From 4da80ca9c17bdd28e2689895ab6acb1ec0c70d33 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Wed, 7 Jun 2023 09:39:58 +0300 Subject: 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 --- gn3/db/rdf.py | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gn3/db') diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py index 5b62b46..c559774 100644 --- a/gn3/db/rdf.py +++ b/gn3/db/rdf.py @@ -156,6 +156,46 @@ CONSTRUCT { ): response[key] = value.map(get_url_local_name) # type: ignore return response + + +def get_publication_metadata( + sparql_conn: SPARQLWrapper, name: str +): + """Return info about a publication with a given NAME""" + __metadata_query = """ +$prefix + +CONSTRUCT { + gn:publication ?publicationTerm ?publicationValue . + gn:publication ?predicate ?subject . +} WHERE { + $name ?publicationTerm ?publicationValue . + ?publication ?publicationTerm ?publicationValue . + OPTIONAL { + ?subject ?predicate ?publication . + } . + VALUES ?publicationTerm { + gn:pubMedId gn:title gn:volume + gn:abstract gn:pages gn:month gn:year gn:author + } + VALUES ?predicate { + gn:phenotypeOfPublication + } +} +""" + response: MonadicDict = MonadicDict() + + for key, value in sparql_query( + sparql_conn, + Template(__metadata_query) + .substitute( + prefix=RDF_PREFIXES, + name=name + ) + )[0].items(): + response[key] = value + if isinstance(value, str) and not key.endswith("pubMedId"): + response[key] = value.map(get_url_local_name) # type: ignore return response -- cgit v1.2.3