| Age | Commit message (Expand) | Author |
|---|
| 2024-01-26 | Feature/gn llm caching (#148)•••* add logic for querying user gnqa search result
* add api endpoints for querying users:qnqa-search-terms,gnqa-results | Alexander Kabui |
| 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)•••* refactor code for processing response from fahamu client
* Add tests for gn-llm | Alexander Kabui |
| 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.•••* .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>
| Munyoki Kilyungi |
| 2024-01-10 | Optionally fetch dataset metadata if provided during genotype fetch.•••* 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>
| Munyoki Kilyungi |
| 2024-01-10 | Switch to gnt:belongsToSpecies in genotype queries.•••* gn3/api/metadata.py (genotypes): Use gnt:belongsToSpecies instead of
xkos:classifiedUnder when querying for species.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-10 | Remove hard-coded dataset name.•••* gn3/api/metadata.py (probesets): Remove hard-coded "HC_M2_0606_P" in
probeset RDF query.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-08 | add json file for all references | Alexander_Kabui |
| 2024-01-08 | Update retry parameters for custom requests to Fahamu AI endpoint.•••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>
| Munyoki Kilyungi |
| 2024-01-08 | disable process wait | Alexander_Kabui |
| 2024-01-06 | Remove extra gene metadata from query as it's un-necessary.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-06 | Add extra keys to the Probeset's json-ld context.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-06 | Refactor gene symbol handling and add references to probeset.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-06 | Use gnt:geneSymbol property to fetch genes in Probeset RDF query.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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.•••* guix-system.scm: Delete file.
| Arun Isaac |
| 2024-01-03 | Do not log user information.•••* gn3/app.py (create_app): Do not log user information.
| Arun Isaac |
| 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)•••* 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 | Alexander Kabui |
| 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.•••* .guix/genenetwork3-package.scm: Import python-pylint from (gnu packages
check) and python-mypy from (gnu packages python-check).
(genenetwork3-all-tests): New variable.
| Arun Isaac |
| 2023-12-15 | Update RDF ProbeSet query.•••* gn3/api/metadata.py (probesets): Update RDF query.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-15 | First frame and then compact probeset results.•••* 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>
| Munyoki Kilyungi |
| 2023-12-15 | Update ProbeSet's context.•••* gn3/api/metadata.py (probesets): Update context.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-15 | Update BASE_CONTEXT entries.•••* gn3/api/metadata.py: (PHENOTYPE_CONTEXT): Move "rdfs", "gnt",
"gnc"...
(BASE_CONTEXT): ... here.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-07 | Fix typo in GoTree prefix.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-07 | Add optional property for platform info in dataset representation.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-07 | Fetch normalization metadata correctly.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-07 | Fix typo in platform prefix.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-07 | Refactor metadata mappings for improved dataset representation.•••* gn3/api/metadata.py: (DATASET_CONTEXT): Remove "ex:" prefixes. Add
new prefixes for citation, platform, GoTree, tissueInfo, contactWebUrl
and contactName.
(datasets): Update query.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-07 | Update phenotype queries to use gnt:belongsToGroup.•••* gn3/api/metadata.py (phenotypes): Use gnt:belongsToGroup instead of xkos:classifiedUnder.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
