Sync: align ncbo/ncbo_cron with the AgroPortal codebase#121
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Sync: align ncbo/ncbo_cron with the AgroPortal codebase#121
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…e old code was causing intermittent test errors
…hat were evident in tests
…ors due to non-deterministic order of test executions
…rking - convert test_ontology_pull from WEBrick server threads to WebMock stubs - remove webrick from test dependencies (Gemfile, gemspec, lockfile) - refactor scheduler tests to bind TCPServer on 127.0.0.1:0 and reuse the open socket - remove TestCase.unused_port helper and all call sites - keep cleanup explicit (server.close in ensure) to avoid port leaks
Infra/ontoportal testkit integration
Setting $0 = "ncbo_cron" before `require` calls causes Ruby to misreport errors as "cannot load such file -- ncbo_cron"
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Overview
This PR aligns
ncbo/ncbo_cronwith the implementation maintained by the AgroPortal team inagroportal/ncbo_cron(developmentbranch), incorporating selected updates while preserving NCBO-specific behavior where required.The changes bring
ncbo_croninto compatibility with the synchronized OntoPortal stack and include scheduler fixes, ontology processing enhancements, and test infrastructure improvements.Unlike the full replacements performed for
gooandsparql-client, this PR incrementally aligns the existing codebase with AgroPortal while maintaining compatibility with the NCBO deployment.Prerequisites
This PR depends on the following changes being merged:
Key Changes
Alignment and compatibility
developmentbranchRuntime and scheduler improvements
Ontology processing and graph management
extract_metadata,index_all_data)Test and CI updates
Notes
This PR is part of a broader effort to reduce divergence between BioPortal and AgroPortal codebases and improve maintainability across OntoPortal deployments.