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2024-01-17temp fix:disable pylint checkAlexander_Kabui
2024-01-17Refactor llms.process: Rename getGNQA to get_gnqaAlexander_Kabui
2024-01-17Feature/gn llm refactoring (#147)Alexander Kabui
* refactor code for processing response from fahamu client * Add tests for gn-llm
2024-01-16add api endpoint for rating reference documents (#146)Alexander Kabui
2024-01-10Add 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>
2024-01-10Optionally 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>
2024-01-10Switch 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>
2024-01-10Remove 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>
2024-01-08merge for latest commitsAlexander_Kabui
2024-01-08fix query formatting and increase no retriesAlexander_Kabui
2024-01-08Optionally fetch dataset metadata if provided during probeset fetch.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-08add json file for all referencesAlexander_Kabui
2024-01-08Update 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>
2024-01-08disable process waitAlexander_Kabui
2024-01-06Remove extra gene metadata from query as it's un-necessary.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-06Add extra keys to the Probeset's json-ld context.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-06Refactor gene symbol handling and add references to probeset.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-06Use gnt:geneSymbol property to fetch genes in Probeset RDF query.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-05http request header fixesAlexander_Kabui
2024-01-05max delay timeAlexander_Kabui
2024-01-05increase number of retriesAlexander_Kabui
2024-01-03fix fetch token error from curent appAlexander_Kabui
2024-01-03pylint fixesAlexander_Kabui
2024-01-03fetch auth token from current appAlexander_Kabui
2024-01-03load gn3 secret fileAlexander_Kabui
2024-01-03Delete obsolete Guix system definition.Arun Isaac
* guix-system.scm: Delete file.
2024-01-03Do not log user information.Arun Isaac
* gn3/app.py (create_app): Do not log user information.
2023-12-29handle exception for request errorAlexander_Kabui
2023-12-29fix mypy issuesAlexander_Kabui
2023-12-22Feature/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
2023-12-22setup.py: Find packages automatically using find_packages.Arun Isaac
2023-12-19README: Replace pylint and mypy CI badges with all-tests CI badge.Arun Isaac
2023-12-19guix: 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.
2023-12-15Update RDF ProbeSet query.Munyoki Kilyungi
* gn3/api/metadata.py (probesets): Update RDF query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15First 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>
2023-12-15Update ProbeSet's context.Munyoki Kilyungi
* gn3/api/metadata.py (probesets): Update context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Update 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>
2023-12-07Fix typo in GoTree prefix.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Add optional property for platform info in dataset representation.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Fetch normalization metadata correctly.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Fix typo in platform prefix.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Refactor metadata mappings for improved dataset representation.Munyoki Kilyungi
* 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>
2023-12-07Update phenotype queries to use gnt:belongsToGroup.Munyoki Kilyungi
* gn3/api/metadata.py (phenotypes): Use gnt:belongsToGroup instead of xkos:classifiedUnder. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-05Move script to gn-authFrederick Muriuki Muriithi
The script is not used in GN3.
2023-11-30Add a phenotype's chromosome location to the Phenotype fetch.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-30Place publication details on a sub-graph of its own.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-30Replace LRS with lodScore.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Remove unused variable "args".Munyoki Kilyungi
* gn3/api/metadata.py (phenotypes): Delete "args". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Attach phenotype endpoints to one function.Munyoki Kilyungi
* 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>
2023-11-27Use "dcat:Dataset" when framing when fetching phenotypes.Munyoki Kilyungi
* gn3/api/metadata.py (phenotypes): Filter for "dcat:Dataset" in json-ld context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 01:48:26 +0000