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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
2024-01-03Do 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
2023-12-15Update 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
2023-12-07Fetch normalization metadata correctly.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-07Fix typo in platform prefix.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-07Refactor 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
2023-12-07Update 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
2023-11-30Add a phenotype's chromosome location to the Phenotype fetch.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-30Place publication details on a sub-graph of its own.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-30Replace LRS with lodScore.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Remove unused variable "args".•••* gn3/api/metadata.py (phenotypes): Delete "args". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Attach phenotype endpoints to one function.•••* 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> Munyoki Kilyungi
2023-11-27Use "dcat:Dataset" when framing when fetching phenotypes.•••* gn3/api/metadata.py (phenotypes): Filter for "dcat:Dataset" in json-ld context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Construct a more semantic graph for phenotypes.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Remove unused argument during template substitution.•••* gn3/api/metadata.py (phenotypes): Delete "name" from template substitution. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Replace "ex:" prefix with a semantic prefix when fetching phenotype.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Add "gnt:abbreviation" and "ex:inbredSet" to PHENOTYPE_CONTEXT.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Add "ex:species" to phenotypes json-ld context.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Return distinct results after a dataset search.•••* gn3/api/metadata.py (search_datasets): Return distinct search results. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Add ex:pages and ex:hits to the search context.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27First fram and compact the jsonld results during dataset search.•••* gn3/api/metadata.py (search_datasets): Replace query_and_frame with query_frame_and_compact. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Add "inbredSet" to the dataset's search context.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Fetch a dataset's contributors in RDF.•••* gn3/api/metadata.py (DATASET_CONTEXT): Add key for "contributors." (datasets): Fetch a dataset's contributors. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Fetch dataset specifics in RDF.•••* gn3/api/metadata.py (DATASET_CONTEXT): Add key for "specifics". (datasets): Fetch a dataset's specifics. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-02Remove files depending on yoyo-migrations.Frederick Muriuki Muriithi
2023-10-27Refactor to use new rdf.query_* abstractions.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Fix pylint error.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Refactor to use new rdf.query_* abstractions.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Add functions that wrap around the common jsonld patterns.•••* 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> Munyoki Kilyungi
2023-10-27Break up long line.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove reimport "Optional".•••* gn3/computations/gemma.py: Delete reimport "Qptional". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Ignore construct result for mypy compliance•••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] ``` Munyoki Kilyungi
2023-10-27Make implicit optional type hints PEP 484 compliant.•••Ran the command: pipx run no_implicit_optional ./ in the root directory. Munyoki Kilyungi
2023-10-27Abstract out (sparql) CONSTRUCT into a function.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
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