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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>
2024-09-18Add method that inserts new RIF comments.Munyoki Kilyungi
* gn3/db/rdf/wiki.py: Import datetime, update_rdf. (update_wiki_comment): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Fetch symbol by it's name.Munyoki Kilyungi
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>
2024-09-18Fetch the next comment version in RDF.Munyoki Kilyungi
* gn3/db/rdf/wiki.py (get_next_comment_version): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Rename sparql_construct_query -> sparql_query.Munyoki Kilyungi
* 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>
2024-09-18Add new method for updating RDF Graph content.Munyoki Kilyungi
* gn3/db/rdf/__init__.py: Import POST, DIGEST, JSON. (update_rdf): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-18Run python-black against file.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>
2024-09-17fix: error when result dict contains NoneJohn Nduli
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
2024-09-12BugFix: assign value and use variable.Frederick Muriuki Muriithi
2024-09-12Fix failing tests after merging in Pjotr's pull request.Frederick Muriuki Muriithi
2024-09-12Gracefully print out debug messages even outside app contextFrederick 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.
2024-09-12From gn3 only use TMPDIR/gn3 pathsPjotr Prins
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
2024-09-12Modify script paths so they can be edited in GuixPjotr Prins
2024-09-12rqtl_wrapper: minor fixesPjotr Prins
2024-09-12Mistake using envvarPjotr Prins
2024-09-12Make sure TMPDIR directories exist!Pjotr Prins
2024-09-12Getting Rqtl to run on fallbackPjotr Prins
2024-09-12assert_paths_exist: make throw_error optionalPjotr Prins
2024-09-12gn3/errors.py: add stack trace to error logPjotr 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
2024-09-12assert_paths_exist: make throw_error optionalPjotr 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
2024-09-11Minor typo fix.Alexander_Kabui
2024-09-11Update docs on use for custom request when query fahamu Api.Alexander_Kabui
2024-09-11Update 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>
2024-09-11Handle case when result is empty when sanitizing json-ld result.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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>
2024-09-11Fix mypy errors.Munyoki Kilyungi
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>
2024-09-11Move comment on the manual sort to the doc-string.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-11Abstract 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>
2024-09-11Update 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>
2024-09-06Modify endpoint to use query string.Alexander_Kabui
2024-09-06Merge pull request #188 from genenetwork/chores/merge-gnqa-apiAlexander Kabui
Chores/merge gnqa api
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 05:02:09 +0000