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-rw-r--r--gn3/api/metadata.py128
1 files changed, 6 insertions, 122 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index 8c900df..2e26489 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -17,132 +17,16 @@ from gn3.db.datasets import (retrieve_metadata,
from gn3.db.rdf import RDF_PREFIXES
from gn3.db.rdf import (query_frame_and_compact,
query_and_compact)
+from gn3.db.constants import (
+ RDF_PREFIXES, BASE_CONTEXT,
+ DATASET_CONTEXT, SEARCH_CONTEXT,
+ DATASET_SEARCH_CONTEXT, PUBLICATION_CONTEXT,
+ PHENOTYPE_CONTEXT
+)
from gn3.api.metadata_api import wiki
-BASE_CONTEXT = {
- "data": "@graph",
- "id": "@id",
- "type": "@type",
- "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",
-}
-
metadata = Blueprint("metadata", __name__)
metadata.register_blueprint(wiki.wiki_blueprint)