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2024-09-27Bug: Use absolute path in place of relative pathFrederick 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.
2024-09-19Remove 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>
2024-09-18Pass 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>
2024-09-18Pass 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>
2024-09-18Get 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>
2024-09-18Update "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>
2024-09-18Fix typo.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-17Fix 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>
2024-09-17feat: require auth for edit api callJohn Nduli
2024-09-12Fix pylint errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-12feat: pick results from sqlite3 if they were storedJohn Nduli
2024-09-12Initialise the package to ensure setuptools finds it.Frederick Muriuki Muriithi
2024-09-12Make sure dir exists before running R/qtlPjotr Prins
2024-09-12Replace TMPDIR/output with TMPDIR/gn3 so it is clear where it comes fromPjotr Prins
2024-09-12rqtl_wrapper: minor fixesPjotr Prins
2024-09-12Make sure TMPDIR directories exist!Pjotr Prins
2024-09-12Move assert_paths_exist into fs_helpersPjotr Prins
2024-09-12Change behavior of do_paths_exist to actually throw useful errorPjotr Prins
2024-09-12Getting Rqtl to run on fallbackPjotr Prins
2024-09-12Move assert_paths_exist into fs_helpersPjotr Prins
2024-09-12Change behavior of do_paths_exist to actually throw useful errorPjotr Prins
2024-09-12Make the gnqa search endpoint a get request.Alexander_Kabui
2024-09-11Replace 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>
2024-09-11Run python-black against file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-06Modify endpoint to use query string.Alexander_Kabui
2024-09-06Merge pull request #188 from genenetwork/chores/merge-gnqa-apiAlexander Kabui
Chores/merge gnqa api
2024-09-05Fix 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>
2024-09-05Use 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>
2024-09-05Add 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>
2024-09-05Ignore type error and add a FIXME stub.Munyoki 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>
2024-09-05Sort previos records by datetime.Alexander_Kabui
2024-09-05Apply pep8 formatting.Alexander_Kabui
2024-09-05Create new endpoints for fetching user previous records.Alexander_Kabui
2024-09-03Remove unused imports.Alexander_Kabui
2024-09-03Use Jsonb for storing results.Alexander_Kabui
2024-09-02Fix spacing after punctuation.Alexander_Kabui
2024-09-02Use default datetime for table.Alexander_Kabui
2024-09-02Add spacing after punctuation.Alexander_Kabui
2024-08-30Fix merge conflict.Alexander_Kabui
2024-08-29docs: add function commentsJohn Nduli
2024-08-29feat: add api calls to get categories and last commentJohn Nduli
2024-08-29Add default timestamp and and primary key for Rating table.Alexander_Kabui
2024-08-29Fix minor typo.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Check for empty values when fetching search history.Alexander_Kabui
2024-08-29Use correct http method `Delete` for search history.Alexander_Kabui
2024-08-29Update gnqa search endpoint from POST to PUT.Alexander_Kabui
2024-08-26Fix mypy errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-26Move "GET /wiki/<symbol>" end-point to gn3.api.metadata.wiki.Munyoki Kilyungi
* gn3/api/metadata.py (get_wiki_entries): Move this... * gn3/api/metadata_api/wiki.py (edit_wiki): ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-26Auto-pep8 buffer and ignore type check for payload.Munyoki Kilyungi
* gn3/api/metadata_api/wiki.py (edit_wiki): Ignore type-check for payload. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 08:32:19 +0000