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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>
2023-10-27Implement "GET /metadata/datasets/:group/list".Munyoki Kilyungi
* gn3/api/metadata.py (list_datasets_by_group): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Support using AccessionId to fetch datasets.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Remove PREFIXES when querying datasets.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Add extra prefixes to the context.Munyoki Kilyungi
* gn3/api/metadata.py (groups): Update the json-ld's context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /group/: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/groups".Munyoki Kilyungi
* gn3/api/metadata.py (fetch_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /species/:name".Munyoki Kilyungi
* gn3/api/metadata.py (fetch_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /species".Munyoki Kilyungi
* gn3/api/metadata.py (list_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /genewikis/ncbi/:symbol".Munyoki Kilyungi
* gn3/api/metadata.py (get_ncbi_genewiki_entries): New end-point.
2023-10-27Delete gn3.db.rdf.sparql_query.Munyoki Kilyungi
* gn3/api/metadata.py: Remove sparql_query import. * gn3/db/rdf.py: Remove unused imports. (sparql_query): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /genewikis/gn/:symbol".Munyoki Kilyungi
* gn3/api/metadata.py (get_genewiki_entries): Rename this to ... (get_gn_genewiki_entries): ... this. Create an end-point for querying GN GeneRIF entries. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Delete db.rdf.get_url_local_name.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/phenotypes/:name".Munyoki Kilyungi
* gn3/api/metadata.py: Delete gn3.db.rdf.get_phenotype_metadata. (phenotype): Rename this to ... (phenotypes): ... this and implement update logic. * gn3/db/rdf.py (get_phenotype_metadata): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Remove un-used get_dataset_metadata import.Munyoki Kilyungi
* gn3/api/metadata.py: Delete gn3.db.rdf.get_dataset_metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Delete get_dataset_metadata.Munyoki Kilyungi
* gn3/db/rdf.py (get_dataset_metadata): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/genotypes/:name".Munyoki Kilyungi
* gn3/api/metadata.py: Delete gn3.db.rdf.get_genotype_metadata. (genotype): Rename this to ... (genotypes): ... this. Construct a query for fetching genotypes and return a response as json-ld.
2023-10-27Implement "GET /metadata/publications/search/:term".Munyoki Kilyungi
* gn3/api/metadata.py (search_publications): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/publications/:name".Munyoki Kilyungi
* gn3/api/metadata.py: Delete gn3.db.rdf.get_publication_metadata. (publication): Rename this ... (publications): ... to this. Return a json-ld result. * gn3/db/rdf.py (get_publication_metadata): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Add fabio: and prism: to PREFIXES.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/datasets/search/:term".Munyoki Kilyungi
* gn3/api/metadata.py (search_datasets): New search endpoint with pagination. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/datasets/:name".Munyoki Kilyungi
* gn3/api/metadata.py: Import json, SPARQLWrapper.{JSON, JSONLD}. (dataset): Rename this to ... (datasets): ... this. Return a well formatted JSONLD result from a dataset. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 15:02:30 +0000