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2024-06-18refactor: drop global variablesJohn Nduli
2024-06-17Check table names in Xapian; if not, default to "-1".Munyoki Kilyungi
Without this check, there will always be an error when this script is run with the "is-data-modified" flag should there be no database in the XAPIAN_DIRECTORY. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-17Fetch distinct comments.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-14fix: typehints in index-genenetwork scriptJohn Nduli
2024-06-14fix: fix incorrect parameters in index_query functionJohn Nduli
2024-06-12Move the generated xapian files to the correct directory.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Set the file path for the logger.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Change the date format for the logger.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Log how long it takes to run the indexing script.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Check for a running process by viewing the build dir's contents.Munyoki Kilyungi
In the CI build, the actual build is run in the xapian_directory/build, which is seen as the xapian_directory in this script. The CI handles clean up WRT removing files related to the build process. * scripts/index-genenetwork (create_xapian_index): Create the xapian directory if it doesn't exist. If the xapian directory has files, exit. Create the temporary directory inside the xapian_directory. Remove "build_directory.rmdir()" Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Return 0 if data changes, else exit with 1.Munyoki Kilyungi
* scripts/index-genenetwork (is_data_modified): Replace click.echo with the respective sys.exit call. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Explicitly pass sparql_uri to script.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Rework how the indexes are built.Munyoki Kilyungi
Right now, the checks are done in Guix's build expression. This moves that work to the index-genenetwork script.
2024-06-12Add method to check the validity of the tables+RDF checksums.Munyoki Kilyungi
* scripts/index-genenetwork (verify_checksums): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Generate a SHA256 checksum for the generif graph.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12refactor: add db_utils global logger that will be the defaultJohn Nduli
2024-06-12fix: use current_app's logger to log db errorsJohn Nduli
2024-06-12fix: log errors when an exception occurs due to db_utilsJohn Nduli
2024-06-01Use global cache to store generif metadata.Munyoki Kilyungi
This global caches has 3,528 entries and there's no expectation for it to grow significantly. Since child processes inherit the parent’s memory, we can pass the global cache to them, reducing fetch times from 0.001s to 0.00001s, significantly boosting performance when indexing the entire database and enriching results with RDF metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-01Add geneRIF prefix.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-01Add geneRIF to gene index.Munyoki Kilyungi
* scripts/index-genenetwork: Import Template, lru_cache, SPARQLWrapper, JSON (get_rif_metadata): New function. (index_rif_comments): New function. (index_genes): Add rif comments to probeset index. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-20Delete search endpoints for datasets/publications.Munyoki Kilyungi
* gn3/api/metadata.py: Delete "query_and_frame" import. (search_datasets): Delete. (search_publications): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-20Remove unused variable.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-09Improve error messaging for use of invalid fahamu token.Alexander_Kabui
2024-05-01pep8 formattingAlexander_Kabui
2024-05-01Delete debug codeAlexander_Kabui
2024-05-01Debug: check for if config is loaded in gn3.Alexander_Kabui
2024-05-01Fix: fix string formatting error and remove unused imports.Alexander_Kabui
2024-05-01RefactoringAlexander_Kabui
*general cleanup for debug code * improve error messaging for successful rating
2024-05-01Debug:fix issue use current_app to fetch configAlexander_Kabui
2024-05-01Debug Process for LLM_DB_PATHAlexander_Kabui
* this commit is a debugging process for llm_path on cd * issue: writes to db but not correct path
2024-05-01Load LLM_DB_PATH as a setting.Alexander_Kabui
2024-05-01Add more error info for Database Open error raisedAlexander_Kabui
2024-04-30Merge pull request #159 from genenetwork/chores/update-llm-db-configurationAlexander Kabui
Chores/update llm db configuration
2024-04-30Add a general Exception for the /rating apiAlexander_Kabui
2024-04-30Replace SQLITE_DB_PATH with LLM_DB_PATH for llm db path.Alexander_Kabui
2024-04-30Update LLM_DB_PATH config.Alexander_Kabui
2024-04-30Add docstring to view_history function.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-30Use JWT tokens from gn-auth.Munyoki Kilyungi
* gn3/api/metadata.py: Import time, jwt, AUthorisationError. (edit_dataset): Use JWT tokens from gn-auth and validate them. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-30Add an endpoint to query a dataset's git history from it's id.Munyoki Kilyungi
* gn3/api/metadata.py: Import get_history. (view_history): New endpoint. * gn3/db/datasets.py (get_history): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-30Add a method for saving a dataset's metadata to git.Munyoki Kilyungi
* gn3/db/datasets.py (retrieve_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-30Rename retrieve_dataset_metadata to retrieve_metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-30Remove an f-string that doesn't have any interpolated variables.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-30Add command function that returns an Either monad.Munyoki Kilyungi
* gn3/commands.py: Import Either, Left, Right. (monadic_run_cmd): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-29Prevent error when group isn't in parents/f1s JSON filezsloan
2024-04-15Delete unused imports.Munyoki Kilyungi
* gn3/api/llm.py: (rate_document, logging): Remove unused imports. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-15Fix error in flycheck-mode check in .dir-locals.pyMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-15Remove empty '() in .dir-locals.elMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-15Show trailing white spaces in python-mode.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-15Update ".dir-locals.el" with same python defaults.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-30 06:44:38 +0000