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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
2024-04-30Add 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>
2024-04-11Include parents/f1s in default samplelist + add boolean options for themzsloan
2024-04-04Rephrase user feedback for Fahamu API in case it takes too long to respond.Alexander_Kabui
2024-03-26add sqlite-db-path configAlexander_Kabui
2024-03-26fetch pubmed file from /gn-meta/litAlexander_Kabui
2024-03-25pep8 formattingAlexander_Kabui
2024-03-25save db data on SQLITE_PATH file pathAlexander_Kabui
2024-03-25fix user_id typeAlexander_Kabui
2024-03-25enable logigng info for api <rating>Alexander_Kabui
2024-03-25match user id to type strAlexander_Kabui
2024-03-25pep8 formattingAlexander_Kabui
2024-03-25fetch tmpdir from current app connfigAlexander_Kabui
2024-03-25fix db path issue for lllmAlexander_Kabui
2024-03-25use data dir for filesAlexander_Kabui
2024-03-22use tmp for test dbAlexander_Kabui
2024-03-22dump gnqa rating data to dbAlexander_Kabui
2024-03-22add gnqa db pathAlexander_Kabui
2024-03-18delete test fileAlexander_Kabui
2024-03-18fetch pubmed data from tmpdirAlexander_Kabui
2024-03-15add pubmed metadataAlexander_Kabui
2024-03-15add error handling for invalid tokensAlexander_Kabui
2024-03-15Remove ALL html templates from GeneNetwork3Frederick Muriuki Muriithi
GN3 provides an API to provide data, and needs no HTML UI.
2024-03-04Check for exception args and provide traceback.Frederick Muriuki Muriithi
2024-03-04Handle generic exceptions gracefully.Frederick Muriuki Muriithi
2024-02-25Disable too-many-arguments for "run_reaper".Munyoki Kilyungi
* gn3/computations/qtlreaper.py: Disable "too-many-arguments" pylint check. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-25Fix line-too-long error.Munyoki Kilyungi
* gn3/heatmaps.py (build_heatmap): Break down call to run_reaper command into many lines to fix pylint error. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-25Correctly handle URLError.Munyoki Kilyungi
Using the `internal_server_error` function to handle URLError raised an exception because the `pnf` exception did not have some attributes. * gn3/errors.py (url_server_error): New function. (register_error_handlers): Register above function to handle URLError. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-25Construct genofile_path using pathlib module.Munyoki Kilyungi
* gn3/db/datasets.py: Remove os import. (retrieve_sample_list): Replace os.path with Path. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>