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ODM-12453: fix dictionary overriding by non-owners #603

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Merged
natalyatodorova merged 4 commits into from
Jan 30, 2026
Merged

ODM-12453: fix dictionary overriding by non-owners #603

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416a425
ODM-12453: fix existing dictionary search
natalyatodorova Jan 26, 2026
679a194
!!ODM-12453: add replace flag to args
natalyatodorova Jan 27, 2026
9f56365
ODM-12453: pass strings as params
natalyatodorova Jan 27, 2026
0d93559
ODM-12453: clean all existing dictionaries on replace option
natalyatodorova Jan 28, 2026
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35 changes: 31 additions & 4 deletions odm_sdk/files_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,7 @@ class FilesUtil(Application):
ALIGNED_READS = 'com.genestack.bio.files.IAlignedReads'
VARIATION_FILE = 'com.genestack.bio.files.IVariationFile'
APPLICATION_PAGE_FILE = 'com.genestack.api.files.IApplicationPageFile'
DICTIONARY_FILE = 'com.genestack.api.files.IDictionaryFile'
REFERENCE_GENOME = 'com.genestack.bio.files.IReferenceGenome'
AUXILIARY_FILE = 'com.genestack.api.files.IAuxiliaryFile'
INDEX_FILE = 'com.genestack.api.files.IIndexFile'
Expand Down Expand Up @@ -366,7 +367,33 @@ def load_info(self, accessions):
"""
return self.invoke('loadInfo', accessions)

def search_files(self, accession):
return self.invoke('searchFiles',
accession, # type: str
{}, [], 100, 0, None, False)
def search_files(self, search_string, parameters=None, data_types=None,
max_on_page=100, page_num=0, sort_order=None, ascending=False):
"""
Search for files.

:param search_string: search string (e.g. accession)
:type search_string: str
:param parameters: dictionary of search parameters
:type parameters: dict[str, str]
:param data_types: list of Java class names for file types
:type data_types: list[str]
:param max_on_page: maximum number of results per page
:param page_num: page number
:param sort_order: sort order (see SortOrder class)
:param ascending: sort direction
:return: list of file infos
"""
parameters = parameters or {}
data_types = data_types or []

return self.invoke(
'searchFiles',
search_string, # type: str
parameters, # type: dict
data_types, # type: list
max_on_page, # type: int
page_num, # type: int
sort_order, # type: str
ascending # type: bool
)
46 changes: 25 additions & 21 deletions odm_sdk/scripts/dictionaries/load_init_share_dictionaries.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,7 @@
from odm_sdk.scripts.utils import colored, GREEN, BLUE, RED


def load_dictionary(connection, data, parent_dictionary=None, replace=True,
reuse_old_version=False, metainfo=None):
def load_dictionary(connection, data, parent_dictionary=None, replace=False, metainfo=None):

if metainfo:
metainfo.add_string(Metainfo.DESCRIPTION, data.get('description'))
Expand All @@ -32,29 +31,32 @@ def load_dictionary(connection, data, parent_dictionary=None, replace=True,
term_type = data.get('term_type')

fu = FilesUtil(connection)
parent = fu.get_folder(
fu.get_special_folder(SpecialFolders.CREATED),
'Data samples',
'Dictionaries',
create=True)

di = DataImporter(connection)
old_dictionary_version = fu.find_file_by_name(name, parent=parent)
if old_dictionary_version:

search_dictionaries = fu.search_files(
search_string=name,
parameters={'type': FilesUtil.DICTIONARY_FILE, 'name': name, 'obsolete': 'false'})
if search_dictionaries['count'] > 0:
if replace:
print('Old version of dictionary %s / %s is removed'
% (colored(old_dictionary_version, GREEN), colored(name, BLUE)))
fu.mark_obsolete(old_dictionary_version)
fu.unlink_file(old_dictionary_version, parent)
# Mark all existing dictionaries as obsolete
for dictionary_file in search_dictionaries['files']:
accession = dictionary_file['accessions'][0]
fu.mark_obsolete(accession)
print('Old version of dictionary %s / %s is marked as obsolete'
% (colored(accession, GREEN), colored(name, BLUE)))
else:
if reuse_old_version:
print('Dictionary %s / %s already exists and will be reused'
% (colored(old_dictionary_version, GREEN), colored(name, BLUE)))
return old_dictionary_version
existing_accessions = []
for dictionary_file in search_dictionaries['files']:
existing_accessions.extend(dictionary_file['accessions'])
raise GenestackException(
"Dictionary %s / %s already exists, set replace=True to replace it"
% (colored(old_dictionary_version, GREEN), colored(name, BLUE)))
"Dictionary %s already exists with accessions: %s. Use --replace flag to overwrite it"
% (colored(name, BLUE), ', '.join([colored(acc, GREEN) for acc in existing_accessions])))

parent = fu.get_folder(
fu.get_special_folder(SpecialFolders.CREATED),
'Data samples',
'Dictionaries',
create=True)
accession = di.create_dictionary(
parent=parent,
name=name,
Expand Down Expand Up @@ -103,7 +105,7 @@ def main():
connection = get_connection(args)
with open(args.file_with_dictionaries, 'r') as data_file:
dictionaries = json.load(data_file)
accessions = [load_dictionary(connection, data) for data in dictionaries]
accessions = [load_dictionary(connection, data, replace=args.replace) for data in dictionaries]
initialization(connection, accessions)
sharing(connection, accessions)

Expand All @@ -117,6 +119,8 @@ def get_arguments():
group.add_argument('--file_with_dictionaries', metavar='<file_with_dictionaries>',
default="dictionaries.json",
help='dictionaries to load', required=True)
parser.add_argument('--replace', action='store_true', default=False,
help='replace existing dictionaries')
args = parser.parse_args()
return args

Expand Down