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-rw-r--r--gn3/db/rdf/__init__.py188
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+"""RDF
+
+Constants for prefixes and contexts; and wrapper functions around
+creating contexts to be used by jsonld when framing and/or compacting.
+
+"""
+import json
+
+from SPARQLWrapper import SPARQLWrapper
+from pyld import jsonld # type: ignore
+
+
+PREFIXES = {
+ "dcat": "http://www.w3.org/ns/dcat#",
+ "dct": "http://purl.org/dc/terms/",
+ "ex": "http://example.org/stuff/1.0/",
+ "fabio": "http://purl.org/spar/fabio/",
+ "foaf": "http://xmlns.com/foaf/0.1/",
+ "generif": "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=",
+ "genotype": "http://genenetwork.org/genotype/",
+ "gn": "http://genenetwork.org/id/",
+ "gnc": "http://genenetwork.org/category/",
+ "gnt": "http://genenetwork.org/term/",
+ "owl": "http://www.w3.org/2002/07/owl#",
+ "phenotype": "http://genenetwork.org/phenotype/",
+ "prism": "http://prismstandard.org/namespaces/basic/2.0/",
+ "publication": "http://genenetwork.org/publication/",
+ "pubmed": "http://rdf.ncbi.nlm.nih.gov/pubmed/",
+ "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "skos": "http://www.w3.org/2004/02/skos/core#",
+ "taxon": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=",
+ "up": "http://purl.uniprot.org/core/",
+ "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#",
+ "xsd": "http://www.w3.org/2001/XMLSchema#",
+}
+
+RDF_PREFIXES = "\n".join([f"PREFIX {key}: <{value}>"
+ for key, value in PREFIXES.items()])
+
+BASE_CONTEXT = {
+ "data": "@graph",
+ "type": "@type",
+ "gn": "http://genenetwork.org/id/",
+ "gnc": "http://genenetwork.org/category/",
+ "gnt": "http://genenetwork.org/term/",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#>",
+}
+
+DATASET_CONTEXT = {
+ "accessRights": "dct:accessRights",
+ "accessionId": "dct:identifier",
+ "acknowledgement": "gnt:hasAcknowledgement",
+ "altLabel": "skos:altLabel",
+ "caseInfo": "gnt:hasCaseInfo",
+ "classifiedUnder": "xkos:classifiedUnder",
+ "contributors": "dct:creator",
+ "contactPoint": "dcat:contactPoint",
+ "created": "dct:created",
+ "dcat": "http://www.w3.org/ns/dcat#",
+ "dct": "http://purl.org/dc/terms/",
+ "description": "dct:description",
+ "ex": "http://example.org/stuff/1.0/",
+ "experimentDesignInfo": "gnt:hasExperimentDesignInfo",
+ "experimentType": "gnt:hasExperimentType",
+ "foaf": "http://xmlns.com/foaf/0.1/",
+ "geoSeriesId": "gnt:hasGeoSeriesId",
+ "gnt": "http://genenetwork.org/term/",
+ "inbredSet": "gnt:belongsToGroup",
+ "label": "rdfs:label",
+ "normalization": "gnt:usesNormalization",
+ "platformInfo": "gnt:hasPlatformInfo",
+ "notes": "gnt:hasNotes",
+ "organization": "foaf:Organization",
+ "prefLabel": "skos:prefLabel",
+ "citation": "dct:isReferencedBy",
+ "GoTree": "gnt:hasGOTreeValue",
+ "platform": "gnt:usesPlatform",
+ "processingInfo": "gnt:hasDataProcessingInfo",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "skos": "http://www.w3.org/2004/02/skos/core#",
+ "specifics": "gnt:hasContentInfo",
+ "title": "dct:title",
+ "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#",
+ "tissueInfo": "gnt:hasTissueInfo",
+ "tissue": "gnt:hasTissue",
+ "contactWebUrl": "foaf:homepage",
+ "contactName": "foaf:name",
+}
+
+SEARCH_CONTEXT = {
+ "pages": "ex:pages",
+ "hits": "ex:hits",
+ "result": "ex:result",
+ "results": "ex:items",
+ "resultItem": "ex:resultType",
+ "currentPage": "ex:currentPage",
+}
+
+DATASET_SEARCH_CONTEXT = SEARCH_CONTEXT | {
+ "classifiedUnder": "xkos:classifiedUnder",
+ "created": "dct:created",
+ "dct": "http://purl.org/dc/terms/",
+ "ex": "http://example.org/stuff/1.0/",
+ "inbredSet": "ex:belongsToInbredSet",
+ "title": "dct:title",
+ "name": "rdfs:label",
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+ "type": "@type",
+ "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#",
+}
+
+PUBLICATION_CONTEXT = {
+ "dct": "http://purl.org/dc/terms/",
+ "fabio": "http://purl.org/spar/fabio/",
+ "prism": "http://prismstandard.org/namespaces/basic/2.0/",
+ "xsd": "http://www.w3.org/2001/XMLSchema#",
+ "title": "dct:title",
+ "journal": "fabio:Journal",
+ "volume": "prism:volume",
+ "page": "fabio:page",
+ "creator": "dct:creator",
+ "abstract": "dct:abstract",
+ "year": {
+ "@id": "fabio:hasPublicationYear",
+ "@type": "xsd:gYear",
+ },
+ "month": {
+ "@id": "prism:publicationDate",
+ "@type": "xsd:gMonth"
+ },
+}
+
+PHENOTYPE_CONTEXT = BASE_CONTEXT | PUBLICATION_CONTEXT | {
+ "skos": "http://www.w3.org/2004/02/skos/core#",
+ "dcat": "http://www.w3.org/ns/dcat#",
+ "prism": "http://prismstandard.org/namespaces/basic/2.0/",
+ "traitName": "skos:altLabel",
+ "trait": "rdfs:label",
+ "altName": "rdfs:altLabel",
+ "description": "dct:description",
+ "abbreviation": "gnt:abbreviation",
+ "labCode": "gnt:labCode",
+ "submitter": "gnt:submitter",
+ "dataset": "dcat:Distribution",
+ "contributor": "dct:contributor",
+ "mean": "gnt:mean",
+ "locus": "gnt:locus",
+ "lodScore": "gnt:lodScore",
+ "references": "dct:isReferencedBy",
+ "additive": "gnt:additive",
+ "sequence": "gnt:sequence",
+ "prefLabel": "skos:prefLabel",
+ "identifier": "dct:identifier",
+ "chromosome": "gnt:chr",
+ "mb": "gnt:mb",
+ "peakLocation": "gnt:locus",
+ "species": "gnt:belongsToSpecies",
+ "group": "gnt:belongsToGroup",
+}
+
+
+def sparql_construct_query(query: str, endpoint: str) -> dict:
+ """Query virtuoso using a CONSTRUCT query and return a json-ld
+ dictionary"""
+ sparql = SPARQLWrapper(endpoint)
+ sparql.setQuery(query)
+ results = sparql.queryAndConvert()
+ return json.loads(results.serialize(format="json-ld")) # type: ignore
+
+
+def query_frame_and_compact(query: str, context: dict, endpoint: str) -> dict:
+ """Frame and then compact the results given a context"""
+ results = sparql_construct_query(query, endpoint)
+ return jsonld.compact(jsonld.frame(results, context), context)
+
+
+def query_and_compact(query: str, context: dict, endpoint: str) -> dict:
+ """Compact the results given a context"""
+ results = sparql_construct_query(query, endpoint)
+ return jsonld.compact(results, context)
+
+
+def query_and_frame(query: str, context: dict, endpoint: str) -> dict:
+ """Frame the results given a context"""
+ results = sparql_construct_query(query, endpoint)
+ return jsonld.frame(results, context)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 01:04:57 +0000