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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>
2023-11-27Construct a more semantic graph for phenotypes.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Remove unused argument during template substitution.Munyoki Kilyungi
* gn3/api/metadata.py (phenotypes): Delete "name" from template substitution. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Replace "ex:" prefix with a semantic prefix when fetching phenotype.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Add "gnt:abbreviation" and "ex:inbredSet" to PHENOTYPE_CONTEXT.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Add "ex:species" to phenotypes json-ld context.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Return distinct results after a dataset search.Munyoki Kilyungi
* gn3/api/metadata.py (search_datasets): Return distinct search results. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Add ex:pages and ex:hits to the search context.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27First fram and compact the jsonld results during dataset search.Munyoki Kilyungi
* gn3/api/metadata.py (search_datasets): Replace query_and_frame with query_frame_and_compact. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Add "inbredSet" to the dataset's search context.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Fetch a dataset's contributors in RDF.Munyoki Kilyungi
* gn3/api/metadata.py (DATASET_CONTEXT): Add key for "contributors." (datasets): Fetch a dataset's contributors. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Fetch dataset specifics in RDF.Munyoki Kilyungi
* gn3/api/metadata.py (DATASET_CONTEXT): Add key for "specifics". (datasets): Fetch a dataset's specifics. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-02Make scripts directory a package to eliminate path issues.Frederick Muriuki Muriithi
2023-11-02Remove files depending on yoyo-migrations.Frederick Muriuki Muriithi
2023-10-30Use correct upstream guix-bioinformatics channel.Munyoki Kilyungi
* .guix-channel: Use git.genenetwork.org instead of gitlab. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-28Revert "Roll back to python 3.9 in .guix-channel"Arun Isaac
This reverts commit 38b2241d31fdbc4f239eae2b3e3b1a8e31a2f4c6.
2023-10-27Trigger CI build.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Add pyld to setup.py file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Refactor to use new rdf.query_* abstractions.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Fix pylint error.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Refactor to use new rdf.query_* abstractions.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Add functions that wrap around the common jsonld patterns.Munyoki Kilyungi
* gn3/db/rdf.py: Import jsonld. (query_frame_and_compact, query_and_compact, query_and_frame): New functions. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Break up long line.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Remove reimport "Optional".Munyoki Kilyungi
* gn3/computations/gemma.py: Delete reimport "Qptional". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Make scripts/ a module since it referenced in argparse_actions.py.Munyoki Kilyungi
* scripts/__init__.py: New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Ignore construct result for mypy complianceMunyoki Kilyungi
This commit addresses the mypy issue below by ignoring the construct result. ``` error: Item "None" of "bytes | str | dict[Any, Any] | Graph | Document | None" has no attribute "serialize" [union-attr] ```
2023-10-27Make implicit optional type hints PEP 484 compliant.Munyoki Kilyungi
Ran the command: pipx run no_implicit_optional ./ in the root directory.
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-12 17:03:08 +0000