| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-05-01 | Delete debug code | Alexander_Kabui | |
| 2024-05-01 | Debug: check for if config is loaded in gn3. | Alexander_Kabui | |
| 2024-05-01 | Fix: fix string formatting error and remove unused imports. | Alexander_Kabui | |
| 2024-05-01 | Refactoring | Alexander_Kabui | |
| *general cleanup for debug code * improve error messaging for successful rating | |||
| 2024-05-01 | Debug:fix issue use current_app to fetch config | Alexander_Kabui | |
| 2024-05-01 | Debug Process for LLM_DB_PATH | Alexander_Kabui | |
| * this commit is a debugging process for llm_path on cd * issue: writes to db but not correct path | |||
| 2024-05-01 | Load LLM_DB_PATH as a setting. | Alexander_Kabui | |
| 2024-05-01 | Add more error info for Database Open error raised | Alexander_Kabui | |
| 2024-04-30 | Add a general Exception for the /rating api | Alexander_Kabui | |
| 2024-04-30 | Replace SQLITE_DB_PATH with LLM_DB_PATH for llm db path. | Alexander_Kabui | |
| 2024-04-30 | Update LLM_DB_PATH config. | Alexander_Kabui | |
| 2024-04-30 | Add docstring to view_history function. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-30 | Use 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> | |||
| 2024-04-30 | Add 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> | |||
| 2024-04-30 | Add 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> | |||
| 2024-04-30 | Rename retrieve_dataset_metadata to retrieve_metadata. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-30 | Remove an f-string that doesn't have any interpolated variables. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-30 | Add 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> | |||
| 2024-04-29 | Prevent error when group isn't in parents/f1s JSON file | zsloan | |
| 2024-04-15 | Delete unused imports. | Munyoki Kilyungi | |
| * gn3/api/llm.py: (rate_document, logging): Remove unused imports. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-11 | Include parents/f1s in default samplelist + add boolean options for them | zsloan | |
| 2024-04-04 | Rephrase user feedback for Fahamu API in case it takes too long to respond. | Alexander_Kabui | |
| 2024-03-26 | add sqlite-db-path config | Alexander_Kabui | |
| 2024-03-26 | fetch pubmed file from /gn-meta/lit | Alexander_Kabui | |
| 2024-03-25 | pep8 formatting | Alexander_Kabui | |
| 2024-03-25 | save db data on SQLITE_PATH file path | Alexander_Kabui | |
| 2024-03-25 | fix user_id type | Alexander_Kabui | |
| 2024-03-25 | enable logigng info for api <rating> | Alexander_Kabui | |
| 2024-03-25 | match user id to type str | Alexander_Kabui | |
| 2024-03-25 | pep8 formatting | Alexander_Kabui | |
| 2024-03-25 | fetch tmpdir from current app connfig | Alexander_Kabui | |
| 2024-03-25 | fix db path issue for lllm | Alexander_Kabui | |
| 2024-03-25 | use data dir for files | Alexander_Kabui | |
| 2024-03-22 | use tmp for test db | Alexander_Kabui | |
| 2024-03-22 | dump gnqa rating data to db | Alexander_Kabui | |
| 2024-03-22 | add gnqa db path | Alexander_Kabui | |
| 2024-03-18 | delete test file | Alexander_Kabui | |
| 2024-03-18 | fetch pubmed data from tmpdir | Alexander_Kabui | |
| 2024-03-15 | add pubmed metadata | Alexander_Kabui | |
| 2024-03-15 | add error handling for invalid tokens | Alexander_Kabui | |
| 2024-03-15 | Remove ALL html templates from GeneNetwork3 | Frederick Muriuki Muriithi | |
| GN3 provides an API to provide data, and needs no HTML UI. | |||
| 2024-03-04 | Check for exception args and provide traceback. | Frederick Muriuki Muriithi | |
| 2024-03-04 | Handle generic exceptions gracefully. | Frederick Muriuki Muriithi | |
| 2024-02-25 | Disable 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> | |||
| 2024-02-25 | Fix 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> | |||
| 2024-02-25 | Correctly 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> | |||
| 2024-02-25 | Construct 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> | |||
| 2024-02-19 | Pass qtlreaper command path as argument to run_reaper | zsloan | |
| Originally the system would get the path from the environment | |||
| 2024-02-15 | Use correct names for dataset entries in json result. | Munyoki Kilyungi | |
| 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> | |||
| 2024-02-14 | Delete type hints from handle_sparql_errors. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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