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2024-02-13Retrieve metadata from text files given a path....* gn3/db/datasets.py (retrieve_trait_dataset): New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-12pep8 formattingAlexander_Kabui
2024-01-30Add the traceback to the exceptions for display.Frederick Muriuki Muriithi
2024-01-26centralize common errorsAlexander_Kabui
2024-01-26Feature/gn llm caching (#148)...* add logic for querying user gnqa search result * add api endpoints for querying users:qnqa-search-terms,gnqa-resultsAlexander Kabui
2024-01-17fix error message for empty responsesAlexander_Kabui
2024-01-17Adjust retry parameters and response handling in custom_requestAlexander_Kabui
2024-01-17Increase timeout to 30s to fix 'Read timed out issueAlexander_Kabui
2024-01-17Enhance error response message in API endpointAlexander_Kabui
2024-01-17max no of retries for user to fahamu apiAlexander_Kabui
2024-01-17fix pylint errorsAlexander_Kabui
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)...* refactor code for processing response from fahamu client * Add tests for gn-llmAlexander Kabui
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....* .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
2024-01-10Optionally 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
2024-01-10Switch 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
2024-01-10Remove 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
2024-01-08merge 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....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-01-08add json file for all referencesAlexander_Kabui
2024-01-08Update 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
2024-01-08disable process waitAlexander_Kabui
2024-01-06Remove extra gene metadata from query as it's un-necessary....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-01-06Add extra keys to the Probeset's json-ld context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-01-06Refactor gene symbol handling and add references to probeset....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-01-06Use gnt:geneSymbol property to fetch genes in Probeset RDF query....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
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....* guix-system.scm: Delete file. Arun Isaac
2024-01-03Do not log user information....* gn3/app.py (create_app): Do not log user information. Arun Isaac
2023-12-29handle exception for request errorAlexander_Kabui
2023-12-29fix mypy issuesAlexander_Kabui
2023-12-22Feature/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 cdAlexander Kabui
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....* .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
2023-12-15Update RDF ProbeSet query....* gn3/api/metadata.py (probesets): Update RDF query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-15First 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
2023-12-15Update ProbeSet's context....* gn3/api/metadata.py (probesets): Update context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-15Update 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
2023-12-07Fix typo in GoTree prefix....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-07Add optional property for platform info in dataset representation....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi