| Age | Commit message (Expand) | Author |
|---|
| 2023-10-27 | Implement "GET /metadata/genotypes/:name".•••* 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.
| Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/publications/search/:term".•••* gn3/api/metadata.py (search_publications): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/publications/:name".•••* 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>
| Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/datasets/search/:term".•••* gn3/api/metadata.py (search_datasets): New search endpoint with
pagination.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/datasets/:name".•••* 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>
| Munyoki Kilyungi |
| 2023-10-27 | Simplify CONSTRUCT query when fetching a dataset's metadata.•••* gn3/api/metadata.py (dataset): Update docstring.
* gn3/db/rdf.py (get_dataset_metadata): Simplify CONSTRUCT query.
Also, now you can fetch metadata using either an accession_id or the
dataset's name.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-15 | Fetch genotypes from virtuoso•••* gn3/api/metadata.py: Import get_genotype_metadata.
(genotype): New end-point.
* gn3/db/rdf.py (get_phenotype_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-12 | Fetch phenotypes from virtuoso•••* gn3/api/metadata.py: Import get_phenotype_metadata.
(phenotype): New end-point.
* gn3/db/rdf.py (get_phenotype_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-12 | Correct publication function docstring•••* gn3/api/metadata.py (publication): Update docstring.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-07 | Add publication end-point•••* gn3/api/metadata.py: Import get_publication_metadata
(publication): New endpoint.
* gn3/db/rdf.py (get_dataset_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-07 | Remove trait_metadata endpoint•••* gn3/api/metadata.py: Remove get_trait_metadata import.
(trait_metadata): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-06 | Rename dataset_metadata -> dataset•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-17 | Create new endpoint for fetching GeneRIF entries•••* gn3/api/metadata.py: Import Template, sparql_query and RDF_PREFIXES.
(get_genewiki_entries): New endpoint.
* gn3/db/rdf.py: Add new constant for storing rdf prefixes.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-03-01 | Create API endpoint for fetching trait metadata•••* gn3/api/metadata.py (dataset_metadata): New function and endpoint.
(jsonify_dataset_metadata): Rename to dataset_metadata.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2022-12-06 | Use a dataset's name to fetch it's metadata from RDF•••* gn3/api/metadata.py (jsonify_dataset_metadata): Rewrite metadata
end-point to use a dataset's name instead of it's accession_id.
* gn3/db/rdf.py (get_dataset_metadata): Replace accession_id with
name. Use one single RDF query instead of multiple queries.
| Munyoki Kilyungi |
| 2022-11-28 | Catch a URLError when virtuoso isn't running at all•••* gn3/api/metadata.py: Import URLError.
(jsonify_dataset_metadata): Add URLError in except block.
| Munyoki Kilyungi |
| 2022-11-28 | Fix pylint errors•••* gn3/api/general.py: Delete rdf import. Delete trailing white
spaces.
* gn3/api/metadata.py: Delete trailing white spaces.
| Munyoki Kilyungi |
| 2022-11-28 | Fail gracefully when virtuoso is not accessible•••* gn3/api/metadata.py: import RemoteDisconnected.
(jsonify_dataset_metadata): Wrap get_dataset_metadata in try block.
| Munyoki Kilyungi |
| 2022-11-23 | Create a new REST endpoint for fetching a phenotype's metadata•••* gn3/api/general.py: (dataset_metadata) Delete.
* gn3/api/metadata.py: Import Blueprint, jsonify, current_app,
SPARQLWrapper and get_dataset_metadata.
(metadata): New Blueprint
(jsonify_dataset_metadata): New function/end-point.
* gn3/app.py: Import metadata
(create_app): Register metadata blueprint.
| Munyoki Kilyungi |
