diff --git a/context.json b/context.json index a652029..d095ea7 100644 --- a/context.json +++ b/context.json @@ -1,8 +1,8 @@ -[ - "https://w3id.org/ro/crate/1.1/context", - { +{ + "@context": { "Person": "https://w3id.org/ro/terms/#Person", "fullName": "https://w3id.org/ro/terms/#fullName", - "friend_of": "https://w3id.org/ro/terms/#friend_of" + "friend_of": "https://w3id.org/ro/terms/#friend_of", + "sdConformsTo": "https://w3id.org/ro/terms/#sdConformsTo" } -] \ No newline at end of file +} \ No newline at end of file diff --git a/context.jsonld b/context.jsonld index a652029..d095ea7 100644 --- a/context.jsonld +++ b/context.jsonld @@ -1,8 +1,8 @@ -[ - "https://w3id.org/ro/crate/1.1/context", - { +{ + "@context": { "Person": "https://w3id.org/ro/terms/#Person", "fullName": "https://w3id.org/ro/terms/#fullName", - "friend_of": "https://w3id.org/ro/terms/#friend_of" + "friend_of": "https://w3id.org/ro/terms/#friend_of", + "sdConformsTo": "https://w3id.org/ro/terms/#sdConformsTo" } -] \ No newline at end of file +} \ No newline at end of file diff --git a/copo/context.json b/copo/context.json index 9df4680..3475e88 100644 --- a/copo/context.json +++ b/copo/context.json @@ -1,7 +1,5 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { + "@context": { "associated_tol_project": "https://w3id.org/ro/terms/copo#associated_tol_project", "biosampleAccession": "https://w3id.org/ro/terms/copo#biosampleAccession", "boldAccession": "https://w3id.org/ro/terms/copo#boldAccession", @@ -90,5 +88,4 @@ "VOUCHER_INSTITUTION": "https://w3id.org/ro/terms/sample#VOUCHER_INSTITUTION", "OTHER_INFORMATION": "https://w3id.org/ro/terms/sample#OTHER_INFORMATION" } - ] } diff --git a/copo/context.jsonld b/copo/context.jsonld index 9df4680..3475e88 100644 --- a/copo/context.jsonld +++ b/copo/context.jsonld @@ -1,7 +1,5 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { + "@context": { "associated_tol_project": "https://w3id.org/ro/terms/copo#associated_tol_project", "biosampleAccession": "https://w3id.org/ro/terms/copo#biosampleAccession", "boldAccession": "https://w3id.org/ro/terms/copo#boldAccession", @@ -90,5 +88,4 @@ "VOUCHER_INSTITUTION": "https://w3id.org/ro/terms/sample#VOUCHER_INSTITUTION", "OTHER_INFORMATION": "https://w3id.org/ro/terms/sample#OTHER_INFORMATION" } - ] } diff --git a/criminalcharacters/context.json b/criminalcharacters/context.json index 70b25d5..3d35a78 100644 --- a/criminalcharacters/context.json +++ b/criminalcharacters/context.json @@ -1,10 +1,7 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "education": "https://w3id.org/ro/terms/criminalcharacters#education", - "interests": "https://w3id.org/ro/terms/criminalcharacters#interests", - "Person": "https://w3id.org/ro/terms/criminalcharacters#Person" - } - ] + "@context": { + "education": "https://w3id.org/ro/terms/criminalcharacters#education", + "interests": "https://w3id.org/ro/terms/criminalcharacters#interests", + "Person": "https://w3id.org/ro/terms/criminalcharacters#Person" + } } \ No newline at end of file diff --git a/criminalcharacters/context.jsonld b/criminalcharacters/context.jsonld index 70b25d5..3d35a78 100644 --- a/criminalcharacters/context.jsonld +++ b/criminalcharacters/context.jsonld @@ -1,10 +1,7 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "education": "https://w3id.org/ro/terms/criminalcharacters#education", - "interests": "https://w3id.org/ro/terms/criminalcharacters#interests", - "Person": "https://w3id.org/ro/terms/criminalcharacters#Person" - } - ] + "@context": { + "education": "https://w3id.org/ro/terms/criminalcharacters#education", + "interests": "https://w3id.org/ro/terms/criminalcharacters#interests", + "Person": "https://w3id.org/ro/terms/criminalcharacters#Person" + } } \ No newline at end of file diff --git a/example/context.json b/example/context.json index f78aaf8..8f2b683 100644 --- a/example/context.json +++ b/example/context.json @@ -1,9 +1,6 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "Book": "https://w3id.org/ro/terms/example#Book", - "title": "https://w3id.org/ro/terms/example#title" - } - ] + "@context": { + "Book": "https://w3id.org/ro/terms/example#Book", + "title": "https://w3id.org/ro/terms/example#title" + } } \ No newline at end of file diff --git a/example/context.jsonld b/example/context.jsonld index f78aaf8..8f2b683 100644 --- a/example/context.jsonld +++ b/example/context.jsonld @@ -1,9 +1,6 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "Book": "https://w3id.org/ro/terms/example#Book", - "title": "https://w3id.org/ro/terms/example#title" - } - ] + "@context": { + "Book": "https://w3id.org/ro/terms/example#Book", + "title": "https://w3id.org/ro/terms/example#title" + } } \ No newline at end of file diff --git a/gen_context.py b/gen_context.py index bdd8301..4362de6 100644 --- a/gen_context.py +++ b/gen_context.py @@ -9,13 +9,11 @@ from pathlib import Path -RO_CRATE_VERSION = "1.1" RO_TERMS_PREFIX = "https://w3id.org/ro/terms" VOCAB_FN = "vocabulary.csv" -def build_context(namespace, vocab_path, ro_crate_version=RO_CRATE_VERSION): - ro_crate_context = f"https://w3id.org/ro/crate/{ro_crate_version}/context" +def build_context(namespace, vocab_path): add_terms = {} with open(vocab_path, newline="") as f: reader = csv.DictReader(f) @@ -26,7 +24,7 @@ def build_context(namespace, vocab_path, ro_crate_version=RO_CRATE_VERSION): if not k: continue # empty line! add_terms[k] = f"{RO_TERMS_PREFIX}/{namespace}#{k}" - return {"@context": [ro_crate_context, add_terms]} + return {"@context": add_terms} def main(args): @@ -34,18 +32,18 @@ def main(args): vocab_path = ns_dir / VOCAB_FN if not vocab_path.is_file(): raise RuntimeError(f"{vocab_path} not found") - context = build_context(ns_dir.name, vocab_path, - ro_crate_version=args.ro_crate_version) + context = build_context(ns_dir.name, vocab_path) if not args.output: - args.output = ns_dir / "context.jsonld" - with open(args.output, "wt", encoding="utf8") as f: - json.dump(context, f, ensure_ascii=False, indent=4, sort_keys=False) + args.output = [ns_dir / f"context.{ext}" for ext in ("json", "jsonld")] + else: + args.output = [args.output] + for out_fn in args.output: + with open(out_fn, "wt", encoding="utf8") as f: + json.dump(context, f, ensure_ascii=False, indent=4, sort_keys=False) if __name__ == "__main__": parser = argparse.ArgumentParser(description=__doc__) parser.add_argument("ns_dir", metavar="NAMESPACE", help="namespace dir") - parser.add_argument("-v", "--ro-crate-version", metavar="string", - default=RO_CRATE_VERSION, help="RO-Crate version") parser.add_argument('-o', '--output', metavar="FILE") main(parser.parse_args(sys.argv[1:])) diff --git a/ods/context.json b/ods/context.json index 52feaa7..3912927 100644 --- a/ods/context.json +++ b/ods/context.json @@ -1,16 +1,13 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "Specimen": "https://w3id.org/ro/terms/ods#Specimen", - "SpecimenRecord": "https://w3id.org/ro/terms/ods#SpecimenRecord", - "authoritative": "https://w3id.org/ro/terms/ods#authoritative", - "modified": "https://w3id.org/ro/terms/ods#modified", - "midsLevel": "https://w3id.org/ro/terms/ods#midsLevel", - "physicalSpecimenId": "https://w3id.org/ro/terms/ods#physicalSpecimenId", - "institution": "https://w3id.org/ro/terms/ods#institution", - "materialType": "https://w3id.org/ro/terms/ods#materialType", - "name": "https://w3id.org/ro/terms/ods#name" - } - ] + "@context": { + "Specimen": "https://w3id.org/ro/terms/ods#Specimen", + "SpecimenRecord": "https://w3id.org/ro/terms/ods#SpecimenRecord", + "authoritative": "https://w3id.org/ro/terms/ods#authoritative", + "modified": "https://w3id.org/ro/terms/ods#modified", + "midsLevel": "https://w3id.org/ro/terms/ods#midsLevel", + "physicalSpecimenId": "https://w3id.org/ro/terms/ods#physicalSpecimenId", + "institution": "https://w3id.org/ro/terms/ods#institution", + "materialType": "https://w3id.org/ro/terms/ods#materialType", + "name": "https://w3id.org/ro/terms/ods#name" + } } \ No newline at end of file diff --git a/ods/context.jsonld b/ods/context.jsonld index 52feaa7..3912927 100644 --- a/ods/context.jsonld +++ b/ods/context.jsonld @@ -1,16 +1,13 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "Specimen": "https://w3id.org/ro/terms/ods#Specimen", - "SpecimenRecord": "https://w3id.org/ro/terms/ods#SpecimenRecord", - "authoritative": "https://w3id.org/ro/terms/ods#authoritative", - "modified": "https://w3id.org/ro/terms/ods#modified", - "midsLevel": "https://w3id.org/ro/terms/ods#midsLevel", - "physicalSpecimenId": "https://w3id.org/ro/terms/ods#physicalSpecimenId", - "institution": "https://w3id.org/ro/terms/ods#institution", - "materialType": "https://w3id.org/ro/terms/ods#materialType", - "name": "https://w3id.org/ro/terms/ods#name" - } - ] + "@context": { + "Specimen": "https://w3id.org/ro/terms/ods#Specimen", + "SpecimenRecord": "https://w3id.org/ro/terms/ods#SpecimenRecord", + "authoritative": "https://w3id.org/ro/terms/ods#authoritative", + "modified": "https://w3id.org/ro/terms/ods#modified", + "midsLevel": "https://w3id.org/ro/terms/ods#midsLevel", + "physicalSpecimenId": "https://w3id.org/ro/terms/ods#physicalSpecimenId", + "institution": "https://w3id.org/ro/terms/ods#institution", + "materialType": "https://w3id.org/ro/terms/ods#materialType", + "name": "https://w3id.org/ro/terms/ods#name" + } } \ No newline at end of file diff --git a/sample/context.json b/sample/context.json index 4ed184d..6e4106a 100644 --- a/sample/context.json +++ b/sample/context.json @@ -1,74 +1,71 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "Sample": "https://w3id.org/ro/terms/sample#Sample", - "SERIES": "https://w3id.org/ro/terms/sample#SERIES", - "RACK_OR_PLATE_ID": "https://w3id.org/ro/terms/sample#RACK_OR_PLATE_ID", - "TUBE_OR_WELL_ID": "https://w3id.org/ro/terms/sample#TUBE_OR_WELL_ID", - "SPECIMEN_ID": "https://w3id.org/ro/terms/sample#SPECIMEN_ID", - "ORDER_OR_GROUP": "https://w3id.org/ro/terms/sample#ORDER_OR_GROUP", - "FAMILY": "https://w3id.org/ro/terms/sample#FAMILY", - "GENUS": "https://w3id.org/ro/terms/sample#GENUS", - "TAXON_ID": "https://w3id.org/ro/terms/sample#TAXON_ID", - "SCIENTIFIC_NAME": "https://w3id.org/ro/terms/sample#SCIENTIFIC_NAME", - "TAXON_REMARKS": "https://w3id.org/ro/terms/sample#TAXON_REMARKS", - "INFRASPECIFIC_EPITHET": "https://w3id.org/ro/terms/sample#INFRASPECIFIC_EPITHET", - "CULTURE_OR_STRAIN_ID": "https://w3id.org/ro/terms/sample#CULTURE_OR_STRAIN_ID", - "COMMON_NAME": "https://w3id.org/ro/terms/sample#COMMON_NAME", - "LIFESTAGE": "https://w3id.org/ro/terms/sample#LIFESTAGE", - "SEX": "https://w3id.org/ro/terms/sample#SEX", - "ORGANISM_PART": "https://w3id.org/ro/terms/sample#ORGANISM_PART", - "SYMBIONT": "https://w3id.org/ro/terms/sample#SYMBIONT", - "RELATIONSHIP": "https://w3id.org/ro/terms/sample#RELATIONSHIP", - "GAL": "https://w3id.org/ro/terms/sample#GAL", - "GAL_SAMPLE_ID": "https://w3id.org/ro/terms/sample#GAL_SAMPLE_ID", - "COLLECTOR_SAMPLE_ID": "https://w3id.org/ro/terms/sample#COLLECTOR_SAMPLE_ID", - "COLLECTED_BY": "https://w3id.org/ro/terms/sample#COLLECTED_BY", - "COLLECTOR_AFFILIATION": "https://w3id.org/ro/terms/sample#COLLECTOR_AFFILIATION", - "DATE_OF_COLLECTION": "https://w3id.org/ro/terms/sample#DATE_OF_COLLECTION", - "COLLECTION_LOCATION": "https://w3id.org/ro/terms/sample#COLLECTION_LOCATION", - "DECIMAL_LATITUDE": "https://w3id.org/ro/terms/sample#DECIMAL_LATITUDE", - "DECIMAL_LONGITUDE": "https://w3id.org/ro/terms/sample#DECIMAL_LONGITUDE", - "GRID_REFERENCE": "https://w3id.org/ro/terms/sample#GRID_REFERENCE", - "HABITAT": "https://w3id.org/ro/terms/sample#HABITAT", - "DEPTH": "https://w3id.org/ro/terms/sample#DEPTH", - "ELEVATION": "https://w3id.org/ro/terms/sample#ELEVATION", - "ORIGINAL_COLLECTION_DATE": "https://w3id.org/ro/terms/sample#ORIGINAL_COLLECTION_DATE", - "ORIGINAL_GEOGRAPHIC_LOCATION": "https://w3id.org/ro/terms/sample#ORIGINAL_GEOGRAPHIC_LOCATION", - "ORIGINAL_DECIMAL_LATITUDE": "https://w3id.org/ro/terms/sample#ORIGINAL_DECIMAL_LATITUDE", - "ORIGINAL_DECIMAL_LONGITUDE": "https://w3id.org/ro/terms/sample#ORIGINAL_DECIMAL_LONGITUDE", - "TIME_OF_COLLECTION": "https://w3id.org/ro/terms/sample#TIME_OF_COLLECTION", - "DESCRIPTION_OF_COLLECTION_METHOD": "https://w3id.org/ro/terms/sample#DESCRIPTION_OF_COLLECTION_METHOD", - "DIFFICULT_OR_HIGH_PRIORITY_SAMPLE": "https://w3id.org/ro/terms/sample#DIFFICULT_OR_HIGH_PRIORITY_SAMPLE", - "IDENTIFIED_BY": "https://w3id.org/ro/terms/sample#IDENTIFIED_BY", - "IDENTIFIER_AFFILIATION": "https://w3id.org/ro/terms/sample#IDENTIFIER_AFFILIATION", - "IDENTIFIED_HOW": "https://w3id.org/ro/terms/sample#IDENTIFIED_HOW", - "SPECIMEN_IDENTITY_RISK": "https://w3id.org/ro/terms/sample#SPECIMEN_IDENTITY_RISK", - "MIXED_SAMPLE_RISK": "https://w3id.org/ro/terms/sample#MIXED_SAMPLE_RISK", - "PRESERVED_BY": "https://w3id.org/ro/terms/sample#PRESERVED_BY", - "PRESERVER_AFFILIATION": "https://w3id.org/ro/terms/sample#PRESERVER_AFFILIATION", - "PRESERVATION_APPROACH": "https://w3id.org/ro/terms/sample#PRESERVATION_APPROACH", - "PRESERVATIVE_SOLUTION": "https://w3id.org/ro/terms/sample#PRESERVATIVE_SOLUTION", - "TIME_ELAPSED_FROM_COLLECTION_TO_PRESERVATION": "https://w3id.org/ro/terms/sample#TIME_ELAPSED_FROM_COLLECTION_TO_PRESERVATION", - "DATE_OF_PRESERVATION": "https://w3id.org/ro/terms/sample#DATE_OF_PRESERVATION", - "SIZE_OF_TISSUE_IN_TUBE": "https://w3id.org/ro/terms/sample#SIZE_OF_TISSUE_IN_TUBE", - "BARCODE_HUB": "https://w3id.org/ro/terms/sample#BARCODE_HUB", - "TISSUE_REMOVED_FOR_BARCODING": "https://w3id.org/ro/terms/sample#TISSUE_REMOVED_FOR_BARCODING", - "PLATE_ID_FOR_BARCODING": "https://w3id.org/ro/terms/sample#PLATE_ID_FOR_BARCODING", - "TUBE_OR_WELL_ID_FOR_BARCODING": "https://w3id.org/ro/terms/sample#TUBE_OR_WELL_ID_FOR_BARCODING", - "TISSUE_FOR_BARCODING": "https://w3id.org/ro/terms/sample#TISSUE_FOR_BARCODING", - "BARCODE_PLATE_PRESERVATIVE": "https://w3id.org/ro/terms/sample#BARCODE_PLATE_PRESERVATIVE", - "BARCODING_STATUS": "https://w3id.org/ro/terms/sample#BARCODING_STATUS", - "PURPOSE_OF_SPECIMEN": "https://w3id.org/ro/terms/sample#PURPOSE_OF_SPECIMEN", - "HAZARD_GROUP": "https://w3id.org/ro/terms/sample#HAZARD_GROUP", - "REGULATORY_COMPLIANCE": "https://w3id.org/ro/terms/sample#REGULATORY_COMPLIANCE", - "VOUCHER_ID": "https://w3id.org/ro/terms/sample#VOUCHER_ID", - "PROXY_VOUCHER_ID": "https://w3id.org/ro/terms/sample#PROXY_VOUCHER_ID", - "VOUCHER_LINK": "https://w3id.org/ro/terms/sample#VOUCHER_LINK", - "PROXY_VOUCHER_LINK": "https://w3id.org/ro/terms/sample#PROXY_VOUCHER_LINK", - "VOUCHER_INSTITUTION": "https://w3id.org/ro/terms/sample#VOUCHER_INSTITUTION", - "OTHER_INFORMATION": "https://w3id.org/ro/terms/sample#OTHER_INFORMATION" - } - ] + "@context": { + "Sample": "https://w3id.org/ro/terms/sample#Sample", + "SERIES": "https://w3id.org/ro/terms/sample#SERIES", + "RACK_OR_PLATE_ID": "https://w3id.org/ro/terms/sample#RACK_OR_PLATE_ID", + "TUBE_OR_WELL_ID": "https://w3id.org/ro/terms/sample#TUBE_OR_WELL_ID", + "SPECIMEN_ID": "https://w3id.org/ro/terms/sample#SPECIMEN_ID", + "ORDER_OR_GROUP": "https://w3id.org/ro/terms/sample#ORDER_OR_GROUP", + "FAMILY": "https://w3id.org/ro/terms/sample#FAMILY", + "GENUS": "https://w3id.org/ro/terms/sample#GENUS", + "TAXON_ID": "https://w3id.org/ro/terms/sample#TAXON_ID", + "SCIENTIFIC_NAME": "https://w3id.org/ro/terms/sample#SCIENTIFIC_NAME", + "TAXON_REMARKS": "https://w3id.org/ro/terms/sample#TAXON_REMARKS", + "INFRASPECIFIC_EPITHET": "https://w3id.org/ro/terms/sample#INFRASPECIFIC_EPITHET", + "CULTURE_OR_STRAIN_ID": "https://w3id.org/ro/terms/sample#CULTURE_OR_STRAIN_ID", + "COMMON_NAME": "https://w3id.org/ro/terms/sample#COMMON_NAME", + "LIFESTAGE": "https://w3id.org/ro/terms/sample#LIFESTAGE", + "SEX": "https://w3id.org/ro/terms/sample#SEX", + "ORGANISM_PART": "https://w3id.org/ro/terms/sample#ORGANISM_PART", + "SYMBIONT": "https://w3id.org/ro/terms/sample#SYMBIONT", + "RELATIONSHIP": "https://w3id.org/ro/terms/sample#RELATIONSHIP", + "GAL": "https://w3id.org/ro/terms/sample#GAL", + "GAL_SAMPLE_ID": "https://w3id.org/ro/terms/sample#GAL_SAMPLE_ID", + "COLLECTOR_SAMPLE_ID": "https://w3id.org/ro/terms/sample#COLLECTOR_SAMPLE_ID", + "COLLECTED_BY": "https://w3id.org/ro/terms/sample#COLLECTED_BY", + "COLLECTOR_AFFILIATION": "https://w3id.org/ro/terms/sample#COLLECTOR_AFFILIATION", + "DATE_OF_COLLECTION": "https://w3id.org/ro/terms/sample#DATE_OF_COLLECTION", + "COLLECTION_LOCATION": "https://w3id.org/ro/terms/sample#COLLECTION_LOCATION", + "DECIMAL_LATITUDE": "https://w3id.org/ro/terms/sample#DECIMAL_LATITUDE", + "DECIMAL_LONGITUDE": "https://w3id.org/ro/terms/sample#DECIMAL_LONGITUDE", + "GRID_REFERENCE": "https://w3id.org/ro/terms/sample#GRID_REFERENCE", + "HABITAT": "https://w3id.org/ro/terms/sample#HABITAT", + "DEPTH": "https://w3id.org/ro/terms/sample#DEPTH", + "ELEVATION": "https://w3id.org/ro/terms/sample#ELEVATION", + "ORIGINAL_COLLECTION_DATE": "https://w3id.org/ro/terms/sample#ORIGINAL_COLLECTION_DATE", + "ORIGINAL_GEOGRAPHIC_LOCATION": "https://w3id.org/ro/terms/sample#ORIGINAL_GEOGRAPHIC_LOCATION", + "ORIGINAL_DECIMAL_LATITUDE": "https://w3id.org/ro/terms/sample#ORIGINAL_DECIMAL_LATITUDE", + "ORIGINAL_DECIMAL_LONGITUDE": "https://w3id.org/ro/terms/sample#ORIGINAL_DECIMAL_LONGITUDE", + "TIME_OF_COLLECTION": "https://w3id.org/ro/terms/sample#TIME_OF_COLLECTION", + "DESCRIPTION_OF_COLLECTION_METHOD": "https://w3id.org/ro/terms/sample#DESCRIPTION_OF_COLLECTION_METHOD", + "DIFFICULT_OR_HIGH_PRIORITY_SAMPLE": "https://w3id.org/ro/terms/sample#DIFFICULT_OR_HIGH_PRIORITY_SAMPLE", + "IDENTIFIED_BY": "https://w3id.org/ro/terms/sample#IDENTIFIED_BY", + "IDENTIFIER_AFFILIATION": "https://w3id.org/ro/terms/sample#IDENTIFIER_AFFILIATION", + "IDENTIFIED_HOW": "https://w3id.org/ro/terms/sample#IDENTIFIED_HOW", + "SPECIMEN_IDENTITY_RISK": "https://w3id.org/ro/terms/sample#SPECIMEN_IDENTITY_RISK", + "MIXED_SAMPLE_RISK": "https://w3id.org/ro/terms/sample#MIXED_SAMPLE_RISK", + "PRESERVED_BY": "https://w3id.org/ro/terms/sample#PRESERVED_BY", + "PRESERVER_AFFILIATION": "https://w3id.org/ro/terms/sample#PRESERVER_AFFILIATION", + "PRESERVATION_APPROACH": "https://w3id.org/ro/terms/sample#PRESERVATION_APPROACH", + "PRESERVATIVE_SOLUTION": "https://w3id.org/ro/terms/sample#PRESERVATIVE_SOLUTION", + "TIME_ELAPSED_FROM_COLLECTION_TO_PRESERVATION": "https://w3id.org/ro/terms/sample#TIME_ELAPSED_FROM_COLLECTION_TO_PRESERVATION", + "DATE_OF_PRESERVATION": "https://w3id.org/ro/terms/sample#DATE_OF_PRESERVATION", + "SIZE_OF_TISSUE_IN_TUBE": "https://w3id.org/ro/terms/sample#SIZE_OF_TISSUE_IN_TUBE", + "BARCODE_HUB": "https://w3id.org/ro/terms/sample#BARCODE_HUB", + "TISSUE_REMOVED_FOR_BARCODING": "https://w3id.org/ro/terms/sample#TISSUE_REMOVED_FOR_BARCODING", + "PLATE_ID_FOR_BARCODING": "https://w3id.org/ro/terms/sample#PLATE_ID_FOR_BARCODING", + "TUBE_OR_WELL_ID_FOR_BARCODING": "https://w3id.org/ro/terms/sample#TUBE_OR_WELL_ID_FOR_BARCODING", + "TISSUE_FOR_BARCODING": "https://w3id.org/ro/terms/sample#TISSUE_FOR_BARCODING", + "BARCODE_PLATE_PRESERVATIVE": "https://w3id.org/ro/terms/sample#BARCODE_PLATE_PRESERVATIVE", + "BARCODING_STATUS": "https://w3id.org/ro/terms/sample#BARCODING_STATUS", + "PURPOSE_OF_SPECIMEN": "https://w3id.org/ro/terms/sample#PURPOSE_OF_SPECIMEN", + "HAZARD_GROUP": "https://w3id.org/ro/terms/sample#HAZARD_GROUP", + "REGULATORY_COMPLIANCE": "https://w3id.org/ro/terms/sample#REGULATORY_COMPLIANCE", + "VOUCHER_ID": "https://w3id.org/ro/terms/sample#VOUCHER_ID", + "PROXY_VOUCHER_ID": "https://w3id.org/ro/terms/sample#PROXY_VOUCHER_ID", + "VOUCHER_LINK": "https://w3id.org/ro/terms/sample#VOUCHER_LINK", + "PROXY_VOUCHER_LINK": "https://w3id.org/ro/terms/sample#PROXY_VOUCHER_LINK", + "VOUCHER_INSTITUTION": "https://w3id.org/ro/terms/sample#VOUCHER_INSTITUTION", + "OTHER_INFORMATION": "https://w3id.org/ro/terms/sample#OTHER_INFORMATION" + } } \ No newline at end of file diff --git a/sample/context.jsonld b/sample/context.jsonld index 4ed184d..6e4106a 100644 --- a/sample/context.jsonld +++ b/sample/context.jsonld @@ -1,74 +1,71 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "Sample": "https://w3id.org/ro/terms/sample#Sample", - "SERIES": "https://w3id.org/ro/terms/sample#SERIES", - "RACK_OR_PLATE_ID": "https://w3id.org/ro/terms/sample#RACK_OR_PLATE_ID", - "TUBE_OR_WELL_ID": "https://w3id.org/ro/terms/sample#TUBE_OR_WELL_ID", - "SPECIMEN_ID": "https://w3id.org/ro/terms/sample#SPECIMEN_ID", - "ORDER_OR_GROUP": 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"mappedRate": "https://w3id.org/ro/terms/sapporo#mappedRate", - "unmappedRate": "https://w3id.org/ro/terms/sapporo#unmappedRate", - "duplicateRate": "https://w3id.org/ro/terms/sapporo#duplicateRate", - "variantCount": "https://w3id.org/ro/terms/sapporo#variantCount", - "snpsCount": "https://w3id.org/ro/terms/sapporo#snpsCount", - "indelsCount": "https://w3id.org/ro/terms/sapporo#indelsCount", - "wesState": "https://w3id.org/ro/terms/sapporo#wesState", - "exitCode": "https://w3id.org/ro/terms/sapporo#exitCode" - } - ] + "@context": { + "lineCount": "https://w3id.org/ro/terms/sapporo#lineCount", + "FileStats": "https://w3id.org/ro/terms/sapporo#FileStats", + "stats": "https://w3id.org/ro/terms/sapporo#stats", + "generatedBy": "https://w3id.org/ro/terms/sapporo#generatedBy", + "totalReads": "https://w3id.org/ro/terms/sapporo#totalReads", + "mappedReads": "https://w3id.org/ro/terms/sapporo#mappedReads", + "unmappedReads": "https://w3id.org/ro/terms/sapporo#unmappedReads", + 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a/test/context.json b/test/context.json index 8129651..6bd0c3e 100644 --- a/test/context.json +++ b/test/context.json @@ -1,20 +1,17 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "TestSuite": "https://w3id.org/ro/terms/test#TestSuite", - "TestInstance": "https://w3id.org/ro/terms/test#TestInstance", - "TestService": "https://w3id.org/ro/terms/test#TestService", - "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition", - "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine", - "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", - "TravisService": "https://w3id.org/ro/terms/test#TravisService", - "GithubService": "https://w3id.org/ro/terms/test#GithubService", - "instance": "https://w3id.org/ro/terms/test#instance", - "runsOn": "https://w3id.org/ro/terms/test#runsOn", - "resource": "https://w3id.org/ro/terms/test#resource", - "definition": "https://w3id.org/ro/terms/test#definition", - "engineVersion": 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8129651..6bd0c3e 100644 --- a/test/context.jsonld +++ b/test/context.jsonld @@ -1,20 +1,17 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "TestSuite": "https://w3id.org/ro/terms/test#TestSuite", - "TestInstance": "https://w3id.org/ro/terms/test#TestInstance", - "TestService": "https://w3id.org/ro/terms/test#TestService", - "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition", - "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine", - "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", - "TravisService": "https://w3id.org/ro/terms/test#TravisService", - "GithubService": "https://w3id.org/ro/terms/test#GithubService", - "instance": "https://w3id.org/ro/terms/test#instance", - "runsOn": "https://w3id.org/ro/terms/test#runsOn", - "resource": "https://w3id.org/ro/terms/test#resource", - "definition": "https://w3id.org/ro/terms/test#definition", - "engineVersion": "https://w3id.org/ro/terms/test#engineVersion" - } - ] + "@context": 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b/text-commons/context.json @@ -1,101 +1,98 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "AnalyticalLexicon": "https://w3id.org/ro/terms/text-commons#AnalyticalLexicon", - "Annotation": "https://w3id.org/ro/terms/text-commons#Annotation", - "BilingualLexicon": "https://w3id.org/ro/terms/text-commons#BilingualLexicon", - "ComparativeDescription": "https://w3id.org/ro/terms/text-commons#ComparativeDescription", - "DictionaryLexicon": "https://w3id.org/ro/terms/text-commons#DictionaryLexicon", - "DiscourseAnnotation": "https://w3id.org/ro/terms/text-commons#DiscourseAnnotation", - "DiscourseDataset": "https://w3id.org/ro/terms/text-commons#DiscourseDataset", - "DiscourseDescription": "https://w3id.org/ro/terms/text-commons#DiscourseDescription", - "DramaText": "https://w3id.org/ro/terms/text-commons#DramaText", - "EtymologicalLexicon": "https://w3id.org/ro/terms/text-commons#EtymologicalLexicon", - "FormulaicText": 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"OrthographicTranscription": "https://w3id.org/ro/terms/text-commons#OrthographicTranscription", - "Part-of-speechAnnotation": "https://w3id.org/ro/terms/text-commons#Part-of-speechAnnotation", - "Part-of-speechDataset": "https://w3id.org/ro/terms/text-commons#Part-of-speechDataset", - "Part-of-speechDescription": "https://w3id.org/ro/terms/text-commons#Part-of-speechDescription", - "PedagogicalDescription": "https://w3id.org/ro/terms/text-commons#PedagogicalDescription", - "PhonemicTranscription": "https://w3id.org/ro/terms/text-commons#PhonemicTranscription", - "PhoneticAnnotation": "https://w3id.org/ro/terms/text-commons#PhoneticAnnotation", - "PhoneticDataset": "https://w3id.org/ro/terms/text-commons#PhoneticDataset", - "PhoneticDescription": "https://w3id.org/ro/terms/text-commons#PhoneticDescription", - "PhoneticLexicon": "https://w3id.org/ro/terms/text-commons#PhoneticLexicon", - "PhoneticTranscription": "https://w3id.org/ro/terms/text-commons#PhoneticTranscription", - 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"MusicalAnnotation": "https://w3id.org/ro/terms/text-commons#MusicalAnnotation", + "MusicalDataset": "https://w3id.org/ro/terms/text-commons#MusicalDataset", + "MusicalTranscription": "https://w3id.org/ro/terms/text-commons#MusicalTranscription", + "NarrativeText": "https://w3id.org/ro/terms/text-commons#NarrativeText", + "OratoryText": "https://w3id.org/ro/terms/text-commons#OratoryText", + "OrthographicDataset": "https://w3id.org/ro/terms/text-commons#OrthographicDataset", + "OrthographicDescription": "https://w3id.org/ro/terms/text-commons#OrthographicDescription", + "OrthographicText": "https://w3id.org/ro/terms/text-commons#OrthographicText", + "OrthographicTranscription": "https://w3id.org/ro/terms/text-commons#OrthographicTranscription", + "Part-of-speechAnnotation": "https://w3id.org/ro/terms/text-commons#Part-of-speechAnnotation", + "Part-of-speechDataset": "https://w3id.org/ro/terms/text-commons#Part-of-speechDataset", + "Part-of-speechDescription": 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"https://w3id.org/ro/terms/workflow-run#registry", + "tag": "https://w3id.org/ro/terms/workflow-run#tag", + "containerImage": "https://w3id.org/ro/terms/workflow-run#containerImage", + "resourceUsage": "https://w3id.org/ro/terms/workflow-run#resourceUsage" + } } \ No newline at end of file diff --git a/workflow-run/context.jsonld b/workflow-run/context.jsonld index 7ac0141..72948f6 100644 --- a/workflow-run/context.jsonld +++ b/workflow-run/context.jsonld @@ -1,23 +1,20 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "ParameterConnection": "https://w3id.org/ro/terms/workflow-run#ParameterConnection", - "ContainerImage": "https://w3id.org/ro/terms/workflow-run#ContainerImage", - "DockerImage": "https://w3id.org/ro/terms/workflow-run#DockerImage", - "SIFImage": "https://w3id.org/ro/terms/workflow-run#SIFImage", - "connection": "https://w3id.org/ro/terms/workflow-run#connection", - "sourceParameter": "https://w3id.org/ro/terms/workflow-run#sourceParameter", - "targetParameter": "https://w3id.org/ro/terms/workflow-run#targetParameter", - "md5": "https://w3id.org/ro/terms/workflow-run#md5", - "sha1": "https://w3id.org/ro/terms/workflow-run#sha1", - "sha256": "https://w3id.org/ro/terms/workflow-run#sha256", - "sha512": "https://w3id.org/ro/terms/workflow-run#sha512", - "environment": "https://w3id.org/ro/terms/workflow-run#environment", - "registry": "https://w3id.org/ro/terms/workflow-run#registry", - "tag": "https://w3id.org/ro/terms/workflow-run#tag", - "containerImage": "https://w3id.org/ro/terms/workflow-run#containerImage", - "resourceUsage": "https://w3id.org/ro/terms/workflow-run#resourceUsage" - } - ] + "@context": { + "ParameterConnection": "https://w3id.org/ro/terms/workflow-run#ParameterConnection", + "ContainerImage": "https://w3id.org/ro/terms/workflow-run#ContainerImage", + "DockerImage": "https://w3id.org/ro/terms/workflow-run#DockerImage", + "SIFImage": "https://w3id.org/ro/terms/workflow-run#SIFImage", + "connection": "https://w3id.org/ro/terms/workflow-run#connection", + "sourceParameter": "https://w3id.org/ro/terms/workflow-run#sourceParameter", + "targetParameter": "https://w3id.org/ro/terms/workflow-run#targetParameter", + "md5": "https://w3id.org/ro/terms/workflow-run#md5", + "sha1": "https://w3id.org/ro/terms/workflow-run#sha1", + "sha256": "https://w3id.org/ro/terms/workflow-run#sha256", + "sha512": "https://w3id.org/ro/terms/workflow-run#sha512", + "environment": "https://w3id.org/ro/terms/workflow-run#environment", + "registry": "https://w3id.org/ro/terms/workflow-run#registry", + "tag": "https://w3id.org/ro/terms/workflow-run#tag", + "containerImage": "https://w3id.org/ro/terms/workflow-run#containerImage", + "resourceUsage": "https://w3id.org/ro/terms/workflow-run#resourceUsage" + } } \ No newline at end of file diff --git a/workflow-run/wfrun.jsonld b/workflow-run/wfrun.jsonld index 388345e..5aa8b7d 100644 --- a/workflow-run/wfrun.jsonld +++ b/workflow-run/wfrun.jsonld @@ -1,30 +1,27 @@ { - "@context": [ - "https://w3id.org/ro/crate/1.1/context", - { - "ParameterConnection": "https://w3id.org/ro/terms/workflow-run#ParameterConnection", - "ContainerImage": "https://w3id.org/ro/terms/workflow-run#ContainerImage", - "DockerImage": "https://w3id.org/ro/terms/workflow-run#DockerImage", - "SIFImage": "https://w3id.org/ro/terms/workflow-run#SIFImage", - "connection": "https://w3id.org/ro/terms/workflow-run#connection", - "sourceParameter": "https://w3id.org/ro/terms/workflow-run#sourceParameter", - "targetParameter": "https://w3id.org/ro/terms/workflow-run#targetParameter", - "md5": "https://w3id.org/ro/terms/workflow-run#md5", - "sha1": "https://w3id.org/ro/terms/workflow-run#sha1", - "sha256": "https://w3id.org/ro/terms/workflow-run#sha256", - "sha512": "https://w3id.org/ro/terms/workflow-run#sha512", - "environment": "https://w3id.org/ro/terms/workflow-run#environment", - "registry": "https://w3id.org/ro/terms/workflow-run#registry", - "tag": "https://w3id.org/ro/terms/workflow-run#tag", - "containerImage": "https://w3id.org/ro/terms/workflow-run#containerImage", - "resourceUsage": "https://w3id.org/ro/terms/workflow-run#resourceUsage", + "@context": { + "ParameterConnection": "https://w3id.org/ro/terms/workflow-run#ParameterConnection", + "ContainerImage": "https://w3id.org/ro/terms/workflow-run#ContainerImage", + "DockerImage": "https://w3id.org/ro/terms/workflow-run#DockerImage", + "SIFImage": "https://w3id.org/ro/terms/workflow-run#SIFImage", + "connection": "https://w3id.org/ro/terms/workflow-run#connection", + "sourceParameter": "https://w3id.org/ro/terms/workflow-run#sourceParameter", + "targetParameter": "https://w3id.org/ro/terms/workflow-run#targetParameter", + "md5": "https://w3id.org/ro/terms/workflow-run#md5", + "sha1": "https://w3id.org/ro/terms/workflow-run#sha1", + "sha256": "https://w3id.org/ro/terms/workflow-run#sha256", + "sha512": "https://w3id.org/ro/terms/workflow-run#sha512", + "environment": "https://w3id.org/ro/terms/workflow-run#environment", + "registry": "https://w3id.org/ro/terms/workflow-run#registry", + "tag": "https://w3id.org/ro/terms/workflow-run#tag", + "containerImage": "https://w3id.org/ro/terms/workflow-run#containerImage", + "resourceUsage": "https://w3id.org/ro/terms/workflow-run#resourceUsage", "input": "https://bioschemas.org/properties/input", "output": "https://bioschemas.org/properties/output", - "wfrun": "https://w3id.org/ro/terms/workflow-run#", - "owl": "http://www.w3.org/2002/07/owl#", - "vann": "http://purl.org/vocab/vann/" - } - ], + "wfrun": "https://w3id.org/ro/terms/workflow-run#", + "owl": "http://www.w3.org/2002/07/owl#", + "vann": "http://purl.org/vocab/vann/" + }, "@graph": [ { "@id": "wfrun:registry",