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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 GeneNetwork3...GN3 provides an API to provide data, and needs no HTML UI. Frederick Muriuki Muriithi
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"....* gn3/computations/qtlreaper.py: Disable "too-many-arguments" pylint check. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-25Fix line-too-long error....* 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> Munyoki Kilyungi
2024-02-25Correctly handle URLError....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> Munyoki Kilyungi
2024-02-25Construct genofile_path using pathlib module....* gn3/db/datasets.py: Remove os import. (retrieve_sample_list): Replace os.path with Path. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-19Pass qtlreaper command path as argument to run_reaper...Originally the system would get the path from the environment zsloan
2024-02-15Use correct names for dataset entries in json result....Since we are appending to an already flattened json-ld file, we don't need to add the prefixes. * gn3/api/metadata.py (DATASET_CONTEXT): Add missing "experimentType" key. * gn3/db/datasets.py (retrieve_dataset_metadata): Match the __subject dict with entries from DATASET_CONTEXT. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-14Delete type hints from handle_sparql_errors....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-14Delete trailing space....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-14Remove try ... except clauses around RDF endpoints....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-14Minor pep-8 fixes....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-14Handle sparql errors at the app level....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-14raise error for fahamu api 0 task_idAlexander_Kabui
2024-02-14Stem the dataset's id before constructing the path....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-13Use correct path for dataset metadata files....* gn3/api/metadata.py (datasets): Use "gn-docs/general/datasets". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-13Fetch extra metadata from text-files when fetching datasets....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-13Update "dataset/<name>" API endpoint to fetch metadata from files....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-13Retrieve metadata from text files given a path....* gn3/db/datasets.py (retrieve_trait_dataset): New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-12pep8 formattingAlexander_Kabui
2024-01-30Add the traceback to the exceptions for display.Frederick Muriuki Muriithi
2024-01-26centralize common errorsAlexander_Kabui
2024-01-26Feature/gn llm caching (#148)...* add logic for querying user gnqa search result * add api endpoints for querying users:qnqa-search-terms,gnqa-resultsAlexander Kabui
2024-01-17fix error message for empty responsesAlexander_Kabui
2024-01-17Adjust retry parameters and response handling in custom_requestAlexander_Kabui
2024-01-17Increase timeout to 30s to fix 'Read timed out issueAlexander_Kabui
2024-01-17Enhance error response message in API endpointAlexander_Kabui
2024-01-17max no of retries for user to fahamu apiAlexander_Kabui
2024-01-17Refactor llms.process: Rename getGNQA to get_gnqaAlexander_Kabui