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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.•••* .guix-channel: Use git.genenetwork.org instead of gitlab. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-28Revert "Roll back to python 3.9 in .guix-channel"•••This reverts commit 38b2241d31fdbc4f239eae2b3e3b1a8e31a2f4c6. Arun Isaac
2023-10-27Trigger CI build.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Add pyld to setup.py file.•••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
2023-10-27Fix 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
2023-10-27Make scripts/ a module since it referenced in argparse_actions.py.•••* scripts/__init__.py: New file. 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
2023-10-27Delete unused imports.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove duplicate key in dictionary.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /metadata/probesets/:name".•••* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Delete duplicate function.•••* gn3/api/metadata.py (genotypes): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /metadata/groups/:name".•••* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /metadata/group".•••* gn3/api/metadata.py (groups): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /metadata/species/:name".•••* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /metadata/species".•••* gn3/api/metadata.py (list_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /metadata/genewikis/ncbi/:symbol".•••* gn3/api/metadata.py (get_ncbi_genewiki_entries): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /metadata/genewikis/gn/:symbol".•••* gn3/api/metadata.py (get_gn_genewiki_entries): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /metadata/genotypes/:name".•••* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Add missing prefixes.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Rename "limit" query paramater to "per-page".•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove un-necessary prefixes when fetching NCBI genewiki entries.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove un-necessary prefixes when fetching gn genewiki entries.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /phenotype/:group/:name".•••* gn3/api/metadata.py (fetch_phenotype_by_group): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove un-necessary prefixes when fetching a phenotype.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove un-necessary prefixes when searching publications.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Use virtuoso's full text search when searching datasets.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27REmove un-necessary prefixes when searching datasets.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /metadata/datasets/:group/list".•••* gn3/api/metadata.py (list_datasets_by_group): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Support using AccessionId to fetch datasets.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove PREFIXES when querying datasets.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Add extra prefixes to the context.•••* gn3/api/metadata.py (groups): Update the json-ld's context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /group/:name".•••* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET metadata/groups".•••* gn3/api/metadata.py (fetch_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /species/:name".•••* gn3/api/metadata.py (fetch_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /species".•••* gn3/api/metadata.py (list_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /genewikis/ncbi/:symbol".•••* gn3/api/metadata.py (get_ncbi_genewiki_entries): New end-point. Munyoki Kilyungi
2023-10-27Delete gn3.db.rdf.sparql_query.•••* 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> Munyoki Kilyungi
2023-10-27Implement "GET /genewikis/gn/:symbol".•••* 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> Munyoki Kilyungi
2023-10-27Delete db.rdf.get_url_local_name.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /metadata/phenotypes/:name".•••* 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> Munyoki Kilyungi
2023-10-27Remove un-used get_dataset_metadata import.•••* gn3/api/metadata.py: Delete gn3.db.rdf.get_dataset_metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
generated by cgit v1.2.3 (git 2.47.1) at 2025-02-27 22:47:56 +0000