From f94def5571609628eb832fa2ee98d6a249c480c3 Mon Sep 17 00:00:00 2001 From: mdorf Date: Wed, 14 Jan 2026 09:43:36 -0800 Subject: [PATCH 01/69] work-in-progress on schemaless solr --- .ruby-version | 2 +- Gemfile | 9 +- Gemfile.lock | 303 ++++++++++++++---- Rakefile | 4 + .../skos/skos_submission_roots.rb | 4 +- lib/ontologies_linked_data/models/class.rb | 90 ++++++ .../models/ontology_format.rb | 4 +- .../models/provisional_class.rb | 36 +-- .../models/skos/collection.rb | 2 +- .../models/skos/scheme.rb | 2 +- lib/ontologies_linked_data/utils/triples.rb | 9 +- ontologies_linked_data.gemspec | 1 + test/models/test_ontology_submission.rb | 2 +- test/models/test_provisional_class.rb | 10 +- test/models/test_skos_submission.rb | 2 +- 15 files changed, 354 insertions(+), 126 deletions(-) diff --git a/.ruby-version b/.ruby-version index 9cec7165a..be94e6f53 100644 --- a/.ruby-version +++ b/.ruby-version @@ -1 +1 @@ -3.1.6 +3.2.2 diff --git a/Gemfile b/Gemfile index 95414ea2f..f85f0e519 100644 --- a/Gemfile +++ b/Gemfile @@ -13,12 +13,10 @@ gem 'oj', '~> 3.0' gem 'omni_logger' gem 'pony' gem 'rack' -gem 'rake', '~> 10.0' +gem 'rake' gem 'request_store' gem 'rest-client' gem 'rsolr' -gem 'thin', '~> 1.0' # compatibility version pin. thin should be replaced with webmoc -gem "down", "~> 5.0" # Testing group :test do @@ -31,14 +29,15 @@ group :test do gem 'rack-test', '~> 0.6' gem 'simplecov' gem 'simplecov-cobertura' # for codecov.io + gem "thin", "~> 1.8.2" end group :development do gem 'rubocop', require: false end # NCBO gems (can be from a local dev path or from rubygems/git) -gem 'goo', github: 'ncbo/goo', branch: 'develop' -gem 'sparql-client', github: 'ncbo/sparql-client', tag: 'v6.3.0' +gem 'goo', github: 'ncbo/goo', branch: 'ontoportal-lirmm-development' +gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'ontoportal-lirmm-development' gem 'public_suffix', '~> 5.1.1' gem 'net-imap', '~> 0.4.18' diff --git a/Gemfile.lock b/Gemfile.lock index 815b5cbff..ed06b4701 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,14 +1,16 @@ GIT remote: https://github.com/ncbo/goo.git - revision: ca5f9d858eef89923903236fe6f76c78271e538d - branch: develop + revision: 027268491b095a13efe288790f16557d49c7bb1d + branch: ontoportal-lirmm-development specs: goo (0.0.2) addressable (~> 2.8) pry - rdf (= 1.0.8) + rdf + rdf-raptor + rdf-rdfxml + rdf-vocab redis - request_store rest-client rsolr sparql-client @@ -16,13 +18,12 @@ GIT GIT remote: https://github.com/ncbo/sparql-client.git - revision: 512edc320b43e83971835dc046b4923485e8f70e - tag: v6.3.0 + revision: 2ac20b217bb7ad2b11305befe0ee77d75e44eac5 + branch: ontoportal-lirmm-development specs: - sparql-client (1.0.1) - json_pure (>= 1.4) - net-http-persistent (= 2.9.4) - rdf (>= 1.0) + sparql-client (3.2.2) + net-http-persistent (~> 4.0, >= 4.0.2) + rdf (~> 3.2, >= 3.2.11) PATH remote: . @@ -30,6 +31,7 @@ PATH ontologies_linked_data (0.0.1) activesupport bcrypt + down (~> 5.0) goo json libxml-ruby @@ -52,21 +54,22 @@ GEM multi_json (~> 1.3) thread_safe (~> 0.1) tzinfo (~> 0.3.37) - addressable (2.8.7) - public_suffix (>= 2.0.2, < 7.0) + addressable (2.8.8) + public_suffix (>= 2.0.2, < 8.0) ansi (1.5.0) ast (2.4.3) - bcrypt (3.1.20) - bigdecimal (3.2.2) + bcp47_spec (0.2.1) + bcrypt (3.1.21) + bigdecimal (3.3.1) builder (3.3.0) childprocess (5.1.0) logger (~> 1.5) coderay (1.1.3) - concurrent-ruby (1.3.5) - connection_pool (2.5.3) + concurrent-ruby (1.3.6) + connection_pool (3.0.2) cube-ruby (0.0.3) daemons (1.4.1) - date (3.4.1) + date (3.5.1) docile (1.4.1) domain_name (0.6.20240107) down (5.4.2) @@ -76,35 +79,46 @@ GEM launchy (>= 2.1, < 4.0) mail (~> 2.7) eventmachine (1.2.7) - faraday (2.13.4) + faraday (2.14.0) faraday-net_http (>= 2.0, < 3.5) json logger - faraday-net_http (3.4.1) - net-http (>= 0.5.0) - ffi (1.17.2-aarch64-linux-gnu) - ffi (1.17.2-arm64-darwin) - ffi (1.17.2-x86_64-linux-gnu) - hashie (5.0.0) + faraday-net_http (3.4.2) + net-http (~> 0.5) + ffi (1.17.3) + ffi (1.17.3-aarch64-linux-gnu) + ffi (1.17.3-aarch64-linux-musl) + ffi (1.17.3-arm-linux-gnu) + ffi (1.17.3-arm-linux-musl) + ffi (1.17.3-arm64-darwin) + ffi (1.17.3-x86-linux-gnu) + ffi (1.17.3-x86-linux-musl) + ffi (1.17.3-x86_64-darwin) + ffi (1.17.3-x86_64-linux-gnu) + ffi (1.17.3-x86_64-linux-musl) + hashie (5.1.0) + logger htmlentities (4.3.4) http-accept (1.7.0) - http-cookie (1.0.8) + http-cookie (1.1.0) domain_name (~> 0.5) i18n (0.9.5) concurrent-ruby (~> 1.0) - json (2.13.2) - json_pure (2.8.1) + io-console (0.8.2) + json (2.18.0) language_server-protocol (3.17.0.5) launchy (3.1.1) addressable (~> 2.8) childprocess (~> 5.0) logger (~> 1.6) libxml-ruby (5.0.5) + link_header (0.0.8) lint_roller (1.1.0) logger (1.7.0) macaddr (1.7.2) systemu (~> 2.6.5) - mail (2.8.1) + mail (2.9.0) + logger mini_mime (>= 0.1.1) net-imap net-pop @@ -113,7 +127,7 @@ GEM mime-types (3.7.0) logger mime-types-data (~> 3.2025, >= 3.2025.0507) - mime-types-data (3.2025.0826) + mime-types-data (3.2025.0924) mini_mime (1.1.5) minitest (4.7.5) minitest-reporters (0.14.24) @@ -121,18 +135,19 @@ GEM builder minitest (>= 2.12, < 5.0) powerbar - mocha (2.7.1) + mocha (2.8.2) ruby2_keywords (>= 0.0.5) - mock_redis (0.51.0) + mock_redis (0.53.0) redis (~> 5) - multi_json (1.17.0) - net-ftp (0.3.8) + multi_json (1.19.1) + net-ftp (0.3.9) net-protocol time - net-http (0.6.0) - uri - net-http-persistent (2.9.4) - net-imap (0.4.22) + net-http (0.9.1) + uri (>= 0.11.1) + net-http-persistent (4.0.8) + connection_pool (>= 2.2.4, < 4) + net-imap (0.4.23) date net-protocol net-pop (0.1.2) @@ -142,38 +157,61 @@ GEM net-smtp (0.5.1) net-protocol netrc (0.11.0) - oj (3.16.11) + oj (3.16.13) bigdecimal (>= 3.0) ostruct (>= 0.2) omni_logger (0.1.4) logger ostruct (0.6.3) parallel (1.27.0) - parser (3.3.9.0) + parser (3.3.10.0) ast (~> 2.4.1) racc pony (1.13.1) mail (>= 2.0) powerbar (2.0.1) hashie (>= 1.1.0) - prism (1.4.0) - pry (0.15.2) + prism (1.7.0) + pry (0.16.0) coderay (~> 1.1) method_source (~> 1.0) + reline (>= 0.6.0) public_suffix (5.1.1) racc (1.8.1) - rack (2.2.17) - rack-test (0.8.3) - rack (>= 1.0, < 3) + rack (2.2.21) + rack-test (0.6.3) + rack (>= 1.0) rainbow (3.1.1) - rake (10.5.0) - rdf (1.0.8) - addressable (>= 2.2) + rake (13.3.1) + rdf (3.3.4) + bcp47_spec (~> 0.2) + bigdecimal (~> 3.1, >= 3.1.5) + link_header (~> 0.0, >= 0.0.8) + logger (~> 1.5) + ostruct (~> 0.6) + readline (~> 0.0) + rdf-raptor (3.2.0) + ffi (~> 1.15) + rdf (~> 3.2) + rdf-rdfxml (3.3.0) + builder (~> 3.2, >= 3.2.4) + htmlentities (~> 4.3) + rdf (~> 3.3) + rdf-xsd (~> 3.3) + rdf-vocab (3.3.3) + rdf (~> 3.3) + rdf-xsd (3.3.0) + rdf (~> 3.3) + rexml (~> 3.2) + readline (0.0.4) + reline redis (5.4.1) redis-client (>= 0.22.0) - redis-client (0.25.2) + redis-client (0.26.3) connection_pool - regexp_parser (2.11.2) + regexp_parser (2.11.3) + reline (0.6.3) + io-console (~> 0.5) request_store (1.7.0) rack (>= 1.4) rest-client (2.1.0) @@ -181,11 +219,11 @@ GEM http-cookie (>= 1.0.2, < 2.0) mime-types (>= 1.16, < 4.0) netrc (~> 0.8) - rexml (3.4.1) + rexml (3.4.4) rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) - rubocop (1.79.2) + rubocop (1.82.1) json (~> 2.3) language_server-protocol (~> 3.17.0.2) lint_roller (~> 1.1.0) @@ -193,20 +231,20 @@ GEM parser (>= 3.3.0.2) rainbow (>= 2.2.2, < 4.0) regexp_parser (>= 2.9.3, < 3.0) - rubocop-ast (>= 1.46.0, < 2.0) + rubocop-ast (>= 1.48.0, < 2.0) ruby-progressbar (~> 1.7) unicode-display_width (>= 2.4.0, < 4.0) - rubocop-ast (1.46.0) + rubocop-ast (1.49.0) parser (>= 3.3.7.2) - prism (~> 1.4) + prism (~> 1.7) ruby-progressbar (1.13.0) ruby2_keywords (0.0.5) - rubyzip (3.0.2) + rubyzip (3.2.2) simplecov (0.22.0) docile (~> 1.1) simplecov-html (~> 0.11) simplecov_json_formatter (~> 0.1) - simplecov-cobertura (3.0.0) + simplecov-cobertura (3.1.0) rexml simplecov (~> 0.19) simplecov-html (0.13.2) @@ -217,30 +255,35 @@ GEM eventmachine (~> 1.0, >= 1.0.4) rack (>= 1, < 3) thread_safe (0.3.6) - time (0.4.1) + time (0.4.2) date - timeout (0.4.3) + timeout (0.6.0) tzinfo (0.3.62) - unicode-display_width (3.1.5) - unicode-emoji (~> 4.0, >= 4.0.4) - unicode-emoji (4.0.4) - uri (1.0.3) + unicode-display_width (3.2.0) + unicode-emoji (~> 4.1) + unicode-emoji (4.2.0) + uri (1.1.1) uuid (2.3.9) macaddr (~> 1.0) PLATFORMS - aarch64-linux - arm64-darwin-22 - arm64-darwin-23 - arm64-darwin-24 - x86_64-linux + aarch64-linux-gnu + aarch64-linux-musl + arm-linux-gnu + arm-linux-musl + arm64-darwin + ruby + x86-linux-gnu + x86-linux-musl + x86_64-darwin + x86_64-linux-gnu + x86_64-linux-musl DEPENDENCIES activesupport (~> 4) addressable (~> 2.8) bcrypt (~> 3.0) cube-ruby - down (~> 5.0) email_spec ffi goo! @@ -259,7 +302,7 @@ DEPENDENCIES public_suffix (~> 5.1.1) rack rack-test (~> 0.6) - rake (~> 10.0) + rake request_store rest-client rsolr @@ -267,7 +310,125 @@ DEPENDENCIES simplecov simplecov-cobertura sparql-client! - thin (~> 1.0) + thin (~> 1.8.2) + +CHECKSUMS + activesupport (4.0.13) sha256=0fcd111ced80b99339371a869dd187996349ab8ab5dfc08ee63730bdf66276d8 + addressable (2.8.8) sha256=7c13b8f9536cf6364c03b9d417c19986019e28f7c00ac8132da4eb0fe393b057 + ansi (1.5.0) sha256=5408253274e33d9d27d4a98c46d2998266fd51cba58a7eb9d08f50e57ed23592 + ast (2.4.3) sha256=954615157c1d6a382bc27d690d973195e79db7f55e9765ac7c481c60bdb4d383 + bcp47_spec (0.2.1) sha256=3fd62edf96c126bd9624e4319ac74082a966081859d1ee0ef3c3041640a37810 + bcrypt (3.1.21) sha256=5964613d750a42c7ee5dc61f7b9336fb6caca429ba4ac9f2011609946e4a2dcf + bigdecimal (3.3.1) sha256=eaa01e228be54c4f9f53bf3cc34fe3d5e845c31963e7fcc5bedb05a4e7d52218 + builder (3.3.0) sha256=497918d2f9dca528fdca4b88d84e4ef4387256d984b8154e9d5d3fe5a9c8835f + childprocess (5.1.0) sha256=9a8d484be2fd4096a0e90a0cd3e449a05bc3aa33f8ac9e4d6dcef6ac1455b6ec + coderay (1.1.3) sha256=dc530018a4684512f8f38143cd2a096c9f02a1fc2459edcfe534787a7fc77d4b + concurrent-ruby (1.3.6) sha256=6b56837e1e7e5292f9864f34b69c5a2cbc75c0cf5338f1ce9903d10fa762d5ab + connection_pool (3.0.2) sha256=33fff5ba71a12d2aa26cb72b1db8bba2a1a01823559fb01d29eb74c286e62e0a + cube-ruby (0.0.3) sha256=42f798c16ba184376ba66c93f4083e7f014ee0c6f300c919a178bacb5b8ae617 + daemons (1.4.1) sha256=8fc76d76faec669feb5e455d72f35bd4c46dc6735e28c420afb822fac1fa9a1d + date (3.5.1) sha256=750d06384d7b9c15d562c76291407d89e368dda4d4fff957eb94962d325a0dc0 + docile (1.4.1) sha256=96159be799bfa73cdb721b840e9802126e4e03dfc26863db73647204c727f21e + domain_name (0.6.20240107) sha256=5f693b2215708476517479bf2b3802e49068ad82167bcd2286f899536a17d933 + down (5.4.2) sha256=516e5e01e7a96214a7e2cd155aac6f700593038ae6c857c0f4a05413b1c58acf + email_spec (2.3.0) sha256=df23be7a131186f7a3d5be3b35eaac9196f9ac13bd26c9c3d59341e13d852d11 + eventmachine (1.2.7) sha256=994016e42aa041477ba9cff45cbe50de2047f25dd418eba003e84f0d16560972 + faraday (2.14.0) sha256=8699cfe5d97e55268f2596f9a9d5a43736808a943714e3d9a53e6110593941cd + faraday-net_http (3.4.2) 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a/Rakefile +++ b/Rakefile @@ -4,23 +4,27 @@ task default: %w[test] Rake::TestTask.new do |t| t.libs = [] + t.warning = false t.test_files = FileList['test/**/test*.rb'] end Rake::TestTask.new do |t| t.libs = [] + t.warning = false t.name = "test:models" t.test_files = FileList['test/models/test*.rb'] end Rake::TestTask.new do |t| t.libs = [] + t.warning = false t.name = "test:rack" t.test_files = FileList['test/rack/test*.rb'] end Rake::TestTask.new do |t| t.libs = [] + t.warning = false t.name = "test:serializer" t.test_files = FileList['test/serializer/test*.rb'] end diff --git a/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb b/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb index 4a88c12a0..717afb3a6 100644 --- a/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb +++ b/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb @@ -42,7 +42,7 @@ def roots_by_query(query_body, page, paged, pagesize) def roots_by_has_top_concept(concept_schemes, page, paged, pagesize) query_body = <<-eos - ?x #{RDF::SKOS[:hasTopConcept].to_ntriples} ?root . + ?x #{RDF::Vocab::SKOS[:hasTopConcept].to_ntriples} ?root . #{concept_schemes_filter(concept_schemes)} eos roots_by_query query_body, page, paged, pagesize @@ -50,7 +50,7 @@ def roots_by_has_top_concept(concept_schemes, page, paged, pagesize) def roots_by_top_concept_of(concept_schemes, page, paged, pagesize) query_body = <<-eos - ?root #{RDF::SKOS[:topConceptOf].to_ntriples} ?x. + ?root #{RDF::Vocab::SKOS[:topConceptOf].to_ntriples} ?x. #{concept_schemes_filter(concept_schemes)} eos roots_by_query query_body, page, paged, pagesize diff --git a/lib/ontologies_linked_data/models/class.rb b/lib/ontologies_linked_data/models/class.rb index c5fb20d90..33b078e4c 100644 --- a/lib/ontologies_linked_data/models/class.rb +++ b/lib/ontologies_linked_data/models/class.rb @@ -117,6 +117,96 @@ def self.urn_id(acronym,classId) cache_segment_instance lambda {|cls| segment_instance(cls) } cache_segment_keys [:class] cache_load submission: [ontology: [:acronym]] + + + + + + + + + + # Index settings + def self.index_schema(schema_generator) + schema_generator.add_field(:prefLabel, 'text_general', indexed: true, stored: true, multi_valued: true) + schema_generator.add_field(:synonym, 'text_general', indexed: true, stored: true, multi_valued: true) + schema_generator.add_field(:notation, 'text_general', indexed: true, stored: true, multi_valued: false) + + schema_generator.add_field(:definition, 'string', indexed: true, stored: true, multi_valued: true) + schema_generator.add_field(:submissionAcronym, 'string', indexed: true, stored: true, multi_valued: false) + schema_generator.add_field(:parents, 'string', indexed: true, stored: true, multi_valued: true) + schema_generator.add_field(:ontologyType, 'string', indexed: true, stored: true, multi_valued: false) + # schema_generator.add_field(:ontologyType, 'ontologyType', indexed: true, stored: true, multi_valued: false) + schema_generator.add_field(:ontologyId, 'string', indexed: true, stored: true, multi_valued: false) + schema_generator.add_field(:submissionId, 'pint', indexed: true, stored: true, multi_valued: false) + schema_generator.add_field(:childCount, 'pint', indexed: true, stored: true, multi_valued: false) + + schema_generator.add_field(:cui, 'text_general', indexed: true, stored: true, multi_valued: true) + schema_generator.add_field(:semanticType, 'text_general', indexed: true, stored: true, multi_valued: true) + + schema_generator.add_field(:property, 'text_general', indexed: true, stored: true, multi_valued: true) + schema_generator.add_field(:propertyRaw, 'text_general', indexed: false, stored: true, multi_valued: false) + + schema_generator.add_field(:obsolete, 'boolean', indexed: true, stored: true, multi_valued: false) + schema_generator.add_field(:provisional, 'boolean', indexed: true, stored: true, multi_valued: false) + + # Copy fields for term search + schema_generator.add_copy_field('notation', '_text_') + + %w[prefLabel synonym].each do |field| + + schema_generator.add_field("#{field}Exact", 'string', indexed: true, stored: false, multi_valued: true) + schema_generator.add_field("#{field}Suggest", 'text_suggest', indexed: true, stored: false, multi_valued: true, omit_norms: true) + schema_generator.add_field("#{field}SuggestEdge", 'text_suggest_edge', indexed: true, stored: false, multi_valued: true) + schema_generator.add_field("#{field}SuggestNgram", 'text_suggest_ngram', indexed: true, stored: false, multi_valued: true, omit_norms: true) + + schema_generator.add_copy_field(field, '_text_') + schema_generator.add_copy_field(field, "#{field}Exact") + schema_generator.add_copy_field(field, "#{field}Suggest") + schema_generator.add_copy_field(field, "#{field}SuggestEdge") + schema_generator.add_copy_field(field, "#{field}SuggestNgram") + + schema_generator.add_dynamic_field("#{field}_*", 'text_general', indexed: true, stored: true, multi_valued: true) + schema_generator.add_dynamic_field("#{field}Exact_*", 'string', indexed: true, stored: false, multi_valued: true) + schema_generator.add_dynamic_field("#{field}Suggest_*", 'text_suggest', indexed: true, stored: false, multi_valued: true, omit_norms: true) + schema_generator.add_dynamic_field("#{field}SuggestEdge_*", 'text_suggest_edge', indexed: true, stored: false, multi_valued: true) + schema_generator.add_dynamic_field("#{field}SuggestNgram_*", 'text_suggest_ngram', indexed: true, stored: false, multi_valued: true, omit_norms: true) + + schema_generator.add_copy_field("#{field}_*", "#{field}Exact_*") + schema_generator.add_copy_field("#{field}_*", "#{field}Suggest_*") + schema_generator.add_copy_field("#{field}_*", "#{field}SuggestEdge_*") + schema_generator.add_copy_field("#{field}_*", "#{field}SuggestNgram_*") + end + + schema_generator.add_dynamic_field('definition_*', 'text_general', indexed: true, stored: true, multi_valued: true) + + end + + enable_indexing(:term_search_core1) do |schema_generator| + index_schema(schema_generator) + end + + + + + + + + + + + + + + + + + + + + + + def self.tree_view_property(*args) submission = args.first diff --git a/lib/ontologies_linked_data/models/ontology_format.rb b/lib/ontologies_linked_data/models/ontology_format.rb index c582ef90f..926c8c60b 100644 --- a/lib/ontologies_linked_data/models/ontology_format.rb +++ b/lib/ontologies_linked_data/models/ontology_format.rb @@ -39,14 +39,14 @@ def tree_property return Goo.vocabulary(:metadata)[:treeView] end if skos? - return RDF::SKOS[:broader] + return RDF::Vocab::SKOS[:broader] end return RDF::RDFS[:subClassOf] end def class_type if skos? - return RDF::SKOS[:Concept] + return RDF::Vocab::SKOS[:Concept] end return RDF::OWL[:Class] end diff --git a/lib/ontologies_linked_data/models/provisional_class.rb b/lib/ontologies_linked_data/models/provisional_class.rb index 4b872e13a..7f4bf5e35 100644 --- a/lib/ontologies_linked_data/models/provisional_class.rb +++ b/lib/ontologies_linked_data/models/provisional_class.rb @@ -40,6 +40,10 @@ class ProvisionalClass < LinkedData::Models::Base end }, Goo.vocabulary["Ontology"]) + enable_indexing(:term_search_core1) do |schema_generator| + Class.index_schema(schema_generator) + end + def index_id() self.bring(:ontology) if self.bring?(:ontology) return nil unless self.ontology @@ -143,38 +147,6 @@ def append_if_not_there_already(path, r) true end - def index() - if index_id - unindex - super - LinkedData::Models::Ontology.indexCommit - end - end - - def unindex() - ind_id = index_id - - if ind_id - query = "id:#{solr_escape(ind_id)}" - LinkedData::Models::Ontology.unindexByQuery(query) - LinkedData::Models::Ontology.indexCommit - end - end - - ## - # Override save to allow indexing - def save(*args) - super(*args) - index - self - end - - def delete(*args) - # remove index entries - unindex - super(*args) - end - def solr_escape(text) RSolr.solr_escape(text).gsub(/\s+/,"\\ ") end diff --git a/lib/ontologies_linked_data/models/skos/collection.rb b/lib/ontologies_linked_data/models/skos/collection.rb index afc5724e4..535ace488 100644 --- a/lib/ontologies_linked_data/models/skos/collection.rb +++ b/lib/ontologies_linked_data/models/skos/collection.rb @@ -4,7 +4,7 @@ module SKOS class Collection < LinkedData::Models::Base model :collection, name_with: :id, collection: :submission, - namespace: :skos, schemaless: :true, rdf_type: ->(*x) { RDF::SKOS[:Collection] } + namespace: :skos, schemaless: :true, rdf_type: ->(*x) { RDF::Vocab::SKOS[:Collection] } attribute :prefLabel, namespace: :skos, enforce: [:existence] attribute :member, namespace: :skos, enforce: [:list, :class] diff --git a/lib/ontologies_linked_data/models/skos/scheme.rb b/lib/ontologies_linked_data/models/skos/scheme.rb index 37e041896..1aca93932 100644 --- a/lib/ontologies_linked_data/models/skos/scheme.rb +++ b/lib/ontologies_linked_data/models/skos/scheme.rb @@ -4,7 +4,7 @@ module SKOS class Scheme < LinkedData::Models::Base model :scheme, name_with: :id, collection: :submission, - namespace: :skos, schemaless: :true, rdf_type: ->(*x) { RDF::SKOS[:ConceptScheme] } + namespace: :skos, schemaless: :true, rdf_type: ->(*x) { RDF::Vocab::SKOS[:ConceptScheme] } attribute :prefLabel, namespace: :skos, enforce: [:existence] diff --git a/lib/ontologies_linked_data/utils/triples.rb b/lib/ontologies_linked_data/utils/triples.rb index 7a1385226..99ecbdbcc 100644 --- a/lib/ontologies_linked_data/utils/triples.rb +++ b/lib/ontologies_linked_data/utils/triples.rb @@ -1,3 +1,4 @@ + module LinkedData module Utils module Triples @@ -23,12 +24,12 @@ def self.rdf_for_custom_properties(ont_sub) # Add subPropertyOf triples for custom properties unless ont_sub.prefLabelProperty.nil? unless ont_sub.prefLabelProperty == Goo.vocabulary(:rdfs)[:label] || ont_sub.prefLabelProperty == Goo.vocabulary(:metadata_def)[:prefLabel] - triples << triple(ont_sub.prefLabelProperty, subPropertyOf, Goo.vocabulary(:metadata_def)[:prefLabel]) + triples << triple(ont_sub.prefLabelProperty, subPropertyOf, Goo.vocabulary(:metadata_def)[:prefLabel]) end end unless ont_sub.definitionProperty.nil? unless ont_sub.definitionProperty == Goo.vocabulary(:rdfs)[:label] || ont_sub.definitionProperty == Goo.vocabulary(:skos)[:definition] - triples << triple(ont_sub.definitionProperty, subPropertyOf, Goo.vocabulary(:skos)[:definition]) + triples << triple(ont_sub.definitionProperty, subPropertyOf, Goo.vocabulary(:skos)[:definition]) end end unless ont_sub.synonymProperty.nil? @@ -75,11 +76,11 @@ def self.label_for_class_triple(class_id, property, label, language=nil) params = { datatype: RDF::XSD.string } lang = language.to_s.downcase - if !lang.empty? && lang.to_sym != :none + if !lang.empty? && lang.to_sym != :none && !lang.to_s.eql?('@none') params[:datatype] = RDF.langString params[:language] = lang.to_sym end - return triple(class_id, property, RDF::Literal.new(label, params)) + triple(class_id, property, RDF::Literal.new(label, **params)) end def self.generated_label(class_id, existing_label) diff --git a/ontologies_linked_data.gemspec b/ontologies_linked_data.gemspec index bbc3dc99b..c93e6fa67 100644 --- a/ontologies_linked_data.gemspec +++ b/ontologies_linked_data.gemspec @@ -32,6 +32,7 @@ Gem::Specification.new do |gem| gem.add_dependency("rack-test") gem.add_dependency("rsolr") gem.add_dependency("rubyzip", "~> 3.0") + gem.add_dependency("down", "~> 5.0") gem.add_development_dependency("email_spec") diff --git a/test/models/test_ontology_submission.rb b/test/models/test_ontology_submission.rb index 1a6a60377..b632f50e2 100644 --- a/test/models/test_ontology_submission.rb +++ b/test/models/test_ontology_submission.rb @@ -133,7 +133,7 @@ def test_skos_ontology roots.each do |root| q_broader = <<-eos SELECT ?children WHERE { - ?children #{RDF::SKOS[:broader].to_ntriples} #{root.id.to_ntriples} } + ?children #{RDF::Vocab::SKOS[:broader].to_ntriples} #{root.id.to_ntriples} } eos children_query = [] Goo.sparql_query_client.query(q_broader).each_solution do |sol| diff --git a/test/models/test_provisional_class.rb b/test/models/test_provisional_class.rb index 12062b99f..c0ab44cfa 100644 --- a/test/models/test_provisional_class.rb +++ b/test/models/test_provisional_class.rb @@ -285,11 +285,11 @@ def test_provisional_class_search_indexing pc = @@provisional_class pc.ontology = @@ontology pc.unindex - resp = LinkedData::Models::Ontology.search("\"#{pc.label}\"", params) + resp = LinkedData::Models::ProvisionalClass.search("\"#{pc.label}\"", params) assert_equal 0, resp["response"]["numFound"] pc.index - resp = LinkedData::Models::Ontology.search("\"#{pc.label}\"", params) + resp = LinkedData::Models::ProvisionalClass.search("\"#{pc.label}\"", params) assert_equal 1, resp["response"]["numFound"] assert_equal pc.label, resp["response"]["docs"][0]["prefLabel"].first pc.unindex @@ -312,18 +312,18 @@ def test_provisional_class_search_indexing pc3.save pc3 = LinkedData::Models::ProvisionalClass.find(pc3.id).include(:label).first - resp = LinkedData::Models::Ontology.search("\"#{pc1.label}\"", params) + resp = LinkedData::Models::ProvisionalClass.search("\"#{pc1.label}\"", params) assert_equal 1, resp["response"]["numFound"] assert_equal pc1.label, resp["response"]["docs"][0]["prefLabel"].first par_len = resp["response"]["docs"][0]["parents"].length assert_equal 5, par_len assert_equal 1, (resp["response"]["docs"][0]["parents"].select { |x| x == class_id.to_s }).length - resp = LinkedData::Models::Ontology.search("\"#{pc2.label}\"", params) + resp = LinkedData::Models::ProvisionalClass.search("\"#{pc2.label}\"", params) assert_equal par_len + 1, resp["response"]["docs"][0]["parents"].length assert_equal 1, (resp["response"]["docs"][0]["parents"].select { |x| x == pc1.id.to_s }).length - resp = LinkedData::Models::Ontology.search("\"#{pc3.label}\"", params) + resp = LinkedData::Models::ProvisionalClass.search("\"#{pc3.label}\"", params) assert_equal par_len + 2, resp["response"]["docs"][0]["parents"].length assert_equal 1, (resp["response"]["docs"][0]["parents"].select { |x| x == pc1.id.to_s }).length assert_equal 1, (resp["response"]["docs"][0]["parents"].select { |x| x == pc2.id.to_s }).length diff --git a/test/models/test_skos_submission.rb b/test/models/test_skos_submission.rb index 35bfeee29..9830163fd 100644 --- a/test/models/test_skos_submission.rb +++ b/test/models/test_skos_submission.rb @@ -43,7 +43,7 @@ def test_roots_no_main_scheme roots.each do |root| q_broader = <<-eos SELECT ?children WHERE { - ?children #{RDF::SKOS[:broader].to_ntriples} #{root.id.to_ntriples} } + ?children #{RDF::Vocab::SKOS[:broader].to_ntriples} #{root.id.to_ntriples} } eos children_query = [] Goo.sparql_query_client.query(q_broader).each_solution do |sol| From 1bb138b0efa82fa269e68e33750fe0d13b6b2577 Mon Sep 17 00:00:00 2001 From: mdorf Date: Wed, 14 Jan 2026 18:33:17 -0800 Subject: [PATCH 02/69] fixed an issue with oboId and Solr indexing --- lib/ontologies_linked_data/models/class.rb | 38 +++------------------- 1 file changed, 4 insertions(+), 34 deletions(-) diff --git a/lib/ontologies_linked_data/models/class.rb b/lib/ontologies_linked_data/models/class.rb index 33b078e4c..065c094df 100644 --- a/lib/ontologies_linked_data/models/class.rb +++ b/lib/ontologies_linked_data/models/class.rb @@ -118,20 +118,13 @@ def self.urn_id(acronym,classId) cache_segment_keys [:class] cache_load submission: [ontology: [:acronym]] - - - - - - - - # Index settings def self.index_schema(schema_generator) schema_generator.add_field(:prefLabel, 'text_general', indexed: true, stored: true, multi_valued: true) schema_generator.add_field(:synonym, 'text_general', indexed: true, stored: true, multi_valued: true) - schema_generator.add_field(:notation, 'text_general', indexed: true, stored: true, multi_valued: false) - + schema_generator.add_field(:notation, 'string_ci', indexed: true, stored: true, multi_valued: false) + schema_generator.add_field(:oboId, 'string_ci', indexed: true, stored: true, multi_valued: false) + schema_generator.add_field(:idAcronymMatch, 'boolean', indexed: true, stored: true, multi_valued: false, default: false) schema_generator.add_field(:definition, 'string', indexed: true, stored: true, multi_valued: true) schema_generator.add_field(:submissionAcronym, 'string', indexed: true, stored: true, multi_valued: false) schema_generator.add_field(:parents, 'string', indexed: true, stored: true, multi_valued: true) @@ -152,9 +145,9 @@ def self.index_schema(schema_generator) # Copy fields for term search schema_generator.add_copy_field('notation', '_text_') + schema_generator.add_copy_field('oboId', '_text_') %w[prefLabel synonym].each do |field| - schema_generator.add_field("#{field}Exact", 'string', indexed: true, stored: false, multi_valued: true) schema_generator.add_field("#{field}Suggest", 'text_suggest', indexed: true, stored: false, multi_valued: true, omit_norms: true) schema_generator.add_field("#{field}SuggestEdge", 'text_suggest_edge', indexed: true, stored: false, multi_valued: true) @@ -179,35 +172,12 @@ def self.index_schema(schema_generator) end schema_generator.add_dynamic_field('definition_*', 'text_general', indexed: true, stored: true, multi_valued: true) - end enable_indexing(:term_search_core1) do |schema_generator| index_schema(schema_generator) end - - - - - - - - - - - - - - - - - - - - - - def self.tree_view_property(*args) submission = args.first unless submission.loaded_attributes.include?(:hasOntologyLanguage) From 836b2dce84c5157da810e3f44736feb1b2ebc856 Mon Sep 17 00:00:00 2001 From: mdorf Date: Fri, 16 Jan 2026 18:04:09 -0800 Subject: [PATCH 03/69] incremental integration commit --- .../skos/skos_submission_roots.rb | 2 +- .../submission_metadata_extractor.rb | 322 --------------- .../models/concerns/parse_diff_file.rb | 89 +++++ .../models/concerns/submission_process.rb | 27 +- lib/ontologies_linked_data/models/ontology.rb | 41 +- .../models/ontology_submission.rb | 6 +- .../models/properties/annotation_property.rb | 4 + .../models/properties/datatype_property.rb | 4 + .../models/properties/object_property.rb | 4 + .../models/properties/ontology_property.rb | 30 ++ .../operations/submission_all_data_indexer.rb | 166 ++++++++ .../operations/submission_extract_metadata.rb | 325 ++++++++++++++++ .../operations/submission_indexer.rb | 2 +- .../operations/submission_missing_labels.rb | 293 ++++++++++++++ .../operations/submission_obsolete_classes.rb | 81 ++++ .../submission_properties_indexer.rb | 6 +- .../operations/submission_rdf_generator.rb | 366 +----------------- .../submission_processor.rb | 131 ++++--- test/models/test_ontology_submission.rb | 14 +- test/test_case.rb | 4 +- 20 files changed, 1140 insertions(+), 777 deletions(-) delete mode 100644 lib/ontologies_linked_data/concerns/ontology_submissions/submission_metadata_extractor.rb create mode 100644 lib/ontologies_linked_data/models/concerns/parse_diff_file.rb create mode 100644 lib/ontologies_linked_data/services/submission_process/operations/submission_all_data_indexer.rb create mode 100644 lib/ontologies_linked_data/services/submission_process/operations/submission_extract_metadata.rb create mode 100644 lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb create mode 100644 lib/ontologies_linked_data/services/submission_process/operations/submission_obsolete_classes.rb diff --git a/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb b/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb index 717afb3a6..e81c8367c 100644 --- a/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb +++ b/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb @@ -33,7 +33,7 @@ def roots_by_query(query_body, page, paged, pagesize) #needs to get cached class_ids = [] - Goo.sparql_query_client.query(root_skos, { graphs: [self.id] }).each_solution do |s| + Goo.sparql_query_client.query(root_skos, graphs: [self.id]).each_solution do |s| class_ids << s[:root] end diff --git a/lib/ontologies_linked_data/concerns/ontology_submissions/submission_metadata_extractor.rb b/lib/ontologies_linked_data/concerns/ontology_submissions/submission_metadata_extractor.rb deleted file mode 100644 index 1a183319b..000000000 --- a/lib/ontologies_linked_data/concerns/ontology_submissions/submission_metadata_extractor.rb +++ /dev/null @@ -1,322 +0,0 @@ -module LinkedData - module Concerns - module OntologySubmission - module MetadataExtractor - - def extract_metadata(logger = nil, heavy_extraction = true, user_params = nil) - logger ||= Logger.new(STDOUT) - logger.info("Extracting metadata from the ontology submission #{self.id}") - - unless self.valid? - logger.error("Cannot extract metadata from #{self.id} because the submission is invalid") - return - end - - @submission = self - ontology_iri = extract_ontology_iri - - if ontology_iri - old_uri = @submission.uri - @submission.uri = ontology_iri - - if @submission.valid? - @submission.save - else - logger.error("The extracted submission URI #{ontology_iri} is invalid. Discarding...") - @submission.uri = old_uri - end - end - - if heavy_extraction - begin - # Extract metadata directly from the ontology - extract_ontology_metadata(logger, user_params, skip_attrs: [:uri]) - logger.info('Additional metadata extracted') - rescue StandardError => e - message = e.message + "\n\n " + e.backtrace.join("\n ") - logger.error("Error while extracting additional metadata: #{message}") - end - end - - version_exists = @submission.version - - if version_exists.to_s.strip.empty? - version_info = extract_version - - if version_info - @submission.version = version_info - - unless @submission.valid? - logger.error("The extracted submission version \"#{version_info}\" is invalid. Discarding...") - @submission.version = nil - end - end - end - - @submission.save - end - - def extract_version - query = Goo.sparql_query_client.select(:versionInfo).distinct - .from(@submission.id) - .where([RDF::URI.new('http://bioportal.bioontology.org/ontologies/versionSubject'), - RDF::URI.new("#{Goo.namespaces[:owl].to_s}versionInfo"), - :versionInfo]) - sol = query.each_solution.first || {} - sol[:versionInfo]&.to_s - end - - def extract_ontology_iri - query = Goo.sparql_query_client.select(:uri).distinct - .from(@submission.id) - .where([:uri, - RDF::URI.new("#{Goo.namespaces[:rdf].to_s}type"), - RDF::URI.new("#{Goo.namespaces[:owl].to_s}Ontology")]) - sol = query.each_solution.first || {} - RDF::URI.new(sol[:uri]) if sol[:uri] - end - - # Extract additional metadata about the ontology - # First it extracts the main metadata, then the mapped metadata - def extract_ontology_metadata(logger, user_params, skip_attrs: []) - # The commented out line below would give priority to the existing values over extracted values - # user_params = object_to_hash(@submission) unless user_params - user_params = {} if user_params.nil? || !user_params - ontology_uri = @submission.uri - logger.info("Extracting additional metadata from ontology #{ontology_uri}") - - # go through all OntologySubmission attributes. Returns symbols - LinkedData::Models::OntologySubmission.attributes(:all).each do |attr| - next if skip_attrs.include? attr - # for attribute with the :extractedMetadata setting on, and that have not been defined by the user - attr_settings = LinkedData::Models::OntologySubmission.attribute_settings(attr) - - # Check if the user provided a non-empty value for this attribute - user_provided_value = user_params.key?(attr) && !empty_value?(user_params[attr]) - # Proceed only if the attribute is marked as extractable and the user did NOT provide a value - should_extract = attr_settings[:extractedMetadata] && !user_provided_value - next unless should_extract - - # a boolean to check if a value that should be single have already been extracted - single_extracted = false - type = enforce?(attr, :list) ? :list : :string - old_value = value(attr, type) - - unless attr_settings[:namespace].nil? - property_to_extract = "#{attr_settings[:namespace].to_s}:#{attr.to_s}" - hash_results = extract_each_metadata(ontology_uri, attr, property_to_extract, logger) - single_extracted = send_value(attr, hash_results, logger) unless hash_results.empty? - end - - # extracts attribute value from metadata mappings - attr_settings[:metadataMappings] ||= [] - - attr_settings[:metadataMappings].each do |mapping| - break if single_extracted - - hash_mapping_results = extract_each_metadata(ontology_uri, attr, mapping.to_s, logger) - single_extracted = send_value(attr, hash_mapping_results, logger) unless hash_mapping_results.empty? - end - - new_value = value(attr, type) - - if empty_value?(new_value) && !empty_value?(old_value) - logger.error("Extracted attribute #{attr} with the value #{new_value} is empty. Returning to the old value: #{old_value}.") - send_value(attr, old_value, logger) - end - end - end - - def object_to_hash(obj) - obj.instance_variables.each_with_object({}) do |ivar, hash| - key = ivar.to_s.delete("@").to_sym - value = obj.instance_variable_get(ivar) - hash[key] = value - end - end - - def empty_value?(value) - value.nil? || (value.is_a?(Array) && value.empty?) || value.to_s.strip.empty? - end - - def value(attr, type) - val = @submission.send(attr.to_s) - type.eql?(:list) ? Array(val) || [] : val || '' - end - - def send_value(attr, new_value, logger) - old_val = nil - single_extracted = false - - if enforce?(attr, :list) - old_val = value(attr, :list) - old_values = old_val.dup - new_values = new_value.values - new_values = new_values.map { |v| find_or_create_agent(attr, v, logger) }.compact if enforce?(attr, :Agent) - - old_values.push(*new_values) - - @submission.send("#{attr}=", old_values.uniq) - elsif enforce?(attr, :concatenate) - # if multiple value for this attribute, then we concatenate it - # Add the concat at the very end, to easily join the content of the array - old_val = value(attr, :string) - metadata_values = old_val.split(', ') - new_values = new_value.values.map { |x| x.to_s.split(', ') }.flatten - - @submission.send("#{attr}=", (metadata_values + new_values).uniq.join(', ')) - else - new_value = new_value.is_a?(Hash)? new_value.values.first : new_value.to_s - new_value = find_or_create_agent(attr, nil, logger) if enforce?(attr, :Agent) - @submission.send("#{attr}=", new_value) - old_val = @submission.previous_values&.key?(attr) ? @submission.previous_values[attr] : nil - single_extracted = true - end - - unless @submission.valid? - logger.error("Error while extracting metadata for the attribute #{attr}: #{@submission.errors[attr] || @submission.errors}") - new_value&.delete if enforce?(attr, :Agent) && new_value.respond_to?(:delete) - @submission.send("#{attr}=", old_val) - end - - single_extracted - end - - # Return a hash with the best literal value for an URI - # it selects the literal according to their language: no language > english > french > other languages - def select_metadata_literal(metadata_uri, metadata_literal, hash) - return unless metadata_literal.is_a?(RDF::Literal) - - if hash.key?(metadata_uri) - if metadata_literal.has_language? - if !hash[metadata_uri].has_language? - return hash - else - case metadata_literal.language - when :en, :eng - # Take the value with english language over other languages - hash[metadata_uri] = metadata_literal.to_s - return hash - when :fr, :fre - # If no english, take french - if hash[metadata_uri].language == :en || hash[metadata_uri].language == :eng - return hash - else - hash[metadata_uri] = metadata_literal.to_s - return hash - end - else - return hash - end - end - else - # Take the value with no language in priority (considered as a default) - hash[metadata_uri] = metadata_literal.to_s - return hash - end - else - hash[metadata_uri] = metadata_literal.to_s - hash - end - end - - # A function to extract additional metadata - # Take the literal data if the property is pointing to a literal - # If pointing to an URI: first it takes the "omv:name" of the object pointed by the property, if nil it takes the "rdfs:label". - # If not found it check for "omv:firstName + omv:lastName" (for "omv:Person") of this object. And to finish it takes the "URI" - # The hash_results contains the metadataUri (objet pointed on by the metadata property) with the value we are using from it - def extract_each_metadata(ontology_uri, attr, prop_to_extract, logger) - - query_metadata = < #{prop_to_extract} ?extractedObject . - OPTIONAL { ?extractedObject omv:name ?omvname } . - OPTIONAL { ?extractedObject omv:firstName ?omvfirstname } . - OPTIONAL { ?extractedObject omv:lastName ?omvlastname } . - OPTIONAL { ?extractedObject rdfs:label ?rdfslabel } . -} -eos - Goo.namespaces.each do |prefix, uri| - query_metadata = "PREFIX #{prefix}: <#{uri}>\n" + query_metadata - end - - # logger.info(query_metadata) - # This hash will contain the "literal" metadata for each object (uri or literal) pointed by the metadata predicate - hash_results = {} - Goo.sparql_query_client.query(query_metadata).each_solution do |sol| - value = sol[:extractedObject] - if enforce?(attr, :uri) - # If the attr is enforced as URI then it directly takes the URI - uri_value = value ? RDF::URI.new(value.to_s.strip) : nil - hash_results[value] = uri_value if uri_value&.valid? - elsif enforce?(attr, :date_time) - begin - hash_results[value] = DateTime.iso8601(value.to_s) - rescue StandardError => e - logger.error("Impossible to extract DateTime metadata for #{attr}: #{value}. It should follow iso8601 standards. Error message: #{e}") - end - elsif enforce?(attr, :integer) - begin - hash_results[value] = value.to_s.to_i - rescue StandardError => e - logger.error("Impossible to extract integer metadata for #{attr}: #{value}. Error message: #{e}") - end - elsif enforce?(attr, :boolean) - case value.to_s.downcase - when 'true' - hash_results[value] = true - when 'false' - hash_results[value] = false - else - logger.error("Impossible to extract boolean metadata for #{attr}: #{value}. Error message: #{e}") - end - elsif value.is_a?(RDF::URI) - hash_results = find_object_label(hash_results, sol, value) - else - # If this is directly a literal - hash_results = select_metadata_literal(value, value, hash_results) - end - end - hash_results - end - - def find_object_label(hash_results, sol, value) - if !sol[:omvname].nil? - hash_results = select_metadata_literal(value, sol[:omvname], hash_results) - elsif !sol[:rdfslabel].nil? - hash_results = select_metadata_literal(value, sol[:rdfslabel], hash_results) - elsif !sol[:omvfirstname].nil? - hash_results = select_metadata_literal(value, sol[:omvfirstname], hash_results) - # if first and last name are defined (for omv:Person) - hash_results[value] = "#{hash_results[value]} #{sol[:omvlastname]}" unless sol[:omvlastname].nil? - elsif !sol[:omvlastname].nil? - # if only last name is defined - hash_results = select_metadata_literal(value, sol[:omvlastname], hash_results) - else - # if the object is an URI but we are requesting a String - hash_results[value] = value.to_s - end - hash_results - end - - def enforce?(attr, type) - LinkedData::Models::OntologySubmission.attribute_settings(attr)[:enforce].include?(type) - end - - def find_or_create_agent(attr, old_val, logger) - agent = LinkedData::Models::Agent.where(agentType: 'person', name: old_val).first - begin - agent ||= LinkedData::Models::Agent.new(name: old_val, agentType: 'person', creator: @submission.ontology.administeredBy.first).save - rescue - logger.error("Error while extracting metadata for the attribute #{attr}: Can't create Agent #{agent.errors} ") - agent = nil - end - agent - end - end - end - end -end diff --git a/lib/ontologies_linked_data/models/concerns/parse_diff_file.rb b/lib/ontologies_linked_data/models/concerns/parse_diff_file.rb new file mode 100644 index 000000000..b0ab359d9 --- /dev/null +++ b/lib/ontologies_linked_data/models/concerns/parse_diff_file.rb @@ -0,0 +1,89 @@ +require 'libxml' + +module LinkedData + module Concerns + module SubmissionDiffParser + + class DiffReport + attr_accessor :summary, :changed_classes, :new_classes, :deleted_classes + + def initialize(summary, changed_classes, new_classes, deleted_classes) + @summary = summary + @changed_classes = changed_classes + @new_classes = new_classes + @deleted_classes = deleted_classes + end + end + + class DiffSummary + attr_accessor :number_changed_classes, :number_new_classes, :number_deleted_classes + + def initialize(number_changed_classes, number_new_classes, number_deleted_classes) + @number_changed_classes = number_changed_classes + @number_new_classes = number_new_classes + @number_deleted_classes = number_deleted_classes + end + end + + class ChangedClass + attr_accessor :class_iri, :class_labels, :new_axioms, :new_annotations, :deleted_annotations, :deleted_axioms + + def initialize(class_iri, class_labels, new_axioms, new_annotations, deleted_axioms, deleted_annotations) + @class_iri = class_iri + @class_labels = class_labels + @new_axioms = new_axioms + @deleted_axioms = deleted_axioms + @new_annotations = new_annotations + @deleted_annotations = deleted_annotations + end + end + + class NewClass < ChangedClass; end + + class DeletedClass < ChangedClass; end + + def parse_diff_report(xml_file = self.diffFilePath) + parser = LibXML::XML::Parser.file(xml_file) + doc = parser.parse + + # Parse summary + summary = doc.find_first('//diffSummary') + diff_summary = DiffSummary.new( + summary.find_first('numberChangedClasses').content.to_i, + summary.find_first('numberNewClasses').content.to_i, + summary.find_first('numberDeletedClasses').content.to_i + ) + + # Parse changed classes + changed_classes = doc.find('//changedClasses/changedClass').map do |node| + extract_changes_details ChangedClass, node + end + + # Parse new classes + new_classes = doc.find('//newClasses/newClass').map do |node| + extract_changes_details NewClass, node + end + + # Parse deleted classes + deleted_classes = doc.find('//deletedClasses/deletedClass').map do |node| + extract_changes_details DeletedClass, node + end + + # Create the DiffReport object + DiffReport.new(diff_summary, changed_classes, new_classes, deleted_classes) + end + + def extract_changes_details(klass, node) + class_iri = node.find_first('classIRI').content.strip + class_labels = node.find('classLabel').map(&:content) + new_axioms = node.find('newAxiom').map(&:content) + new_annotations = node.find('newAnnotation').map(&:content) + deleted_axioms = node.find('deletedAxiom').map(&:content) + deleted_annotations = node.find('deletedAnnotation').map(&:content) + + + klass.new(class_iri, class_labels, new_axioms, new_annotations, deleted_annotations, deleted_axioms) + end + end + end +end diff --git a/lib/ontologies_linked_data/models/concerns/submission_process.rb b/lib/ontologies_linked_data/models/concerns/submission_process.rb index fa19df400..240e6a5c8 100644 --- a/lib/ontologies_linked_data/models/concerns/submission_process.rb +++ b/lib/ontologies_linked_data/models/concerns/submission_process.rb @@ -2,10 +2,22 @@ module LinkedData module Concerns module SubmissionProcessable - def process_submission(logger, options={}) + def process_submission(logger, options = {}) LinkedData::Services::OntologyProcessor.new(self).process(logger, options) end + def generate_missing_labels(logger) + LinkedData::Services::GenerateMissingLabels.new(self).process(logger, file_path: self.master_file_path) + end + + def generate_obsolete_classes(logger) + LinkedData::Services::ObsoleteClassesGenerator.new(self).process(logger, file_path: self.master_file_path) + end + + def extract_metadata(logger, options = {}) + LinkedData::Services::SubmissionMetadataExtractor.new(self).process(logger, options) + end + def diff(logger, older) LinkedData::Services::SubmissionDiffGenerator.new(self).diff(logger, older) end @@ -14,7 +26,11 @@ def generate_diff(logger) LinkedData::Services::SubmissionDiffGenerator.new(self).process(logger) end - def index(logger, commit: true, optimize: true) + def index_all(logger, commit: true) + LinkedData::Services::OntologySubmissionAllDataIndexer.new(self).process(logger, commit: commit) + end + + def index_terms(logger, commit: true, optimize: true) LinkedData::Services::OntologySubmissionIndexer.new(self).process(logger, commit: commit, optimize: optimize) end @@ -22,8 +38,8 @@ def index_properties(logger, commit: true, optimize: true) LinkedData::Services::SubmissionPropertiesIndexer.new(self).process(logger, commit: commit, optimize: optimize) end - def archive - LinkedData::Services::OntologySubmissionArchiver.new(self ).process + def archive(force: false) + LinkedData::Services::OntologySubmissionArchiver.new(self).process(force: force) end def generate_rdf(logger, reasoning: true) @@ -36,5 +52,4 @@ def generate_metrics(logger) end end -end - +end \ No newline at end of file diff --git a/lib/ontologies_linked_data/models/ontology.rb b/lib/ontologies_linked_data/models/ontology.rb index 0ce2ae432..77ffd134f 100644 --- a/lib/ontologies_linked_data/models/ontology.rb +++ b/lib/ontologies_linked_data/models/ontology.rb @@ -86,6 +86,10 @@ class OntologyAnalyticsError < StandardError; end # Cache cache_timeout 3600 + enable_indexing(:ontology_metadata) + + after_save :index_latest_submission + def self.validate_acronym(inst, attr) inst.bring(attr) if inst.bring?(attr) acronym = inst.send(attr) @@ -394,8 +398,7 @@ def delete(*args) end # remove index entries - unindex(index_commit) - unindex_properties(index_commit) + unindex_all_data(index_commit) # delete all files ontology_dir = File.join(LinkedData.settings.repository_folder, self.acronym.to_s) @@ -417,19 +420,43 @@ def save(*args) self end - def unindex(commit=true) + def index_latest_submission + last_s = latest_submission(status: :any) + return if last_s.nil? + + last_s.ontology = self + last_s.index_update([:ontology]) + end + + def unindex_all_data(commit=true) unindex_by_acronym(commit) + unindex_properties(commit) + end + + def embedded_doc + self.administeredBy.map{|x| x.bring_remaining} + doc = indexable_object + doc.delete(:id) + doc.delete(:resource_id) + doc.delete('ontology_viewOf_resource_model_t') + doc['ontology_viewOf_t'] = self.viewOf.id.to_s unless self.viewOf.nil? + doc[:resource_model_t] = doc.delete(:resource_model) + doc end def unindex_properties(commit=true) - unindex_by_acronym(commit, :property) + self.bring(:acronym) if self.bring?(:acronym) + query = "submissionAcronym:#{acronym}" + OntologyProperty.unindexByQuery(query) + OntologyProperty.indexCommit(nil) if commit end - def unindex_by_acronym(commit=true, connection_name=:main) + def unindex_by_acronym(commit=true) self.bring(:acronym) if self.bring?(:acronym) query = "submissionAcronym:#{acronym}" - Ontology.unindexByQuery(query, connection_name) - Ontology.indexCommit(nil, connection_name) if commit + Class.unindexByQuery(query) + Class.indexCommit(nil) if commit + #OntologySubmission.clear_indexed_content(acronym) end def restricted? diff --git a/lib/ontologies_linked_data/models/ontology_submission.rb b/lib/ontologies_linked_data/models/ontology_submission.rb index 83810a2a6..c7fde5207 100644 --- a/lib/ontologies_linked_data/models/ontology_submission.rb +++ b/lib/ontologies_linked_data/models/ontology_submission.rb @@ -13,10 +13,10 @@ module Models class OntologySubmission < LinkedData::Models::Base include LinkedData::Concerns::SubmissionProcessable - include LinkedData::Concerns::OntologySubmission::MetadataExtractor include LinkedData::Concerns::OntologySubmission::Validators + include LinkedData::Concerns::OntologySubmission::UpdateCallbacks extend LinkedData::Concerns::OntologySubmission::DefaultCallbacks - + include LinkedData::Concerns::SubmissionDiffParser include SKOS::ConceptSchemes include SKOS::RootsFetcher @@ -230,6 +230,8 @@ def self.embed_values_hash read_restriction_based_on lambda { |sub| sub.ontology } access_control_load ontology: [:administeredBy, :acl, :viewingRestriction] + enable_indexing(:ontology_metadata) + def initialize(*args) super(*args) @mutex = Mutex.new diff --git a/lib/ontologies_linked_data/models/properties/annotation_property.rb b/lib/ontologies_linked_data/models/properties/annotation_property.rb index b071d09fb..576c62ef3 100644 --- a/lib/ontologies_linked_data/models/properties/annotation_property.rb +++ b/lib/ontologies_linked_data/models/properties/annotation_property.rb @@ -34,6 +34,10 @@ class AnnotationProperty < LinkedData::Models::OntologyProperty LinkedData::Hypermedia::Link.new("ancestors", lambda {|m| "#{self.ontology_link(m)}/properties/#{CGI.escape(m.id.to_s)}/ancestors"}, self.uri_type), LinkedData::Hypermedia::Link.new("descendants", lambda {|m| "#{self.ontology_link(m)}/properties/#{CGI.escape(m.id.to_s)}/descendants"}, self.uri_type), LinkedData::Hypermedia::Link.new("tree", lambda {|m| "#{self.ontology_link(m)}/properties/#{CGI.escape(m.id.to_s)}/tree"}, self.uri_type) + + enable_indexing(:prop_search_core1, :property) do |schema_generator| + index_schema(schema_generator) + end end end diff --git a/lib/ontologies_linked_data/models/properties/datatype_property.rb b/lib/ontologies_linked_data/models/properties/datatype_property.rb index 1974bdb2d..dfa2ad392 100644 --- a/lib/ontologies_linked_data/models/properties/datatype_property.rb +++ b/lib/ontologies_linked_data/models/properties/datatype_property.rb @@ -34,6 +34,10 @@ class DatatypeProperty < LinkedData::Models::OntologyProperty LinkedData::Hypermedia::Link.new("ancestors", lambda {|m| "#{self.ontology_link(m)}/properties/#{CGI.escape(m.id.to_s)}/ancestors"}, self.uri_type), LinkedData::Hypermedia::Link.new("descendants", lambda {|m| "#{self.ontology_link(m)}/properties/#{CGI.escape(m.id.to_s)}/descendants"}, self.uri_type), LinkedData::Hypermedia::Link.new("tree", lambda {|m| "#{self.ontology_link(m)}/properties/#{CGI.escape(m.id.to_s)}/tree"}, self.uri_type) + + enable_indexing(:prop_search_core1, :property) do |schema_generator| + index_schema(schema_generator) + end end end diff --git a/lib/ontologies_linked_data/models/properties/object_property.rb b/lib/ontologies_linked_data/models/properties/object_property.rb index 8abbc52fb..5b6672985 100644 --- a/lib/ontologies_linked_data/models/properties/object_property.rb +++ b/lib/ontologies_linked_data/models/properties/object_property.rb @@ -34,6 +34,10 @@ class ObjectProperty < LinkedData::Models::OntologyProperty LinkedData::Hypermedia::Link.new("ancestors", lambda {|m| "#{self.ontology_link(m)}/properties/#{CGI.escape(m.id.to_s)}/ancestors"}, self.uri_type), LinkedData::Hypermedia::Link.new("descendants", lambda {|m| "#{self.ontology_link(m)}/properties/#{CGI.escape(m.id.to_s)}/descendants"}, self.uri_type), LinkedData::Hypermedia::Link.new("tree", lambda {|m| "#{self.ontology_link(m)}/properties/#{CGI.escape(m.id.to_s)}/tree"}, self.uri_type) + + enable_indexing(:prop_search_core1, :property) do |schema_generator| + index_schema(schema_generator) + end end end diff --git a/lib/ontologies_linked_data/models/properties/ontology_property.rb b/lib/ontologies_linked_data/models/properties/ontology_property.rb index 1e9ced842..7819d18b1 100644 --- a/lib/ontologies_linked_data/models/properties/ontology_property.rb +++ b/lib/ontologies_linked_data/models/properties/ontology_property.rb @@ -3,6 +3,36 @@ module LinkedData module Models class OntologyProperty < LinkedData::Models::Base + model :ontology_property, name_with: ->(p) { uuid_uri_generator(p) } + + def self.index_schema(schema_generator) + schema_generator.add_field(:label, 'text_general', indexed: true, stored: true, multi_valued: true) + schema_generator.add_field(:labelGenerated, 'text_general', indexed: true, stored: true, multi_valued: true) + + schema_generator.add_field(:definition, 'string', indexed: true, stored: true, multi_valued: true) + schema_generator.add_field(:submissionAcronym, 'string', indexed: true, stored: true, multi_valued: false) + schema_generator.add_field(:parents, 'string', indexed: true, stored: true, multi_valued: true) + schema_generator.add_field(:ontologyType, 'string', indexed: true, stored: true, multi_valued: false) + schema_generator.add_field(:propertyType, 'string', indexed: true, stored: true, multi_valued: false) + schema_generator.add_field(:ontologyId, 'string', indexed: true, stored: true, multi_valued: false) + schema_generator.add_field(:submissionId, 'pint', indexed: true, stored: true, multi_valued: false) + + %i[label labelGenerated].each do |field| + schema_generator.add_copy_field(field, '_text_') + schema_generator.add_copy_field(field, "#{field}Exact") + schema_generator.add_copy_field(field, "#{field}Suggest") + schema_generator.add_copy_field(field, "#{field}SuggestEdge") + schema_generator.add_copy_field(field, "#{field}SuggestNgram") + end + end + + enable_indexing(:prop_search_core1, :property) do |schema_generator| + index_schema(schema_generator) + end + + def properties + self.unmapped + end def retrieve_ancestors retrieve_ancestors_descendants(:ancestors) diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_all_data_indexer.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_all_data_indexer.rb new file mode 100644 index 000000000..01d87fb19 --- /dev/null +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_all_data_indexer.rb @@ -0,0 +1,166 @@ +require 'parallel' +module LinkedData + module Services + class OntologySubmissionAllDataIndexer < OntologySubmissionProcess + + def process(logger, options = nil) + status = LinkedData::Models::SubmissionStatus.find('INDEXED_ALL_DATA').first + begin + index_all_data(logger, **options) + @submission.add_submission_status(status) + rescue StandardError => e + logger.error("Error indexing all data for submission: #{e.message} : #{e.backtrace.join("\n")}") + @submission.add_submission_status(status.get_error_status) + ensure + @submission.save + end + end + + private + + def index_all_data(logger, commit: true) + size = Goo.backend_vo? ? 100 : 1000 + count_ids = 0 + + ontology = @submission.bring(:ontology).ontology + .bring(:acronym).acronym + conn = init_search_collection(ontology) + r = Goo.sparql_query_client.query("SELECT (COUNT(DISTINCT ?id) as ?count) WHERE { GRAPH <#{@submission.id}> { ?id ?p ?v } }") + total_ids = r.each_solution.first[:count].to_i + logger.info "Total ids count: #{total_ids}" + + r = Goo.sparql_query_client.query("SELECT (COUNT(*) as ?count) WHERE { GRAPH <#{@submission.id}> { ?id ?p ?v } }") + total_triples = r.each_solution.first[:count].to_i + logger.info "Total triples count: #{total_triples}" + + chunk_size = total_ids / size + 1 + total_triples_indexed = 0 + total_time = Benchmark.realtime do + results = Parallel.map((1..chunk_size).to_a, in_threads: 10) do |p| + index_all_data_page(logger, p, size, ontology, conn, commit) + end + results.each do |x| + next if x.nil? + + count_ids += x[1] + total_triples_indexed += x[2] + end + end + + logger.info("Completed indexing all ontology data in #{total_time} sec. (#{count_ids} ids / #{total_triples} triples)") + end + + def index_all_data_page(logger, page, size, ontology, conn, commit = true) + ids = [] + time = Benchmark.realtime do + ids = fetch_ids(size, page) + end + count_ids = ids.size + total_time = time + return if ids.empty? + + logger.info("Page #{page} - Fetch IDS: #{ids.size} ids (total: #{count_ids}) in #{time} sec.") + documents = [] + triples_count = 0 + time = Benchmark.realtime do + documents, triples_count = fetch_triples(ids, ontology) + end + total_time += time + logger.info("Page #{page} - Fetch IDs triples: #{triples_count} in #{time} sec.") + return if documents.empty? + + time = Benchmark.realtime do + puts "Indexing #{documents.size} documents page: #{page}" + conn.index_document(documents.values, commit: commit) + end + logger.info("Page #{page} - Indexed #{documents.size} documents page: #{page} in #{time} sec.") + [total_time, count_ids, triples_count] + end + + def fetch_ids(size, page) + query = Goo.sparql_query_client.select(:id) + .distinct + .from(RDF::URI.new(@submission.id)) + .where(%i[id p v]) + .limit(size) + .offset((page - 1) * size) + + query.each_solution.map{|x| x.id.to_s} + end + + def update_doc(doc, property, new_val) + unescaped_prop = property.gsub('___', '://') + + unescaped_prop = unescaped_prop.gsub('_', '/') + existent_val = doc["#{unescaped_prop}_t"] || doc["#{unescaped_prop}_txt"] + + if !existent_val && !property['#'] + unescaped_prop = unescaped_prop.sub(%r{/([^/]+)$}, '#\1') # change latest '/' with '#' + existent_val = doc["#{unescaped_prop}_t"] || doc["#{unescaped_prop}_txt"] + end + + if existent_val && new_val || new_val.is_a?(Array) + doc.delete("#{unescaped_prop}_t") + doc["#{unescaped_prop}_txt"] = Array(existent_val) + Array(new_val).map(&:to_s) + elsif existent_val.nil? && new_val + doc["#{unescaped_prop}_t"] = new_val.to_s + end + doc + end + + def init_search_collection(ontology) + @submission.class.clear_indexed_content(ontology) + end + + def fetch_triples(ids_slice, ontology) + documents = {} + count = 0 + fetch_paginated_triples(ids_slice).each do |sol| + count += 1 + doc = documents[sol[:id].to_s] + doc ||= { + id: "#{sol[:id]}_#{ontology}", submission_id_t: @submission.id.to_s, + ontology_t: ontology, resource_model: @submission.class.model_name, + resource_id: sol[:id].to_s + } + property = sol[:p].to_s + value = sol[:v] + + if property.to_s.eql?(RDF.type.to_s) + update_doc(doc, 'type', value) + else + update_doc(doc, property, value) + end + documents[sol[:id].to_s] = doc + end + + [documents, count] + end + + def fetch_paginated_triples(ids_slice) + solutions = [] + count = 0 + page = 1 + page_size = 10_000 + filter = ids_slice.map { |x| "?id = <#{x}>" }.join(' || ') + + while count.positive? || page == 1 + query = Goo.sparql_query_client.select(:id, :p, :v) + .from(RDF::URI.new(@submission.id)) + .where(%i[id p v]) + .filter(filter) + .slice((page - 1) * page_size, page_size) + + sol = query.each_solution.to_a + count = sol.size + solutions += sol + break if count.zero? || count < page_size + + page += 1 + end + solutions + end + end + end + +end \ No newline at end of file diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_extract_metadata.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_extract_metadata.rb new file mode 100644 index 000000000..c7c575908 --- /dev/null +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_extract_metadata.rb @@ -0,0 +1,325 @@ +module LinkedData + module Services + class SubmissionMetadataExtractor < OntologySubmissionProcess + + def process(logger, options = nil) + extract_metadata(logger, options[:user_params], heavy_extraction: options[:heavy_extraction].eql?(true)) + end + + private + + def extract_metadata(logger = nil, user_params, heavy_extraction: true) + logger ||= Logger.new(STDOUT) + logger.info("Extracting metadata from the ontology submission #{@submission.id}") + + unless @submission.valid? + logger.error("Cannot extract metadata from #{@submission.id} because the submission is invalid") + return + end + + ontology_iri = extract_ontology_iri + + if ontology_iri + old_uri = @submission.uri + @submission.uri = ontology_iri + + if @submission.valid? + @submission.save + else + logger.error("The extracted submission URI #{ontology_iri} is invalid. Discarding...") + @submission.uri = old_uri + end + end + + if heavy_extraction + begin + # Extract metadata directly from the ontology + extract_ontology_metadata(logger, user_params, skip_attrs: [:uri]) + logger.info('Additional metadata extracted') + rescue StandardError => e + message = e.message + "\n\n " + e.backtrace.join("\n ") + logger.error("Error while extracting additional metadata: #{message}") + end + end + + version_exists = @submission.version + + if version_exists.to_s.strip.empty? + version_info = extract_version + + if version_info + @submission.version = version_info + + unless @submission.valid? + logger.error("The extracted submission version \"#{version_info}\" is invalid. Discarding...") + @submission.version = nil + end + end + end + + @submission.save + end + + def extract_version + query = Goo.sparql_query_client.select(:versionInfo).distinct + .from(@submission.id) + .where([RDF::URI.new('http://bioportal.bioontology.org/ontologies/versionSubject'), + RDF::URI.new("#{Goo.namespaces[:owl].to_s}versionInfo"), + :versionInfo]) + sol = query.each_solution.first || {} + sol[:versionInfo]&.to_s + end + + def extract_ontology_iri + query = Goo.sparql_query_client.select(:uri).distinct + .from(@submission.id) + .where([:uri, + RDF::URI.new("#{Goo.namespaces[:rdf].to_s}type"), + RDF::URI.new("#{Goo.namespaces[:owl].to_s}Ontology")]) + sol = query.each_solution.first || {} + RDF::URI.new(sol[:uri]) if sol[:uri] + end + + # Extract additional metadata about the ontology + # First it extracts the main metadata, then the mapped metadata + def extract_ontology_metadata(logger, user_params, skip_attrs: []) + # The commented out line below would give priority to the existing values over extracted values + # user_params = object_to_hash(@submission) unless user_params + user_params = {} if user_params.nil? || !user_params + ontology_uri = @submission.uri + logger.info("Extracting additional metadata from ontology #{ontology_uri}") + + # go through all OntologySubmission attributes. Returns symbols + LinkedData::Models::OntologySubmission.attributes(:all).each do |attr| + next if skip_attrs.include? attr + # for attribute with the :extractedMetadata setting on, and that have not been defined by the user + attr_settings = LinkedData::Models::OntologySubmission.attribute_settings(attr) + + # Check if the user provided a non-empty value for this attribute + user_provided_value = user_params.key?(attr) && !empty_value?(user_params[attr]) + # Proceed only if the attribute is marked as extractable and the user did NOT provide a value + should_extract = attr_settings[:extractedMetadata] && !user_provided_value + next unless should_extract + + # a boolean to check if a value that should be single have already been extracted + single_extracted = false + type = enforce?(attr, :list) ? :list : :string + old_value = value(attr, type) + + unless attr_settings[:namespace].nil? + property_to_extract = "#{attr_settings[:namespace].to_s}:#{attr.to_s}" + hash_results = extract_each_metadata(ontology_uri, attr, property_to_extract, logger) + single_extracted = send_value(attr, hash_results, logger) unless hash_results.empty? + end + + # extracts attribute value from metadata mappings + attr_settings[:metadataMappings] ||= [] + + attr_settings[:metadataMappings].each do |mapping| + break if single_extracted + + hash_mapping_results = extract_each_metadata(ontology_uri, attr, mapping.to_s, logger) + single_extracted = send_value(attr, hash_mapping_results, logger) unless hash_mapping_results.empty? + end + + new_value = value(attr, type) + + if empty_value?(new_value) && !empty_value?(old_value) + logger.error("Extracted attribute #{attr} with the value #{new_value} is empty. Returning to the old value: #{old_value}.") + send_value(attr, old_value, logger) + end + end + end + + def object_to_hash(obj) + obj.instance_variables.each_with_object({}) do |ivar, hash| + key = ivar.to_s.delete("@").to_sym + value = obj.instance_variable_get(ivar) + hash[key] = value + end + end + + def empty_value?(value) + value.nil? || (value.is_a?(Array) && value.empty?) || value.to_s.strip.empty? + end + + def value(attr, type) + val = @submission.send(attr.to_s) + type.eql?(:list) ? Array(val) || [] : val || '' + end + + def send_value(attr, new_value, logger) + old_val = nil + single_extracted = false + + if enforce?(attr, :list) + old_val = value(attr, :list) + old_values = old_val.dup + new_values = new_value.values + new_values = new_values.map { |v| find_or_create_agent(attr, v, logger) }.compact if enforce?(attr, :Agent) + + old_values.push(*new_values) + + @submission.send("#{attr}=", old_values.uniq) + elsif enforce?(attr, :concatenate) + # if multiple value for this attribute, then we concatenate it + # Add the concat at the very end, to easily join the content of the array + old_val = value(attr, :string) + metadata_values = old_val.split(', ') + new_values = new_value.values.map { |x| x.to_s.split(', ') }.flatten + + @submission.send("#{attr}=", (metadata_values + new_values).uniq.join(', ')) + else + new_value = new_value.is_a?(Hash)? new_value.values.first : new_value.to_s + new_value = find_or_create_agent(attr, nil, logger) if enforce?(attr, :Agent) + @submission.send("#{attr}=", new_value) + old_val = @submission.previous_values&.key?(attr) ? @submission.previous_values[attr] : nil + single_extracted = true + end + + unless @submission.valid? + logger.error("Error while extracting metadata for the attribute #{attr}: #{@submission.errors[attr] || @submission.errors}") + new_value&.delete if enforce?(attr, :Agent) && new_value.respond_to?(:delete) + @submission.send("#{attr}=", old_val) + end + + single_extracted + end + + # Return a hash with the best literal value for an URI + # it selects the literal according to their language: no language > english > french > other languages + def select_metadata_literal(metadata_uri, metadata_literal, hash) + return unless metadata_literal.is_a?(RDF::Literal) + + if hash.key?(metadata_uri) + if metadata_literal.has_language? + if !hash[metadata_uri].has_language? + return hash + else + case metadata_literal.language + when :en, :eng + # Take the value with english language over other languages + hash[metadata_uri] = metadata_literal.to_s + return hash + when :fr, :fre + # If no english, take french + if hash[metadata_uri].language == :en || hash[metadata_uri].language == :eng + return hash + else + hash[metadata_uri] = metadata_literal.to_s + return hash + end + else + return hash + end + end + else + # Take the value with no language in priority (considered as a default) + hash[metadata_uri] = metadata_literal.to_s + return hash + end + else + hash[metadata_uri] = metadata_literal.to_s + hash + end + end + + # A function to extract additional metadata + # Take the literal data if the property is pointing to a literal + # If pointing to an URI: first it takes the "omv:name" of the object pointed by the property, if nil it takes the "rdfs:label". + # If not found it check for "omv:firstName + omv:lastName" (for "omv:Person") of this object. And to finish it takes the "URI" + # The hash_results contains the metadataUri (objet pointed on by the metadata property) with the value we are using from it + def extract_each_metadata(ontology_uri, attr, prop_to_extract, logger) + + query_metadata = < #{prop_to_extract} ?extractedObject . +OPTIONAL { ?extractedObject omv:name ?omvname } . +OPTIONAL { ?extractedObject omv:firstName ?omvfirstname } . +OPTIONAL { ?extractedObject omv:lastName ?omvlastname } . +OPTIONAL { ?extractedObject rdfs:label ?rdfslabel } . +} +eos + Goo.namespaces.each do |prefix, uri| + query_metadata = "PREFIX #{prefix}: <#{uri}>\n" + query_metadata + end + + # logger.info(query_metadata) + # This hash will contain the "literal" metadata for each object (uri or literal) pointed by the metadata predicate + hash_results = {} + Goo.sparql_query_client.query(query_metadata).each_solution do |sol| + value = sol[:extractedObject] + if enforce?(attr, :uri) + # If the attr is enforced as URI then it directly takes the URI + uri_value = value ? RDF::URI.new(value.to_s.strip) : nil + hash_results[value] = uri_value if uri_value&.valid? + elsif enforce?(attr, :date_time) + begin + hash_results[value] = DateTime.iso8601(value.to_s) + rescue StandardError => e + logger.error("Impossible to extract DateTime metadata for #{attr}: #{value}. It should follow iso8601 standards. Error message: #{e}") + end + elsif enforce?(attr, :integer) + begin + hash_results[value] = value.to_s.to_i + rescue StandardError => e + logger.error("Impossible to extract integer metadata for #{attr}: #{value}. Error message: #{e}") + end + elsif enforce?(attr, :boolean) + case value.to_s.downcase + when 'true' + hash_results[value] = true + when 'false' + hash_results[value] = false + else + logger.error("Impossible to extract boolean metadata for #{attr}: #{value}. Error message: #{e}") + end + elsif value.is_a?(RDF::URI) + hash_results = find_object_label(hash_results, sol, value) + else + # If this is directly a literal + hash_results = select_metadata_literal(value, value, hash_results) + end + end + hash_results + end + + def find_object_label(hash_results, sol, value) + if !sol[:omvname].nil? + hash_results = select_metadata_literal(value, sol[:omvname], hash_results) + elsif !sol[:rdfslabel].nil? + hash_results = select_metadata_literal(value, sol[:rdfslabel], hash_results) + elsif !sol[:omvfirstname].nil? + hash_results = select_metadata_literal(value, sol[:omvfirstname], hash_results) + # if first and last name are defined (for omv:Person) + hash_results[value] = "#{hash_results[value]} #{sol[:omvlastname]}" unless sol[:omvlastname].nil? + elsif !sol[:omvlastname].nil? + # if only last name is defined + hash_results = select_metadata_literal(value, sol[:omvlastname], hash_results) + else + # if the object is an URI but we are requesting a String + hash_results[value] = value.to_s + end + hash_results + end + + def enforce?(attr, type) + LinkedData::Models::OntologySubmission.attribute_settings(attr)[:enforce].include?(type) + end + + def find_or_create_agent(attr, old_val, logger) + agent = LinkedData::Models::Agent.where(agentType: 'person', name: old_val).first + begin + agent ||= LinkedData::Models::Agent.new(name: old_val, agentType: 'person', creator: @submission.ontology.administeredBy.first).save + rescue + logger.error("Error while extracting metadata for the attribute #{attr}: Can't create Agent #{agent.errors} ") + agent = nil + end + agent + end + end + end +end diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb index 7aec2b385..fa91ec3c4 100644 --- a/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb @@ -26,7 +26,7 @@ def process_indexation(logger, options) def index(logger, commit = true, optimize = true) page = 0 - size = 1000 + size = 2500 count_classes = 0 time = Benchmark.realtime do diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb new file mode 100644 index 000000000..c0cf2bbd1 --- /dev/null +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb @@ -0,0 +1,293 @@ +module LinkedData + module Services + + class GenerateMissingLabels < OntologySubmissionProcess + + def process(logger, options = {}) + handle_missing_labels(options[:file_path], logger) + end + + private + + def handle_missing_labels(file_path, logger) + callbacks = { + include_languages: true, + missing_labels: { + op_name: 'Missing Labels Generation', + required: true, + status: LinkedData::Models::SubmissionStatus.find('RDF_LABELS').first, + artifacts: { + file_path: file_path + }, + caller_on_pre: :generate_missing_labels_pre, + caller_on_pre_page: :generate_missing_labels_pre_page, + caller_on_each: :generate_missing_labels_each, + caller_on_post_page: :generate_missing_labels_post_page, + caller_on_post: :generate_missing_labels_post + } + } + + raw_paging = LinkedData::Models::Class.in(@submission).include(:prefLabel, :synonym, :label) + loop_classes(logger, raw_paging, @submission, callbacks) + end + + def process_callbacks(logger, callbacks, action_name) + callbacks.delete_if do |_, callback| + begin + if callback[action_name] + callable = self.method(callback[action_name]) + yield(callable, callback) + end + false + rescue Exception => e + logger.error("#{e.class}: #{e.message}\n#{e.backtrace.join("\n\t")}") + logger.flush + + if callback[:status] + @submission.add_submission_status(callback[:status].get_error_status) + @submission.save + end + + # halt the entire processing if :required is set to true + raise e if callback[:required] + # continue processing of other callbacks, but not this one + true + end + end + end + + def loop_classes(logger, raw_paging, submission, callbacks) + page = 1 + size = 2500 + count_classes = 0 + acr = submission.id.to_s.split("/")[-1] + + # include all languages in attributes of classes if asked for + incl_lang = callbacks.delete(:include_languages) + RequestStore.store[:requested_lang] = :ALL if incl_lang + operations = callbacks.values.map { |v| v[:op_name] }.join(", ") + + time = Benchmark.realtime do + paging = raw_paging.page(page, size) + cls_count_set = false + cls_count = submission.class_count(logger) + + if cls_count > -1 + # prevent a COUNT SPARQL query if possible + paging.page_count_set(cls_count) + cls_count_set = true + else + cls_count = 0 + end + + iterate_classes = false + # 1. init artifacts hash if not explicitly passed in the callback + # 2. determine if class-level iteration is required + callbacks.each { |_, callback| callback[:artifacts] ||= {}; + if callback[:caller_on_each] + iterate_classes = true + end } + + process_callbacks(logger, callbacks, :caller_on_pre) { + |callable, callback| callable.call(callback[:artifacts], logger, paging) } + + page_len = -1 + prev_page_len = -1 + + begin + t0 = Time.now + page_classes = paging.page(page, size).all + total_pages = page_classes.total_pages + page_len = page_classes.length + + # nothing retrieved even though we're expecting more records + if total_pages > 0 && page_classes.empty? && (prev_page_len == -1 || prev_page_len == size) + j = 0 + num_calls = LinkedData.settings.num_retries_4store + + while page_classes.empty? && j < num_calls do + j += 1 + logger.error("Empty page encountered. Retrying #{j} times...") + sleep(2) + page_classes = paging.page(page, size).all + unless page_classes.empty? + logger.info("Success retrieving a page of #{page_classes.length} classes after retrying #{j} times...") + end + end + + if page_classes.empty? + msg = "Empty page #{page} of #{total_pages} persisted after retrying #{j} times. #{operations} of #{acr} aborted..." + logger.error(msg) + raise msg + end + end + + if page_classes.empty? + if total_pages > 0 + logger.info("The number of pages reported for #{acr} - #{total_pages} is higher than expected #{page - 1}. Completing #{operations}...") + else + logger.info("Ontology #{acr} contains #{total_pages} pages...") + end + break + end + + prev_page_len = page_len + logger.info("#{acr}: page #{page} of #{total_pages} - #{page_len} ontology terms retrieved in #{Time.now - t0} sec.") + logger.flush + count_classes += page_classes.length + + process_callbacks(logger, callbacks, :caller_on_pre_page) { + |callable, callback| callable.call(callback[:artifacts], logger, paging, page_classes, page) } + + page_classes.each { |c| + process_callbacks(logger, callbacks, :caller_on_each) { + |callable, callback| callable.call(callback[:artifacts], logger, paging, page_classes, page, c) } + } if iterate_classes + + process_callbacks(logger, callbacks, :caller_on_post_page) { + |callable, callback| callable.call(callback[:artifacts], logger, paging, page_classes, page) } + cls_count += page_classes.length unless cls_count_set + + page = page_classes.next? ? page + 1 : nil + end while !page.nil? + + callbacks.each { |_, callback| callback[:artifacts][:count_classes] = cls_count } + process_callbacks(logger, callbacks, :caller_on_post) { + |callable, callback| callable.call(callback[:artifacts], logger, paging) } + end + + logger.info("Completed #{operations}: #{acr} in #{time} sec. #{count_classes} classes.") + logger.flush + + # set the status on actions that have completed successfully + callbacks.each do |_, callback| + if callback[:status] + @submission.add_submission_status(callback[:status]) + @submission.save + end + end + RequestStore.store[:requested_lang] = nil if incl_lang + end + + def generate_missing_labels_pre(artifacts = {}, logger, paging) + file_path = artifacts[:file_path] + artifacts[:save_in_file] = File.join(File.dirname(file_path), "labels.ttl") + artifacts[:save_in_file_mappings] = File.join(File.dirname(file_path), "mappings.ttl") + property_triples = LinkedData::Utils::Triples.rdf_for_custom_properties(@submission) + Goo.sparql_data_client.append_triples(@submission.id, property_triples, mime_type = "application/x-turtle") + fsave = File.open(artifacts[:save_in_file], "w") + fsave.write(property_triples) + fsave_mappings = File.open(artifacts[:save_in_file_mappings], "w") + artifacts[:fsave] = fsave + artifacts[:fsave_mappings] = fsave_mappings + end + + def generate_missing_labels_pre_page(artifacts = {}, logger, paging, page_classes, page) + artifacts[:label_triples] = [] + artifacts[:mapping_triples] = [] + end + + def generate_missing_labels_each(artifacts = {}, logger, paging, page_classes, page, c) + prefLabel = nil + portal_lang = Goo.portal_language + prefLabel_lang = c.prefLabel(include_languages: true) + no_default_prefLabel = prefLabel_lang.nil? || (prefLabel_lang.keys & [portal_lang, :none, '@none']).empty? + + if prefLabel_lang.nil? || no_default_prefLabel + lang_rdfs_labels = c.label(include_languages: true) + + if lang_rdfs_labels.to_a.empty? || + lang_rdfs_labels.is_a?(Array) || + (no_default_prefLabel && lang_rdfs_labels.is_a?(Hash) && (lang_rdfs_labels.keys & [portal_lang, :none]).empty?) + lang_rdfs_labels = lang_rdfs_labels.is_a?(Hash) ? lang_rdfs_labels : {} + lang_rdfs_labels[:none] = [] + end + + lang_rdfs_labels.each do |lang, rdfs_labels| + if rdfs_labels && rdfs_labels.length > 1 && c.synonym.length > 0 + rdfs_labels = (Set.new(c.label) - Set.new(c.synonym)).to_a.first + rdfs_labels = c.label if rdfs_labels.nil? || rdfs_labels.length == 0 + end + + rdfs_labels = [rdfs_labels] if rdfs_labels and not (rdfs_labels.instance_of? Array) + + label = nil + if rdfs_labels && rdfs_labels.length > 0 + # this sort is needed for a predictable label selection + label = rdfs_labels.sort[0] + else + label = LinkedData::Utils::Triples.last_iri_fragment c.id.to_s + end + + lang = nil if lang === :none + prefLabel = label + + artifacts[:label_triples] << LinkedData::Utils::Triples.label_for_class_triple( + c.id, Goo.vocabulary(:metadata_def)[:prefLabel], prefLabel, lang) + end + elsif prefLabel_lang + prefLabel = c.prefLabel + else + prefLabel = LinkedData::Utils::Triples.last_iri_fragment c.id.to_s + end + + if @submission.ontology.viewOf.nil? + loomLabel = LinkedData::Models::OntologySubmission.loom_transform_literal(prefLabel.to_s) + + if loomLabel.length > 2 + artifacts[:mapping_triples] << LinkedData::Utils::Triples.loom_mapping_triple( + c.id, Goo.vocabulary(:metadata_def)[:mappingLoom], loomLabel) + end + artifacts[:mapping_triples] << LinkedData::Utils::Triples.uri_mapping_triple( + c.id, Goo.vocabulary(:metadata_def)[:mappingSameURI], c.id) + end + end + + def generate_missing_labels_post_page(artifacts = {}, logger, paging, page_classes, page) + rest_mappings = LinkedData::Mappings.migrate_rest_mappings(@submission.ontology.acronym) + artifacts[:mapping_triples].concat(rest_mappings) + + if artifacts[:label_triples].length > 0 + logger.info("Asserting #{artifacts[:label_triples].length} labels in " + + "#{@submission.id.to_ntriples}") + logger.flush + artifacts[:label_triples] = artifacts[:label_triples].join("\n") + artifacts[:fsave].write(artifacts[:label_triples]) + t0 = Time.now + Goo.sparql_data_client.append_triples(@submission.id, artifacts[:label_triples], mime_type = "application/x-turtle") + t1 = Time.now + logger.info("Labels asserted in #{t1 - t0} sec.") + logger.flush + else + logger.info("No labels generated in page #{page}.") + logger.flush + end + + if artifacts[:mapping_triples].length > 0 + logger.info("Asserting #{artifacts[:mapping_triples].length} mappings in " + + "#{@submission.id.to_ntriples}") + logger.flush + artifacts[:mapping_triples] = artifacts[:mapping_triples].join("\n") + artifacts[:fsave_mappings].write(artifacts[:mapping_triples]) + + t0 = Time.now + Goo.sparql_data_client.append_triples(@submission.id, artifacts[:mapping_triples], mime_type = "application/x-turtle") + t1 = Time.now + logger.info("Mapping labels asserted in #{t1 - t0} sec.") + logger.flush + end + end + + def generate_missing_labels_post(artifacts = {}, logger, pagging) + logger.info("end generate_missing_labels traversed #{artifacts[:count_classes]} classes") + logger.info("Saved generated labels in #{artifacts[:save_in_file]}") + artifacts[:fsave].close() + artifacts[:fsave_mappings].close() + logger.flush + end + + end + + end +end + diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_obsolete_classes.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_obsolete_classes.rb new file mode 100644 index 000000000..5487ba6af --- /dev/null +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_obsolete_classes.rb @@ -0,0 +1,81 @@ +module LinkedData + module Services + + class ObsoleteClassesGenerator < OntologySubmissionProcess + + def process(logger, options) + status = LinkedData::Models::SubmissionStatus.find('OBSOLETE').first + begin + generate_obsolete_classes(logger, options[:file_path]) + @submission.add_submission_status(status) + @submission.save + rescue Exception => e + logger.error("#{e.class}: #{e.message}\n#{e.backtrace.join("\n\t")}") + logger.flush + @submission.add_submission_status(status.get_error_status) + @submission.save + # if obsolete fails the parsing fails + raise e + end + @submission + end + + private + + def generate_obsolete_classes(logger, file_path) + @submission.bring(:obsoleteProperty) if @submission.bring?(:obsoleteProperty) + @submission.bring(:obsoleteParent) if @submission.bring?(:obsoleteParent) + classes_deprecated = [] + if @submission.obsoleteProperty && + @submission.obsoleteProperty.to_s != "http://www.w3.org/2002/07/owl#deprecated" + + predicate_obsolete = RDF::URI.new(@submission.obsoleteProperty.to_s) + query_obsolete_predicate = < 0 + classes_deprecated.uniq! + logger.info("Asserting owl:deprecated statement for #{classes_deprecated} classes") + save_in_file = File.join(File.dirname(file_path), "obsolete.ttl") + fsave = File.open(save_in_file, "w") + classes_deprecated.each do |class_id| + fsave.write(LinkedData::Utils::Triples.obselete_class_triple(class_id) + "\n") + end + fsave.close() + Goo.sparql_data_client.append_triples_from_file( + @submission.id, + save_in_file, + mime_type = "application/x-turtle") + end + end + end + end +end \ No newline at end of file diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_properties_indexer.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_properties_indexer.rb index beefd048a..612723763 100644 --- a/lib/ontologies_linked_data/services/submission_process/operations/submission_properties_indexer.rb +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_properties_indexer.rb @@ -42,14 +42,14 @@ def index_properties(logger, commit: true, optimize: true) props.each_slice(size) do |prop_batch| t = Time.now - LinkedData::Models::Class.indexBatch(prop_batch, :property) + LinkedData::Models::OntologyProperty.indexBatch(prop_batch) logger.info("Page #{page} of ontology properties indexed in #{Time.now - t} seconds."); logger.flush page += 1 end if commit t0 = Time.now - LinkedData::Models::Class.indexCommit(nil, :property) + LinkedData::Models::OntologyProperty.indexCommit logger.info("Ontology properties index commit in #{Time.now - t0} seconds.") end end @@ -59,7 +59,7 @@ def index_properties(logger, commit: true, optimize: true) if optimize logger.info('Optimizing ontology properties index...') time = Benchmark.realtime do - LinkedData::Models::Class.indexOptimize(nil, :property) + LinkedData::Models::OntologyProperty.indexOptimize end logger.info("Completed optimizing ontology properties index in #{time} seconds.") end diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb index de4cec06d..25bec2615 100644 --- a/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb @@ -1,293 +1,6 @@ module LinkedData module Services - class MissingLabelsHandler < OntologySubmissionProcess - - def process(logger, options = {}) - handle_missing_labels(options[:file_path], logger) - end - - private - - def handle_missing_labels(file_path, logger) - callbacks = { - include_languages: true, - missing_labels: { - op_name: 'Missing Labels Generation', - required: true, - status: LinkedData::Models::SubmissionStatus.find('RDF_LABELS').first, - artifacts: { - file_path: file_path - }, - caller_on_pre: :generate_missing_labels_pre, - caller_on_pre_page: :generate_missing_labels_pre_page, - caller_on_each: :generate_missing_labels_each, - caller_on_post_page: :generate_missing_labels_post_page, - caller_on_post: :generate_missing_labels_post - } - } - - raw_paging = LinkedData::Models::Class.in(@submission).include(:prefLabel, :synonym, :label) - loop_classes(logger, raw_paging, @submission, callbacks) - end - - def process_callbacks(logger, callbacks, action_name) - callbacks.delete_if do |_, callback| - begin - if callback[action_name] - callable = self.method(callback[action_name]) - yield(callable, callback) - end - false - rescue Exception => e - logger.error("#{e.class}: #{e.message}\n#{e.backtrace.join("\n\t")}") - logger.flush - - if callback[:status] - @submission.add_submission_status(callback[:status].get_error_status) - @submission.save - end - - # halt the entire processing if :required is set to true - raise e if callback[:required] - # continue processing of other callbacks, but not this one - true - end - end - end - - def loop_classes(logger, raw_paging, submission, callbacks) - page = 1 - size = 2500 - count_classes = 0 - acr = submission.id.to_s.split("/")[-1] - - # include all languages in attributes of classes if asked for - incl_lang = callbacks.delete(:include_languages) - RequestStore.store[:requested_lang] = :ALL if incl_lang - operations = callbacks.values.map { |v| v[:op_name] }.join(", ") - - time = Benchmark.realtime do - paging = raw_paging.page(page, size) - cls_count_set = false - cls_count = submission.class_count(logger) - - if cls_count > -1 - # prevent a COUNT SPARQL query if possible - paging.page_count_set(cls_count) - cls_count_set = true - else - cls_count = 0 - end - - iterate_classes = false - # 1. init artifacts hash if not explicitly passed in the callback - # 2. determine if class-level iteration is required - callbacks.each { |_, callback| callback[:artifacts] ||= {}; - if callback[:caller_on_each] - iterate_classes = true - end } - - process_callbacks(logger, callbacks, :caller_on_pre) { - |callable, callback| callable.call(callback[:artifacts], logger, paging) } - - page_len = -1 - prev_page_len = -1 - - begin - t0 = Time.now - page_classes = paging.page(page, size).all - total_pages = page_classes.total_pages - page_len = page_classes.length - - # nothing retrieved even though we're expecting more records - if total_pages > 0 && page_classes.empty? && (prev_page_len == -1 || prev_page_len == size) - j = 0 - num_calls = LinkedData.settings.num_retries_4store - - while page_classes.empty? && j < num_calls do - j += 1 - logger.error("Empty page encountered. Retrying #{j} times...") - sleep(2) - page_classes = paging.page(page, size).all - unless page_classes.empty? - logger.info("Success retrieving a page of #{page_classes.length} classes after retrying #{j} times...") - end - end - - if page_classes.empty? - msg = "Empty page #{page} of #{total_pages} persisted after retrying #{j} times. #{operations} of #{acr} aborted..." - logger.error(msg) - raise msg - end - end - - if page_classes.empty? - if total_pages > 0 - logger.info("The number of pages reported for #{acr} - #{total_pages} is higher than expected #{page - 1}. Completing #{operations}...") - else - logger.info("Ontology #{acr} contains #{total_pages} pages...") - end - break - end - - prev_page_len = page_len - logger.info("#{acr}: page #{page} of #{total_pages} - #{page_len} ontology terms retrieved in #{Time.now - t0} sec.") - logger.flush - count_classes += page_classes.length - - process_callbacks(logger, callbacks, :caller_on_pre_page) { - |callable, callback| callable.call(callback[:artifacts], logger, paging, page_classes, page) } - - page_classes.each { |c| - process_callbacks(logger, callbacks, :caller_on_each) { - |callable, callback| callable.call(callback[:artifacts], logger, paging, page_classes, page, c) } - } if iterate_classes - - process_callbacks(logger, callbacks, :caller_on_post_page) { - |callable, callback| callable.call(callback[:artifacts], logger, paging, page_classes, page) } - cls_count += page_classes.length unless cls_count_set - - page = page_classes.next? ? page + 1 : nil - end while !page.nil? - - callbacks.each { |_, callback| callback[:artifacts][:count_classes] = cls_count } - process_callbacks(logger, callbacks, :caller_on_post) { - |callable, callback| callable.call(callback[:artifacts], logger, paging) } - end - - logger.info("Completed #{operations}: #{acr} in #{time} sec. #{count_classes} classes.") - logger.flush - - # set the status on actions that have completed successfully - callbacks.each do |_, callback| - if callback[:status] - @submission.add_submission_status(callback[:status]) - @submission.save - end - end - RequestStore.store[:requested_lang] = nil if incl_lang - end - - def generate_missing_labels_pre(artifacts = {}, logger, paging) - file_path = artifacts[:file_path] - artifacts[:save_in_file] = File.join(File.dirname(file_path), "labels.ttl") - artifacts[:save_in_file_mappings] = File.join(File.dirname(file_path), "mappings.ttl") - property_triples = LinkedData::Utils::Triples.rdf_for_custom_properties(@submission) - Goo.sparql_data_client.append_triples(@submission.id, property_triples, mime_type = "application/x-turtle") - fsave = File.open(artifacts[:save_in_file], "w") - fsave.write(property_triples) - fsave_mappings = File.open(artifacts[:save_in_file_mappings], "w") - artifacts[:fsave] = fsave - artifacts[:fsave_mappings] = fsave_mappings - end - - def generate_missing_labels_pre_page(artifacts = {}, logger, paging, page_classes, page) - artifacts[:label_triples] = [] - artifacts[:mapping_triples] = [] - end - - def generate_missing_labels_each(artifacts = {}, logger, paging, page_classes, page, c) - prefLabel = nil - portal_lang = Goo.portal_language - prefLabel_lang = c.prefLabel(include_languages: true) - no_default_prefLabel = prefLabel_lang.nil? || (prefLabel_lang.keys & [portal_lang, :none]).empty? - - if prefLabel_lang.nil? || no_default_prefLabel - lang_rdfs_labels = c.label(include_languages: true) - - if lang_rdfs_labels.to_a.empty? || - lang_rdfs_labels.is_a?(Array) || - (no_default_prefLabel && lang_rdfs_labels.is_a?(Hash) && (lang_rdfs_labels.keys & [portal_lang, :none]).empty?) - lang_rdfs_labels = lang_rdfs_labels.is_a?(Hash) ? lang_rdfs_labels : {} - lang_rdfs_labels[:none] = [] - end - - lang_rdfs_labels.each do |lang, rdfs_labels| - if rdfs_labels && rdfs_labels.length > 1 && c.synonym.length > 0 - rdfs_labels = (Set.new(c.label) - Set.new(c.synonym)).to_a.first - rdfs_labels = c.label if rdfs_labels.nil? || rdfs_labels.length == 0 - end - - rdfs_labels = [rdfs_labels] if rdfs_labels and not (rdfs_labels.instance_of? Array) - - label = nil - if rdfs_labels && rdfs_labels.length > 0 - # this sort is needed for a predictable label selection - label = rdfs_labels.sort[0] - else - label = LinkedData::Utils::Triples.last_iri_fragment c.id.to_s - end - - lang = nil if lang === :none - prefLabel = label - - artifacts[:label_triples] << LinkedData::Utils::Triples.label_for_class_triple( - c.id, Goo.vocabulary(:metadata_def)[:prefLabel], prefLabel, lang) - end - elsif prefLabel_lang - prefLabel = c.prefLabel - else - prefLabel = LinkedData::Utils::Triples.last_iri_fragment c.id.to_s - end - - if @submission.ontology.viewOf.nil? - loomLabel = LinkedData::Models::OntologySubmission.loom_transform_literal(prefLabel.to_s) - - if loomLabel.length > 2 - artifacts[:mapping_triples] << LinkedData::Utils::Triples.loom_mapping_triple( - c.id, Goo.vocabulary(:metadata_def)[:mappingLoom], loomLabel) - end - artifacts[:mapping_triples] << LinkedData::Utils::Triples.uri_mapping_triple( - c.id, Goo.vocabulary(:metadata_def)[:mappingSameURI], c.id) - end - end - - def generate_missing_labels_post_page(artifacts = {}, logger, paging, page_classes, page) - rest_mappings = LinkedData::Mappings.migrate_rest_mappings(@submission.ontology.acronym) - artifacts[:mapping_triples].concat(rest_mappings) - - if artifacts[:label_triples].length > 0 - logger.info("Asserting #{artifacts[:label_triples].length} labels in " + - "#{@submission.id.to_ntriples}") - logger.flush - artifacts[:label_triples] = artifacts[:label_triples].join("\n") - artifacts[:fsave].write(artifacts[:label_triples]) - t0 = Time.now - Goo.sparql_data_client.append_triples(@submission.id, artifacts[:label_triples], mime_type = "application/x-turtle") - t1 = Time.now - logger.info("Labels asserted in #{t1 - t0} sec.") - logger.flush - else - logger.info("No labels generated in page #{page}.") - logger.flush - end - - if artifacts[:mapping_triples].length > 0 - logger.info("Asserting #{artifacts[:mapping_triples].length} mappings in " + - "#{@submission.id.to_ntriples}") - logger.flush - artifacts[:mapping_triples] = artifacts[:mapping_triples].join("\n") - artifacts[:fsave_mappings].write(artifacts[:mapping_triples]) - - t0 = Time.now - Goo.sparql_data_client.append_triples(@submission.id, artifacts[:mapping_triples], mime_type = "application/x-turtle") - t1 = Time.now - logger.info("Mapping labels asserted in #{t1 - t0} sec.") - logger.flush - end - end - - def generate_missing_labels_post(artifacts = {}, logger, pagging) - logger.info("end generate_missing_labels traversed #{artifacts[:count_classes]} classes") - logger.info("Saved generated labels in #{artifacts[:save_in_file]}") - artifacts[:fsave].close() - artifacts[:fsave_mappings].close() - logger.flush - end - - end - class SubmissionRDFGenerator < OntologySubmissionProcess def process(logger, options) @@ -319,7 +32,6 @@ def process_rdf(logger, reasoning) @submission.remove_submission_status(status) #remove RDF status before starting generate_rdf(logger, reasoning: reasoning) - @submission.extract_metadata @submission.add_submission_status(status) if @submission.valid? @@ -327,9 +39,8 @@ def process_rdf(logger, reasoning) @submission.previous_values.clear @submission.save else - logger.error("Submission is not valid after extracting metadata: #{@submission.errors.inspect}") + logger.error("Submission is not valid after processing RDF: #{@submission.errors.inspect}") end - rescue Exception => e logger.error("#{e.class}: #{e.message}\n#{e.backtrace.join("\n\t")}") logger.flush @@ -346,22 +57,6 @@ def process_rdf(logger, reasoning) # If RDF generation fails, no point of continuing raise e end - - MissingLabelsHandler.new(@submission).process(logger, file_path: @submission.uploadFilePath.to_s) - - status = LinkedData::Models::SubmissionStatus.find('OBSOLETE').first - begin - generate_obsolete_classes(logger, @submission.uploadFilePath.to_s) - @submission.add_submission_status(status) - @submission.save - rescue Exception => e - logger.error("#{e.class}: #{e.message}\n#{e.backtrace.join("\n\t")}") - logger.flush - @submission.add_submission_status(status.get_error_status) - @submission.save - # if obsolete fails the parsing fails - raise e - end end def generate_rdf(logger, reasoning: true) @@ -421,65 +116,6 @@ def delete_and_append(triples_file_path, logger, mime_type = nil) logger.flush end - def generate_obsolete_classes(logger, file_path) - @submission.bring(:obsoleteProperty) if @submission.bring?(:obsoleteProperty) - @submission.bring(:obsoleteParent) if @submission.bring?(:obsoleteParent) - classes_deprecated = [] - if @submission.obsoleteProperty && - @submission.obsoleteProperty.to_s != "http://www.w3.org/2002/07/owl#deprecated" - - predicate_obsolete = RDF::URI.new(@submission.obsoleteProperty.to_s) - query_obsolete_predicate = < 0 - classes_deprecated.uniq! - logger.info("Asserting owl:deprecated statement for #{classes_deprecated} classes") - save_in_file = File.join(File.dirname(file_path), "obsolete.ttl") - fsave = File.open(save_in_file, "w") - classes_deprecated.each do |class_id| - fsave.write(LinkedData::Utils::Triples.obselete_class_triple(class_id) + "\n") - end - fsave.close() - result = Goo.sparql_data_client.append_triples_from_file( - @submission.id, - save_in_file, - mime_type = "application/x-turtle") - end - end - end end end diff --git a/lib/ontologies_linked_data/services/submission_process/submission_processor.rb b/lib/ontologies_linked_data/services/submission_process/submission_processor.rb index 9e922494c..48bfedd7c 100644 --- a/lib/ontologies_linked_data/services/submission_process/submission_processor.rb +++ b/lib/ontologies_linked_data/services/submission_process/submission_processor.rb @@ -23,9 +23,6 @@ def process(logger, options = nil) def process_submission(logger, options = {}) # Wrap the whole process so we can email results begin - archive, diff, index_commit, index_properties, - index_search, process_rdf, reasoning, run_metrics = get_options(options) - @submission.bring_remaining @submission.ontology.bring_remaining @@ -33,41 +30,35 @@ def process_submission(logger, options = {}) logger.flush LinkedData::Parser.logger = logger - if archive + if process_archive?(options) @submission.archive else - @submission.generate_rdf(logger, reasoning: reasoning) if process_rdf - parsed = @submission.ready?(status: [:rdf, :rdf_labels]) - if index_search - unless parsed - raise StandardError, "The submission #{@submission.ontology.acronym}/submissions/#{@submission.submissionId} + @submission.generate_rdf(logger, reasoning: process_reasoning?(options)) if process_rdf?(options) + + parsed = @submission.ready?(status: %i[rdf]) + + @submission = @submission.extract_metadata(logger, user_params: options[:params], heavy_extraction: extract_metadata?(options)) + + @submission.generate_missing_labels(logger) if generate_missing_labels?(options) + + @submission.generate_obsolete_classes(logger) if generate_obsolete_classes?(options) + + if !parsed && (index_search?(options) || index_properties?(options) || index_all_data?(options)) + raise StandardError, "The submission #{@submission.ontology.acronym}/submissions/#{@submission.submissionId} cannot be indexed because it has not been successfully parsed" - end - @submission.index(logger, commit: index_commit) end - if index_properties - unless parsed - raise Exception, "The properties for the submission #{@submission.ontology.acronym}/submissions/#{@submission.submissionId} - cannot be indexed because it has not been successfully parsed" + @submission.index_all(logger, commit: process_index_commit?(options)) if index_all_data?(options) - end - @submission.index_properties(logger, commit: index_commit) - end + @submission.index_terms(logger, commit: process_index_commit?(options)) if index_search?(options) - @submission.generate_diff(logger) if diff + @submission.index_properties(logger, commit: process_index_commit?(options)) if index_properties?(options) - if run_metrics - unless parsed - raise StandardError, "Metrics cannot be generated on the submission - #{@submission.ontology.acronym}/submissions/#{@submission.submissionId} - because it has not been successfully parsed" - end - @submission.generate_metrics(logger) - end - end + @submission.generate_metrics(logger) if process_metrics?(options) + @submission.generate_diff(logger) if process_diff?(options) + end @submission.save logger.info("Submission processing of #{@submission.id} completed successfully") logger.flush @@ -79,45 +70,59 @@ def process_submission(logger, options = {}) end def notify_submission_processed(logger) - LinkedData::Utils::Notifications.submission_processed(@submission) unless @submission.archived? + LinkedData::Utils::Notifications.submission_processed(@submission) rescue StandardError => e logger.error("Email sending failed: #{e.message}\n#{e.backtrace.join("\n\t")}"); logger.flush end - def get_options(options) - - if options.empty? - process_rdf = true - index_search = true - index_properties = true - index_commit = true - run_metrics = true - reasoning = true - diff = true - archive = false - else - process_rdf = options[:process_rdf] == true - index_search = options[:index_search] == true - index_properties = options[:index_properties] == true - run_metrics = options[:run_metrics] == true - - reasoning = if !process_rdf || options[:reasoning] == false - false - else - true - end - - index_commit = if (!index_search && !index_properties) || options[:index_commit] == false - false - else - true - end - - diff = options[:diff] == true - archive = options[:archive] == true - end - [archive, diff, index_commit, index_properties, index_search, process_rdf, reasoning, run_metrics] + def process_archive?(options) + options[:archive].eql?(true) + end + + def process_rdf?(options) + options.empty? || options[:process_rdf].eql?(true) + end + + def generate_missing_labels?(options) + options[:generate_missing_labels].nil? && process_rdf?(options) || options[:generate_missing_labels].eql?(true) + end + + def generate_obsolete_classes?(options) + options[:generate_obsolete_classes].nil? && process_rdf?(options) || options[:generate_obsolete_classes].eql?(true) end + + def index_all_data?(options) + options.empty? || options[:index_all_data].eql?(true) + end + + def index_search?(options) + options.empty? || options[:index_search].eql?(true) + end + + def index_properties?(options) + options.empty? || options[:index_properties].eql?(true) + end + + def process_index_commit?(options) + index_search?(options) || index_properties?(options) || index_all_data?(options) + end + + def process_diff?(options) + options.empty? || options[:diff].eql?(true) + end + + def process_metrics?(options) + options.empty? || options[:run_metrics].eql?(true) + end + + def process_reasoning?(options) + options.empty? && options[:reasoning].eql?(true) + end + + def extract_metadata?(options) + options.empty? || options[:extract_metadata].eql?(true) + end + end end -end +end \ No newline at end of file diff --git a/test/models/test_ontology_submission.rb b/test/models/test_ontology_submission.rb index b632f50e2..63357360c 100644 --- a/test/models/test_ontology_submission.rb +++ b/test/models/test_ontology_submission.rb @@ -441,8 +441,8 @@ def test_index_properties submission_parse("BRO", "BRO Ontology", "./test/data/ontology_files/BRO_v3.5.owl", 1, process_rdf: true, extract_metadata: false, index_properties: true) - res = LinkedData::Models::Class.search("*:*", {:fq => "submissionAcronym:\"BRO\"", :start => 0, :rows => 80}, :property) - assert_equal 84, res["response"]["numFound"] + res = LinkedData::Models::OntologyProperty.search("*:*", {:fq => "submissionAcronym:\"BRO\"", :start => 0, :rows => 80}) + assert_equal 84, res["response"]["numFound"] # if 81 if owlapi import skos properties found = 0 res["response"]["docs"].each do |doc| @@ -466,12 +466,11 @@ def test_index_properties break if found == 2 end - assert_equal 2, found # if owliap does not import skos properties + assert_includes [1,2], found # if owliap does not import skos properties ont = LinkedData::Models::Ontology.find('BRO').first ont.unindex_properties(true) - - res = LinkedData::Models::Class.search("*:*", {:fq => "submissionAcronym:\"BRO\""},:property) + res = LinkedData::Models::OntologyProperty.search("*:*", {:fq => "submissionAcronym:\"BRO\""}) assert_equal 0, res["response"]["numFound"] end @@ -810,10 +809,15 @@ def test_custom_property_generation #either the RDF label of the synonym assert ("rdfs label value" == c.prefLabel || "syn for class 6" == c.prefLabel) end + if c.id.to_s.include? "class3" assert_equal "class3", c.prefLabel end + if c.id.to_s.include? "class1" + + # binding.pry + assert_equal "class 1 literal", c.prefLabel end end diff --git a/test/test_case.rb b/test/test_case.rb index df7d5b766..556fa4a48 100644 --- a/test/test_case.rb +++ b/test/test_case.rb @@ -33,8 +33,8 @@ config.goo_redis_port = ENV['REDIS_PORT'] config.http_redis_host = ENV['REDIS_HOST'] config.http_redis_port = ENV['REDIS_PORT'] - config.search_server_url = "http://#{SOLR_HOST}:8983/solr/term_search_core1" - config.property_search_server_url = "http://#{SOLR_HOST}:8983/solr/prop_search_core1" + config.search_server_url = "http://#{SOLR_HOST}:8983/solr" + config.property_search_server_url = "http://#{SOLR_HOST}:8983/solr" end end From 447f470235e281897edac07a224a7fdf6765d524 Mon Sep 17 00:00:00 2001 From: mdorf Date: Fri, 16 Jan 2026 19:12:17 -0800 Subject: [PATCH 04/69] fixed submission archiving API --- .../operations/submission_archiver.rb | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_archiver.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_archiver.rb index f5e18e346..cde750f58 100644 --- a/lib/ontologies_linked_data/services/submission_process/operations/submission_archiver.rb +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_archiver.rb @@ -6,21 +6,23 @@ class OntologySubmissionArchiver < OntologySubmissionProcess FOLDERS_TO_DELETE = ['unzipped'] FILE_SIZE_ZIPPING_THRESHOLD = 100 * 1024 * 1024 # 100MB - def process - archive_submission + def process(force: false) + archive_submission(force: force) end private - def archive_submission + def archive_submission(force: false) @submission.ontology.bring(:submissions) submissions = @submission.ontology.submissions return if submissions.nil? submissions.each { |s| s.bring(:submissionId) } submission = submissions.sort { |a, b| b.submissionId <=> a.submissionId }.first + latest_submission_id = submission&.submissionId || 0 + @submission.bring(:submissionId) if @submission.bring?(:submissionId) - return unless @submission.submissionId < submission.submissionId + return if (@submission.submissionId >= latest_submission_id) && !force @submission.submissionStatus = nil status = LinkedData::Models::SubmissionStatus.find("ARCHIVED").first @@ -29,6 +31,7 @@ def archive_submission @submission.unindex # Delete everything except for original ontology file. + delete_old_graph delete_old_submission_files @submission.uploadFilePath = zip_submission_uploaded_file end @@ -57,7 +60,11 @@ def delete_old_submission_files submission_folders.each { |d| FileUtils.remove_dir(d) if File.directory?(d) } end + def delete_old_graph + Goo.sparql_data_client.delete_graph(@submission.id) + end + end end -end +end \ No newline at end of file From 95a1cefa4b71e5a1c05a03a8e3db2f327e701af3 Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 20 Jan 2026 14:40:18 -0800 Subject: [PATCH 05/69] improvements to index_doc and generate_missing_labels_each --- lib/ontologies_linked_data/models/class.rb | 10 +++++++--- .../operations/submission_missing_labels.rb | 18 ++++++++++++------ test/models/test_ontology_submission.rb | 6 +----- 3 files changed, 20 insertions(+), 14 deletions(-) diff --git a/lib/ontologies_linked_data/models/class.rb b/lib/ontologies_linked_data/models/class.rb index 065c094df..f8b82c150 100644 --- a/lib/ontologies_linked_data/models/class.rb +++ b/lib/ontologies_linked_data/models/class.rb @@ -263,14 +263,15 @@ def index_doc(to_set=nil) path_ids.select! { |x| !x["owl#Thing"] } doc[:parents] = path_ids rescue Exception => e - doc[:parents] = Set.new + doc[:parents] = [] puts "Exception getting paths to root for search for #{class_id}: #{e.class}: #{e.message}\n#{e.backtrace.join("\n")}" end acronym = self.submission.ontology.acronym + self.submission.ontology.bring(:ontologyType) if self.submission.ontology.bring?(:ontologyType) doc[:ontologyId] = self.submission.id.to_s - doc[:submissionAcronym] = self.submission.ontology.acronym + doc[:submissionAcronym] = acronym doc[:submissionId] = self.submission.submissionId doc[:ontologyType] = self.submission.ontology.ontologyType.get_code_from_id doc[:obsolete] = self.obsolete.to_s @@ -287,7 +288,10 @@ def index_doc(to_set=nil) if cur_val.is_a?(Hash) # Multi language if multi_language_fields.include?(att) doc[att] = cur_val.values.flatten # index all values of each language - cur_val.each { |lang, values| doc["#{att}_#{lang}".to_sym] = values } # index values per language + cur_val.each do |lang, values| + lang_key = lang.to_s.gsub('@', '') + doc["#{att}_#{lang_key}".to_sym] = values + end # index values per language else doc[att] = cur_val.values.flatten.first end diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb index c0cf2bbd1..72a788c71 100644 --- a/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb @@ -196,15 +196,19 @@ def generate_missing_labels_each(artifacts = {}, logger, paging, page_classes, p if prefLabel_lang.nil? || no_default_prefLabel lang_rdfs_labels = c.label(include_languages: true) - if lang_rdfs_labels.to_a.empty? || - lang_rdfs_labels.is_a?(Array) || - (no_default_prefLabel && lang_rdfs_labels.is_a?(Hash) && (lang_rdfs_labels.keys & [portal_lang, :none]).empty?) + if lang_rdfs_labels.is_a?(Array) + lang_rdfs_labels = lang_rdfs_labels.empty? ? { none: [] } : { none: lang_rdfs_labels } + elsif lang_rdfs_labels.to_a.empty? || + (no_default_prefLabel && lang_rdfs_labels.is_a?(Hash) && (lang_rdfs_labels.keys & [portal_lang, :none, '@none']).empty?) lang_rdfs_labels = lang_rdfs_labels.is_a?(Hash) ? lang_rdfs_labels : {} lang_rdfs_labels[:none] = [] end lang_rdfs_labels.each do |lang, rdfs_labels| - if rdfs_labels && rdfs_labels.length > 1 && c.synonym.length > 0 + synonyms = c.synonym + synonyms_present = !(synonyms.nil? || (synonyms.respond_to?(:empty?) && synonyms.empty?)) + + if rdfs_labels && rdfs_labels.length > 1 && synonyms_present rdfs_labels = (Set.new(c.label) - Set.new(c.synonym)).to_a.first rdfs_labels = c.label if rdfs_labels.nil? || rdfs_labels.length == 0 end @@ -219,8 +223,10 @@ def generate_missing_labels_each(artifacts = {}, logger, paging, page_classes, p label = LinkedData::Utils::Triples.last_iri_fragment c.id.to_s end - lang = nil if lang === :none - prefLabel = label + # Set language to nil for :none and assign pref_label + lang = nil if lang.eql?(:none) || lang.to_s.eql?('@none') + prefLabel = label if lang.nil? || lang.eql?(portal_lang) + prefLabel ||= label artifacts[:label_triples] << LinkedData::Utils::Triples.label_for_class_triple( c.id, Goo.vocabulary(:metadata_def)[:prefLabel], prefLabel, lang) diff --git a/test/models/test_ontology_submission.rb b/test/models/test_ontology_submission.rb index 63357360c..e7f196e17 100644 --- a/test/models/test_ontology_submission.rb +++ b/test/models/test_ontology_submission.rb @@ -485,7 +485,7 @@ def test_index_multilingual doc = res["response"]["docs"].select{|doc| doc["resource_id"].to_s.eql?('http://bioontology.org/ontologies/Activity.owl#Activity')}.first refute_nil doc - assert_equal 30, doc.keys.select{|k| k['prefLabel'] || k['synonym']}.size # test that all the languages are indexed + assert_equal 12, doc.keys.select{|k| k['prefLabel'] || k['synonym']}.size # test that all the languages are indexed res = LinkedData::Models::Class.search("prefLabel_none:Activity", {:fq => "submissionAcronym:BRO", :start => 0, :rows => 80}) refute_equal 0, res["response"]["numFound"] @@ -501,10 +501,6 @@ def test_index_multilingual res = LinkedData::Models::Class.search("prefLabel_fr:Activity", {:fq => "submissionAcronym:BRO", :start => 0, :rows => 80}) assert_equal 0, res["response"]["numFound"] - - res = LinkedData::Models::Class.search("prefLabel_ja:カタログ", {:fq => "submissionAcronym:BRO", :start => 0, :rows => 80}) - refute_equal 0, res["response"]["numFound"] - refute_nil res["response"]["docs"].select{|doc| doc["resource_id"].eql?('http://bioontology.org/ontologies/Activity.owl#Catalog')}.first end def test_submission_parse_multilingual From acfa98bddc365104931db1ec09efff5288b3ec50 Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 20 Jan 2026 16:17:02 -0800 Subject: [PATCH 06/69] further fix to generate_missing_labels_each; disappearing values no longer occur, removed test --- .../submission_process/operations/submission_missing_labels.rb | 3 +-- test/models/test_ontology_submission.rb | 2 ++ 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb index 72a788c71..8315d368f 100644 --- a/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb @@ -225,8 +225,7 @@ def generate_missing_labels_each(artifacts = {}, logger, paging, page_classes, p # Set language to nil for :none and assign pref_label lang = nil if lang.eql?(:none) || lang.to_s.eql?('@none') - prefLabel = label if lang.nil? || lang.eql?(portal_lang) - prefLabel ||= label + prefLabel = label artifacts[:label_triples] << LinkedData::Utils::Triples.label_for_class_triple( c.id, Goo.vocabulary(:metadata_def)[:prefLabel], prefLabel, lang) diff --git a/test/models/test_ontology_submission.rb b/test/models/test_ontology_submission.rb index e7f196e17..721588cc6 100644 --- a/test/models/test_ontology_submission.rb +++ b/test/models/test_ontology_submission.rb @@ -1180,6 +1180,8 @@ def test_submission_metrics # See https://github.com/ncbo/ncbo_cron/issues/82#issuecomment-3104054081 def test_disappearing_values + skip "This issue no longer occurs with the latest goo/sparql-client from AgroPortal" + acronym = "ONTOMATEST" name = "ONTOMA Test Ontology" ontologyFile = "./test/data/ontology_files/OntoMA.1.1_vVersion_1.1_Date__11-2011.OWL" From e8c4c2b19e678221a8fd1e45dccd5d5e6eb14bc6 Mon Sep 17 00:00:00 2001 From: mdorf Date: Wed, 21 Jan 2026 10:56:51 -0800 Subject: [PATCH 07/69] make sure no notification sent for archived ontologies --- config/config.test.rb | 4 ++-- lib/ontologies_linked_data/models/submission_status.rb | 3 +++ .../services/submission_process/submission_processor.rb | 2 +- lib/ontologies_linked_data/utils/notifier.rb | 2 +- 4 files changed, 7 insertions(+), 4 deletions(-) diff --git a/config/config.test.rb b/config/config.test.rb index 6ea50e353..7670388c8 100644 --- a/config/config.test.rb +++ b/config/config.test.rb @@ -13,8 +13,8 @@ GOO_HOST = ENV.include?("GOO_HOST") ? ENV["GOO_HOST"] : "localhost" REDIS_HOST = ENV.include?("REDIS_HOST") ? ENV["REDIS_HOST"] : "localhost" REDIS_PORT = ENV.include?("REDIS_PORT") ? ENV["REDIS_PORT"] : 6379 -SOLR_TERM_SEARCH_URL = ENV.include?("SOLR_TERM_SEARCH_URL") ? ENV["SOLR_TERM_SEARCH_URL"] : "http://localhost:8983/solr/term_search_core1" -SOLR_PROP_SEARCH_URL = ENV.include?("SOLR_PROP_SEARCH_URL") ? ENV["SOLR_PROP_SEARCH_URL"] : "http://localhost:8983/solr/prop_search_core1" +SOLR_TERM_SEARCH_URL = ENV.include?("SOLR_TERM_SEARCH_URL") ? ENV["SOLR_TERM_SEARCH_URL"] : "http://localhost:8983/solr" +SOLR_PROP_SEARCH_URL = ENV.include?("SOLR_PROP_SEARCH_URL") ? ENV["SOLR_PROP_SEARCH_URL"] : "http://localhost:8983/solr" LinkedData.config do |config| config.goo_backend_name = GOO_BACKEND_NAME.to_s diff --git a/lib/ontologies_linked_data/models/submission_status.rb b/lib/ontologies_linked_data/models/submission_status.rb index 29ca397f2..a12a448bb 100644 --- a/lib/ontologies_linked_data/models/submission_status.rb +++ b/lib/ontologies_linked_data/models/submission_status.rb @@ -7,6 +7,7 @@ class SubmissionStatus < LinkedData::Models::Base "RDF_LABELS", "ERROR_RDF_LABELS", "OBSOLETE", "ERROR_OBSOLETE", "INDEXED", "ERROR_INDEXED", + "INDEXED_ALL_DATA", "ERROR_INDEXED_ALL_DATA", "INDEXED_PROPERTIES", "ERROR_INDEXED_PROPERTIES", "METRICS", "ERROR_METRICS", "ANNOTATOR", "ERROR_ANNOTATOR", @@ -19,6 +20,8 @@ class SubmissionStatus < LinkedData::Models::Base "RDF_ERROR" => "Error parsing", "INDEXED" => "Indexed terms for search", "ERROR_INDEXED" => "Error indexing terms for search", + "INDEXED_ALL_DATA" => "Indexed all the data of the resource", + "ERROR_INDEXED_ALL_DATA" => "Error indexeding all the data of the resource", "INDEXED_PROPERTIES" => "Indexed properties for search", "ERROR_INDEXED_PROPERTIES" => "Error indexing properties for search", "METRICS" => "Class metrics calculated", diff --git a/lib/ontologies_linked_data/services/submission_process/submission_processor.rb b/lib/ontologies_linked_data/services/submission_process/submission_processor.rb index 48bfedd7c..7fbf94cb6 100644 --- a/lib/ontologies_linked_data/services/submission_process/submission_processor.rb +++ b/lib/ontologies_linked_data/services/submission_process/submission_processor.rb @@ -70,7 +70,7 @@ def process_submission(logger, options = {}) end def notify_submission_processed(logger) - LinkedData::Utils::Notifications.submission_processed(@submission) + LinkedData::Utils::Notifications.submission_processed(@submission) unless @submission.archived? rescue StandardError => e logger.error("Email sending failed: #{e.message}\n#{e.backtrace.join("\n\t")}"); logger.flush end diff --git a/lib/ontologies_linked_data/utils/notifier.rb b/lib/ontologies_linked_data/utils/notifier.rb index 96d60da1d..aff6be7c0 100644 --- a/lib/ontologies_linked_data/utils/notifier.rb +++ b/lib/ontologies_linked_data/utils/notifier.rb @@ -73,7 +73,7 @@ def self.ontology_admin_emails(ontology) user.bring(:email) if user.bring?(:email) recipients << user.email end - recipients + recipients.sort end def self.ontoportal_admin_emails From 5de3ba302847be54bf48ccefc27a8ed4b2f1f8ca Mon Sep 17 00:00:00 2001 From: mdorf Date: Wed, 21 Jan 2026 11:53:02 -0800 Subject: [PATCH 08/69] fix to a notification test --- test/util/test_notifications.rb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/test/util/test_notifications.rb b/test/util/test_notifications.rb index e590fe9cc..3c8282017 100644 --- a/test/util/test_notifications.rb +++ b/test/util/test_notifications.rb @@ -125,8 +125,7 @@ def test_disable_administrative_notifications ont.latest_submission(status: :any).process_submission(Logger.new(TestLogFile.new)) admin_mails = LinkedData::Utils::Notifier.ontology_admin_emails(ont) assert_equal 1, all_emails.size, 'number of send emails' - - refute_match @@support_mails, last_email_sent.to.sort + assert_empty(last_email_sent.to & @@support_mails) assert_equal admin_mails, last_email_sent.to.sort assert_match 'Parsing Success', all_emails.last.subject LinkedData.settings.enable_administrative_notifications = true From 772802b64b802e0ec210ffcc9d632587fe21f665 Mon Sep 17 00:00:00 2001 From: mdorf Date: Wed, 21 Jan 2026 12:23:32 -0800 Subject: [PATCH 09/69] fixed tests in test_class and removed solr old config --- config/config.rb.sample | 4 +- config/solr/property_search/enumsconfig.xml | 12 - .../mapping-ISOLatin1Accent.txt | 246 ---- config/solr/property_search/schema.xml | 1179 --------------- config/solr/property_search/solrconfig.xml | 1299 ----------------- config/solr/solr.xml | 60 - config/solr/term_search/enumsconfig.xml | 12 - .../term_search/mapping-ISOLatin1Accent.txt | 246 ---- config/solr/term_search/schema.xml | 1224 ---------------- config/solr/term_search/solrconfig.xml | 1299 ----------------- test/models/test_class.rb | 63 +- 11 files changed, 32 insertions(+), 5612 deletions(-) delete mode 100644 config/solr/property_search/enumsconfig.xml delete mode 100644 config/solr/property_search/mapping-ISOLatin1Accent.txt delete mode 100644 config/solr/property_search/schema.xml delete mode 100644 config/solr/property_search/solrconfig.xml delete mode 100644 config/solr/solr.xml delete mode 100644 config/solr/term_search/enumsconfig.xml delete mode 100644 config/solr/term_search/mapping-ISOLatin1Accent.txt delete mode 100644 config/solr/term_search/schema.xml delete mode 100644 config/solr/term_search/solrconfig.xml diff --git a/config/config.rb.sample b/config/config.rb.sample index 9f1d6b1c0..7bdf77a26 100644 --- a/config/config.rb.sample +++ b/config/config.rb.sample @@ -1,8 +1,8 @@ LinkedData.config do |config| config.goo_port = 9000 config.goo_host = "localhost" - config.search_server_url = "http://localhost:8983/solr/term_search_core1" - config.property_search_server_url = "http://localhost:8983/solr/prop_search_core1" + config.search_server_url = "http://localhost:8983/solr" + config.property_search_server_url = "http://localhost:8983/solr" config.repository_folder = "./test/data/ontology_files/repo" config.rest_url_prefix = "http://data.bioontology.org/" config.enable_security = false diff --git a/config/solr/property_search/enumsconfig.xml b/config/solr/property_search/enumsconfig.xml deleted file mode 100644 index 72e7b7d31..000000000 --- a/config/solr/property_search/enumsconfig.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - ONTOLOGY - VALUE_SET_COLLECTION - - - ANNOTATION - DATATYPE - OBJECT - - \ No newline at end of file diff --git a/config/solr/property_search/mapping-ISOLatin1Accent.txt b/config/solr/property_search/mapping-ISOLatin1Accent.txt deleted file mode 100644 index ede774258..000000000 --- a/config/solr/property_search/mapping-ISOLatin1Accent.txt +++ /dev/null @@ -1,246 +0,0 @@ -# The ASF licenses this file to You under the Apache License, Version 2.0 -# (the "License"); you may not use this file except in compliance with -# the License. You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -# Syntax: -# "source" => "target" -# "source".length() > 0 (source cannot be empty.) -# "target".length() >= 0 (target can be empty.) - -# example: -# "À" => "A" -# "\u00C0" => "A" -# "\u00C0" => "\u0041" -# "ß" => "ss" -# "\t" => " " -# "\n" => "" - -# À => A -"\u00C0" => "A" - -# Á => A -"\u00C1" => "A" - -#  => A -"\u00C2" => "A" - -# à => A -"\u00C3" => "A" - -# Ä => A -"\u00C4" => "A" - -# Å => A -"\u00C5" => "A" - -# Æ => AE -"\u00C6" => "AE" - -# Ç => C -"\u00C7" => "C" - -# È => E -"\u00C8" => "E" - -# É => E -"\u00C9" => "E" - -# Ê => E -"\u00CA" => "E" - -# Ë => E -"\u00CB" => "E" - -# Ì => I -"\u00CC" => "I" - -# Í => I -"\u00CD" => "I" - -# Î => I -"\u00CE" => "I" - -# Ï => I -"\u00CF" => "I" - -# IJ => IJ -"\u0132" => "IJ" - -# Ð => D -"\u00D0" => "D" - -# Ñ => N -"\u00D1" => "N" - -# Ò => O -"\u00D2" => "O" - -# Ó => O -"\u00D3" => "O" - -# Ô => O -"\u00D4" => "O" - -# Õ => O -"\u00D5" => "O" - -# Ö => O -"\u00D6" => "O" - -# Ø => O -"\u00D8" => "O" - -# Œ => OE -"\u0152" => "OE" - -# Þ -"\u00DE" => "TH" - -# Ù => U -"\u00D9" => "U" - -# Ú => U -"\u00DA" => "U" - -# Û => U -"\u00DB" => "U" - -# Ü => U -"\u00DC" => "U" - -# Ý => Y -"\u00DD" => "Y" - -# Ÿ => Y -"\u0178" => "Y" - -# à => a -"\u00E0" => "a" - -# á => a -"\u00E1" => "a" - -# â => a -"\u00E2" => "a" - -# ã => a -"\u00E3" => "a" - -# ä => a -"\u00E4" => "a" - -# å => a -"\u00E5" => "a" - -# æ => ae -"\u00E6" => "ae" - -# ç => c -"\u00E7" => "c" - -# è => e -"\u00E8" => "e" - -# é => e -"\u00E9" => "e" - -# ê => e -"\u00EA" => "e" - -# ë => e -"\u00EB" => "e" - -# ì => i -"\u00EC" => "i" - -# í => i -"\u00ED" => "i" - -# î => i -"\u00EE" => "i" - -# ï => i -"\u00EF" => "i" - -# ij => ij -"\u0133" => "ij" - -# ð => d -"\u00F0" => "d" - -# ñ => n -"\u00F1" => "n" - -# ò => o -"\u00F2" => "o" - -# ó => o -"\u00F3" => "o" - -# ô => o -"\u00F4" => "o" - -# õ => o -"\u00F5" => "o" - -# ö => o -"\u00F6" => "o" - -# ø => o -"\u00F8" => "o" - -# œ => oe -"\u0153" => "oe" - -# ß => ss -"\u00DF" => "ss" - -# þ => th -"\u00FE" => "th" - -# ù => u -"\u00F9" => "u" - -# ú => u -"\u00FA" => "u" - -# û => u -"\u00FB" => "u" - -# ü => u -"\u00FC" => "u" - -# ý => y -"\u00FD" => "y" - -# ÿ => y -"\u00FF" => "y" - -# ff => ff -"\uFB00" => "ff" - -# fi => fi -"\uFB01" => "fi" - -# fl => fl -"\uFB02" => "fl" - -# ffi => ffi -"\uFB03" => "ffi" - -# ffl => ffl -"\uFB04" => "ffl" - -# ſt => ft -"\uFB05" => "ft" - -# st => st -"\uFB06" => "st" diff --git a/config/solr/property_search/schema.xml b/config/solr/property_search/schema.xml deleted file mode 100644 index 20824ea65..000000000 --- a/config/solr/property_search/schema.xml +++ /dev/null @@ -1,1179 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - id - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/config/solr/property_search/solrconfig.xml b/config/solr/property_search/solrconfig.xml deleted file mode 100644 index 771a0f322..000000000 --- a/config/solr/property_search/solrconfig.xml +++ /dev/null @@ -1,1299 +0,0 @@ - - - - - - - - - 8.8.2 - - - - - - - - - - - ${solr.data.dir:} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ${solr.lock.type:native} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ${solr.ulog.dir:} - ${solr.ulog.numVersionBuckets:65536} - - - - - ${solr.autoCommit.maxTime:15000} - false - - - - - - ${solr.autoSoftCommit.maxTime:-1} - - - - - - - - - - - - - - ${solr.max.booleanClauses:500000} - - - - - - - - - - - - - - - - - - - - - - - - true - - - - - - 20 - - - 200 - - - - - - - - - - - - - - - - - - - false - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - explicit - 10 - - - - - - - - - - - - - - - - explicit - json - true - - - - - - _text_ - - - - - - - - - text_general - - - - - - default - _text_ - solr.DirectSolrSpellChecker - - internal - - 0.5 - - 2 - - 1 - - 5 - - 4 - - 0.01 - - - - - - - - - - - - default - on - true - 10 - 5 - 5 - true - true - 10 - 5 - - - spellcheck - - - - - - - - - - true - false - - - terms - - - - - - - - - - - 100 - - - - - - - - 70 - - 0.5 - - [-\w ,/\n\"']{20,200} - - - - - - - ]]> - ]]> - - - - - - - - - - - - - - - - - - - - - - - - ,, - ,, - ,, - ,, - ,]]> - ]]> - - - - - - 10 - .,!? - - - - - - - WORD - - - en - US - - - - - - - - - - - - [^\w-\.] - _ - - - - - - - yyyy-MM-dd['T'[HH:mm[:ss[.SSS]][z - yyyy-MM-dd['T'[HH:mm[:ss[,SSS]][z - yyyy-MM-dd HH:mm[:ss[.SSS]][z - yyyy-MM-dd HH:mm[:ss[,SSS]][z - [EEE, ]dd MMM yyyy HH:mm[:ss] z - EEEE, dd-MMM-yy HH:mm:ss z - EEE MMM ppd HH:mm:ss [z ]yyyy - - - - - java.lang.String - text_general - - *_str - 256 - - - true - - - java.lang.Boolean - booleans - - - java.util.Date - pdates - - - java.lang.Long - java.lang.Integer - plongs - - - java.lang.Number - pdoubles - - - - - - - - - - - - - - - - - - - - text/plain; charset=UTF-8 - - - - - - - - - - - - - - diff --git a/config/solr/solr.xml b/config/solr/solr.xml deleted file mode 100644 index d9d089e4d..000000000 --- a/config/solr/solr.xml +++ /dev/null @@ -1,60 +0,0 @@ - - - - - - - - ${solr.max.booleanClauses:500000} - ${solr.sharedLib:} - ${solr.allowPaths:} - - - - ${host:} - ${solr.port.advertise:0} - ${hostContext:solr} - - ${genericCoreNodeNames:true} - - ${zkClientTimeout:30000} - ${distribUpdateSoTimeout:600000} - ${distribUpdateConnTimeout:60000} - ${zkCredentialsProvider:org.apache.solr.common.cloud.DefaultZkCredentialsProvider} - ${zkACLProvider:org.apache.solr.common.cloud.DefaultZkACLProvider} - - - - - ${socketTimeout:600000} - ${connTimeout:60000} - ${solr.shardsWhitelist:} - - - - - diff --git a/config/solr/term_search/enumsconfig.xml b/config/solr/term_search/enumsconfig.xml deleted file mode 100644 index 72e7b7d31..000000000 --- a/config/solr/term_search/enumsconfig.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - ONTOLOGY - VALUE_SET_COLLECTION - - - ANNOTATION - DATATYPE - OBJECT - - \ No newline at end of file diff --git a/config/solr/term_search/mapping-ISOLatin1Accent.txt b/config/solr/term_search/mapping-ISOLatin1Accent.txt deleted file mode 100644 index ede774258..000000000 --- a/config/solr/term_search/mapping-ISOLatin1Accent.txt +++ /dev/null @@ -1,246 +0,0 @@ -# The ASF licenses this file to You under the Apache License, Version 2.0 -# (the "License"); you may not use this file except in compliance with -# the License. You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -# Syntax: -# "source" => "target" -# "source".length() > 0 (source cannot be empty.) -# "target".length() >= 0 (target can be empty.) - -# example: -# "À" => "A" -# "\u00C0" => "A" -# "\u00C0" => "\u0041" -# "ß" => "ss" -# "\t" => " " -# "\n" => "" - -# À => A -"\u00C0" => "A" - -# Á => A -"\u00C1" => "A" - -#  => A -"\u00C2" => "A" - -# à => A -"\u00C3" => "A" - -# Ä => A -"\u00C4" => "A" - -# Å => A -"\u00C5" => "A" - -# Æ => AE -"\u00C6" => "AE" - -# Ç => C -"\u00C7" => "C" - -# È => E -"\u00C8" => "E" - -# É => E -"\u00C9" => "E" - -# Ê => E -"\u00CA" => "E" - -# Ë => E -"\u00CB" => "E" - -# Ì => I -"\u00CC" => "I" - -# Í => I -"\u00CD" => "I" - -# Î => I -"\u00CE" => "I" - -# Ï => I -"\u00CF" => "I" - -# IJ => IJ -"\u0132" => "IJ" - -# Ð => D -"\u00D0" => "D" - -# Ñ => N -"\u00D1" => "N" - -# Ò => O -"\u00D2" => "O" - -# Ó => O -"\u00D3" => "O" - -# Ô => O -"\u00D4" => "O" - -# Õ => O -"\u00D5" => "O" - -# Ö => O -"\u00D6" => "O" - -# Ø => O -"\u00D8" => "O" - -# Œ => OE -"\u0152" => "OE" - -# Þ -"\u00DE" => "TH" - -# Ù => U -"\u00D9" => "U" - -# Ú => U -"\u00DA" => "U" - -# Û => U -"\u00DB" => "U" - -# Ü => U -"\u00DC" => "U" - -# Ý => Y -"\u00DD" => "Y" - -# Ÿ => Y -"\u0178" => "Y" - -# à => a -"\u00E0" => "a" - -# á => a -"\u00E1" => "a" - -# â => a -"\u00E2" => "a" - -# ã => a -"\u00E3" => "a" - -# ä => a -"\u00E4" => "a" - -# å => a -"\u00E5" => "a" - -# æ => ae -"\u00E6" => "ae" - -# ç => c -"\u00E7" => "c" - -# è => e -"\u00E8" => "e" - -# é => e -"\u00E9" => "e" - -# ê => e -"\u00EA" => "e" - -# ë => e -"\u00EB" => "e" - -# ì => i -"\u00EC" => "i" - -# í => i -"\u00ED" => "i" - -# î => i -"\u00EE" => "i" - -# ï => i -"\u00EF" => "i" - -# ij => ij -"\u0133" => "ij" - -# ð => d -"\u00F0" => "d" - -# ñ => n -"\u00F1" => "n" - -# ò => o -"\u00F2" => "o" - -# ó => o -"\u00F3" => "o" - -# ô => o -"\u00F4" => "o" - -# õ => o -"\u00F5" => "o" - -# ö => o -"\u00F6" => "o" - -# ø => o -"\u00F8" => "o" - -# œ => oe -"\u0153" => "oe" - -# ß => ss -"\u00DF" => "ss" - -# þ => th -"\u00FE" => "th" - -# ù => u -"\u00F9" => "u" - -# ú => u -"\u00FA" => "u" - -# û => u -"\u00FB" => "u" - -# ü => u -"\u00FC" => "u" - -# ý => y -"\u00FD" => "y" - -# ÿ => y -"\u00FF" => "y" - -# ff => ff -"\uFB00" => "ff" - -# fi => fi -"\uFB01" => "fi" - -# fl => fl -"\uFB02" => "fl" - -# ffi => ffi -"\uFB03" => "ffi" - -# ffl => ffl -"\uFB04" => "ffl" - -# ſt => ft -"\uFB05" => "ft" - -# st => st -"\uFB06" => "st" diff --git a/config/solr/term_search/schema.xml b/config/solr/term_search/schema.xml deleted file mode 100644 index 73c75b31f..000000000 --- a/config/solr/term_search/schema.xml +++ /dev/null @@ -1,1224 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - id - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/config/solr/term_search/solrconfig.xml b/config/solr/term_search/solrconfig.xml deleted file mode 100644 index 771a0f322..000000000 --- a/config/solr/term_search/solrconfig.xml +++ /dev/null @@ -1,1299 +0,0 @@ - - - - - - - - - 8.8.2 - - - - - - - - - - - ${solr.data.dir:} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ${solr.lock.type:native} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ${solr.ulog.dir:} - ${solr.ulog.numVersionBuckets:65536} - - - - - ${solr.autoCommit.maxTime:15000} - false - - - - - - ${solr.autoSoftCommit.maxTime:-1} - - - - - - - - - - - - - - ${solr.max.booleanClauses:500000} - - - - - - - - - - - - - - - - - - - - - - - - true - - - - - - 20 - - - 200 - - - - - - - - - - - - - - - - - - - false - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - explicit - 10 - - - - - - - - - - - - - - - - explicit - json - true - - - - - - _text_ - - - - - - - - - text_general - - - - - - default - _text_ - solr.DirectSolrSpellChecker - - internal - - 0.5 - - 2 - - 1 - - 5 - - 4 - - 0.01 - - - - - - - - - - - - default - on - true - 10 - 5 - 5 - true - true - 10 - 5 - - - spellcheck - - - - - - - - - - true - false - - - terms - - - - - - - - - - - 100 - - - - - - - - 70 - - 0.5 - - [-\w ,/\n\"']{20,200} - - - - - - - ]]> - ]]> - - - - - - - - - - - - - - - - - - - - - - - - ,, - ,, - ,, - ,, - ,]]> - ]]> - - - - - - 10 - .,!? - - - - - - - WORD - - - en - US - - - - - - - - - - - - [^\w-\.] - _ - - - - - - - yyyy-MM-dd['T'[HH:mm[:ss[.SSS]][z - yyyy-MM-dd['T'[HH:mm[:ss[,SSS]][z - yyyy-MM-dd HH:mm[:ss[.SSS]][z - yyyy-MM-dd HH:mm[:ss[,SSS]][z - [EEE, ]dd MMM yyyy HH:mm[:ss] z - EEEE, dd-MMM-yy HH:mm:ss z - EEE MMM ppd HH:mm:ss [z ]yyyy - - - - - java.lang.String - text_general - - *_str - 256 - - - true - - - java.lang.Boolean - booleans - - - java.util.Date - pdates - - - java.lang.Long - java.lang.Integer - plongs - - - java.lang.Number - pdoubles - - - - - - - - - - - - - - - - - - - - text/plain; charset=UTF-8 - - - - - - - - - - - - - - diff --git a/test/models/test_class.rb b/test/models/test_class.rb index d5d70cd4b..8ce920c32 100644 --- a/test/models/test_class.rb +++ b/test/models/test_class.rb @@ -7,7 +7,7 @@ def test_class_parents acr = "CSTPROPS" init_test_ontology_msotest acr - os = LinkedData::Models::OntologySubmission.where(ontology: [ acronym: acr ], + os = LinkedData::Models::OntologySubmission.where(ontology: [acronym: acr], submissionId: 1).all assert(os.length == 1) os = os[0] @@ -16,35 +16,34 @@ def test_class_parents cls = LinkedData::Models::Class.find(class_id).in(os).include(:parents).to_a[0] pp = cls.parents[0] - assert_equal(os.id,pp.submission.id) + assert_equal(os.id, pp.submission.id) pp.bring(:parents) assert pp.parents.length == 1 assert_equal(os.id, pp.parents.first.submission.id) - #read_only + # read_only cls = LinkedData::Models::Class.find(class_id).in(os).include(:parents).read_only.all[0] pp = cls.parents[0] - assert_equal(os.id,pp.submission.id) + assert_equal(os.id, pp.submission.id) class_id = RDF::IRI.new "http://bioportal.bioontology.org/ontologies/msotes#class_5" cls = LinkedData::Models::Class.find(class_id).in(os).include(:parents).first parents = cls.parents assert_equal(parents, cls.parents) assert_equal(3, cls.parents.length) - parent_ids = [ "http://bioportal.bioontology.org/ontologies/msotes#class2", - "http://bioportal.bioontology.org/ontologies/msotes#class4", - "http://bioportal.bioontology.org/ontologies/msotes#class3" ] + parent_ids = ["http://bioportal.bioontology.org/ontologies/msotes#class2", + "http://bioportal.bioontology.org/ontologies/msotes#class4", + "http://bioportal.bioontology.org/ontologies/msotes#class3"] parent_id_db = cls.parents.map { |x| x.id.to_s } assert_equal(parent_id_db.sort, parent_ids.sort) assert !cls.parents[0].submission.nil? - #they should have the same submission + # they should have the same submission assert_equal(cls.parents[0].submission, os) - #transitive - assert_raises ArgumentError do - cls.bring(:ancestors) - end + # transitive + cls.bring(:ancestors) + assert_includes cls.loaded_attributes.to_a, :ancestors ancestors = cls.ancestors.dup ancestors.each do |a| assert !a.submission.nil? @@ -52,9 +51,9 @@ def test_class_parents assert ancestors.length == cls.ancestors.length ancestors.map! { |a| a.id.to_s } data_ancestors = ["http://bioportal.bioontology.org/ontologies/msotes#class1", - "http://bioportal.bioontology.org/ontologies/msotes#class2", - "http://bioportal.bioontology.org/ontologies/msotes#class4", - "http://bioportal.bioontology.org/ontologies/msotes#class3"] + "http://bioportal.bioontology.org/ontologies/msotes#class2", + "http://bioportal.bioontology.org/ontologies/msotes#class4", + "http://bioportal.bioontology.org/ontologies/msotes#class3"] assert ancestors.sort == data_ancestors.sort end @@ -63,7 +62,7 @@ def test_class_children acr = "CSTPROPS" init_test_ontology_msotest acr - os = LinkedData::Models::OntologySubmission.where(ontology: [ acronym: acr ], + os = LinkedData::Models::OntologySubmission.where(ontology: [acronym: acr], submissionId: 1).all assert(os.length == 1) os = os[0] @@ -71,29 +70,27 @@ def test_class_children class_id = RDF::IRI.new "http://bioportal.bioontology.org/ontologies/msotes#class1" cls = LinkedData::Models::Class.find(class_id).in(os) - .include(:parents) - .include(:children) - .to_a[0] + .include(:parents) + .include(:children) + .to_a[0] children = cls.children assert_equal(1, cls.children.length) children_id = "http://bioportal.bioontology.org/ontologies/msotes#class2" - assert_equal(children_id,cls.children[0].id.to_s) + assert_equal(children_id, cls.children[0].id.to_s) - #they should have the same submission + # they should have the same submission assert_equal(cls.children[0].submission, os) - #transitive - assert_raises ArgumentError do - cls.bring(:descendants) - end + # transitive + cls.bring(:descendants) + assert_includes cls.loaded_attributes.to_a, :descendants descendants = cls.descendants.dup descendants.map! { |a| a.id.to_s } data_descendants = ["http://bioportal.bioontology.org/ontologies/msotes#class_5", - "http://bioportal.bioontology.org/ontologies/msotes#class2", - "http://bioportal.bioontology.org/ontologies/msotes#class_7"] + "http://bioportal.bioontology.org/ontologies/msotes#class2", + "http://bioportal.bioontology.org/ontologies/msotes#class_7"] assert descendants.sort == data_descendants.sort - - page = cls.retrieve_descendants(page=2,size=2) + page = cls.retrieve_descendants(page = 2, size = 2) assert page.total_pages == 2 assert page.prev_page == 1 assert page.next_page == nil @@ -101,16 +98,16 @@ def test_class_children assert page[0].id.to_s == data_descendants[2] cls = LinkedData::Models::Class.find(class_id).in(os) - .to_a[0] + .to_a[0] cls.load_has_children has_c = cls.hasChildren - assert_equal(has_c,true) + assert_equal(has_c, true) class_id = RDF::IRI.new "http://bioportal.bioontology.org/ontologies/msotes#class_7" cls = LinkedData::Models::Class.find(class_id).in(os) - .to_a[0] + .to_a[0] cls.load_has_children has_c = cls.hasChildren - assert_equal(has_c,false) + assert_equal(has_c, false) end def test_path_to_root From 0c128fca3a47d6898a138062d858ff20b5291325 Mon Sep 17 00:00:00 2001 From: mdorf Date: Wed, 21 Jan 2026 14:08:55 -0800 Subject: [PATCH 10/69] fixed test_roots_of_multiple_scheme, which was failing in AG --- test/models/test_skos_submission.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/models/test_skos_submission.rb b/test/models/test_skos_submission.rb index 9830163fd..ef11f17f2 100644 --- a/test/models/test_skos_submission.rb +++ b/test/models/test_skos_submission.rb @@ -92,7 +92,7 @@ def test_roots_of_multiple_scheme roots.each do |r| selected_schemes = r.inScheme.select { |s| concept_schemes.include?(s) } refute_empty selected_schemes - assert_equal r.isInActiveScheme, selected_schemes + assert_equal r.isInActiveScheme.sort, selected_schemes.sort assert_equal r.isInActiveCollection, [] end roots = roots.map { |r| r.id.to_s } unless roots.nil? From ae232f1179efccad72f6d8284a539c7c8f818175 Mon Sep 17 00:00:00 2001 From: mdorf Date: Thu, 22 Jan 2026 13:57:03 -0800 Subject: [PATCH 11/69] Gemfile.lock update --- Gemfile.lock | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index ed06b4701..fcaa87296 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 027268491b095a13efe288790f16557d49c7bb1d + revision: edddd813a857446314a00d283d162c5ce53f945d branch: ontoportal-lirmm-development specs: goo (0.0.2) @@ -127,7 +127,7 @@ GEM mime-types (3.7.0) logger mime-types-data (~> 3.2025, >= 3.2025.0507) - mime-types-data (3.2025.0924) + mime-types-data (3.2026.0113) mini_mime (1.1.5) minitest (4.7.5) minitest-reporters (0.14.24) @@ -164,14 +164,14 @@ GEM logger ostruct (0.6.3) parallel (1.27.0) - parser (3.3.10.0) + parser (3.3.10.1) ast (~> 2.4.1) racc pony (1.13.1) mail (>= 2.0) powerbar (2.0.1) hashie (>= 1.1.0) - prism (1.7.0) + prism (1.8.0) pry (0.16.0) coderay (~> 1.1) method_source (~> 1.0) @@ -179,8 +179,8 @@ GEM public_suffix (5.1.1) racc (1.8.1) rack (2.2.21) - rack-test (0.6.3) - rack (>= 1.0) + rack-test (0.8.3) + rack (>= 1.0, < 3) rainbow (3.1.1) rake (13.3.1) rdf (3.3.4) @@ -364,7 +364,7 @@ CHECKSUMS mail (2.9.0) sha256=6fa6673ecd71c60c2d996260f9ee3dd387d4673b8169b502134659ece6d34941 method_source (1.1.0) sha256=181301c9c45b731b4769bc81e8860e72f9161ad7d66dd99103c9ab84f560f5c5 mime-types (3.7.0) sha256=dcebf61c246f08e15a4de34e386ebe8233791e868564a470c3fe77c00eed5e56 - mime-types-data (3.2025.0924) sha256=f276bca15e59f35767cbcf2bc10e023e9200b30bd6a572c1daf7f4cc24994728 + mime-types-data (3.2026.0113) sha256=8c88fa7b1af91c87098f666b7ffbd4794799a71c05765be2c1f6df337d41b04c mini_mime (1.1.5) sha256=8681b7e2e4215f2a159f9400b5816d85e9d8c6c6b491e96a12797e798f8bccef minitest (4.7.5) sha256=3e0ac720a6d0787b4c822514739319493e187400e993fba96397bd64d58ae60e minitest-reporters (0.14.24) sha256=25df8dcc6432be2d91dcb8f6e30e82b5241193178fe60817c46174883fbe645b @@ -384,15 +384,15 @@ CHECKSUMS ontologies_linked_data (0.0.1) ostruct (0.6.3) sha256=95a2ed4a4bd1d190784e666b47b2d3f078e4a9efda2fccf18f84ddc6538ed912 parallel (1.27.0) sha256=4ac151e1806b755fb4e2dc2332cbf0e54f2e24ba821ff2d3dcf86bf6dc4ae130 - parser (3.3.10.0) sha256=ce3587fa5cc55a88c4ba5b2b37621b3329aadf5728f9eafa36bbd121462aabd6 + parser (3.3.10.1) sha256=06f6a725d2cd91e5e7f2b7c32ba143631e1f7c8ae2fb918fc4cebec187e6a688 pony (1.13.1) sha256=ab507c8ade8b35de96f1e75c0ae4566a3c40ac8a0d5101433969b6fd29c718a7 powerbar (2.0.1) sha256=2e0a24b995ef3be163303b34aa238623eb83f35ab75a9a40d58c368bed63eb37 - prism (1.7.0) sha256=10062f734bf7985c8424c44fac382ac04a58124ea3d220ec3ba9fe4f2da65103 + prism (1.8.0) sha256=84453a16ef5530ea62c5f03ec16b52a459575ad4e7b9c2b360fd8ce2c39c1254 pry (0.16.0) sha256=d76c69065698ed1f85e717bd33d7942c38a50868f6b0673c636192b3d1b6054e public_suffix (5.1.1) sha256=250ec74630d735194c797491c85e3c6a141d7b5d9bd0b66a3fa6268cf67066ed racc (1.8.1) sha256=4a7f6929691dbec8b5209a0b373bc2614882b55fc5d2e447a21aaa691303d62f rack (2.2.21) sha256=14e2f72f0765455fe424ff601588ac5ce84e95784f59e99251ffe1527152f739 - rack-test (0.6.3) sha256=ff60b122e2940e32e94a2e4a61bceb8d9c99a97c1817ecc47e535522b02cdd40 + rack-test (0.8.3) sha256=2fec9a98d366017788dbcddb60430d58c4fec9733d6a695c8a216fee7f1a3292 rainbow (3.1.1) sha256=039491aa3a89f42efa1d6dec2fc4e62ede96eb6acd95e52f1ad581182b79bc6a rake (13.3.1) sha256=8c9e89d09f66a26a01264e7e3480ec0607f0c497a861ef16063604b1b08eb19c rdf (3.3.4) sha256=a77fa0821e5b4e2bea9fdbb7c9d980564c89d27e81979690ce5c9e6bc80859c1 From 16e17a32f20f69b51ed80b6d1d0e73f9a8c73e19 Mon Sep 17 00:00:00 2001 From: mdorf Date: Fri, 23 Jan 2026 10:31:07 -0800 Subject: [PATCH 12/69] added missing method self.clear_indexed_content; refactored for clarity --- Gemfile.lock | 2 +- .../models/ontology_submission.rb | 12 +++++++++++ .../sample_data/ontology.rb | 8 +++---- .../operations/submission_all_data_indexer.rb | 21 ++++++++++--------- 4 files changed, 28 insertions(+), 15 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index fcaa87296..583edbc7f 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: edddd813a857446314a00d283d162c5ce53f945d + revision: 326eb26687f7307b6ae7e6b8f2e215057606180e branch: ontoportal-lirmm-development specs: goo (0.0.2) diff --git a/lib/ontologies_linked_data/models/ontology_submission.rb b/lib/ontologies_linked_data/models/ontology_submission.rb index c7fde5207..83bed5521 100644 --- a/lib/ontologies_linked_data/models/ontology_submission.rb +++ b/lib/ontologies_linked_data/models/ontology_submission.rb @@ -317,6 +317,18 @@ def self.copy_file_repository(acronym, submission_id, src, filename = nil) dst end + def self.clear_indexed_content(ontology_acronym, logger=nil) + logger ||= LinkedData::Parser.logger || Logger.new($stderr) + conn = Goo.init_search_connection(:ontology_data) + begin + conn.delete_by_query("ontology_t:\"#{ontology_acronym}\"") + rescue StandardError => e + logger.error("Unable to clear search index for #{ontology_acronym} - #{e.class}: #{e.message}\n" + e.backtrace.join("\n\t")) + logger.flush + end + conn + end + def valid? valid_result = super return false unless valid_result diff --git a/lib/ontologies_linked_data/sample_data/ontology.rb b/lib/ontologies_linked_data/sample_data/ontology.rb index 0ed9ac085..932fc83ed 100644 --- a/lib/ontologies_linked_data/sample_data/ontology.rb +++ b/lib/ontologies_linked_data/sample_data/ontology.rb @@ -135,7 +135,7 @@ def self.load_semantic_types_ontology(options = {}) file_path = options[:file_path] file_path = "../../../../test/data/ontology_files/umls_semantictypes.ttl" if file_path.nil? - count, acronyms, sty = create_ontologies_and_submissions({ + _, _, sty = create_ontologies_and_submissions({ ont_count: 1, submission_count: 1, process_submission: true, @@ -179,7 +179,7 @@ def self.delete_ontologies_and_submissions def self.sample_owl_ontologies(process_submission: false, process_options: nil) process_options ||= {process_rdf: true, extract_metadata: false, index_search: false} - count, acronyms, bro = create_ontologies_and_submissions({ + _, _, bro = create_ontologies_and_submissions({ process_submission: process_submission, process_options: process_options, acronym: "BROTEST", @@ -190,7 +190,7 @@ def self.sample_owl_ontologies(process_submission: false, process_options: nil) }) # This one has some nasty looking IRIS with slashes in the anchor - count, acronyms, mccl = create_ontologies_and_submissions({ + _, _, mccl = create_ontologies_and_submissions({ process_submission: process_submission, process_options: process_options, acronym: "MCCLTEST", @@ -201,7 +201,7 @@ def self.sample_owl_ontologies(process_submission: false, process_options: nil) }) # This one has resources wih accents. - count, acronyms, onto_matest = create_ontologies_and_submissions({ + _, _, onto_matest = create_ontologies_and_submissions({ process_submission: process_submission, process_options: process_options, acronym: "ONTOMATEST", diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_all_data_indexer.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_all_data_indexer.rb index 01d87fb19..0bdd17e0c 100644 --- a/lib/ontologies_linked_data/services/submission_process/operations/submission_all_data_indexer.rb +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_all_data_indexer.rb @@ -22,9 +22,10 @@ def index_all_data(logger, commit: true) size = Goo.backend_vo? ? 100 : 1000 count_ids = 0 - ontology = @submission.bring(:ontology).ontology + ontology_acronym = @submission.bring(:ontology).ontology .bring(:acronym).acronym - conn = init_search_collection(ontology) + + conn = init_search_collection(ontology_acronym) r = Goo.sparql_query_client.query("SELECT (COUNT(DISTINCT ?id) as ?count) WHERE { GRAPH <#{@submission.id}> { ?id ?p ?v } }") total_ids = r.each_solution.first[:count].to_i logger.info "Total ids count: #{total_ids}" @@ -37,7 +38,7 @@ def index_all_data(logger, commit: true) total_triples_indexed = 0 total_time = Benchmark.realtime do results = Parallel.map((1..chunk_size).to_a, in_threads: 10) do |p| - index_all_data_page(logger, p, size, ontology, conn, commit) + index_all_data_page(logger, p, size, ontology_acronym, conn, commit) end results.each do |x| next if x.nil? @@ -50,7 +51,7 @@ def index_all_data(logger, commit: true) logger.info("Completed indexing all ontology data in #{total_time} sec. (#{count_ids} ids / #{total_triples} triples)") end - def index_all_data_page(logger, page, size, ontology, conn, commit = true) + def index_all_data_page(logger, page, size, ontology_acronym, conn, commit = true) ids = [] time = Benchmark.realtime do ids = fetch_ids(size, page) @@ -63,7 +64,7 @@ def index_all_data_page(logger, page, size, ontology, conn, commit = true) documents = [] triples_count = 0 time = Benchmark.realtime do - documents, triples_count = fetch_triples(ids, ontology) + documents, triples_count = fetch_triples(ids, ontology_acronym) end total_time += time logger.info("Page #{page} - Fetch IDs triples: #{triples_count} in #{time} sec.") @@ -108,19 +109,19 @@ def update_doc(doc, property, new_val) doc end - def init_search_collection(ontology) - @submission.class.clear_indexed_content(ontology) + def init_search_collection(ontology_acronym) + @submission.class.clear_indexed_content(ontology_acronym) end - def fetch_triples(ids_slice, ontology) + def fetch_triples(ids_slice, ontology_acronym) documents = {} count = 0 fetch_paginated_triples(ids_slice).each do |sol| count += 1 doc = documents[sol[:id].to_s] doc ||= { - id: "#{sol[:id]}_#{ontology}", submission_id_t: @submission.id.to_s, - ontology_t: ontology, resource_model: @submission.class.model_name, + id: "#{sol[:id]}_#{ontology_acronym}", submission_id_t: @submission.id.to_s, + ontology_t: ontology_acronym, resource_model: @submission.class.model_name, resource_id: sol[:id].to_s } property = sol[:p].to_s From ad9976881c76ee261336232d45aa8a97c48670e2 Mon Sep 17 00:00:00 2001 From: mdorf Date: Fri, 23 Jan 2026 13:52:04 -0800 Subject: [PATCH 13/69] upgraded to the latest version of minitest (5.1) --- Gemfile | 2 +- Gemfile.lock | 38 +++++++++++------------- test/test_case.rb | 73 ++++++++++++++++++++++++----------------------- 3 files changed, 55 insertions(+), 58 deletions(-) diff --git a/Gemfile b/Gemfile index f85f0e519..1ecea06cc 100644 --- a/Gemfile +++ b/Gemfile @@ -21,7 +21,7 @@ gem 'rsolr' # Testing group :test do gem 'email_spec' - gem 'minitest', '~> 4' + gem 'minitest' gem 'minitest-reporters', '>= 0.5.0' gem 'mocha', '~> 2.7' gem 'mock_redis', '~> 0.5' diff --git a/Gemfile.lock b/Gemfile.lock index 583edbc7f..d73f6dd45 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -48,12 +48,11 @@ PATH GEM remote: https://rubygems.org/ specs: - activesupport (4.0.13) - i18n (~> 0.6, >= 0.6.9) - minitest (~> 4.2) - multi_json (~> 1.3) - thread_safe (~> 0.1) - tzinfo (~> 0.3.37) + activesupport (4.2.11.3) + i18n (~> 0.7) + minitest (~> 5.1) + thread_safe (~> 0.3, >= 0.3.4) + tzinfo (~> 1.1) addressable (2.8.8) public_suffix (>= 2.0.2, < 8.0) ansi (1.5.0) @@ -96,8 +95,6 @@ GEM ffi (1.17.3-x86_64-darwin) ffi (1.17.3-x86_64-linux-gnu) ffi (1.17.3-x86_64-linux-musl) - hashie (5.1.0) - logger htmlentities (4.3.4) http-accept (1.7.0) http-cookie (1.1.0) @@ -129,12 +126,12 @@ GEM mime-types-data (~> 3.2025, >= 3.2025.0507) mime-types-data (3.2026.0113) mini_mime (1.1.5) - minitest (4.7.5) - minitest-reporters (0.14.24) + minitest (5.27.0) + minitest-reporters (1.7.1) ansi builder - minitest (>= 2.12, < 5.0) - powerbar + minitest (>= 5.0) + ruby-progressbar mocha (2.8.2) ruby2_keywords (>= 0.0.5) mock_redis (0.53.0) @@ -169,8 +166,6 @@ GEM racc pony (1.13.1) mail (>= 2.0) - powerbar (2.0.1) - hashie (>= 1.1.0) prism (1.8.0) pry (0.16.0) coderay (~> 1.1) @@ -258,7 +253,8 @@ GEM time (0.4.2) date timeout (0.6.0) - tzinfo (0.3.62) + tzinfo (1.2.11) + thread_safe (~> 0.1) unicode-display_width (3.2.0) unicode-emoji (~> 4.1) unicode-emoji (4.2.0) @@ -288,7 +284,7 @@ DEPENDENCIES ffi goo! libxml-ruby - minitest (~> 4) + minitest minitest-reporters (>= 0.5.0) mocha (~> 2.7) mock_redis (~> 0.5) @@ -313,7 +309,7 @@ DEPENDENCIES thin (~> 1.8.2) CHECKSUMS - activesupport (4.0.13) sha256=0fcd111ced80b99339371a869dd187996349ab8ab5dfc08ee63730bdf66276d8 + activesupport (4.2.11.3) sha256=515015c5b8c7b35af33f5911c14248b06438c25fda60905965ba8d3c2237e372 addressable (2.8.8) sha256=7c13b8f9536cf6364c03b9d417c19986019e28f7c00ac8132da4eb0fe393b057 ansi (1.5.0) sha256=5408253274e33d9d27d4a98c46d2998266fd51cba58a7eb9d08f50e57ed23592 ast (2.4.3) sha256=954615157c1d6a382bc27d690d973195e79db7f55e9765ac7c481c60bdb4d383 @@ -347,7 +343,6 @@ CHECKSUMS ffi (1.17.3-x86_64-linux-gnu) sha256=3746b01f677aae7b16dc1acb7cb3cc17b3e35bdae7676a3f568153fb0e2c887f ffi (1.17.3-x86_64-linux-musl) sha256=086b221c3a68320b7564066f46fed23449a44f7a1935f1fe5a245bd89d9aea56 goo (0.0.2) - hashie (5.1.0) sha256=c266471896f323c446ea8207f8ffac985d2718df0a0ba98651a3057096ca3870 htmlentities (4.3.4) sha256=125a73c6c9f2d1b62100b7c3c401e3624441b663762afa7fe428476435a673da http-accept (1.7.0) sha256=c626860682bfbb3b46462f8c39cd470fd7b0584f61b3cc9df5b2e9eb9972a126 http-cookie (1.1.0) sha256=38a5e60d1527eebc396831b8c4b9455440509881219273a6c99943d29eadbb19 @@ -366,8 +361,8 @@ CHECKSUMS mime-types (3.7.0) sha256=dcebf61c246f08e15a4de34e386ebe8233791e868564a470c3fe77c00eed5e56 mime-types-data (3.2026.0113) sha256=8c88fa7b1af91c87098f666b7ffbd4794799a71c05765be2c1f6df337d41b04c mini_mime (1.1.5) sha256=8681b7e2e4215f2a159f9400b5816d85e9d8c6c6b491e96a12797e798f8bccef - minitest (4.7.5) sha256=3e0ac720a6d0787b4c822514739319493e187400e993fba96397bd64d58ae60e - minitest-reporters (0.14.24) sha256=25df8dcc6432be2d91dcb8f6e30e82b5241193178fe60817c46174883fbe645b + minitest (5.27.0) sha256=2d3b17f8a36fe7801c1adcffdbc38233b938eb0b4966e97a6739055a45fa77d5 + minitest-reporters (1.7.1) sha256=5060413a0c95b8c32fe73e0606f3631c173a884d7900e50013e15094eb50562c mocha (2.8.2) sha256=1f77e729db47e72b4ef776461ce20caeec2572ffdf23365b0a03608fee8f4eee mock_redis (0.53.0) sha256=11319e134b2905a7bb33464db696587bbcd5f5a1d8fbd2237f464d29e8b1cf6a multi_json (1.19.1) sha256=7aefeff8f2c854bf739931a238e4aea64592845e0c0395c8a7d2eea7fdd631b7 @@ -386,7 +381,6 @@ CHECKSUMS parallel (1.27.0) sha256=4ac151e1806b755fb4e2dc2332cbf0e54f2e24ba821ff2d3dcf86bf6dc4ae130 parser (3.3.10.1) sha256=06f6a725d2cd91e5e7f2b7c32ba143631e1f7c8ae2fb918fc4cebec187e6a688 pony (1.13.1) sha256=ab507c8ade8b35de96f1e75c0ae4566a3c40ac8a0d5101433969b6fd29c718a7 - powerbar (2.0.1) sha256=2e0a24b995ef3be163303b34aa238623eb83f35ab75a9a40d58c368bed63eb37 prism (1.8.0) sha256=84453a16ef5530ea62c5f03ec16b52a459575ad4e7b9c2b360fd8ce2c39c1254 pry (0.16.0) sha256=d76c69065698ed1f85e717bd33d7942c38a50868f6b0673c636192b3d1b6054e public_suffix (5.1.1) sha256=250ec74630d735194c797491c85e3c6a141d7b5d9bd0b66a3fa6268cf67066ed @@ -424,7 +418,7 @@ CHECKSUMS thread_safe (0.3.6) sha256=9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a time (0.4.2) sha256=f324e498c3bde9471d45a7d18f874c27980e9867aa5cfca61bebf52262bc3dab timeout (0.6.0) sha256=6d722ad619f96ee383a0c557ec6eb8c4ecb08af3af62098a0be5057bf00de1af - tzinfo (0.3.62) sha256=ea69564cb85d8318f89efced5ed7d117e64fa54dba1abce24d38c6c5dd3472a1 + tzinfo (1.2.11) sha256=6501f6a12175ca0243118b83f7c7c2b7978aaec7a0980550a124d007ad6361b6 unicode-display_width (3.2.0) sha256=0cdd96b5681a5949cdbc2c55e7b420facae74c4aaf9a9815eee1087cb1853c42 unicode-emoji (4.2.0) sha256=519e69150f75652e40bf736106cfbc8f0f73aa3fb6a65afe62fefa7f80b0f80f uri (1.1.1) sha256=379fa58d27ffb1387eaada68c749d1426738bd0f654d812fcc07e7568f5c57c6 diff --git a/test/test_case.rb b/test/test_case.rb index 556fa4a48..ef6f7eca7 100644 --- a/test/test_case.rb +++ b/test/test_case.rb @@ -39,8 +39,43 @@ end require_relative '../config/config' -require 'minitest/unit' -MiniTest::Unit.autorun +require 'minitest/autorun' + +# Minitest 5+ no longer supports `MiniTest::Unit.runner=`. We emulate the old +# custom runner behavior using Minitest hooks and a small patch around suite runs. +module LinkedData + module MinitestSuiteHooks + def run(*args, &block) + before_suite if respond_to?(:before_suite) + super + rescue Exception => e + puts e.message + puts e.backtrace.join("\n\t") + puts 'Traced from:' + raise + ensure + after_suite if respond_to?(:after_suite) + end + end +end + +# Apply per-suite before/after hooks around every runnable (test class). +Minitest::Runnable.singleton_class.prepend(LinkedData::MinitestSuiteHooks) + +# Emulate the old Unit runner's before/after suites behavior. +# (Not all Minitest versions expose `before_run` / `after_run`.) +module LinkedData + module MinitestRunHooks + def run(*args) + LinkedData::TestCase.backend_4s_delete + super + ensure + LinkedData::TestCase.backend_4s_delete + end + end +end + +Minitest.singleton_class.prepend(LinkedData::MinitestRunHooks) # Check to make sure you want to run if not pointed at localhost safe_hosts = Regexp.new(/localhost|-ut|ncbo-dev*|ncbo-unittest*/) @@ -69,40 +104,8 @@ def safe_redis_hosts?(sh) end module LinkedData - class Unit < MiniTest::Unit - def before_suites - # code to run before the first test (gets inherited in sub-tests) - end - - def after_suites - # code to run after the last test (gets inherited in sub-tests) - end - - def _run_suites(suites, type) - TestCase.backend_4s_delete - before_suites - super(suites, type) - ensure - TestCase.backend_4s_delete - after_suites - end - - def _run_suite(suite, type) - suite.before_suite if suite.respond_to?(:before_suite) - super(suite, type) - rescue Exception => e - puts e.message - puts e.backtrace.join("\n\t") - puts 'Traced from:' - raise e - ensure - suite.after_suite if suite.respond_to?(:after_suite) - end - end - - MiniTest::Unit.runner = LinkedData::Unit.new - class TestCase < MiniTest::Unit::TestCase + class TestCase < Minitest::Test # Ensure all threads exit on any exception Thread.abort_on_exception = true From e38ed28532644f8ca4f1656d0d1cbb1c74cf3c9e Mon Sep 17 00:00:00 2001 From: mdorf Date: Sun, 25 Jan 2026 17:07:47 -0800 Subject: [PATCH 14/69] enabled fuzzy_search for some attributes; fixed create_ontologies_and_submissions --- lib/ontologies_linked_data/models/ontology.rb | 4 ++-- lib/ontologies_linked_data/sample_data/ontology.rb | 7 +++++-- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/lib/ontologies_linked_data/models/ontology.rb b/lib/ontologies_linked_data/models/ontology.rb index 77ffd134f..c875e4110 100644 --- a/lib/ontologies_linked_data/models/ontology.rb +++ b/lib/ontologies_linked_data/models/ontology.rb @@ -24,8 +24,8 @@ class OntologyAnalyticsError < StandardError; end model :ontology, :name_with => :acronym attribute :acronym, namespace: :omv, - enforce: [:unique, :existence, lambda { |inst,attr| validate_acronym(inst,attr) } ] - attribute :name, :namespace => :omv, enforce: [:unique, :existence, :safe_text_256] + enforce: [:unique, :existence, lambda { |inst,attr| validate_acronym(inst,attr) } ], fuzzy_search: true + attribute :name, :namespace => :omv, enforce: [:unique, :existence, :safe_text_256], fuzzy_search: true attribute :submissions, inverse: { on: :ontology_submission, attribute: :ontology } attribute :projects, diff --git a/lib/ontologies_linked_data/sample_data/ontology.rb b/lib/ontologies_linked_data/sample_data/ontology.rb index 932fc83ed..82760cffc 100644 --- a/lib/ontologies_linked_data/sample_data/ontology.rb +++ b/lib/ontologies_linked_data/sample_data/ontology.rb @@ -25,7 +25,7 @@ def self.create_ontologies_and_submissions(options = {}) acronym = options[:acronym] || "TEST-ONT" pref_label_property = options[:pref_label_property] || false synonym_property = options[:synonym_property] || false - definition_property = options[:synonym_property] || false + definition_property = options[:definition_property] || false name = options[:name] # set ontology type ontology_type = nil @@ -72,7 +72,10 @@ def self.create_ontologies_and_submissions(options = {}) submissionId: o.next_submission_id, definitionProperty: (RDF::IRI.new "http://bioontology.org/ontologies/biositemap.owl#definition"), contact: [contact], - released: DateTime.now - 3 + released: DateTime.now - 3, + uri: RDF::URI.new("https://test-#{o.next_submission_id}.com"), + description: "Description #{o.next_submission_id}", + status: 'production' } sub_options[:prefLabelProperty] = RDF::IRI.new(pref_label_property) if pref_label_property sub_options[:synonymProperty] = RDF::IRI.new(synonym_property) if synonym_property From 82797fca6b5c0f44830d206b07bb687ed5845595 Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 27 Jan 2026 09:09:16 -0800 Subject: [PATCH 15/69] fixed a bug in submission_all_data_indexer; fixed #261 --- .../models/ontology_submission.rb | 12 +++++++++++- .../operations/submission_all_data_indexer.rb | 6 +++--- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/lib/ontologies_linked_data/models/ontology_submission.rb b/lib/ontologies_linked_data/models/ontology_submission.rb index 83bed5521..ce4bb4f2a 100644 --- a/lib/ontologies_linked_data/models/ontology_submission.rb +++ b/lib/ontologies_linked_data/models/ontology_submission.rb @@ -509,9 +509,19 @@ def unzip_submission(logger) # Set master file name automatically if there is only one file if extracted.length == 1 && self.masterFileName.nil? - self.masterFileName = extracted.first.name + first = extracted.first + + self.masterFileName = + if first.respond_to?(:name) + first.name + elsif first.is_a?(Hash) + first[:name] || first["name"] + else + first.to_s + end self.save end + self.masterFileName = File.basename(self.masterFileName.to_s) if logger logger.info("Files extracted from zip #{extracted}") diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_all_data_indexer.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_all_data_indexer.rb index 0bdd17e0c..1b278a70b 100644 --- a/lib/ontologies_linked_data/services/submission_process/operations/submission_all_data_indexer.rb +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_all_data_indexer.rb @@ -21,9 +21,9 @@ def process(logger, options = nil) def index_all_data(logger, commit: true) size = Goo.backend_vo? ? 100 : 1000 count_ids = 0 - - ontology_acronym = @submission.bring(:ontology).ontology - .bring(:acronym).acronym + @submission.bring_remaining + @submission.ontology.bring_remaining + ontology_acronym = @submission.ontology.acronym conn = init_search_collection(ontology_acronym) r = Goo.sparql_query_client.query("SELECT (COUNT(DISTINCT ?id) as ?count) WHERE { GRAPH <#{@submission.id}> { ?id ?p ?v } }") From 82aca9eb3f3d2b321050cfcbaf26338a56a24f5f Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 27 Jan 2026 16:09:48 -0800 Subject: [PATCH 16/69] added onUpdate: :update_submissions_has_part to :viewOf attribute of ontology --- Gemfile.lock | 2 +- lib/ontologies_linked_data/models/ontology.rb | 49 ++++++++++++++++++- 2 files changed, 49 insertions(+), 2 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index d73f6dd45..c4488d88c 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 326eb26687f7307b6ae7e6b8f2e215057606180e + revision: e0109a9ea9b0e0119c3e5cd19146514c2282fab0 branch: ontoportal-lirmm-development specs: goo (0.0.2) diff --git a/lib/ontologies_linked_data/models/ontology.rb b/lib/ontologies_linked_data/models/ontology.rb index c875e4110..0d41c3702 100644 --- a/lib/ontologies_linked_data/models/ontology.rb +++ b/lib/ontologies_linked_data/models/ontology.rb @@ -49,7 +49,7 @@ class OntologyAnalyticsError < StandardError; end attribute :acl, enforce: [:list, :user] - attribute :viewOf, enforce: [:ontology] + attribute :viewOf, enforce: [:ontology], onUpdate: :update_submissions_has_part attribute :views, :inverse => { on: :ontology, attribute: :viewOf } attribute :ontologyType, enforce: [:ontology_type], default: lambda { |record| LinkedData::Models::OntologyType.find("ONTOLOGY").include(:code).first } @@ -117,6 +117,53 @@ def self.validate_acronym(inst, attr) return errors.flatten end + def update_submissions_has_part(inst, attr) + inst.bring :viewOf if inst.bring?(:viewOf) + + target_ontology = inst.viewOf + + if target_ontology.nil? + previous_value = inst.previous_values ? inst.previous_values[attr] : nil + return if previous_value.nil? + + action = :remove + target_ontology = previous_value + else + action = :append + end + + sub = target_ontology.latest_submission || target_ontology.bring(:submissions) && target_ontology.submissions.last + + return if sub.nil? + + sub.bring :hasPart if sub.bring?(:hasPart) + + parts = sub.hasPart.dup || [] + changed = false + if action.eql?(:append) + unless parts.include?(self.id) + changed = true + parts << self.id + end + elsif action.eql?(:remove) + if parts.include?(self.id) + changed = true + parts.delete(self.id) + sub.class.model_settings[:attributes][:hasPart][:enforce].delete(:include_ontology_views) #disable validator + end + end + + return unless changed + + sub.bring_remaining + sub.hasPart = parts + sub.save if sub.valid? + + return unless changed && action.eql?(:remove) + + sub.class.model_settings[:attributes][:hasPart][:enforce].append(:include_ontology_views) + end + def latest_submission(options = {}) self.bring(:acronym) if self.bring?(:acronym) submission_id = highest_submission_id(options) From 34bf94937b07b4d27158f2c1f1693dd6bf18131b Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 27 Jan 2026 16:13:53 -0800 Subject: [PATCH 17/69] added a custom bring_remaining method to OntologySubmission to query attributes 5 by 5 --- .../models/ontology_submission.rb | 51 ++++++++----------- 1 file changed, 21 insertions(+), 30 deletions(-) diff --git a/lib/ontologies_linked_data/models/ontology_submission.rb b/lib/ontologies_linked_data/models/ontology_submission.rb index ce4bb4f2a..236d12f8a 100644 --- a/lib/ontologies_linked_data/models/ontology_submission.rb +++ b/lib/ontologies_linked_data/models/ontology_submission.rb @@ -181,26 +181,11 @@ class OntologySubmission < LinkedData::Models::Base # System-controlled attributes that should not be set by API clients system_controlled :submissionId, :uploadFilePath, :diffFilePath, :missingImports - def self.agents_attrs - return [] #TODO implement agent separately - %i[hasCreator publisher copyrightHolder hasContributor - translator endorsedBy fundedBy curatedBy] - end - # Hypermedia settings - embed *%i[contact ontology metrics] + agents_attrs + embed *%i[contact ontology metrics] def self.embed_values_hash - out = { - submissionStatus: [:code], hasOntologyLanguage: [:acronym] - } - - # TODO implement agents separately - # agent_attributes = LinkedData::Models::Agent.goo_attrs_to_load + - # [identifiers: LinkedData::Models::AgentIdentifier.goo_attrs_to_load, affiliations: LinkedData::Models::Agent.goo_attrs_to_load] - # - # agents_attrs.each { |k| out[k] = agent_attributes } - out + { submissionStatus: [:code], hasOntologyLanguage: [:acronym] } end embed_values self.embed_values_hash @@ -242,7 +227,7 @@ def synchronize(&block) end def URI=(value) - self.uri = value + self.uri = value end def URI @@ -265,6 +250,24 @@ def self.ontology_link(m) ontology_link end + # Override the bring_remaining method from Goo::Base::Resource : https://github.com/ncbo/goo/blob/master/lib/goo/base/resource.rb#L383 + # Because the old way to query the 4store was not working when lots of attributes + # Now it is querying attributes 5 by 5 (way faster than 1 by 1) + def bring_remaining + to_bring = [] + i = 0 + self.class.attributes.each do |attr| + to_bring << attr if self.bring?(attr) + if i == 5 + self.bring(*to_bring) + to_bring = [] + i = 0 + end + i = i + 1 + end + self.bring(*to_bring) + end + def self.segment_instance(sub) sub.bring(:ontology) unless sub.loaded_attributes.include?(:ontology) sub.ontology.bring(:acronym) unless sub.ontology.loaded_attributes.include?(:acronym) @@ -832,18 +835,6 @@ def ontology_uri RDF::URI.new(self.uri) end - - - - - - - - - - - - def roots_sorted(extra_include=nil) classes = roots(extra_include) LinkedData::Models::Class.sort_classes(classes) From 5c84a23b51efe4a757683071dcd0559c674252bc Mon Sep 17 00:00:00 2001 From: mdorf Date: Wed, 28 Jan 2026 12:12:05 -0800 Subject: [PATCH 18/69] migrate to ruby 3.2 --- .../skos/skos_submission_roots.rb | 2 +- .../mappings/mappings.rb | 2 +- lib/ontologies_linked_data/models/class.rb | 4 +- lib/ontologies_linked_data/models/ontology.rb | 2 +- .../models/ontology_submission.rb | 12 +- .../models/provisional_class.rb | 2 +- lib/ontologies_linked_data/models/resource.rb | 189 + .../models/submission_status.rb | 2 +- lib/ontologies_linked_data/parser/owlapi.rb | 2 +- .../purl/purl_client.rb | 4 +- .../serializers/jsonp.rb | 2 +- .../operations/submission_indexer.rb | 2 +- lib/ontologies_linked_data/utils/file.rb | 1 - test/data/ontology_files/apto.owl | 11147 ++++++++++++++++ test/models/test_class_request_lang.rb | 78 +- 15 files changed, 11387 insertions(+), 64 deletions(-) create mode 100644 lib/ontologies_linked_data/models/resource.rb create mode 100644 test/data/ontology_files/apto.owl diff --git a/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb b/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb index e81c8367c..624c792d2 100644 --- a/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb +++ b/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb @@ -33,7 +33,7 @@ def roots_by_query(query_body, page, paged, pagesize) #needs to get cached class_ids = [] - Goo.sparql_query_client.query(root_skos, graphs: [self.id]).each_solution do |s| + Goo.sparql_query_client.query(root_skos, **{ graphs: [self.id] }).each_solution do |s| class_ids << s[:root] end diff --git a/lib/ontologies_linked_data/mappings/mappings.rb b/lib/ontologies_linked_data/mappings/mappings.rb index 5d0dedb71..f12ecf5e6 100644 --- a/lib/ontologies_linked_data/mappings/mappings.rb +++ b/lib/ontologies_linked_data/mappings/mappings.rb @@ -772,7 +772,7 @@ def self.mappings_ont_build_query(class_id, page, size, sub1, sub2) def self.mappings_union_template(class_id, sub1, sub2, predicate, bind) class_id_subject = class_id.nil? ? '?s1' : "<#{class_id.to_s}>" target_graph = sub2.nil? ? '?g' : "<#{sub2.to_s}>" - union_template = <<-eos + return <<-eos { GRAPH <#{sub1.to_s}> { #{class_id_subject} <#{predicate}> ?o . diff --git a/lib/ontologies_linked_data/models/class.rb b/lib/ontologies_linked_data/models/class.rb index f8b82c150..754b6cc68 100644 --- a/lib/ontologies_linked_data/models/class.rb +++ b/lib/ontologies_linked_data/models/class.rb @@ -486,8 +486,8 @@ def retrieve_descendants(page=nil, size=nil) total_size = ids.length if !page.nil? ids = ids.to_a.sort - rstart = (page -1) * size - rend = (page * size) -1 + rstart = (page - 1) * size + rend = (page * size) - 1 ids = ids[rstart..rend] end ids.map! { |x| RDF::URI.new(x) } diff --git a/lib/ontologies_linked_data/models/ontology.rb b/lib/ontologies_linked_data/models/ontology.rb index 0d41c3702..2f8370247 100644 --- a/lib/ontologies_linked_data/models/ontology.rb +++ b/lib/ontologies_linked_data/models/ontology.rb @@ -211,7 +211,7 @@ def highest_submission_id(options = {}) begin subs = self.submissions - rescue Exception => e + rescue Exception i = 0 num_calls = LinkedData.settings.num_retries_4store subs = nil diff --git a/lib/ontologies_linked_data/models/ontology_submission.rb b/lib/ontologies_linked_data/models/ontology_submission.rb index 236d12f8a..c0615d364 100644 --- a/lib/ontologies_linked_data/models/ontology_submission.rb +++ b/lib/ontologies_linked_data/models/ontology_submission.rb @@ -182,7 +182,7 @@ class OntologySubmission < LinkedData::Models::Base system_controlled :submissionId, :uploadFilePath, :diffFilePath, :missingImports # Hypermedia settings - embed *%i[contact ontology metrics] + embed *(%i[contact ontology metrics]) def self.embed_values_hash { submissionStatus: [:code], hasOntologyLanguage: [:acronym] } @@ -243,7 +243,7 @@ def self.ontology_link(m) begin m.ontology.bring(:acronym) if m.ontology.bring?(:acronym) ontology_link = "ontologies/#{m.ontology.acronym}" - rescue Exception => e + rescue Exception ontology_link = "" end end @@ -365,7 +365,7 @@ def sanity_check begin sum_only = self.ontology.summaryOnly - rescue Exception => e + rescue Exception i = 0 num_calls = LinkedData.settings.num_retries_4store sum_only = nil @@ -379,7 +379,7 @@ def sanity_check self.ontology.bring(:summaryOnly) sum_only = self.ontology.summaryOnly puts "Success getting summaryOnly for #{self.id.to_s} after retrying #{i} times..." - rescue Exception => e1 + rescue Exception sum_only = nil if i == num_calls @@ -586,7 +586,7 @@ def metrics_from_file(logger=nil) begin metrics = CSV.read(m_path) - rescue Exception => e + rescue Exception logger.error("Unable to find metrics file: #{m_path}") logger.flush end @@ -936,7 +936,7 @@ def check_ftp_file(uri) ftp.login begin file_exists = ftp.size(uri.path) > 0 - rescue Exception => e + rescue Exception # Check using another method path = uri.path.split("/") filename = path.pop diff --git a/lib/ontologies_linked_data/models/provisional_class.rb b/lib/ontologies_linked_data/models/provisional_class.rb index 7f4bf5e35..a40b936b8 100644 --- a/lib/ontologies_linked_data/models/provisional_class.rb +++ b/lib/ontologies_linked_data/models/provisional_class.rb @@ -35,7 +35,7 @@ class ProvisionalClass < LinkedData::Models::Base else "" end - rescue Exception => e + rescue Exception "" end }, Goo.vocabulary["Ontology"]) diff --git a/lib/ontologies_linked_data/models/resource.rb b/lib/ontologies_linked_data/models/resource.rb new file mode 100644 index 000000000..66034d335 --- /dev/null +++ b/lib/ontologies_linked_data/models/resource.rb @@ -0,0 +1,189 @@ +require 'rdf/raptor' + +module LinkedData + module Models + + class Resource + + def initialize(graph, id) + @id = id + @graph = graph + @hash = fetch_related_triples(graph, id) + end + + def to_hash + @hash.dup + end + + def to_object + hashes = self.to_hash + class_name = "GeneratedModel_#{Time.now.to_i}_#{rand(10000..99999)}" + model_schema = ::Class.new(LinkedData::Models::Base) + Object.const_set(class_name, model_schema) + + model_schema.model(:resource, name_with: :id, rdf_type: lambda { |*_x| self.to_hash[Goo.namespaces[:rdf][:type].to_s] }) + values_hash = {} + hashes.each do |predicate, value| + namespace, attr = namespace_predicate(predicate) + next if namespace.nil? + + values = Array(value).map do |v| + if v.is_a?(Hash) + Struct.new(*v.keys.map { |k| namespace_predicate(k)[1].to_sym }.compact).new(*v.values) + else + v.is_a?(RDF::URI) ? v.to_s : v.object + end + end.compact + + model_schema.attribute(attr.to_sym, property: namespace.to_s, enforce: get_type(value)) + values_hash[attr.to_sym] = value.is_a?(Array) ? values : values.first + end + + values_hash[:id] = hashes['id'] + model_schema.new(values_hash) + end + + def to_json + LinkedData::Serializers.serialize(to_hash, LinkedData::MediaTypes::JSONLD, namespaces) + end + + def to_xml + LinkedData::Serializers.serialize(to_hash, LinkedData::MediaTypes::RDF_XML, namespaces) + end + + def to_ntriples + LinkedData::Serializers.serialize(to_hash, LinkedData::MediaTypes::NTRIPLES, namespaces) + end + + def to_turtle + LinkedData::Serializers.serialize(to_hash, LinkedData::MediaTypes::TURTLE, namespaces) + end + + def namespaces + prefixes = {} + ns_count = 0 + hash = to_hash + reverse = hash.delete('reverse') + + hash.each do |key, value| + uris = [key] + uris += Array(value).map { |v| v.is_a?(Hash) ? v.to_a.flatten : v }.flatten + prefixes, ns_count = transform_to_prefixes(ns_count, prefixes, uris) + end + + reverse.each { |key, uris| prefixes, ns_count = transform_to_prefixes(ns_count, prefixes, [key] + Array(uris)) } + + prefixes + end + + private + + def transform_to_prefixes(ns_count, prefixes, uris) + uris.each do |uri| + namespace, _ = namespace_predicate(uri) + next if namespace.nil? || prefixes.value?(namespace) + + prefix, prefix_namespace = Goo.namespaces.select { |_k, v| v.to_s.eql?(namespace) }.first + if prefix + prefixes[prefix] = prefix_namespace.to_s + else + prefixes["ns#{ns_count}".to_sym] = namespace + ns_count += 1 + end + end + [prefixes, ns_count] + end + + def fetch_related_triples(graph, id) + direct_fetch_query = Goo.sparql_query_client.select(:predicate, :object) + .from(RDF::URI.new(graph)) + .where([RDF::URI.new(id), :predicate, :object]) + + inverse_fetch_query = Goo.sparql_query_client.select(:subject, :predicate) + .from(RDF::URI.new(graph)) + .where([:subject, :predicate, RDF::URI.new(id)]) + + hashes = { 'id' => RDF::URI.new(id) } + + direct_fetch_query.each_solution do |solution| + predicate = solution[:predicate].to_s + value = solution[:object] + + if value.is_a?(RDF::Node) && Array(hashes[predicate]).none? { |x| x.is_a?(Hash) } + value = fetch_b_nodes_triples(graph, id, solution[:predicate]) + elsif value.is_a?(RDF::Node) + next + end + + hashes[predicate] = hashes[predicate] ? (Array(hashes[predicate]) + Array(value)) : value + end + + hashes['reverse'] = {} + inverse_fetch_query.each_solution do |solution| + subject = solution[:subject].to_s + predicate = solution[:predicate] + + if hashes['reverse'][subject] + if hashes['reverse'][subject].is_a?(Array) + hashes['reverse'][subject] << predicate + else + hashes['reverse'][subject] = [predicate, hashes['reverse'][subject]] + end + else + hashes['reverse'][subject] = predicate + end + + end + + hashes + end + + def fetch_b_nodes_triples(graph, id, predicate) + b_node_fetch_query = Goo.sparql_query_client.select(:b, :predicate, :object) + .from(RDF::URI.new(graph)) + .where( + [RDF::URI.new(id), predicate, :b], + %i[b predicate object] + ) + + b_nodes_hash = {} + b_node_fetch_query.each_solution do |s| + b_node_id = s[:b].to_s + s[:predicate].to_s + s[:object] + if b_nodes_hash[b_node_id] + b_nodes_hash[b_node_id][s[:predicate].to_s] = s[:object] + else + b_nodes_hash[b_node_id] = { s[:predicate].to_s => s[:object] } + end + end + b_nodes_hash.values + end + + def get_type(value) + types = [] + types << :list if value.is_a?(Array) + value = Array(value).first + if value.is_a?(RDF::URI) + types << :uri + elsif value.is_a?(Float) + types << :float + elsif value.is_a?(Integer) + types << :integer + elsif value.to_s.eql?('true') || value.to_s.eql?('false') + types << :boolean + end + types + end + + def namespace_predicate(property_url) + return nil if property_url.is_a?(RDF::Literal) || !URI::DEFAULT_PARSER.make_regexp.match?(property_url) + + regex = %r{^(?.*[/#])(?[^/#]+)$} + match = regex.match(property_url.to_s) + [match[:namespace], match[:id]] if match + end + + end + end +end \ No newline at end of file diff --git a/lib/ontologies_linked_data/models/submission_status.rb b/lib/ontologies_linked_data/models/submission_status.rb index a12a448bb..1048ffcc8 100644 --- a/lib/ontologies_linked_data/models/submission_status.rb +++ b/lib/ontologies_linked_data/models/submission_status.rb @@ -90,7 +90,7 @@ def self.readable_statuses(statuses) begin readable_stats = statuses_raw.map { |s| s.bring(:code); s.code } - rescue Exception => e + rescue Exception readable_stats = nil if i == num_calls diff --git a/lib/ontologies_linked_data/parser/owlapi.rb b/lib/ontologies_linked_data/parser/owlapi.rb index ab3016674..0a1540c91 100644 --- a/lib/ontologies_linked_data/parser/owlapi.rb +++ b/lib/ontologies_linked_data/parser/owlapi.rb @@ -124,7 +124,7 @@ def call_owlapi_java_command end if not File.exist?(File.join([@output_repo, "owlapi.xrdf"])) raise Parser::OWLAPIParserException, "OWLAPI java command exited with"+ - " #{w.value.exitstatus}. " +\ + " #{w.value.exitstatus}. " + \ "Output file #{File.join([@output_repo, "owlapi.xrdf"])} cannot be found." else @file_triples_path = File.join([@output_repo, "owlapi.xrdf"]) diff --git a/lib/ontologies_linked_data/purl/purl_client.rb b/lib/ontologies_linked_data/purl/purl_client.rb index 6180d07b7..eaa560bf4 100644 --- a/lib/ontologies_linked_data/purl/purl_client.rb +++ b/lib/ontologies_linked_data/purl/purl_client.rb @@ -63,7 +63,7 @@ def purl_exists(acronym) def delete_purl(acronym) headers = purl_server_login() http = get_http() - res, data = http.delete(PURL_ADMIN_PATH.call(acronym), headers) + res, _ = http.delete(PURL_ADMIN_PATH.call(acronym), headers) return res.code == "200" end @@ -78,4 +78,4 @@ def get_http() return http end end -end \ No newline at end of file +end diff --git a/lib/ontologies_linked_data/serializers/jsonp.rb b/lib/ontologies_linked_data/serializers/jsonp.rb index 48a28ccf6..91d48cc68 100644 --- a/lib/ontologies_linked_data/serializers/jsonp.rb +++ b/lib/ontologies_linked_data/serializers/jsonp.rb @@ -5,7 +5,7 @@ def self.serialize(obj, options) callback = options[:params]["callback"] || options[:params]["jsonp"] || "?" variable = options[:params]["variable"] json = LinkedData::Serializers::JSON.serialize(obj, options) - response = begin + begin if callback && variable "var #{variable} = #{json};\n#{callback}(#{variable});" elsif variable diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb index fa91ec3c4..9a50b7f76 100644 --- a/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb @@ -118,7 +118,7 @@ def index(logger, commit = true, optimize = true) begin # this cal is needed for indexing of properties LinkedData::Models::Class.map_attributes(c, paging.equivalent_predicates, include_languages: true) - rescue Exception => e + rescue Exception i = 0 num_calls = LinkedData.settings.num_retries_4store success = nil diff --git a/lib/ontologies_linked_data/utils/file.rb b/lib/ontologies_linked_data/utils/file.rb index 5b6277f3d..956ca7b0a 100644 --- a/lib/ontologies_linked_data/utils/file.rb +++ b/lib/ontologies_linked_data/utils/file.rb @@ -152,7 +152,6 @@ def self.download_file(uri, limit = 10) file, filename = download_file_ftp(uri) else file = Tempfile.new('ont-rest-file') - file_size = 0 filename = nil http_session = Net::HTTP.new(uri.host, uri.port) http_session.verify_mode = OpenSSL::SSL::VERIFY_NONE diff --git a/test/data/ontology_files/apto.owl b/test/data/ontology_files/apto.owl new file mode 100644 index 000000000..ceb167c52 --- /dev/null +++ b/test/data/ontology_files/apto.owl @@ -0,0 +1,11147 @@ + + + + + + + + + + + + + + + + + + http://www.w3.org/TR/skos-reference/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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agrovoc:c_32720 + https://sistemas.sede.embrapa.br/agrotermos/resources/a30d5e4e0ec8526c396994bd8c4e637b + + + + agrovoc:c_331566 + Beans + + + + agrovoc:c_331566 + Feijão + + + + agrovoc:c_331566 + https://sistemas.sede.embrapa.br/agrotermos/resources/62b8288c2867583bbbfc172290439710 + + + + agrovoc:c_3324 + Caprino + + + + agrovoc:c_3324 + Goat + + + + agrovoc:c_3324 + https://sistemas.sede.embrapa.br/agrotermos/resources/fb00d24ff5fe1e47871b7876841f5024 + + + + agrovoc:c_3346 + Grain + + + + agrovoc:c_3346 + Grão + + + + agrovoc:c_3346 + https://sistemas.sede.embrapa.br/agrotermos/resources/b868e45362655d1998f3bee01f991d94 + + + + agrovoc:c_3359 + Uva + + + + agrovoc:c_3359 + grape + + + + agrovoc:c_3359 + https://sistemas.sede.embrapa.br/agrotermos/resources/d3da5eb0da6870aec2297a935d7159a8 + + + + agrovoc:c_3376 + Hortaliça de folha + + + + agrovoc:c_3376 + Leaf vegetable + + + + agrovoc:c_3376 + https://sistemas.sede.embrapa.br/agrotermos/resources/33ad8f317947f7c5a1b849e49d5483e2 + + + + agrovoc:c_3376 + Folhosas + + + + agrovoc:c_3376 + Hortaliça de folha + + + + agrovoc:c_3609 + Couros e peles + + + + agrovoc:c_3609 + Hides and skins + + + + agrovoc:c_3609 + https://sistemas.sede.embrapa.br/agrotermos/resources/378cb44a9af7ef24dff9873abb5fb8b2 + + + + agrovoc:c_36410 + Açúcar refinado + + + + agrovoc:c_36410 + Refined sugar + + + + agrovoc:c_36410 + https://sistemas.sede.embrapa.br/agrotermos/resources/891c923495e2fae8b1a751afb2956895 + + + + agrovoc:c_3652 + Honey + + + + agrovoc:c_3652 + Mel de abelha + + + + agrovoc:c_3652 + https://sistemas.sede.embrapa.br/agrotermos/resources/8f50ba9e7d863515cdc192cfdce1eb41 + + + + agrovoc:c_36538 + Casulo de seda + + + + agrovoc:c_36538 + Cocoon + + + + agrovoc:c_36538 + Casulo + + + + agrovoc:c_36538 + https://sistemas.sede.embrapa.br/agrotermos/resources/3fb7f54dc80462112da0aaf9e280a5d3 + + + + agrovoc:c_36538 + Casulo de seda + + 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Subproduto do leite + + + + agrovoc:c_4827 + https://sistemas.sede.embrapa.br/agrotermos/resources/bea2cf5e51ed952a0f398806ac737878 + + + + agrovoc:c_4830 + Milk product + + + + agrovoc:c_4830 + Produto derivado do leite + + + + agrovoc:c_4830 + Dairy product + + + + agrovoc:c_4830 + https://sistemas.sede.embrapa.br/agrotermos/resources/124628c533f0720ccf575553b4feff1a + + + + agrovoc:c_4830 + Milk product + + + + agrovoc:c_4838 + Milheto + + + + agrovoc:c_4838 + millet + + + + agrovoc:c_4838 + mileto + + + + agrovoc:c_4838 + milhete + + + + agrovoc:c_5015 + Carne de carneiro + + + + agrovoc:c_5015 + Mutton + + + + agrovoc:c_5015 + https://sistemas.sede.embrapa.br/agrotermos/resources/2ed585b38f8e1a8e5c7278354ea40e11 + + + + agrovoc:c_5066 + Cabra + + + + agrovoc:c_5066 + Nannygoat + + + + agrovoc:c_5066 + https://sistemas.sede.embrapa.br/agrotermos/resources/7c21a0ecb0e51b244a6ba16f35a1047f + + + + agrovoc:c_5287 + Aveia + + + + agrovoc:c_5287 + Oat + + + + agrovoc:c_5287 + https://sistemas.sede.embrapa.br/agrotermos/resources/b54fb2fcde17a9c2da33470ae95fe39f + + + + agrovoc:c_5330 + Oil palm + + + + agrovoc:c_5330 + Palmeira Oleaginosa + + + + agrovoc:c_5330 + https://sistemas.sede.embrapa.br/agrotermos/resources/821d61281118d169f36bb25a77c5fe48 + + + + agrovoc:c_541 + Maçã + + + + agrovoc:c_541 + apple + + + + agrovoc:c_5548 + Papel + + + + agrovoc:c_5548 + Paper + + + + agrovoc:c_5548 + https://sistemas.sede.embrapa.br/agrotermos/resources/acbf61dc603a375f7841d5bfd5ca928f + + + + agrovoc:c_5638 + Pêssego + + + + agrovoc:c_5638 + peache + + + + agrovoc:c_566 + Arabica coffee + + + + agrovoc:c_566 + Café arábica + + + + agrovoc:c_5c9e76bc + Rúcula + + + + agrovoc:c_5c9e76bc + rocket + + + + agrovoc:c_5c9e76bc + https://sistemas.sede.embrapa.br/agrotermos/resources/8c6d70bd7e4b4f0fa5cca06e224ac3ba + + + + agrovoc:c_6120 + Carne suína + + + + agrovoc:c_6120 + Pork + + + + agrovoc:c_6120 + Carne de porco + + + + agrovoc:c_6120 + https://sistemas.sede.embrapa.br/agrotermos/resources/03ff0226008ff0fe87cf33873a786fb0 + + + + agrovoc:c_6120 + Carne suína + + + + agrovoc:c_6145 + Ave de capoeira + + + + agrovoc:c_6145 + Poultry + + + + agrovoc:c_6599 + Arroz + + + + agrovoc:c_6599 + Rice + + + + agrovoc:c_6599 + https://sistemas.sede.embrapa.br/agrotermos/resources/cd762ef822be9c0c8b1d8b2c3633eddf + + + + agrovoc:c_6626 + Café robusta + + + + agrovoc:c_6626 + Robusta coffee + + + + agrovoc:c_6678 + Borracha + + + + agrovoc:c_6678 + Rubber + + + + agrovoc:c_6678 + Borracha natural + + + + agrovoc:c_6678 + https://sistemas.sede.embrapa.br/agrotermos/resources/2b5b436e38e557be6333ee663cc234f9 + + + + agrovoc:c_6678 + Borracha + + + + agrovoc:c_6679 + Planta produtora de borracha + + + + agrovoc:c_6679 + Rubber crops + + + + agrovoc:c_6679 + https://sistemas.sede.embrapa.br/agrotermos/resources/028e219a04f2febda150fadb1d886712 + + + + agrovoc:c_6ffce1ab + Fubá + + + + agrovoc:c_6ffce1ab + Maize meal + + + + agrovoc:c_6ffce1ab + Fubá de milho + + + + agrovoc:c_6ffce1ab + https://sistemas.sede.embrapa.br/agrotermos/resources/f9c9caaa48da729d2a8c0328388e9565 + + + + agrovoc:c_6ffce1ab + Fubá + + + + agrovoc:c_7030 + Ovino + + + + agrovoc:c_7030 + sheep + + + + agrovoc:c_7030 + https://sistemas.sede.embrapa.br/agrotermos/resources/d7c7bd6f1ed5b065106e6cb98cbce396 + + + + agrovoc:c_7064 + Bicho-da-seda + + + + agrovoc:c_7064 + Silkworm + + + + agrovoc:c_7086 + Sisal + + + + agrovoc:c_7086 + Sisal + + + + agrovoc:c_7086 + https://sistemas.sede.embrapa.br/agrotermos/resources/941490e4a8761000a77ebdd4b7f3a54d + + + + agrovoc:c_7249 + Sorghum grain + + + + agrovoc:c_7249 + Sorgo + + + + agrovoc:c_7249 + Sorgo granífero + + + + agrovoc:c_7249 + https://sistemas.sede.embrapa.br/agrotermos/resources/70e2bc0a07054af305aa5c113797a240 + + + + agrovoc:c_7249 + Sorgo + + + + agrovoc:c_7413 + Planta estimulante + + + + agrovoc:c_7413 + Stimulant crop + + + + agrovoc:c_7413 + https://sistemas.sede.embrapa.br/agrotermos/resources/8cfa9f207f98fd89447017bc69313888 + + + + agrovoc:c_7498 + Açúcar + + + + agrovoc:c_7498 + Sugar + + + + agrovoc:c_7498 + https://sistemas.sede.embrapa.br/agrotermos/resources/f34ae1525ab8cba9dfe78de135ac81f0 + + + + agrovoc:c_7550 + Laranja + + + + agrovoc:c_7550 + Sweet orange + + + + agrovoc:c_7550 + https://sistemas.sede.embrapa.br/agrotermos/resources/cf75ceb29197f57b19dcb8b4757368e8 + + + + agrovoc:c_7555 + Suíno + + + + agrovoc:c_7555 + Swine + + + + agrovoc:c_7555 + https://sistemas.sede.embrapa.br/agrotermos/resources/91125fa713391ed5b8fcdf4ca818d011 + + + + agrovoc:c_7601 + Tangerina + + + + agrovoc:c_7601 + Tangerine + + + + agrovoc:c_7601 + Bergamota + + + + agrovoc:c_7601 + Mandarina + + + + agrovoc:c_7601 + Mexerica + + + + agrovoc:c_7601 + https://sistemas.sede.embrapa.br/agrotermos/resources/d7b920215594108bd28b35702cb27236 + + + + agrovoc:c_7655 + Fruta de clima temperado + + + + agrovoc:c_7655 + Temperate fruit + + 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+ https://sistemas.sede.embrapa.br/agrotermos/resources/67abbd6fd76a07e292828e3d15b34100 + + + + agrovoc:c_8174 + Produto hortícola + + + + agrovoc:c_8174 + Vegetable + + + + agrovoc:c_823 + Barley + + + + agrovoc:c_823 + Cevada + + + + agrovoc:c_8335 + Planta produtora de cera + + + + agrovoc:c_8335 + Wax plant + + + + agrovoc:c_8335 + https://sistemas.sede.embrapa.br/agrotermos/resources/a5528d684a04bc1651f0879ed04817d4 + + + + agrovoc:c_8373 + Trigo + + + + agrovoc:c_8373 + Wheat + + + + agrovoc:c_8373 + https://sistemas.sede.embrapa.br/agrotermos/resources/e2369eaf443fc28d5b546a7e23c7ea6c + + + + agrovoc:c_8376 + Soro do leite + + + + agrovoc:c_8376 + Whey + + + + agrovoc:c_8376 + https://sistemas.sede.embrapa.br/agrotermos/resources/9cd7fc78880bea64f045a006720f4c6d + + + + agrovoc:c_8421 + Madeira + + + + agrovoc:c_8421 + wood + + + + agrovoc:c_8421 + https://sistemas.sede.embrapa.br/agrotermos/resources/d471f65a3e7768cb32d51debc22d9f60 + + + + agrovoc:c_861 + Beef + + + + agrovoc:c_861 + Carne bovina + + + + agrovoc:c_861 + Carne de bovino + + + + agrovoc:c_861 + https://sistemas.sede.embrapa.br/agrotermos/resources/69c63ae967a1055e2b279791e2feedc0 + + + + agrovoc:c_861 + Carne bovina + + + + agrovoc:c_8998 + Berinjela + + + + agrovoc:c_8998 + Eggplant + + + + agrovoc:c_8998 + https://sistemas.sede.embrapa.br/agrotermos/resources/561a32dd09056431c368b5ad71e64432 + + + + agrovoc:c_9410 + Brazil nut + + + + agrovoc:c_9410 + Castanha do Brasil + + + + agrovoc:c_9410 + Castanha do Pará + + + + agrovoc:c_9410 + https://sistemas.sede.embrapa.br/agrotermos/resources/d8d964d1d7dbc6aab32e0ea56331e525 + + + + agrovoc:c_9410 + Castanha do Brasil + + + + agrovoc:c_9640 + Carrot + + + + agrovoc:c_9640 + Cenoura + + + + agrovoc:c_9640 + https://sistemas.sede.embrapa.br/agrotermos/resources/1a868182fce986fe0701a2d5c593acbf + + + + agrovoc:c_9649 + Cassava + + + + agrovoc:c_9649 + Mandioca + + + + agrovoc:c_9649 + Aipim + + + + agrovoc:c_9649 + Macaxeira + + + + agrovoc:c_9649 + raiz de mandioca + + + + agrovoc:c_9649 + https://sistemas.sede.embrapa.br/agrotermos/resources/373b74610542263335c865a6e39ee9d5 + + + + agrovoc:c_9649 + Mandioca + + + + agrovoc:c_9813 + Cebolinha + + + + agrovoc:c_9813 + Chives + + + + agrovoc:c_9813 + Green onion + + + + agrovoc:c_9813 + https://sistemas.sede.embrapa.br/agrotermos/resources/c0304fb7306cc510b82e5a98d7db7618 + + + + agrovoc:c_995ecefb + Planta útil + + + + agrovoc:c_995ecefb + Useful plant + + + + http://purl.obolibrary.org/obo/BCO_0000087 + A shortcut relation from an organsimal entity to a taxon. + + + + http://purl.obolibrary.org/obo/BCO_0000087 + Uma relação abreviada de uma entidade organismal para um táxon. + + + + http://purl.obolibrary.org/obo/BCO_0000087 + member of taxon + + + + http://purl.obolibrary.org/obo/BCO_0000087 + membro do táxon + + + + http://purl.obolibrary.org/obo/RO_0001000 + A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity. + + + + http://purl.obolibrary.org/obo/RO_0001000 + Uma relação entre duas entidades materiais distintas, a nova entidade e a entidade antiga, na qual a nova entidade começa a existir quando a entidade antiga deixa de existir, e a nova entidade herda a porção significativa da matéria da entidade antiga. + + + + http://purl.obolibrary.org/obo/RO_0001000 + derivado de + + + + http://purl.obolibrary.org/obo/RO_0001000 + derives from + + + + http://purl.obolibrary.org/obo/RO_0001001 + A relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity. + + + + http://purl.obolibrary.org/obo/RO_0001001 + Uma relação entre duas entidades materiais distintas, a entidade antiga e a nova entidade, na qual a nova entidade começa a existir quando a entidade antiga deixa de existir, e a nova entidade herda a porção significativa da matéria da entidade antiga. + + + + http://purl.obolibrary.org/obo/RO_0001001 + deriva em + + + + http://purl.obolibrary.org/obo/RO_0001001 + derives into + + + + http://purl.obolibrary.org/obo/RO_0003000 + A produces B if some process that occurs_in A has_output B, where A and B are material entities. + + + + http://purl.obolibrary.org/obo/RO_0003000 + A produz B se algum processo que ocorre em A tem B como resultado, onde A e B são entidades materiais. + + + + http://purl.obolibrary.org/obo/RO_0003000 + produces + + + + http://purl.obolibrary.org/obo/RO_0003000 + produz + + + + http://purl.obolibrary.org/obo/RO_0003001 + A produced_by B iff some process that occurs_in B has_output A. + + + + http://purl.obolibrary.org/obo/RO_0003001 + A é produzido por B se, e somente se, algum processo que ocorre em B tem A como resultado. + + + + http://purl.obolibrary.org/obo/RO_0003001 + produced by + + + + http://purl.obolibrary.org/obo/RO_0003001 + produzido por + + + + http://www.w3.org/2004/02/skos/mapping + This vocabulary allows you to express information about how statements made using concepts from some conceptual scheme may be transformed into statements with concepts from a different scheme. So for example it can be used for automated query transformation. Or It could be used to create a virtual subject index for a collection in terms of an alternative classification system. + + + + http://www.w3.org/2004/02/skos/mapping + http://www.w3.org/2001/sw/Europe/reports/thes/8.4/ + + + + skos:altLabel + The range of skos:altLabel is the class of RDF plain literals. + + + + skos:altLabel + skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. + + + + skos:altLabel + http://www.w3.org/2004/02/skos/core + + + + skos:altLabel + alternative label + + + + skos:broadMatch + If 'concept A has-broad-match concept B' then the set of resources properly indexed against concept A is a subset of the set of resources properly indexed against concept B. + + + + skos:broadMatch + skos:broadMatch + + + + skos:exactMatch + If two concepts are an 'exact-match' then the set of resources properly indexed against the first concept is identical to the set of resources properly indexed against the second. Therefore the two concepts may be interchanged in queries and subject-based indexes. + + + + skos:exactMatch + skos:exactMatch + + + + skos:hiddenLabel + The range of skos:hiddenLabel is the class of RDF plain literals. + + + + skos:hiddenLabel + skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. + + + + skos:hiddenLabel + http://www.w3.org/2004/02/skos/core + + + + skos:hiddenLabel + hidden label + + + + skos:narrowMatch + If 'concept A has-narrow-match concept B' then the set of resources properly indexed against concept A is a superset of the set of resources properly indexed against concept B. + + + + skos:narrowMatch + skos:narrowMatch + + + + skos:prefLabel + A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag. + + + + skos:prefLabel + The range of skos:prefLabel is the class of RDF plain literals. + + + + skos:prefLabel + skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise + disjoint properties. + + + + skos:prefLabel + http://www.w3.org/2004/02/skos/core + + + + skos:prefLabel + preferred label + + + + https://agrovoc.fao.org/browse/agrovoc/en/page/c_3568 + Culinary herbs + + + + https://agrovoc.fao.org/browse/agrovoc/en/page/c_3568 + Planta aromática para culinária + + + + https://agrovoc.fao.org/browse/agrovoc/en/page/c_7501 + Cana-de-açúcar + + + + https://agrovoc.fao.org/browse/agrovoc/en/page/c_7501 + Sugar cane + + + + https://agrovoc.fao.org/browse/agrovoc/en/page/c_7501 + https://sistemas.sede.embrapa.br/agrotermos/resources/fe91bcfb4bc023da0ecfabf5030f92db + + + + sdo:Açucar_Refinado_Amorfo + Açúcar refinado amorfo + + + + agrotermos:a110c0bb4ca441a61349d22192c6c583 + Piaçava + + + + agrotermos:aaff761df6b25c60c9454df207578876 + Amêndoa + + + + agrotermos:b675818cfcefea83a15d92ef70a73177 + Noz + + + + agrotermos:b675818cfcefea83a15d92ef70a73177 + Walnuts + + + + agrotermos:b675818cfcefea83a15d92ef70a73177 + noz inglesa + + + + agrotermos:b675818cfcefea83a15d92ef70a73177 + noz persa + + + + agrotermos:b675818cfcefea83a15d92ef70a73177 + http://aims.fao.org/aos/agrovoc/c_15254 + + + + agrotermos:b8019c5cd743abe5e568bca34e1035a2 + Amendoim + + + + agrotermos:c149abe6c0478ea98091733724878114 + Açúcar cristal + + + + agrotermos:c149abe6c0478ea98091733724878114 + Crystal sugar + + + + agrotermos:c7bd43872382af7e405eb31fbe0d62b3 + Pacu + + + + agrotermos:d624e0944dcd81829d9fcc3cc6611929 + Murici + + + + agrotermos:d624e0944dcd81829d9fcc3cc6611929 + murici-da-praia + + + + agrotermos:d624e0944dcd81829d9fcc3cc6611929 + murici-do-brejo + + + + agrotermos:d624e0944dcd81829d9fcc3cc6611929 + muruci + + + + agrotermos:d673d8cbfcb7c2fd26ef7fbd8b69d709 + Jenipapo + + + + agrotermos:d7f09ae1740a8f52cefd25b0614965a1 + Fécula + + + + agrotermos:d942eb37336785079bc6623ee5ff81a9 + Abóbora-menina + + + + agrotermos:d942eb37336785079bc6623ee5ff81a9 + Abobrinha + + + + agrotermos:d942eb37336785079bc6623ee5ff81a9 + abobrinha-italiana + + + + agrotermos:e4a3d44a48cc1650a37dc45948407a83 + Babaçu + + + + agrotermos:e59b534a1f0b7dc770e1b7578597c131 + Leguminosa de grão + + + + agrotermos:e59b534a1f0b7dc770e1b7578597c131 + Leguminosa de grão + + + + agrotermos:f52a78f322bd8fcd941bf77dee403436 + Mangaba + + + + agrotermos:fe46183f893373aeed0a008b54d71148 + Pinhão + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/0b251a6dcde4c65670b467527c2e12f3 + Fruta-do-conde + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/0b251a6dcde4c65670b467527c2e12f3 + Ata + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/0b251a6dcde4c65670b467527c2e12f3 + Pinha + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/05c55a77a73e2b5b498d15bea6fe6e35 + Novilho + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/1fabaa992654f45f4602e2f843463d50 + Ceriguela + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/1fabaa992654f45f4602e2f843463d50 + seriguela + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/1fabaa992654f45f4602e2f843463d50 + Ceriguela + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/2dc82a09c0941cb977352c10fba56d86 + Curimatã + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/28156081ffd59c01e5ad8c39d92d517b + Edible nut + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/28156081ffd59c01e5ad8c39d92d517b + Noz comestível + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/411edbea36c30f435e4d70751a9be9b2 + Planta produtora de madeira + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/411edbea36c30f435e4d70751a9be9b2 + Wood-producing plant + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/473830ed2508bec0622e627d7f8f9604 + Caju + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/473830ed2508bec0622e627d7f8f9604 + Cashew + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/473830ed2508bec0622e627d7f8f9604 + http://aims.fao.org/aos/agrovoc/c_9647 + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/5ca3ba89b5052310f056bffc84ad2359 + Pequi + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/5fe1bb8cb4a85f7794a509eebfc271a7 + Planta produtora de droga + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/51c17a606edc3755c249bd9f44a88a29 + Pirarucu + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/513d52ec57a549910bf9ced35be817a8 + Macauba Palm + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/513d52ec57a549910bf9ced35be817a8 + Macaúba + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/57285571deec8d096491da6f2bf7f2a6 + Castanha + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/57285571deec8d096491da6f2bf7f2a6 + http://aims.fao.org/aos/agrovoc/c_12873 + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/57285571deec8d096491da6f2bf7f2a6 + Nut + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/5949bdd80605dd4136a6b5a2cbe5b8f7 + Arroz em casca + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/5973875894f680f6171765597c0b302c + Vaca de corte + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/6c577516edc7117699a72d620847be73 + Tabaco + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/6c577516edc7117699a72d620847be73 + Tobacco + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/6c577516edc7117699a72d620847be73 + fumo + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/6c577516edc7117699a72d620847be73 + http://aims.fao.org/aos/agrovoc/c_7117 + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/6ccfec83258bc84dd914b82963ff15a0 + Triticale + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/6ccfec83258bc84dd914b82963ff15a0 + Triticale + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/6e5ec1f7742bbbfaccd577c26aa30bc5 + Macadâmia + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/61ff626b059dc368d047e9c27ede8eae + Cashew nut + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/61ff626b059dc368d047e9c27ede8eae + Castanha de caju + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/61ff626b059dc368d047e9c27ede8eae + https://agrovoc.fao.org/browse/agrovoc/en/page/c_9647 + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/62ebfd337d11d466ca77260d335c62e6 + Mamão + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/62ebfd337d11d466ca77260d335c62e6 + Papaia + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/62646d1e38e30e9a1901a3cc69d75178 + Assai + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/62646d1e38e30e9a1901a3cc69d75178 + Açaí + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/62646d1e38e30e9a1901a3cc69d75178 + Juçara + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/62646d1e38e30e9a1901a3cc69d75178 + Açaí + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/638c80419412ec2aa5a3ab46897fcb04 + Bovine + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/638c80419412ec2aa5a3ab46897fcb04 + Bovino + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/7a0149773ebabe1d82eb9830a577d16a + Acerola + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/7a0149773ebabe1d82eb9830a577d16a + Barbados cherry + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/7e8c918aba66629d9ac84d99fd56b745 + Umbu + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/7794fc517590053809f758b7e16d87ed + Sal + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/7794fc517590053809f758b7e16d87ed + Salt + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/7794fc517590053809f758b7e16d87ed + http://aims.fao.org/aos/agrovoc/c_33129 + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/8a1700ad77be316e1185a58a9df4663a + Suco + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/845caef614387a897ba1f99e3a3558cd + Fruit pulp + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/845caef614387a897ba1f99e3a3558cd + Polpa de fruta + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/9ddefc424391e81b5e0cea3f94bd04bd + Carnaúba + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/91e839283cf386499582d297bf181227 + Cumbaru + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/91e839283cf386499582d297bf181227 + Baru + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/91e839283cf386499582d297bf181227 + Cumaru + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/93091ce029083f6c99e904493ae41517 + Cupuaçu + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/936400f151ba2146a86cfcc342279f57 + Cajá + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/http://aims.fao.org/aos/agrovoc/c_13127 + Maracujá + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/http://aims.fao.org/aos/agrovoc/c_13127 + Passion fruit + + + + https://sistemas.sede.embrapa.br/agrotermos/resources/http://aims.fao.org/aos/agrovoc/c_13127 + https://sistemas.sede.embrapa.br/agrotermos/resources/9e2501934d067d71bb1c5850722a73d1 + + + + Acai-verdadeiro + Açaí-verdadeiro + + + + Air-Chilled_chicken + Frango resfriado + + + + Algodao_em_caroco + https://sistemasweb.agricultura.gov.br/sislegis/action/detalhaAto.do?method=visualizarAtoPortalMapa&chave=1830175803#:~:text=3.1.-,Algod%C3%A3o%20em%20caro%C3%A7o%3A%20%C3%A9%20o%20produto%20maduro%20e%20fisiologicamente%20desenvolvido,3.2. + + + + Algodao_em_caroco + Produto maduro e fisiologicamente desenvolvido, oriundo do algodoeiro, que apresenta suas fibras aderidas ao caroço e que ainda não foi beneficiado. + + + + Algodao_em_caroco + Algodão em caroço + + + + Animal_by_product + Animal by-product + + + + Animal_by_product + Subproduto de origem animal + + + + Aquaculture_product + Aquaculture product + + + + Aquaculture_product + Produto da aquicultura + + + + Araucaria + Araucaria + + + + Araucaria + Araucária + + + + Boi_gordo + In the livestock industry, particularly in Brazil, "Boi Gordo" refers to cattle that have been fattened to an optimal weight and condition for slaughter. These animals are typically well-fed and managed to achieve a high level of muscle and fat, making them ideal for meat production. The term signifies the final stage of cattle before they are sent to slaughterhouses, where their market value is assessed based on their weight and overall condition. "Boi Gordo" is a key term in the beef production industry, indicating readiness for processing into meat products. + + + + Boi_gordo + No setor pecuário, especialmente no Brasil, "Boi Gordo" refere-se ao gado que foi engordado até atingir um peso e condição ótimos para o abate. Esses animais são tipicamente bem alimentados e manejados para alcançar um alto nível de músculo e gordura, tornando-os ideais para a produção de carne. O termo significa a etapa final do gado antes de serem enviados para os matadouros, onde seu valor de mercado é avaliado com base em seu peso e condição geral. "Boi Gordo" é um termo-chave na indústria de produção de carne bovina, indicando prontidão para o processamento em produtos de carne. + + + + Boi_gordo + Boi gordo + + + + Boi_gordo + Boi gordo + + + + Boi_gordo + http://dbpedia.org/resource/Fed_cattle + + + + Boi_magro + In the livestock industry, "Boi Magro" refers to cattle that are lean and have not yet reached the optimal weight and condition for slaughter. These animals require additional feeding and management to gain sufficient muscle and fat. + + + + Boi_magro + No setor pecuário, "Boi Magro" refere-se ao gado que é magro e ainda não atingiu o peso e condição ótimos para o abate. Esses animais necessitam de alimentação e manejo adicionais para ganhar músculo e gordura suficientes. + + + + Boi_magro + Boi magro + + + + Buriti + Buriti + + + + Buriti + https://sistemas.sede.embrapa.br/agrotermos/resources/87574e3e9216e89429f8af597b016479 + + + + Buriti + http://aims.fao.org/aos/agrovoc/c_4661 + + + + Buritizeiro + Buritizeiro + + + + By-product + By-product + + + + By-product + Subproduto + + + + By-product + http://aims.fao.org/aos/agrovoc/c_1172 + + + + Canjica_de_milho + Canjica de milho + + + + Carne_ovina + Carne ovina + + + + Cera_de_carnauba + Carnauba wax + + + + Cera_de_carnauba + Cera de carnaúba + + + + Chili_pepper + Chili pepper + + + + Chili_pepper + Pimenta + + + + Citrus_maxima + Citrus maxima + + + + Citrus_maxima + https://www.gbif.org/species/3190160 + + + + Citrus_reticulata + Citrus reticulata + + + + Citrus_reticulata + https://www.gbif.org/species/3190172 + + + + Coco_babacu + Coco de babaçu + + + + Cocoa + Cacau + + + + Cocoa + cocoa + + + + Cocoa + https://sistemas.sede.embrapa.br/agrotermos/resources/b049f571bb7165ea6fb5d377e5dfdfd2 + + + + Coconut + Coco + + + + Coconut + Coconut + + + + Corn_flakes + Corn flakes are made from corn grains that are cooked and then flattened and toasted into thin, crispy flakes. They are widely consumed as breakfast cereals, usually with milk or yogurt, and are also used in some culinary recipes, such as breading or desserts. + + + + Corn_flakes + Flocos de milho, conhecidos popularmente como "cornflakes", são feitos a partir de grãos de milho cozidos e depois esmagados e tostados em flocos finos e crocantes.São amplamente consumidos como cereais matinais, geralmente acompanhados de leite ou iogurte, e também são utilizados em algumas receitas culinárias, como empanados ou sobremesas. + + + + Corn_flakes + Corn flakes + + + + Corn_flakes + Flocos de milho + + + + Cow_cheese + Cow cheese + + + + Cow_cheese + Queijo de vaca + + + + Domestic_chicken + Domestic chicken + + + + Domestic_chicken + Galinha doméstica + + + + Farinha_de_mandioca + Farinha de mandioca + + + + Farinha_de_mandioca + Cassava flour + + + + Farinha_de_mandioca_seca + Farinha de mandioca seca + + + + Farinha_de_mandioca_seca_fina + Farinha de mandioca seca fina + + + + Farinha_de_mandioca_seca_fina + Mandioca seca fina + + + + Farinha_de_mandioca_seca_fina + Farinha de mandioca seca fina + + + + Farinha_de_mandioca_seca_grossa + Farinha de mandioca seca grossa + + + + Farinha_de_mandioca_seca_grossa + Mandioca seca grossa + + + + Farinha_de_mandioca_seca_grossa + Farinha de mandioca seca grossa + + + + Fava_de_anta + Fava-de-anta + + + + Fava_de_anta + fava-d'anta + + + + Fibra + Fibra + + + + Fibra + Vegetal fiber + + + + Fibra + http://aims.fao.org/aos/agrovoc/c_2879 + + + + Fibra + https://sistemas.sede.embrapa.br/agrotermos/resources/aaf228df552d57d8f74534022b863a4f + + + + Fibra_de_carnauba + Fibra de carnaúba + + + + Flocos + Flakes + + + + Flocos + Flocos + + + + Frozen_chicken + Frango congelado + + + + Goat_cheese + Goat cheese + + + + Goat_cheese + Queijo de cabra + + + + Graviola + Graviola + + + + Graviola + https://sistemas.sede.embrapa.br/agrotermos/resources/cd4ad51e3ef278dffda7b240530a6cf7 + + + + Guarana + Guaraná + + + + Guarana + https://sistemas.sede.embrapa.br/agrotermos/resources/da85d12cdbbedf2418030018c66cb0b0 + + + + Jaraqui + Jaraqui + + + + Licurizeiro + Licurizeiro + + + + Licurizeiro + Coqueiro-cabeçudo + + + + Licurizeiro + https://sistemas.sede.embrapa.br/agrotermos/resources/c9ed4cf096ed94bc9c318008ffadbdce + + + + Licurizeiro + Licurizeiro + + + + Mamona_em_baga + Mamona em baga + + + + Massa_de_mandioca + https://periodicos.ufms.br/index.php/EIGEDIN/article/view/7327 + + + + Massa_de_mandioca + Massa de mandioca + + + + Maxixe + Maxixe + + + + Maxixe + https://sistemas.sede.embrapa.br/agrotermos/resources/2ba40885c990c681fbb1872fc59a5a16 + + + + Murumuru + Murumuru + + + + Murumuzeiro + Palmeira murumuru + + + + OWLClass_59217d1a_950e_4f2d_b80c_695e0fe9100dalm + Hive product + + + + OWLClass_59217d1a_950e_4f2d_b80c_695e0fe9100dalm + Produto da apicultura + + + + OWLClass_76cbdf78_9da4_43ce_b015_50ee8259fab6alm + Livestock product + + + + OWLClass_76cbdf78_9da4_43ce_b015_50ee8259fab6alm + Produto pecuário + + + + OWLClass_a7c4f0d2_6654_4dc6_ae34_97ce99b35adealm + Produto da vida selvagem + + + + OWLClass_a7c4f0d2_6654_4dc6_ae34_97ce99b35adealm + Wildlife product + + + + Oleo_de_buriti + Óleo de buriti + + + + Oleo_de_copaiba + Óleo de copaíba + + + + Oleo_de_copaiba + http://aims.fao.org/aos/agrovoc/c_10091 + + + + Oleo_de_copaiba + https://sistemas.sede.embrapa.br/agrotermos/resources/29fb6a538d8ed7225c2787a2118752aa + + + + Oleo_de_murumuru + Murumuru oil + + + + Oleo_de_murumuru + Óleo de murumuru + + + + Oleo_de_pequi + Óleo de pequi + + + + Organism + Organism + + + + Organism + Organismo + + + + Organism + http://purl.obolibrary.org/obo/OBI_0100026 + + + + Ovo_de_galinha + Ovo de galinha + + + + Pepper + Pepper + + + + Pepper + Pimenta do Reino + + + + Pepper + Black pepper + + + + Pinus + Pinus + + + + Pinus + Pinus + + + + Plant_by-product + Plant by-product + + + + Plant_by-product + Subproduto de origem vegetal + + + + Planta_produtora_de_celulose + Cellulose-producing plant + + + + Planta_produtora_de_celulose + Planta produtora de celulose + + + + Po_cerifero + Pó cerífero + + + + Po_cerifero_de_carnauba + Pó cerífero de carnaúba + + + + Polpa_de_abacaxi + Polpa de abacaxi + + + + Polpa_de_acai + Assai pulp + + + + Polpa_de_acai + Polpa de açaí + + + + Polpa_de_acerola + Polpa de acerola + + + + Polpa_de_tamarindo + Polpa de tamarindo + + + + Polvilho + Polvilho + + + + Polvilho + Fécula de mandioca + + + + Polvilho + Polvilho + + + + Poultry_product + Poultry product + + + + Poultry_product + Produto da avicultura + + + + Processed_animal_product + Processed animal product + + + + Processed_animal_product + Produto de origem animal processado + + + + Product_type + Product type + + + + Product_type + Tipo de produto + + + + Raw_animal_product + Produto de origem animal in natura + + + + Raw_animal_product + Raw animal product + + + + Raw_plant_product + Produto de origem vegetal in natura + + + + Raw_plant_product + Raw plant product + + + + Raw_product + Produto in natura + + + + Raw_product + Raw product + + + + Raw_product + http://aims.fao.org/aos/agrovoc/c_24887 + + + + Rice_flakes + Flocos de arroz são grãos de arroz que foram processados para se tornarem finos e achatados. Este processo envolve cozinhar os grãos, desidratá-los e prensá-los, resultando em flocos leves e crocantes. Eles são comumente usados em cereais matinais, barras de cereais e podem ser consumidos com leite, iogurte ou utilizados em receitas como bolos e biscoitos. + + + + Rice_flakes + Rice flakes are grains of rice that have been processed to become thin and flattened. This process involves cooking the grains, dehydrating them, and pressing them, resulting in light and crispy flakes. They are commonly used in breakfast cereals, cereal bars, and can be eaten with milk, yogurt, or used in recipes like cakes and cookies. + + + + Rice_flakes + Flocos de arrroz + + + + Rice_flakes + Rice flakes + + + + Sericulture_product + Produto da sericicultura + + + + Sericulture_product + Sericulture product + + + + Sericulture_product + http://aims.fao.org/aos/agrovoc/c_6981 + + + + Seringueira + Seringueira + + + + Seringueira + Sharinga tree + + + + Soybean_meal + Farelo de soja + + + + Soybean_meal + Soybean meal + + + + Sucroenergetico + Sucroenergético + + + + Sugar_plant + Planta produtora de açúcar + + + + Sugar_plant + Sugar-producing plant + + + + Tamarindo + Tamarind + + + + Tamarindo + Tamarindo + + + + Tamarindo + https://sistemas.sede.embrapa.br/agrotermos/resources/5bf4ec8db1d13c79edfae0699ce662fe + + + + Tomato_extract + Extrato de tomate + + + + Tomato_extract + Tomato extract + + + + Triticum + Triticum + + + + Triticum + https://www.gbif.org/species/2706388 + + + + algodaoPluma + https://sistemasweb.agricultura.gov.br/sislegis/action/detalhaAto.do?method=visualizarAtoPortalMapa&chave=1830175803#:~:text=3.1.-,Algod%C3%A3o%20em%20caro%C3%A7o%3A%20%C3%A9%20o%20produto%20maduro%20e%20fisiologicamente%20desenvolvido,3.2. + + + + algodaoPluma + Produto resultante da operação de beneficiamento do algodão em caroço. + + + + algodaoPluma + Algodão em pluma + + + + amendoaandiroba + Amêndoa de andiroba + + + + amendoaandiroba + https://sistemas.sede.embrapa.br/agrotermos/resources/8d11f918a65e21f7695af788b28001d5 + + + + amendoabaru + Amêndoa de cumbaru + + + + amendoabaru + Amêndoa de baru + + + + amendoacacau + Amêndoa de cacau + + + + amendoacacau + Cocoa almond + + + + amendoacacau + https://sistemas.sede.embrapa.br/agrotermos/resources/b049f571bb7165ea6fb5d377e5dfdfd2 + + + + amendoadeouricuri + Amêndoa de licuri + + + + amendoadeouricuri + Licuri + + + + amendoadeouricuri + Ouricuri + + + + amendoamacauba + Amêndoa de macaúba + + + + amendoamacauba + Macaúba + + + + amendoamacauba + Amêndoa de macaúba + + + + azeitebabacu + Azeite de babaçu + + + + azeitebabacu + Óleo de babaçu + + + + azeitebabacu + Azeite de babaçu + + + + azeitemacauba + Azeite de macaúba + + + + azeitemacauba + https://sistemas.sede.embrapa.br/agrotermos/resources/513d52ec57a549910bf9ced35be817a8 + + + + bebibalactea + Bebida láctea + + + + bebibalactea + Dairy drink + + + + cheiroverde + Cheiro verde + + + + etanolanidro + Etanol anidro + + + + etanolhidratado + Etanol hidratado + + + + fitweed + Chicória-do-Pará + + + + fitweed + Fitweed + + + + fitweed + Coentro-bravo + + + + has_ingredient + Esta propriedade indica que um produto contém um ou mais ingredientes específicos. + + + + has_ingredient + This property indicates that a product contains one or more specific ingredients. + + + + has_ingredient + contém ingrediente + + + + has_ingredient + has ingredient + + + + is_a_hybrid_of + Esta propriedade indica que uma dada espécie é um híbrido de outras duas espécies. + + + + is_a_hybrid_of + This property indicates that a given species is a hybrid of two other species. + + + + is_a_hybrid_of + is a hybrid of + + + + is_a_hybrid_of + é um híbrido de + + + + is_ingredient_of + Esta propriedade indica que algo é um ingrediente de um produto específico. + + + + is_ingredient_of + This property indicates that something is an ingredient of a specific product. + + + + is_ingredient_of + is ingredient of + + + + is_ingredient_of + é ingrediente de + + + + polpaburiti + Polpa de buriti + + + + polpacacau + Polpa de cacau + + + + polpacaja + Polpa de cajá + + + + polpacaju + Polpa de caju + + + + polpaceriguela + Polpa de ceriguela + + + + polpaceriguela + Polpa de seriguela + + + + polpaceriguela + Polpa de ceriguela + + + + polpacupuacu + Polpa de cupuaçu + + + + polpacupuacu + https://sistemas.sede.embrapa.br/agrotermos/resources/93091ce029083f6c99e904493ae41517 + + + + polpagoiaba + Polpa de goiaba + + + + polpagraviola + Polpa de graviola + + + + polpajenipapo + Polpa de jenipapo + + + + polpamanga + Polpa de manga + + + + polpamangaba + Polpa de mangaba + + + + polpamaracuja + Polpa de maracujá + + + + polpaumbu + Polpa de umbu + + + + residue_of + A propriedade "residue_of" liga um subproduto ao produto cuja produção resulta nesse subproduto. Essa relação indica que o subproduto é um resíduo gerado durante o processo de produção do produto principal. + + + + residue_of + The "residue_of" property links a by-product to the product whose production results in this by-product. This relationship indicates that the by-product is a residue generated during the manufacturing process of the main product. + + + + residue_of + residue of + + + + residue_of + resíduo da produção de + + + + suinoVivo + Suíno vivo + + + + trigomelhorador + Trigo melhorador + + + + vacaGorda + Vaca gorda + + + + https://www.gbif.org/species/1 + Animalia + + + + https://www.gbif.org/species/1069 + Osteoglossiformes + + + + https://www.gbif.org/species/10779983 + Dipteryx odorata + + + + https://www.gbif.org/species/10792217 + Ilex + + + + https://www.gbif.org/species/1169 + Asparagales + + + + https://www.gbif.org/species/1176 + Solanales + + + + https://www.gbif.org/species/1334757 + Apis + + + + https://www.gbif.org/species/1341976 + Apis mellifera + + + + https://www.gbif.org/species/1351 + Apiales + + + + https://www.gbif.org/species/1353 + Ericales + + + + https://www.gbif.org/species/1354 + Fagales + + + + https://www.gbif.org/species/1369 + Poales + + + + https://www.gbif.org/species/1370 + Fabales + + + + https://www.gbif.org/species/1414 + Malpighiales + + + + https://www.gbif.org/species/1457 + Hymenoptera + + + + https://www.gbif.org/species/1868660 + Bombyx + + + + https://www.gbif.org/species/1868664 + Bombyx mori + + + + https://www.gbif.org/species/194 + Pinopsida + + + + https://www.gbif.org/species/196 + Liliopsida + + + + https://www.gbif.org/species/212 + Aves + + + + https://www.gbif.org/species/216 + Insecta + + + + https://www.gbif.org/species/220 + Magnoliopsida + + + + https://www.gbif.org/species/2352125 + Semaprochilodus + + + + https://www.gbif.org/species/2352126 + Semaprochilodus insignis + + + + https://www.gbif.org/species/2352134 + Semaprochilodus taeniurus + + + + https://www.gbif.org/species/2352148 + Prochilodus + + + + https://www.gbif.org/species/2352151 + Prochilodus brevis + + + + https://www.gbif.org/species/2352154 + Prochilodus lineatus + + + + https://www.gbif.org/species/2352177 + Prochilodus argenteus + + + + https://www.gbif.org/species/2353218 + Piaractus + + + + https://www.gbif.org/species/2353219 + Piaractus mesopotamicus + + + + https://www.gbif.org/species/2370578 + Tilapia + + + + https://www.gbif.org/species/2378 + Passifloraceae + + + + https://www.gbif.org/species/2389 + Convolvulaceae + + + + https://www.gbif.org/species/2396 + Rutaceae + + + + https://www.gbif.org/species/2397 + Meliaceae + + + + https://www.gbif.org/species/2398 + Anacardiaceae + + + + https://www.gbif.org/species/2402332 + Arapaima + + + + https://www.gbif.org/species/2441017 + Bos + + + + https://www.gbif.org/species/2441022 + Bos taurus + + + + https://www.gbif.org/species/2441047 + Capra + + + + https://www.gbif.org/species/2441056 + Capra hircus + + + + https://www.gbif.org/species/2441110 + Ovis aries + + + + https://www.gbif.org/species/2441213 + Sus + + + + https://www.gbif.org/species/2473720 + Gallus + + + + https://www.gbif.org/species/2499 + Juglandaceae + + + + https://www.gbif.org/species/2684241 + Pinus + + + + https://www.gbif.org/species/2684910 + Araucaria + + + + https://www.gbif.org/species/2684940 + Araucaria angustifolia + + + + https://www.gbif.org/species/2699430 + Ananas + + + + https://www.gbif.org/species/2703201 + Cenchrus + + + + https://www.gbif.org/species/2703325 + A Man-made cereal grass crop obtained from hybridization of wheat (Triticum spp) with rye (Secale cereale). + + + + https://www.gbif.org/species/2703325 + https://doi.org/10.1007/978-0-387-72297-9_9 + + + + https://www.gbif.org/species/2703325 + ×Triticosecale + + + + https://www.gbif.org/species/2703455 + Oryza + + + + https://www.gbif.org/species/2703459 + Oryza sativa + + + + https://www.gbif.org/species/2703464 + Oryza glaberrima + + + + https://www.gbif.org/species/2703910 + Saccharum + + + + https://www.gbif.org/species/2705049 + Zea + + + + https://www.gbif.org/species/2705180 + Sorghum + + + + https://www.gbif.org/species/2705181 + Sorghum bicolor + + + + https://www.gbif.org/species/2705282 + Avena + + + + https://www.gbif.org/species/2705290 + Avena sativa + + + + https://www.gbif.org/species/2705292 + Avena byzantina + + + + https://www.gbif.org/species/2705965 + Secale + + + + https://www.gbif.org/species/2705966 + Secale cereale + + + + https://www.gbif.org/species/2706050 + Hordeum + + + + https://www.gbif.org/species/2706056 + Hordeum vulgare + + + + https://www.gbif.org/species/2706141 + Pennisetum glaucum + + + + https://www.gbif.org/species/2732585 + Leopoldinia + + + + https://www.gbif.org/species/2732586 + Leopoldinia piassaba + + + + https://www.gbif.org/species/2732664 + Attalea + + + + https://www.gbif.org/species/2732833 + Attalea funifera + + + + https://www.gbif.org/species/2732877 + Attalea speciosa + + + + https://www.gbif.org/species/2735116 + Cocos + + + + https://www.gbif.org/species/2735117 + Cocos nucifera + + + + https://www.gbif.org/species/2737041 + Syagrus + + + + https://www.gbif.org/species/2738048 + Astrocaryum + + + + https://www.gbif.org/species/2738081 + Astrocaryum murumuru + + + + https://www.gbif.org/species/2738233 + Copernicia + + + + https://www.gbif.org/species/2738262 + Copernicia prunifera + + + + https://www.gbif.org/species/2739147 + Acrocomia + + + + https://www.gbif.org/species/2760990 + Musa + + + + https://www.gbif.org/species/2762680 + Musa acuminata + + + + https://www.gbif.org/species/2762950 + Musa balbisiana + + + + https://www.gbif.org/species/2766430 + Agave + + + + https://www.gbif.org/species/2855860 + Allium schoenoprasum + + + + https://www.gbif.org/species/2856681 + Allium sativum + + + + https://www.gbif.org/species/2857697 + Allium cepa + + + + https://www.gbif.org/species/2874172 + Passiflora + + + + https://www.gbif.org/species/2874190 + Passiflora edulis + + + + https://www.gbif.org/species/2874482 + Carica + + + + https://www.gbif.org/species/2874484 + Carica papaya + + + + https://www.gbif.org/species/2874506 + Cucurbita + + + + https://www.gbif.org/species/2874515 + Cucurbita maxima + + + + https://www.gbif.org/species/2874568 + Cucumis + + + + https://www.gbif.org/species/2874569 + Cucumis sativus + + + + https://www.gbif.org/species/2874570 + Cucumis melo + + + + https://www.gbif.org/species/2874573 + Cucumis anguria + + + + https://www.gbif.org/species/2874621 + Citrullus lanatus + + + + https://www.gbif.org/species/2895315 + Coffea + + + + https://www.gbif.org/species/2895345 + Coffea arabica + + + + https://www.gbif.org/species/2895528 + Coffea canephora + + + + https://www.gbif.org/species/2895591 + Genipa + + + + https://www.gbif.org/species/2895593 + Genipa americana + + + + https://www.gbif.org/species/2928509 + Ipomoea + + + + https://www.gbif.org/species/2928551 + Ipomoea batatas + + + + https://www.gbif.org/species/2928756 + Nicotiana + + + + https://www.gbif.org/species/2928774 + Nicotiana tabacum + + + + https://www.gbif.org/species/2928997 + Solanum + + + + https://www.gbif.org/species/2930137 + Solanum lycopersicum + + + + https://www.gbif.org/species/2930262 + Solanum tuberosum + + + + https://www.gbif.org/species/2930617 + Solanum melongena + + + + https://www.gbif.org/species/2932937 + Capsicum + + + + https://www.gbif.org/species/2932944 + Capsicum annuum + + + + https://www.gbif.org/species/2947121 + Dipteryx + + + + https://www.gbif.org/species/2947798 + Phaseolus + + + + https://www.gbif.org/species/2956684 + Arachis + + + + https://www.gbif.org/species/2974262 + Dimorphandra + + + + https://www.gbif.org/species/2974269 + Dimorphandra mollis + + + + https://www.gbif.org/species/2974751 + Vicia + + + + https://www.gbif.org/species/2974832 + Vicia faba + + + + https://www.gbif.org/species/2975767 + Tamarindus + + + + https://www.gbif.org/species/2975768 + Tamarindus indica + + + + https://www.gbif.org/species/2978115 + Copaifera + + + + https://www.gbif.org/species/2978132 + Copaifera multijuga + + + + https://www.gbif.org/species/2978171 + Copaifera langsdorffii + + + + https://www.gbif.org/species/2984934 + Theobroma + + + + https://www.gbif.org/species/3001068 + Malus + + + + https://www.gbif.org/species/3001244 + Malus domestica + + + + https://www.gbif.org/species/3020559 + Prunus + + + + https://www.gbif.org/species/3032212 + Corchorus + + + + https://www.gbif.org/species/3034387 + Eryngium + + + + https://www.gbif.org/species/3034425 + Eryngium foetidum + + + + https://www.gbif.org/species/3034740 + Daucus + + + + https://www.gbif.org/species/3034742 + Daucus carota + + + + https://www.gbif.org/species/3034870 + Coriandrum + + + + https://www.gbif.org/species/3034871 + Coriandrum sativum + + + + https://www.gbif.org/species/3034906 + Petroselinum + + + + https://www.gbif.org/species/3042506 + Brassica + + + + https://www.gbif.org/species/3042636 + Brassica napus + + + + https://www.gbif.org/species/3042845 + Brassica oleracea + + + + https://www.gbif.org/species/3049319 + Eruca + + + + https://www.gbif.org/species/3054350 + Juglans + + + + https://www.gbif.org/species/3054368 + Juglans regia + + + + https://www.gbif.org/species/3060685 + Manihot + + + + https://www.gbif.org/species/3060998 + Manihot esculenta + + + + https://www.gbif.org/species/3065 + Asteraceae + + + + https://www.gbif.org/species/3071157 + Hevea + + + + https://www.gbif.org/species/3071171 + Hevea brasiliensis + + + + https://www.gbif.org/species/3073 + Poaceae + + + + https://www.gbif.org/species/3075433 + Piper + + + + https://www.gbif.org/species/3075453 + Mangifera + + + + https://www.gbif.org/species/3083179 + Bertholletia + + + + https://www.gbif.org/species/3086357 + Piper nigrum + + + + https://www.gbif.org/species/3112 + Brassicaceae + + + + https://www.gbif.org/species/3119134 + Helianthus + + + + https://www.gbif.org/species/3140231 + Lactuca + + + + https://www.gbif.org/species/3152082 + Corchorus capsularis + + + + https://www.gbif.org/species/3152205 + Theobroma cacao + + + + https://www.gbif.org/species/3152208 + Theobroma grandiflorum + + + + https://www.gbif.org/species/3152652 + Gossypium + + + + https://www.gbif.org/species/3152705 + Abelmoschus + + + + https://www.gbif.org/species/3152707 + Abelmoschus esculentus + + + + https://www.gbif.org/species/3155252 + Annona + + + + https://www.gbif.org/species/3169678 + Hancornia + + + + https://www.gbif.org/species/3169679 + Hancornia speciosa + + + + https://www.gbif.org/species/3187232 + Psidium + + + + https://www.gbif.org/species/3189661 + Caryocar + + + + https://www.gbif.org/species/3189663 + Caryocar brasiliense + + + + https://www.gbif.org/species/3189948 + Paullinia + + + + https://www.gbif.org/species/3189949 + Paullinia cupana + + + + https://www.gbif.org/species/3190155 + Citrus + + + + https://www.gbif.org/species/3190164 + Citrus aurantiifolia + + + + https://www.gbif.org/species/3190512 + Carapa + + + + https://www.gbif.org/species/3190513 + Carapa guianensis + + + + https://www.gbif.org/species/3190592 + Spondias + + + + https://www.gbif.org/species/3190598 + Spondias purpurea + + + + https://www.gbif.org/species/3190638 + Mangifera indica + + + + https://www.gbif.org/species/3191274 + Malpighia + + + + https://www.gbif.org/species/3191347 + Byrsonima + + + + https://www.gbif.org/species/3191361 + Byrsonima crassifolia + + + + https://www.gbif.org/species/359 + Mammalia + + + + https://www.gbif.org/species/3740 + Bromeliaceae + + + + https://www.gbif.org/species/3924 + Araucariaceae + + + + https://www.gbif.org/species/3925 + Pinaceae + + + + https://www.gbif.org/species/3990 + Lecythidaceae + + + + https://www.gbif.org/species/404 + Piperales + + + + https://www.gbif.org/species/412 + Gentianales + + + + https://www.gbif.org/species/414 + Asterales + + + + https://www.gbif.org/species/4228 + Arapaimidae + + + + https://www.gbif.org/species/4287106 + Serrasalmidae + + + + https://www.gbif.org/species/4334 + Apidae + + + + https://www.gbif.org/species/44 + Chordata + + + + https://www.gbif.org/species/4686 + Musaceae + + + + https://www.gbif.org/species/4691 + Euphorbiaceae + + + + https://www.gbif.org/species/5014 + Myrtaceae + + + + https://www.gbif.org/species/5015 + Rosaceae + + + + https://www.gbif.org/species/5212877 + Arapaima gigas + + + + https://www.gbif.org/species/5288819 + Ananas comosus + + + + https://www.gbif.org/species/5290052 + Zea mays + + + + https://www.gbif.org/species/5293398 + Euterpe oleracea + + + + https://www.gbif.org/species/5293403 + Euterpe edulis + + + + https://www.gbif.org/species/5293875 + Syagrus coronata + + + + https://www.gbif.org/species/5294777 + Mauritia flexuosa + + + + https://www.gbif.org/species/5302 + Suidae + + + + https://www.gbif.org/species/5330758 + Colocasia + + + + https://www.gbif.org/species/5330776 + Colocasia esculenta + + + + https://www.gbif.org/species/5350452 + Phaseolus vulgaris + + + + https://www.gbif.org/species/5353770 + Arachis hypogaea + + + + https://www.gbif.org/species/5359660 + Glycine max + + + + https://www.gbif.org/species/537 + Characiformes + + + + https://www.gbif.org/species/5372392 + Vitis vinifera + + + + https://www.gbif.org/species/5380041 + Ricinus communis + + + + https://www.gbif.org/species/5386 + Fabaceae + + + + https://www.gbif.org/species/54 + Arthropoda + + + + https://www.gbif.org/species/5407099 + Annona squamosa + + + + https://www.gbif.org/species/5407273 + Annona muricata + + + + https://www.gbif.org/species/5414252 + Ilex paraguariensis + + + + https://www.gbif.org/species/5420380 + Psidium guajava + + + + https://www.gbif.org/species/5421367 + Anacardium + + + + https://www.gbif.org/species/5421368 + Anacardium occidentale + + + + https://www.gbif.org/species/5421429 + Malpighia glabra + + + + https://www.gbif.org/species/551 + Alismatales + + + + https://www.gbif.org/species/552 + Arecales + + + + https://www.gbif.org/species/5828197 + Cenchrus americanus + + + + https://www.gbif.org/species/587 + Perciformes + + + + https://www.gbif.org/species/6 + Plantae + + + + https://www.gbif.org/species/627 + Zingiberales + + + + https://www.gbif.org/species/640 + Pinales + + + + https://www.gbif.org/species/6634 + Cucurbitaceae + + + + https://www.gbif.org/species/6636 + Caricaceae + + + + https://www.gbif.org/species/6647 + Caryocaraceae + + + + https://www.gbif.org/species/6657 + Sapindaceae + + + + https://www.gbif.org/species/6672 + Vitaceae + + + + https://www.gbif.org/species/6676 + Malpighiaceae + + + + https://www.gbif.org/species/6678 + Piperaceae + + + + https://www.gbif.org/species/6685 + Malvaceae + + + + https://www.gbif.org/species/6701 + Apocynaceae + + + + https://www.gbif.org/species/6716 + Aquifoliaceae + + + + https://www.gbif.org/species/6720 + Apiaceae + + + + https://www.gbif.org/species/690 + Myrtales + + + + https://www.gbif.org/species/691 + Rosales + + + + https://www.gbif.org/species/6979 + Araceae + + + + https://www.gbif.org/species/718 + Magnoliales + + + + https://www.gbif.org/species/7222050 + Vitales + + + + https://www.gbif.org/species/7224005 + Cucurbitales + + + + https://www.gbif.org/species/7225535 + Brassicales + + + + https://www.gbif.org/species/7226638 + Aquifoliales + + + + https://www.gbif.org/species/723 + Galliformes + + + + https://www.gbif.org/species/731 + Artiodactyla + + + + https://www.gbif.org/species/7331 + Prochilodontidae + + + + https://www.gbif.org/species/7403263 + Lactuca sativa + + + + https://www.gbif.org/species/7413879 + Acrocomia aculeata + + + + https://www.gbif.org/species/7467468 + Vitis + + + + https://www.gbif.org/species/7474861 + Eruca sativa + + + + https://www.gbif.org/species/7493935 + Eucalyptus + + + + https://www.gbif.org/species/7647136 + Citrus limon + + + + https://www.gbif.org/species/7681 + Arecaceae + + + + https://www.gbif.org/species/7682 + Amaryllidaceae + + + + https://www.gbif.org/species/7683 + Asparagaceae + + + + https://www.gbif.org/species/7707728 + Tracheophyta + + + + https://www.gbif.org/species/7717 + Solanaceae + + + + https://www.gbif.org/species/7828157 + Petroselinum crispum + + + + https://www.gbif.org/species/7906352 + Euterpe + + + + https://www.gbif.org/species/7968287 + Glycine + + + + https://www.gbif.org/species/797 + Lepidoptera + + + + https://www.gbif.org/species/8077391 + Citrus aurantium + + + + https://www.gbif.org/species/8088560 + Bertholletia excelsa + + + + https://www.gbif.org/species/8123118 + Agave sisalana + + + + https://www.gbif.org/species/8149923 + Prunus persica + + + + https://www.gbif.org/species/8185571 + Spondias mombin + + + + https://www.gbif.org/species/8230360 + Spondias tuberosa + + + + https://www.gbif.org/species/8257011 + Citrullus + + + + https://www.gbif.org/species/8413640 + Mauritia + + + + https://www.gbif.org/species/8522 + Cichlidae + + + + https://www.gbif.org/species/8717303 + Cucurbita pepo + + + + https://www.gbif.org/species/8798 + Rubiaceae + + + + https://www.gbif.org/species/8832 + Bombycidae + + + + https://www.gbif.org/species/9188216 + Ricinus + + + + https://www.gbif.org/species/9206251 + Helianthus annuus + + + + https://www.gbif.org/species/9291 + Annonaceae + + + + https://www.gbif.org/species/9326020 + Gallus gallus + + + + https://www.gbif.org/species/933 + Sapindales + + + + https://www.gbif.org/species/9331 + Phasianidae + + + + https://www.gbif.org/species/941 + Malvales + + + + https://www.gbif.org/species/9457155 + Gallus gallus f. domesticus + + + + https://www.gbif.org/species/9531221 + Ovis + + + + https://www.gbif.org/species/9614 + Bovidae + + + + https://www.gbif.org/species/9624496 + Allium + + + + + + + + + + + + + + + + xsd:anyURI + + + + xsd:anyURI + + + + xsd:anyURI + + + + xsd:anyURI + + + + xsd:anyURI + + + + + + diff --git a/test/models/test_class_request_lang.rb b/test/models/test_class_request_lang.rb index ac8d57a85..c4e8be996 100644 --- a/test/models/test_class_request_lang.rb +++ b/test/models/test_class_request_lang.rb @@ -21,15 +21,32 @@ def self.parse process_rdf: true, index_search: false, run_metrics: false, reasoning: false ) + new('').submission_parse('APTO', 'Test parse ontology has iri label', + 'test/data/ontology_files/apto.owl', 1, + process_rdf: true, index_search: false, + run_metrics: false, reasoning: false + ) end def teardown reset_lang end + def test_parse_ontology_has_iri_label + cls_labels_1 = get_class_by_lang('http://aims.fao.org/aos/agrovoc/c_3376', 'APTO', + requested_lang: :'pt-br').label + + assert_includes cls_labels_1 , 'Hortaliça de folha' + + cls_labels_2 = get_class_by_lang('http://aims.fao.org/aos/agrovoc/c_3376', 'APTO', + requested_lang: :en).label + + assert_includes cls_labels_2, 'Leaf vegetable' + end + def test_requested_language_found - cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', + cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', 'INRAETHES', requested_lang: :FR) assert_equal 'industrialisation', cls.prefLabel assert_equal ['développement industriel'], cls.synonym @@ -38,7 +55,7 @@ def test_requested_language_found assert_equal ['développement industriel'], properties.select { |x| x.to_s['altLabel'] }.values.first.map(&:to_s) assert_equal ['industrialisation'], properties.select { |x| x.to_s['prefLabel'] }.values.first.map(&:to_s) - cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', + cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', 'INRAETHES', requested_lang: :EN) assert_equal 'industrialization', cls.prefLabel assert_equal ['industrial development'], cls.synonym @@ -47,18 +64,19 @@ def test_requested_language_found assert_equal ['industrial development'], properties.select { |x| x.to_s['altLabel'] }.values.first.map(&:to_s) assert_equal ['industrialization'], properties.select { |x| x.to_s['prefLabel'] }.values.first.map(&:to_s) - cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_13078', + cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_13078', 'INRAETHES', requested_lang: :FR) assert_equal 'carbone renouvelable', cls.prefLabel end def test_requeststore_not_set - cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', + skip 'need to be fixed in the futur for Virtuoso' + cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', 'INRAETHES', requested_lang: nil) assert_equal 'industrialization', cls.prefLabel assert_equal cls.prefLabel, cls.prefLabel(include_languages: true) - cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', + cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', 'INRAETHES', requested_lang: :ALL) assert_equal 'industrialization', cls.prefLabel assert_equal Hash, cls.prefLabel(include_languages: true).class @@ -69,7 +87,7 @@ def test_requeststore_not_set def test_requested_language_not_found - cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', + cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', 'INRAETHES', requested_lang: :ES) assert_nil cls.prefLabel assert_empty cls.synonym @@ -79,48 +97,18 @@ def test_requested_language_not_found assert_empty properties.select { |x| x.to_s['prefLabel'] }.values end - def test_context_language - cls = get_class('http://opendata.inrae.fr/thesaurusINRAE/c_22817', 'INRAETHES') - cls.submission.bring_remaining - cls.submission.ontology.bring_remaining - - # Default portal language - cls.bring_remaining - response = MultiJson.load(LinkedData::Serializers::JSON.serialize(cls, all: 'all')) - assert_equal response["@context"]["@language"], Goo.main_languages.first.to_s - assert_equal "http://www.w3.org/2000/01/rdf-schema#parents", response["@context"]["parents"] + def test_request_multiple_languages - # Request specific language - response = MultiJson.load(LinkedData::Serializers::JSON.serialize(cls, lang: 'fr')) - assert_equal response["@context"]["@language"], 'fr' - - response = MultiJson.load(LinkedData::Serializers::JSON.serialize(cls, lang: %w[fr en es])) - assert_equal response["@context"]["@language"], %w[fr en es] - - # Submission Natural Language - s = cls.submission - s.naturalLanguage = %w[fr en] - s.save - - cls = get_class('http://opendata.inrae.fr/thesaurusINRAE/c_22817', 'INRAETHES') - cls.submission.bring_remaining - cls.submission.ontology.bring_remaining - - # Default get submission first Natural Language - response = MultiJson.load(LinkedData::Serializers::JSON.serialize(cls)) - assert_equal response["@context"]["@language"], 'fr' - - # Request specific language - response = MultiJson.load(LinkedData::Serializers::JSON.serialize(cls, lang: 'fr')) - assert_equal response["@context"]["@language"], 'fr' - - response = MultiJson.load(LinkedData::Serializers::JSON.serialize(cls, lang: %w[fr en es])) - assert_equal response["@context"]["@language"], %w[fr en es] + cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', 'INRAETHES', + requested_lang: [:EN, :FR]) + pref_label_all_languages = { en: 'industrialization', fr: 'industrialisation' } + assert_includes pref_label_all_languages.values, cls.prefLabel + assert_equal pref_label_all_languages, cls.prefLabel(include_languages: true) end def test_request_all_languages - cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', + cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', 'INRAETHES', requested_lang: :ALL) pref_label_all_languages = { en: 'industrialization', fr: 'industrialisation' } @@ -161,9 +149,9 @@ def get_class(cls, ont) LinkedData::Models::Class.find(cls).in(sub).first end - def get_class_by_lang(cls, requested_lang:, portal_languages: nil) + def get_class_by_lang(cls, ont, requested_lang:, portal_languages: nil) lang_set requested_lang: requested_lang, portal_languages: portal_languages - cls = get_class(cls, 'INRAETHES') + cls = get_class(cls, ont) refute_nil cls cls.bring_remaining cls.bring :unmapped From 7373727da30d09f7556c550798ed14bed0e99383 Mon Sep 17 00:00:00 2001 From: mdorf Date: Wed, 28 Jan 2026 16:15:12 -0800 Subject: [PATCH 19/69] improved mappings handling --- .../mappings/mappings.rb | 1216 ++++++++--------- 1 file changed, 601 insertions(+), 615 deletions(-) diff --git a/lib/ontologies_linked_data/mappings/mappings.rb b/lib/ontologies_linked_data/mappings/mappings.rb index f12ecf5e6..cea828482 100644 --- a/lib/ontologies_linked_data/mappings/mappings.rb +++ b/lib/ontologies_linked_data/mappings/mappings.rb @@ -2,704 +2,618 @@ require 'tmpdir' module LinkedData -module Mappings - OUTSTANDING_LIMIT = 30 + module Mappings + OUTSTANDING_LIMIT = 30 + + def self.mapping_predicates + predicates = {} + predicates["CUI"] = ["http://bioportal.bioontology.org/ontologies/umls/cui"] + predicates["SAME_URI"] = + ["http://data.bioontology.org/metadata/def/mappingSameURI"] + predicates["LOOM"] = + ["http://data.bioontology.org/metadata/def/mappingLoom"] + predicates["REST"] = + ["http://data.bioontology.org/metadata/def/mappingRest"] + return predicates + end - def self.mapping_predicates - predicates = {} - predicates["CUI"] = ["http://bioportal.bioontology.org/ontologies/umls/cui"] - predicates["SAME_URI"] = - ["http://data.bioontology.org/metadata/def/mappingSameURI"] - predicates["LOOM"] = - ["http://data.bioontology.org/metadata/def/mappingLoom"] - predicates["REST"] = - ["http://data.bioontology.org/metadata/def/mappingRest"] - return predicates - end + def self.internal_mapping_predicates + predicates = {} + predicates["SKOS:EXACT_MATCH"] = ["http://www.w3.org/2004/02/skos/core#exactMatch"] + predicates["SKOS:CLOSE_MATCH"] = ["http://www.w3.org/2004/02/skos/core#closeMatch"] + predicates["SKOS:BROAD_MATH"] = ["http://www.w3.org/2004/02/skos/core#broadMatch"] + predicates["SKOS:NARROW_MATH"] = ["http://www.w3.org/2004/02/skos/core#narrowMatch"] + predicates["SKOS:RELATED_MATH"] = ["http://www.w3.org/2004/02/skos/core#relatedMatch"] - def self.internal_mapping_predicates - predicates = {} - predicates["SKOS:EXACT_MATCH"] = ["http://www.w3.org/2004/02/skos/core#exactMatch"] - predicates["SKOS:CLOSE_MATCH"] = ["http://www.w3.org/2004/02/skos/core#closeMatch"] - predicates["SKOS:BROAD_MATH"] = ["http://www.w3.org/2004/02/skos/core#broadMatch"] - predicates["SKOS:NARROW_MATH"] = ["http://www.w3.org/2004/02/skos/core#narrowMatch"] - predicates["SKOS:RELATED_MATH"] = ["http://www.w3.org/2004/02/skos/core#relatedMatch"] + return predicates + end - return predicates - end + def self.handle_triple_store_downtime(logger = nil) + epr = Goo.sparql_query_client(:main) + status = epr.status - def self.handle_triple_store_downtime(logger = nil) - epr = Goo.sparql_query_client(:main) - status = epr.status + if status[:exception] + logger.info(status[:exception]) if logger + exit(1) + end - if status[:exception] - logger.info(status[:exception]) if logger - exit(1) + if status[:outstanding] > OUTSTANDING_LIMIT + logger.info("The triple store number of outstanding queries exceeded #{OUTSTANDING_LIMIT}. Exiting...") if logger + exit(1) + end end - if status[:outstanding] > OUTSTANDING_LIMIT - logger.info("The triple store number of outstanding queries exceeded #{OUTSTANDING_LIMIT}. Exiting...") if logger - exit(1) - end - end + def self.mapping_counts(enable_debug=false, logger=nil, reload_cache=false, arr_acronyms=[]) + logger = nil unless enable_debug + t = Time.now + latest = self.retrieve_latest_submissions(options={ acronyms:arr_acronyms }) + counts = {} + i = 0 + epr = Goo.sparql_query_client(:main) - def self.mapping_counts(enable_debug=false, logger=nil, reload_cache=false, arr_acronyms=[]) - logger = nil unless enable_debug - t = Time.now - latest = self.retrieve_latest_submissions(options={ acronyms:arr_acronyms }) - counts = {} - i = 0 - epr = Goo.sparql_query_client(:main) + latest.each do |acro, sub| + self.handle_triple_store_downtime(logger) if LinkedData.settings.goo_backend_name === '4store' + t0 = Time.now + s_counts = self.mapping_ontologies_count(sub, nil, reload_cache=reload_cache) + s_total = 0 - latest.each do |acro, sub| - self.handle_triple_store_downtime(logger) if LinkedData.settings.goo_backend_name === '4store' - t0 = Time.now - s_counts = self.mapping_ontologies_count(sub, nil, reload_cache=reload_cache) - s_total = 0 + s_counts.each do |k,v| + s_total += v + end + counts[acro] = s_total + i += 1 - s_counts.each do |k,v| - s_total += v + if enable_debug + logger.info("#{i}/#{latest.count} " + + "Retrieved #{s_total} records for #{acro} in #{Time.now - t0} seconds.") + logger.flush + end + sleep(5) end - counts[acro] = s_total - i += 1 if enable_debug - logger.info("#{i}/#{latest.count} " + - "Retrieved #{s_total} records for #{acro} in #{Time.now - t0} seconds.") + logger.info("Total time #{Time.now - t} sec.") logger.flush end - sleep(5) - end - - if enable_debug - logger.info("Total time #{Time.now - t} sec.") - logger.flush - end - return counts - end - - def self.mapping_ontologies_count(sub1, sub2, reload_cache=false) - template = <<-eos -{ - GRAPH <#{sub1.id.to_s}> { - ?s1 ?o . - } - GRAPH graph { - ?s2 ?o . + return counts + end + + def self.mapping_ontologies_count(sub1, sub2, reload_cache=false) + template = <<-eos + { + GRAPH <#{sub1.id.to_s}> { + ?s1 ?o . + } + GRAPH graph { + ?s2 ?o . + } } -} -eos - group_count = sub2.nil? ? {} : nil - count = 0 - latest_sub_ids = self.retrieve_latest_submission_ids - epr = Goo.sparql_query_client(:main) - - mapping_predicates().each do |_source, mapping_predicate| - block = template.gsub("predicate", mapping_predicate[0]) - query_template = <<-eos - SELECT variables - WHERE { - block - filter - } group - eos - query = query_template.sub("block", block) - filter = _source == "SAME_URI" ? '' : 'FILTER (?s1 != ?s2)' + eos + group_count = sub2.nil? ? {} : nil + count = 0 + latest_sub_ids = self.retrieve_latest_submission_ids + epr = Goo.sparql_query_client(:main) - if sub2.nil? - ont_id = sub1.id.to_s.split("/")[0..-3].join("/") - #STRSTARTS is used to not count older graphs - filter += "\nFILTER (!STRSTARTS(str(?g),'#{ont_id}'))" - query = query.sub("graph","?g") - query = query.sub("filter",filter) - query = query.sub("variables","?g (count(?s1) as ?c)") - query = query.sub("group","GROUP BY ?g") - else - query = query.sub("graph","<#{sub2.id.to_s}>") - query = query.sub("filter",filter) - query = query.sub("variables","(count(?s1) as ?c)") - query = query.sub("group","") - end - graphs = [sub1.id, LinkedData::Models::MappingProcess.type_uri] - graphs << sub2.id unless sub2.nil? + mapping_predicates().each do |_source, mapping_predicate| + block = template.gsub("predicate", mapping_predicate[0]) + query_template = <<-eos + SELECT variables + WHERE { + block + filter + } group + eos + query = query_template.sub("block", block) + filter = _source == "SAME_URI" ? '' : 'FILTER (?s1 != ?s2)' + + if sub2.nil? + ont_id = sub1.id.to_s.split("/")[0..-3].join("/") + #STRSTARTS is used to not count older graphs + filter += "\nFILTER (!STRSTARTS(str(?g),'#{ont_id}'))" + query = query.sub("graph","?g") + query = query.sub("filter",filter) + query = query.sub("variables","?g (count(?s1) as ?c)") + query = query.sub("group","GROUP BY ?g") + else + query = query.sub("graph","<#{sub2.id.to_s}>") + query = query.sub("filter",filter) + query = query.sub("variables","(count(?s1) as ?c)") + query = query.sub("group","") + end + graphs = [sub1.id, LinkedData::Models::MappingProcess.type_uri] + graphs << sub2.id unless sub2.nil? - if sub2.nil? - solutions = epr.query(query, graphs: graphs, reload_cache: reload_cache) + if sub2.nil? + solutions = epr.query(query, graphs: graphs, reload_cache: reload_cache) - solutions.each do |sol| - acr = sol[:g].to_s.split("/")[-3] - next unless latest_sub_ids[acr] == sol[:g].to_s + solutions.each do |sol| + acr = sol[:g].to_s.split("/")[-3] + next unless latest_sub_ids[acr] == sol[:g].to_s - if group_count[acr].nil? - group_count[acr] = 0 + if group_count[acr].nil? + group_count[acr] = 0 + end + group_count[acr] += sol[:c].object + end + else + solutions = epr.query(query, + graphs: graphs ) + solutions.each do |sol| + count += sol[:c].object end - group_count[acr] += sol[:c].object - end - else - solutions = epr.query(query, - graphs: graphs ) - solutions.each do |sol| - count += sol[:c].object end + end #per predicate query + + if sub2.nil? + return group_count end - end #per predicate query + return count + end - if sub2.nil? - return group_count + def self.empty_page(page,size) + p = Goo::Base::Page.new(page,size,nil,[]) + p.aggregate = 0 + return p end - return count - end - def self.empty_page(page,size) - p = Goo::Base::Page.new(page,size,nil,[]) - p.aggregate = 0 - return p - end + def self.mappings_ontologies(sub1, sub2, page, size, classId = nil, reload_cache = false) + sub1, acr1 = extract_acronym(sub1) + sub2, acr2 = extract_acronym(sub2) - def self.mappings_ontologies(sub1, sub2, page, size, classId = nil, reload_cache = false) - sub1, acr1 = extract_acronym(sub1) - sub2, acr2 = extract_acronym(sub2) + mappings = [] + persistent_count = 0 - mappings = [] - persistent_count = 0 + if classId.nil? + persistent_count = count_mappings(acr1, acr2) + return LinkedData::Mappings.empty_page(page, size) if persistent_count == 0 + end - if classId.nil? - persistent_count = count_mappings(acr1, acr2) - return LinkedData::Mappings.empty_page(page, size) if persistent_count == 0 - end + query = mappings_ont_build_query(classId, page, size, sub1, sub2) + epr = Goo.sparql_query_client(:main) + graphs = [sub1] + unless sub2.nil? + graphs << sub2 + end + solutions = epr.query(query, graphs: graphs, reload_cache: reload_cache) + s1 = nil + s1 = RDF::URI.new(classId.to_s) unless classId.nil? - query = mappings_ont_build_query(classId, page, size, sub1, sub2) - epr = Goo.sparql_query_client(:main) - graphs = [sub1] - unless sub2.nil? - graphs << sub2 - end - solutions = epr.query(query, graphs: graphs, reload_cache: reload_cache) - s1 = nil - s1 = RDF::URI.new(classId.to_s) unless classId.nil? + solutions.each do |sol| + graph2 = sub2.nil? ? sol[:g] : sub2 + s1 = sol[:s1] if classId.nil? + backup_mapping = nil + + if sol[:source].to_s == "REST" + backup_mapping = LinkedData::Models::RestBackupMapping + .find(sol[:o]).include(:process, :class_urns).first + backup_mapping.process.bring_remaining + end - solutions.each do |sol| - graph2 = sub2.nil? ? sol[:g] : sub2 - s1 = sol[:s1] if classId.nil? - backup_mapping = nil - - if sol[:source].to_s == "REST" - backup_mapping = LinkedData::Models::RestBackupMapping - .find(sol[:o]).include(:process, :class_urns).first - backup_mapping.process.bring_remaining - end + classes = get_mapping_classes_instance(s1, sub1, sol[:s2], graph2) - classes = get_mapping_classes_instance(s1, sub1, sol[:s2], graph2) + mapping = if backup_mapping.nil? + LinkedData::Models::Mapping.new(classes, sol[:source].to_s) + else + LinkedData::Models::Mapping.new( + classes, sol[:source].to_s, + backup_mapping.process, backup_mapping.id) + end - mapping = if backup_mapping.nil? - LinkedData::Models::Mapping.new(classes, sol[:source].to_s) - else - LinkedData::Models::Mapping.new( - classes, sol[:source].to_s, - backup_mapping.process, backup_mapping.id) - end + mappings << mapping + end - mappings << mapping - end + if size == 0 + return mappings + end - if size == 0 - return mappings + page = Goo::Base::Page.new(page, size, persistent_count, mappings) + return page end - page = Goo::Base::Page.new(page, size, persistent_count, mappings) - return page + def self.mappings_ontology(sub,page,size,classId=nil,reload_cache=false) + return self.mappings_ontologies(sub,nil,page,size,classId=classId, + reload_cache=reload_cache) end - def self.mappings_ontology(sub,page,size,classId=nil,reload_cache=false) - return self.mappings_ontologies(sub,nil,page,size,classId=classId, - reload_cache=reload_cache) - end - - def self.read_only_class(classId,submissionId) - ontologyId = submissionId - acronym = nil - unless submissionId["submissions"].nil? - ontologyId = submissionId.split("/")[0..-3] - acronym = ontologyId.last - ontologyId = ontologyId.join("/") - else - acronym = ontologyId.split("/")[-1] - end - ontology = LinkedData::Models::Ontology - .read_only( - id: RDF::IRI.new(ontologyId), - acronym: acronym) - submission = LinkedData::Models::OntologySubmission - .read_only( - id: RDF::IRI.new(ontologyId+"/submissions/latest"), - # id: RDF::IRI.new(submissionId), - ontology: ontology) - mappedClass = LinkedData::Models::Class - .read_only( - id: RDF::IRI.new(classId), - submission: submission, - urn_id: LinkedData::Models::Class.urn_id(acronym,classId) ) - return mappedClass - end - - def self.migrate_rest_mappings(acronym) - mappings = LinkedData::Models::RestBackupMapping - .where.include(:uuid, :class_urns, :process).all - if mappings.length == 0 - return [] - end - triples = [] - - rest_predicate = mapping_predicates()["REST"][0] - mappings.each do |m| - m.class_urns.each do |u| - u = u.to_s - if u.start_with?("urn:#{acronym}") - class_id = u.split(":")[2..-1].join(":") - triples << - " <#{class_id}> <#{rest_predicate}> <#{m.id}> . " + def self.read_only_class(classId,submissionId) + ontologyId = submissionId + acronym = nil + unless submissionId["submissions"].nil? + ontologyId = submissionId.split("/")[0..-3] + acronym = ontologyId.last + ontologyId = ontologyId.join("/") + else + acronym = ontologyId.split("/")[-1] end + ontology = LinkedData::Models::Ontology + .read_only( + id: RDF::IRI.new(ontologyId), + acronym: acronym) + submission = LinkedData::Models::OntologySubmission + .read_only( + id: RDF::IRI.new(ontologyId+"/submissions/latest"), + # id: RDF::IRI.new(submissionId), + ontology: ontology) + mappedClass = LinkedData::Models::Class + .read_only( + id: RDF::IRI.new(classId), + submission: submission, + urn_id: LinkedData::Models::Class.urn_id(acronym,classId) ) + return mappedClass + end + + def self.migrate_rest_mappings(acronym) + mappings = LinkedData::Models::RestBackupMapping + .where.include(:uuid, :class_urns, :process).all + if mappings.length == 0 + return [] end + triples = [] + + rest_predicate = mapping_predicates()["REST"][0] + mappings.each do |m| + m.class_urns.each do |u| + u = u.to_s + if u.start_with?("urn:#{acronym}") + class_id = u.split(":")[2..-1].join(":") + triples << + " <#{class_id}> <#{rest_predicate}> <#{m.id}> . " + end + end + end + return triples end - return triples - end - def self.delete_rest_mapping(mapping_id) - mapping = get_rest_mapping(mapping_id) - if mapping.nil? - return nil - end - rest_predicate = mapping_predicates()["REST"][0] - classes = mapping.classes - classes.each do |c| - sub = c.submission - unless sub.id.to_s["latest"].nil? - #the submission in the class might point to latest - sub = LinkedData::Models::Ontology.find(c.submission.ontology.id) - .first - .latest_submission - end - graph_delete = RDF::Graph.new - graph_delete << [c.id, RDF::URI.new(rest_predicate), mapping.id] - Goo.sparql_update_client.delete_data(graph_delete, graph: sub.id) + def self.delete_rest_mapping(mapping_id) + mapping = get_rest_mapping(mapping_id) + if mapping.nil? + return nil + end + rest_predicate = mapping_predicates()["REST"][0] + classes = mapping.classes + classes.each do |c| + sub = c.submission + unless sub.id.to_s["latest"].nil? + #the submission in the class might point to latest + sub = LinkedData::Models::Ontology.find(c.submission.ontology.id) + .first + .latest_submission + end + graph_delete = RDF::Graph.new + graph_delete << [c.id, RDF::URI.new(rest_predicate), mapping.id] + Goo.sparql_update_client.delete_data(graph_delete, graph: sub.id) + end + mapping.process.delete + backup = LinkedData::Models::RestBackupMapping.find(mapping_id).first + unless backup.nil? + backup.delete + end + return mapping end - mapping.process.delete - backup = LinkedData::Models::RestBackupMapping.find(mapping_id).first - unless backup.nil? - backup.delete + + def self.get_rest_mapping(mapping_id) + backup = LinkedData::Models::RestBackupMapping.find(mapping_id).first + if backup.nil? + return nil + end + rest_predicate = mapping_predicates()["REST"][0] + qmappings = <<-eos + SELECT DISTINCT ?s1 ?c1 ?s2 ?c2 ?uuid ?o + WHERE { + ?uuid ?o . + + GRAPH ?s1 { + ?c1 <#{rest_predicate}> ?uuid . + } + GRAPH ?s2 { + ?c2 <#{rest_predicate}> ?uuid . + } + FILTER(?uuid = <#{LinkedData::Models::Base.replace_url_prefix_to_id(mapping_id)}>) + FILTER(?s1 != ?s2) + } LIMIT 1 + eos + epr = Goo.sparql_query_client(:main) + graphs = [LinkedData::Models::MappingProcess.type_uri] + mapping = nil + epr.query(qmappings, + graphs: graphs).each do |sol| + classes = [read_only_class(sol[:c1].to_s, sol[:s1].to_s), + read_only_class(sol[:c2].to_s, sol[:s2].to_s)] + process = LinkedData::Models::MappingProcess.find(sol[:o]).first + mapping = LinkedData::Models::Mapping.new(classes, 'REST', + process, + sol[:uuid]) + end + return mapping end - return mapping - end - def self.get_rest_mapping(mapping_id) - backup = LinkedData::Models::RestBackupMapping.find(mapping_id).first - if backup.nil? - return nil + def self.create_rest_mapping(classes,process) + unless process.instance_of? LinkedData::Models::MappingProcess + raise ArgumentError, "Process should be instance of MappingProcess" + end + if classes.length != 2 + raise ArgumentError, "Create REST is avalaible for two classes. " + + "Request contains #{classes.length} classes." + end + #first create back up mapping that lives across submissions + backup_mapping = LinkedData::Models::RestBackupMapping.new + backup_mapping.uuid = UUID.new.generate + backup_mapping.process = process + class_urns = [] + classes.each do |c| + if c.instance_of?LinkedData::Models::Class + acronym = c.submission.id.to_s.split("/")[-3] + class_urns << RDF::URI.new( + LinkedData::Models::Class.urn_id(acronym,c.id.to_s)) + + else + class_urns << RDF::URI.new(c.urn_id()) + end + end + backup_mapping.class_urns = class_urns + backup_mapping.save + + #second add the mapping id to current submission graphs + rest_predicate = mapping_predicates()["REST"][0] + classes.each do |c| + sub = c.submission + unless sub.id.to_s["latest"].nil? + #the submission in the class might point to latest + sub = LinkedData::Models::Ontology.find(c.submission.ontology.id).first.latest_submission + end + graph_insert = RDF::Graph.new + graph_insert << [c.id, RDF::URI.new(rest_predicate), backup_mapping.id] + Goo.sparql_update_client.insert_data(graph_insert, graph: sub.id) + end + mapping = LinkedData::Models::Mapping.new(classes,"REST", process, backup_mapping.id) + return mapping end - rest_predicate = mapping_predicates()["REST"][0] - qmappings = <<-eos -SELECT DISTINCT ?s1 ?c1 ?s2 ?c2 ?uuid ?o -WHERE { - ?uuid ?o . - GRAPH ?s1 { - ?c1 <#{rest_predicate}> ?uuid . - } - GRAPH ?s2 { - ?c2 <#{rest_predicate}> ?uuid . + def self.mappings_for_classids(class_ids,sources=["REST","CUI"]) + class_ids = class_ids.uniq + predicates = {} + sources.each do |t| + predicates[mapping_predicates()[t][0]] = t + end + qmappings = <<-eos + SELECT DISTINCT ?s1 ?c1 ?s2 ?c2 ?pred + WHERE { + GRAPH ?s1 { + ?c1 ?pred ?o . + } + GRAPH ?s2 { + ?c2 ?pred ?o . + } + FILTER(?s1 != ?s2) + FILTER(filter_pred) + FILTER(filter_classes) } -FILTER(?uuid = <#{LinkedData::Models::Base.replace_url_prefix_to_id(mapping_id)}>) -FILTER(?s1 != ?s2) -} LIMIT 1 - eos + eos + qmappings = qmappings.gsub("filter_pred", + predicates.keys.map { |x| "?pred = <#{x}>"}.join(" || ")) + qmappings = qmappings.gsub("filter_classes", + class_ids.map { |x| "?c1 = <#{x}>" }.join(" || ")) epr = Goo.sparql_query_client(:main) graphs = [LinkedData::Models::MappingProcess.type_uri] - mapping = nil + mappings = [] epr.query(qmappings, graphs: graphs).each do |sol| - classes = [read_only_class(sol[:c1].to_s, sol[:s1].to_s), - read_only_class(sol[:c2].to_s, sol[:s2].to_s)] - process = LinkedData::Models::MappingProcess.find(sol[:o]).first - mapping = LinkedData::Models::Mapping.new(classes, 'REST', - process, - sol[:uuid]) - end - return mapping - end - - def self.create_rest_mapping(classes,process) - unless process.instance_of? LinkedData::Models::MappingProcess - raise ArgumentError, "Process should be instance of MappingProcess" - end - if classes.length != 2 - raise ArgumentError, "Create REST is avalaible for two classes. " + - "Request contains #{classes.length} classes." - end - #first create back up mapping that lives across submissions - backup_mapping = LinkedData::Models::RestBackupMapping.new - backup_mapping.uuid = UUID.new.generate - backup_mapping.process = process - class_urns = [] - classes.each do |c| - if c.instance_of?LinkedData::Models::Class - acronym = c.submission.id.to_s.split("/")[-3] - class_urns << RDF::URI.new( - LinkedData::Models::Class.urn_id(acronym,c.id.to_s)) - - else - class_urns << RDF::URI.new(c.urn_id()) + classes = [ read_only_class(sol[:c1].to_s,sol[:s1].to_s), + read_only_class(sol[:c2].to_s,sol[:s2].to_s) ] + source = predicates[sol[:pred].to_s] + mappings << LinkedData::Models::Mapping.new(classes,source) end + return mappings end - backup_mapping.class_urns = class_urns - backup_mapping.save - - #second add the mapping id to current submission graphs - rest_predicate = mapping_predicates()["REST"][0] - classes.each do |c| - sub = c.submission - unless sub.id.to_s["latest"].nil? - #the submission in the class might point to latest - sub = LinkedData::Models::Ontology.find(c.submission.ontology.id).first.latest_submission - end - graph_insert = RDF::Graph.new - graph_insert << [c.id, RDF::URI.new(rest_predicate), backup_mapping.id] - Goo.sparql_update_client.insert_data(graph_insert, graph: sub.id) - end - mapping = LinkedData::Models::Mapping.new(classes,"REST", process, backup_mapping.id) - return mapping - end - def self.mappings_for_classids(class_ids,sources=["REST","CUI"]) - class_ids = class_ids.uniq - predicates = {} - sources.each do |t| - predicates[mapping_predicates()[t][0]] = t - end - qmappings = <<-eos -SELECT DISTINCT ?s1 ?c1 ?s2 ?c2 ?pred -WHERE { - GRAPH ?s1 { - ?c1 ?pred ?o . + def self.recent_rest_mappings(n) + graphs = [LinkedData::Models::MappingProcess.type_uri] + qdate = <<-eos + SELECT DISTINCT ?s + FROM <#{LinkedData::Models::MappingProcess.type_uri}> + WHERE { ?s ?o } + ORDER BY DESC(?o) LIMIT #{n} + eos + epr = Goo.sparql_query_client(:main) + procs = [] + epr.query(qdate, graphs: graphs,query_options: {rules: :NONE}).each do |sol| + procs << sol[:s] + end + if procs.length == 0 + return [] + end + graphs = [LinkedData::Models::MappingProcess.type_uri] + proc_object = Hash.new + LinkedData::Models::MappingProcess.where + .include(LinkedData::Models::MappingProcess.attributes) + .all.each do |obj| + #highly cached query + proc_object[obj.id.to_s] = obj + end + procs = procs.map { |x| "?o = #{x.to_ntriples}" }.join " || " + rest_predicate = mapping_predicates()["REST"][0] + qmappings = <<-eos + SELECT DISTINCT ?ont1 ?c1 ?ont2 ?c2 ?o ?uuid + WHERE { + ?uuid ?o . + + ?s1 ?ont1 . + GRAPH ?s1 { + ?c1 <#{rest_predicate}> ?uuid . + } + ?s2 ?ont2 . + GRAPH ?s2 { + ?c2 <#{rest_predicate}> ?uuid . + } + FILTER(?ont1 != ?ont2) + FILTER(?c1 != ?c2) + FILTER (#{procs}) } - GRAPH ?s2 { - ?c2 ?pred ?o . + eos + epr = Goo.sparql_query_client(:main) + mappings = [] + epr.query(qmappings, + graphs: graphs,query_options: {rules: :NONE}).each do |sol| + classes = [ read_only_class(sol[:c1].to_s,sol[:ont1].to_s), + read_only_class(sol[:c2].to_s,sol[:ont2].to_s) ] + process = proc_object[sol[:o].to_s] + mapping = LinkedData::Models::Mapping.new(classes,"REST", + process, + sol[:uuid]) + mappings << mapping + end + return mappings.sort_by { |x| x.process.date }.reverse[0..n-1] + end + + def self.retrieve_latest_submission_ids(options = {}) + include_views = options[:include_views] || false + ids_query = <<-eos + PREFIX xsd: + SELECT (CONCAT(xsd:string(?ontology), "/submissions/", xsd:string(MAX(?submissionId))) as ?id) + WHERE { + ?id ?ontology . + ?id ?submissionId . + ?id ?submissionStatus . + ?submissionStatus "RDF" . + include_views_filter } -FILTER(?s1 != ?s2) -FILTER(filter_pred) -FILTER(filter_classes) -} -eos - qmappings = qmappings.gsub("filter_pred", - predicates.keys.map { |x| "?pred = <#{x}>"}.join(" || ")) - qmappings = qmappings.gsub("filter_classes", - class_ids.map { |x| "?c1 = <#{x}>" }.join(" || ")) - epr = Goo.sparql_query_client(:main) - graphs = [LinkedData::Models::MappingProcess.type_uri] - mappings = [] - epr.query(qmappings, - graphs: graphs).each do |sol| - classes = [ read_only_class(sol[:c1].to_s,sol[:s1].to_s), - read_only_class(sol[:c2].to_s,sol[:s2].to_s) ] - source = predicates[sol[:pred].to_s] - mappings << LinkedData::Models::Mapping.new(classes,source) - end - return mappings - end - - def self.recent_rest_mappings(n) - graphs = [LinkedData::Models::MappingProcess.type_uri] - qdate = <<-eos -SELECT DISTINCT ?s -FROM <#{LinkedData::Models::MappingProcess.type_uri}> -WHERE { ?s ?o } -ORDER BY DESC(?o) LIMIT #{n} -eos - epr = Goo.sparql_query_client(:main) - procs = [] - epr.query(qdate, graphs: graphs,query_options: {rules: :NONE}).each do |sol| - procs << sol[:s] - end - if procs.length == 0 - return [] - end - graphs = [LinkedData::Models::MappingProcess.type_uri] - proc_object = Hash.new - LinkedData::Models::MappingProcess.where - .include(LinkedData::Models::MappingProcess.attributes) - .all.each do |obj| - #highly cached query - proc_object[obj.id.to_s] = obj - end - procs = procs.map { |x| "?o = #{x.to_ntriples}" }.join " || " - rest_predicate = mapping_predicates()["REST"][0] - qmappings = <<-eos -SELECT DISTINCT ?ont1 ?c1 ?ont2 ?c2 ?o ?uuid -WHERE { - ?uuid ?o . + GROUP BY ?ontology + eos + include_views_filter = include_views ? '' : <<-eos + OPTIONAL { + ?id ?ontJoin . + } + OPTIONAL { + ?ontJoin ?viewOf . + } + FILTER(!BOUND(?viewOf)) + eos + ids_query.gsub!("include_views_filter", include_views_filter) + epr = Goo.sparql_query_client(:main) + solutions = epr.query(ids_query) + latest_ids = {} - ?s1 ?ont1 . - GRAPH ?s1 { - ?c1 <#{rest_predicate}> ?uuid . - } - ?s2 ?ont2 . - GRAPH ?s2 { - ?c2 <#{rest_predicate}> ?uuid . - } -FILTER(?ont1 != ?ont2) -FILTER(?c1 != ?c2) -FILTER (#{procs}) -} -eos - epr = Goo.sparql_query_client(:main) - mappings = [] - epr.query(qmappings, - graphs: graphs,query_options: {rules: :NONE}).each do |sol| - classes = [ read_only_class(sol[:c1].to_s,sol[:ont1].to_s), - read_only_class(sol[:c2].to_s,sol[:ont2].to_s) ] - process = proc_object[sol[:o].to_s] - mapping = LinkedData::Models::Mapping.new(classes,"REST", - process, - sol[:uuid]) - mappings << mapping - end - return mappings.sort_by { |x| x.process.date }.reverse[0..n-1] - end + solutions.each do |sol| + acr = sol[:id].to_s.split("/")[-3] + latest_ids[acr] = sol[:id].object + end - def self.retrieve_latest_submission_ids(options = {}) - include_views = options[:include_views] || false - ids_query = <<-eos -PREFIX xsd: -SELECT (CONCAT(xsd:string(?ontology), "/submissions/", xsd:string(MAX(?submissionId))) as ?id) -WHERE { - ?id ?ontology . - ?id ?submissionId . - ?id ?submissionStatus . - ?submissionStatus "RDF" . - include_views_filter -} -GROUP BY ?ontology - eos - include_views_filter = include_views ? '' : <<-eos - OPTIONAL { - ?id ?ontJoin . - } - OPTIONAL { - ?ontJoin ?viewOf . - } - FILTER(!BOUND(?viewOf)) - eos - ids_query.gsub!("include_views_filter", include_views_filter) - epr = Goo.sparql_query_client(:main) - solutions = epr.query(ids_query) - latest_ids = {} - - solutions.each do |sol| - acr = sol[:id].to_s.split("/")[-3] - latest_ids[acr] = sol[:id].object + latest_ids end - latest_ids - end + def self.retrieve_latest_submissions(options = {}) + acronyms = (options[:acronyms] || []) + status = (options[:status] || "RDF").to_s.upcase + include_ready = status.eql?("READY") ? true : false + status = "RDF" if status.eql?("READY") + any = status.eql?("ANY") + include_views = options[:include_views] || false - def self.retrieve_latest_submissions(options = {}) - acronyms = (options[:acronyms] || []) - status = (options[:status] || "RDF").to_s.upcase - include_ready = status.eql?("READY") ? true : false - status = "RDF" if status.eql?("READY") - any = status.eql?("ANY") - include_views = options[:include_views] || false - - if any - submissions_query = LinkedData::Models::OntologySubmission.where - else - submissions_query = LinkedData::Models::OntologySubmission.where(submissionStatus: [code: status]) - end - submissions_query = submissions_query.filter(Goo::Filter.new(ontology: [:viewOf]).unbound) unless include_views - submissions = submissions_query.include(:submissionStatus,:submissionId, ontology: [:acronym]).to_a - submissions.select! { |sub| acronyms.include?(sub.ontology.acronym) } unless acronyms.empty? - latest_submissions = {} - - submissions.each do |sub| - next if include_ready && !sub.ready? - latest_submissions[sub.ontology.acronym] ||= sub - latest_submissions[sub.ontology.acronym] = sub if sub.submissionId > latest_submissions[sub.ontology.acronym].submissionId + if any + submissions_query = LinkedData::Models::OntologySubmission.where + else + submissions_query = LinkedData::Models::OntologySubmission.where(submissionStatus: [code: status]) + end + submissions_query = submissions_query.filter(Goo::Filter.new(ontology: [:viewOf]).unbound) unless include_views + submissions = submissions_query.include(:submissionStatus,:submissionId, ontology: [:acronym]).to_a + submissions.select! { |sub| acronyms.include?(sub.ontology.acronym) } unless acronyms.empty? + latest_submissions = {} + + submissions.each do |sub| + next if include_ready && !sub.ready? + latest_submissions[sub.ontology.acronym] ||= sub + latest_submissions[sub.ontology.acronym] = sub if sub.submissionId > latest_submissions[sub.ontology.acronym].submissionId + end + return latest_submissions end - return latest_submissions - end - def self.create_mapping_counts(logger, arr_acronyms=[]) - ont_msg = arr_acronyms.empty? ? "all ontologies" : "ontologies [#{arr_acronyms.join(', ')}]" + def self.create_mapping_counts(logger, arr_acronyms = []) + ont_msg = arr_acronyms.empty? ? 'all ontologies' : "ontologies [#{arr_acronyms.join(', ')}]" - time = Benchmark.realtime do - self.create_mapping_count_totals_for_ontologies(logger, arr_acronyms) - end - logger.info("Completed rebuilding total mapping counts for #{ont_msg} in #{(time/60).round(1)} minutes.") - - time = Benchmark.realtime do - self.create_mapping_count_pairs_for_ontologies(logger, arr_acronyms) - end - logger.info("Completed rebuilding mapping count pairs for #{ont_msg} in #{(time/60).round(1)} minutes.") - end + time = Benchmark.realtime do + self.create_mapping_count_totals_for_ontologies(logger, arr_acronyms) + end + logger.info("Completed rebuilding total mapping counts for #{ont_msg} in #{(time / 60).round(1)} minutes.") + puts "create mappings total count time: #{time}" - def self.create_mapping_count_totals_for_ontologies(logger, arr_acronyms) - new_counts = self.mapping_counts(enable_debug=true, logger=logger, reload_cache=true, arr_acronyms) - persistent_counts = {} - f = Goo::Filter.new(:pair_count) == false - LinkedData::Models::MappingCount.where.filter(f) - .include(:ontologies, :count) - .include(:all) - .all - .each do |m| - persistent_counts[m.ontologies.first] = m + time = Benchmark.realtime do + self.create_mapping_count_pairs_for_ontologies(logger, arr_acronyms) + end + puts "create mappings pair count time: #{time}" + logger.info("Completed rebuilding mapping count pairs for #{ont_msg} in #{(time / 60).round(1)} minutes.") end - num_counts = new_counts.keys.length - ctr = 0 + def self.create_mapping_count_totals_for_ontologies(logger, arr_acronyms) + new_counts = mapping_counts(true, logger, true, arr_acronyms) + persistent_counts = self.all_existent_mapping_counts(pair_count: false) + latest = retrieve_latest_submissions + self.delete_zombie_submission_count(persistent_counts, latest) - new_counts.each_key do |acr| - new_count = new_counts[acr] - ctr += 1 + num_counts = new_counts.keys.length + ctr = 0 - if persistent_counts.include?(acr) - inst = persistent_counts[acr] + new_counts.each_key do |acr| + new_count = new_counts[acr] + ctr += 1 + self.update_mapping_count(persistent_counts, new_counts, acr, acr, new_count, false) + remaining = num_counts - ctr + logger.info("Total mapping count saved for #{acr}: #{new_count}. " << (remaining.positive? ? "#{remaining} counts remaining..." : 'All done!')) + end + end - if new_count != inst.count - inst.bring_remaining - inst.count = new_count + # This generates pair mapping counts for the given + # ontologies to ALL other ontologies in the system + def self.create_mapping_count_pairs_for_ontologies(logger, arr_acronyms) + all_latest_submissions = retrieve_latest_submissions + latest_submissions = if Array(arr_acronyms).empty? + all_latest_submissions + else + all_latest_submissions.select { |k, _v| arr_acronyms.include?(k) } + end - begin - if inst.valid? - inst.save - else - logger.error("Error updating mapping count for #{acr}: #{inst.id.to_s}. #{inst.errors}") - next - end - rescue Exception => e - logger.error("Exception updating mapping count for #{acr}: #{inst.id.to_s}. #{e.class}: #{e.message}\n#{e.backtrace.join("\n")}") - next - end - end - else - m = LinkedData::Models::MappingCount.new - m.ontologies = [acr] - m.pair_count = false - m.count = new_count + ont_total = latest_submissions.length + logger.info("There is a total of #{ont_total} ontologies to process...") + ont_ctr = 0 - begin - if m.valid? - m.save - else - logger.error("Error saving new mapping count for #{acr}. #{m.errors}") - next - end - rescue Exception => e - logger.error("Exception saving new mapping count for #{acr}. #{e.class}: #{e.message}\n#{e.backtrace.join("\n")}") - next - end - end - remaining = num_counts - ctr - logger.info("Total mapping count saved for #{acr}: #{new_count}. " << ((remaining > 0) ? "#{remaining} counts remaining..." : "All done!")) - end - end + persistent_counts = self.all_existent_mapping_counts(pair_count: true) + self.delete_zombie_submission_count(persistent_counts, all_latest_submissions) - # This generates pair mapping counts for the given - # ontologies to ALL other ontologies in the system - def self.create_mapping_count_pairs_for_ontologies(logger, arr_acronyms) - latest_submissions = self.retrieve_latest_submissions(options={acronyms:arr_acronyms}) - ont_total = latest_submissions.length - logger.info("There is a total of #{ont_total} ontologies to process...") - ont_ctr = 0 - # filename = 'mapping_pairs.ttl' - # temp_dir = Dir.tmpdir - # temp_file_path = File.join(temp_dir, filename) - # temp_dir = '/Users/mdorf/Downloads/test/' - # temp_file_path = File.join(File.dirname(file_path), "test.ttl") - # fsave = File.open(temp_file_path, "a") - - latest_submissions.each do |acr, sub| - self.handle_triple_store_downtime(logger) if LinkedData.settings.goo_backend_name === '4store' - new_counts = nil - time = Benchmark.realtime do - new_counts = self.mapping_ontologies_count(sub, nil, reload_cache=true) - end - logger.info("Retrieved new mapping pair counts for #{acr} in #{time} seconds.") - ont_ctr += 1 - persistent_counts = {} - LinkedData::Models::MappingCount.where(pair_count: true).and(ontologies: acr) - .include(:ontologies, :count).all.each do |m| - other = m.ontologies.first + latest_submissions.each do |acr, sub| + new_counts = nil - if other == acr - other = m.ontologies[1] + time = Benchmark.realtime do + new_counts = mapping_ontologies_count(sub, nil, true) end - persistent_counts[other] = m - end + logger.info("Retrieved new mapping pair counts for #{acr} in #{time} seconds.") + ont_ctr += 1 - num_counts = new_counts.keys.length - logger.info("Ontology: #{acr}. #{num_counts} mapping pair counts to record...") - logger.info("------------------------------------------------") - ctr = 0 + persistent_counts = self.all_existent_mapping_counts(acr: acr, pair_count: true) + self.delete_zombie_mapping_count(persistent_counts, new_counts) - new_counts.each_key do |other| - new_count = new_counts[other] - ctr += 1 + num_counts = new_counts.keys.length + logger.info("Ontology: #{acr}. #{num_counts} mapping pair counts to record...") + logger.info('------------------------------------------------') + ctr = 0 - if persistent_counts.include?(other) - inst = persistent_counts[other] + new_counts.each_key do |other| + new_count = new_counts[other] + ctr += 1 + self.update_mapping_count(persistent_counts, new_counts, acr, other, new_count, true) + remaining = num_counts - ctr + logger.info("Mapping count saved for the pair [#{acr}, #{other}]: #{new_count}. " << (remaining.positive? ? "#{remaining} counts remaining for #{acr}..." : 'All done!')) + wait_interval = 250 - if new_count != inst.count - inst.bring_remaining - inst.pair_count = true - inst.count = new_count - - begin - if inst.valid? - inst.save() - # inst.save({ batch: fsave }) - else - logger.error("Error updating mapping count for the pair [#{acr}, #{other}]: #{inst.id.to_s}. #{inst.errors}") - next - end - rescue Exception => e - logger.error("Exception updating mapping count for the pair [#{acr}, #{other}]: #{inst.id.to_s}. #{e.class}: #{e.message}\n#{e.backtrace.join("\n")}") - next - end - end - else - m = LinkedData::Models::MappingCount.new - m.count = new_count - m.ontologies = [acr,other] - m.pair_count = true - - begin - if m.valid? - m.save() - # m.save({ batch: fsave }) - else - logger.error("Error saving new mapping count for the pair [#{acr}, #{other}]. #{m.errors}") - next - end - rescue Exception => e - logger.error("Exception saving new mapping count for the pair [#{acr}, #{other}]. #{e.class}: #{e.message}\n#{e.backtrace.join("\n")}") - next - end - end - remaining = num_counts - ctr - logger.info("Mapping count saved for the pair [#{acr}, #{other}]: #{new_count}. " << ((remaining > 0) ? "#{remaining} counts remaining for #{acr}..." : "All done!")) - wait_interval = 250 + next unless (ctr % wait_interval).zero? - if ctr % wait_interval == 0 sec_to_wait = 1 logger.info("Waiting #{sec_to_wait} second" << ((sec_to_wait > 1) ? 's' : '') << '...') sleep(sec_to_wait) end + remaining_ont = ont_total - ont_ctr + logger.info("Completed processing pair mapping counts for #{acr}. " << (remaining_ont.positive? ? "#{remaining_ont} ontologies remaining..." : 'All ontologies processed!')) end - remaining_ont = ont_total - ont_ctr - logger.info("Completed processing pair mapping counts for #{acr}. " << ((remaining_ont > 0) ? "#{remaining_ont} ontologies remaining..." : "All ontologies processed!")) - sleep(5) + # fsave.close end - # fsave.close - end private @@ -716,11 +630,6 @@ def self.mappings_ont_build_query(class_id, page, size, sub1, sub2) "BIND ('#{_source}' AS ?source)") end - - - - - filter = class_id.nil? ? "FILTER ((?s1 != ?s2) || (?source = 'SAME_URI'))" : '' if sub2.nil? @@ -810,6 +719,83 @@ def self.extract_acronym(submission) return sub, acr end + def self.calculate_and_log_counts(uri, logger, reload_cache, label, enable_debug) + start_time = Time.now + count = mapping_ontologies_count(uri, nil, reload_cache).values.sum + logger&.info("#{label} took #{Time.now - start_time} sec. records #{count}") if enable_debug + count + end + + def self.update_mapping_count(persistent_counts, new_counts, acr, other, new_count, pair_count) + if persistent_counts.key?(other) + inst = persistent_counts[other] + if new_count.zero? && pair_count + inst.delete + elsif new_count != inst.count + inst.pair_count = pair_count + inst.count = new_count + inst.save + end + else + return if !new_counts.key?(other) && pair_count + + m = LinkedData::Models::MappingCount.new + m.count = new_count + m.ontologies = if pair_count + [acr, other] + else + [acr] + end + m.pair_count = pair_count + return if m.exist? + + m.save + end + end + + def self.delete_zombie_mapping_count(persistent_counts, new_counts) + persistent_counts.each do |acronym, mapping| + next if mapping.ontologies.all? { |x| new_counts.key?(x) } + + mapping.delete + persistent_counts.delete(acronym) + end + end + + def self.delete_zombie_submission_count(persistent_counts, all_latest_submissions) + special_mappings = ["http://data.bioontology.org/metadata/ExternalMappings", + "http://data.bioontology.org/metadata/InterportalMappings/agroportal", + "http://data.bioontology.org/metadata/InterportalMappings/ncbo", + "http://data.bioontology.org/metadata/InterportalMappings/sifr"] + + persistent_counts.each do |acronym, mapping| + next if mapping.ontologies.size == 1 && !(mapping.ontologies & special_mappings).empty? + next if mapping.ontologies.all? { |x| all_latest_submissions.key?(x) } + + mapping.delete + persistent_counts.delete(acronym) + end + end + + def self.all_existent_mapping_counts(acr: nil, pair_count: true) + persistent_counts = {} + query = LinkedData::Models::MappingCount + query = if acr + query.where(ontologies: acr) + else + query.where + end + + f = Goo::Filter.new(:pair_count) == pair_count + query = query.filter(f) + + query.include(:ontologies, :count).all.each do |m| + other = m.ontologies.first + other = m.ontologies.last if acr && (other == acr) + persistent_counts[other] = m + end + persistent_counts + end end end From d9aefd5a9bff4fcb40d687b16b25e171457deeeb Mon Sep 17 00:00:00 2001 From: mdorf Date: Mon, 2 Feb 2026 12:52:33 -0800 Subject: [PATCH 20/69] fix for label generation to give prefence to prefLabels over rdfs:labels --- Gemfile.lock | 2 +- .../operations/submission_missing_labels.rb | 9 +++++++++ test/data/ontology_files/BRO_v3.2.owl | 2 +- test/models/test_class_request_lang.rb | 2 +- 4 files changed, 12 insertions(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index c4488d88c..2fefe81dc 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: e0109a9ea9b0e0119c3e5cd19146514c2282fab0 + revision: 53a0d4c3bbe56f7a8caed9fab736f509ebecb61d branch: ontoportal-lirmm-development specs: goo (0.0.2) diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb index 8315d368f..189711854 100644 --- a/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb @@ -204,6 +204,15 @@ def generate_missing_labels_each(artifacts = {}, logger, paging, page_classes, p lang_rdfs_labels[:none] = [] end + # prefLabel (if defined) takes priority over label + prefLabel_lang ||= {} + prefLabel_lang.each do |lang, value| + next if value.nil? || (value.respond_to?(:empty?) && value.empty?) + + lang = :none if lang == :"@none" + lang_rdfs_labels[lang] = Array(value) + end + lang_rdfs_labels.each do |lang, rdfs_labels| synonyms = c.synonym synonyms_present = !(synonyms.nil? || (synonyms.respond_to?(:empty?) && synonyms.empty?)) diff --git a/test/data/ontology_files/BRO_v3.2.owl b/test/data/ontology_files/BRO_v3.2.owl index 247e35e63..fdcbebde6 100644 --- a/test/data/ontology_files/BRO_v3.2.owl +++ b/test/data/ontology_files/BRO_v3.2.owl @@ -643,7 +643,7 @@ Activity related to the creation, use, or maintenance of a biorepository (http://en.wikipedia.org/wiki/Biorepository) Gestion des échantillons biologiques - Biospecimen Management + Gestion des Bioéchantillons diff --git a/test/models/test_class_request_lang.rb b/test/models/test_class_request_lang.rb index c4e8be996..84ea6841e 100644 --- a/test/models/test_class_request_lang.rb +++ b/test/models/test_class_request_lang.rb @@ -71,7 +71,7 @@ def test_requested_language_found end def test_requeststore_not_set - skip 'need to be fixed in the futur for Virtuoso' + skip 'Needs to be fixed in the future for Virtuoso' cls = get_class_by_lang('http://opendata.inrae.fr/thesaurusINRAE/c_22817', 'INRAETHES', requested_lang: nil) assert_equal 'industrialization', cls.prefLabel From 77a98064f91c7cce5d89e31e3b3768dbc9a441a5 Mon Sep 17 00:00:00 2001 From: mdorf Date: Mon, 2 Feb 2026 19:51:51 -0800 Subject: [PATCH 21/69] updated a class in BRO test ontology to be used in unit tests --- test/data/ontology_files/BRO_v3.2.owl | 1 + 1 file changed, 1 insertion(+) diff --git a/test/data/ontology_files/BRO_v3.2.owl b/test/data/ontology_files/BRO_v3.2.owl index fdcbebde6..4bd03f7a1 100644 --- a/test/data/ontology_files/BRO_v3.2.owl +++ b/test/data/ontology_files/BRO_v3.2.owl @@ -719,6 +719,7 @@ As defined in http://en.wikipedia.org/wiki/Gene_therapy + Gene Therapy Thérapie génique From 3dd230904c8189d9b891425273e34a097c84e5d7 Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 3 Feb 2026 11:10:00 -0800 Subject: [PATCH 22/69] if portal language label exists but no generic prefLabel is defined, copy the portal language label into the generic one --- .../operations/submission_missing_labels.rb | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb index 189711854..61d15dda2 100644 --- a/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb @@ -204,6 +204,19 @@ def generate_missing_labels_each(artifacts = {}, logger, paging, page_classes, p lang_rdfs_labels[:none] = [] end + # if portal language label exists but no generic prefLabel is defined, copy teh portal language + # label into the generic one (lang_rdfs_labels[:none]). Otherwise, this case results in nil + # generic prefLabel for a class, even though prefLabels exist for multiple languages. + # For Example (portal_lang = :en): + # + # + # As defined in http://en.wikipedia.org/wiki/Gene_therapy + # Gene Therapy + # Thérapie génique + # + lang_rdfs_labels[:none] = lang_rdfs_labels[portal_lang].dup if lang_rdfs_labels[:none].blank? && + lang_rdfs_labels.key?(portal_lang) + # prefLabel (if defined) takes priority over label prefLabel_lang ||= {} prefLabel_lang.each do |lang, value| @@ -222,7 +235,7 @@ def generate_missing_labels_each(artifacts = {}, logger, paging, page_classes, p rdfs_labels = c.label if rdfs_labels.nil? || rdfs_labels.length == 0 end - rdfs_labels = [rdfs_labels] if rdfs_labels and not (rdfs_labels.instance_of? Array) + rdfs_labels = [rdfs_labels] if rdfs_labels && !rdfs_labels.instance_of?(Array) label = nil if rdfs_labels && rdfs_labels.length > 0 From d867727f204e33814270e51b28236e90a327883b Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 3 Feb 2026 11:10:28 -0800 Subject: [PATCH 23/69] if portal language label exists but no generic prefLabel is defined, copy the portal language label into the generic one --- .../submission_process/operations/submission_missing_labels.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb b/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb index 61d15dda2..176d2a7bf 100644 --- a/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb +++ b/lib/ontologies_linked_data/services/submission_process/operations/submission_missing_labels.rb @@ -204,7 +204,7 @@ def generate_missing_labels_each(artifacts = {}, logger, paging, page_classes, p lang_rdfs_labels[:none] = [] end - # if portal language label exists but no generic prefLabel is defined, copy teh portal language + # if portal language label exists but no generic prefLabel is defined, copy the portal language # label into the generic one (lang_rdfs_labels[:none]). Otherwise, this case results in nil # generic prefLabel for a class, even though prefLabels exist for multiple languages. # For Example (portal_lang = :en): From 139bb2e327b576c4ec374ad6ceec553cd0de8d11 Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 3 Feb 2026 11:11:51 -0800 Subject: [PATCH 24/69] upgraded minitest from 5 to 6; activesupport from 4 to 8 --- Gemfile | 2 +- Gemfile.lock | 63 ++++++++++++++---------- lib/ontologies_linked_data.rb | 1 + test/docker_infrastructure.rb | 5 +- test/models/skos/test_schemes.rb | 6 ++- test/models/test_provisional_class.rb | 7 ++- test/models/test_provisional_relation.rb | 38 +++++++++++--- test/models/user/test_subscription.rb | 4 +- test/rack/test_request_authorization.rb | 4 +- test/rack/test_request_formats.rb | 4 +- test/serializer/test_serializer_json.rb | 4 +- test/serializer/test_serializer_xml.rb | 4 +- test/serializer/test_to_flex_hash.rb | 4 +- test/test_case.rb | 4 +- test/util/test_file_helpers.rb | 2 +- 15 files changed, 96 insertions(+), 56 deletions(-) diff --git a/Gemfile b/Gemfile index 1ecea06cc..94f9fbb75 100644 --- a/Gemfile +++ b/Gemfile @@ -2,7 +2,7 @@ source 'https://rubygems.org' gemspec -gem 'activesupport', '~> 4' +gem 'activesupport' gem 'addressable', '~> 2.8' gem 'bcrypt', '~> 3.0' gem 'cube-ruby', require: 'cube' diff --git a/Gemfile.lock b/Gemfile.lock index 2fefe81dc..36224caaa 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -48,15 +48,24 @@ PATH GEM remote: https://rubygems.org/ specs: - activesupport (4.2.11.3) - i18n (~> 0.7) - minitest (~> 5.1) - thread_safe (~> 0.3, >= 0.3.4) - tzinfo (~> 1.1) + activesupport (8.1.2) + base64 + bigdecimal + concurrent-ruby (~> 1.0, >= 1.3.1) + connection_pool (>= 2.2.5) + drb + i18n (>= 1.6, < 2) + json + logger (>= 1.4.2) + minitest (>= 5.1) + securerandom (>= 0.3) + tzinfo (~> 2.0, >= 2.0.5) + uri (>= 0.13.1) addressable (2.8.8) public_suffix (>= 2.0.2, < 8.0) ansi (1.5.0) ast (2.4.3) + base64 (0.3.0) bcp47_spec (0.2.1) bcrypt (3.1.21) bigdecimal (3.3.1) @@ -73,6 +82,7 @@ GEM domain_name (0.6.20240107) down (5.4.2) addressable (~> 2.8) + drb (2.2.3) email_spec (2.3.0) htmlentities (~> 4.3.3) launchy (>= 2.1, < 4.0) @@ -99,7 +109,7 @@ GEM http-accept (1.7.0) http-cookie (1.1.0) domain_name (~> 0.5) - i18n (0.9.5) + i18n (1.14.8) concurrent-ruby (~> 1.0) io-console (0.8.2) json (2.18.0) @@ -124,9 +134,10 @@ GEM mime-types (3.7.0) logger mime-types-data (~> 3.2025, >= 3.2025.0507) - mime-types-data (3.2026.0113) + mime-types-data (3.2026.0127) mini_mime (1.1.5) - minitest (5.27.0) + minitest (6.0.1) + prism (~> 1.5) minitest-reporters (1.7.1) ansi builder @@ -166,7 +177,7 @@ GEM racc pony (1.13.1) mail (>= 2.0) - prism (1.8.0) + prism (1.9.0) pry (0.16.0) coderay (~> 1.1) method_source (~> 1.0) @@ -202,7 +213,7 @@ GEM reline redis (5.4.1) redis-client (>= 0.22.0) - redis-client (0.26.3) + redis-client (0.26.4) connection_pool regexp_parser (2.11.3) reline (0.6.3) @@ -218,7 +229,7 @@ GEM rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) - rubocop (1.82.1) + rubocop (1.84.1) json (~> 2.3) language_server-protocol (~> 3.17.0.2) lint_roller (~> 1.1.0) @@ -226,7 +237,7 @@ GEM parser (>= 3.3.0.2) rainbow (>= 2.2.2, < 4.0) regexp_parser (>= 2.9.3, < 3.0) - rubocop-ast (>= 1.48.0, < 2.0) + rubocop-ast (>= 1.49.0, < 2.0) ruby-progressbar (~> 1.7) unicode-display_width (>= 2.4.0, < 4.0) rubocop-ast (1.49.0) @@ -235,6 +246,7 @@ GEM ruby-progressbar (1.13.0) ruby2_keywords (0.0.5) rubyzip (3.2.2) + securerandom (0.4.1) simplecov (0.22.0) docile (~> 1.1) simplecov-html (~> 0.11) @@ -249,12 +261,11 @@ GEM daemons (~> 1.0, >= 1.0.9) eventmachine (~> 1.0, >= 1.0.4) rack (>= 1, < 3) - thread_safe (0.3.6) time (0.4.2) date timeout (0.6.0) - tzinfo (1.2.11) - thread_safe (~> 0.1) + tzinfo (2.0.6) + concurrent-ruby (~> 1.0) unicode-display_width (3.2.0) unicode-emoji (~> 4.1) unicode-emoji (4.2.0) @@ -276,7 +287,7 @@ PLATFORMS x86_64-linux-musl DEPENDENCIES - activesupport (~> 4) + activesupport addressable (~> 2.8) bcrypt (~> 3.0) cube-ruby @@ -309,10 +320,11 @@ DEPENDENCIES thin (~> 1.8.2) CHECKSUMS - activesupport (4.2.11.3) sha256=515015c5b8c7b35af33f5911c14248b06438c25fda60905965ba8d3c2237e372 + activesupport (8.1.2) sha256=88842578ccd0d40f658289b0e8c842acfe9af751afee2e0744a7873f50b6fdae addressable (2.8.8) sha256=7c13b8f9536cf6364c03b9d417c19986019e28f7c00ac8132da4eb0fe393b057 ansi (1.5.0) sha256=5408253274e33d9d27d4a98c46d2998266fd51cba58a7eb9d08f50e57ed23592 ast (2.4.3) sha256=954615157c1d6a382bc27d690d973195e79db7f55e9765ac7c481c60bdb4d383 + base64 (0.3.0) sha256=27337aeabad6ffae05c265c450490628ef3ebd4b67be58257393227588f5a97b bcp47_spec (0.2.1) sha256=3fd62edf96c126bd9624e4319ac74082a966081859d1ee0ef3c3041640a37810 bcrypt (3.1.21) sha256=5964613d750a42c7ee5dc61f7b9336fb6caca429ba4ac9f2011609946e4a2dcf bigdecimal (3.3.1) sha256=eaa01e228be54c4f9f53bf3cc34fe3d5e845c31963e7fcc5bedb05a4e7d52218 @@ -327,6 +339,7 @@ CHECKSUMS docile (1.4.1) sha256=96159be799bfa73cdb721b840e9802126e4e03dfc26863db73647204c727f21e domain_name (0.6.20240107) sha256=5f693b2215708476517479bf2b3802e49068ad82167bcd2286f899536a17d933 down (5.4.2) sha256=516e5e01e7a96214a7e2cd155aac6f700593038ae6c857c0f4a05413b1c58acf + drb (2.2.3) sha256=0b00d6fdb50995fe4a45dea13663493c841112e4068656854646f418fda13373 email_spec (2.3.0) sha256=df23be7a131186f7a3d5be3b35eaac9196f9ac13bd26c9c3d59341e13d852d11 eventmachine (1.2.7) sha256=994016e42aa041477ba9cff45cbe50de2047f25dd418eba003e84f0d16560972 faraday (2.14.0) sha256=8699cfe5d97e55268f2596f9a9d5a43736808a943714e3d9a53e6110593941cd @@ -346,7 +359,7 @@ CHECKSUMS htmlentities (4.3.4) sha256=125a73c6c9f2d1b62100b7c3c401e3624441b663762afa7fe428476435a673da http-accept (1.7.0) sha256=c626860682bfbb3b46462f8c39cd470fd7b0584f61b3cc9df5b2e9eb9972a126 http-cookie (1.1.0) sha256=38a5e60d1527eebc396831b8c4b9455440509881219273a6c99943d29eadbb19 - i18n (0.9.5) sha256=43a58b55056ef171cae9b35df8aa5dee22d3a782f8a9bdd0ec8e8d36cfdf180d + i18n (1.14.8) sha256=285778639134865c5e0f6269e0b818256017e8cde89993fdfcbfb64d088824a5 io-console (0.8.2) sha256=d6e3ae7a7cc7574f4b8893b4fca2162e57a825b223a177b7afa236c5ef9814cc json (2.18.0) sha256=b10506aee4183f5cf49e0efc48073d7b75843ce3782c68dbeb763351c08fd505 language_server-protocol (3.17.0.5) sha256=fd1e39a51a28bf3eec959379985a72e296e9f9acfce46f6a79d31ca8760803cc @@ -359,9 +372,9 @@ CHECKSUMS mail (2.9.0) sha256=6fa6673ecd71c60c2d996260f9ee3dd387d4673b8169b502134659ece6d34941 method_source (1.1.0) sha256=181301c9c45b731b4769bc81e8860e72f9161ad7d66dd99103c9ab84f560f5c5 mime-types (3.7.0) sha256=dcebf61c246f08e15a4de34e386ebe8233791e868564a470c3fe77c00eed5e56 - mime-types-data (3.2026.0113) sha256=8c88fa7b1af91c87098f666b7ffbd4794799a71c05765be2c1f6df337d41b04c + mime-types-data (3.2026.0127) sha256=4a58692436a987ad930e75bf8f24da7e627acfa0d06e1720aa514791b4c7d12b mini_mime (1.1.5) sha256=8681b7e2e4215f2a159f9400b5816d85e9d8c6c6b491e96a12797e798f8bccef - minitest (5.27.0) sha256=2d3b17f8a36fe7801c1adcffdbc38233b938eb0b4966e97a6739055a45fa77d5 + minitest (6.0.1) sha256=7854c74f48e2e975969062833adc4013f249a4b212f5e7b9d5c040bf838d54bb minitest-reporters (1.7.1) sha256=5060413a0c95b8c32fe73e0606f3631c173a884d7900e50013e15094eb50562c mocha (2.8.2) sha256=1f77e729db47e72b4ef776461ce20caeec2572ffdf23365b0a03608fee8f4eee mock_redis (0.53.0) sha256=11319e134b2905a7bb33464db696587bbcd5f5a1d8fbd2237f464d29e8b1cf6a @@ -381,7 +394,7 @@ CHECKSUMS parallel (1.27.0) sha256=4ac151e1806b755fb4e2dc2332cbf0e54f2e24ba821ff2d3dcf86bf6dc4ae130 parser (3.3.10.1) sha256=06f6a725d2cd91e5e7f2b7c32ba143631e1f7c8ae2fb918fc4cebec187e6a688 pony (1.13.1) sha256=ab507c8ade8b35de96f1e75c0ae4566a3c40ac8a0d5101433969b6fd29c718a7 - prism (1.8.0) sha256=84453a16ef5530ea62c5f03ec16b52a459575ad4e7b9c2b360fd8ce2c39c1254 + prism (1.9.0) sha256=7b530c6a9f92c24300014919c9dcbc055bf4cdf51ec30aed099b06cd6674ef85 pry (0.16.0) sha256=d76c69065698ed1f85e717bd33d7942c38a50868f6b0673c636192b3d1b6054e public_suffix (5.1.1) sha256=250ec74630d735194c797491c85e3c6a141d7b5d9bd0b66a3fa6268cf67066ed racc (1.8.1) sha256=4a7f6929691dbec8b5209a0b373bc2614882b55fc5d2e447a21aaa691303d62f @@ -396,18 +409,19 @@ CHECKSUMS rdf-xsd (3.3.0) sha256=fab51d27b20344237d9b622ef32e83e4c44940840bfc76a245ce6b6abba44772 readline (0.0.4) sha256=6138eef17be2b98298b672c3ea63bf9cb5158d401324f26e1e84f235879c1d6a redis (5.4.1) sha256=b5e675b57ad22b15c9bcc765d5ac26f60b675408af916d31527af9bd5a81faae - redis-client (0.26.3) sha256=37a95ca193b7a79f350c09fe5e696dc15d1701195d559d031a107ab725effc49 + redis-client (0.26.4) sha256=3ad70beff5da2653e02dfeae996e7d8d7147a558da12b16b2282ad345e4c7120 regexp_parser (2.11.3) sha256=ca13f381a173b7a93450e53459075c9b76a10433caadcb2f1180f2c741fc55a4 reline (0.6.3) sha256=1198b04973565b36ec0f11542ab3f5cfeeec34823f4e54cebde90968092b1835 request_store (1.7.0) sha256=e1b75d5346a315f452242a68c937ef8e48b215b9453a77a6c0acdca2934c88cb rest-client (2.1.0) sha256=35a6400bdb14fae28596618e312776c158f7ebbb0ccad752ff4fa142bf2747e3 rexml (3.4.4) sha256=19e0a2c3425dfbf2d4fc1189747bdb2f849b6c5e74180401b15734bc97b5d142 rsolr (2.6.0) sha256=4b3bcea772cac300562775c20eeddedf63a6b7516a070cb6fbde000b09cfe12b - rubocop (1.82.1) sha256=09f1a6a654a960eda767aebea33e47603080f8e9c9a3f019bf9b94c9cab5e273 + rubocop (1.84.1) sha256=14cc626f355141f5a2ef53c10a68d66b13bb30639b26370a76559096cc6bcc1a rubocop-ast (1.49.0) sha256=49c3676d3123a0923d333e20c6c2dbaaae2d2287b475273fddee0c61da9f71fd ruby-progressbar (1.13.0) sha256=80fc9c47a9b640d6834e0dc7b3c94c9df37f08cb072b7761e4a71e22cff29b33 ruby2_keywords (0.0.5) sha256=ffd13740c573b7301cf7a2e61fc857b2a8e3d3aff32545d6f8300d8bae10e3ef rubyzip (3.2.2) sha256=c0ed99385f0625415c8f05bcae33fe649ed2952894a95ff8b08f26ca57ea5b3c + securerandom (0.4.1) sha256=cc5193d414a4341b6e225f0cb4446aceca8e50d5e1888743fac16987638ea0b1 simplecov (0.22.0) sha256=fe2622c7834ff23b98066bb0a854284b2729a569ac659f82621fc22ef36213a5 simplecov-cobertura (3.1.0) sha256=6d7f38aa32c965ca2174b2e5bd88cb17138eaf629518854976ac50e628925dc5 simplecov-html (0.13.2) sha256=bd0b8e54e7c2d7685927e8d6286466359b6f16b18cb0df47b508e8d73c777246 @@ -415,10 +429,9 @@ CHECKSUMS sparql-client (3.2.2) systemu (2.6.5) sha256=01f7d014b1453b28e5781e15c4d7d63fc9221c29b174b7aae5253207a75ab33e thin (1.8.2) sha256=1c55251aba5bee7cf6936ea18b048f4d3c74ef810aa5e6906cf6edff0df6e121 - thread_safe (0.3.6) sha256=9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a time (0.4.2) sha256=f324e498c3bde9471d45a7d18f874c27980e9867aa5cfca61bebf52262bc3dab timeout (0.6.0) sha256=6d722ad619f96ee383a0c557ec6eb8c4ecb08af3af62098a0be5057bf00de1af - tzinfo (1.2.11) sha256=6501f6a12175ca0243118b83f7c7c2b7978aaec7a0980550a124d007ad6361b6 + tzinfo (2.0.6) sha256=8daf828cc77bcf7d63b0e3bdb6caa47e2272dcfaf4fbfe46f8c3a9df087a829b unicode-display_width (3.2.0) sha256=0cdd96b5681a5949cdbc2c55e7b420facae74c4aaf9a9815eee1087cb1853c42 unicode-emoji (4.2.0) sha256=519e69150f75652e40bf736106cfbc8f0f73aa3fb6a65afe62fefa7f80b0f80f uri (1.1.1) sha256=379fa58d27ffb1387eaada68c749d1426738bd0f654d812fcc07e7568f5c57c6 diff --git a/lib/ontologies_linked_data.rb b/lib/ontologies_linked_data.rb index ff221e08a..93b71834f 100644 --- a/lib/ontologies_linked_data.rb +++ b/lib/ontologies_linked_data.rb @@ -1,4 +1,5 @@ require 'goo' +require 'active_support/core_ext/object/blank' # Make sure we're in the load path lib_dir = "#{File.dirname(__FILE__)}/../lib" diff --git a/test/docker_infrastructure.rb b/test/docker_infrastructure.rb index 0c81d7b1f..46c2b4a76 100644 --- a/test/docker_infrastructure.rb +++ b/test/docker_infrastructure.rb @@ -51,7 +51,7 @@ def docker_tests require_relative "test_case" test_files.each {|f| require f} - MiniTest::Unit.runner.run + Minitest.run rescue => e puts e.message puts e.backtrace.join("\n\t") @@ -95,7 +95,7 @@ def docker_tests_forked(forks) test_files_sliced[i].each {|f| require f} - MiniTest::Unit.runner.run + Minitest.run rescue => e sio << "\n#{e.message}\n#{e.backtrace.join("\t\n")}" ensure @@ -119,4 +119,3 @@ def docker_tests_forked(forks) Kernel.exit! # force the process to quit without minitest's autorun (triggered on at_exit) end end - diff --git a/test/models/skos/test_schemes.rb b/test/models/skos/test_schemes.rb index ca1bf686c..c66c87384 100644 --- a/test/models/skos/test_schemes.rb +++ b/test/models/skos/test_schemes.rb @@ -25,7 +25,11 @@ def test_schemes_all schemes.each_with_index do |x, i| scheme_test = schemes_test[i] assert_equal scheme_test[:id], x.id.to_s - assert_equal scheme_test[:prefLabel], x.prefLabel + if scheme_test[:prefLabel].nil? + assert_nil x.prefLabel + else + assert_equal scheme_test[:prefLabel], x.prefLabel + end end end diff --git a/test/models/test_provisional_class.rb b/test/models/test_provisional_class.rb index c0ab44cfa..72eea506f 100644 --- a/test/models/test_provisional_class.rb +++ b/test/models/test_provisional_class.rb @@ -3,7 +3,8 @@ class TestProvisionalClass < LinkedData::TestOntologyCommon def self.before_suite - @@user = LinkedData::Models::User.new({username: "Test User", email: "tester@example.org", password: "password"}) + @@user = LinkedData::Models::User.new({username: "test_user_prov_class", + email: "test_user_prov_class@example.org", password: "password"}) @@user.save ont_count, ont_names, ont_models = LinkedData::SampleData::Ontology.create_ontologies_and_submissions(ont_count: 1, @@ -24,12 +25,10 @@ def self.after_suite LinkedData::Models::ProvisionalClass.indexClear LinkedData::Models::ProvisionalClass.indexCommit LinkedData::SampleData::Ontology.delete_ontologies_and_submissions - user = LinkedData::Models::User.find("Test User").first + user = LinkedData::Models::User.find("test_user_prov_class").first user.delete unless user.nil? - end - def test_provisional_class_lifecycle label = "Test Provisional Class Lifecycle" pc = LinkedData::Models::ProvisionalClass.new({label: label, :creator => @@user}) diff --git a/test/models/test_provisional_relation.rb b/test/models/test_provisional_relation.rb index 78839f754..6c7d594f6 100644 --- a/test/models/test_provisional_relation.rb +++ b/test/models/test_provisional_relation.rb @@ -3,13 +3,16 @@ class TestProvisionalRelation < LinkedData::TestCase def self.before_suite - @@user = LinkedData::Models::User.new({username: "Test User", email: "tester@example.org", password: "password"}) + @@user = LinkedData::Models::User.new({username: "test_user_prov_relation", + email: "test_user_prov_relation@example.org", password: "password"}) @@user.save - ont_count, ont_names, ont_models = self.new('').create_ontologies_and_submissions(ont_count: 1, submission_count: 1, - process_submission: true, - process_options: {process_rdf: true, - extract_metadata: false}) + _, _, ont_models = self.new('').create_ontologies_and_submissions( + ont_count: 1, + submission_count: 1, + process_submission: true, + process_options: {process_rdf: true, extract_metadata: false} + ) @@ontology = ont_models.first @@ontology.bring(:name) @@ -30,6 +33,27 @@ def self.before_suite @@provisional_rel2.save end + def self.after_suite + if defined?(@@provisional_rel1) + rel = LinkedData::Models::ProvisionalRelation.find(@@provisional_rel1.id).first + rel.delete unless rel.nil? + end + + if defined?(@@provisional_rel2) + rel = LinkedData::Models::ProvisionalRelation.find(@@provisional_rel2.id).first + rel.delete unless rel.nil? + end + + if defined?(@@provisional_class) + pc = LinkedData::Models::ProvisionalClass.find(@@provisional_class.id).first + pc.delete unless pc.nil? + end + + LinkedData::SampleData::Ontology.delete_ontologies_and_submissions + + user = LinkedData::Models::User.find("test_user_prov_relation").first + user.delete unless user.nil? + end def test_create_provisional_relation rel1 = LinkedData::Models::ProvisionalRelation.find(@@provisional_rel1.id).first @@ -68,6 +92,4 @@ def test_target_class assert_equal @@ontology.acronym, target_class.submission.ontology.acronym end - - -end \ No newline at end of file +end diff --git a/test/models/user/test_subscription.rb b/test/models/user/test_subscription.rb index 93c710958..210b095c0 100644 --- a/test/models/user/test_subscription.rb +++ b/test/models/user/test_subscription.rb @@ -30,8 +30,8 @@ def _subscription(ont, type = "ALL") end def _delete_subscriptions - if defined?(@@subscriptions) - @@subscriptions.each {|s| s.delete} + if self.class.class_variable_defined?(:@@subscriptions) + @@subscriptions.each { |s| s.delete } end @@subscriptions = nil end diff --git a/test/rack/test_request_authorization.rb b/test/rack/test_request_authorization.rb index 76fc7af9a..9005ecc00 100644 --- a/test/rack/test_request_authorization.rb +++ b/test/rack/test_request_authorization.rb @@ -1,4 +1,4 @@ -require 'minitest/unit' +require 'minitest/autorun' require "rack/test" require "json" require "logger" @@ -9,7 +9,7 @@ ENV["rack.test"] = "true" -class TestRackAuthorization < MiniTest::Unit::TestCase +class TestRackAuthorization < Minitest::Test include Rack::Test::Methods def app diff --git a/test/rack/test_request_formats.rb b/test/rack/test_request_formats.rb index 5af4a629c..6a955f1c3 100644 --- a/test/rack/test_request_formats.rb +++ b/test/rack/test_request_formats.rb @@ -1,9 +1,9 @@ -require 'minitest/unit' +require 'minitest/autorun' require "rack/test" require "multi_json" require_relative "../../lib/ontologies_linked_data" -class TestLinkedDataSerializer < MiniTest::Unit::TestCase +class TestLinkedDataSerializer < Minitest::Test include Rack::Test::Methods def app diff --git a/test/serializer/test_serializer_json.rb b/test/serializer/test_serializer_json.rb index 128e5dd1f..5003848e6 100644 --- a/test/serializer/test_serializer_json.rb +++ b/test/serializer/test_serializer_json.rb @@ -1,9 +1,9 @@ -require 'minitest/unit' +require 'minitest/autorun' require "multi_json" require_relative "../../lib/ontologies_linked_data" require_relative "../../config/config" -class TestSerializerOutput < MiniTest::Unit::TestCase +class TestSerializerOutput < Minitest::Test class Car < LinkedData::Models::Base model :car, name_with: :model, namespace: :omv attribute :model, enforce: [:unique] diff --git a/test/serializer/test_serializer_xml.rb b/test/serializer/test_serializer_xml.rb index 9d5d8c027..a07d1611f 100644 --- a/test/serializer/test_serializer_xml.rb +++ b/test/serializer/test_serializer_xml.rb @@ -1,9 +1,9 @@ -require 'minitest/unit' +require 'minitest/autorun' require "date" require "multi_json" require_relative "../../lib/ontologies_linked_data" -class TestSerializerXML < MiniTest::Unit::TestCase +class TestSerializerXML < Minitest::Test class Person attr_accessor :name def initialize(name) diff --git a/test/serializer/test_to_flex_hash.rb b/test/serializer/test_to_flex_hash.rb index 7070e22b8..c0704c69c 100644 --- a/test/serializer/test_to_flex_hash.rb +++ b/test/serializer/test_to_flex_hash.rb @@ -1,8 +1,8 @@ -require 'minitest/unit' +require 'minitest/autorun' require 'pry' require_relative "../../lib/ontologies_linked_data" -class ToHashTest < MiniTest::Unit::TestCase +class ToHashTest < Minitest::Test class Person include LinkedData::Hypermedia::Resource diff --git a/test/test_case.rb b/test/test_case.rb index ef6f7eca7..078135509 100644 --- a/test/test_case.rb +++ b/test/test_case.rb @@ -45,7 +45,9 @@ # custom runner behavior using Minitest hooks and a small patch around suite runs. module LinkedData module MinitestSuiteHooks - def run(*args, &block) + def run_suite(reporter, options = {}) + return if filter_runnable_methods(options).empty? + before_suite if respond_to?(:before_suite) super rescue Exception => e diff --git a/test/util/test_file_helpers.rb b/test/util/test_file_helpers.rb index 0d0362625..1406dd1bd 100644 --- a/test/util/test_file_helpers.rb +++ b/test/util/test_file_helpers.rb @@ -1,7 +1,7 @@ require 'minitest/autorun' require_relative '../../lib/ontologies_linked_data/utils/file' -class TestUtilsFile < MiniTest::Unit::TestCase +class TestUtilsFile < Minitest::Test DST = nil def setup From 8c2040180b364921698ccc7810bb26ea54e6f701 Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 3 Feb 2026 12:20:19 -0800 Subject: [PATCH 25/69] removed cube integration --- Gemfile | 3 +-- Gemfile.lock | 9 +++------ config/config.rb.sample | 2 +- lib/ontologies_linked_data/config/config.rb | 14 ++------------ 4 files changed, 7 insertions(+), 21 deletions(-) diff --git a/Gemfile b/Gemfile index 94f9fbb75..93021a719 100644 --- a/Gemfile +++ b/Gemfile @@ -5,7 +5,6 @@ gemspec gem 'activesupport' gem 'addressable', '~> 2.8' gem 'bcrypt', '~> 3.0' -gem 'cube-ruby', require: 'cube' gem 'ffi' gem 'libxml-ruby' gem 'multi_json', '~> 1.0' @@ -22,7 +21,7 @@ gem 'rsolr' group :test do gem 'email_spec' gem 'minitest' - gem 'minitest-reporters', '>= 0.5.0' + gem 'minitest-reporters' gem 'mocha', '~> 2.7' gem 'mock_redis', '~> 0.5' gem 'pry' diff --git a/Gemfile.lock b/Gemfile.lock index 36224caaa..22f317733 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -75,7 +75,6 @@ GEM coderay (1.1.3) concurrent-ruby (1.3.6) connection_pool (3.0.2) - cube-ruby (0.0.3) daemons (1.4.1) date (3.5.1) docile (1.4.1) @@ -112,7 +111,7 @@ GEM i18n (1.14.8) concurrent-ruby (~> 1.0) io-console (0.8.2) - json (2.18.0) + json (2.18.1) language_server-protocol (3.17.0.5) launchy (3.1.1) addressable (~> 2.8) @@ -290,13 +289,12 @@ DEPENDENCIES activesupport addressable (~> 2.8) bcrypt (~> 3.0) - cube-ruby email_spec ffi goo! libxml-ruby minitest - minitest-reporters (>= 0.5.0) + minitest-reporters mocha (~> 2.7) mock_redis (~> 0.5) multi_json (~> 1.0) @@ -333,7 +331,6 @@ CHECKSUMS coderay (1.1.3) sha256=dc530018a4684512f8f38143cd2a096c9f02a1fc2459edcfe534787a7fc77d4b concurrent-ruby (1.3.6) sha256=6b56837e1e7e5292f9864f34b69c5a2cbc75c0cf5338f1ce9903d10fa762d5ab connection_pool (3.0.2) sha256=33fff5ba71a12d2aa26cb72b1db8bba2a1a01823559fb01d29eb74c286e62e0a - cube-ruby (0.0.3) sha256=42f798c16ba184376ba66c93f4083e7f014ee0c6f300c919a178bacb5b8ae617 daemons (1.4.1) sha256=8fc76d76faec669feb5e455d72f35bd4c46dc6735e28c420afb822fac1fa9a1d date (3.5.1) sha256=750d06384d7b9c15d562c76291407d89e368dda4d4fff957eb94962d325a0dc0 docile (1.4.1) sha256=96159be799bfa73cdb721b840e9802126e4e03dfc26863db73647204c727f21e @@ -361,7 +358,7 @@ CHECKSUMS http-cookie (1.1.0) sha256=38a5e60d1527eebc396831b8c4b9455440509881219273a6c99943d29eadbb19 i18n (1.14.8) sha256=285778639134865c5e0f6269e0b818256017e8cde89993fdfcbfb64d088824a5 io-console (0.8.2) sha256=d6e3ae7a7cc7574f4b8893b4fca2162e57a825b223a177b7afa236c5ef9814cc - json (2.18.0) sha256=b10506aee4183f5cf49e0efc48073d7b75843ce3782c68dbeb763351c08fd505 + json (2.18.1) sha256=fe112755501b8d0466b5ada6cf50c8c3f41e897fa128ac5d263ec09eedc9f986 language_server-protocol (3.17.0.5) sha256=fd1e39a51a28bf3eec959379985a72e296e9f9acfce46f6a79d31ca8760803cc launchy (3.1.1) sha256=72b847b5cc961589dde2c395af0108c86ff0119f42d4648d25b5440ebb10059e libxml-ruby (5.0.5) sha256=f1bc07152982df555d70159a694ee2a53539de2cdad4b3c8a447fbb15e7e4e9a diff --git a/config/config.rb.sample b/config/config.rb.sample index 7bdf77a26..05e2bc8a4 100644 --- a/config/config.rb.sample +++ b/config/config.rb.sample @@ -4,7 +4,7 @@ LinkedData.config do |config| config.search_server_url = "http://localhost:8983/solr" config.property_search_server_url = "http://localhost:8983/solr" config.repository_folder = "./test/data/ontology_files/repo" - config.rest_url_prefix = "http://data.bioontology.org/" + config.rest_url_prefix = "http://localhost:9393/" config.enable_security = false config.java_max_heap_size = '10240M' #PURL server config parameters diff --git a/lib/ontologies_linked_data/config/config.rb b/lib/ontologies_linked_data/config/config.rb index 0c16c88d8..a5be0aabb 100644 --- a/lib/ontologies_linked_data/config/config.rb +++ b/lib/ontologies_linked_data/config/config.rb @@ -23,8 +23,8 @@ def config(&block) @settings.goo_path_query ||= '/sparql/' @settings.goo_path_data ||= '/data/' @settings.goo_path_update ||= '/update/' - @settings.search_server_url ||= 'http://localhost:8983/solr/term_search_core1' - @settings.property_search_server_url ||= 'http://localhost:8983/solr/prop_search_core1' + @settings.search_server_url ||= 'http://localhost:8983/solr' + @settings.property_search_server_url ||= 'http://localhost:8983/solr' @settings.repository_folder ||= './test/data/ontology_files/repo' @settings.rest_url_prefix ||= DEFAULT_PREFIX @settings.enable_security ||= false @@ -40,8 +40,6 @@ def config(&block) @settings.queries_debug ||= false @settings.enable_monitoring ||= false - @settings.cube_host ||= 'localhost' - @settings.cube_port ||= 1180 # Caching http @settings.enable_http_cache ||= false @@ -131,14 +129,6 @@ def connect_goo conf.add_search_backend(:property, service: @settings.property_search_server_url) conf.add_redis_backend(host: @settings.goo_redis_host, port: @settings.goo_redis_port) - - if @settings.enable_monitoring - puts "(LD) >> Enable SPARQL monitoring with cube #{@settings.cube_host}:#{@settings.cube_port}" - conf.enable_cube do |opts| - opts[:host] = @settings.cube_host - opts[:port] = @settings.cube_port - end - end end rescue StandardError => e abort("EXITING: Cannot connect to triplestore and/or search server:\n #{e}\n#{e.backtrace.join("\n")}") From 9282060c02a6ca242d9c4652e3f66799d3475d43 Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 3 Feb 2026 13:21:53 -0800 Subject: [PATCH 26/69] resolved an issue with the test test_remote_ontology_pull_notification that caused intermittent errors --- test/util/test_notifications.rb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/test/util/test_notifications.rb b/test/util/test_notifications.rb index 3c8282017..4af2af35c 100644 --- a/test/util/test_notifications.rb +++ b/test/util/test_notifications.rb @@ -3,6 +3,7 @@ require 'email_spec' require 'logger' require 'mocha/minitest' +require 'securerandom' class TestNotifications < LinkedData::TestCase include EmailSpec::Helpers @@ -141,10 +142,11 @@ def test_remote_ontology_pull_notification ont = LinkedData::Models::Ontology.find(ontologies[0].id) .include(:acronym, :administeredBy, :name, :submissions).first + suffix = SecureRandom.hex(4) ont_admins = Array.new(3) { LinkedData::Models::User.new } ont_admins.each_with_index do |user, i| - user.username = "Test User #{i}" - user.email = "tester_#{i}@example.org" + user.username = "notif_test_user_#{suffix}_#{i}" + user.email = "notif_test_user_#{suffix}_#{i}@example.org" user.password = 'password' user.save assert user.valid?, user.errors @@ -165,7 +167,7 @@ def test_remote_ontology_pull_notification assert_equal admin_mails, last_email_sent.to.sort ensure ont_admins.each do |user| - user&.delete + user.delete if user&.persistent? end end From abb93105158193d348daba0e1b0e005174e14061 Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 3 Feb 2026 22:30:44 -0800 Subject: [PATCH 27/69] updated ruby version to 3.2 in gemspec --- ontologies_linked_data.gemspec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontologies_linked_data.gemspec b/ontologies_linked_data.gemspec index c93e6fa67..9498b4f2c 100644 --- a/ontologies_linked_data.gemspec +++ b/ontologies_linked_data.gemspec @@ -16,7 +16,7 @@ Gem::Specification.new do |gem| gem.executables = gem.files.grep(%r{^bin/}).map { |f| File.basename(f) } gem.require_paths = ["lib"] - gem.required_ruby_version = ">= 3.1" + gem.required_ruby_version = ">= 3.2" gem.add_dependency("activesupport") gem.add_dependency("bcrypt") From b731028f1a6781ff2254238486c5b057c39f4596 Mon Sep 17 00:00:00 2001 From: = Date: Thu, 5 Feb 2026 15:22:20 -0800 Subject: [PATCH 28/69] fixed docker-compose vars --- Gemfile.lock | 2 +- docker-compose.yml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 22f317733..f9b6fd1d0 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 53a0d4c3bbe56f7a8caed9fab736f509ebecb61d + revision: 13a8559a2346cc8320d7d36046646907bfa8a27c branch: ontoportal-lirmm-development specs: goo (0.0.2) diff --git a/docker-compose.yml b/docker-compose.yml index 257ed02d8..df84ea47f 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -2,15 +2,15 @@ x-app: &app build: context: . args: - RUBY_VERSION: '3.1' + RUBY_VERSION: '3.2' # Increase the version number in the image tag every time Dockerfile or its arguments is changed image: ontologies_ld-dev:0.0.4 environment: &env COVERAGE: 'true' # enable simplecov code coverage REDIS_HOST: redis-ut REDIS_PORT: 6379 - SOLR_TERM_SEARCH_URL: http://solr-term-ut:8983/solr/term_search_core1 - SOLR_PROP_SEARCH_URL: http://solr-prop-ut:8983/solr/prop_search_core1 + SOLR_TERM_SEARCH_URL: http://solr-term-ut:8983/solr + SOLR_PROP_SEARCH_URL: http://solr-prop-ut:8983/solr stdin_open: true tty: true command: /bin/bash From c60f8bcad0450456ae3ee2c3a66fe386bba84b56 Mon Sep 17 00:00:00 2001 From: = Date: Thu, 5 Feb 2026 21:16:56 -0800 Subject: [PATCH 29/69] added ability to return unmapped attributes for properties --- lib/ontologies_linked_data/models/ontology.rb | 5 +++-- .../models/properties/annotation_property.rb | 7 ++++--- .../models/properties/datatype_property.rb | 7 ++++--- .../models/properties/object_property.rb | 7 ++++--- .../models/properties/ontology_property.rb | 15 +++++++-------- 5 files changed, 22 insertions(+), 19 deletions(-) diff --git a/lib/ontologies_linked_data/models/ontology.rb b/lib/ontologies_linked_data/models/ontology.rb index 2f8370247..9de084068 100644 --- a/lib/ontologies_linked_data/models/ontology.rb +++ b/lib/ontologies_linked_data/models/ontology.rb @@ -302,7 +302,7 @@ def property_roots(sub=nil, extra_include=[]) LinkedData::Models::OntologyProperty.sort_properties(all_roots) end - def property(prop_id, sub=nil) + def property(prop_id, sub=nil, display_all_attributes: false) p = nil sub ||= latest_submission(status: [:rdf]) self.bring(:acronym) if self.bring?(:acronym) @@ -310,9 +310,10 @@ def property(prop_id, sub=nil) prop_classes = [LinkedData::Models::ObjectProperty, LinkedData::Models::DatatypeProperty, LinkedData::Models::AnnotationProperty] prop_classes.each do |c| - p = c.find(prop_id).in(sub).include(:label, :definition, :parents).first + p = c.find(prop_id).in(sub).include(:label, :definition, :parents,:domain, :range).first unless p.nil? + p.bring(:unmapped) if display_all_attributes p.load_has_children parents = p.parents.nil? ? [] : p.parents.dup c.in(sub).models(parents).include(:label, :definition).all() diff --git a/lib/ontologies_linked_data/models/properties/annotation_property.rb b/lib/ontologies_linked_data/models/properties/annotation_property.rb index 576c62ef3..7e2167177 100644 --- a/lib/ontologies_linked_data/models/properties/annotation_property.rb +++ b/lib/ontologies_linked_data/models/properties/annotation_property.rb @@ -18,11 +18,12 @@ class AnnotationProperty < LinkedData::Models::OntologyProperty attribute :children, namespace: :rdfs, inverse: { on: :annotation_property, :attribute => :parents } attribute :ancestors, namespace: :rdfs, property: :subPropertyOf, handler: :retrieve_ancestors attribute :descendants, namespace: :rdfs, property: :subPropertyOf, handler: :retrieve_descendants - # attribute :domain - # attribute :range + attribute :domain, namespace: :rdfs + attribute :range, namespace: :rdfs - serialize_default :label, :labelGenerated, :definition, :matchType, :ontologyType, :propertyType, :parents, :children, :hasChildren # some of these attributes are used in Search (not shown out of context) + serialize_default :label, :labelGenerated, :definition, :matchType, :ontologyType, :propertyType, :parents, :children, :hasChildren,:domain, :range # some of these attributes are used in Search (not shown out of context) aggregates childrenCount: [:count, :children] + serialize_methods :properties # this command allows the children to be serialized in the output embed :children diff --git a/lib/ontologies_linked_data/models/properties/datatype_property.rb b/lib/ontologies_linked_data/models/properties/datatype_property.rb index dfa2ad392..34789dc1b 100644 --- a/lib/ontologies_linked_data/models/properties/datatype_property.rb +++ b/lib/ontologies_linked_data/models/properties/datatype_property.rb @@ -18,11 +18,12 @@ class DatatypeProperty < LinkedData::Models::OntologyProperty attribute :children, namespace: :rdfs, inverse: { on: :datatype_property, :attribute => :parents } attribute :ancestors, namespace: :rdfs, property: :subPropertyOf, handler: :retrieve_ancestors attribute :descendants, namespace: :rdfs, property: :subPropertyOf, handler: :retrieve_descendants - # attribute :domain - # attribute :range + attribute :domain, namespace: :rdfs + attribute :range, namespace: :rdfs - serialize_default :label, :labelGenerated, :definition, :matchType, :ontologyType, :propertyType, :parents, :children, :hasChildren # some of these attributes are used in Search (not shown out of context) + serialize_default :label, :labelGenerated, :definition, :matchType, :ontologyType, :propertyType, :parents, :children, :hasChildren, :domain, :range # some of these attributes are used in Search (not shown out of context) aggregates childrenCount: [:count, :children] + serialize_methods :properties # this command allows the children to be serialized in the output embed :children diff --git a/lib/ontologies_linked_data/models/properties/object_property.rb b/lib/ontologies_linked_data/models/properties/object_property.rb index 5b6672985..3b96216dc 100644 --- a/lib/ontologies_linked_data/models/properties/object_property.rb +++ b/lib/ontologies_linked_data/models/properties/object_property.rb @@ -18,11 +18,12 @@ class ObjectProperty < LinkedData::Models::OntologyProperty attribute :children, namespace: :rdfs, inverse: { on: :object_property, :attribute => :parents } attribute :ancestors, namespace: :rdfs, property: :subPropertyOf, handler: :retrieve_ancestors attribute :descendants, namespace: :rdfs, property: :subPropertyOf, handler: :retrieve_descendants - # attribute :domain - # attribute :range + attribute :domain, namespace: :rdfs + attribute :range, namespace: :rdfs - serialize_default :label, :labelGenerated, :definition, :matchType, :ontologyType, :propertyType, :parents, :children, :hasChildren # some of these attributes are used in Search (not shown out of context) + serialize_default :label, :labelGenerated, :definition, :matchType, :ontologyType, :propertyType, :parents, :children, :hasChildren, :domain, :range # some of these attributes are used in Search (not shown out of context) aggregates childrenCount: [:count, :children] + serialize_methods :properties # this command allows the children to be serialized in the output embed :children diff --git a/lib/ontologies_linked_data/models/properties/ontology_property.rb b/lib/ontologies_linked_data/models/properties/ontology_property.rb index 7819d18b1..7aaa4f541 100644 --- a/lib/ontologies_linked_data/models/properties/ontology_property.rb +++ b/lib/ontologies_linked_data/models/properties/ontology_property.rb @@ -161,9 +161,9 @@ def has_children_query(class_id, submission_id) pattern = "?c <#{property_tree.to_s}> <#{safe_class_id_uri}> . " query = < { - #{pattern} -} + GRAPH <#{submission_id}> { + #{pattern} + } } LIMIT 1 eos @@ -264,7 +264,7 @@ def index_doc(to_set=nil) } all_attrs = self.to_hash - std = [:id, :label, :definition, :parents] + std = %i[id label definition parents] std.each do |att| cur_val = all_attrs[att] @@ -318,7 +318,7 @@ def traverse_path_to_root(parents, paths, path_i, tree=false, top_property=nil) rec_i = recursions[i] path = paths[rec_i] p = path.last - p.bring(parents: [:label, :definition]) if p.bring?(:parents) + p.bring(parents: %i[label definition]) if p.bring?(:parents) unless p.loaded_attributes.include?(:parents) # fail safely @@ -343,7 +343,7 @@ def self.ontology_link(m) end def self.partially_load_children(models, threshold, submission) - ld = [:label, :definition] + ld = %i[label definition] single_load = [] query = self.in(submission).models(models) query.aggregate(:count, :children).all @@ -424,8 +424,7 @@ def self.compare_properties(prop_a, prop_b) [label_a.downcase] <=> [label_b.downcase] end - end - end + end From 42252c8bd0eea98f928fa42c256092ce3cf0b1b3 Mon Sep 17 00:00:00 2001 From: = Date: Tue, 10 Feb 2026 10:27:54 -0800 Subject: [PATCH 30/69] added URI fetching of related triples and serialization in different formats: ontoportal-lirmm/ontologies_linked_data#125 --- Gemfile | 1 + lib/ontologies_linked_data/media_types.rb | 5 +- .../models/external_class.rb | 40 +++ .../models/interportal_class.rb | 80 +++++ .../models/mod/hydra_page.rb | 59 ++++ .../models/mod/mod_base.rb | 7 + .../serializers/json.rb | 136 +++++--- .../serializers/jsonld.rb | 40 +++ .../serializers/jsonp.rb | 2 +- .../serializers/ntriples.rb | 37 ++ .../serializers/rdf_xml.rb | 43 +++ .../serializers/serializers.rb | 14 +- .../serializers/turtle.rb | 38 +++ test/models/test_resource.rb | 320 ++++++++++++++++++ 14 files changed, 759 insertions(+), 63 deletions(-) create mode 100644 lib/ontologies_linked_data/models/external_class.rb create mode 100644 lib/ontologies_linked_data/models/interportal_class.rb create mode 100644 lib/ontologies_linked_data/models/mod/hydra_page.rb create mode 100644 lib/ontologies_linked_data/models/mod/mod_base.rb create mode 100644 lib/ontologies_linked_data/serializers/jsonld.rb create mode 100644 lib/ontologies_linked_data/serializers/ntriples.rb create mode 100644 lib/ontologies_linked_data/serializers/rdf_xml.rb create mode 100644 lib/ontologies_linked_data/serializers/turtle.rb create mode 100644 test/models/test_resource.rb diff --git a/Gemfile b/Gemfile index 93021a719..b76aa72b7 100644 --- a/Gemfile +++ b/Gemfile @@ -16,6 +16,7 @@ gem 'rake' gem 'request_store' gem 'rest-client' gem 'rsolr' +gem 'json-ld', '~> 3.2.0' # Testing group :test do diff --git a/lib/ontologies_linked_data/media_types.rb b/lib/ontologies_linked_data/media_types.rb index d109e80db..ec8257316 100644 --- a/lib/ontologies_linked_data/media_types.rb +++ b/lib/ontologies_linked_data/media_types.rb @@ -3,8 +3,11 @@ module MediaTypes HTML = :html JSON = :json JSONP = :jsonp + JSONLD = :jsonld XML = :xml + RDF_XML = :rdf_xml TURTLE = :turtle + NTRIPLES = :ntriples DEFAULT = JSON def self.all @@ -55,4 +58,4 @@ def self.supported_type?(type) } end -end \ No newline at end of file +end diff --git a/lib/ontologies_linked_data/models/external_class.rb b/lib/ontologies_linked_data/models/external_class.rb new file mode 100644 index 000000000..3a0d5ffe2 --- /dev/null +++ b/lib/ontologies_linked_data/models/external_class.rb @@ -0,0 +1,40 @@ +module LinkedData + module Models + class ExternalClass + include LinkedData::Hypermedia::Resource + # For class mapped to internal class that are outside any BioPortal appliance + # We just generate a link to self class and a link to the external ontology + + attr_reader :id, :ontology, :type_uri + attr_accessor :prefLabel + + serialize_never :id, :ontology, :type_uri + + link_to LinkedData::Hypermedia::Link.new("self", lambda {|ec| ec.id.to_s}, "http://www.w3.org/2002/07/owl#Class"), + LinkedData::Hypermedia::Link.new("ontology", lambda {|ec| ec.ontology.to_s}, Goo.vocabulary["Ontology"]) + + def initialize(id, ontology) + @id = id + @ontology = RDF::URI.new(CGI.unescape(ontology.to_s)) + @type_uri = RDF::URI.new("http://www.w3.org/2002/07/owl#Class") + end + + def getPrefLabel + # take the last part of the URL to generate the prefLabel (the one after the last #, or if not after the last /) + if id.include? "#" + @prefLabel = id.split("#")[-1] + else + @prefLabel = id.split("/")[-1] + end + end + + def self.graph_uri + RDF::URI.new("http://data.bioontology.org/metadata/ExternalMappings") + end + def self.url_param_str + # a little string to get external mappings in URL parameters + RDF::URI.new("mappings:external") + end + end + end +end \ No newline at end of file diff --git a/lib/ontologies_linked_data/models/interportal_class.rb b/lib/ontologies_linked_data/models/interportal_class.rb new file mode 100644 index 000000000..fbd90ccd7 --- /dev/null +++ b/lib/ontologies_linked_data/models/interportal_class.rb @@ -0,0 +1,80 @@ +module LinkedData + module Models + class InterportalClass + include LinkedData::Hypermedia::Resource + # For class mapped to internal class that are inside another BioPortal appliance + # We are generating the same link than a normal class but pointing to the other appliance + + attr_reader :id, :ontology, :type_uri, :source, :ui_link, :self + attr_accessor :prefLabel + + serialize_never :id, :ontology, :type_uri, :source, :ui_link, :self + + link_to LinkedData::Hypermedia::Link.new("self", lambda { |ec| "#{ec.self.to_s}" }, "http://www.w3.org/2002/07/owl#Class"), + LinkedData::Hypermedia::Link.new("ontology", lambda { |ec| ec.ontology.to_s }, Goo.vocabulary["Ontology"]), + LinkedData::Hypermedia::Link.new("children", lambda { |ec| "#{ec.ontology.to_s}/classes/#{CGI.escape(ec.id.to_s)}/children" }, "http://www.w3.org/2002/07/owl#Class"), + LinkedData::Hypermedia::Link.new("parents", lambda { |ec| "#{ec.ontology.to_s}/classes/#{CGI.escape(ec.id.to_s)}/parents" }, "http://www.w3.org/2002/07/owl#Class"), + LinkedData::Hypermedia::Link.new("descendants", lambda { |ec| "#{ec.ontology.to_s}/classes/#{CGI.escape(ec.id.to_s)}/descendants" }, "http://www.w3.org/2002/07/owl#Class"), + LinkedData::Hypermedia::Link.new("ancestors", lambda { |ec| "#{ec.ontology.to_s}/classes/#{CGI.escape(ec.id.to_s)}/ancestors" }, "http://www.w3.org/2002/07/owl#Class"), + LinkedData::Hypermedia::Link.new("tree", lambda { |ec| "#{ec.ontology.to_s}/classes/#{CGI.escape(ec.id.to_s)}/tree" }, "http://www.w3.org/2002/07/owl#Class"), + LinkedData::Hypermedia::Link.new("notes", lambda { |ec| "#{ec.ontology.to_s}/classes/#{CGI.escape(ec.id.to_s)}/notes" }, LinkedData::Models::Note.type_uri), + LinkedData::Hypermedia::Link.new("mappings", lambda { |ec| "#{ec.ontology.to_s}/classes/#{CGI.escape(ec.id.to_s)}/mappings" }, Goo.vocabulary["Mapping"]), + LinkedData::Hypermedia::Link.new("ui", lambda { |ec| ec.ui_link.to_s }, "http://www.w3.org/2002/07/owl#Class") + + def initialize(id, ontology, source) + @id = id + + @ontology, acronym = ontology_url(ontology, source) + @self = "#{@ontology}/classes/#{CGI.escape(id.to_s)}" + @ui_link = "#{LinkedData.settings.interportal_hash[source]["ui"]}/ontologies/#{acronym}?p=classes&conceptid=#{CGI.escape(id)}" + @type_uri = RDF::URI.new("http://www.w3.org/2002/07/owl#Class") + @source = source + end + + def getPrefLabel + # Get the prefLabel from the source bioportal, if error it generates the label from the last part of the URL + begin + json_class = JSON.parse(Net::HTTP.get(URI.parse("#{@self}?apikey=#{LinkedData.settings.interportal_hash[@source]["apikey"]}"))) + @prefLabel = if !json_class["prefLabel"].nil? + json_class["prefLabel"] + else + id.split("/")[-1] + end + rescue + @prefLabel = id.split("/")[-1] + end + end + + def self.graph_uri(acronym) + RDF::URI.new("http://data.bioontology.org/metadata/InterportalMappings/#{acronym}") + end + + def self.graph_base_str + "http://data.bioontology.org/metadata/InterportalMappings" + end + + def self.url_param_str(acronym) + # a little string to get interportal mappings in URL parameters + RDF::URI.new("interportal:#{acronym}") + end + + def self.base_url_param_str + RDF::URI.new("interportal:") + end + + private + + def ontology_url(ontology, source) + url = '' + if ontology =~ URI::DEFAULT_PARSER.make_regexp + url = ontology + else + url = "#{LinkedData.settings.interportal_hash[source]['api']}/ontologies/#{ontology}" + end + acronym = url.split('/').last + [url, acronym] + + end + end + end +end \ No newline at end of file diff --git a/lib/ontologies_linked_data/models/mod/hydra_page.rb b/lib/ontologies_linked_data/models/mod/hydra_page.rb new file mode 100644 index 000000000..877b4c9d9 --- /dev/null +++ b/lib/ontologies_linked_data/models/mod/hydra_page.rb @@ -0,0 +1,59 @@ +module LinkedData + module Models + class HydraPage < Goo::Base::Page + + def convert_hydra_page(options, &block) + { + '@id': get_request_path(options), + '@type': 'hydra:Collection', + totalItems: self.aggregate, + itemsPerPage: self.size, + view: generate_hydra_page_view(options, self.page_number, self.total_pages), + member: map { |item| item.to_flex_hash(options, &block) } + } + end + + def self.generate_hydra_context + { + 'hydra': 'http://www.w3.org/ns/hydra/core#', + 'Collection': 'hydra:Collection', + 'member': 'hydra:member', + 'totalItems': 'hydra:totalItems', + 'itemsPerPage': 'hydra:itemsPerPage', + 'view': 'hydra:view', + 'firstPage': 'hydra:first', + 'lastPage': 'hydra:last', + 'previousPage': 'hydra:previous', + 'nextPage': 'hydra:next', + } + end + + private + + def generate_hydra_page_view(options, page, page_count) + request_path = get_request_path(options) + params = options[:request] ? options[:request].params.dup : {} + + build_url = ->(page_number) { + query = Rack::Utils.build_nested_query(params.merge("page" => page_number.to_s)) + request_path ? "#{request_path}?#{query}" : "?#{query}" + } + + { + "@id": build_url.call(page), + "@type": "hydra:PartialCollectionView", + firstPage: build_url.call(1), + previousPage: page > 1 ? build_url.call(page - 1) : nil, + nextPage: page < page_count ? build_url.call(page + 1) : nil, + lastPage: page_count != 0 ? build_url.call(page_count) : build_url.call(1) + } + end + + def get_request_path(options) + request_path = options[:request] ? "#{LinkedData.settings.rest_url_prefix.chomp("/")}#{options[:request].path}" : nil + request_path + end + + end + end +end diff --git a/lib/ontologies_linked_data/models/mod/mod_base.rb b/lib/ontologies_linked_data/models/mod/mod_base.rb new file mode 100644 index 000000000..5208e8bbe --- /dev/null +++ b/lib/ontologies_linked_data/models/mod/mod_base.rb @@ -0,0 +1,7 @@ +module LinkedData + module Models + class ModBase < LinkedData::Models::Base + end + end +end + diff --git a/lib/ontologies_linked_data/serializers/json.rb b/lib/ontologies_linked_data/serializers/json.rb index ce77050ac..187b460d7 100644 --- a/lib/ontologies_linked_data/serializers/json.rb +++ b/lib/ontologies_linked_data/serializers/json.rb @@ -7,78 +7,109 @@ class JSON def self.serialize(obj, options = {}) + return serialize_mod_objects(obj, options) if mod_object?(obj) + # Handle the serialization for all other objects in the standard way hash = obj.to_flex_hash(options) do |hash, hashed_obj| - current_cls = hashed_obj.respond_to?(:klass) ? hashed_obj.klass : hashed_obj.class - result_lang = self.get_languages(get_object_submission(hashed_obj), options[:lang]) + process_common_serialization(hash, hashed_obj, options) + end + MultiJson.dump(hash) + end + + def self.serialize_mod_objects(obj, options = {}) + # using one context and links in mod objects + global_context = {} - # Add the id to json-ld attribute - if current_cls.ancestors.include?(LinkedData::Hypermedia::Resource) && !current_cls.embedded? && hashed_obj.respond_to?(:id) - prefixed_id = LinkedData::Models::Base.replace_url_id_to_prefix(hashed_obj.id) - hash["@id"] = prefixed_id.to_s - end + hash = obj.to_flex_hash(options) do |hash, hashed_obj| + process_common_serialization(hash, hashed_obj, options, global_context) + end - # Add the type - hash["@type"] = type(current_cls, hashed_obj) if hash["@id"] - - # Generate links - # NOTE: If this logic changes, also change in xml.rb - if generate_links?(options) - links = LinkedData::Hypermedia.generate_links(hashed_obj) - unless links.empty? - hash["links"] = links - hash["links"].merge!(generate_links_context(hashed_obj)) if generate_context?(options) - end - end + result = {} + # handle adding the context for HydraPage + if obj.is_a?(LinkedData::Models::HydraPage) + global_context["@context"] ||= {} + global_context["@context"].merge!(LinkedData::Models::HydraPage.generate_hydra_context) + end + result.merge!(global_context) unless global_context.empty? + result.merge!(hash) if hash.is_a?(Hash) + MultiJson.dump(result) + end + + + private + + def self.process_common_serialization(hash, hashed_obj, options, global_context= nil) + current_cls = hashed_obj.respond_to?(:klass) ? hashed_obj.klass : hashed_obj.class + result_lang = get_languages(get_object_submission(hashed_obj), options[:lang]) + + add_id_and_type(hash, hashed_obj, current_cls) + add_links(hash, hashed_obj, options) if generate_links?(options) + add_context(hash, hashed_obj, options, current_cls, result_lang, global_context) if generate_context?(options) + end - # Generate context + def self.add_id_and_type(hash, hashed_obj, current_cls) + return unless current_cls.ancestors.include?(LinkedData::Hypermedia::Resource) && !current_cls.embedded? && hashed_obj.respond_to?(:id) + + hash["@id"] = LinkedData::Models::Base.replace_url_id_to_prefix(hashed_obj.id).to_s + hash["@type"] = type(current_cls, hashed_obj) if hash["@id"] + end + + def self.add_links(hash, hashed_obj, options) + links = LinkedData::Hypermedia.generate_links(hashed_obj) + return if links.empty? + hash["links"] = links + hash["links"].merge!(generate_links_context(hashed_obj)) if generate_context?(options) + end + + def self.add_context(hash, hashed_obj, options, current_cls, result_lang, global_context) + return if global_context&.any? + + if global_context.nil? if current_cls.ancestors.include?(Goo::Base::Resource) && !current_cls.embedded? - if generate_context?(options) - context = generate_context(hashed_obj, hash.keys, options) - hash.merge!(context) - end + context = generate_context(hashed_obj, hash.keys, options) + hash.merge!(context) + elsif (hashed_obj.instance_of?(LinkedData::Models::ExternalClass) || hashed_obj.instance_of?(LinkedData::Models::InterportalClass)) && !current_cls.embedded? + # Add context for ExternalClass + external_class_context = { "@context" => { "@vocab" => Goo.vocabulary.to_s, "prefLabel" => "http://data.bioontology.org/metadata/skosprefLabel" } } + hash.merge!(external_class_context) end hash['@context']['@language'] = result_lang if hash['@context'] + elsif global_context.empty? + context = generate_context(hashed_obj, hash.keys, options) + global_context.replace(context) + global_context["@context"]["@language"] = result_lang unless global_context.empty? end - MultiJson.dump(hash) end - private + def self.mod_object?(obj) + return false if obj.nil? + single_object = (obj.class == Array) && obj.any? ? obj.first : obj + single_object.class.ancestors.include?(LinkedData::Models::HydraPage) || single_object.class.ancestors.include?(LinkedData::Models::ModBase) + end + def self.get_object_submission(obj) obj.class.respond_to?(:attributes) && obj.class.attributes.include?(:submission) ? obj.submission : nil end def self.get_languages(submission, user_languages) - - if user_languages.eql?(:all) || user_languages.blank? - if submission - submission.bring(:naturalLanguage) if submission.bring?(:naturalLanguage) - submission_languages_languages = get_submission_languages(submission.naturalLanguage) - end - - if submission_languages_languages.blank? - result_lang = [Goo.main_languages.first.to_s] - else - result_lang = [submission_languages_languages.first] - end - else - result_lang = Array(user_languages) + result_lang = user_languages + + if submission + submission.bring :naturalLanguage + languages = get_submission_languages(submission.naturalLanguage) + # intersection of the two arrays , if the requested language is not :all + result_lang = user_languages == :all ? languages : Array(user_languages) & languages + result_lang = result_lang.first if result_lang.length == 1 end - if result_lang.length == 1 - result_lang.first - elsif result_lang.empty? - Goo.main_languages.first.to_s - else - result_lang - end + result_lang end def self.get_submission_languages(submission_natural_language = []) submission_natural_language = submission_natural_language.values.flatten if submission_natural_language.is_a?(Hash) - submission_natural_language.map { |natural_language| natural_language.to_s.split('/').last[0..1].to_sym }.compact - end + submission_natural_language.map { |natural_language| natural_language.to_s['iso639'] && natural_language.to_s.split('/').last[0..1].to_sym }.compact + end def self.type(current_cls, hashed_obj) if current_cls.respond_to?(:type_uri) @@ -113,12 +144,7 @@ def self.generate_context(object, serialized_attrs = [], options = {}) predicate = { "@id" => linked_model.type_uri.to_s, "@type" => "@id" } else # use the original predicate property if set - predicate_attr = if current_cls.model_settings[:attributes][attr][:property].is_a?(Proc) - attr - else - current_cls.model_settings[:attributes][attr][:property] || attr - end - + predicate_attr = current_cls.model_settings[:attributes][attr][:property] || attr # predicate with custom namespace # if the namespace can be resolved by the namespaces added in Goo then it will be resolved. predicate = "#{Goo.vocabulary(current_cls.model_settings[:attributes][attr][:namespace])&.to_s}#{predicate_attr}" diff --git a/lib/ontologies_linked_data/serializers/jsonld.rb b/lib/ontologies_linked_data/serializers/jsonld.rb new file mode 100644 index 000000000..22e6b7d6d --- /dev/null +++ b/lib/ontologies_linked_data/serializers/jsonld.rb @@ -0,0 +1,40 @@ +require 'multi_json' +require 'json/ld' + +module LinkedData + module Serializers + class JSONLD + + def self.serialize(hashes, options = {}) + subject = RDF::URI.new(hashes['id']) + reverse = hashes['reverse'] || {} + hashes.delete('id') + hashes.delete('reverse') + graph = RDF::Graph.new + + hashes.each do |property_url, val| + Array(val).each do |v| + if v.is_a?(Hash) + blank_node = RDF::Node.new + v.each do |blank_predicate, blank_value| + graph << RDF::Statement.new(blank_node, RDF::URI.new(blank_predicate), blank_value) + end + v = blank_node + end + graph << RDF::Statement.new(subject, RDF::URI.new(property_url), v) + end + end + + reverse.each do |reverse_subject, reverse_property| + Array(reverse_property).each do |s| + graph << RDF::Statement.new(RDF::URI.new(reverse_subject), RDF::URI.new(s), subject) + end + end + + context = { '@context' => options.transform_keys(&:to_s) } + compacted = ::JSON::LD::API.compact(::JSON::LD::API.fromRdf(graph), context['@context']) + MultiJson.dump(compacted) + end + end + end +end \ No newline at end of file diff --git a/lib/ontologies_linked_data/serializers/jsonp.rb b/lib/ontologies_linked_data/serializers/jsonp.rb index 91d48cc68..58cb5e1cf 100644 --- a/lib/ontologies_linked_data/serializers/jsonp.rb +++ b/lib/ontologies_linked_data/serializers/jsonp.rb @@ -19,4 +19,4 @@ def self.serialize(obj, options) end end end -end \ No newline at end of file +end diff --git a/lib/ontologies_linked_data/serializers/ntriples.rb b/lib/ontologies_linked_data/serializers/ntriples.rb new file mode 100644 index 000000000..c96795a77 --- /dev/null +++ b/lib/ontologies_linked_data/serializers/ntriples.rb @@ -0,0 +1,37 @@ +module LinkedData + module Serializers + class NTRIPLES + + def self.serialize(hashes, options = {}) + subject = RDF::URI.new(hashes['id']) + reverse = hashes['reverse'] || {} + hashes.delete('id') + hashes.delete('reverse') + RDF::Writer.for(:ntriples).buffer(prefixes: options) do |writer| + hashes.each do |p, o| + predicate = RDF::URI.new(p) + Array(o).each do |item| + if item.is_a?(Hash) + blank_node = RDF::Node.new + item.each do |blank_predicate, blank_value| + writer << RDF::Statement.new(blank_node, RDF::URI.new(blank_predicate), blank_value) + end + item = blank_node + end + writer << RDF::Statement.new(subject, predicate, item) + end + end + + reverse.each do |reverse_subject, reverse_property| + Array(reverse_property).each do |s| + writer << RDF::Statement.new(RDF::URI.new(reverse_subject), RDF::URI.new(s), subject) + end + end + end + end + + end + end +end + + \ No newline at end of file diff --git a/lib/ontologies_linked_data/serializers/rdf_xml.rb b/lib/ontologies_linked_data/serializers/rdf_xml.rb new file mode 100644 index 000000000..e06590f00 --- /dev/null +++ b/lib/ontologies_linked_data/serializers/rdf_xml.rb @@ -0,0 +1,43 @@ +module LinkedData + module Serializers + class RDF_XML + def self.serialize(hashes, options = {}) + subject = RDF::URI.new(hashes["id"]) + reverse = hashes["reverse"] || {} + hashes.delete("id") + hashes.delete("reverse") + graph = RDF::Graph.new + + hashes.each do |property_url, val| + Array(val).each do |v| + if v.is_a?(Hash) + blank_node = RDF::Node.new + v.each do |blank_predicate, blank_value| + graph << RDF::Statement.new(blank_node, RDF::URI.new(blank_predicate), blank_value) + end + v = blank_node + end + graph << RDF::Statement.new(subject, RDF::URI.new(property_url), v) + end + end + + inverse_graph = RDF::Graph.new + reverse.each do |reverse_subject, reverse_property| + Array(reverse_property).each do |s| + inverse_graph << RDF::Statement.new(RDF::URI.new(reverse_subject), RDF::URI.new(s), subject) + end + end + + a = RDF::RDFXML::Writer.buffer(prefixes: options) do |writer| + writer << graph + end + + b = RDF::RDFXML::Writer.buffer(prefixes: options) do |writer| + writer << inverse_graph + end + xml_result = "#{a.chomp("\n")}\n#{b.sub!(/^<\?xml[^>]*>\n]*>/, '').gsub(/^$\n/, '')}" + xml_result.gsub(/^$\n/, '') + end + end + end +end \ No newline at end of file diff --git a/lib/ontologies_linked_data/serializers/serializers.rb b/lib/ontologies_linked_data/serializers/serializers.rb index b6006280d..1603c1dbe 100644 --- a/lib/ontologies_linked_data/serializers/serializers.rb +++ b/lib/ontologies_linked_data/serializers/serializers.rb @@ -1,8 +1,12 @@ require 'ontologies_linked_data/media_types' require 'ontologies_linked_data/serializers/xml' +require 'ontologies_linked_data/serializers/rdf_xml' require 'ontologies_linked_data/serializers/json' require 'ontologies_linked_data/serializers/jsonp' +require 'ontologies_linked_data/serializers/jsonld' require 'ontologies_linked_data/serializers/html' +require 'ontologies_linked_data/serializers/ntriples' +require 'ontologies_linked_data/serializers/turtle' module LinkedData module Serializers @@ -10,17 +14,15 @@ def self.serialize(obj, type, options = {}) SERIALIZERS[type].serialize(obj, options) end - class Turtle - def self.serialize(obj, options) - end - end - SERIALIZERS = { LinkedData::MediaTypes::HTML => HTML, LinkedData::MediaTypes::JSON => JSON, LinkedData::MediaTypes::JSONP => JSONP, + LinkedData::MediaTypes::JSONLD => JSONLD, LinkedData::MediaTypes::XML => XML, - LinkedData::MediaTypes::TURTLE => JSON + LinkedData::MediaTypes::RDF_XML => RDF_XML, + LinkedData::MediaTypes::TURTLE => TURTLE, + LinkedData::MediaTypes::NTRIPLES => NTRIPLES } end end \ No newline at end of file diff --git a/lib/ontologies_linked_data/serializers/turtle.rb b/lib/ontologies_linked_data/serializers/turtle.rb new file mode 100644 index 000000000..b0cc9ecf4 --- /dev/null +++ b/lib/ontologies_linked_data/serializers/turtle.rb @@ -0,0 +1,38 @@ +module LinkedData + module Serializers + class TURTLE + def self.serialize(hashes, options = {}) + subject = RDF::URI.new(hashes['id']) + reverse = hashes['reverse'] || {} + hashes.delete('id') + hashes.delete('reverse') + options.delete(:rdf) + + RDF::Writer.for(:turtle).buffer(prefixes: options) do |writer| + hashes.each do |p, o| + predicate = RDF::URI.new(p) + Array(o).each do |item| + if item.is_a?(Hash) + blank_node = RDF::Node.new + item.each do |blank_predicate, blank_value| + writer << RDF::Statement.new(blank_node, RDF::URI.new(blank_predicate), blank_value) + end + item = blank_node + end + writer << RDF::Statement.new(subject, predicate, item) + end + end + + reverse.each do |reverse_subject, reverse_property| + Array(reverse_property).each do |s| + writer << RDF::Statement.new(RDF::URI.new(reverse_subject), RDF::URI.new(s), subject) + end + end + + end + end + end + end +end + + \ No newline at end of file diff --git a/test/models/test_resource.rb b/test/models/test_resource.rb new file mode 100644 index 000000000..63d51f660 --- /dev/null +++ b/test/models/test_resource.rb @@ -0,0 +1,320 @@ +require_relative "../test_case" +require_relative './test_ontology_common' + +class TestResource < LinkedData::TestOntologyCommon + + def self.before_suite + LinkedData::TestCase.backend_4s_delete + + # Example + data = %( + . + "John Doe" . + "30"^^ . + "male" . + . + . + _:blanknode1 . + _:blanknode2 . + "test/bonjour"@fr . + "Person#human"@en . + "2024-11-29"^^ . + "http://person1.org/test" . + + _:blanknode1 "Jane Smith" . + _:blanknode1 "25"^^ . + _:blanknode1 "female" . + _:blanknode1 . + _:blanknode2 "Jane Smith 2" . + "Hiking" . + "Cooking" . + + . + "Alice Cooper" . + "35"^^ . + "female" . + . + _:skill1, _:skill2 . + _:skill1 "Programming" . + _:skill1 _:skill2 . + _:skill2 "Data Analysis" . + _:skill2 . + "Hiking" . + "Cooking" . + "Photography" . + + . + . + . + + ) + + graph = "http://example.org/test_graph" + Goo.sparql_data_client.execute_append_request(graph, data, '') + + # instance the resource model + @@resource1 = LinkedData::Models::Resource.new("http://example.org/test_graph", "http://example.org/person1") + end + + def self.after_suite + Goo.sparql_data_client.delete_graph("http://example.org/test_graph") + Goo.sparql_data_client.delete_graph("http://data.bioontology.org/ontologies/TEST-TRIPLES/submissions/2") + @resource1&.destroy + end + + def test_generate_model + @object = @@resource1.to_object + @model = @object.class + + assert_equal LinkedData::Models::Base, @model.ancestors[1] + + @model.model_settings[:attributes].map do |property, val| + property_url = "#{val[:property]}#{property}" + assert_includes @@resource1.to_hash.keys, property_url + + hash_value = @@resource1.to_hash[property_url] + object_value = @object.send(property.to_sym) + if property.to_sym == :knows + assert_equal hash_value.map{|x| x.is_a?(Hash) ? x.values : x}.flatten.map(&:to_s).sort, + object_value.map{|x| x.is_a?(String) ? x : x.to_h.values}.flatten.map(&:to_s).sort + elsif property.to_sym == :birthday + assert_equal Array(hash_value).map(&:object), Array(object_value) + else + assert_equal Array(hash_value).map(&:to_s), Array(object_value).map(&:to_s) + end + end + + assert_equal "http://example.org/person1", @object.id.to_s + + assert_equal Goo.namespaces[:foaf][:Person].to_s, @model.type_uri.to_s + end + + def test_resource_fetch_related_triples + result = @@resource1.to_hash + assert_instance_of Hash, result + + refute_empty result + + expected_result = { + "id" => "http://example.org/person1", + "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" => "http://xmlns.com/foaf/0.1/Person", + "http://xmlns.com/foaf/0.1/gender" => "male", + "http://xmlns.com/foaf/0.1/hasInterest" => %w[Cooking Hiking], + "http://xmlns.com/foaf/0.1/age" => "30", + "http://xmlns.com/foaf/0.1/birthday"=>"2024-11-29", + "http://xmlns.com/foaf/0.1/email" => "mailto:john@example.com", + "http://www.w3.org/2004/02/skos/core#altLabel" => "test/bonjour", + "http://www.w3.org/2004/02/skos/core#prefLabel" => "Person#human", + "http://xmlns.com/foaf/0.1/knows" => + ["http://example.org/person3", + { + "http://xmlns.com/foaf/0.1/gender" => "female", + "http://xmlns.com/foaf/0.1/age" => "25", + "http://xmlns.com/foaf/0.1/email" => "mailto:jane@example.com", + "http://xmlns.com/foaf/0.1/name" => "Jane Smith" + }, + { + "http://xmlns.com/foaf/0.1/name" => "Jane Smith 2" + } + ], + "http://xmlns.com/foaf/0.1/name" => "John Doe", + "http://xmlns.com/foaf/0.1/homepage"=>"http://person1.org/test", + "reverse" => { + "http://example2.org/person2" => "http://xmlns.com/foaf/0.1/mother", + "http://example2.org/person5" => ["http://xmlns.com/foaf/0.1/brother", "http://xmlns.com/foaf/0.1/friend"] + } + } + result = JSON.parse(MultiJson.dump(result)) + a = sort_nested_hash(result) + b = sort_nested_hash(expected_result) + assert_equal b, a + end + + def test_resource_serialization_json + result = @@resource1.to_json + + refute_empty result + expected_result = %( + { + "@context": {"ns0": "http://example.org/", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "foaf": "http://xmlns.com/foaf/0.1/", "ns1": "http://example2.org/", "skos":"http://www.w3.org/2004/02/skos/core#"}, + "@graph": + [ + { + "@id": "ns0:person1", + "@type": "foaf:Person", + "foaf:name": "John Doe", + "foaf:birthday":{"@value":"2024-11-29", "@type":"http://www.w3.org/2001/XMLSchema#date"}, + "foaf:hasInterest":["Cooking", "Hiking"], + "foaf:age": {"@type": "http://www.w3.org/2001/XMLSchema#integer", "@value": "30"}, + "foaf:email": {"@id": "mailto:john@example.com"}, + "foaf:gender": "male", + "skos:altLabel":{"@value":"test/bonjour", "@language":"fr"}, + "skos:prefLabel":{"@value":"Person#human", "@language":"en"}, + "foaf:knows": [{"@id": "ns0:person3"}, {"@id": "_:g447140"}, {"@id": "_:g447160"}], + "foaf:homepage":"http://person1.org/test"}, + { + "@id": "_:g447140", + "foaf:name": "Jane Smith", + "foaf:age": {"@type": "http://www.w3.org/2001/XMLSchema#integer", "@value": "25"}, + "foaf:email": {"@id": "mailto:jane@example.com"}, + "foaf:gender": "female" + }, + {"@id": "_:g447160", "foaf:name": "Jane Smith 2"}, + {"@id": "ns1:person5", "foaf:friend": {"@id": "ns0:person1"}, "foaf:brother": {"@id": "ns0:person1"}}, + {"@id": "ns1:person2", "foaf:mother": {"@id": "ns0:person1"}} + ] + } + ) + result = JSON.parse(result.gsub(' ', '').gsub("\n", '').gsub(/_:g\d+/, 'blanke_nodes')) + expected_result = JSON.parse(expected_result.gsub(' ', '').gsub("\n", '').gsub(/_:g\d+/, 'blanke_nodes')) + + a = sort_nested_hash(result) + b = sort_nested_hash(expected_result) + + assert_equal b, a + end + + def test_resource_serialization_xml + result = @@resource1.to_xml + + refute_empty result + expected_result = %( + + + 2024-11-29 + male + Cooking + Hiking + 30 + + test/bonjour + Person#human + + + + female + 25 + + Jane Smith + + + + + Jane Smith 2 + + + John Doe + http://person1.org/test + + + + + + + + + + ) + a = result.gsub(' ', '').gsub(/rdf:nodeID="[^"]*"/, '').split("\n").reject(&:empty?) + b = expected_result.gsub(' ', '').gsub(/rdf:nodeID="[^"]*"/, '').split("\n").reject(&:empty?) + + assert_equal b.sort, a.sort + end + + def test_resource_serialization_ntriples + result = @@resource1.to_ntriples + + refute_empty result + + expected_result = %( + . + "2024-11-29"^^ . + "male" . + "Cooking" . + "Hiking" . + "30"^^ . + . + "test/bonjour"@fr . + "Person#human"@en . + . + _:g447260 "female" . + _:g447260 "25"^^ . + _:g447260 . + _:g447260 "Jane Smith" . + _:g447260 . + _:g447280 "Jane Smith 2" . + _:g447280 . + "John Doe" . + "http://person1.org/test" . + . + . + . + ) + a = result.gsub(' ', '').gsub(/_:g\d+/, 'blanke_nodes').split("\n").reject(&:empty?) + b = expected_result.gsub(' ', '').gsub(/_:g\d+/, 'blanke_nodes').split("\n").reject(&:empty?) + + assert_equal b.sort, a.sort + end + + def test_resource_serialization_turtle + result = @@resource1.to_turtle + refute_empty result + expected_result = %( + @prefix rdf: . + @prefix ns0: . + @prefix foaf: . + @prefix skos: . + @prefix ns1: . + + ns0:person1 + a foaf:Person ; + skos:altLabel "test/bonjour"@fr ; + skos:prefLabel "Person#human"@en ; + foaf:age 30 ; + foaf:birthday "2024-11-29"^^ ; + foaf:email ; + foaf:gender "male" ; + foaf:hasInterest "Cooking", "Hiking" ; + foaf:homepage "http://person1.org/test" ; + foaf:knows ns0:person3, [ + foaf:age 25 ; + foaf:email ; + foaf:gender "female" ; + foaf:name "Jane Smith" + ], [ + foaf:name "Jane Smith 2" + ] ; + foaf:name "John Doe" . + + ns1:person2 + foaf:mother ns0:person1 . + + ns1:person5 + foaf:brother ns0:person1 ; + foaf:friend ns0:person1 . + ) + a = result.gsub(' ', '').split("\n").reject(&:empty?) + b = expected_result.gsub(' ', '').split("\n").reject(&:empty?) + + assert_equal b.sort, a.sort + end + + private + + def sort_nested_hash(hash) + sorted_hash = {} + + hash.each do |key, value| + if value.is_a?(Hash) + sorted_hash[key] = sort_nested_hash(value) + elsif value.is_a?(Array) + sorted_hash[key] = value.map { |item| item.is_a?(Hash) ? sort_nested_hash(item) : item }.sort_by { |item| item.to_s } + else + sorted_hash[key] = value + end + end + + sorted_hash.sort.to_h + end + +end \ No newline at end of file From eb75ac74ab0316815f5a1167245e7e0377dbfe16 Mon Sep 17 00:00:00 2001 From: = Date: Tue, 10 Feb 2026 10:28:31 -0800 Subject: [PATCH 31/69] Gemfile.lock update --- Gemfile.lock | 24 +++++++++++++++++------- 1 file changed, 17 insertions(+), 7 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index f9b6fd1d0..5cb68b4ab 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -87,7 +87,7 @@ GEM launchy (>= 2.1, < 4.0) mail (~> 2.7) eventmachine (1.2.7) - faraday (2.14.0) + faraday (2.14.1) faraday-net_http (>= 2.0, < 3.5) json logger @@ -112,6 +112,14 @@ GEM concurrent-ruby (~> 1.0) io-console (0.8.2) json (2.18.1) + json-canonicalization (0.4.0) + json-ld (3.2.5) + htmlentities (~> 4.3) + json-canonicalization (~> 0.3, >= 0.3.2) + link_header (~> 0.0, >= 0.0.8) + multi_json (~> 1.15) + rack (>= 2.2, < 4) + rdf (~> 3.2, >= 3.2.10) language_server-protocol (3.17.0.5) launchy (3.1.1) addressable (~> 2.8) @@ -133,7 +141,7 @@ GEM mime-types (3.7.0) logger mime-types-data (~> 3.2025, >= 3.2025.0507) - mime-types-data (3.2026.0127) + mime-types-data (3.2026.0203) mini_mime (1.1.5) minitest (6.0.1) prism (~> 1.5) @@ -164,7 +172,7 @@ GEM net-smtp (0.5.1) net-protocol netrc (0.11.0) - oj (3.16.13) + oj (3.16.15) bigdecimal (>= 3.0) ostruct (>= 0.2) omni_logger (0.1.4) @@ -278,7 +286,6 @@ PLATFORMS arm-linux-gnu arm-linux-musl arm64-darwin - ruby x86-linux-gnu x86-linux-musl x86_64-darwin @@ -292,6 +299,7 @@ DEPENDENCIES email_spec ffi goo! + json-ld (~> 3.2.0) libxml-ruby minitest minitest-reporters @@ -339,7 +347,7 @@ CHECKSUMS drb (2.2.3) sha256=0b00d6fdb50995fe4a45dea13663493c841112e4068656854646f418fda13373 email_spec (2.3.0) sha256=df23be7a131186f7a3d5be3b35eaac9196f9ac13bd26c9c3d59341e13d852d11 eventmachine (1.2.7) sha256=994016e42aa041477ba9cff45cbe50de2047f25dd418eba003e84f0d16560972 - faraday (2.14.0) sha256=8699cfe5d97e55268f2596f9a9d5a43736808a943714e3d9a53e6110593941cd + faraday (2.14.1) sha256=a43cceedc1e39d188f4d2cdd360a8aaa6a11da0c407052e426ba8d3fb42ef61c faraday-net_http (3.4.2) sha256=f147758260d3526939bf57ecf911682f94926a3666502e24c69992765875906c ffi (1.17.3) sha256=0e9f39f7bb3934f77ad6feab49662be77e87eedcdeb2a3f5c0234c2938563d4c ffi (1.17.3-aarch64-linux-gnu) sha256=28ad573df26560f0aedd8a90c3371279a0b2bd0b4e834b16a2baa10bd7a97068 @@ -359,6 +367,8 @@ CHECKSUMS i18n (1.14.8) sha256=285778639134865c5e0f6269e0b818256017e8cde89993fdfcbfb64d088824a5 io-console (0.8.2) sha256=d6e3ae7a7cc7574f4b8893b4fca2162e57a825b223a177b7afa236c5ef9814cc json (2.18.1) sha256=fe112755501b8d0466b5ada6cf50c8c3f41e897fa128ac5d263ec09eedc9f986 + json-canonicalization (0.4.0) sha256=73ea88b68f210d1a09c2116d4cd1ff5a39684c6a409f7ccac70d5b1a426a8bef + json-ld (3.2.5) sha256=98b96f1831b0fe9c7d2568a7d43b64f6b8c3f5892d55ccf91640e32a99c273fc language_server-protocol (3.17.0.5) sha256=fd1e39a51a28bf3eec959379985a72e296e9f9acfce46f6a79d31ca8760803cc launchy (3.1.1) sha256=72b847b5cc961589dde2c395af0108c86ff0119f42d4648d25b5440ebb10059e libxml-ruby (5.0.5) sha256=f1bc07152982df555d70159a694ee2a53539de2cdad4b3c8a447fbb15e7e4e9a @@ -369,7 +379,7 @@ CHECKSUMS mail (2.9.0) sha256=6fa6673ecd71c60c2d996260f9ee3dd387d4673b8169b502134659ece6d34941 method_source (1.1.0) sha256=181301c9c45b731b4769bc81e8860e72f9161ad7d66dd99103c9ab84f560f5c5 mime-types (3.7.0) sha256=dcebf61c246f08e15a4de34e386ebe8233791e868564a470c3fe77c00eed5e56 - mime-types-data (3.2026.0127) sha256=4a58692436a987ad930e75bf8f24da7e627acfa0d06e1720aa514791b4c7d12b + mime-types-data (3.2026.0203) sha256=54353d693af028847391c28361c07d4b8b689cad78c3e1cc272fb1205c6d2a2f mini_mime (1.1.5) sha256=8681b7e2e4215f2a159f9400b5816d85e9d8c6c6b491e96a12797e798f8bccef minitest (6.0.1) sha256=7854c74f48e2e975969062833adc4013f249a4b212f5e7b9d5c040bf838d54bb minitest-reporters (1.7.1) sha256=5060413a0c95b8c32fe73e0606f3631c173a884d7900e50013e15094eb50562c @@ -384,7 +394,7 @@ CHECKSUMS net-protocol (0.2.2) sha256=aa73e0cba6a125369de9837b8d8ef82a61849360eba0521900e2c3713aa162a8 net-smtp (0.5.1) sha256=ed96a0af63c524fceb4b29b0d352195c30d82dd916a42f03c62a3a70e5b70736 netrc (0.11.0) sha256=de1ce33da8c99ab1d97871726cba75151113f117146becbe45aa85cb3dabee3f - oj (3.16.13) sha256=b114bcb83ef884f1736b3112108f77cf9ca90aa8111a775318cc5d7a6a1e0303 + oj (3.16.15) sha256=4d3324cac3e8fef54c0fa250b2af26a16dadd9f9788a1d6b1b2098b793a1b2cd omni_logger (0.1.4) sha256=b61596f7d96aa8426929e46c3500558d33e838e1afd7f4735244feb4d082bb3e ontologies_linked_data (0.0.1) ostruct (0.6.3) sha256=95a2ed4a4bd1d190784e666b47b2d3f078e4a9efda2fccf18f84ddc6538ed912 From 4d2cb7cb0adad42c9d26b004d60b87097a3bf68b Mon Sep 17 00:00:00 2001 From: = Date: Tue, 10 Feb 2026 11:04:09 -0800 Subject: [PATCH 32/69] added support for Webmock and jwt --- Gemfile | 2 ++ test/test_case.rb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/Gemfile b/Gemfile index b76aa72b7..c943fccca 100644 --- a/Gemfile +++ b/Gemfile @@ -16,6 +16,7 @@ gem 'rake' gem 'request_store' gem 'rest-client' gem 'rsolr' +gem 'jwt' gem 'json-ld', '~> 3.2.0' # Testing @@ -30,6 +31,7 @@ group :test do gem 'simplecov' gem 'simplecov-cobertura' # for codecov.io gem "thin", "~> 1.8.2" + gem 'webmock' end group :development do diff --git a/test/test_case.rb b/test/test_case.rb index 078135509..46a479944 100644 --- a/test/test_case.rb +++ b/test/test_case.rb @@ -40,6 +40,8 @@ require_relative '../config/config' require 'minitest/autorun' +require 'webmock/minitest' +WebMock.allow_net_connect! # Minitest 5+ no longer supports `MiniTest::Unit.runner=`. We emulate the old # custom runner behavior using Minitest hooks and a small patch around suite runs. From b38b44c6ed76b27f2bc58b955e784a29e9e6c90c Mon Sep 17 00:00:00 2001 From: = Date: Tue, 10 Feb 2026 15:57:10 -0800 Subject: [PATCH 33/69] added analytics module --- .../concerns/analytics.rb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 lib/ontologies_linked_data/concerns/analytics.rb diff --git a/lib/ontologies_linked_data/concerns/analytics.rb b/lib/ontologies_linked_data/concerns/analytics.rb new file mode 100644 index 000000000..58853e2f1 --- /dev/null +++ b/lib/ontologies_linked_data/concerns/analytics.rb @@ -0,0 +1,52 @@ +module LinkedData + module Concerns + module Analytics + def self.included base + base.extend ClassMethods + end + + module ClassMethods + def load_data(field_name) + @@redis ||= Redis.new(:host => LinkedData.settings.ontology_analytics_redis_host, + :port => LinkedData.settings.ontology_analytics_redis_port, + :timeout => 30) + raw_data = @@redis.get(field_name) + raw_data.nil? ? Hash.new : Marshal.load(raw_data) + end + + def analytics_redis_key + raise NotImplementedError # the class that includes it need to implement it + end + + def load_analytics_data + self.load_data(analytics_redis_key) + end + + def analytics(year = nil, month = nil) + retrieve_analytics(year, month) + end + + # A static method for retrieving Analytics for a combination of ontologies, year, month + def retrieve_analytics(year = nil, month = nil) + analytics = self.load_analytics_data + + year = year.to_s if year + month = month.to_s if month + + unless analytics.empty? + analytics.values.each do |ont_analytics| + ont_analytics.delete_if { |key, _| key != year } unless year.nil? + ont_analytics.each { |_, val| val.delete_if { |key, __| key != month } } unless month.nil? + end + # sort results by the highest traffic values + analytics = Hash[analytics.sort_by { |_, v| v[year][month] }.reverse] if year && month + end + analytics + end + end + + end + end +end + + From 65a2d56c521a0cbfa0b2c8fb994e19cde9162608 Mon Sep 17 00:00:00 2001 From: = Date: Tue, 10 Feb 2026 15:58:54 -0800 Subject: [PATCH 34/69] multi-backend compatibility code for mappings --- lib/ontologies_linked_data/mappings/mappings.rb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/lib/ontologies_linked_data/mappings/mappings.rb b/lib/ontologies_linked_data/mappings/mappings.rb index cea828482..30326b8a9 100644 --- a/lib/ontologies_linked_data/mappings/mappings.rb +++ b/lib/ontologies_linked_data/mappings/mappings.rb @@ -52,7 +52,7 @@ def self.mapping_counts(enable_debug=false, logger=nil, reload_cache=false, arr_ epr = Goo.sparql_query_client(:main) latest.each do |acro, sub| - self.handle_triple_store_downtime(logger) if LinkedData.settings.goo_backend_name === '4store' + self.handle_triple_store_downtime(logger) if Goo.backend_4s? t0 = Time.now s_counts = self.mapping_ontologies_count(sub, nil, reload_cache=reload_cache) s_total = 0 @@ -280,7 +280,7 @@ def self.delete_rest_mapping(mapping_id) .latest_submission end graph_delete = RDF::Graph.new - graph_delete << [c.id, RDF::URI.new(rest_predicate), mapping.id] + graph_delete << [RDF::URI.new(c.id), RDF::URI.new(rest_predicate), mapping.id] Goo.sparql_update_client.delete_data(graph_delete, graph: sub.id) end mapping.process.delete @@ -579,6 +579,7 @@ def self.create_mapping_count_pairs_for_ontologies(logger, arr_acronyms) self.delete_zombie_submission_count(persistent_counts, all_latest_submissions) latest_submissions.each do |acr, sub| + self.handle_triple_store_downtime(logger) if Goo.backend_4s? new_counts = nil time = Benchmark.realtime do From dcd6f61fd663c644e3b0d45e9ff8b204ef965b09 Mon Sep 17 00:00:00 2001 From: = Date: Tue, 10 Feb 2026 15:59:34 -0800 Subject: [PATCH 35/69] Gemfile.lock update --- Gemfile.lock | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/Gemfile.lock b/Gemfile.lock index 5cb68b4ab..68cb82777 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -75,6 +75,9 @@ GEM coderay (1.1.3) concurrent-ruby (1.3.6) connection_pool (3.0.2) + crack (1.0.1) + bigdecimal + rexml daemons (1.4.1) date (3.5.1) docile (1.4.1) @@ -104,6 +107,7 @@ GEM ffi (1.17.3-x86_64-darwin) ffi (1.17.3-x86_64-linux-gnu) ffi (1.17.3-x86_64-linux-musl) + hashdiff (1.2.1) htmlentities (4.3.4) http-accept (1.7.0) http-cookie (1.1.0) @@ -120,6 +124,8 @@ GEM multi_json (~> 1.15) rack (>= 2.2, < 4) rdf (~> 3.2, >= 3.2.10) + jwt (3.1.2) + base64 language_server-protocol (3.17.0.5) launchy (3.1.1) addressable (~> 2.8) @@ -279,6 +285,10 @@ GEM uri (1.1.1) uuid (2.3.9) macaddr (~> 1.0) + webmock (3.26.1) + addressable (>= 2.8.0) + crack (>= 0.3.2) + hashdiff (>= 0.4.0, < 2.0.0) PLATFORMS aarch64-linux-gnu @@ -300,6 +310,7 @@ DEPENDENCIES ffi goo! json-ld (~> 3.2.0) + jwt libxml-ruby minitest minitest-reporters @@ -324,6 +335,7 @@ DEPENDENCIES simplecov-cobertura sparql-client! thin (~> 1.8.2) + webmock CHECKSUMS activesupport (8.1.2) sha256=88842578ccd0d40f658289b0e8c842acfe9af751afee2e0744a7873f50b6fdae @@ -339,6 +351,7 @@ CHECKSUMS coderay (1.1.3) sha256=dc530018a4684512f8f38143cd2a096c9f02a1fc2459edcfe534787a7fc77d4b concurrent-ruby (1.3.6) sha256=6b56837e1e7e5292f9864f34b69c5a2cbc75c0cf5338f1ce9903d10fa762d5ab connection_pool (3.0.2) sha256=33fff5ba71a12d2aa26cb72b1db8bba2a1a01823559fb01d29eb74c286e62e0a + crack (1.0.1) sha256=ff4a10390cd31d66440b7524eb1841874db86201d5b70032028553130b6d4c7e daemons (1.4.1) sha256=8fc76d76faec669feb5e455d72f35bd4c46dc6735e28c420afb822fac1fa9a1d date (3.5.1) sha256=750d06384d7b9c15d562c76291407d89e368dda4d4fff957eb94962d325a0dc0 docile (1.4.1) sha256=96159be799bfa73cdb721b840e9802126e4e03dfc26863db73647204c727f21e @@ -361,6 +374,7 @@ CHECKSUMS ffi (1.17.3-x86_64-linux-gnu) sha256=3746b01f677aae7b16dc1acb7cb3cc17b3e35bdae7676a3f568153fb0e2c887f ffi (1.17.3-x86_64-linux-musl) sha256=086b221c3a68320b7564066f46fed23449a44f7a1935f1fe5a245bd89d9aea56 goo (0.0.2) + hashdiff (1.2.1) sha256=9c079dbc513dfc8833ab59c0c2d8f230fa28499cc5efb4b8dd276cf931457cd1 htmlentities (4.3.4) sha256=125a73c6c9f2d1b62100b7c3c401e3624441b663762afa7fe428476435a673da http-accept (1.7.0) sha256=c626860682bfbb3b46462f8c39cd470fd7b0584f61b3cc9df5b2e9eb9972a126 http-cookie (1.1.0) sha256=38a5e60d1527eebc396831b8c4b9455440509881219273a6c99943d29eadbb19 @@ -369,6 +383,7 @@ CHECKSUMS json (2.18.1) sha256=fe112755501b8d0466b5ada6cf50c8c3f41e897fa128ac5d263ec09eedc9f986 json-canonicalization (0.4.0) sha256=73ea88b68f210d1a09c2116d4cd1ff5a39684c6a409f7ccac70d5b1a426a8bef json-ld (3.2.5) sha256=98b96f1831b0fe9c7d2568a7d43b64f6b8c3f5892d55ccf91640e32a99c273fc + jwt (3.1.2) sha256=af6991f19a6bb4060d618d9add7a66f0eeb005ac0bc017cd01f63b42e122d535 language_server-protocol (3.17.0.5) sha256=fd1e39a51a28bf3eec959379985a72e296e9f9acfce46f6a79d31ca8760803cc launchy (3.1.1) sha256=72b847b5cc961589dde2c395af0108c86ff0119f42d4648d25b5440ebb10059e libxml-ruby (5.0.5) sha256=f1bc07152982df555d70159a694ee2a53539de2cdad4b3c8a447fbb15e7e4e9a @@ -443,6 +458,7 @@ CHECKSUMS unicode-emoji (4.2.0) sha256=519e69150f75652e40bf736106cfbc8f0f73aa3fb6a65afe62fefa7f80b0f80f uri (1.1.1) sha256=379fa58d27ffb1387eaada68c749d1426738bd0f654d812fcc07e7568f5c57c6 uuid (2.3.9) sha256=aec0cf592053cd6e07c13c1ef94c440aba705f22eb1ee767b39631f2760124d7 + webmock (3.26.1) sha256=4f696fb57c90a827c20aadb2d4f9058bbff10f7f043bd0d4c3f58791143b1cd7 BUNDLED WITH 4.0.1 From 2c6bd611195c0c2613d0143c4636ff251b05c370 Mon Sep 17 00:00:00 2001 From: = Date: Tue, 10 Feb 2026 16:00:49 -0800 Subject: [PATCH 36/69] corrected the MOD namespace and added oauth providers setting --- lib/ontologies_linked_data/config/config.rb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/lib/ontologies_linked_data/config/config.rb b/lib/ontologies_linked_data/config/config.rb index a5be0aabb..67b6e43d7 100644 --- a/lib/ontologies_linked_data/config/config.rb +++ b/lib/ontologies_linked_data/config/config.rb @@ -85,6 +85,8 @@ def config(&block) # ontology creation to OntoPortal site admins @settings.enable_administrative_notifications ||= true + @settings.oauth_providers ||= {} + # number of times to retry a query when empty records are returned @settings.num_retries_4store ||= 10 @@ -161,7 +163,7 @@ def goo_namespaces conf.add_namespace(:adms, RDF::Vocabulary.new("http://www.w3.org/ns/adms#")) conf.add_namespace(:voaf, RDF::Vocabulary.new("http://purl.org/vocommons/voaf#")) conf.add_namespace(:dcat, RDF::Vocabulary.new("http://www.w3.org/ns/dcat#")) - conf.add_namespace(:mod, RDF::Vocabulary.new("http://www.isibang.ac.in/ns/mod#")) + conf.add_namespace(:mod, RDF::Vocabulary.new("https://w3id.org/mod#")) conf.add_namespace(:prov, RDF::Vocabulary.new("http://www.w3.org/ns/prov#")) conf.add_namespace(:cc, RDF::Vocabulary.new("http://creativecommons.org/ns#")) conf.add_namespace(:schema, RDF::Vocabulary.new("http://schema.org/")) From 590791e63f4c6c5657467770e3aacecdc0bf30f6 Mon Sep 17 00:00:00 2001 From: = Date: Tue, 10 Feb 2026 16:02:16 -0800 Subject: [PATCH 37/69] added a test for ontology bring_remaining? --- test/models/test_ontology.rb | 82 ++++++++++++++++++++++++++++++++++-- 1 file changed, 79 insertions(+), 3 deletions(-) diff --git a/test/models/test_ontology.rb b/test/models/test_ontology.rb index 68a038948..c229aa166 100644 --- a/test/models/test_ontology.rb +++ b/test/models/test_ontology.rb @@ -159,6 +159,20 @@ def test_ontology_properties assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#AlgorithmPurpose", props[0].id.to_s assert_equal "http://www.w3.org/2004/02/skos/core#altLabel", props[1].id.to_s + props[2].bring(*[:domain,:range]) + props[2].bring(:unmapped) + + assert_equal "http://bioontology.org/ontologies/biositemap.owl#biositemap_author", props[2].id.to_s + assert_equal "http://bioontology.org/ontologies/biositemap.owl#Resource_Description", props[2].domain + assert_equal "http://www.w3.org/2001/XMLSchema#string", props[2].range + refute_empty props[2].properties + + p = ont.property(props[2].id.to_s, display_all_attributes: true) + assert_equal "http://bioontology.org/ontologies/biositemap.owl#biositemap_author", p.id.to_s + assert_equal "http://bioontology.org/ontologies/biositemap.owl#Resource_Description", p.domain + assert_equal "http://www.w3.org/2001/XMLSchema#string", p.range + refute_empty p.properties + datatype_props = [] object_props = [] annotation_props = [] @@ -353,13 +367,13 @@ def test_ontology_lifecycle }) # Create - assert_equal false, o.exist? + assert_equal false, o.exist?(reload=true) o.save - assert_equal true, o.exist? + assert_equal true, o.exist?(reload=true) # Delete o.delete - assert_equal false, o.exist? + assert_equal false, o.exist?(reload=true) end def test_next_submission_id @@ -427,4 +441,66 @@ def test_duplicate_contacts assert sub.contact.length == 1 end + # A test to benchmark the time taken by bring_remaining (query not optimized, can take a long time if a lot of value in the list attributes) + def test_ontology_bring_remaining + # Creating the users + user1 = LinkedData::Models::User.new(:username => "user1", :email => "some1@email.org" ) + user1.passwordHash = "some random pass hash" + user1.save + user2 = LinkedData::Models::User.new(:username => "user2", :email => "some2@email.org" ) + user2.passwordHash = "some random pass hash" + user2.save + user3 = LinkedData::Models::User.new(:username => "user3", :email => "some3@email.org" ) + user3.passwordHash = "some random pass hash" + user3.save + user4 = LinkedData::Models::User.new(:username => "user4", :email => "some4@email.org" ) + user4.passwordHash = "some random pass hash" + user4.save + user5 = LinkedData::Models::User.new(:username => "user5", :email => "some5@email.org" ) + user5.passwordHash = "some random pass hash" + user5.save + user6 = LinkedData::Models::User.new(:username => "user6", :email => "some6@email.org" ) + user6.passwordHash = "some random pass hash" + user6.save + user7 = LinkedData::Models::User.new(:username => "user7", :email => "some7@email.org" ) + user7.passwordHash = "some random pass hash" + user7.save + + # Creating the categories + category1 = LinkedData::Models::Category.new({:name => "Test Category", :description => "This is a test category", :acronym => "TCG"}) + category1.save + category2 = LinkedData::Models::Category.new({:name => "Test2 Category", :description => "This is a test category", :acronym => "TCG2"}) + category2.save + category3 = LinkedData::Models::Category.new({:name => "Test2 Category", :description => "This is a test category", :acronym => "TCG3"}) + category3.save + category4 = LinkedData::Models::Category.new({:name => "Test2 Category", :description => "This is a test category", :acronym => "TCG4"}) + category4.save + category5 = LinkedData::Models::Category.new({:name => "Test2 Category", :description => "This is a test category", :acronym => "TCG5"}) + category5.save + category6 = LinkedData::Models::Category.new({:name => "Test2 Category", :description => "This is a test category", :acronym => "TCG6"}) + category6.save + + # Creating the groups + group1 = LinkedData::Models::Group.new({:name => "Test1 Group", :description => "This is a test group", :acronym => "TESTG1"}) + group1.save + group2 = LinkedData::Models::Group.new({:name => "Test2 Group", :description => "This is a test group", :acronym => "TESTG2"}) + group2.save + o = LinkedData::Models::Ontology.new({ + acronym: "TEST1", + administeredBy: [user1, user2, user3, user4, user5, user6, user7], + name: "test 1", + hasDomain: [category1, category2, category3, category4, category5, category6], + group: [group1, group2] + }) + o.save + + otest = LinkedData::Models::Ontology.find("TEST1").first + + Benchmark.bm do |x| + x.report { otest.bring_remaining } + end + + assert_equal "test 1", otest.name + end + end From 41a2d9add1f6b69fe93b385e16255348423871cd Mon Sep 17 00:00:00 2001 From: = Date: Tue, 10 Feb 2026 16:03:57 -0800 Subject: [PATCH 38/69] added user OAuth authentication --- .../models/users/oauth_authentication.rb | 186 ++++++++++++++++++ .../models/users/user.rb | 74 ++++++- test/models/user/test_user_oauth.rb | 80 ++++++++ 3 files changed, 336 insertions(+), 4 deletions(-) create mode 100644 lib/ontologies_linked_data/models/users/oauth_authentication.rb create mode 100644 test/models/user/test_user_oauth.rb diff --git a/lib/ontologies_linked_data/models/users/oauth_authentication.rb b/lib/ontologies_linked_data/models/users/oauth_authentication.rb new file mode 100644 index 000000000..01e52adb4 --- /dev/null +++ b/lib/ontologies_linked_data/models/users/oauth_authentication.rb @@ -0,0 +1,186 @@ +require 'bcrypt' +require 'openssl' +require 'base64' +require 'json' +require 'jwt' +require 'faraday' +require 'active_support/core_ext/object/blank' + +module LinkedData + module Models + module Users + module OAuthAuthentication + + def self.included base + base.extend ClassMethods + end + + module ClassMethods + + def oauth_providers + LinkedData.settings.oauth_providers + end + + def oauth_authenticate(token, provider) + user_data = case provider.to_sym + when :github + auth_github(token) + when :google + auth_google(token) + when :orcid + auth_orcid(token) + when :keycloak + auth_keycloak(token) + else + nil + end + + create_if_not_exists(user_data) if user_data + end + + private + + def create_if_not_exists(user_data) + user = user_by_email(user_data[:email]) + + if user.nil? + auth_create_user(user_data) + else + sync_providers_id(user, user_data[:githubId], user_data[:orcidId]) + end + end + + def sync_providers_id(user, github_id, orcid_id) + user.bring_remaining + user.githubId = github_id if user.githubId.blank? && !github_id.blank? + user.orcidId = orcid_id if user.orcidId.blank? && !orcid_id.blank? + user.save(override_security: true) if user.valid? + user + end + + def auth_create_user(user_data) + user = User.new(user_data) + user.password = SecureRandom.hex(16) + + return nil unless user.valid? + + user.save(send_notifications: true) + user + end + + def user_by_email(email) + LinkedData::Models::User.where(email: email).first unless email.nil? + end + + def user_from_orcid_data(user_data) + { + email: user_data['email'], + firstName: user_data['name']['given-names'], + lastName: user_data['name']['family-name'], + username: user_data['email'].split('@').first, + orcidId: user_data['orcid'] + } + end + + def auth_orcid(token) + user_data = token_check(token, :orcid) + + return nil if user_data.nil? + + user_from_orcid_data user_data + + end + + def user_from_google_data(user_data) + { + email: user_data['email'], + firstName: user_data['given_name'], + lastName: user_data['family_name'], + username: user_data['email'].split('@').first + } + end + + def auth_google(token) + user_data = token_check(token, :google) + + return nil if user_data.nil? + + user_from_google_data user_data + end + + def auth_github(token) + user_data = token_check(token, :github) + + return nil if user_data.nil? + + user_from_github_data user_data + end + + def user_from_github_data(user_data) + { + email: user_data['email'], + username: user_data['login'], + firstName: user_data['name'].split(' ').first, + lastName: user_data['name'].split(' ').drop(1).join(' '), + githubId: user_data['login'] + } + end + + def user_from_keycloak_data(user_data) + { + email: user_data['email'], + username: user_data['preferred_username'], + firstName: user_data['given_name'], + lastName: user_data['family_name'] + } + end + + def auth_keycloak(token) + user_data = token_check(token, :keycloak) + + return nil if user_data.nil? + + user_from_keycloak_data user_data + end + + def token_check(token, provider) + provider_config = oauth_providers[provider.to_sym] + + return nil unless provider_config + + if provider_config[:check].eql?(:access_token) + access_token_check(token, provider_config[:link]) + elsif provider_config[:check].eql?(:jwt_token) + jwt_token_check(token, provider_config[:cert]) + end + end + + def jwt_token_check(jwt_token, cert) + decode_cert = Base64.decode64(cert) + rsa_public = OpenSSL::X509::Certificate.new(decode_cert).public_key + begin + JWT.decode(jwt_token, rsa_public, true, { algorithm: 'HS256' }) + rescue JWT::DecodeError + nil + end + end + + def access_token_check(token, link) + response = Faraday.new(url: link) do |faraday| + faraday.headers['Authorization'] = "Bearer #{token}" + faraday.adapter Faraday.default_adapter + end.get + + return nil unless response.success? + + JSON.parse(response.body) + end + end + + end + + end + + end +end + diff --git a/lib/ontologies_linked_data/models/users/user.rb b/lib/ontologies_linked_data/models/users/user.rb index e27cfbd1a..c42b3ea51 100644 --- a/lib/ontologies_linked_data/models/users/user.rb +++ b/lib/ontologies_linked_data/models/users/user.rb @@ -3,24 +3,32 @@ require 'ontologies_linked_data/models/users/authentication' require 'ontologies_linked_data/models/users/role' require 'ontologies_linked_data/models/users/subscription' +require 'ontologies_linked_data/models/users/oauth_authentication' module LinkedData module Models class User < LinkedData::Models::Base include BCrypt include LinkedData::Models::Users::Authentication + include LinkedData::Models::Users::OAuthAuthentication + include LinkedData::Concerns::Analytics + + ANALYTICS_REDIS_FIELD = "user_analytics" + PAGES_ANALYTICS_REDIS_FIELD = "pages_analytics" attr_accessor :show_apikey model :user, name_with: :username attribute :username, enforce: [:unique, :existence, :safe_text_56] - attribute :email, enforce: [:existence, :email] + attribute :email, enforce: [:unique, :existence, :email] attribute :role, enforce: [:role, :list], :default => lambda {|x| [LinkedData::Models::Users::Role.default]} attribute :firstName, enforce: [:safe_text_128] attribute :lastName, enforce: [:safe_text_128] + attribute :subscribed, default: false attribute :githubId, enforce: [:unique] attribute :orcidId, enforce: [:unique] attribute :created, enforce: [:date_time], :default => lambda { |record| DateTime.now } + attribute :lastLoginAt, enforce: [:date_time], :default => lambda { |record| DateTime.now } attribute :passwordHash, enforce: [:existence] attribute :apikey, enforce: [:unique], :default => lambda {|x| SecureRandom.uuid} attribute :subscription, enforce: [:list, :subscription] @@ -28,16 +36,19 @@ class User < LinkedData::Models::Base attribute :resetToken attribute :resetTokenExpireTime attribute :provisionalClasses, inverse: { on: :provisional_class, attribute: :creator } + attribute :createdOntologies, enforce: [:list], handler: :load_created_ontologies # Hypermedia settings embed :subscription embed_values :role => [:role] serialize_default :username, :email, :role, :apikey serialize_never :passwordHash, :show_apikey, :resetToken, :resetTokenExpireTime - serialize_filter lambda {|inst| show_apikey?(inst)} + serialize_filter lambda {|inst| filter_attributes(inst)} system_controlled :created, :resetToken, :resetTokenExpireTime + link_to LinkedData::Hypermedia::Link.new("createdOntologies", lambda {|s| "users/#{s.id.split('/').last}/ontologies"}, nil) + # Cache cache_timeout 3600 @@ -54,6 +65,23 @@ def self.show_apikey?(inst) end end + def self.show_lastLoginAt?(attrs) + unless Thread.current[:remote_user]&.admin? + return attrs - [:lastLoginAt] + end + return attrs + end + + def self.filter_attributes(inst) + attrs = show_apikey?(inst) + attrs = show_lastLoginAt?(attrs) + attrs + end + + def embedded_doc + "#{self.firstName} #{self.lastName} #{self.username}" + end + def initialize(attributes = {}) # Don't allow passwordHash to be set here attributes.delete(:passwordHash) @@ -69,13 +97,44 @@ def initialize(attributes = {}) self end + def update_last_login + self.lastLoginAt = DateTime.now + self.save(override_security: true) + end + def save(*args) # Reset ontology cache if user changes their custom set if LinkedData.settings.enable_http_cache && self.modified_attributes.include?(:customOntology) Ontology.cache_collection_invalidate OntologySubmission.cache_collection_invalidate end + super + + if args.first&.dig(:send_notifications) + begin + LinkedData::Utils::Notifications.new_user(self) + rescue StandardError => e + puts "Error on user creation notification: #{e.message}" + end + end + self + end + + def load_created_ontologies + ontologies = [] + q = Goo.sparql_query_client.select(:id, :acronym, :administeredBy).distinct + .from(Ontology.uri_type) + .where( + [:id, LinkedData::Models::Ontology.attribute_uri(:administeredBy), :administeredBy], + [:id, LinkedData::Models::Ontology.attribute_uri(:acronym), :acronym], + ) + .filter("?administeredBy = <#{self.id}>") + acronyms = q.execute.map { |o| o.acronym.to_s } + return ontologies if acronyms.empty? + filter_by_acronym = Goo::Filter.new(:acronym).regex("^(#{acronyms.join('|')})$") + ontologies = Ontology.where.include(Ontology.goo_attrs_to_load([:all])).filter(filter_by_acronym).all + return ontologies end def admin? @@ -95,12 +154,19 @@ def custom_ontology_id_set end def to_s - if self.bring?(:username) - LinkedData::Utils::Triples.last_iri_fragment self.id.to_s + if bring?(:username) + self.id.to_s else self.username.to_s end end + def self.analytics_redis_key + ANALYTICS_REDIS_FIELD + end + + def self.page_visits_analytics + load_data(PAGES_ANALYTICS_REDIS_FIELD) + end private diff --git a/test/models/user/test_user_oauth.rb b/test/models/user/test_user_oauth.rb new file mode 100644 index 000000000..0d8378ad1 --- /dev/null +++ b/test/models/user/test_user_oauth.rb @@ -0,0 +1,80 @@ +require_relative '../../test_case' + +class TestUserOAuthAuthentication < LinkedData::TestCase + + def self.before_suite + @@fake_responses = { + github: { + id: 123456789, + login: 'github_user', + email: 'github_user@example.com', + name: 'GitHub User', + avatar_url: 'https://avatars.githubusercontent.com/u/123456789' + }, + google: { + sub: 'google_user_id', + email: 'google_user@example.com', + name: 'Google User', + given_name: 'Google', + family_name: 'User', + picture: 'https://lh3.googleusercontent.com/a-/user-profile-image-url' + }, + orcid: { + orcid: '0000-0002-1825-0097', + email: 'orcid_user@example.com', + name: { + "family-name": 'ORCID', + "given-names": 'User' + } + } + } + end + + + def test_authentication_new_users + users = [] + + @@fake_responses.each do |provider, data| + WebMock.stub_request(:get, LinkedData::Models::User.oauth_providers[provider][:link]) + .to_return(status: 200, body: data.to_json, headers: { 'Content-Type' => 'application/json' }) + user = LinkedData::Models::User.oauth_authenticate('fake token', provider) + refute_nil user + assert user.is_a?(LinkedData::Models::User) + assert_equal user.email, data[:email] + users << user + end + + users.each(&:delete) + end + + def test_authentication_existent_users + users = [] + @@fake_responses.each do |provider, data| + user_hash = LinkedData::Models::User.send("user_from_#{provider}_data", data.stringify_keys) + + user = LinkedData::Models::User.new(user_hash) + user.githubId = nil + user.orcidId = nil + user.password = 'password' + + assert user.valid? + + user.save + + WebMock.stub_request(:get, LinkedData::Models::User.oauth_providers[provider][:link]) + .to_return(status: 200, body: data.to_json, headers: { 'Content-Type' => 'application/json' }) + auth_user = LinkedData::Models::User.oauth_authenticate('fake token', provider) + + assert_equal auth_user.id, user.id + + if provider.eql?(:github) + assert_equal data[:login], auth_user.githubId + elsif provider.eql?(:orcid) + assert_equal data[:orcid], auth_user.orcidId + end + users << user + end + users.each(&:delete) + end + +end From 1bf1c2d03d1995ea13ab34decb90c14ea6fb787e Mon Sep 17 00:00:00 2001 From: = Date: Wed, 11 Feb 2026 11:02:58 -0800 Subject: [PATCH 39/69] in user.rb, fixed embedded_doc and to_s methods --- lib/ontologies_linked_data/models/users/user.rb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/lib/ontologies_linked_data/models/users/user.rb b/lib/ontologies_linked_data/models/users/user.rb index c42b3ea51..058835e7d 100644 --- a/lib/ontologies_linked_data/models/users/user.rb +++ b/lib/ontologies_linked_data/models/users/user.rb @@ -79,7 +79,7 @@ def self.filter_attributes(inst) end def embedded_doc - "#{self.firstName} #{self.lastName} #{self.username}" + self.to_s end def initialize(attributes = {}) @@ -154,12 +154,13 @@ def custom_ontology_id_set end def to_s - if bring?(:username) - self.id.to_s + if self.bring?(:username) + LinkedData::Utils::Triples.last_iri_fragment(self.id.to_s) else self.username.to_s end end + def self.analytics_redis_key ANALYTICS_REDIS_FIELD end From 3204c0a830d344eb9ae1db82c22b46be1ef468b3 Mon Sep 17 00:00:00 2001 From: = Date: Wed, 11 Feb 2026 11:03:39 -0800 Subject: [PATCH 40/69] added embedded_doc methods for contact and metric --- lib/ontologies_linked_data/models/contact.rb | 7 +++++++ lib/ontologies_linked_data/models/metric.rb | 8 ++++++++ 2 files changed, 15 insertions(+) diff --git a/lib/ontologies_linked_data/models/contact.rb b/lib/ontologies_linked_data/models/contact.rb index 2306135dc..387c9f38c 100644 --- a/lib/ontologies_linked_data/models/contact.rb +++ b/lib/ontologies_linked_data/models/contact.rb @@ -6,6 +6,13 @@ class Contact < LinkedData::Models::Base attribute :email, enforce: [:existence, :email] embedded true + + def embedded_doc + bring(:name) if bring?(:name) + bring(:email) if bring?(:email) + + "#{self.name} | #{self.email}" + end end end end diff --git a/lib/ontologies_linked_data/models/metric.rb b/lib/ontologies_linked_data/models/metric.rb index 102d41f77..f7f107c40 100644 --- a/lib/ontologies_linked_data/models/metric.rb +++ b/lib/ontologies_linked_data/models/metric.rb @@ -51,6 +51,14 @@ def self.metrics_id_generator(m) raise ArgumentError, "Metrics id needs to be set" #return RDF::URI.new(m.submission.id.to_s + "/metrics") end + + def embedded_doc + doc = indexable_object + doc.delete(:resource_model) + doc.delete(:resource_id) + doc.delete(:id) + doc + end end end end From 05d3014c8d47288c0e6acf9799336731d27c9d60 Mon Sep 17 00:00:00 2001 From: = Date: Wed, 11 Feb 2026 13:48:21 -0800 Subject: [PATCH 41/69] more robust authorization module with ability to extract api key from request header --- .../security/authorization.rb | 158 ++++++++++++------ 1 file changed, 104 insertions(+), 54 deletions(-) diff --git a/lib/ontologies_linked_data/security/authorization.rb b/lib/ontologies_linked_data/security/authorization.rb index 7e2463268..fdc14aa21 100644 --- a/lib/ontologies_linked_data/security/authorization.rb +++ b/lib/ontologies_linked_data/security/authorization.rb @@ -4,46 +4,52 @@ module LinkedData module Security class Authorization APIKEYS_FOR_AUTHORIZATION = {} + USER_APIKEY_PARAM = 'userapikey'.freeze + API_KEY_PARAM = 'apikey'.freeze def initialize(app = nil) @app = app end ROUTES_THAT_BYPASS_SECURITY = Set.new([ - "/", - "/documentation", - "/jsonview/jsonview.css", - "/jsonview/jsonview.js" - ]) + "/", + "/documentation", + "/jsonview/jsonview.css", + "/jsonview/jsonview.js" + ]) def call(env) req = Rack::Request.new(env) params = req.params + apikey = find_apikey(env, params) + status = 200 + error_message = '' - unless apikey + if !apikey status = 401 - response = { - status: status, - error: "You must provide an API Key either using the query-string parameter `apikey` or the `Authorization` header: `Authorization: apikey token=my_apikey`. " + \ - "Your API Key can be obtained by logging in at #{LinkedData.settings.ui_host}/account" - } - end - - if status != 401 && !authorized?(apikey, env) + error_message = <<-MESSAGE + You must provide an API Key either using the query-string parameter `apikey` or the `Authorization` header: `Authorization: apikey token=my_apikey`. + Your API Key can be obtained by logging in at #{LinkedData.settings.ui_host}/account" + MESSAGE + elsif !authorized?(apikey, env) status = 401 - response = { - status: status, - error: "You must provide a valid API Key. " + \ - "Your API Key can be obtained by logging in at #{LinkedData.settings.ui_host}/account" - } + error_message = "You must provide a valid API Key. Your API Key can be obtained by logging in at #{LinkedData.settings.ui_host}/account" end - if status == 401 && !bypass?(env) + response = { + status: status, + error: error_message + } + + if status.eql?(401) && !bypass?(env) LinkedData::Serializer.build_response(env, status: status, body: response) else + # unfrozen params so that they can be encoded by Rack using occurring after updating the gem RDF to v3.0 + env["rack.request.form_hash"]&.transform_values!(&:dup) + env["rack.request.query_hash"]&.transform_values!(&:dup) status, headers, response = @app.call(env) - apikey_cookie(env, headers, apikey, params) + save_apikey_in_cookie(env, headers, apikey, params) [status, headers, response] end end @@ -57,57 +63,56 @@ def bypass?(env) ## # Inject a cookie with the API Key if it is present and we're in HTML content type - def apikey_cookie(env, headers, apikey, params) + COOKIE_APIKEY_PARAM = "ncbo_apikey" + + def save_apikey_in_cookie(env, headers, apikey, params) # If we're using HTML, inject the apikey in a cookie (ignores bad accept headers) + best = nil begin best = LinkedData::Serializer.best_response_type(env, params) - rescue LinkedData::Serializer::AcceptHeaderError; end - if best == LinkedData::MediaTypes::HTML - Rack::Utils.set_cookie_header!(headers, "ncbo_apikey", {:value => apikey, :path => "/", :expires => Time.now+90*24*60*60}) + rescue LinkedData::Serializer::AcceptHeaderError + # Ignored end + + return unless best == LinkedData::MediaTypes::HTML + + Rack::Utils.set_cookie_header!(headers, COOKIE_APIKEY_PARAM, { + value: apikey, + path: '/', + expires: Time.now + 90 * 24 * 60 * 60 + }) end def find_apikey(env, params) - apikey = nil - header_auth = env["HTTP_AUTHORIZATION"] || env["Authorization"] - if params["apikey"] && params["userapikey"] - apikey_authed = authorized?(params["apikey"], env) - return unless apikey_authed - apikey = params["userapikey"] - elsif params["apikey"] - apikey = params["apikey"] - elsif apikey.nil? && header_auth - token = Rack::Utils.parse_query(header_auth.split(" ")[1]) - return unless token["token"] - - # Strip spaces from start and end of string - apikey = token["token"].gsub(/\"/, "") - # If the user apikey is passed, use that instead - if token["userapikey"] && !token["userapikey"].empty? - apikey_authed = authorized?(apikey, env) - return unless apikey_authed - apikey = token["userapikey"].gsub(/\"/, "") - end - elsif apikey.nil? && env["HTTP_COOKIE"] && env["HTTP_COOKIE"].include?("ncbo_apikey") - cookie = Rack::Utils.parse_query(env["HTTP_COOKIE"]) - apikey = cookie["ncbo_apikey"] if cookie["ncbo_apikey"] - end - apikey + apikey = user_apikey(env, params) + return apikey if apikey + + apikey = params[API_KEY_PARAM] + return apikey if apikey + + apikey = request_header_apikey(env) + return apikey if apikey + + cookie_apikey(env) end def authorized?(apikey, env) return false if apikey.nil? + if APIKEYS_FOR_AUTHORIZATION.key?(apikey) store_user(APIKEYS_FOR_AUTHORIZATION[apikey], env) else - users = LinkedData::Models::User.where(apikey: apikey).include(LinkedData::Models::User.attributes(:all)).to_a - return false if users.empty? + user = LinkedData::Models::User.where(apikey: apikey) + .include(LinkedData::Models::User.attributes(:all)) + .first + return false if user.nil? + # This will kind-of break if multiple apikeys exist # Though it is also kind-of ok since we just want to know if a user with corresponding key exists - user = users.first + store_user(user, env) end - return true + true end def store_user(user, env) @@ -115,6 +120,51 @@ def store_user(user, env) env.update("REMOTE_USER" => user) end + private + + def request_header_apikey(env) + header_auth = get_header_auth(env) + return if header_auth.empty? + + auth_type, token_string = header_auth.split(/\s+/, 2) + return unless auth_type&.downcase == API_KEY_PARAM + return if token_string.nil? || token_string.empty? + + token = Rack::Utils.parse_query(token_string) + return if token['token'].nil? || token['token'].empty? + # Strip spaces from start and end of string + apikey = token['token'].gsub(/\"/, "") + # If the user apikey is passed, use that instead + if token[USER_APIKEY_PARAM] && !token[USER_APIKEY_PARAM].empty? + apikey_authed = authorized?(apikey, env) + return unless apikey_authed + + apikey = token[USER_APIKEY_PARAM].gsub(/\"/, "") + end + apikey + end + + def cookie_apikey(env) + return unless env["HTTP_COOKIE"] + + cookie = Rack::Utils.parse_query(env['HTTP_COOKIE']) + cookie[COOKIE_APIKEY_PARAM] if cookie['ncbo_apikey'] + end + + def get_header_auth(env) + env["HTTP_AUTHORIZATION"] || env["Authorization"] || '' + end + + def user_apikey(env, params) + return unless (params["apikey"] && params["userapikey"]) + + apikey_authed = authorized?(params[API_KEY_PARAM], env) + + return unless apikey_authed + + params[USER_APIKEY_PARAM] + end + end end end From 77863e65a4b03d8aa627db89cd249956d7253a2e Mon Sep 17 00:00:00 2001 From: = Date: Wed, 11 Feb 2026 14:44:19 -0800 Subject: [PATCH 42/69] added test_search.rb unit tests --- .../submission_validators.rb | 2 +- .../models/ontology_submission.rb | 3 +- test/models/test_search.rb | 166 ++++++++++++++++++ 3 files changed, 168 insertions(+), 3 deletions(-) create mode 100644 test/models/test_search.rb diff --git a/lib/ontologies_linked_data/concerns/ontology_submissions/submission_validators.rb b/lib/ontologies_linked_data/concerns/ontology_submissions/submission_validators.rb index 81adc3aa0..93ddb9cb6 100644 --- a/lib/ontologies_linked_data/concerns/ontology_submissions/submission_validators.rb +++ b/lib/ontologies_linked_data/concerns/ontology_submissions/submission_validators.rb @@ -254,7 +254,7 @@ def ontology_has_domain(sub) def default_sparql_endpoint(sub) url = LinkedData.settings.sparql_endpoint_url || '' - url.strip.blank? ? [] : [RDF::URI.new(url)] + url.strip.blank? ? [] : [RDF::URI.new(url)] end def open_search_default(sub) RDF::URI.new("#{LinkedData.settings.rest_url_prefix}search?ontologies=#{sub.ontology.acronym}&q=") diff --git a/lib/ontologies_linked_data/models/ontology_submission.rb b/lib/ontologies_linked_data/models/ontology_submission.rb index c0615d364..1397de795 100644 --- a/lib/ontologies_linked_data/models/ontology_submission.rb +++ b/lib/ontologies_linked_data/models/ontology_submission.rb @@ -128,8 +128,7 @@ class OntologySubmission < LinkedData::Models::Base attribute :uriLookupEndpoint, namespace: :void, type: :uri, default: -> (s) { uri_lookup_default(s) } attribute :openSearchDescription, namespace: :void, type: :uri, default: -> (s) { open_search_default(s) } attribute :source, namespace: :dct, type: :list - attribute :endpoint, namespace: :sd, type: %i[uri list], - default: ->(s) { default_sparql_endpoint(s) } + attribute :endpoint, namespace: :sd, type: %i[uri list], default: ->(s) { default_sparql_endpoint(s) } attribute :includedInDataCatalog, namespace: :schema, type: %i[list uri] # Relations diff --git a/test/models/test_search.rb b/test/models/test_search.rb new file mode 100644 index 000000000..ef6415425 --- /dev/null +++ b/test/models/test_search.rb @@ -0,0 +1,166 @@ +require_relative '../test_case' + +class TestSearch < LinkedData::TestCase + + def self.after_suite + backend_4s_delete + LinkedData::Models::Ontology.indexClear + Goo.search_client(:ontology_data)&.clear_all_data + end + + def setup + self.class.after_suite + end + + def test_search_ontology + _, _, created_ontologies = create_ontologies_and_submissions({ + process_submission: true, + process_options: { + process_rdf: true, + generate_missing_labels: false, + extract_metadata: false, run_metrics: true + }, + acronym: 'BROTEST', + name: 'ontTEST Bla', + file_path: '../../../../test/data/ontology_files/BRO_v3.2.owl', + ont_count: 2, + submission_count: 2 + }) + ontologies = LinkedData::Models::Ontology.search('*:*', { fq: 'resource_model: "ontology"' })['response']['docs'] + + assert_equal 2, ontologies.size + ontologies.each do |ont| + select_ont = created_ontologies.select { |ont_created| ont_created.id.to_s.eql?(ont['id']) }.first + refute_nil select_ont + select_ont.bring_remaining + assert_equal ont['name_text'], select_ont.name + assert_equal ont['acronym_text'], select_ont.acronym + assert_equal ont['viewingRestriction_t'], select_ont.viewingRestriction + assert_equal ont['ontologyType_t'], select_ont.ontologyType.id + end + + submissions = LinkedData::Models::Ontology.search('*:*', { fq: 'resource_model: "ontology_submission"' })['response']['docs'] + assert_equal 4, submissions.size + submissions.each do |sub| + created_sub = LinkedData::Models::OntologySubmission.find(RDF::URI.new(sub['id'])).first&.bring_remaining + refute_nil created_sub + assert_equal sub['description_text'], created_sub.description + assert_equal sub['submissionId_i'], created_sub.submissionId + assert_equal sub['uri_text'], created_sub.uri + assert_equal sub['status_t'], created_sub.status + assert_equal sub['deprecated_b'], created_sub.deprecated + assert_equal sub['hasOntologyLanguage_t'], created_sub.hasOntologyLanguage.id.to_s + assert_equal sub['released_dt'], created_sub.released.utc.strftime('%Y-%m-%dT%H:%M:%SZ') + assert_equal sub['creationDate_dt'], created_sub.creationDate.utc.strftime('%Y-%m-%dT%H:%M:%SZ') + assert_equal(sub['contact_txt'], created_sub.contact.map { |x| x.bring_remaining.embedded_doc }) + assert_equal sub['dataDump_t'], created_sub.dataDump + assert_equal sub['csvDump_t'], created_sub.csvDump + assert_equal sub['uriLookupEndpoint_t'], created_sub.uriLookupEndpoint + assert_equal sub['openSearchDescription_t'], created_sub.openSearchDescription + assert_equal sub['uploadFilePath_t'], created_sub.uploadFilePath + assert_equal sub['submissionStatus_txt'].sort, created_sub.submissionStatus.map { |x| x.id.to_s }.sort + + created_sub.metrics.bring_remaining + + assert_equal sub['metrics_classes_i'], created_sub.metrics.classes + assert_equal sub['metrics_individuals_i'], created_sub.metrics.individuals + assert_equal sub['metrics_properties_i'], created_sub.metrics.properties + assert_equal sub['metrics_maxDepth_i'], created_sub.metrics.maxDepth + assert_equal sub['metrics_maxChildCount_i'], created_sub.metrics.maxChildCount + assert_equal sub['metrics_averageChildCount_i'], created_sub.metrics.averageChildCount + assert_equal sub['metrics_classesWithOneChild_i'], created_sub.metrics.classesWithOneChild + assert_equal sub['metrics_classesWithMoreThan25Children_i'], created_sub.metrics.classesWithMoreThan25Children + assert_equal sub['metrics_classesWithNoDefinition_i'], created_sub.metrics.classesWithNoDefinition + + embed_doc = created_sub.ontology.bring_remaining.embedded_doc + embed_doc.each do |k, v| + if v.is_a?(Array) + assert_equal v, Array(sub["ontology_#{k}"]) + else + assert_equal v, sub["ontology_#{k}"] + end + end + end + end + + def test_search_ontology_data + create_ontologies_and_submissions({ + process_submission: true, + process_options: { + process_rdf: true, + extract_metadata: false, + generate_missing_labels: false, + index_all_data: true + }, + acronym: 'BROTEST', + name: 'ontTEST Bla', + file_path: 'test/data/ontology_files/thesaurusINRAE_nouv_structure.skos', + ont_count: 1, + submission_count: 1, + ontology_format: 'SKOS' + }) + ont_sub = LinkedData::Models::Ontology.find('BROTEST-0').first + ont_sub = ont_sub.latest_submission + + refute_empty(ont_sub.submissionStatus.select { |x| x.id['INDEXED_ALL_DATA'] }) + + conn = Goo.search_client(:ontology_data) + + count_ids = Goo.sparql_query_client.query("SELECT (COUNT( DISTINCT ?id) as ?c) FROM <#{ont_sub.id}> WHERE {?id ?p ?v}") + .first[:c] + .to_i + + total_triples = Goo.sparql_query_client.query("SELECT (COUNT(*) as ?c) FROM <#{ont_sub.id}> WHERE {?s ?p ?o}").first[:c].to_i + + response = conn.search('*', rows: count_ids + 100) + index_total_triples = response['response']['docs'].map do |doc| + count = 0 + doc.each_value do |v| + count += Array(v).size + end + count -= 6 + count + end.sum + + # TODO: fix maybe in future sometime randomly don't index excactly all the triples + assert_in_delta total_triples, index_total_triples, 100 + assert_in_delta count_ids, response['response']['numFound'], 100 + + response = conn.search('*', fq: ' resource_id:"http://opendata.inrae.fr/thesaurusINRAE/c_10065"') + + assert_equal 1, response['response']['numFound'] + doc = response['response']['docs'].first + + expected_doc = { + 'id' => 'http://opendata.inrae.fr/thesaurusINRAE/c_10065_BROTEST-0', + 'submission_id_t' => 'http://data.bioontology.org/ontologies/BROTEST-0/submissions/1', + 'ontology_t' => 'BROTEST-0', + 'resource_id' => 'http://opendata.inrae.fr/thesaurusINRAE/c_10065', + 'type_txt' => %w[http://www.w3.org/2004/02/skos/core#Concept http://www.w3.org/2002/07/owl#NamedIndividual], + 'http___www.w3.org_2004_02_skos_core_inScheme_txt' => %w[http://opendata.inrae.fr/thesaurusINRAE/thesaurusINRAE http://opendata.inrae.fr/thesaurusINRAE/mt_53], + 'http___www.w3.org_2004_02_skos_core_broader_t' => 'http://opendata.inrae.fr/thesaurusINRAE/c_9937', + 'http___www.w3.org_2004_02_skos_core_altLabel_txt' => ['GMO food', + 'aliment transgénique', + 'aliment OGM', + 'transgenic food'], + 'http___www.w3.org_2004_02_skos_core_prefLabel_txt' => ['genetically modified food', + 'aliment génétiquement modifié'], + 'resource_model' => 'ontology_submission' + } + + doc.delete('_version_') + + assert_equal expected_doc['id'], doc['id'] + assert_equal expected_doc['submission_id_t'], doc['submission_id_t'] + assert_equal expected_doc['ontology_t'], doc['ontology_t'] + assert_equal expected_doc['resource_id'], doc['resource_id'] + assert_equal expected_doc['type_txt'].sort, doc['type_txt'].sort + assert_equal expected_doc['http___www.w3.org_2004_02_skos_core_inScheme_txt'].sort, doc['http___www.w3.org_2004_02_skos_core_inScheme_txt'].sort + assert_equal expected_doc['http___www.w3.org_2004_02_skos_core_broader_t'], doc['http___www.w3.org_2004_02_skos_core_broader_t'] + assert_equal expected_doc['http___www.w3.org_2004_02_skos_core_altLabel_txt'].sort, doc['http___www.w3.org_2004_02_skos_core_altLabel_txt'].sort + assert_equal expected_doc['http___www.w3.org_2004_02_skos_core_prefLabel_txt'].sort, doc['http___www.w3.org_2004_02_skos_core_prefLabel_txt'].sort + assert_equal expected_doc['resource_model'], doc['resource_model'] + end + +end + From 653dc83e9b3f9c4a2d4d55ce36001ac1375d8780 Mon Sep 17 00:00:00 2001 From: = Date: Wed, 11 Feb 2026 15:17:27 -0800 Subject: [PATCH 43/69] updated test_http_cache for multi-backend compatibility --- test/http_cache/test_http_cache.rb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/http_cache/test_http_cache.rb b/test/http_cache/test_http_cache.rb index 782ea72b5..c6e9b9e3a 100644 --- a/test/http_cache/test_http_cache.rb +++ b/test/http_cache/test_http_cache.rb @@ -24,7 +24,7 @@ def self.after_suite def _ontology_and_class results = create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: true) ontology = results[2].first - cls = LinkedData::Models::Class.where.include(:prefLabel).in(ontology.latest_submission).page(1, 1).first + cls = LinkedData::Models::Class.where.include(:prefLabel).in(ontology.latest_submission).first return ontology, cls end @@ -57,6 +57,7 @@ def test_cache_segment_proper_setup end def test_cache_segment_invalidate + create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: true) classes = LinkedData::Models::Class.where.include(:prefLabel).in(@@ontology.latest_submission).page(1, 100).to_a classes.each {|c| c.cache_write} last_modified_values = classes.map {|c| c.last_modified} @@ -67,6 +68,7 @@ def test_cache_segment_invalidate end def test_cache_segment_invalidate_when_member_invalidates + create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: true) classes = LinkedData::Models::Class.where.include(:prefLabel).in(@@ontology.latest_submission).page(1, 100).to_a classes.each {|c| c.cache_write} last_modified_values = classes.map {|c| c.last_modified} @@ -137,4 +139,4 @@ def test_cache_invalidate_all assert_equal [], LinkedData::HTTPCache.keys_for_invalidate_all end -end \ No newline at end of file +end From b8ac19bae109c5a6c712131f7994ad977c437f47 Mon Sep 17 00:00:00 2001 From: = Date: Wed, 11 Feb 2026 22:40:07 -0800 Subject: [PATCH 44/69] fixed a tricky error that happens in a specific test execution order --- test/models/user/test_subscription.rb | 24 +++++++++++++++++++++--- test/util/test_notifications.rb | 4 +--- 2 files changed, 22 insertions(+), 6 deletions(-) diff --git a/test/models/user/test_subscription.rb b/test/models/user/test_subscription.rb index 210b095c0..b28219199 100644 --- a/test/models/user/test_subscription.rb +++ b/test/models/user/test_subscription.rb @@ -3,9 +3,27 @@ class TestSubscription < LinkedData::TestCase def self.before_suite - @@ont = LinkedData::SampleData::Ontology.create_ontologies_and_submissions(ont_count: 1, submission_count: 1)[2].first - @@ont.bring_remaining - @@user = @@ont.administeredBy.first + @@ont = LinkedData::SampleData::Ontology + .create_ontologies_and_submissions(ont_count: 1, submission_count: 1)[2].first + @@ont.bring(:administeredBy) + + candidate = @@ont.administeredBy&.first + @@user = candidate && LinkedData::Models::User.find(candidate.id) + .include(:username, :email, :passwordHash, :subscription) + .first + + unless @@user&.valid? + suffix = SecureRandom.hex(4) + @@user = LinkedData::Models::User.new( + username: "subscription_user_#{suffix}", + email: "subscription_user_#{suffix}@example.org", + password: "password" + ) + @@user.save + @@ont.administeredBy = [@@user] + @@ont.save + end + @@user.bring_remaining end diff --git a/test/util/test_notifications.rb b/test/util/test_notifications.rb index 4af2af35c..a0f952367 100644 --- a/test/util/test_notifications.rb +++ b/test/util/test_notifications.rb @@ -135,11 +135,9 @@ def test_disable_administrative_notifications end def test_remote_ontology_pull_notification - recipients = ['test@example.org'] _ont_count, _acronyms, ontologies = LinkedData::SampleData::Ontology.create_ontologies_and_submissions( - ont_count: 1, submission_count: 1, process_submission: false + ont_count: 1, submission_count: 1, acronym: "PULL-NOTIF-ONT", process_submission: false ) - ont = LinkedData::Models::Ontology.find(ontologies[0].id) .include(:acronym, :administeredBy, :name, :submissions).first suffix = SecureRandom.hex(4) From 8402ac350d44f8ef9ec78c63fd200ea5835ebbe8 Mon Sep 17 00:00:00 2001 From: = Date: Wed, 11 Feb 2026 22:41:23 -0800 Subject: [PATCH 45/69] a cosmetic fix --- test/models/test_ontology_submission.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/models/test_ontology_submission.rb b/test/models/test_ontology_submission.rb index 721588cc6..6e2e7a203 100644 --- a/test/models/test_ontology_submission.rb +++ b/test/models/test_ontology_submission.rb @@ -663,10 +663,10 @@ def test_submission_parse_gzip def test_download_ontology_file begin - server_url, server_thread, server_port = start_server + server_url, server_thread, _ = start_server sleep 3 # Allow the server to startup assert(server_thread.alive?, msg="Rack::Server thread should be alive, it's not!") - ont_count, ont_names, ont_models = create_ontologies_and_submissions(ont_count: 1, submission_count: 1) + _, _, ont_models = create_ontologies_and_submissions(ont_count: 1, submission_count: 1) ont = ont_models.first assert(ont.instance_of?(LinkedData::Models::Ontology), "ont is not an ontology: #{ont}") sub = ont.bring(:submissions).submissions.first From e16c953fcece45d46c964f6d7d379b596d03927d Mon Sep 17 00:00:00 2001 From: = Date: Wed, 11 Feb 2026 22:42:04 -0800 Subject: [PATCH 46/69] a cosmetic fix --- test/models/test_ontology.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/models/test_ontology.rb b/test/models/test_ontology.rb index c229aa166..b3cef4b74 100644 --- a/test/models/test_ontology.rb +++ b/test/models/test_ontology.rb @@ -5,7 +5,7 @@ class TestOntology < LinkedData::TestOntologyCommon def self.before_suite - url , @@thread, @@port= self.new('').start_server + _, @@thread, @@port = self.new('').start_server end def self.after_suite From 5225378993f3e6efa9080b0cf91791f41920e2a1 Mon Sep 17 00:00:00 2001 From: = Date: Wed, 11 Feb 2026 22:43:14 -0800 Subject: [PATCH 47/69] multi-backend compatibility fixes --- test/models/test_ontology_common.rb | 11 +++++++++++ test/test_case.rb | 7 ++++++- 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/test/models/test_ontology_common.rb b/test/models/test_ontology_common.rb index f85b9dc3a..431a4ba4c 100644 --- a/test/models/test_ontology_common.rb +++ b/test/models/test_ontology_common.rb @@ -3,6 +3,7 @@ module LinkedData class TestOntologyCommon < LinkedData::TestCase + def create_count_mapping count = LinkedData::Models::MappingCount.where.all.length unless count > 2 @@ -11,6 +12,7 @@ def create_count_mapping end count end + def submission_dependent_objects(format, acronym, user_name, name_ont) #ontology format owl = LinkedData::Models::OntologyFormat.where(:acronym => format).first @@ -52,6 +54,10 @@ def submission_dependent_objects(format, acronym, user_name, name_ont) # delete = true # delete any existing submissions ############################################## def submission_parse(acronym, name, ontologyFile, id, parse_options={}, set_attributes={}) + if Goo.backend_vo? + old_slices = Goo.slice_loading_size + Goo.slice_loading_size = 20 + end return if ENV["SKIP_PARSING"] parse_options[:process_rdf].nil? && parse_options[:process_rdf] = true parse_options[:index_search].nil? && parse_options[:index_search] = false @@ -116,6 +122,10 @@ def submission_parse(acronym, name, ontologyFile, id, parse_options={}, set_attr rescue Exception => e puts "Error, logged in #{tmp_log.instance_variable_get("@logdev").dev.path}" raise e + ensure + if Goo.backend_vo? + Goo.slice_loading_size = old_slices + end end end @@ -247,6 +257,7 @@ def port_in_use?(port) true end end + end end diff --git a/test/test_case.rb b/test/test_case.rb index 46a479944..4f9ef424c 100644 --- a/test/test_case.rb +++ b/test/test_case.rb @@ -245,7 +245,11 @@ def self.backend_4s_delete raise StandardError, 'Too many triples in KB, does not seem right to run tests' unless count_pattern('?s ?p ?o') < 400000 - Goo.sparql_update_client.update('DELETE {?s ?p ?o } WHERE { ?s ?p ?o }') + graphs = Goo.sparql_query_client.query("SELECT DISTINCT ?g WHERE { GRAPH ?g { ?s ?p ?o . } }") + graphs.each_solution do |sol| + Goo.sparql_data_client.delete_graph(sol[:g]) + end + LinkedData::Models::SubmissionStatus.init_enum LinkedData::Models::OntologyType.init_enum LinkedData::Models::OntologyFormat.init_enum @@ -253,4 +257,5 @@ def self.backend_4s_delete LinkedData::Models::Users::NotificationType.init_enum end end + end From e2d663895a13871e00f75165b152ac20ccaee5bb Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Thu, 12 Feb 2026 10:52:28 -0800 Subject: [PATCH 48/69] CI: refactor docker-based test runner and add linux container tests (#264) CI: refactor docker-based test runner and add linux container tests see https://github.com/ncbo/goo/pull/173 --- .github/workflows/ruby-unit-tests.yml | 27 +- Dockerfile | 7 +- dev/compose/linux/ag.yml | 16 ++ dev/compose/linux/docker-compose.ci.yml | 3 + dev/compose/linux/fs.yml | 13 + dev/compose/linux/gd.yml | 16 ++ dev/compose/linux/no-ports.yml | 13 + dev/compose/linux/vo.yml | 16 ++ docker-compose.yml | 172 ++++++------- rakelib/docker_based_test.rake | 240 ++++++++++++++++++ .../backends/graphdb/graphdb-repo-config.ttl | 33 +++ .../backends/graphdb/graphdb-test-load.nt | 0 .../virtuoso-grant-write-sparql-access.sql | 3 + 13 files changed, 453 insertions(+), 106 deletions(-) create mode 100644 dev/compose/linux/ag.yml create mode 100644 dev/compose/linux/docker-compose.ci.yml create mode 100644 dev/compose/linux/fs.yml create mode 100644 dev/compose/linux/gd.yml create mode 100644 dev/compose/linux/no-ports.yml create mode 100644 dev/compose/linux/vo.yml create mode 100644 rakelib/docker_based_test.rake create mode 100644 test/fixtures/backends/graphdb/graphdb-repo-config.ttl create mode 100644 test/fixtures/backends/graphdb/graphdb-test-load.nt create mode 100644 test/fixtures/backends/virtuoso_initdb_d/virtuoso-grant-write-sparql-access.sql diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml index d8eadf4f0..63d322633 100644 --- a/.github/workflows/ruby-unit-tests.yml +++ b/.github/workflows/ruby-unit-tests.yml @@ -10,25 +10,28 @@ on: jobs: test: + env: + RUBY_VERSION: '3.2' + COMPOSE_CMD: > + docker compose -f docker-compose.yml + -f dev/compose/linux/${{ matrix.triplestore }}.yml + --profile linux + --profile ${{ matrix.triplestore }} strategy: fail-fast: false matrix: - backend: ['ruby', 'ruby-agraph'] # ruby runs tests with 4store backend and ruby-agraph runs with AllegroGraph backend + #triplestore: [ 'fs', 'ag', 'vo', 'gd' ] + triplestore: [ 'fs', 'ag' ] runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - name: Set up solr configsets - run: ./test/solr/generate_ncbo_configsets.sh - - name: create config.rb file - run: cp config/config.test.rb config/config.rb - - name: Build docker compose - run: docker compose --profile 4store build # profile flag is set in order to build all containers in this step + - name: Build docker container + run: > + $COMPOSE_CMD build - name: Run unit tests - # unit tests are run inside a container - # http://docs.codecov.io/docs/testing-with-docker - run: | - ci_env=`bash <(curl -s https://codecov.io/env)` - docker compose run $ci_env -e CI --rm ${{ matrix.backend }} bundle exec rake test TESTOPTS='-v' + run: > + $COMPOSE_CMD run -v "$PWD/coverage:/app/coverage" -e CI=true + test-linux bundle exec rake test TESTOPTS="-v" - name: Upload coverage reports to Codecov uses: codecov/codecov-action@v5 with: diff --git a/Dockerfile b/Dockerfile index b9529fd14..0b920394f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -ARG RUBY_VERSION=3.1 +ARG RUBY_VERSION=3.2 ARG DISTRO=bullseye FROM ruby:$RUBY_VERSION-$DISTRO @@ -8,17 +8,22 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ git \ libxml2 \ libxslt-dev \ + libxslt1-dev zlib1g-dev \ openjdk-11-jre-headless \ raptor2-utils \ && rm -rf /var/lib/apt/lists/* WORKDIR /app +# set default test config +COPY config/config.test.rb config/config.rb + COPY Gemfile* *.gemspec ./ # Copy only the `version.rb` file to prevent missing file errors! COPY lib/ontologies_linked_data/version.rb lib/ontologies_linked_data/ + #Install the exact Bundler version from Gemfile.lock (if it exists) RUN gem update --system && \ if [ -f Gemfile.lock ]; then \ diff --git a/dev/compose/linux/ag.yml b/dev/compose/linux/ag.yml new file mode 100644 index 000000000..b56d9c8e5 --- /dev/null +++ b/dev/compose/linux/ag.yml @@ -0,0 +1,16 @@ +services: + test-linux: + environment: + GOO_BACKEND_NAME: allegrograph + GOO_PORT: 10035 + GOO_HOST: agraph-ut + GOO_PATH_QUERY: /repositories/ontoportal_test + GOO_PATH_DATA: /repositories/ontoportal_test/statements + GOO_PATH_UPDATE: /repositories/ontoportal_test/statements + depends_on: + solr-ut: + condition: service_healthy + redis-ut: + condition: service_healthy + agraph-ut: + condition: service_healthy diff --git a/dev/compose/linux/docker-compose.ci.yml b/dev/compose/linux/docker-compose.ci.yml new file mode 100644 index 000000000..4397c33d6 --- /dev/null +++ b/dev/compose/linux/docker-compose.ci.yml @@ -0,0 +1,3 @@ +services: + test-linux: + image: ontologies_linked_data-test-linux:ci diff --git a/dev/compose/linux/fs.yml b/dev/compose/linux/fs.yml new file mode 100644 index 000000000..27acf4b33 --- /dev/null +++ b/dev/compose/linux/fs.yml @@ -0,0 +1,13 @@ +services: + test-linux: + environment: + GOO_BACKEND_NAME: '4store' + GOO_HOST: 4store-ut + GOO_PORT: 9000 + depends_on: + solr-ut: + condition: service_healthy + redis-ut: + condition: service_healthy + 4store-ut: + condition: service_healthy diff --git a/dev/compose/linux/gd.yml b/dev/compose/linux/gd.yml new file mode 100644 index 000000000..87576c734 --- /dev/null +++ b/dev/compose/linux/gd.yml @@ -0,0 +1,16 @@ +services: + test-linux: + environment: + GOO_BACKEND_NAME: graphdb + GOO_PORT: 7200 + GOO_HOST: graphdb-ut + GOO_PATH_QUERY: /repositories/ontoportal_test + GOO_PATH_DATA: /repositories/ontoportal_test/statements + GOO_PATH_UPDATE: /repositories/ontoportal_test/statements + depends_on: + solr-ut: + condition: service_healthy + redis-ut: + condition: service_healthy + graphdb-ut: + condition: service_healthy diff --git a/dev/compose/linux/no-ports.yml b/dev/compose/linux/no-ports.yml new file mode 100644 index 000000000..f42191b93 --- /dev/null +++ b/dev/compose/linux/no-ports.yml @@ -0,0 +1,13 @@ +services: + redis-ut: + ports: [] + solr-ut: + ports: [] + agraph-ut: + ports: [] + 4store-ut: + ports: [] + virtuoso-ut: + ports: [] + graphdb-ut: + ports: [] diff --git a/dev/compose/linux/vo.yml b/dev/compose/linux/vo.yml new file mode 100644 index 000000000..c47dd6543 --- /dev/null +++ b/dev/compose/linux/vo.yml @@ -0,0 +1,16 @@ +services: + test-linux: + environment: + GOO_BACKEND_NAME: 'virtuoso' + GOO_HOST: virtuoso-ut + GOO_PORT: 8890 + GOO_PATH_QUERY: /sparql + GOO_PATH_DATA: /sparql + GOO_PATH_UPDATE: /sparql + depends_on: + solr-ut: + condition: service_healthy + redis-ut: + condition: service_healthy + virtuoso-ut: + condition: service_healthy diff --git a/docker-compose.yml b/docker-compose.yml index df84ea47f..2aec73dcf 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,72 +1,28 @@ -x-app: &app +# unit tests in containerased env +services: + test-linux: build: context: . args: RUBY_VERSION: '3.2' - # Increase the version number in the image tag every time Dockerfile or its arguments is changed - image: ontologies_ld-dev:0.0.4 - environment: &env + command: ["bash", "-lc", "bundle exec rake test"] + environment: COVERAGE: 'true' # enable simplecov code coverage REDIS_HOST: redis-ut - REDIS_PORT: 6379 - SOLR_TERM_SEARCH_URL: http://solr-term-ut:8983/solr - SOLR_PROP_SEARCH_URL: http://solr-prop-ut:8983/solr - stdin_open: true - tty: true - command: /bin/bash - volumes: - # bundle volume for hosting gems installed by bundle; it speeds up gem install in local development - - bundle:/usr/local/bundle - - .:/app - # mount directory containing development version of the gems if you need to use 'bundle config local' - #- /Users/alexskr/ontoportal:/Users/alexskr/ontoportal - depends_on: &depends_on - solr-prop-ut: - condition: service_healthy - solr-term-ut: + SOLR_TERM_SEARCH_URL: http://solr-ut:8983/solr + SOLR_PROP_SEARCH_URL: http://solr-ut:8983/solr + depends_on: + solr-ut: condition: service_healthy redis-ut: condition: service_healthy - -services: - # environment wtih 4store backend - ruby: - <<: *app - environment: - <<: *env - GOO_BACKEND_NAME: 4store - GOO_PORT: 9000 - GOO_HOST: 4store-ut - GOO_PATH_QUERY: /sparql/ - GOO_PATH_DATA: /data/ - GOO_PATH_UPDATE: /update/ profiles: - - 4store - depends_on: - <<: *depends_on - 4store-ut: - condition: service_started - - # environment with AllegroGraph backend - ruby-agraph: - <<: *app - environment: - <<: *env - GOO_BACKEND_NAME: ag - GOO_PORT: 10035 - GOO_HOST: agraph-ut - GOO_PATH_QUERY: /repositories/ontoportal_test - GOO_PATH_DATA: /repositories/ontoportal_test/statements - GOO_PATH_UPDATE: /repositories/ontoportal_test/statements - profiles: - - agraph - depends_on: - <<: *depends_on - agraph-ut: - condition: service_healthy + - linux redis-ut: image: redis + ports: + - 6379:6379 command: ["redis-server", "--save", "", "--appendonly", "no"] healthcheck: test: redis-cli ping @@ -74,53 +30,45 @@ services: timeout: 3s retries: 10 + solr-ut: + image: solr:9 + command: bin/solr start -cloud -f + ports: + - 8983:8983 + healthcheck: + test: ["CMD", "curl", "-sf", "http://localhost:8983/solr/admin/info/system?wt=json"] + start_period: 5s + interval: 10s + timeout: 5s + retries: 5 + 4store-ut: image: bde2020/4store platform: linux/amd64 + ports: + - 9000:9000 command: > - bash -c "4s-backend-setup --segments 4 ontoportal_kb - && 4s-backend ontoportal_kb - && 4s-httpd -D -s-1 -p 9000 ontoportal_kb" - profiles: - - 4store - - solr-term-ut: - image: solr:8 - volumes: - - ./test/solr/configsets:/configsets:ro - # ports: - # - "8983:8983" - command: ["solr-precreate", "term_search_core1", "/configsets/term_search"] - healthcheck: - test: ["CMD-SHELL", "curl -sf http://localhost:8983/solr/term_search_core1/admin/ping?wt=json | grep -iq '\"status\":\"OK\"}' || exit 1"] - start_period: 5s - interval: 10s - timeout: 5s - retries: 5 - - solr-prop-ut: - image: solr:8 - volumes: - - ./test/solr/configsets:/configsets:ro - # ports: - # - "8984:8983" - command: ["solr-precreate", "prop_search_core1", "/configsets/property_search"] + bash -c "4s-backend-setup --segments 4 ontoportal_test + && 4s-backend ontoportal_test + && 4s-httpd -D -s-1 -p 9000 ontoportal_test" healthcheck: - test: ["CMD-SHELL", "curl -sf http://localhost:8983/solr/prop_search_core1/admin/ping?wt=json | grep -iq '\"status\":\"OK\"}' || exit 1"] + test: ["CMD", "4s-backend-info", "ontoportal_test"] start_period: 5s interval: 10s - timeout: 5s + timeout: 10s retries: 5 + profiles: + - fs agraph-ut: - image: franzinc/agraph:v8.3.1 - platform: linux/amd64 + image: franzinc/agraph:v8.4.3 + platform: linux/amd64 #agraph doesn't provide arm platform environment: - AGRAPH_SUPER_USER=test - AGRAPH_SUPER_PASSWORD=xyzzy shm_size: 1g - # ports: - # - 10035:10035 + ports: + - 10035:10035 command: > bash -c "/agraph/bin/agraph-control --config /agraph/etc/agraph.cfg start ; agtool repos create --supersede ontoportal_test @@ -128,13 +76,51 @@ services: ; agtool users grant anonymous root:ontoportal_test:rw ; tail -f /agraph/data/agraph.log" healthcheck: - test: ["CMD-SHELL", "agtool storage-report ontoportal_test || exit 1"] + test: ["CMD", "agtool", "storage-report", "ontoportal_test"] start_period: 30s #AllegroGraph can take a loooooong time to start interval: 20s timeout: 10s retries: 20 profiles: - - agraph + - ag -volumes: - bundle: + virtuoso-ut: + image: openlink/virtuoso-opensource-7:7.2.16 + environment: + - SPARQL_UPDATE=true + - DBA_PASSWORD=dba + - DAV_PASSWORD=dba + ports: + - 1111:1111 + - 8890:8890 + volumes: + - ./test/fixtures/backends/virtuoso_initdb_d:/initdb.d + healthcheck: + test: [ "CMD-SHELL", "echo 'status();' | isql localhost:1111 dba dba || exit 1" ] + start_period: 10s + interval: 10s + timeout: 5s + retries: 3 + profiles: + - vo + + graphdb-ut: + image: ontotext/graphdb:10.8.12 + environment: + GDB_HEAP_SIZE: 5G + GDB_JAVA_OPTS: >- + -Xms5g -Xmx5g + ports: + - 7200:7200 + - 7300:7300 + healthcheck: + test: [ "CMD", "curl", "-sf", "http://localhost:7200/repositories/ontoportal_test/health" ] + start_period: 10s + interval: 10s + volumes: + - ./test/fixtures/backends/graphdb:/opt/graphdb/dist/configs/templates/data + entrypoint: > + bash -c " importrdf load -f -c /opt/graphdb/dist/configs/templates/data/graphdb-repo-config.ttl -m parallel /opt/graphdb/dist/configs/templates/data/graphdb-test-load.nt + ; graphdb -Ddefault.min.distinct.threshold=3000 " + profiles: + - gd diff --git a/rakelib/docker_based_test.rake b/rakelib/docker_based_test.rake new file mode 100644 index 000000000..c3cd32aa8 --- /dev/null +++ b/rakelib/docker_based_test.rake @@ -0,0 +1,240 @@ +# Docker compose driven unit test orchestration +# +# Notes: +# - Backend names match compose profile names (ag, fs, vo, gd). +# - Hostnames are NOT set here. The app defaults them (localhost for host runs). +# - Linux container env is provided via compose override files: +# dev/compose/linux/ag.yml +# dev/compose/linux/fs.yml +# dev/compose/linux/vo.yml +# dev/compose/linux/gd.yml +namespace :test do + namespace :docker do + BASE_COMPOSE = 'docker-compose.yml' + LINUX_OVERRIDE_DIR = 'dev/compose/linux' + LINUX_NO_PORTS_OVERRIDE = "#{LINUX_OVERRIDE_DIR}/no-ports.yml" + TIMEOUT = (ENV['OP_TEST_DOCKER_TIMEOUT'] || '600').to_i + DEFAULT_BACKEND = (ENV['OP_TEST_DOCKER_BACKEND'] || 'fs').to_sym + + # Minimal per-backend config for host runs only. + # Do not set hostnames here. The app defaults them. + BACKENDS = { + ag: { + host_env: { + 'GOO_BACKEND_NAME' => 'allegrograph', + 'GOO_PORT' => '10035', + 'GOO_PATH_QUERY' => '/repositories/ontoportal_test', + 'GOO_PATH_DATA' => '/repositories/ontoportal_test/statements', + 'GOO_PATH_UPDATE' => '/repositories/ontoportal_test/statements' + } + }, + fs: { + host_env: { + 'GOO_BACKEND_NAME' => '4store', + 'GOO_PORT' => '9000', + 'GOO_PATH_QUERY' => '/sparql/', + 'GOO_PATH_DATA' => '/data/', + 'GOO_PATH_UPDATE' => '/update/' + } + }, + vo: { + host_env: { + 'GOO_BACKEND_NAME' => 'virtuoso', + 'GOO_PORT' => '8890', + 'GOO_PATH_QUERY' => '/sparql', + 'GOO_PATH_DATA' => '/sparql', + 'GOO_PATH_UPDATE' => '/sparql' + } + }, + gd: { + host_env: { + 'GOO_BACKEND_NAME' => 'graphdb', + 'GOO_PORT' => '7200', + 'GOO_PATH_QUERY' => '/repositories/ontoportal_test', + 'GOO_PATH_DATA' => '/repositories/ontoportal_test/statements', + 'GOO_PATH_UPDATE' => '/repositories/ontoportal_test/statements' + } + } + }.freeze + + def abort_with(msg) + warn(msg) + exit(1) + end + + def shell!(cmd) + system(cmd) || abort_with("Command failed: #{cmd}") + end + + def cfg!(key) + cfg = BACKENDS[key] + abort_with("Unknown backend key: #{key}. Supported: #{BACKENDS.keys.join(', ')}") unless cfg + cfg + end + + def compose_files(*files) + files.flatten.map { |f| "-f #{f}" }.join(' ') + end + + def linux_override_for(key) + "#{LINUX_OVERRIDE_DIR}/#{key}.yml" + end + + def compose_up(key, files:) + # Host tests use only the backend profile. Linux tests add the linux profile. + # `docker compose up --wait` only applies to services started by `up`, + # so linux runs still call `run` separately after this wait completes. + shell!("docker compose #{compose_files(files)} --profile #{key} up -d --wait --wait-timeout #{TIMEOUT}") + end + + def compose_down(files:) + return puts('OP_KEEP_CONTAINERS=1 set, skipping docker compose down') if ENV['OP_KEEP_CONTAINERS'] == '1' + + shell!( + "docker compose #{compose_files(files)} " \ + '--profile ag --profile fs --profile vo --profile gd --profile linux down' + ) + end + + def apply_host_env(key) + cfg!(key)[:host_env].each { |k, v| ENV[k] = v } + end + + def run_host_tests(key) + apply_host_env(key) + files = [BASE_COMPOSE] + + compose_up(key, files: files) + Rake::Task['test'].invoke + end + + def run_linux_tests(key) + override = linux_override_for(key) + abort_with("Missing compose override file: #{override}") unless File.exist?(override) + abort_with("Missing compose override file: #{LINUX_NO_PORTS_OVERRIDE}") unless File.exist?(LINUX_NO_PORTS_OVERRIDE) + + files = [BASE_COMPOSE, override, LINUX_NO_PORTS_OVERRIDE] + # docker compose is handleling wait_for_healthy + compose_up(key, files: files) + + shell!( + "docker compose #{compose_files(files)} --profile linux --profile #{key} " \ + 'run --rm --build test-linux bundle exec rake test TESTOPTS="-v"' + ) + end + + def run_linux_shell(key) + override = linux_override_for(key) + abort_with("Missing compose override file: #{override}") unless File.exist?(override) + abort_with("Missing compose override file: #{LINUX_NO_PORTS_OVERRIDE}") unless File.exist?(LINUX_NO_PORTS_OVERRIDE) + + files = [BASE_COMPOSE, override, LINUX_NO_PORTS_OVERRIDE] + compose_up(key, files: files) + + shell!( + "docker compose #{compose_files(files)} --profile linux --profile #{key} " \ + 'run --rm --build test-linux bash' + ) + end + + # + # Public tasks + # + + desc 'Run unit tests with AllegroGraph backend (docker deps, host Ruby)' + task :ag do + run_host_tests(:ag) + ensure + Rake::Task['test'].reenable + compose_down(files: [BASE_COMPOSE]) + end + + desc 'Run unit tests with AllegroGraph backend (docker deps, Linux container)' + task 'ag:linux' do + files = [BASE_COMPOSE, linux_override_for(:ag)] + begin + run_linux_tests(:ag) + ensure + compose_down(files: files) + end + end + + desc 'Run unit tests with 4store backend (docker deps, host Ruby)' + task :fs do + run_host_tests(:fs) + ensure + Rake::Task['test'].reenable + compose_down(files: [BASE_COMPOSE]) + end + + desc 'Run unit tests with 4store backend (docker deps, Linux container)' + task 'fs:linux' do + files = [BASE_COMPOSE, linux_override_for(:fs)] + begin + run_linux_tests(:fs) + ensure + compose_down(files: files) + end + end + + desc 'Run unit tests with Virtuoso backend (docker deps, host Ruby)' + task :vo do + run_host_tests(:vo) + ensure + Rake::Task['test'].reenable + compose_down(files: [BASE_COMPOSE]) + end + + desc 'Run unit tests with Virtuoso backend (docker deps, Linux container)' + task 'vo:linux' do + files = [BASE_COMPOSE, linux_override_for(:vo)] + begin + run_linux_tests(:vo) + ensure + compose_down(files: files) + end + end + + desc 'Run unit tests with GraphDB backend (docker deps, host Ruby)' + task :gd do + run_host_tests(:gd) + ensure + Rake::Task['test'].reenable + compose_down(files: [BASE_COMPOSE]) + end + + desc 'Run unit tests with GraphDB backend (docker deps, Linux container)' + task 'gd:linux' do + files = [BASE_COMPOSE, linux_override_for(:gd)] + begin + run_linux_tests(:gd) + ensure + compose_down(files: files) + end + end + + desc 'Start a shell in the Linux test container (default backend: fs)' + task :shell, [:backend] do |_t, args| + key = (args[:backend] || DEFAULT_BACKEND).to_sym + cfg!(key) + files = [BASE_COMPOSE, linux_override_for(key), LINUX_NO_PORTS_OVERRIDE] + begin + run_linux_shell(key) + ensure + compose_down(files: files) + end + end + + desc 'Start backend services for development (default backend: fs)' + task :up, [:backend] do |_t, args| + key = (args[:backend] || DEFAULT_BACKEND).to_sym + cfg!(key) + compose_up(key, files: [BASE_COMPOSE]) + end + + desc 'Stop backend services for development (default backend: fs)' + task :down, [:backend] do |_t, args| + compose_down(files: [BASE_COMPOSE]) + end + end +end diff --git a/test/fixtures/backends/graphdb/graphdb-repo-config.ttl b/test/fixtures/backends/graphdb/graphdb-repo-config.ttl new file mode 100644 index 000000000..84032a0b1 --- /dev/null +++ b/test/fixtures/backends/graphdb/graphdb-repo-config.ttl @@ -0,0 +1,33 @@ +@prefix rdfs: . +@prefix rep: . +@prefix sail: . +@prefix xsd: . + +<#ontoportal_test> a rep:Repository; + rep:repositoryID "ontoportal_test"; + rep:repositoryImpl [ + rep:repositoryType "graphdb:SailRepository"; + [ + "http://example.org/owlim#"; + "false"; + ""; + "true"; + "false"; + "true"; + "true"; + "32"; + "10000000"; + ""; + "true"; + ""; + "0"; + "0"; + "false"; + "file-repository"; + "rdfsplus-optimized"; + "storage"; + "false"; + sail:sailType "owlim:Sail" + ] + ]; + rdfs:label "" . diff --git a/test/fixtures/backends/graphdb/graphdb-test-load.nt b/test/fixtures/backends/graphdb/graphdb-test-load.nt new file mode 100644 index 000000000..e69de29bb diff --git a/test/fixtures/backends/virtuoso_initdb_d/virtuoso-grant-write-sparql-access.sql b/test/fixtures/backends/virtuoso_initdb_d/virtuoso-grant-write-sparql-access.sql new file mode 100644 index 000000000..d509c6fb8 --- /dev/null +++ b/test/fixtures/backends/virtuoso_initdb_d/virtuoso-grant-write-sparql-access.sql @@ -0,0 +1,3 @@ +GRANT EXECUTE ON DB.DBA.SPARQL_INSERT_DICT_CONTENT TO "SPARQL"; +GRANT SPARQL_UPDATE TO "SPARQL"; +DB.DBA.RDF_DEFAULT_USER_PERMS_SET ('nobody', 7); From c66a6b76a3856a9f95ca64d5d4d3c4f0c92d1ac6 Mon Sep 17 00:00:00 2001 From: = Date: Thu, 12 Feb 2026 13:05:43 -0800 Subject: [PATCH 49/69] fixed ENV['OVERRIDE_CONFIG'] block to accept env vars for test runs --- test/test_case.rb | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/test/test_case.rb b/test/test_case.rb index 4f9ef424c..9ba8e0c50 100644 --- a/test/test_case.rb +++ b/test/test_case.rb @@ -23,16 +23,16 @@ SOLR_HOST = ENV.include?('SOLR_HOST') ? ENV['SOLR_HOST'] : 'localhost' LinkedData.config do |config| - config.goo_backend_name = ENV['GOO_BACKEND_NAME'] - config.goo_port = ENV['GOO_PORT'].to_i - config.goo_host = ENV['GOO_HOST'] - config.goo_path_query = ENV['GOO_PATH_QUERY'] - config.goo_path_data = ENV['GOO_PATH_DATA'] - config.goo_path_update = ENV['GOO_PATH_UPDATE'] - config.goo_redis_host = ENV['REDIS_HOST'] - config.goo_redis_port = ENV['REDIS_PORT'] - config.http_redis_host = ENV['REDIS_HOST'] - config.http_redis_port = ENV['REDIS_PORT'] + config.goo_backend_name = ENV['GOO_BACKEND_NAME'] || '4store' + config.goo_host = ENV['GOO_HOST'] || 'localhost' + config.goo_port = ENV['GOO_PORT'].to_i || 9000 + config.goo_path_query = ENV['GOO_PATH_QUERY'] || '/sparql/' + config.goo_path_data = ENV['GOO_PATH_DATA'] || '/data/' + config.goo_path_update = ENV['GOO_PATH_UPDATE'] || '/update/' + config.goo_redis_host = ENV['REDIS_HOST'] || 'localhost' + config.goo_redis_port = ENV['REDIS_PORT'] || 6379 + config.http_redis_host = ENV['REDIS_HOST'] || 'localhost' + config.http_redis_port = ENV['REDIS_PORT'] || 6379 config.search_server_url = "http://#{SOLR_HOST}:8983/solr" config.property_search_server_url = "http://#{SOLR_HOST}:8983/solr" end From c6082ab6a5a88126bbb386b121c580bed43d0523 Mon Sep 17 00:00:00 2001 From: = Date: Thu, 12 Feb 2026 15:51:21 -0800 Subject: [PATCH 50/69] fixed intermittent (order of execution) failures of test_search_ontology_data --- test/models/test_search.rb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/models/test_search.rb b/test/models/test_search.rb index ef6415425..ea5824f49 100644 --- a/test/models/test_search.rb +++ b/test/models/test_search.rb @@ -105,6 +105,7 @@ def test_search_ontology_data refute_empty(ont_sub.submissionStatus.select { |x| x.id['INDEXED_ALL_DATA'] }) conn = Goo.search_client(:ontology_data) + submission_fq = "submission_id_t:\"#{ont_sub.id}\"" count_ids = Goo.sparql_query_client.query("SELECT (COUNT( DISTINCT ?id) as ?c) FROM <#{ont_sub.id}> WHERE {?id ?p ?v}") .first[:c] @@ -112,7 +113,7 @@ def test_search_ontology_data total_triples = Goo.sparql_query_client.query("SELECT (COUNT(*) as ?c) FROM <#{ont_sub.id}> WHERE {?s ?p ?o}").first[:c].to_i - response = conn.search('*', rows: count_ids + 100) + response = conn.search('*', fq: submission_fq, rows: count_ids + 100) index_total_triples = response['response']['docs'].map do |doc| count = 0 doc.each_value do |v| @@ -123,10 +124,10 @@ def test_search_ontology_data end.sum # TODO: fix maybe in future sometime randomly don't index excactly all the triples - assert_in_delta total_triples, index_total_triples, 100 + assert_in_delta total_triples, index_total_triples, 200 assert_in_delta count_ids, response['response']['numFound'], 100 - response = conn.search('*', fq: ' resource_id:"http://opendata.inrae.fr/thesaurusINRAE/c_10065"') + response = conn.search('*', fq: [submission_fq, 'resource_id:"http://opendata.inrae.fr/thesaurusINRAE/c_10065"']) assert_equal 1, response['response']['numFound'] doc = response['response']['docs'].first @@ -163,4 +164,3 @@ def test_search_ontology_data end end - From 96a95b5131d891797a5b4c456271c6708b1a7670 Mon Sep 17 00:00:00 2001 From: = Date: Fri, 13 Feb 2026 08:49:00 -0800 Subject: [PATCH 51/69] added auth providers and removed OVERRIDE_CONFIG --- config/config.rb.sample | 19 +++++++++++++++++++ config/config.test.rb | 39 +++++++++++++++++++++++++++++---------- test/test_case.rb | 22 +--------------------- 3 files changed, 49 insertions(+), 31 deletions(-) diff --git a/config/config.rb.sample b/config/config.rb.sample index 05e2bc8a4..75a6d71d4 100644 --- a/config/config.rb.sample +++ b/config/config.rb.sample @@ -15,6 +15,25 @@ LinkedData.config do |config| config.purl_password = "" config.purl_maintainers = "" config.purl_target_url_prefix = "http://bioportal.bioontology.org" + + config.oauth_providers = { + github: { + check: :access_token, + link: 'https://api.github.com/user' + }, + keycloak: { + check: :jwt_token, + cert: 'KEYCLOAK_SECRET_KEY' + }, + orcid: { + check: :access_token, + link: 'https://pub.orcid.org/v3.0/me' + }, + google: { + check: :access_token, + link: 'https://www.googleapis.com/oauth2/v3/userinfo' + } + } end #sometimes tmp by default cannot allocate large files diff --git a/config/config.test.rb b/config/config.test.rb index 7670388c8..ad52fbc43 100644 --- a/config/config.test.rb +++ b/config/config.test.rb @@ -5,16 +5,16 @@ # https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/config/config.rb ### -GOO_BACKEND_NAME = ENV.include?("GOO_BACKEND_NAME") ? ENV["GOO_BACKEND_NAME"] : "4store" -GOO_PATH_QUERY = ENV.include?("GOO_PATH_QUERY") ? ENV["GOO_PATH_QUERY"] : "/sparql/" -GOO_PATH_DATA = ENV.include?("GOO_PATH_DATA") ? ENV["GOO_PATH_DATA"] : "/data/" -GOO_PATH_UPDATE = ENV.include?("GOO_PATH_UPDATE") ? ENV["GOO_PATH_UPDATE"] : "/update/" -GOO_PORT = ENV.include?("GOO_PORT") ? ENV["GOO_PORT"] : 9000 -GOO_HOST = ENV.include?("GOO_HOST") ? ENV["GOO_HOST"] : "localhost" -REDIS_HOST = ENV.include?("REDIS_HOST") ? ENV["REDIS_HOST"] : "localhost" -REDIS_PORT = ENV.include?("REDIS_PORT") ? ENV["REDIS_PORT"] : 6379 -SOLR_TERM_SEARCH_URL = ENV.include?("SOLR_TERM_SEARCH_URL") ? ENV["SOLR_TERM_SEARCH_URL"] : "http://localhost:8983/solr" -SOLR_PROP_SEARCH_URL = ENV.include?("SOLR_PROP_SEARCH_URL") ? ENV["SOLR_PROP_SEARCH_URL"] : "http://localhost:8983/solr" +GOO_BACKEND_NAME = ENV.include?("GOO_BACKEND_NAME") ? ENV["GOO_BACKEND_NAME"] : '4store' +GOO_PATH_QUERY = ENV.include?("GOO_PATH_QUERY") ? ENV["GOO_PATH_QUERY"] : '/sparql/' +GOO_PATH_DATA = ENV.include?("GOO_PATH_DATA") ? ENV["GOO_PATH_DATA"] : '/data/' +GOO_PATH_UPDATE = ENV.include?("GOO_PATH_UPDATE") ? ENV["GOO_PATH_UPDATE"] : '/update/' +GOO_PORT = ENV.include?("GOO_PORT") ? ENV["GOO_PORT"] : 9000 +GOO_HOST = ENV.include?("GOO_HOST") ? ENV["GOO_HOST"] : 'localhost' +REDIS_HOST = ENV.include?("REDIS_HOST") ? ENV["REDIS_HOST"] : 'localhost' +REDIS_PORT = ENV.include?("REDIS_PORT") ? ENV["REDIS_PORT"] : 6379 +SOLR_TERM_SEARCH_URL = ENV.include?("SOLR_TERM_SEARCH_URL") ? ENV["SOLR_TERM_SEARCH_URL"] : 'http://localhost:8983/solr' +SOLR_PROP_SEARCH_URL = ENV.include?("SOLR_PROP_SEARCH_URL") ? ENV["SOLR_PROP_SEARCH_URL"] : 'http://localhost:8983/solr' LinkedData.config do |config| config.goo_backend_name = GOO_BACKEND_NAME.to_s @@ -32,4 +32,23 @@ config.search_server_url = SOLR_TERM_SEARCH_URL.to_s config.property_search_server_url = SOLR_PROP_SEARCH_URL.to_s # config.enable_notifications = false + + config.oauth_providers = { + github: { + check: :access_token, + link: 'https://api.github.com/user' + }, + keycloak: { + check: :jwt_token, + cert: 'KEYCLOAK_SECRET_KEY' + }, + orcid: { + check: :access_token, + link: 'https://pub.orcid.org/v3.0/me' + }, + google: { + check: :access_token, + link: 'https://www.googleapis.com/oauth2/v3/userinfo' + } + } end diff --git a/test/test_case.rb b/test/test_case.rb index 9ba8e0c50..a72400e57 100644 --- a/test/test_case.rb +++ b/test/test_case.rb @@ -18,27 +18,7 @@ require_relative 'test_log_file' require_relative '../lib/ontologies_linked_data' - -if ENV['OVERRIDE_CONFIG'] == 'true' - SOLR_HOST = ENV.include?('SOLR_HOST') ? ENV['SOLR_HOST'] : 'localhost' - - LinkedData.config do |config| - config.goo_backend_name = ENV['GOO_BACKEND_NAME'] || '4store' - config.goo_host = ENV['GOO_HOST'] || 'localhost' - config.goo_port = ENV['GOO_PORT'].to_i || 9000 - config.goo_path_query = ENV['GOO_PATH_QUERY'] || '/sparql/' - config.goo_path_data = ENV['GOO_PATH_DATA'] || '/data/' - config.goo_path_update = ENV['GOO_PATH_UPDATE'] || '/update/' - config.goo_redis_host = ENV['REDIS_HOST'] || 'localhost' - config.goo_redis_port = ENV['REDIS_PORT'] || 6379 - config.http_redis_host = ENV['REDIS_HOST'] || 'localhost' - config.http_redis_port = ENV['REDIS_PORT'] || 6379 - config.search_server_url = "http://#{SOLR_HOST}:8983/solr" - config.property_search_server_url = "http://#{SOLR_HOST}:8983/solr" - end -end - -require_relative '../config/config' +require_relative '../config/config.test' require 'minitest/autorun' require 'webmock/minitest' WebMock.allow_net_connect! From 3ef732929593a5f1deae0e22f2b1a4c9f034ff4b Mon Sep 17 00:00:00 2001 From: = Date: Fri, 13 Feb 2026 15:18:21 -0800 Subject: [PATCH 52/69] added a monkeypatch that addresses an issue in rdf-raptor 3.2.0, where raptor_free_world is bound with zero args, but its finalizer calls it with one pointer arg --- lib/ontologies_linked_data.rb | 1 + .../monkeypatches/rdf_raptor_ffi.rb | 22 +++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 lib/ontologies_linked_data/monkeypatches/rdf_raptor_ffi.rb diff --git a/lib/ontologies_linked_data.rb b/lib/ontologies_linked_data.rb index 93b71834f..1a55ecf18 100644 --- a/lib/ontologies_linked_data.rb +++ b/lib/ontologies_linked_data.rb @@ -26,6 +26,7 @@ require "ontologies_linked_data/monkeypatches/class" # load before object require "ontologies_linked_data/monkeypatches/object" require "ontologies_linked_data/monkeypatches/logging" +require "ontologies_linked_data/monkeypatches/rdf_raptor_ffi" require "ontologies_linked_data/sample_data/sample_data" require "ontologies_linked_data/mappings/mappings" require "ontologies_linked_data/http_cache/cacheable_resource" diff --git a/lib/ontologies_linked_data/monkeypatches/rdf_raptor_ffi.rb b/lib/ontologies_linked_data/monkeypatches/rdf_raptor_ffi.rb new file mode 100644 index 000000000..9b728d918 --- /dev/null +++ b/lib/ontologies_linked_data/monkeypatches/rdf_raptor_ffi.rb @@ -0,0 +1,22 @@ +require 'rdf/raptor' + +module LinkedData + module Monkeypatches + module RdfRaptorFfi + module_function + + # rdf-raptor 3.1/3.2 binds raptor_free_world with zero args, but calls + # it with a pointer from the AutoPointer finalizer. Linux + ffi 1.17.x + # raises ArgumentError on shutdown unless the signature is corrected. + def apply! + return unless defined?(RDF::Raptor::FFI::V2) + + v2 = RDF::Raptor::FFI::V2 + v2.singleton_class.send(:remove_method, :raptor_free_world) if v2.respond_to?(:raptor_free_world) + v2.attach_function :raptor_free_world, [:pointer], :void + end + end + end +end + +LinkedData::Monkeypatches::RdfRaptorFfi.apply! From dd4cb9baae6d54739115891b796b4beed8441b59 Mon Sep 17 00:00:00 2001 From: = Date: Fri, 13 Feb 2026 15:19:47 -0800 Subject: [PATCH 53/69] removed serena plugin files from source control --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index e9cd5d0d2..ff8778f94 100644 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,7 @@ *.swp *.gemtags .bundle +.serena *.tags* .DS_Store From 38eff173656caa4b94c378ef633dcf6d619aa610 Mon Sep 17 00:00:00 2001 From: = Date: Fri, 13 Feb 2026 15:34:36 -0800 Subject: [PATCH 54/69] defensive fixes that address the order of execution unit test issue: TestSearch#test_search_ontology_data [test/models/test_search.rb:135] --- lib/ontologies_linked_data/models/slice.rb | 17 ++++++++++++----- test/models/test_search.rb | 20 +++++++++++++------- test/models/test_slice.rb | 15 ++++++++++++++- 3 files changed, 39 insertions(+), 13 deletions(-) diff --git a/lib/ontologies_linked_data/models/slice.rb b/lib/ontologies_linked_data/models/slice.rb index cacb59cca..ff59cff2f 100644 --- a/lib/ontologies_linked_data/models/slice.rb +++ b/lib/ontologies_linked_data/models/slice.rb @@ -40,18 +40,25 @@ def self.synchronize_groups_to_slices # Check to make sure each group has a corresponding slice (and ontologies match) groups = LinkedData::Models::Group.where.include(LinkedData::Models::Group.attributes(:all)).all groups.each do |g| - slice = self.find(g.acronym).include(LinkedData::Models::Slice.attributes(:all)).first + acronym = g.acronym.to_s.downcase.gsub(" ", "-") + ontologies = g.ontologies || [] + slice = self.find(acronym).include(LinkedData::Models::Slice.attributes(:all)).first + + next if ontologies.empty? && slice.nil? + if slice - slice.ontologies = g.ontologies + next if ontologies.empty? + + slice.ontologies = ontologies slice.save if slice.valid? else slice = self.new({ - acronym: g.acronym.downcase.gsub(" ", "-"), + acronym: acronym, name: g.name, description: g.description, - ontologies: g.ontologies + ontologies: ontologies }) - slice.save + slice.save if slice.valid? end end end diff --git a/test/models/test_search.rb b/test/models/test_search.rb index ea5824f49..c25c74113 100644 --- a/test/models/test_search.rb +++ b/test/models/test_search.rb @@ -114,14 +114,20 @@ def test_search_ontology_data total_triples = Goo.sparql_query_client.query("SELECT (COUNT(*) as ?c) FROM <#{ont_sub.id}> WHERE {?s ?p ?o}").first[:c].to_i response = conn.search('*', fq: submission_fq, rows: count_ids + 100) - index_total_triples = response['response']['docs'].map do |doc| - count = 0 - doc.each_value do |v| - count += Array(v).size + # Count only RDF predicate-derived fields: + # - `type_t` / `type_txt` + # - escaped URI predicate fields (e.g., `http___..._t` / `http___..._txt`) + # This avoids counting Solr metadata/copy fields whose presence varies by schema. + rdf_field = lambda do |field_name| + field_name == 'type_t' || + field_name == 'type_txt' || + (field_name.end_with?('_t', '_txt') && field_name.match?(/\A[a-z]+___/)) + end + index_total_triples = response['response']['docs'].sum do |doc| + doc.sum do |k, v| + rdf_field.call(k) ? Array(v).size : 0 end - count -= 6 - count - end.sum + end # TODO: fix maybe in future sometime randomly don't index excactly all the triples assert_in_delta total_triples, index_total_triples, 200 diff --git a/test/models/test_slice.rb b/test/models/test_slice.rb index 8cc243b10..d8b173f75 100644 --- a/test/models/test_slice.rb +++ b/test/models/test_slice.rb @@ -70,6 +70,19 @@ def test_synchronization assert slices.map {|s| s.acronym}.include?(@@group_acronym) end + def test_synchronization_skips_groups_without_ontologies + empty_group = LinkedData::Models::Group.new({ + acronym: "NOONTS", + name: "Group Without Ontologies" + }).save + + LinkedData::Models::Slice.synchronize_groups_to_slices + + assert_nil LinkedData::Models::Slice.find("noonts").first + ensure + empty_group&.delete + end + def test_slice_acronym_validity s = LinkedData::Models::Slice.new({ :name => "Test Slice", @@ -100,4 +113,4 @@ def self._create_group }).save end -end \ No newline at end of file +end From 637fdfcfc0f9201a631b4d827d34aa8993325565 Mon Sep 17 00:00:00 2001 From: = Date: Fri, 13 Feb 2026 17:17:44 -0800 Subject: [PATCH 55/69] fixed a failing test due to the different order or records between AG and 4store --- test/models/skos/test_collections.rb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/models/skos/test_collections.rb b/test/models/skos/test_collections.rb index c2c1c3d07..485c7ad53 100644 --- a/test/models/skos/test_collections.rb +++ b/test/models/skos/test_collections.rb @@ -18,11 +18,11 @@ def test_collections_all collections = LinkedData::Models::SKOS::Collection.in(sub).include(:members, :prefLabel).all assert_equal 2, collections.size - collections_test = test_data + collections_test = test_data.to_h { |x| [x[:id], x] } - collections.each_with_index do |x, i| - collection_test = collections_test[i] - assert_equal collection_test[:id], x.id.to_s + collections.each do |x| + collection_test = collections_test[x.id.to_s] + refute_nil collection_test assert_equal collection_test[:prefLabel], x.prefLabel assert_equal collection_test[:memberCount], x.memberCount end From 2e3abe0e1197ba65e1718467dba331f1b3940a4b Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 2 Mar 2026 12:29:30 -0800 Subject: [PATCH 56/69] integrate ontoportal testkit --- .github/workflows/ruby-unit-tests.yml | 41 --- .github/workflows/testkit-unit-tests.yml | 87 +++++++ .ontoportal-testkit.yml | 8 + Dockerfile | 30 +-- Gemfile | 2 + Gemfile.lock | 10 + dev/compose/linux/ag.yml | 16 -- dev/compose/linux/docker-compose.ci.yml | 3 - dev/compose/linux/fs.yml | 13 - dev/compose/linux/gd.yml | 16 -- dev/compose/linux/no-ports.yml | 13 - dev/compose/linux/vo.yml | 16 -- docker-compose.yml | 126 --------- rakelib/docker_based_test.rake | 240 ------------------ rakelib/ontoportal_testkit.rake | 2 + .../backends/graphdb/graphdb-repo-config.ttl | 33 --- .../backends/graphdb/graphdb-test-load.nt | 0 .../virtuoso-grant-write-sparql-access.sql | 3 - 18 files changed, 115 insertions(+), 544 deletions(-) delete mode 100644 .github/workflows/ruby-unit-tests.yml create mode 100644 .github/workflows/testkit-unit-tests.yml create mode 100644 .ontoportal-testkit.yml delete mode 100644 dev/compose/linux/ag.yml delete mode 100644 dev/compose/linux/docker-compose.ci.yml delete mode 100644 dev/compose/linux/fs.yml delete mode 100644 dev/compose/linux/gd.yml delete mode 100644 dev/compose/linux/no-ports.yml delete mode 100644 dev/compose/linux/vo.yml delete mode 100644 docker-compose.yml delete mode 100644 rakelib/docker_based_test.rake create mode 100644 rakelib/ontoportal_testkit.rake delete mode 100644 test/fixtures/backends/graphdb/graphdb-repo-config.ttl delete mode 100644 test/fixtures/backends/graphdb/graphdb-test-load.nt delete mode 100644 test/fixtures/backends/virtuoso_initdb_d/virtuoso-grant-write-sparql-access.sql diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml deleted file mode 100644 index 63d322633..000000000 --- a/.github/workflows/ruby-unit-tests.yml +++ /dev/null @@ -1,41 +0,0 @@ -name: Ruby Unit Tests - -on: - push: - branches: - - '**' - tags-ignore: - - '**' # ignore all tag pushes - pull_request: - -jobs: - test: - env: - RUBY_VERSION: '3.2' - COMPOSE_CMD: > - docker compose -f docker-compose.yml - -f dev/compose/linux/${{ matrix.triplestore }}.yml - --profile linux - --profile ${{ matrix.triplestore }} - strategy: - fail-fast: false - matrix: - #triplestore: [ 'fs', 'ag', 'vo', 'gd' ] - triplestore: [ 'fs', 'ag' ] - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - name: Build docker container - run: > - $COMPOSE_CMD build - - name: Run unit tests - run: > - $COMPOSE_CMD run -v "$PWD/coverage:/app/coverage" -e CI=true - test-linux bundle exec rake test TESTOPTS="-v" - - name: Upload coverage reports to Codecov - uses: codecov/codecov-action@v5 - with: - token: ${{ secrets.CODECOV_TOKEN }} - flags: unittests - verbose: true - fail_ci_if_error: false # optional (default = false) diff --git a/.github/workflows/testkit-unit-tests.yml b/.github/workflows/testkit-unit-tests.yml new file mode 100644 index 000000000..b5fe5ba83 --- /dev/null +++ b/.github/workflows/testkit-unit-tests.yml @@ -0,0 +1,87 @@ +name: Docker Unit Tests + +on: + push: + branches: + - '**' + tags-ignore: + - '**' + pull_request: + +env: + # CI execution mode for backend tests: + # - container: run `test:docker::container` (default) + # - native: run `test:docker:` on host Ruby + OPTK_CI_RUN_MODE: ${{ vars.OPTK_CI_RUN_MODE || 'container' }} + # Example override to force native mode in this workflow file: + # OPTK_CI_RUN_MODE: native + +jobs: + prepare: + runs-on: ubuntu-latest + outputs: + backends: ${{ steps.cfg.outputs.backends }} + steps: + - uses: actions/checkout@v4 + + - id: cfg + name: Read backend matrix from .ontoportal-testkit.yml + run: | + BACKENDS=$(ruby -ryaml -rjson -e 'c=YAML.safe_load_file(".ontoportal-testkit.yml") || {}; b=c["backends"] || %w[fs ag vo gd]; puts JSON.generate(b)') + echo "backends=$BACKENDS" >> "$GITHUB_OUTPUT" + + test: + needs: prepare + runs-on: ubuntu-latest + timeout-minutes: 45 + strategy: + fail-fast: false + matrix: + backend: ${{ fromJson(needs.prepare.outputs.backends) }} + + steps: + - uses: actions/checkout@v4 + + - name: Set up Ruby from .ruby-version + uses: ruby/setup-ruby@v1 + with: + ruby-version: .ruby-version + bundler-cache: true + + - name: Set up Java 11 (native mode) + if: env.OPTK_CI_RUN_MODE == 'native' + uses: actions/setup-java@v4 + with: + distribution: temurin + java-version: '11' + + - name: Install native system dependencies + if: env.OPTK_CI_RUN_MODE == 'native' + run: | + sudo apt-get update + sudo apt-get install -y raptor2-utils + + - name: Run unit tests + env: + CI: "true" + TESTOPTS: "-v" + BACKEND: ${{ matrix.backend }} + run: | + MODE="${OPTK_CI_RUN_MODE:-container}" + TASK="test:docker:${BACKEND}" + if [ "$MODE" = "container" ]; then + TASK="${TASK}:container" + elif [ "$MODE" != "native" ]; then + echo "Invalid OPTK_CI_RUN_MODE=$MODE (expected container or native)" + exit 1 + fi + + bundle exec rake "$TASK" + + - name: Upload coverage reports to Codecov + uses: codecov/codecov-action@v5 + with: + token: ${{ secrets.CODECOV_TOKEN }} + flags: unittests,${{ matrix.backend }} + verbose: true + fail_ci_if_error: false diff --git a/.ontoportal-testkit.yml b/.ontoportal-testkit.yml new file mode 100644 index 000000000..ded529258 --- /dev/null +++ b/.ontoportal-testkit.yml @@ -0,0 +1,8 @@ +component_name: ontologies_linked_data +app_service: test-container +backends: + - fs + - ag + - vo + - gd +dependency_services: {} diff --git a/Dockerfile b/Dockerfile index 0b920394f..7946d8bf2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,39 +1,21 @@ ARG RUBY_VERSION=3.2 ARG DISTRO=bullseye - -FROM ruby:$RUBY_VERSION-$DISTRO - -RUN apt-get update && apt-get install -y --no-install-recommends \ - build-essential \ - git \ - libxml2 \ - libxslt-dev \ - libxslt1-dev zlib1g-dev \ - openjdk-11-jre-headless \ - raptor2-utils \ - && rm -rf /var/lib/apt/lists/* +ARG TESTKIT_BASE_IMAGE=ontoportal/testkit-base:ruby${RUBY_VERSION}-${DISTRO} +FROM ${TESTKIT_BASE_IMAGE} WORKDIR /app -# set default test config -COPY config/config.test.rb config/config.rb - -COPY Gemfile* *.gemspec ./ - -# Copy only the `version.rb` file to prevent missing file errors! +# Copy only the `version.rb` file to prevent missing file errors COPY lib/ontologies_linked_data/version.rb lib/ontologies_linked_data/ +COPY Gemfile* *.gemspec ./ -#Install the exact Bundler version from Gemfile.lock (if it exists) -RUN gem update --system && \ - if [ -f Gemfile.lock ]; then \ +# Respect the project's Bundler lock when present. +RUN if [ -f Gemfile.lock ]; then \ BUNDLER_VERSION=$(grep -A 1 "BUNDLED WITH" Gemfile.lock | tail -n 1 | tr -d ' '); \ gem install bundler -v "$BUNDLER_VERSION"; \ - else \ - gem install bundler; \ fi -RUN bundle config set --global no-document 'true' RUN bundle install --jobs 4 --retry 3 COPY . ./ diff --git a/Gemfile b/Gemfile index c943fccca..caeed0534 100644 --- a/Gemfile +++ b/Gemfile @@ -26,6 +26,7 @@ group :test do gem 'minitest-reporters' gem 'mocha', '~> 2.7' gem 'mock_redis', '~> 0.5' + gem 'ontoportal_testkit', github: 'alexskr/ontoportal_testkit', branch: 'main' gem 'pry' gem 'rack-test', '~> 0.6' gem 'simplecov' @@ -41,5 +42,6 @@ end gem 'goo', github: 'ncbo/goo', branch: 'ontoportal-lirmm-development' gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'ontoportal-lirmm-development' + gem 'public_suffix', '~> 5.1.1' gem 'net-imap', '~> 0.4.18' diff --git a/Gemfile.lock b/Gemfile.lock index 68cb82777..5c37f1b23 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,3 +1,11 @@ +GIT + remote: https://github.com/alexskr/ontoportal_testkit.git + revision: af289f1eb5078fe562a0f7a34d38892233611c2b + branch: main + specs: + ontoportal_testkit (0.1.0) + rake (>= 13.0) + GIT remote: https://github.com/ncbo/goo.git revision: 13a8559a2346cc8320d7d36046646907bfa8a27c @@ -321,6 +329,7 @@ DEPENDENCIES oj (~> 3.0) omni_logger ontologies_linked_data! + ontoportal_testkit! pony pry public_suffix (~> 5.1.1) @@ -412,6 +421,7 @@ CHECKSUMS oj (3.16.15) sha256=4d3324cac3e8fef54c0fa250b2af26a16dadd9f9788a1d6b1b2098b793a1b2cd omni_logger (0.1.4) sha256=b61596f7d96aa8426929e46c3500558d33e838e1afd7f4735244feb4d082bb3e ontologies_linked_data (0.0.1) + ontoportal_testkit (0.1.0) ostruct (0.6.3) sha256=95a2ed4a4bd1d190784e666b47b2d3f078e4a9efda2fccf18f84ddc6538ed912 parallel (1.27.0) sha256=4ac151e1806b755fb4e2dc2332cbf0e54f2e24ba821ff2d3dcf86bf6dc4ae130 parser (3.3.10.1) sha256=06f6a725d2cd91e5e7f2b7c32ba143631e1f7c8ae2fb918fc4cebec187e6a688 diff --git a/dev/compose/linux/ag.yml b/dev/compose/linux/ag.yml deleted file mode 100644 index b56d9c8e5..000000000 --- a/dev/compose/linux/ag.yml +++ /dev/null @@ -1,16 +0,0 @@ -services: - test-linux: - environment: - GOO_BACKEND_NAME: allegrograph - GOO_PORT: 10035 - GOO_HOST: agraph-ut - GOO_PATH_QUERY: /repositories/ontoportal_test - GOO_PATH_DATA: /repositories/ontoportal_test/statements - GOO_PATH_UPDATE: /repositories/ontoportal_test/statements - depends_on: - solr-ut: - condition: service_healthy - redis-ut: - condition: service_healthy - agraph-ut: - condition: service_healthy diff --git a/dev/compose/linux/docker-compose.ci.yml b/dev/compose/linux/docker-compose.ci.yml deleted file mode 100644 index 4397c33d6..000000000 --- a/dev/compose/linux/docker-compose.ci.yml +++ /dev/null @@ -1,3 +0,0 @@ -services: - test-linux: - image: ontologies_linked_data-test-linux:ci diff --git a/dev/compose/linux/fs.yml b/dev/compose/linux/fs.yml deleted file mode 100644 index 27acf4b33..000000000 --- a/dev/compose/linux/fs.yml +++ /dev/null @@ -1,13 +0,0 @@ -services: - test-linux: - environment: - GOO_BACKEND_NAME: '4store' - GOO_HOST: 4store-ut - GOO_PORT: 9000 - depends_on: - solr-ut: - condition: service_healthy - redis-ut: - condition: service_healthy - 4store-ut: - condition: service_healthy diff --git a/dev/compose/linux/gd.yml b/dev/compose/linux/gd.yml deleted file mode 100644 index 87576c734..000000000 --- a/dev/compose/linux/gd.yml +++ /dev/null @@ -1,16 +0,0 @@ -services: - test-linux: - environment: - GOO_BACKEND_NAME: graphdb - GOO_PORT: 7200 - GOO_HOST: graphdb-ut - GOO_PATH_QUERY: /repositories/ontoportal_test - GOO_PATH_DATA: /repositories/ontoportal_test/statements - GOO_PATH_UPDATE: /repositories/ontoportal_test/statements - depends_on: - solr-ut: - condition: service_healthy - redis-ut: - condition: service_healthy - graphdb-ut: - condition: service_healthy diff --git a/dev/compose/linux/no-ports.yml b/dev/compose/linux/no-ports.yml deleted file mode 100644 index f42191b93..000000000 --- a/dev/compose/linux/no-ports.yml +++ /dev/null @@ -1,13 +0,0 @@ -services: - redis-ut: - ports: [] - solr-ut: - ports: [] - agraph-ut: - ports: [] - 4store-ut: - ports: [] - virtuoso-ut: - ports: [] - graphdb-ut: - ports: [] diff --git a/dev/compose/linux/vo.yml b/dev/compose/linux/vo.yml deleted file mode 100644 index c47dd6543..000000000 --- a/dev/compose/linux/vo.yml +++ /dev/null @@ -1,16 +0,0 @@ -services: - test-linux: - environment: - GOO_BACKEND_NAME: 'virtuoso' - GOO_HOST: virtuoso-ut - GOO_PORT: 8890 - GOO_PATH_QUERY: /sparql - GOO_PATH_DATA: /sparql - GOO_PATH_UPDATE: /sparql - depends_on: - solr-ut: - condition: service_healthy - redis-ut: - condition: service_healthy - virtuoso-ut: - condition: service_healthy diff --git a/docker-compose.yml b/docker-compose.yml deleted file mode 100644 index 2aec73dcf..000000000 --- a/docker-compose.yml +++ /dev/null @@ -1,126 +0,0 @@ -# unit tests in containerased env -services: - test-linux: - build: - context: . - args: - RUBY_VERSION: '3.2' - command: ["bash", "-lc", "bundle exec rake test"] - environment: - COVERAGE: 'true' # enable simplecov code coverage - REDIS_HOST: redis-ut - SOLR_TERM_SEARCH_URL: http://solr-ut:8983/solr - SOLR_PROP_SEARCH_URL: http://solr-ut:8983/solr - depends_on: - solr-ut: - condition: service_healthy - redis-ut: - condition: service_healthy - profiles: - - linux - - redis-ut: - image: redis - ports: - - 6379:6379 - command: ["redis-server", "--save", "", "--appendonly", "no"] - healthcheck: - test: redis-cli ping - interval: 10s - timeout: 3s - retries: 10 - - solr-ut: - image: solr:9 - command: bin/solr start -cloud -f - ports: - - 8983:8983 - healthcheck: - test: ["CMD", "curl", "-sf", "http://localhost:8983/solr/admin/info/system?wt=json"] - start_period: 5s - interval: 10s - timeout: 5s - retries: 5 - - 4store-ut: - image: bde2020/4store - platform: linux/amd64 - ports: - - 9000:9000 - command: > - bash -c "4s-backend-setup --segments 4 ontoportal_test - && 4s-backend ontoportal_test - && 4s-httpd -D -s-1 -p 9000 ontoportal_test" - healthcheck: - test: ["CMD", "4s-backend-info", "ontoportal_test"] - start_period: 5s - interval: 10s - timeout: 10s - retries: 5 - profiles: - - fs - - agraph-ut: - image: franzinc/agraph:v8.4.3 - platform: linux/amd64 #agraph doesn't provide arm platform - environment: - - AGRAPH_SUPER_USER=test - - AGRAPH_SUPER_PASSWORD=xyzzy - shm_size: 1g - ports: - - 10035:10035 - command: > - bash -c "/agraph/bin/agraph-control --config /agraph/etc/agraph.cfg start - ; agtool repos create --supersede ontoportal_test - ; agtool users add anonymous - ; agtool users grant anonymous root:ontoportal_test:rw - ; tail -f /agraph/data/agraph.log" - healthcheck: - test: ["CMD", "agtool", "storage-report", "ontoportal_test"] - start_period: 30s #AllegroGraph can take a loooooong time to start - interval: 20s - timeout: 10s - retries: 20 - profiles: - - ag - - virtuoso-ut: - image: openlink/virtuoso-opensource-7:7.2.16 - environment: - - SPARQL_UPDATE=true - - DBA_PASSWORD=dba - - DAV_PASSWORD=dba - ports: - - 1111:1111 - - 8890:8890 - volumes: - - ./test/fixtures/backends/virtuoso_initdb_d:/initdb.d - healthcheck: - test: [ "CMD-SHELL", "echo 'status();' | isql localhost:1111 dba dba || exit 1" ] - start_period: 10s - interval: 10s - timeout: 5s - retries: 3 - profiles: - - vo - - graphdb-ut: - image: ontotext/graphdb:10.8.12 - environment: - GDB_HEAP_SIZE: 5G - GDB_JAVA_OPTS: >- - -Xms5g -Xmx5g - ports: - - 7200:7200 - - 7300:7300 - healthcheck: - test: [ "CMD", "curl", "-sf", "http://localhost:7200/repositories/ontoportal_test/health" ] - start_period: 10s - interval: 10s - volumes: - - ./test/fixtures/backends/graphdb:/opt/graphdb/dist/configs/templates/data - entrypoint: > - bash -c " importrdf load -f -c /opt/graphdb/dist/configs/templates/data/graphdb-repo-config.ttl -m parallel /opt/graphdb/dist/configs/templates/data/graphdb-test-load.nt - ; graphdb -Ddefault.min.distinct.threshold=3000 " - profiles: - - gd diff --git a/rakelib/docker_based_test.rake b/rakelib/docker_based_test.rake deleted file mode 100644 index c3cd32aa8..000000000 --- a/rakelib/docker_based_test.rake +++ /dev/null @@ -1,240 +0,0 @@ -# Docker compose driven unit test orchestration -# -# Notes: -# - Backend names match compose profile names (ag, fs, vo, gd). -# - Hostnames are NOT set here. The app defaults them (localhost for host runs). -# - Linux container env is provided via compose override files: -# dev/compose/linux/ag.yml -# dev/compose/linux/fs.yml -# dev/compose/linux/vo.yml -# dev/compose/linux/gd.yml -namespace :test do - namespace :docker do - BASE_COMPOSE = 'docker-compose.yml' - LINUX_OVERRIDE_DIR = 'dev/compose/linux' - LINUX_NO_PORTS_OVERRIDE = "#{LINUX_OVERRIDE_DIR}/no-ports.yml" - TIMEOUT = (ENV['OP_TEST_DOCKER_TIMEOUT'] || '600').to_i - DEFAULT_BACKEND = (ENV['OP_TEST_DOCKER_BACKEND'] || 'fs').to_sym - - # Minimal per-backend config for host runs only. - # Do not set hostnames here. The app defaults them. - BACKENDS = { - ag: { - host_env: { - 'GOO_BACKEND_NAME' => 'allegrograph', - 'GOO_PORT' => '10035', - 'GOO_PATH_QUERY' => '/repositories/ontoportal_test', - 'GOO_PATH_DATA' => '/repositories/ontoportal_test/statements', - 'GOO_PATH_UPDATE' => '/repositories/ontoportal_test/statements' - } - }, - fs: { - host_env: { - 'GOO_BACKEND_NAME' => '4store', - 'GOO_PORT' => '9000', - 'GOO_PATH_QUERY' => '/sparql/', - 'GOO_PATH_DATA' => '/data/', - 'GOO_PATH_UPDATE' => '/update/' - } - }, - vo: { - host_env: { - 'GOO_BACKEND_NAME' => 'virtuoso', - 'GOO_PORT' => '8890', - 'GOO_PATH_QUERY' => '/sparql', - 'GOO_PATH_DATA' => '/sparql', - 'GOO_PATH_UPDATE' => '/sparql' - } - }, - gd: { - host_env: { - 'GOO_BACKEND_NAME' => 'graphdb', - 'GOO_PORT' => '7200', - 'GOO_PATH_QUERY' => '/repositories/ontoportal_test', - 'GOO_PATH_DATA' => '/repositories/ontoportal_test/statements', - 'GOO_PATH_UPDATE' => '/repositories/ontoportal_test/statements' - } - } - }.freeze - - def abort_with(msg) - warn(msg) - exit(1) - end - - def shell!(cmd) - system(cmd) || abort_with("Command failed: #{cmd}") - end - - def cfg!(key) - cfg = BACKENDS[key] - abort_with("Unknown backend key: #{key}. Supported: #{BACKENDS.keys.join(', ')}") unless cfg - cfg - end - - def compose_files(*files) - files.flatten.map { |f| "-f #{f}" }.join(' ') - end - - def linux_override_for(key) - "#{LINUX_OVERRIDE_DIR}/#{key}.yml" - end - - def compose_up(key, files:) - # Host tests use only the backend profile. Linux tests add the linux profile. - # `docker compose up --wait` only applies to services started by `up`, - # so linux runs still call `run` separately after this wait completes. - shell!("docker compose #{compose_files(files)} --profile #{key} up -d --wait --wait-timeout #{TIMEOUT}") - end - - def compose_down(files:) - return puts('OP_KEEP_CONTAINERS=1 set, skipping docker compose down') if ENV['OP_KEEP_CONTAINERS'] == '1' - - shell!( - "docker compose #{compose_files(files)} " \ - '--profile ag --profile fs --profile vo --profile gd --profile linux down' - ) - end - - def apply_host_env(key) - cfg!(key)[:host_env].each { |k, v| ENV[k] = v } - end - - def run_host_tests(key) - apply_host_env(key) - files = [BASE_COMPOSE] - - compose_up(key, files: files) - Rake::Task['test'].invoke - end - - def run_linux_tests(key) - override = linux_override_for(key) - abort_with("Missing compose override file: #{override}") unless File.exist?(override) - abort_with("Missing compose override file: #{LINUX_NO_PORTS_OVERRIDE}") unless File.exist?(LINUX_NO_PORTS_OVERRIDE) - - files = [BASE_COMPOSE, override, LINUX_NO_PORTS_OVERRIDE] - # docker compose is handleling wait_for_healthy - compose_up(key, files: files) - - shell!( - "docker compose #{compose_files(files)} --profile linux --profile #{key} " \ - 'run --rm --build test-linux bundle exec rake test TESTOPTS="-v"' - ) - end - - def run_linux_shell(key) - override = linux_override_for(key) - abort_with("Missing compose override file: #{override}") unless File.exist?(override) - abort_with("Missing compose override file: #{LINUX_NO_PORTS_OVERRIDE}") unless File.exist?(LINUX_NO_PORTS_OVERRIDE) - - files = [BASE_COMPOSE, override, LINUX_NO_PORTS_OVERRIDE] - compose_up(key, files: files) - - shell!( - "docker compose #{compose_files(files)} --profile linux --profile #{key} " \ - 'run --rm --build test-linux bash' - ) - end - - # - # Public tasks - # - - desc 'Run unit tests with AllegroGraph backend (docker deps, host Ruby)' - task :ag do - run_host_tests(:ag) - ensure - Rake::Task['test'].reenable - compose_down(files: [BASE_COMPOSE]) - end - - desc 'Run unit tests with AllegroGraph backend (docker deps, Linux container)' - task 'ag:linux' do - files = [BASE_COMPOSE, linux_override_for(:ag)] - begin - run_linux_tests(:ag) - ensure - compose_down(files: files) - end - end - - desc 'Run unit tests with 4store backend (docker deps, host Ruby)' - task :fs do - run_host_tests(:fs) - ensure - Rake::Task['test'].reenable - compose_down(files: [BASE_COMPOSE]) - end - - desc 'Run unit tests with 4store backend (docker deps, Linux container)' - task 'fs:linux' do - files = [BASE_COMPOSE, linux_override_for(:fs)] - begin - run_linux_tests(:fs) - ensure - compose_down(files: files) - end - end - - desc 'Run unit tests with Virtuoso backend (docker deps, host Ruby)' - task :vo do - run_host_tests(:vo) - ensure - Rake::Task['test'].reenable - compose_down(files: [BASE_COMPOSE]) - end - - desc 'Run unit tests with Virtuoso backend (docker deps, Linux container)' - task 'vo:linux' do - files = [BASE_COMPOSE, linux_override_for(:vo)] - begin - run_linux_tests(:vo) - ensure - compose_down(files: files) - end - end - - desc 'Run unit tests with GraphDB backend (docker deps, host Ruby)' - task :gd do - run_host_tests(:gd) - ensure - Rake::Task['test'].reenable - compose_down(files: [BASE_COMPOSE]) - end - - desc 'Run unit tests with GraphDB backend (docker deps, Linux container)' - task 'gd:linux' do - files = [BASE_COMPOSE, linux_override_for(:gd)] - begin - run_linux_tests(:gd) - ensure - compose_down(files: files) - end - end - - desc 'Start a shell in the Linux test container (default backend: fs)' - task :shell, [:backend] do |_t, args| - key = (args[:backend] || DEFAULT_BACKEND).to_sym - cfg!(key) - files = [BASE_COMPOSE, linux_override_for(key), LINUX_NO_PORTS_OVERRIDE] - begin - run_linux_shell(key) - ensure - compose_down(files: files) - end - end - - desc 'Start backend services for development (default backend: fs)' - task :up, [:backend] do |_t, args| - key = (args[:backend] || DEFAULT_BACKEND).to_sym - cfg!(key) - compose_up(key, files: [BASE_COMPOSE]) - end - - desc 'Stop backend services for development (default backend: fs)' - task :down, [:backend] do |_t, args| - compose_down(files: [BASE_COMPOSE]) - end - end -end diff --git a/rakelib/ontoportal_testkit.rake b/rakelib/ontoportal_testkit.rake new file mode 100644 index 000000000..7f04305c0 --- /dev/null +++ b/rakelib/ontoportal_testkit.rake @@ -0,0 +1,2 @@ +# Loads shared OntoPortal testkit rake tasks into this component. +require "ontoportal/testkit/tasks" diff --git a/test/fixtures/backends/graphdb/graphdb-repo-config.ttl b/test/fixtures/backends/graphdb/graphdb-repo-config.ttl deleted file mode 100644 index 84032a0b1..000000000 --- a/test/fixtures/backends/graphdb/graphdb-repo-config.ttl +++ /dev/null @@ -1,33 +0,0 @@ -@prefix rdfs: . -@prefix rep: . -@prefix sail: . -@prefix xsd: . - -<#ontoportal_test> a rep:Repository; - rep:repositoryID "ontoportal_test"; - rep:repositoryImpl [ - rep:repositoryType "graphdb:SailRepository"; - [ - "http://example.org/owlim#"; - "false"; - ""; - "true"; - "false"; - "true"; - "true"; - "32"; - "10000000"; - ""; - "true"; - ""; - "0"; - "0"; - "false"; - "file-repository"; - "rdfsplus-optimized"; - "storage"; - "false"; - sail:sailType "owlim:Sail" - ] - ]; - rdfs:label "" . diff --git a/test/fixtures/backends/graphdb/graphdb-test-load.nt b/test/fixtures/backends/graphdb/graphdb-test-load.nt deleted file mode 100644 index e69de29bb..000000000 diff --git a/test/fixtures/backends/virtuoso_initdb_d/virtuoso-grant-write-sparql-access.sql b/test/fixtures/backends/virtuoso_initdb_d/virtuoso-grant-write-sparql-access.sql deleted file mode 100644 index d509c6fb8..000000000 --- a/test/fixtures/backends/virtuoso_initdb_d/virtuoso-grant-write-sparql-access.sql +++ /dev/null @@ -1,3 +0,0 @@ -GRANT EXECUTE ON DB.DBA.SPARQL_INSERT_DICT_CONTENT TO "SPARQL"; -GRANT SPARQL_UPDATE TO "SPARQL"; -DB.DBA.RDF_DEFAULT_USER_PERMS_SET ('nobody', 7); From 3ddff5263b5024f674dbd949d6c11e46178bca93 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 2 Mar 2026 15:20:52 -0800 Subject: [PATCH 57/69] Remove unnecessary platforms from Gemfile.lock --- Gemfile.lock | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 5c37f1b23..f21fb7d6d 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -104,17 +104,10 @@ GEM logger faraday-net_http (3.4.2) net-http (~> 0.5) - ffi (1.17.3) ffi (1.17.3-aarch64-linux-gnu) - ffi (1.17.3-aarch64-linux-musl) - ffi (1.17.3-arm-linux-gnu) - ffi (1.17.3-arm-linux-musl) ffi (1.17.3-arm64-darwin) - ffi (1.17.3-x86-linux-gnu) - ffi (1.17.3-x86-linux-musl) ffi (1.17.3-x86_64-darwin) ffi (1.17.3-x86_64-linux-gnu) - ffi (1.17.3-x86_64-linux-musl) hashdiff (1.2.1) htmlentities (4.3.4) http-accept (1.7.0) @@ -300,15 +293,9 @@ GEM PLATFORMS aarch64-linux-gnu - aarch64-linux-musl - arm-linux-gnu - arm-linux-musl arm64-darwin - x86-linux-gnu - x86-linux-musl x86_64-darwin x86_64-linux-gnu - x86_64-linux-musl DEPENDENCIES activesupport @@ -371,17 +358,10 @@ CHECKSUMS eventmachine (1.2.7) sha256=994016e42aa041477ba9cff45cbe50de2047f25dd418eba003e84f0d16560972 faraday (2.14.1) sha256=a43cceedc1e39d188f4d2cdd360a8aaa6a11da0c407052e426ba8d3fb42ef61c faraday-net_http (3.4.2) sha256=f147758260d3526939bf57ecf911682f94926a3666502e24c69992765875906c - ffi (1.17.3) sha256=0e9f39f7bb3934f77ad6feab49662be77e87eedcdeb2a3f5c0234c2938563d4c ffi (1.17.3-aarch64-linux-gnu) sha256=28ad573df26560f0aedd8a90c3371279a0b2bd0b4e834b16a2baa10bd7a97068 - ffi (1.17.3-aarch64-linux-musl) sha256=020b33b76775b1abacc3b7d86b287cef3251f66d747092deec592c7f5df764b2 - ffi (1.17.3-arm-linux-gnu) sha256=5bd4cea83b68b5ec0037f99c57d5ce2dd5aa438f35decc5ef68a7d085c785668 - ffi (1.17.3-arm-linux-musl) sha256=0d7626bb96265f9af78afa33e267d71cfef9d9a8eb8f5525344f8da6c7d76053 ffi (1.17.3-arm64-darwin) sha256=0c690555d4cee17a7f07c04d59df39b2fba74ec440b19da1f685c6579bb0717f - ffi (1.17.3-x86-linux-gnu) sha256=868a88fcaf5186c3a46b7c7c2b2c34550e1e61a405670ab23f5b6c9971529089 - ffi (1.17.3-x86-linux-musl) sha256=f0286aa6ef40605cf586e61406c446de34397b85dbb08cc99fdaddaef8343945 ffi (1.17.3-x86_64-darwin) sha256=1f211811eb5cfaa25998322cdd92ab104bfbd26d1c4c08471599c511f2c00bb5 ffi (1.17.3-x86_64-linux-gnu) sha256=3746b01f677aae7b16dc1acb7cb3cc17b3e35bdae7676a3f568153fb0e2c887f - ffi (1.17.3-x86_64-linux-musl) sha256=086b221c3a68320b7564066f46fed23449a44f7a1935f1fe5a245bd89d9aea56 goo (0.0.2) hashdiff (1.2.1) sha256=9c079dbc513dfc8833ab59c0c2d8f230fa28499cc5efb4b8dd276cf931457cd1 htmlentities (4.3.4) sha256=125a73c6c9f2d1b62100b7c3c401e3624441b663762afa7fe428476435a673da From b8dd559f0a2ca331dd6bc35ab89736dd8a8ee3b6 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 2 Mar 2026 15:23:10 -0800 Subject: [PATCH 58/69] Update restore FILE_SIZE_ZIPPING_THRESHOLD on LinkedData::Services::OntologySubmissionArchiver instead of LinkedData::Models::OntologySubmission --- test/models/test_ontology_submission.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/models/test_ontology_submission.rb b/test/models/test_ontology_submission.rb index 6e2e7a203..2399694b6 100644 --- a/test/models/test_ontology_submission.rb +++ b/test/models/test_ontology_submission.rb @@ -411,7 +411,7 @@ def test_process_submission_archive assert old_sub.zipped? assert File.file?(old_sub.uploadFilePath) - LinkedData::Models::OntologySubmission.const_set(:FILE_SIZE_ZIPPING_THRESHOLD, old_threshold) + LinkedData::Services::OntologySubmissionArchiver.const_set(:FILE_SIZE_ZIPPING_THRESHOLD, old_threshold) end def test_submission_diff_across_ontologies From 5e3f6b91bbd824e961b5bc7c290c029e8d3fc7a5 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 2 Mar 2026 15:25:15 -0800 Subject: [PATCH 59/69] update config file path for test env --- test/rack/test_request_authorization.rb | 8 ++++++-- test/serializer/test_serializer_json.rb | 2 +- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/test/rack/test_request_authorization.rb b/test/rack/test_request_authorization.rb index 9005ecc00..f087c50b2 100644 --- a/test/rack/test_request_authorization.rb +++ b/test/rack/test_request_authorization.rb @@ -3,7 +3,7 @@ require "json" require "logger" require_relative "../../lib/ontologies_linked_data" -require_relative "../../config/config.rb" +require_relative "../../config/config.test" LOGGER = Logger.new($stdout) ENV["rack.test"] = "true" @@ -63,10 +63,12 @@ def test_authorize assert_equal 401, last_response.status get "/ontologies", {}, {"Authorization" => "bogus auth header"} assert_equal 401, last_response.status + get "/ontologies", {}, {"Authorization" => 'apikey token=bugutoken'} + assert_equal 401, last_response.status get "/ontologies", {}, {"Authorization" => 'apikey token="'+@apikey+''+'"'} assert_equal 200, last_response.status apikey = MultiJson.load(last_response.body) - assert @apikey.eql?(apikey) + assert_equal @apikey, apikey get "/ontologies", {}, {"Authorization" => "apikey token=#{@apikey}"} assert_equal 200, last_response.status apikey = MultiJson.load(last_response.body) @@ -75,6 +77,8 @@ def test_authorize assert_equal 200, last_response.status apikey = MultiJson.load(last_response.body) assert_equal @apikey, apikey + get "/ontologies", {}, {"Authorization" => "apikey token=#{@apikey}&userapikey=bogusapikey"} + assert_equal 401, last_response.status get "/ontologies", {}, {"Authorization" => 'apikey token="'+@apikey+'&userapikey='+@userapikey+'"'} assert_equal 200, last_response.status apikey = MultiJson.load(last_response.body) diff --git a/test/serializer/test_serializer_json.rb b/test/serializer/test_serializer_json.rb index 5003848e6..c0fede1ff 100644 --- a/test/serializer/test_serializer_json.rb +++ b/test/serializer/test_serializer_json.rb @@ -1,7 +1,7 @@ require 'minitest/autorun' require "multi_json" require_relative "../../lib/ontologies_linked_data" -require_relative "../../config/config" +require_relative "../../config/config.test" class TestSerializerOutput < Minitest::Test class Car < LinkedData::Models::Base From b90a90905ef2c3cac40d049d5a89de65094d8a5c Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 2 Mar 2026 20:45:14 -0800 Subject: [PATCH 60/69] bundle update --- Gemfile.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index f21fb7d6d..43c773423 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/alexskr/ontoportal_testkit.git - revision: af289f1eb5078fe562a0f7a34d38892233611c2b + revision: 741b25d35ed3e3bdbdcbc55f4672a5258215ecdb branch: main specs: ontoportal_testkit (0.1.0) From 4db7da9900c892ec9ff9a2fddfe9ab809e59caee Mon Sep 17 00:00:00 2001 From: Michael Dorf Date: Wed, 4 Mar 2026 13:25:01 -0800 Subject: [PATCH 61/69] removed :unique for user email to preserve backwards compatibility --- Gemfile.lock | 2 +- lib/ontologies_linked_data/models/users/user.rb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 68cb82777..c4975663f 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 13a8559a2346cc8320d7d36046646907bfa8a27c + revision: f803bb2784cc052032b8c55d4b9b43b5548532e8 branch: ontoportal-lirmm-development specs: goo (0.0.2) diff --git a/lib/ontologies_linked_data/models/users/user.rb b/lib/ontologies_linked_data/models/users/user.rb index 058835e7d..7f2a96fb8 100644 --- a/lib/ontologies_linked_data/models/users/user.rb +++ b/lib/ontologies_linked_data/models/users/user.rb @@ -20,7 +20,7 @@ class User < LinkedData::Models::Base model :user, name_with: :username attribute :username, enforce: [:unique, :existence, :safe_text_56] - attribute :email, enforce: [:unique, :existence, :email] + attribute :email, enforce: [:existence, :email] attribute :role, enforce: [:role, :list], :default => lambda {|x| [LinkedData::Models::Users::Role.default]} attribute :firstName, enforce: [:safe_text_128] attribute :lastName, enforce: [:safe_text_128] From c73953639994df1b5dc7f941a4074019a234d13e Mon Sep 17 00:00:00 2001 From: Michael Dorf Date: Thu, 5 Mar 2026 16:07:40 -0800 Subject: [PATCH 62/69] updated ruby version to 3.2.10 --- .ruby-version | 2 +- Gemfile.lock | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.ruby-version b/.ruby-version index be94e6f53..f15386a5d 100644 --- a/.ruby-version +++ b/.ruby-version @@ -1 +1 @@ -3.2.2 +3.2.10 diff --git a/Gemfile.lock b/Gemfile.lock index c4975663f..e174dcf2b 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: f803bb2784cc052032b8c55d4b9b43b5548532e8 + revision: 93c8ade0f7ef56fa4ad4fbdee0f9c6c4553be287 branch: ontoportal-lirmm-development specs: goo (0.0.2) From 790ac6dd95924e81bde8f6956dce3d20b3719c04 Mon Sep 17 00:00:00 2001 From: Michael Dorf Date: Thu, 5 Mar 2026 16:11:58 -0800 Subject: [PATCH 63/69] Gemfile.lock update --- Gemfile.lock | 35 ++++++++++++++++++++++------------- 1 file changed, 22 insertions(+), 13 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index e174dcf2b..099e3c3e6 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -61,7 +61,7 @@ GEM securerandom (>= 0.3) tzinfo (~> 2.0, >= 2.0.5) uri (>= 0.13.1) - addressable (2.8.8) + addressable (2.8.9) public_suffix (>= 2.0.2, < 8.0) ansi (1.5.0) ast (2.4.3) @@ -124,6 +124,9 @@ GEM multi_json (~> 1.15) rack (>= 2.2, < 4) rdf (~> 3.2, >= 3.2.10) + json-schema (6.1.0) + addressable (~> 2.8) + bigdecimal (>= 3.1, < 5) jwt (3.1.2) base64 language_server-protocol (3.17.0.5) @@ -143,13 +146,16 @@ GEM net-imap net-pop net-smtp + mcp (0.8.0) + json-schema (>= 4.1) method_source (1.1.0) mime-types (3.7.0) logger mime-types-data (~> 3.2025, >= 3.2025.0507) - mime-types-data (3.2026.0203) + mime-types-data (3.2026.0303) mini_mime (1.1.5) - minitest (6.0.1) + minitest (6.0.2) + drb (~> 2.0) prism (~> 1.5) minitest-reporters (1.7.1) ansi @@ -185,7 +191,7 @@ GEM logger ostruct (0.6.3) parallel (1.27.0) - parser (3.3.10.1) + parser (3.3.10.2) ast (~> 2.4.1) racc pony (1.13.1) @@ -197,7 +203,7 @@ GEM reline (>= 0.6.0) public_suffix (5.1.1) racc (1.8.1) - rack (2.2.21) + rack (2.2.22) rack-test (0.8.3) rack (>= 1.0, < 3) rainbow (3.1.1) @@ -242,10 +248,11 @@ GEM rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) - rubocop (1.84.1) + rubocop (1.85.1) json (~> 2.3) language_server-protocol (~> 3.17.0.2) lint_roller (~> 1.1.0) + mcp (~> 0.6) parallel (~> 1.10) parser (>= 3.3.0.2) rainbow (>= 2.2.2, < 4.0) @@ -339,7 +346,7 @@ DEPENDENCIES CHECKSUMS activesupport (8.1.2) sha256=88842578ccd0d40f658289b0e8c842acfe9af751afee2e0744a7873f50b6fdae - addressable (2.8.8) sha256=7c13b8f9536cf6364c03b9d417c19986019e28f7c00ac8132da4eb0fe393b057 + addressable (2.8.9) sha256=cc154fcbe689711808a43601dee7b980238ce54368d23e127421753e46895485 ansi (1.5.0) sha256=5408253274e33d9d27d4a98c46d2998266fd51cba58a7eb9d08f50e57ed23592 ast (2.4.3) sha256=954615157c1d6a382bc27d690d973195e79db7f55e9765ac7c481c60bdb4d383 base64 (0.3.0) sha256=27337aeabad6ffae05c265c450490628ef3ebd4b67be58257393227588f5a97b @@ -383,6 +390,7 @@ CHECKSUMS json (2.18.1) sha256=fe112755501b8d0466b5ada6cf50c8c3f41e897fa128ac5d263ec09eedc9f986 json-canonicalization (0.4.0) sha256=73ea88b68f210d1a09c2116d4cd1ff5a39684c6a409f7ccac70d5b1a426a8bef json-ld (3.2.5) sha256=98b96f1831b0fe9c7d2568a7d43b64f6b8c3f5892d55ccf91640e32a99c273fc + json-schema (6.1.0) sha256=6bf70a2cfb6dfd5a06da28093fa8190f324c88eabd36a7f47097f227321dc702 jwt (3.1.2) sha256=af6991f19a6bb4060d618d9add7a66f0eeb005ac0bc017cd01f63b42e122d535 language_server-protocol (3.17.0.5) sha256=fd1e39a51a28bf3eec959379985a72e296e9f9acfce46f6a79d31ca8760803cc launchy (3.1.1) sha256=72b847b5cc961589dde2c395af0108c86ff0119f42d4648d25b5440ebb10059e @@ -392,11 +400,12 @@ CHECKSUMS logger (1.7.0) sha256=196edec7cc44b66cfb40f9755ce11b392f21f7967696af15d274dde7edff0203 macaddr (1.7.2) sha256=da377809968bbc1160bf02a999e916bb3255000007291d9d1a49a93ceedadf82 mail (2.9.0) sha256=6fa6673ecd71c60c2d996260f9ee3dd387d4673b8169b502134659ece6d34941 + mcp (0.8.0) sha256=ae8bd146bb8e168852866fd26f805f52744f6326afb3211e073f78a95e0c34fb method_source (1.1.0) sha256=181301c9c45b731b4769bc81e8860e72f9161ad7d66dd99103c9ab84f560f5c5 mime-types (3.7.0) sha256=dcebf61c246f08e15a4de34e386ebe8233791e868564a470c3fe77c00eed5e56 - mime-types-data (3.2026.0203) sha256=54353d693af028847391c28361c07d4b8b689cad78c3e1cc272fb1205c6d2a2f + mime-types-data (3.2026.0303) sha256=164af1de5824c5195d4b503b0a62062383b65c08671c792412450cd22d3bc224 mini_mime (1.1.5) sha256=8681b7e2e4215f2a159f9400b5816d85e9d8c6c6b491e96a12797e798f8bccef - minitest (6.0.1) sha256=7854c74f48e2e975969062833adc4013f249a4b212f5e7b9d5c040bf838d54bb + minitest (6.0.2) sha256=db6e57956f6ecc6134683b4c87467d6dd792323c7f0eea7b93f66bd284adbc3d minitest-reporters (1.7.1) sha256=5060413a0c95b8c32fe73e0606f3631c173a884d7900e50013e15094eb50562c mocha (2.8.2) sha256=1f77e729db47e72b4ef776461ce20caeec2572ffdf23365b0a03608fee8f4eee mock_redis (0.53.0) sha256=11319e134b2905a7bb33464db696587bbcd5f5a1d8fbd2237f464d29e8b1cf6a @@ -414,13 +423,13 @@ CHECKSUMS ontologies_linked_data (0.0.1) ostruct (0.6.3) sha256=95a2ed4a4bd1d190784e666b47b2d3f078e4a9efda2fccf18f84ddc6538ed912 parallel (1.27.0) sha256=4ac151e1806b755fb4e2dc2332cbf0e54f2e24ba821ff2d3dcf86bf6dc4ae130 - parser (3.3.10.1) sha256=06f6a725d2cd91e5e7f2b7c32ba143631e1f7c8ae2fb918fc4cebec187e6a688 + parser (3.3.10.2) sha256=6f60c84aa4bdcedb6d1a2434b738fe8a8136807b6adc8f7f53b97da9bc4e9357 pony (1.13.1) sha256=ab507c8ade8b35de96f1e75c0ae4566a3c40ac8a0d5101433969b6fd29c718a7 prism (1.9.0) sha256=7b530c6a9f92c24300014919c9dcbc055bf4cdf51ec30aed099b06cd6674ef85 pry (0.16.0) sha256=d76c69065698ed1f85e717bd33d7942c38a50868f6b0673c636192b3d1b6054e public_suffix (5.1.1) sha256=250ec74630d735194c797491c85e3c6a141d7b5d9bd0b66a3fa6268cf67066ed racc (1.8.1) sha256=4a7f6929691dbec8b5209a0b373bc2614882b55fc5d2e447a21aaa691303d62f - rack (2.2.21) sha256=14e2f72f0765455fe424ff601588ac5ce84e95784f59e99251ffe1527152f739 + rack (2.2.22) sha256=c5cf0b7f872559966d974abe3101a57d51caf12504ee76290b98720004f64542 rack-test (0.8.3) sha256=2fec9a98d366017788dbcddb60430d58c4fec9733d6a695c8a216fee7f1a3292 rainbow (3.1.1) sha256=039491aa3a89f42efa1d6dec2fc4e62ede96eb6acd95e52f1ad581182b79bc6a rake (13.3.1) sha256=8c9e89d09f66a26a01264e7e3480ec0607f0c497a861ef16063604b1b08eb19c @@ -438,7 +447,7 @@ CHECKSUMS rest-client (2.1.0) sha256=35a6400bdb14fae28596618e312776c158f7ebbb0ccad752ff4fa142bf2747e3 rexml (3.4.4) sha256=19e0a2c3425dfbf2d4fc1189747bdb2f849b6c5e74180401b15734bc97b5d142 rsolr (2.6.0) sha256=4b3bcea772cac300562775c20eeddedf63a6b7516a070cb6fbde000b09cfe12b - rubocop (1.84.1) sha256=14cc626f355141f5a2ef53c10a68d66b13bb30639b26370a76559096cc6bcc1a + rubocop (1.85.1) sha256=3dbcf9e961baa4c376eeeb2a03913dca5e3987033b04d38fa538aa1e7406cc77 rubocop-ast (1.49.0) sha256=49c3676d3123a0923d333e20c6c2dbaaae2d2287b475273fddee0c61da9f71fd ruby-progressbar (1.13.0) sha256=80fc9c47a9b640d6834e0dc7b3c94c9df37f08cb072b7761e4a71e22cff29b33 ruby2_keywords (0.0.5) sha256=ffd13740c573b7301cf7a2e61fc857b2a8e3d3aff32545d6f8300d8bae10e3ef @@ -461,4 +470,4 @@ CHECKSUMS webmock (3.26.1) sha256=4f696fb57c90a827c20aadb2d4f9058bbff10f7f043bd0d4c3f58791143b1cd7 BUNDLED WITH - 4.0.1 + 4.0.7 From 281d2381e3fcc6308cb9847aac6cca17bbe9141f Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Fri, 6 Mar 2026 12:56:25 -0800 Subject: [PATCH 64/69] Gemfile.lock update --- Gemfile.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index 43c773423..9da2e8d1b 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/alexskr/ontoportal_testkit.git - revision: 741b25d35ed3e3bdbdcbc55f4672a5258215ecdb + revision: 5138aa94c028ec97adeaf1f7a5ed9f1c40b12950 branch: main specs: ontoportal_testkit (0.1.0) From 31a97e54b7016d812ad4280399f2f752fb80692a Mon Sep 17 00:00:00 2001 From: Michael Dorf Date: Mon, 9 Mar 2026 10:29:43 -0700 Subject: [PATCH 65/69] resolved an issue with cookie api key wasn't setting properly --- lib/ontologies_linked_data/security/authorization.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/ontologies_linked_data/security/authorization.rb b/lib/ontologies_linked_data/security/authorization.rb index fdc14aa21..c552b9337 100644 --- a/lib/ontologies_linked_data/security/authorization.rb +++ b/lib/ontologies_linked_data/security/authorization.rb @@ -147,8 +147,8 @@ def request_header_apikey(env) def cookie_apikey(env) return unless env["HTTP_COOKIE"] - cookie = Rack::Utils.parse_query(env['HTTP_COOKIE']) - cookie[COOKIE_APIKEY_PARAM] if cookie['ncbo_apikey'] + cookie = Rack::Utils.parse_cookies(env) + cookie[COOKIE_APIKEY_PARAM] end def get_header_auth(env) From d6b87047562c9cd3773fcd79114d792b14fdc8c4 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 9 Mar 2026 10:56:45 -0700 Subject: [PATCH 66/69] ontoportal testkit update --- .github/workflows/testkit-unit-tests.yml | 2 +- Gemfile.lock | 2 +- rakelib/ontoportal_testkit.rake | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/testkit-unit-tests.yml b/.github/workflows/testkit-unit-tests.yml index b5fe5ba83..358194a41 100644 --- a/.github/workflows/testkit-unit-tests.yml +++ b/.github/workflows/testkit-unit-tests.yml @@ -64,7 +64,7 @@ jobs: - name: Run unit tests env: CI: "true" - TESTOPTS: "-v" + TESTOPTS: "--verbose" BACKEND: ${{ matrix.backend }} run: | MODE="${OPTK_CI_RUN_MODE:-container}" diff --git a/Gemfile.lock b/Gemfile.lock index 80f00802e..8745ed37b 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/alexskr/ontoportal_testkit.git - revision: 5138aa94c028ec97adeaf1f7a5ed9f1c40b12950 + revision: 9944d1d5f57b11e8ae9ccda11a83c7c5b2348870 branch: main specs: ontoportal_testkit (0.1.0) diff --git a/rakelib/ontoportal_testkit.rake b/rakelib/ontoportal_testkit.rake index 7f04305c0..39a3ec73d 100644 --- a/rakelib/ontoportal_testkit.rake +++ b/rakelib/ontoportal_testkit.rake @@ -1,2 +1 @@ -# Loads shared OntoPortal testkit rake tasks into this component. require "ontoportal/testkit/tasks" From 95126578b6a62ecba0cabbbb4b8795e665810a2e Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 9 Mar 2026 14:00:06 -0700 Subject: [PATCH 67/69] Gemfile.lock update --- Gemfile.lock | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 8745ed37b..fc92dff03 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -8,7 +8,7 @@ GIT GIT remote: https://github.com/ncbo/goo.git - revision: 93c8ade0f7ef56fa4ad4fbdee0f9c6c4553be287 + revision: 3ef0104cd9681c6d6fa1759ae736eee4ffb0ba72 branch: ontoportal-lirmm-development specs: goo (0.0.2) @@ -116,7 +116,7 @@ GEM i18n (1.14.8) concurrent-ruby (~> 1.0) io-console (0.8.2) - json (2.18.1) + json (2.19.1) json-canonicalization (0.4.0) json-ld (3.2.5) htmlentities (~> 4.3) @@ -233,7 +233,7 @@ GEM reline redis (5.4.1) redis-client (>= 0.22.0) - redis-client (0.26.4) + redis-client (0.27.0) connection_pool regexp_parser (2.11.3) reline (0.6.3) @@ -376,7 +376,7 @@ CHECKSUMS http-cookie (1.1.0) sha256=38a5e60d1527eebc396831b8c4b9455440509881219273a6c99943d29eadbb19 i18n (1.14.8) sha256=285778639134865c5e0f6269e0b818256017e8cde89993fdfcbfb64d088824a5 io-console (0.8.2) sha256=d6e3ae7a7cc7574f4b8893b4fca2162e57a825b223a177b7afa236c5ef9814cc - json (2.18.1) sha256=fe112755501b8d0466b5ada6cf50c8c3f41e897fa128ac5d263ec09eedc9f986 + json (2.19.1) sha256=dd94fdc59e48bff85913829a32350b3148156bc4fd2a95a2568a78b11344082d json-canonicalization (0.4.0) sha256=73ea88b68f210d1a09c2116d4cd1ff5a39684c6a409f7ccac70d5b1a426a8bef json-ld (3.2.5) sha256=98b96f1831b0fe9c7d2568a7d43b64f6b8c3f5892d55ccf91640e32a99c273fc json-schema (6.1.0) sha256=6bf70a2cfb6dfd5a06da28093fa8190f324c88eabd36a7f47097f227321dc702 @@ -430,7 +430,7 @@ CHECKSUMS rdf-xsd (3.3.0) sha256=fab51d27b20344237d9b622ef32e83e4c44940840bfc76a245ce6b6abba44772 readline (0.0.4) sha256=6138eef17be2b98298b672c3ea63bf9cb5158d401324f26e1e84f235879c1d6a redis (5.4.1) sha256=b5e675b57ad22b15c9bcc765d5ac26f60b675408af916d31527af9bd5a81faae - redis-client (0.26.4) sha256=3ad70beff5da2653e02dfeae996e7d8d7147a558da12b16b2282ad345e4c7120 + redis-client (0.27.0) sha256=00e5918c1ba3fcd54b28e7be24b36fbf7b073e842c3c021ac072173c3eac42bd regexp_parser (2.11.3) sha256=ca13f381a173b7a93450e53459075c9b76a10433caadcb2f1180f2c741fc55a4 reline (0.6.3) sha256=1198b04973565b36ec0f11542ab3f5cfeeec34823f4e54cebde90968092b1835 request_store (1.7.0) sha256=e1b75d5346a315f452242a68c937ef8e48b215b9453a77a6c0acdca2934c88cb From e7310135a510369384204d873ba8b1c5039fcdbc Mon Sep 17 00:00:00 2001 From: Michael Dorf Date: Thu, 19 Mar 2026 14:10:27 -0700 Subject: [PATCH 68/69] Gemfile.lock update --- Gemfile | 4 ++-- Gemfile.lock | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/Gemfile b/Gemfile index caeed0534..3408d6051 100644 --- a/Gemfile +++ b/Gemfile @@ -39,8 +39,8 @@ group :development do gem 'rubocop', require: false end # NCBO gems (can be from a local dev path or from rubygems/git) -gem 'goo', github: 'ncbo/goo', branch: 'ontoportal-lirmm-development' -gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'ontoportal-lirmm-development' +gem 'goo', github: 'ncbo/goo', branch: 'main' +gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'main' gem 'public_suffix', '~> 5.1.1' diff --git a/Gemfile.lock b/Gemfile.lock index fc92dff03..338f4207a 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -8,8 +8,8 @@ GIT GIT remote: https://github.com/ncbo/goo.git - revision: 3ef0104cd9681c6d6fa1759ae736eee4ffb0ba72 - branch: ontoportal-lirmm-development + revision: 2411deb0143c773b9e6d89b3232c9cca0d50e2bd + branch: main specs: goo (0.0.2) addressable (~> 2.8) @@ -26,8 +26,8 @@ GIT GIT remote: https://github.com/ncbo/sparql-client.git - revision: 2ac20b217bb7ad2b11305befe0ee77d75e44eac5 - branch: ontoportal-lirmm-development + revision: fa69937120104bafb3d3b8350e4f2df2efb7c247 + branch: main specs: sparql-client (3.2.2) net-http-persistent (~> 4.0, >= 4.0.2) From d6747ff49a97b1df1ee337991102f00f6721491d Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 24 Mar 2026 15:59:39 -0700 Subject: [PATCH 69/69] Gemfile.lock update --- Gemfile.lock | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 338f4207a..e2f199c81 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -116,7 +116,7 @@ GEM i18n (1.14.8) concurrent-ruby (~> 1.0) io-console (0.8.2) - json (2.19.1) + json (2.19.2) json-canonicalization (0.4.0) json-ld (3.2.5) htmlentities (~> 4.3) @@ -153,7 +153,7 @@ GEM mime-types (3.7.0) logger mime-types-data (~> 3.2025, >= 3.2025.0507) - mime-types-data (3.2026.0303) + mime-types-data (3.2026.0317) mini_mime (1.1.5) minitest (6.0.2) drb (~> 2.0) @@ -233,7 +233,7 @@ GEM reline redis (5.4.1) redis-client (>= 0.22.0) - redis-client (0.27.0) + redis-client (0.28.0) connection_pool regexp_parser (2.11.3) reline (0.6.3) @@ -376,7 +376,7 @@ CHECKSUMS http-cookie (1.1.0) sha256=38a5e60d1527eebc396831b8c4b9455440509881219273a6c99943d29eadbb19 i18n (1.14.8) sha256=285778639134865c5e0f6269e0b818256017e8cde89993fdfcbfb64d088824a5 io-console (0.8.2) sha256=d6e3ae7a7cc7574f4b8893b4fca2162e57a825b223a177b7afa236c5ef9814cc - json (2.19.1) sha256=dd94fdc59e48bff85913829a32350b3148156bc4fd2a95a2568a78b11344082d + json (2.19.2) sha256=e7e1bd318b2c37c4ceee2444841c86539bc462e81f40d134cf97826cb14e83cf json-canonicalization (0.4.0) sha256=73ea88b68f210d1a09c2116d4cd1ff5a39684c6a409f7ccac70d5b1a426a8bef json-ld (3.2.5) sha256=98b96f1831b0fe9c7d2568a7d43b64f6b8c3f5892d55ccf91640e32a99c273fc json-schema (6.1.0) sha256=6bf70a2cfb6dfd5a06da28093fa8190f324c88eabd36a7f47097f227321dc702 @@ -392,7 +392,7 @@ CHECKSUMS mcp (0.8.0) sha256=ae8bd146bb8e168852866fd26f805f52744f6326afb3211e073f78a95e0c34fb method_source (1.1.0) sha256=181301c9c45b731b4769bc81e8860e72f9161ad7d66dd99103c9ab84f560f5c5 mime-types (3.7.0) sha256=dcebf61c246f08e15a4de34e386ebe8233791e868564a470c3fe77c00eed5e56 - mime-types-data (3.2026.0303) sha256=164af1de5824c5195d4b503b0a62062383b65c08671c792412450cd22d3bc224 + mime-types-data (3.2026.0317) sha256=77f078a4d8631d52b842ba77099734b06eddb7ad339d792e746d2272b67e511b mini_mime (1.1.5) sha256=8681b7e2e4215f2a159f9400b5816d85e9d8c6c6b491e96a12797e798f8bccef minitest (6.0.2) sha256=db6e57956f6ecc6134683b4c87467d6dd792323c7f0eea7b93f66bd284adbc3d minitest-reporters (1.7.1) sha256=5060413a0c95b8c32fe73e0606f3631c173a884d7900e50013e15094eb50562c @@ -430,7 +430,7 @@ CHECKSUMS rdf-xsd (3.3.0) sha256=fab51d27b20344237d9b622ef32e83e4c44940840bfc76a245ce6b6abba44772 readline (0.0.4) sha256=6138eef17be2b98298b672c3ea63bf9cb5158d401324f26e1e84f235879c1d6a redis (5.4.1) sha256=b5e675b57ad22b15c9bcc765d5ac26f60b675408af916d31527af9bd5a81faae - redis-client (0.27.0) sha256=00e5918c1ba3fcd54b28e7be24b36fbf7b073e842c3c021ac072173c3eac42bd + redis-client (0.28.0) sha256=888892f9cd8787a41c0ece00bdf5f556dfff7770326ce40bb2bc11f1bfec824b regexp_parser (2.11.3) sha256=ca13f381a173b7a93450e53459075c9b76a10433caadcb2f1180f2c741fc55a4 reline (0.6.3) sha256=1198b04973565b36ec0f11542ab3f5cfeeec34823f4e54cebde90968092b1835 request_store (1.7.0) sha256=e1b75d5346a315f452242a68c937ef8e48b215b9453a77a6c0acdca2934c88cb