Age | Commit message (Collapse) | Author |
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* gn3/api/metadata.py (genotypes): If a dataset name is provided fetch
the group it belongs to and the dataset's full and short name.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (genotypes): Use gnt:belongsToSpecies instead of
xkos:classifiedUnder when querying for species.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (probesets): Remove hard-coded "HC_M2_0606_P" in
probeset RDF query.
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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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (probesets): Update RDF query.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py: Reshape the data in a nice way by first framing
and compacting the json-ld result.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (probesets): Update context.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py: (PHENOTYPE_CONTEXT): Move "rdfs", "gnt",
"gnc"...
(BASE_CONTEXT): ... here.
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: (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>
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* gn3/api/metadata.py (phenotypes): Use gnt:belongsToGroup instead of xkos:classifiedUnder.
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 (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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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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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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