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2025-07-07Delete "reject_case_attribute."Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Delete "insert_case_attribute_audit."Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Delete "get_unreviewed_diffs."Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Delete "get_case_attributes."Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Move queue_edit to gn3.db.case_attributes.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Move EditStatus to gn3.db.case_attributes.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Move CaseAttributeEdit to gn3.db, rename diff to changes.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-06-17Fix pylint issues in db/sample_data.pyzsloan
2025-06-17Include n_cases in batch update querieszsloan
2025-06-17Add Batch Update code to GN3zsloan
2025-06-17Change sample_data fetch functions so they can use different inputszsloan
2025-06-17Add function for retrieving group_id given group_namezsloan
2025-04-25Handle null species in wiki comment queryMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-25Return a zero when the species is unspecified.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-25Skip adding a species to RDF when the species is unspecified.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-22Add function to delete wiki entries by wiki_id.Munyoki Kilyungi
* delete_wiki_entries_by_id: New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-03-18Order species by species id.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-03-07Convert wikiId and versionId to ints.Munyoki Kilyungi
This fixes failing tests. * gn3/db/rdf/wiki.py (__sanitize_result): Convert versionId and wiki Id to ints. (get_wiki_entries_by_symbol): Get string representation of VersionId and the wikiId instead of the the URI. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-02-28Fix linting errors.Frederick Muriuki Muriithi
2025-01-21Enable new inserts of new wiki entries.Munyoki Kilyungi
* gn3/api/metadata_api/wiki.py: Import Optional (edit_wiki): Add "/edit" route. Add new comment id. * gn3/db/wiki.py (get_next_comment_id): New function for fetching the getting the next comment_id. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-12-04refactor: make pylint fixes.Alexander_Kabui
2024-12-02Fix probeset metadata query to include dataset namezsloan
Previously this attempted to fetch probeset metadata using only the probeset name, but this is wrong. The dataset name is also needed.
2024-10-14Run python black against file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Replace CONSTRUCT with SELECT for fetching RIF NCBI entries.Munyoki Kilyungi
* gn3/db/rdf/wiki.py: Delete datetime import. Import sparql_query. [RIF_CONTEXT]: Delete. (get_rif_entries_by_symbol): Replace CONSTRUCT with SELECT. * tests/unit/db/rdf/test_wiki.py (test_get_rif_entries_by_symbol): Update tests. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Add function for fetching NCBI data.Munyoki Kilyungi
* gn3/db/rdf/wiki.py: Import datetime. [RIF_CONTEXT]: New global variable defining the json-ld context for NCBI rif data. (get_rif_entries_by_symbol): New function. * tests/unit/db/rdf/data.py: New file containing expected NCBI test data. * tests/unit/db/rdf/test_wiki.py (test_update_wiki_comment): New test case. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-30chore: pylint code fixJohn Nduli
2024-09-30fix: rdf and sql queries for fetching rif dataJohn Nduli
SQL queries fail because we get bytes instead of strings which cannot be decoded. We decode results from DictCursor to fix this. For RDF, we cast `?symbol` to a string.
2024-09-23Revert "Remove one-line if/else statement."Munyoki Kilyungi
This reverts commit 0d15840913c9cc401d1e74295aa5e17e34f2987b. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Remove one-line if/else statement.Munyoki Kilyungi
* gn3/db/rdf/wiki.py (__sanitize_result): When fetching pubmed_ids and categories, default to [] if the key misses, and remove the subsequent one-line if/else statement. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Use correct object modifier for a label when inserting a comment.Munyoki Kilyungi
* gn3/db/rdf/wiki.py (update_wiki_comment) [query]: Replace "rdf:label" with "rdfs:label". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Update docstring for "update_wiki_comment".Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Use correct object modifier in triple when fetching comment history.Munyoki Kilyungi
* gn3/db/rdf/wiki.py (get_comment_history) [query]: Replace ?symbolName with ?symbolName. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Use correct modifier when getting species name in SPARQL.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Remove dead variable from RDF query.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Alphabetically sort the categories and pubmed_ids array.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Remove un-necessary triple in comment history RDF query.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-19Use correct return type.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Pass in insert_dict instead of payload in "get_wiki_entries".Munyoki Kilyungi
* gn3/api/metadata_api/wiki.py (edit_wiki) [insert_dict]: Add species, categories fields. [update_wiki_comment]: Pass in insert_dict, and get rid of redundant keys. Directly pass in sparql_auth's conf params instead of a dict. * gn3/db/rdf/wiki.py (get_next_comment_version): Get rid of redundant params. Use fields directly from insert_dict. Directly pass in sparql_auth's conf params instead of a dict. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Pass in the createtime as an arg when inserting into RDF graph.Munyoki Kilyungi
* gn3/api/metadata_api/wiki.py (edit_wiki): Pass in the createtime as an arg. * gn3/db/rdf/wiki.py: Remove un-used imports. (update_wiki_comment): Use passed in "created" arg in the createtime field. This makes sure that the SQL/RDF timestamps match. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Get the next versionId from SQL.Munyoki Kilyungi
* gn3/api/metadata_api/wiki.py (edit_wiki): Get the next version Id from SQL * gn3/db/rdf/wiki.py (get_next_comment_version): Delete. (update_wiki_comment): Provide the next_version id as an extra arg. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Add method that inserts new RIF comments.Munyoki Kilyungi
* gn3/db/rdf/wiki.py: Import datetime, update_rdf. (update_wiki_comment): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Fetch symbol by it's name.Munyoki Kilyungi
The RDF ttl files were updated to have: comment gnt:symbol "name" . instead of: comment gnt:symbol symbolQname . * gn3/db/rdf/wiki.py (get_wiki_entries_by_symbol): Fetch symbol using it's string literal name. (get_comment_history): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Fetch the next comment version in RDF.Munyoki Kilyungi
* gn3/db/rdf/wiki.py (get_next_comment_version): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Rename sparql_construct_query -> sparql_query.Munyoki Kilyungi
* gn3/db/rdf/__init__.py (sparql_construct_query): Rename to... (sparql_query): ... this. Extend function to be able to return JSQN for SELECT queries. (query_frame_and_compact): Ditto. (query_and_compact): Ditto. (query_and_frame): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Add new method for updating RDF Graph content.Munyoki Kilyungi
* gn3/db/rdf/__init__.py: Import POST, DIGEST, JSON. (update_rdf): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Run python-black against file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-17fix: error when result dict contains NoneJohn Nduli
2024-09-17feat: require auth for edit api callJohn Nduli
2024-09-11Update SPARQL queries to fetch from graph with a default value.Munyoki Kilyungi
This makes testing easier since tests will be run against a different graph. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-11Handle case when result is empty when sanitizing json-ld result.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-11-29 18:46:31 +0000