| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | |
| 2024-01-05 | max delay time | Alexander_Kabui | |
| 2024-01-05 | increase number of retries | Alexander_Kabui | |
| 2024-01-03 | fix fetch token error from curent app | Alexander_Kabui | |
| 2024-01-03 | pylint fixes | Alexander_Kabui | |
| 2024-01-03 | fetch auth token from current app | Alexander_Kabui | |
| 2024-01-03 | load gn3 secret file | Alexander_Kabui | |
| 2024-01-03 | Delete obsolete Guix system definition. | Arun Isaac | |
| * guix-system.scm: Delete file. | |||
| 2024-01-03 | Do not log user information. | Arun Isaac | |
| * gn3/app.py (create_app): Do not log user information. | |||
| 2023-12-29 | handle exception for request error | Alexander_Kabui | |
| 2023-12-29 | fix mypy issues | Alexander_Kabui | |
| 2023-12-22 | Feature/gn llms (#140) | Alexander Kabui | |
| * add entry route for gn_llms * add gn_llms reference doc ids * init authorization module for gn-llm * Add class for parsing unprocessable response * add init config file * add clienmodule:gn-llm fahamu interface * Add module descriptor for client file * reponse data handler * add response file handler * add processing file * remove unnecessary files * init code refactoring * Restructure code to module * refactor code:disble pylint for testing on cd | |||
| 2023-12-22 | setup.py: Find packages automatically using find_packages. | Arun Isaac | |
| 2023-12-19 | README: Replace pylint and mypy CI badges with all-tests CI badge. | Arun Isaac | |
| 2023-12-19 | guix: Add genenetwork3-all-tests. | Arun Isaac | |
| * .guix/genenetwork3-package.scm: Import python-pylint from (gnu packages check) and python-mypy from (gnu packages python-check). (genenetwork3-all-tests): New variable. | |||
| 2023-12-15 | Update RDF ProbeSet query. | Munyoki Kilyungi | |
| * gn3/api/metadata.py (probesets): Update RDF query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-15 | First frame and then compact probeset results. | Munyoki Kilyungi | |
| * gn3/api/metadata.py: Reshape the data in a nice way by first framing and compacting the json-ld result. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-15 | Update ProbeSet's context. | Munyoki Kilyungi | |
| * gn3/api/metadata.py (probesets): Update context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-15 | Update BASE_CONTEXT entries. | Munyoki Kilyungi | |
| * gn3/api/metadata.py: (PHENOTYPE_CONTEXT): Move "rdfs", "gnt", "gnc"... (BASE_CONTEXT): ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-07 | Fix typo in GoTree prefix. | 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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