| Age | Commit message (Expand) | Author |
|---|---|---|
| 2023-12-07 | Fix typo in platform prefix....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-12-07 | Refactor 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 |
| 2023-12-07 | Update 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 |
| 2023-12-05 | Move script to gn-auth...The script is not used in GN3. | Frederick Muriuki Muriithi |
| 2023-11-30 | Add a phenotype's chromosome location to the Phenotype fetch....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-30 | Place publication details on a sub-graph of its own....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-30 | Replace LRS with lodScore....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Remove unused variable "args"....* gn3/api/metadata.py (phenotypes): Delete "args". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Attach 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 |
| 2023-11-27 | Use "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 |
| 2023-11-27 | Construct a more semantic graph for phenotypes....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Remove 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 |
| 2023-11-27 | Replace "ex:" prefix with a semantic prefix when fetching phenotype....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Add "gnt:abbreviation" and "ex:inbredSet" to PHENOTYPE_CONTEXT....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Add "ex:species" to phenotypes json-ld context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Return 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 |
| 2023-11-27 | Add ex:pages and ex:hits to the search context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | First 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 |
| 2023-11-27 | Add "inbredSet" to the dataset's search context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Fetch 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 |
| 2023-11-27 | Fetch 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 |
| 2023-11-02 | Make scripts directory a package to eliminate path issues. | Frederick Muriuki Muriithi |
| 2023-11-02 | Remove files depending on yoyo-migrations. | Frederick Muriuki Muriithi |
| 2023-10-30 | Use correct upstream guix-bioinformatics channel....* .guix-channel: Use git.genenetwork.org instead of gitlab. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-28 | Revert "Roll back to python 3.9 in .guix-channel"...This reverts commit 38b2241d31fdbc4f239eae2b3e3b1a8e31a2f4c6. | Arun Isaac |
| 2023-10-27 | Trigger CI build....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Add pyld to setup.py file....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Refactor to use new rdf.query_* abstractions....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Fix pylint error....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Refactor to use new rdf.query_* abstractions....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Add 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 |
| 2023-10-27 | Break up long line....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Remove reimport "Optional"....* gn3/computations/gemma.py: Delete reimport "Qptional". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Make 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 |
| 2023-10-27 | Ignore 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 |
| 2023-10-27 | Make implicit optional type hints PEP 484 compliant....Ran the command: pipx run no_implicit_optional ./ in the root directory. | Munyoki Kilyungi |
| 2023-10-27 | Abstract out (sparql) CONSTRUCT into a function....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Delete unused imports....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Remove duplicate key in dictionary....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Implement "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 |
| 2023-10-27 | Delete duplicate function....* gn3/api/metadata.py (genotypes): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Implement "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 |
| 2023-10-27 | Implement "GET /metadata/group"....* gn3/api/metadata.py (groups): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Implement "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 |
| 2023-10-27 | Implement "GET /metadata/species"....* gn3/api/metadata.py (list_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Implement "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 |
| 2023-10-27 | Implement "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 |
| 2023-10-27 | Implement "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 |
| 2023-10-27 | Add missing prefixes....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Rename "limit" query paramater to "per-page"....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
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