| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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> | |||
| 2024-02-13 | Use correct path for dataset metadata files. | Munyoki Kilyungi | |
| * gn3/api/metadata.py (datasets): Use "gn-docs/general/datasets". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-13 | Fetch extra metadata from text-files when fetching datasets. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-13 | Update "dataset/<name>" API endpoint to fetch metadata from files. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-13 | Retrieve metadata from text files given a path. | Munyoki Kilyungi | |
| * gn3/db/datasets.py (retrieve_trait_dataset): New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-12 | pep8 formatting | Alexander_Kabui | |
| 2024-01-30 | Add the traceback to the exceptions for display. | Frederick Muriuki Muriithi | |
| 2024-01-26 | centralize common errors | Alexander_Kabui | |
| 2024-01-26 | Feature/gn llm caching (#148) | Alexander Kabui | |
| * add logic for querying user gnqa search result * add api endpoints for querying users:qnqa-search-terms,gnqa-results | |||
| 2024-01-17 | fix error message for empty responses | Alexander_Kabui | |
| 2024-01-17 | Adjust retry parameters and response handling in custom_request | Alexander_Kabui | |
| 2024-01-17 | Increase timeout to 30s to fix 'Read timed out issue | Alexander_Kabui | |
| 2024-01-17 | Enhance error response message in API endpoint | Alexander_Kabui | |
| 2024-01-17 | max no of retries for user to fahamu api | Alexander_Kabui | |
| 2024-01-17 | fix pylint errors | Alexander_Kabui | |
| 2024-01-17 | temp fix:disable pylint check | Alexander_Kabui | |
| 2024-01-17 | Refactor llms.process: Rename getGNQA to get_gnqa | Alexander_Kabui | |
| 2024-01-17 | Feature/gn llm refactoring (#147) | Alexander Kabui | |
| * refactor code for processing response from fahamu client * Add tests for gn-llm | |||
| 2024-01-16 | add api endpoint for rating reference documents (#146) | Alexander Kabui | |
| 2024-01-10 | Add extra pylint rule to except files that are too long. | Munyoki Kilyungi | |
| * .pylintrc (disable): Include "too-many-lines" rule in the list of exceptions. The RDF queries are lengthy, causing lines in files to be too long. Currently, a workaround is to disable this rule, as abstracting the queries elsewhere doesn't make sense. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-10 | Optionally fetch dataset metadata if provided during genotype fetch. | Munyoki Kilyungi | |
| * gn3/api/metadata.py (genotypes): If a dataset name is provided fetch the group it belongs to and the dataset's full and short name. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-10 | Switch to gnt:belongsToSpecies in genotype queries. | Munyoki Kilyungi | |
| * gn3/api/metadata.py (genotypes): Use gnt:belongsToSpecies instead of xkos:classifiedUnder when querying for species. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-10 | Remove hard-coded dataset name. | Munyoki Kilyungi | |
| * gn3/api/metadata.py (probesets): Remove hard-coded "HC_M2_0606_P" in probeset RDF query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-08 | merge for latest commits | Alexander_Kabui | |
| 2024-01-08 | fix query formatting and increase no retries | Alexander_Kabui | |
| 2024-01-08 | Optionally fetch dataset metadata if provided during probeset fetch. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-08 | add json file for all references | Alexander_Kabui | |
| 2024-01-08 | Update retry parameters for custom requests to Fahamu AI endpoint. | Munyoki Kilyungi | |
| ATM the GN3 times out with the following trace: ``` 2024-01-08 09:33:08 [2024-01-08 09:33:08 +0000] [50] [CRITICAL] WORKER TIMEOUT (pid:1589) ``` * gn3/llms/client.py (GeneNetworkQAClient.custom_request): Update max_retries and retry_delay. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-08 | disable process wait | Alexander_Kabui | |
| 2024-01-06 | Remove extra gene metadata from query as it's un-necessary. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-06 | Add extra keys to the Probeset's json-ld context. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-06 | Refactor gene symbol handling and add references to probeset. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-06 | Use gnt:geneSymbol property to fetch genes in Probeset RDF query. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-05 | http request header fixes | Alexander_Kabui | |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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