| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-09-12 | Gracefully print out debug messages even outside app context | Frederick Muriuki Muriithi | |
| The flask.current_app object depends on the application context existing. In the case that no such context existing, then we still log out information, gracefully with this commit. | |||
| 2024-09-12 | Bump version | Pjotr Prins | |
| 2024-09-12 | From gn3 only use TMPDIR/gn3 paths | Pjotr Prins | |
| 2024-09-12 | Make sure dir exists before running R/qtl | Pjotr Prins | |
| 2024-09-12 | Replace TMPDIR/output with TMPDIR/gn3 so it is clear where it comes from | Pjotr Prins | |
| 2024-09-12 | Modify script paths so they can be edited in Guix | Pjotr Prins | |
| 2024-09-12 | rqtl_wrapper: minor fixes | Pjotr Prins | |
| 2024-09-12 | Mistake using envvar | Pjotr Prins | |
| 2024-09-12 | Make sure TMPDIR directories exist! | Pjotr Prins | |
| 2024-09-12 | Fix Rqtl test | Pjotr Prins | |
| 2024-09-12 | Getting Rqtl to run on fallback | Pjotr Prins | |
| 2024-09-12 | assert_paths_exist: make throw_error optional | Pjotr Prins | |
| 2024-09-12 | gn3/errors.py: add stack trace to error log | Pjotr Prins | |
| 2024-09-12 | Move assert_paths_exist into fs_helpers | Pjotr Prins | |
| 2024-09-12 | Change behavior of do_paths_exist to actually throw useful error | Pjotr Prins | |
| 2024-09-12 | Getting Rqtl to run on fallback | Pjotr Prins | |
| 2024-09-12 | README | Pjotr Prins | |
| 2024-09-12 | assert_paths_exist: make throw_error optional | Pjotr Prins | |
| 2024-09-12 | Move assert_paths_exist into fs_helpers | Pjotr Prins | |
| 2024-09-12 | Change behavior of do_paths_exist to actually throw useful error | Pjotr Prins | |
| 2024-09-12 | Make the gnqa search endpoint a get request. | Alexander_Kabui | |
| 2024-09-11 | Minor typo fix. | Alexander_Kabui | |
| 2024-09-11 | Update docs on use for custom request when query fahamu Api. | Alexander_Kabui | |
| 2024-09-11 | Update 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> | |||
| 2024-09-11 | Handle case when result is empty when sanitizing json-ld result. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-11 | Replace format-string with f-strings. | Munyoki Kilyungi | |
| * gn3/api/llm.py (delete_records): Using format-strings causes pylint to error out. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-11 | Fix mypy errors. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-11 | Run python-black against file. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-11 | Add test cases for wiki.__sanitize_result. | Munyoki Kilyungi | |
| * tests/unit/db/rdf/test_wiki.py (test_sanitize_result): New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-11 | Move comment on the manual sort to the doc-string. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-11 | Abstract 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> | |||
| 2024-09-11 | Update 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> | |||
| 2024-09-06 | Modify endpoint to use query string. | Alexander_Kabui | |
| 2024-09-06 | Merge pull request #188 from genenetwork/chores/merge-gnqa-api | Alexander Kabui | |
| Chores/merge gnqa api | |||
| 2024-09-05 | Update comment explaining why CONSTRUCT doesn't respect ORDER BY. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Correctly get categories in response. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Sort the RIF history data in reverse order. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Enforce array type to "categories" and "pmids" fields. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Set OPTIONAL values to default to an empty string. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Rename "pubmed_id" -> "pubmed_ids" to be explicit it's an array. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Remove type from wiki history. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Fix type error. | Munyoki Kilyungi | |
| * gn3/api/metadata_api/wiki.py: Remove FIXME comment. * gn3/db/wiki.py: Fix type error. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Use the correct header to request json-ld data. | Munyoki Kilyungi | |
| In HTTP, we use content negotiation to server different representations of a resource to the same URI to help the user agent specify which representation is best suited for the user: <https://developer.mozilla.org/en-US/docs/Web/HTTP/Content_negotiation> The "Accept" requet HTTP indicates which content types the user is supposed to understand: <https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Accept> * gn3/api/metadata_api/wiki.py (get_wiki_entries): Use the "Accept" header. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Add 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> | |||
| 2024-09-05 | Always 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> | |||
| 2024-09-05 | Use correct prefix when querying for email in triple. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Create global wiki context usable by all functions in gn3.rdf.wiki | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Ignore type error and add a FIXME stub. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Add missing doc-strings to make pylint pass. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-05 | Restructure 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> | |||
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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