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2023-10-27Implement "GET /metadata/genewikis/gn/:symbol"....* gn3/api/metadata.py (get_gn_genewiki_entries): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /metadata/genotypes/:name"....* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Add missing prefixes....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Rename "limit" query paramater to "per-page"....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove un-necessary prefixes when fetching NCBI genewiki entries....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove un-necessary prefixes when fetching gn genewiki entries....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /phenotype/:group/:name"....* gn3/api/metadata.py (fetch_phenotype_by_group): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove un-necessary prefixes when fetching a phenotype....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove un-necessary prefixes when searching publications....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Use virtuoso's full text search when searching datasets....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27REmove un-necessary prefixes when searching datasets....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /metadata/datasets/:group/list"....* gn3/api/metadata.py (list_datasets_by_group): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Support using AccessionId to fetch datasets....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove PREFIXES when querying datasets....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Add extra prefixes to the context....* gn3/api/metadata.py (groups): Update the json-ld's context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /group/:name"....* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET metadata/groups"....* gn3/api/metadata.py (fetch_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /species/:name"....* gn3/api/metadata.py (fetch_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /species"....* gn3/api/metadata.py (list_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "GET /genewikis/ncbi/:symbol"....* gn3/api/metadata.py (get_ncbi_genewiki_entries): New end-point. Munyoki Kilyungi
2023-10-27Delete 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
2023-10-27Implement "GET /genewikis/gn/:symbol"....* 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> Munyoki Kilyungi
2023-10-27Delete db.rdf.get_url_local_name....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "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
2023-10-27Remove un-used get_dataset_metadata import....* gn3/api/metadata.py: Delete gn3.db.rdf.get_dataset_metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Delete get_dataset_metadata....* gn3/db/rdf.py (get_dataset_metadata): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "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
2023-10-27Implement "GET /metadata/publications/search/:term"....* gn3/api/metadata.py (search_publications): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "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
2023-10-27Add fabio: and prism: to PREFIXES....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Implement "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
2023-10-27Implement "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
2023-10-27Add missing dcat: prefix.Munyoki Kilyungi
2023-10-27Derive RDF_PREFIXES string from PREFIXES....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Remove 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
2023-10-27Simplify 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
2023-10-27Update RDF prefixes....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-26Fix errors caught by mypy.Frederick Muriuki Muriithi
2023-10-26case-attribute: Fix linting errors.Frederick Muriuki Muriithi
2023-10-25Update __pk__Frederick Muriuki Muriithi
2023-10-25case-attribute: Implement __apply_diff__...Enable the "apply diff" feature which actually makes changes to the database by applying the given diff. Frederick Muriuki Muriithi
2023-10-25case-attribute: Bug: List ALL case-attribute values...Fix bug where only one case-attribute value was returned. Frederick Muriuki Muriithi
2023-10-24case-attribute: use isoformat() for datetime objects.Frederick Muriuki Muriithi
2023-10-23case-attribute: View case attribute diffFrederick Muriuki Muriithi
2023-10-19CaseAttribute: change URL, Create diff dir, fix diff...* Change the URL for listing an inbredset group's case-attribute diffs * Create the diff directory if it does not exist * Add `filename` to the output sent to the browser Frederick Muriuki Muriithi
2023-10-19Handle 404 error(s) at top level.Frederick Muriuki Muriithi
2023-10-12CaseAttributes: List diffs under review...List diffs under review for a given InbredSet. Regenerate any diff files that might be deleted while still under review. Frederick Muriuki Muriithi
2023-10-12CaseAttribute: Bug: Fix bugs with rejecting diffs.Frederick Muriuki Muriithi
2023-10-12CaseAttributes: Bug: Fix privileges checkFrederick Muriuki Muriithi
2023-10-12CaseAttribute: Bug: Fix query - include time_stamp.Frederick Muriuki Muriithi
generated by cgit v1.2.3 (git 2.46.2) at 2024-12-04 14:45:55 +0000