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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
2023-10-27Implement "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
2023-10-27Implement "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
2023-10-27Implement "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
2023-10-27Simplify 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
2023-10-06Provide keyword argument.Frederick Muriuki Muriithi
2023-10-06Pass in configs/settings as function arguments...To avoid reliance of `flask.current_app.config` or on `gn3.settings` modules globally, this commit passes in the appropriate configurations as arguments to the relevant functions. Frederick Muriuki Muriithi
2023-09-05Fix C3001: Lambda expression assigned to a variable...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-15Fetch 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
2023-06-12Fetch 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
2023-06-12Correct publication function docstring...* gn3/api/metadata.py (publication): Update docstring. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-07Add 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
2023-06-07Remove 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
2023-06-06Rename dataset_metadata -> dataset...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-04-17Create 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
2023-04-06Remove deprecated `gn3.db_utils.database_connector` function...Remove the deprecated function and fix a myriad of bugs that arise from removing the function. Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils Frederick Muriuki Muriithi
2023-03-01Fetch sampledata...* gn3/api/sampledata.py (get_sampledata): New end-point. * gn3/app.py: Register above end-point. * gn3/settings.py: Add new conf variable for LMDB. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-03-01Create 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
2023-01-24search: Use decimals, not floats, when converting to megabases....* gn3/api/search.py (parse_location_field): Use decimals, not floats, when converting to megabases. Arun Isaac
2023-01-24search: Support SI suffixes and point locations....* gn3/api/search.py (parse_position_field): New function. (parse_query): Associate the position prefix with the parse_position_field field processor. Arun Isaac
2023-01-24search: Abstract out parsing of position spec into separate function....* gn3/api/search.py (parse_position): New function. (parse_location_field): Use parse_position. * tests/unit/test_search.py: Import parse_position from gn3.api.search. (test_parse_position_close_to_zero_location): New test. Arun Isaac
2023-01-24search: Alias the position prefix with pos....* gn3/api/search.py (parse_query): Alias the position prefix with pos. Arun Isaac
2023-01-24search: Rename the mb prefix to position....* gn3/api/search.py (parse_query): Rename the mb prefix to position. Arun Isaac
2023-01-24search: Assume triplets mean synteny is requested....* gn3/api/search.py (query_subqueries, query_terms, parse_synteny_field, is_synteny_on, remove_synteny_field): Delete functions. (parse_query): Assume triplets mean synteny is requested. Arun Isaac
2023-01-24search: Use comprehension when splitting location....* gn3/api/search.py (parse_location_field): Use comprehension. Arun Isaac
2023-01-20mypy: minor fixes to typing errorsFrederick Muriuki Muriithi
2023-01-19search: Downcase before applying SI suffix....* gn3/api/search.py (apply_si_suffix): Downcase before applying SI suffix. Arun Isaac
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