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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, POST, DIGEST, JSON
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_query(query: str, endpoint: str, format_type="json-ld") -> dict:
"""Query virtuoso using a CONSTRUCT query and return a json-ld
dictionary"""
sparql = SPARQLWrapper(endpoint)
if format_type == "json-ld":
sparql.setQuery(query)
results = sparql.queryAndConvert()
return json.loads(results.serialize(format=format_type)) # type: ignore
# For SELECTs
sparql.setReturnFormat(JSON)
sparql.setQuery(query)
return sparql.queryAndConvert()["results"]["bindings"] # 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_query(query, endpoint)
return jsonld.compact(
jsonld.frame(results, context), context, options={"graph": True}
)
def query_and_compact(query: str, context: dict, endpoint: str) -> dict:
"""Compact the results given a context"""
results = sparql_query(query, endpoint)
return jsonld.compact(results, context, options={"graph": True})
def query_and_frame(query: str, context: dict, endpoint: str) -> dict:
"""Frame the results given a context"""
results = sparql_query(query, endpoint)
return jsonld.frame(results, context)
def update_rdf(
query: str, sparql_user: str, sparql_password: str, sparql_auth_uri: str
) -> str:
"""Update RDF Graph content---INSERT/DELETE---in a Graph Store
using HTTP. Example return:
'Insert into <http://genenetwork.org>, 14 (or less) triples -- done'
"""
sparql = SPARQLWrapper(sparql_auth_uri)
sparql.setHTTPAuth(DIGEST)
sparql.setCredentials(sparql_user, sparql_password)
sparql.setMethod(POST)
sparql.setReturnFormat(JSON)
sparql.setQuery(query)
_r = sparql.queryAndConvert()["results"] # type: ignore
return _r["bindings"][0]["callret-0"]["value"] # type: ignore
|
