Age | Commit message (Collapse) | Author |
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* gn3/api/metadata.py (phenotypes): Delete "args".
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* 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>
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* gn3/api/metadata.py (phenotypes): Filter for "dcat:Dataset" in
json-ld context.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (phenotypes): Delete "name" from template
substitution.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (search_datasets): Return distinct search
results.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (search_datasets): Replace query_and_frame with
query_frame_and_compact.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (DATASET_CONTEXT): Add key for "contributors."
(datasets): Fetch a dataset's contributors.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (DATASET_CONTEXT): Add key for "specifics".
(datasets): Fetch a dataset's specifics.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* .guix-channel: Use git.genenetwork.org instead of gitlab.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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This reverts commit 38b2241d31fdbc4f239eae2b3e3b1a8e31a2f4c6.
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* 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>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/computations/gemma.py: Delete reimport "Qptional".
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* scripts/__init__.py: New file.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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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]
```
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Ran the command:
pipx run no_implicit_optional ./
in the root directory.
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (fetch_group_by_species): New end-point.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (genotypes): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (fetch_group_by_species): New end-point.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (groups): New end-point.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (fetch_group_by_species): New end-point.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (list_species): New end-point.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (get_ncbi_genewiki_entries): New end-point.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (get_gn_genewiki_entries): New end-point.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (fetch_group_by_species): New end-point.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (fetch_phenotype_by_group): New end-point.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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