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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>
2024-09-11Fix mypy errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-11Run python-black against file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-11Move comment on the manual sort to the doc-string.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-11Abstract out sanitizing json-ld result into a function.Munyoki Kilyungi
* gn3/db/rdf/wiki.py (__sanitize_result): New function. (get_wiki_entries_by_symbol): Delete sanitization code. (get_comment_history): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-11Update RDF queries to match ADR/000/gn-transform-databases.Munyoki Kilyungi
See: <https://issues.genenetwork.org/topics/ADR/gn-transform-databases/000-remodel-rif-transform-with-predicateobject-lists> for more context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Update comment explaining why CONSTRUCT doesn't respect ORDER BY.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Correctly get categories in response.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Sort the RIF history data in reverse order.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Enforce array type to "categories" and "pmids" fields.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Set OPTIONAL values to default to an empty string.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Rename "pubmed_id" -> "pubmed_ids" to be explicit it's an array.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Remove type from wiki history.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Add comment history.Munyoki Kilyungi
* gn3/api/metadata_api/wiki.py: Import get_comment_history. (get_history): New end-point. * gn3/db/rdf/wiki.py: (get_comment_history): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Always output the top-level graph when compacting.Munyoki Kilyungi
This makes sure that the API is always consistent. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Use correct prefix when querying for email in triple.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Create global wiki context usable by all functions in gn3.rdf.wikiMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Restructure RDF module.Munyoki Kilyungi
* gn3/api/metadata.py: Import constants from gn3.db.rdf * gn3/api/metadata_api/wiki.py: Ditto. Import "get_wiki_entries_by_symbol" from gn3.db.rdf.wiki. * gn3/db/constants.py: Delete file and move all constants ... * gn3/db/rdf.py: ... and functions ... * gn3/db/rdf/__init__.py: ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 14:54:20 +0000