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2024-09-23Fix or ignore pylint errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Revert "Remove one-line if/else statement."Munyoki Kilyungi
This reverts commit 0d15840913c9cc401d1e74295aa5e17e34f2987b. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Add section on setting up virtuoso locally.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Update docs to use default virtuoso ports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Update docs on how to use SPARQL default ports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Remove one-line if/else statement.Munyoki Kilyungi
* gn3/db/rdf/wiki.py (__sanitize_result): When fetching pubmed_ids and categories, default to [] if the key misses, and remove the subsequent one-line if/else statement. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Load GN3_SECRETS after loading GN3_CONF settings.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Remove dead comment.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Make sure the the test graph is empty before running rdf tests.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Update docs to highlight sparql conf params in SECRETS file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Use correct object modifier for a label when inserting a comment.Munyoki Kilyungi
* gn3/db/rdf/wiki.py (update_wiki_comment) [query]: Replace "rdf:label" with "rdfs:label". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Update docstring for "update_wiki_comment".Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Use correct object modifier in triple when fetching comment history.Munyoki Kilyungi
* gn3/db/rdf/wiki.py (get_comment_history) [query]: Replace ?symbolName with ?symbolName. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Use test fixtures to set-up a test named graph.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Add RDF test cases.Munyoki Kilyungi
* pytest.ini: Add rdf pytest marker. * tests/test_data/ttl-files/test-data.ttl: New file with turtle test data for RIF editing. * tests/unit/db/rdf/test_wiki.py (test_sanitize_result): New test case. (test_get_comment_history): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Use correct modifier when getting species name in SPARQL.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Remove dead variable from RDF query.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Alphabetically sort the categories and pubmed_ids array.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Remove un-necessary triple in comment history RDF query.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-19Use correct return type.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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 docs with extra conf vars for updating virtuoso.Munyoki Kilyungi
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.
2024-09-12Bump versionPjotr Prins
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
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