| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-12-20 | Add todo note for writing rqtl file. | Alexander_Kabui | |
| 2024-12-20 | fix: Pylint fixes. | Alexander_Kabui | |
| 2024-12-20 | feat: Enable streaming for output. | Alexander_Kabui | |
| 2024-12-17 | feat: Init integrate streaming functionality to rqtl1. | Alexander_Kabui | |
| 2024-12-07 | Check whether genofile/phenofile exist separately. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-12-04 | Temp disable with for test Popen processes. | Alexander_Kabui | |
| 2024-12-04 | refactor: make pylint fixes. | Alexander_Kabui | |
| 2024-11-28 | feat: define general endpoint for streaming stdout using unique identifier. | Alexander_Kabui | |
| 2024-11-27 | feat: return run id for compute and streaming api's. | Alexander_Kabui | |
| 2024-11-26 | feat: Implement reading from file functionality | Alexander_Kabui | |
| Implement read from the last position for a file. | |||
| 2024-11-22 | feat: return pointer position from where the file was last read. | Alexander_Kabui | |
| 2024-11-22 | feat: Add new endpoint to read stdout given a file identifier. | Alexander_Kabui | |
| 2024-11-22 | feat: implement ednpoint for computing qtl using rqtl2. | Alexander_Kabui | |
| Capture stdout results to a file. | |||
| 2024-10-18 | refactor: replace gn3.auth.db with gn3.sqlite_db_utils and drop all refs to ↵ | John Nduli | |
| gn3.auth | |||
| 2024-10-18 | refactor: move definition of auth errs and remove auth cli utils | John Nduli | |
| 2024-10-15 | Lint: Fix linting errors. | Frederick Muriuki Muriithi | |
| 2024-10-15 | Pass in correct file path. | Frederick Muriuki Muriithi | |
| 2024-10-15 | fix: use require_token to validate gn3 apis | John Nduli | |
| 2024-10-14 | Add end-point for fetching NCBI metadata. | Munyoki Kilyungi | |
| * gn3/api/metadata.py: Register "wiki.rif_blueprint". * gn3/api/metadata_api/wiki.py: Import "get_rif_entries_by_symbol". [rif_blueprint]: New blueprint. (get_ncbi_rif_entries): New endpoint: "metadata/rif/<symbol>". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-30 | chore: pylint code fix | John Nduli | |
| 2024-09-30 | feat: rollback mysql transaction when rdf insert fails | John Nduli | |
| 2024-09-27 | Bug: Use absolute path in place of relative path | Frederick Muriuki Muriithi | |
| Prior to this commit, an assumption is made that the application is invoked with the root of the repository being the current working directory. If this assumption is not met, then the system will not find the appropriate path. This commit forces the use of an absolute path, which should help avoid issues with misplaced relative paths. | |||
| 2024-09-19 | Remove extraneous keyword. | Munyoki Kilyungi | |
| * gn3/api/metadata_api/wiki.py (edit_wiki): Remove comment_id from args---it's already in the insert_dict. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-18 | Pass in insert_dict instead of payload in "get_wiki_entries". | Munyoki Kilyungi | |
| * 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> | |||
| 2024-09-18 | Pass in the createtime as an arg when inserting into RDF graph. | Munyoki Kilyungi | |
| * 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> | |||
| 2024-09-18 | Get the next versionId from SQL. | Munyoki Kilyungi | |
| * 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> | |||
| 2024-09-18 | Update "POST /wiki/comment_id/edit" to have RDF edits. | Munyoki Kilyungi | |
| * gn3/api/metadata_api/wiki.py: Import update_wiki_comment. (edit_wiki): Update wiki in RDF. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-18 | Fix typo. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-17 | Fix C0411/C0412 pylint errors in gn3.api.metadata.api.wiki. | Munyoki Kilyungi | |
| * gn3/api/metadata_api/wiki.py: Re-order imports to fix pylint errors. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-17 | feat: require auth for edit api call | John Nduli | |
| 2024-09-12 | Fix pylint errors. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-12 | feat: pick results from sqlite3 if they were stored | John Nduli | |
| 2024-09-12 | Initialise the package to ensure setuptools finds it. | Frederick Muriuki Muriithi | |
| 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 | rqtl_wrapper: minor fixes | Pjotr Prins | |
| 2024-09-12 | Make sure TMPDIR directories exist! | 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 | 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 | 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 | Run python-black against file. | Munyoki Kilyungi | |
| 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 | 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> | |||
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
| about summary refs log tree commit diff |