| Age | Commit message (Expand) | Author |
|---|
| 2023-10-27 | Fix pylint error....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 | 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 | Abstract out (sparql) CONSTRUCT into a function....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-10-27 | Delete gn3.db.rdf.sparql_query....* 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>
| Munyoki Kilyungi |
| 2023-10-27 | Delete db.rdf.get_url_local_name....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/phenotypes/:name"....* 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>
| Munyoki Kilyungi |
| 2023-10-27 | Delete get_dataset_metadata....* gn3/db/rdf.py (get_dataset_metadata): Delete.
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 | Add fabio: and prism: to PREFIXES....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 | Add missing dcat: prefix. | Munyoki Kilyungi |
| 2023-10-27 | Derive RDF_PREFIXES string from PREFIXES....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-10-27 | Remove get_url_local_name when processing result keys....* gn3/db/rdf.py (sparql_query): Delete "get_url_local_name".
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 |
| 2023-10-27 | Update RDF prefixes....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 | Delete unused import...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 | Delete unused get_trait_metadata function...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 | Nest duplicate entries into a list from a sparql result...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-06 | Pass geoSeries as a URL...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-06 | Rename gn:geoPlatform -> gn:geoPlatformUrl...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-06 | Match how dataset metadata is fetched with GN1...* gn3/db/rdf.py (sparql_query): Parse CONSTRUCTS and SELECTS
differently.
(strip_url): Rename to ...
(get_url_local_name): ... this.
(get_dataset_metadata): Fetch extra fields in RDF.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-06 | Replace taxon prefix with ncbiTaxon which references NCBI...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-02 | Replace SELECT with CONSTRUCT when fetching a dataset's metadata...* gn3/db/rdf.py: Importh pymonad.Nothing.
(get_dataset_metadata): Replace SELECT with CONSTRUCT.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-02 | Create a function for stripping the last bit from a URL...* gn3/db/rdf.py: Import unquote and urlparse.
(strip_url): New function.
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 | Fetch trait metadata from RDF...* gn3/db/rdf.py (get_dataset_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2022-12-08 | Remove unused import | Frederick Muriuki Muriithi |
| 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 |
| 2022-11-16 | Inject SPARQLWrapper as a parameter...* gn3/db/rdf.py: Delete gn3.setting.SPARQL_ENDPOINT import.
(sparql_query): Inject SPARQLWrapper.
(get_dataset_metadata): Ditto.
| Munyoki Kilyungi |
| 2022-11-02 | Re-implement RDF related code to use monads in its own module...* gn3/api/general.py: Replace gn3.db.datasets import with gn3.db.rdf.
(dataset_metadata) <jsonify>: Replace datasets.dataset_metadata with
rdf.get_dataset_metadata.
* gn3/db/datasets.py: Remove unused imports.
(sparql_query, dataset_metadata): Delete.
* gn3/db/rdf.py: (sparql_query, get_dataset_metadata): New functions.
| Munyoki Kilyungi |
