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2024-11-26feat: Implement reading from file functionalityAlexander_Kabui
Implement read from the last position for a file.
2024-11-22feat: return pointer position from where the file was last read.Alexander_Kabui
2024-11-22feat: Add new endpoint to read stdout given a file identifier.Alexander_Kabui
2024-11-22feat: register rqtl2 blueprint to app.Alexander_Kabui
2024-11-22feat: implement ednpoint for computing qtl using rqtl2.Alexander_Kabui
Capture stdout results to a file.
2024-11-15Fix bug where case attribute editing didn't work if a case attribute waszsloan
called 'Strain' This is because the code was also using 'Strain' for the strain name. At least for the time being, I addressed this by changing those instances to 'Sample' instead (which I don't believe is ever a case attribute name).
2024-11-14Fix auth endpoint for case attribute editingzsloan
2024-11-14Fix case attribute queryzsloan
2024-11-12Remove unused setting.Frederick Muriuki Muriithi
The BCRYPT_SALT setting is not used anywhere in GN3 or GN2
2024-11-12Remove unused import.Frederick Muriuki Muriithi
2024-11-12mypy: Rename and annotate variables to silence mypyFrederick Muriuki Muriithi
2024-11-12Pure aesthetics: No functional change.Frederick Muriuki Muriithi
This commit has no functional change it implements. It is purely a aesthetics change to please Frederick.
2024-11-11Allow extra database connection options on URIFrederick Muriuki Muriithi
Update the database URI parsing to allow setting of extra connection option on the URI string.
2024-10-28fix: remove dangerous default configs and have a detailed error with how to ↵John Nduli
configure
2024-10-18refactor: replace gn3.auth.db with gn3.sqlite_db_utils and drop all refs to ↵John Nduli
gn3.auth
2024-10-18refactor: move definition of auth errs and remove auth cli utilsJohn Nduli
2024-10-18refactor: remove unused gn3.auth modulesJohn Nduli
2024-10-15Lint: Fix linting errors.Frederick Muriuki Muriithi
2024-10-15Pass in correct file path.Frederick Muriuki Muriithi
2024-10-15fix: use require_token to validate gn3 apisJohn Nduli
2024-10-14Run python black against file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Replace CONSTRUCT with SELECT for fetching RIF NCBI entries.Munyoki Kilyungi
* gn3/db/rdf/wiki.py: Delete datetime import. Import sparql_query. [RIF_CONTEXT]: Delete. (get_rif_entries_by_symbol): Replace CONSTRUCT with SELECT. * tests/unit/db/rdf/test_wiki.py (test_get_rif_entries_by_symbol): Update tests. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Add 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>
2024-10-14Add function for fetching NCBI data.Munyoki Kilyungi
* gn3/db/rdf/wiki.py: Import datetime. [RIF_CONTEXT]: New global variable defining the json-ld context for NCBI rif data. (get_rif_entries_by_symbol): New function. * tests/unit/db/rdf/data.py: New file containing expected NCBI test data. * tests/unit/db/rdf/test_wiki.py (test_update_wiki_comment): New test case. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-30chore: pylint code fixJohn Nduli
2024-09-30feat: rollback mysql transaction when rdf insert failsJohn Nduli
2024-09-30fix: rdf and sql queries for fetching rif dataJohn Nduli
SQL queries fail because we get bytes instead of strings which cannot be decoded. We decode results from DictCursor to fix this. For RDF, we cast `?symbol` to a string.
2024-09-27Debug command.Frederick Muriuki Muriithi
2024-09-27Bug: Use absolute paths in place of relative paths.Frederick Muriuki Muriithi
Similar issue to commit 11d543eeca08fe0df4bf2be7222234fadb516a51
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.
2024-09-23Revert "Remove one-line if/else statement."Munyoki Kilyungi
This reverts commit 0d15840913c9cc401d1e74295aa5e17e34f2987b. 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>
2024-09-23Use 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 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 "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>
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-11-24 23:16:05 +0000