Age | Commit message (Collapse) | Author |
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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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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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* gn3/api/metadata.py (list_datasets_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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* gn3/api/metadata.py (groups): Update the json-ld's context.
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 (fetch_species): New end-point.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (fetch_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.
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* 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>
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* 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>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* 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>
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* gn3/api/metadata.py: Delete gn3.db.rdf.get_dataset_metadata.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/db/rdf.py (get_dataset_metadata): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* 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.
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* gn3/api/metadata.py (search_publications): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* 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>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (search_datasets): New search endpoint with
pagination.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* 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>
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