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2024-09-18Fetch symbol by it's name.•••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> Munyoki Kilyungi
2024-09-18Fetch the next comment version in RDF.•••* gn3/db/rdf/wiki.py (get_next_comment_version): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-18Rename sparql_construct_query -> sparql_query.•••* 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> Munyoki Kilyungi
2024-09-18Add new method for updating RDF Graph content.•••* gn3/db/rdf/__init__.py: Import POST, DIGEST, JSON. (update_rdf): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-18Run python-black against file.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-11Update SPARQL queries to fetch from graph with a default value.•••This makes testing easier since tests will be run against a different graph. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-11Handle case when result is empty when sanitizing json-ld result.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-11Fix mypy errors.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-11Run python-black against file.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-11Move comment on the manual sort to the doc-string.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-11Abstract out sanitizing json-ld result into a function.•••* 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> Munyoki Kilyungi
2024-09-11Update RDF queries to match ADR/000/gn-transform-databases.•••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> Munyoki Kilyungi
2024-09-05Update comment explaining why CONSTRUCT doesn't respect ORDER BY.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-05Correctly get categories in response.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-05Sort the RIF history data in reverse order.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-05Enforce array type to "categories" and "pmids" fields.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-05Set OPTIONAL values to default to an empty string.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-05Rename "pubmed_id" -> "pubmed_ids" to be explicit it's an array.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-05Remove type from wiki history.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-05Add comment history.•••* 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> Munyoki Kilyungi
2024-09-05Always output the top-level graph when compacting.•••This makes sure that the API is always consistent. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-05Use correct prefix when querying for email in triple.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-05Create global wiki context usable by all functions in gn3.rdf.wiki•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-09-05Restructure RDF module.•••* 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> Munyoki Kilyungi