| Age | Commit message (Expand) | Author |
|---|---|---|
| 2024-09-18 | Pass in insert_dict instead of payload in "get_wiki_entries"....* 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> | Munyoki Kilyungi |
| 2024-09-18 | Pass in the createtime as an arg when inserting into RDF graph....* 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> | Munyoki Kilyungi |
| 2024-09-18 | Get the next versionId from SQL....* 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> | Munyoki Kilyungi |
| 2024-09-18 | Add method that inserts new RIF comments....* gn3/db/rdf/wiki.py: Import datetime, update_rdf. (update_wiki_comment): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Fetch 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 |
| 2024-09-18 | Fetch 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 |
| 2024-09-18 | Rename 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 |
| 2024-09-18 | Add 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 |
| 2024-09-18 | Run python-black against file....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-11 | Update 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 |
| 2024-09-11 | Handle case when result is empty when sanitizing json-ld result....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-11 | Fix mypy errors....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-11 | Run python-black against file....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-11 | Move comment on the manual sort to the doc-string....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-11 | Abstract 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 |
| 2024-09-11 | Update 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 |
| 2024-09-05 | Update comment explaining why CONSTRUCT doesn't respect ORDER BY....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-05 | Correctly get categories in response....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-05 | Sort the RIF history data in reverse order....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-05 | Enforce array type to "categories" and "pmids" fields....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-05 | Set OPTIONAL values to default to an empty string....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-05 | Rename "pubmed_id" -> "pubmed_ids" to be explicit it's an array....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-05 | Remove type from wiki history....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-05 | Add 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 |
| 2024-09-05 | Always 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 |
| 2024-09-05 | Use correct prefix when querying for email in triple....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-05 | Create global wiki context usable by all functions in gn3.rdf.wiki...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-05 | Restructure 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 |
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