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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>
2023-11-30Add 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>
2023-11-02Remove files depending on yoyo-migrations.Frederick Muriuki Muriithi
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>
2023-10-27Ignore 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.
2023-10-27Abstract out (sparql) CONSTRUCT into a function.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Delete unused imports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Remove duplicate key in dictionary.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/probesets/:name".Munyoki Kilyungi
* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Delete duplicate function.Munyoki Kilyungi
* gn3/api/metadata.py (genotypes): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/groups/:name".Munyoki Kilyungi
* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/group".Munyoki Kilyungi
* gn3/api/metadata.py (groups): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/species/:name".Munyoki Kilyungi
* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/species".Munyoki Kilyungi
* gn3/api/metadata.py (list_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/genewikis/ncbi/:symbol".Munyoki Kilyungi
* gn3/api/metadata.py (get_ncbi_genewiki_entries): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/genewikis/gn/:symbol".Munyoki Kilyungi
* gn3/api/metadata.py (get_gn_genewiki_entries): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/genotypes/:name".Munyoki Kilyungi
* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Add missing prefixes.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Rename "limit" query paramater to "per-page".Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Remove un-necessary prefixes when fetching NCBI genewiki entries.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Remove un-necessary prefixes when fetching gn genewiki entries.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /phenotype/:group/:name".Munyoki Kilyungi
* gn3/api/metadata.py (fetch_phenotype_by_group): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Remove un-necessary prefixes when fetching a phenotype.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Remove un-necessary prefixes when searching publications.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Use virtuoso's full text search when searching datasets.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27REmove un-necessary prefixes when searching datasets.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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