Age | Commit message (Collapse) | Author |
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* refactor code for processing response from fahamu client
* Add tests for gn-llm
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* 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>
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* gn3/api/metadata.py (genotypes): Use gnt:belongsToSpecies instead of
xkos:classifiedUnder when querying for species.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (probesets): Remove hard-coded "HC_M2_0606_P" in
probeset RDF query.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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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>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/app.py (create_app): Do not log user information.
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* 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
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* gn3/api/metadata.py (probesets): Update RDF query.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* 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>
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* gn3/api/metadata.py (probesets): Update context.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py: (PHENOTYPE_CONTEXT): Move "rdfs", "gnt",
"gnc"...
(BASE_CONTEXT): ... here.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* 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>
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* gn3/api/metadata.py (phenotypes): Use gnt:belongsToGroup instead of xkos:classifiedUnder.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (phenotypes): Delete "args".
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (phenotypes): Add "/phenotypes/<group>/<name>"
to this endpoint.
(fetch_phenotype_by_group): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (phenotypes): Filter for "dcat:Dataset" in
json-ld context.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (phenotypes): Delete "name" from template
substitution.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (search_datasets): Return distinct search
results.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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