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2025-10-22Fetch configs from app setting and pass them downFrederick Muriuki Muriithi
Fix the code to avoid using global variables holding configuration variables to avoid the failures caused by action-at-a-distance effects due to change of a value elsewhere. This way, all code consistently receives the same configuration values passed on from callers. We pass on the following configuration settings: * TMPDIR * SQL_URI * TEXTDIR
2025-07-07Ignore pylint rule.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Add null check for cursor.fetchone() in apply_change function.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Fix minor bug in how reviews and approvals are added to LMDB.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Rename dict key.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Fix mypy.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Refactor get_changes to filter by EditStatus; update return dict.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Fix minor spacing issue.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Fix empty change_ids in fetch_case_attrs_changes to return {}.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Fix mypy errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Fix pylint errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Add missing doc-strings for functions.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Delete unused imports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Delete "update_case_attribute"Munyoki Kilyungi
To update an attribute, you can use the "apply_change" function instead. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Add function for adding a change.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Add function for viewing a single diff change.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Return true at the end of for loop when updating case attributes.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Add function for fetching case attribute changes.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Add test cases for "update_case_attributes."Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Add update case-attributes function.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Store edit status in enum class.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Return the change_id for a given case attr edit.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Delete "approve_case_attribute."Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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.
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-11-25 06:13:41 +0000