| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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> | |||
| 2024-04-15 | Fix error in flycheck-mode check in .dir-locals.py | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-15 | Remove empty '() in .dir-locals.el | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-15 | Show trailing white spaces in python-mode. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-15 | Update ".dir-locals.el" with same python defaults. | Munyoki Kilyungi | |
| 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 | |
| 2024-03-25 | ignore missing import for biopython | 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 | Merge pull request #154 from genenetwork/feature/pubmed-metadata | Alexander Kabui | |
| pubmed metadata | |||
| 2024-03-18 | pep8 formatting | Alexander_Kabui | |
| 2024-03-18 | delete test file | Alexander_Kabui | |
| 2024-03-18 | fetch pubmed data from tmpdir | Alexander_Kabui | |
| 2024-03-18 | pep8 formatting | 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. | |||
| 2024-03-13 | Add documentation on what the script is for and does. | Frederick Muriuki Muriithi | |
| 2024-03-13 | Remove debug prints in the script | Frederick Muriuki Muriithi | |
| 2024-03-12 | Commit migration script for CaseAttribute* tables | Frederick Muriuki Muriithi | |
| 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> | |||
| 2024-02-14 | Delete trailing space. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-14 | Remove try ... except clauses around RDF endpoints. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-14 | Minor pep-8 fixes. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-14 | Handle sparql errors at the app level. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-14 | raise error for fahamu api 0 task_id | Alexander_Kabui | |
| 2024-02-14 | Stem the dataset's id before constructing the path. | 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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