def test_basics(self):
BFO = CurieNamespace('bfo', "http://purl.obolibrary.org/obo/BFO_")
self.assertEqual(URIRef("http://purl.obolibrary.org/obo/BFO_test"),
BFO.test)
self.assertEqual("http://purl.obolibrary.org/obo/BFO_", BFO)
self.assertEqual("bfo:test", BFO.curie('test'))
self.assertEqual("bfo:", BFO.curie())
def parse_identifier(cls, identifier: str) -> Tuple[CurieNamespace, str]:
# trivial case of a null identifier?
if not identifier:
return CurieNamespace("", ""), ""
# check if this is a candidate URI...
if identifier.lower().startswith("http"):
# guess that perhaps it is, so try to parse it
return cls.parse_uri(identifier)
else: # attempt to parse as a CURIE
return cls.parse_curie(identifier)
def parse_curie(cls, curie: str) -> Tuple[CurieNamespace, str]:
"""
Parse a candidate CURIE
:param curie: candidate curie string
:return: CURIE namespace and object_id
"""
found = CurieNamespace(
"",
""), curie # default value if not a CURIE or unknown XMLNS prefix
if ':' in curie:
part = curie.split(":")
# Normalize retrieval with upper case of prefix for lookup
prefix = part[0].upper()
if prefix in cls._get_prefix_map():
found = cls._prefix_map[prefix], part[1]
return found
def parse_uri(cls, uri: str) -> Tuple[CurieNamespace, str]:
"""
Parse a candidate URI
:param uri: candidate URI string
:return: namespace and object_id
"""
found = CurieNamespace(
"", ""), uri # default value returned if unknown URI namespace
# TODO: is there a more efficient lookup scheme here than a linear search of namespaces?
for ns in cls._namespaces:
base_uri = str(ns)
if uri.startswith(base_uri):
# simple minded deletion of base_uri to give the object_id
object_id = uri.replace(base_uri, "")
found = ns, object_id
break
return found
from linkml.utils.slot import Slot
from linkml.utils.metamodelcore import empty_list, empty_dict, bnode
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
EX = CurieNamespace('ex', 'https://example.org/linkml/hello-world/')
FOAF = CurieNamespace('foaf', 'http://xmlns.com/foaf/0.1/')
LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
SDO = CurieNamespace('sdo', 'https://schema.org/')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = EX
# Types
class String(str):
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = EX.String
from linkml.utils.slot import Slot
from linkml.utils.metamodelcore import empty_list, empty_dict, bnode
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
EX = CurieNamespace('ex', 'https://example.org/importee/')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = EX
# Types
class String(str):
""" A character string """
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = EX.String
# Class references
class BaseId(extended_str):
if sys.version_info < (3, 7, 6):
from linkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from includes.types import String
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
CLUE = CurieNamespace('CLUE', 'http://ontologies-r.us/clue/')
CS = CurieNamespace('CS', 'http://ontologies-r.us/codesystems/')
BIOLINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
EVIDENCE = CurieNamespace('evidence', 'http://example.org/test/evidence/')
DEFAULT_ = EVIDENCE
# Types
# Class references
class AllEnumsEntryName(extended_str):
pass
@dataclass
class AllEnums(YAMLRoot):
from linkml.utils.metamodelcore import empty_list, empty_dict, bnode
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml.utils.metamodelcore import URI
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = LINKML
# Types
class String(str):
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = LINKML.String
class Uri(URI):
""" a complete URI """
type_class_uri = XSD.anyURI
from dataclasses import dataclass
from linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions
from linkml.utils.slot import Slot
from linkml.utils.metamodelcore import empty_list, empty_dict, bnode
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
DEFAULT_ = CurieNamespace('', 'https://hotecosystem.org/tccm/prefixes/')
# Types
# Class references
# Enumerations
# Slots
class slots:
pass
from linkml.utils.metamodelcore import empty_list, empty_dict, bnode
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml.utils.metamodelcore import Bool
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
FOAF = CurieNamespace('foaf', 'http://xmlns.com/foaf/0.1/')
LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
PERS = CurieNamespace('pers', 'http://example.org/sample/person/')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = PERS
# Types
class String(str):
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = PERS.String
class Int(int):
from linkml.utils.metamodelcore import empty_list, empty_dict, bnode
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
DEFAULT_ = CurieNamespace('', 'https://microbiomedata/schema/mixs/')
# Types
# Class references
class ParentClass(YAMLRoot):
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ParentClass")
class_class_curie: ClassVar[str] = None
class_name: ClassVar[str] = "parent_class"
class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ParentClass")
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml.utils.metamodelcore import ElementIdentifier
from linkml_model.types import Double, Float, String
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
UO = CurieNamespace('UO', 'http://purl.obolibrary.org/obo/UO_')
DCTERMS = CurieNamespace('dcterms', 'http://example.org/UNKNOWN/dcterms/')
LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
NMDC = CurieNamespace('nmdc', 'https://microbiomedata/meta/')
QUD = CurieNamespace('qud', 'http://qudt.org/1.1/schema/qudt#')
RDF = CurieNamespace('rdf', 'http://example.org/UNKNOWN/rdf/')
RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/')
SKOS = CurieNamespace('skos', 'http://example.org/UNKNOWN/skos/')
WGS = CurieNamespace('wgs', 'http://www.w3.org/2003/01/geo/wgs84_pos')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = NMDC
# Types
class IdentifierType(ElementIdentifier):
""" A string that is intended to uniquely identify a thing May be URI in full or compact (CURIE) form """
class BiolinkNameSpace:
"""
Map of BioLink Model registered URI Namespaces
"""
_namespaces = [
CurieNamespace('APO', 'http://purl.obolibrary.org/obo/APO_'),
CurieNamespace('Aeolus', 'http://translator.ncats.nih.gov/Aeolus_'),
CurieNamespace('BIOGRID', 'http://identifiers.org/biogrid/'),
CurieNamespace('BIOSAMPLE', 'http://identifiers.org/biosample/'),
CurieNamespace('BSPO', 'http://purl.obolibrary.org/obo/BSPO_'),
CurieNamespace(
'CAID',
'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid='
),
CurieNamespace('CAS', 'http://identifiers.org/cas/'),
CurieNamespace('CATH', 'http://identifiers.org/cath/'),
CurieNamespace('CATH_SUPERFAMILY',
'http://identifiers.org/cath.superfamily/'),
CurieNamespace('CDD', 'http://identifiers.org/cdd/'),
CurieNamespace('CHADO', 'http://gmod.org/wiki/Chado/'),
CurieNamespace('CHEBI', 'http://purl.obolibrary.org/obo/CHEBI_'),
CurieNamespace('CHEMBL_COMPOUND',
'http://identifiers.org/chembl.compound/'),
CurieNamespace('CHEMBL_MECHANISM',
'https://www.ebi.ac.uk/chembl/mechanism/inspect/'),
CurieNamespace('CHEMBL_TARGET',
'http://identifiers.org/chembl.target/'),
CurieNamespace('CID', 'http://pubchem.ncbi.nlm.nih.gov/compound/'),
CurieNamespace('CL', 'http://purl.obolibrary.org/obo/CL_'),
CurieNamespace('CLINVAR', 'http://identifiers.org/clinvar/'),
CurieNamespace('CLO', 'http://purl.obolibrary.org/obo/CLO_'),
CurieNamespace('COAR_RESOURCE', 'http://purl.org/coar/resource_type/'),
CurieNamespace('CPT',
'https://www.ama-assn.org/practice-management/cpt/'),
CurieNamespace('CTD', 'http://translator.ncats.nih.gov/CTD_'),
CurieNamespace(
'ChemBank',
'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid='
),
CurieNamespace('ClinVarVariant',
'http://www.ncbi.nlm.nih.gov/clinvar/variation/'),
CurieNamespace('DBSNP', 'http://identifiers.org/dbsnp/'),
CurieNamespace('DGIdb', 'https://www.dgidb.org/interaction_types'),
CurieNamespace('DOID', 'http://purl.obolibrary.org/obo/DOID_'),
CurieNamespace('DRUGBANK', 'http://identifiers.org/drugbank/'),
CurieNamespace('DrugCentral',
'http://translator.ncats.nih.gov/DrugCentral_'),
CurieNamespace('EC', 'http://www.enzyme-database.org/query.php?ec='),
CurieNamespace('ECTO', 'http://purl.obolibrary.org/obo/ECTO_'),
CurieNamespace('EDAM-DATA', 'http://edamontology.org/data_'),
CurieNamespace('EDAM-FORMAT', 'http://edamontology.org/format_'),
CurieNamespace('EDAM-OPERATION', 'http://edamontology.org/operation_'),
CurieNamespace('EDAM-TOPIC', 'http://edamontology.org/topic_'),
CurieNamespace('EFO', 'http://www.ebi.ac.uk/efo/EFO_'),
CurieNamespace('EGGNOG', 'http://identifiers.org/eggnog/'),
CurieNamespace('ENSEMBL', 'http://identifiers.org/ensembl/'),
CurieNamespace('ExO', 'http://purl.obolibrary.org/obo/ExO_'),
CurieNamespace('FAO', 'http://purl.obolibrary.org/obo/FAO_'),
CurieNamespace('FB', 'http://identifiers.org/fb/'),
CurieNamespace('FBcv', 'http://purl.obolibrary.org/obo/FBcv_'),
CurieNamespace('GAMMA', 'http://translator.renci.org/GAMMA_'),
CurieNamespace('GO', 'http://purl.obolibrary.org/obo/GO_'),
CurieNamespace('GOLD_META', 'http://identifiers.org/gold.meta/'),
CurieNamespace('GOP', 'http://purl.obolibrary.org/obo/go#'),
CurieNamespace('GOREL', 'http://purl.obolibrary.org/obo/GOREL_'),
CurieNamespace('GSID', 'https://scholar.google.com/citations?user='******'GTEx', 'https://www.gtexportal.org/home/gene/'),
CurieNamespace(
'GTOPDB',
'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId='
),
CurieNamespace('HAMAP', 'http://identifiers.org/hamap/'),
CurieNamespace('HANCESTRO', 'http://www.ebi.ac.uk/ancestro/ancestro_'),
CurieNamespace('HCPCS', 'http://purl.bioontology.org/ontology/HCPCS/'),
CurieNamespace('HGNC', 'http://identifiers.org/hgnc/'),
CurieNamespace('HGNC_FAMILY', 'http://identifiers.org/hgnc.family/'),
CurieNamespace('HMDB', 'http://identifiers.org/hmdb/'),
CurieNamespace('HP', 'http://purl.obolibrary.org/obo/HP_'),
CurieNamespace('HsapDv', 'http://purl.obolibrary.org/obo/HsapDv_'),
CurieNamespace('ICD0', 'http://translator.ncats.nih.gov/ICD0_'),
CurieNamespace('ICD10', 'http://translator.ncats.nih.gov/ICD10_'),
CurieNamespace('ICD9', 'http://translator.ncats.nih.gov/ICD9_'),
CurieNamespace('INCHI', 'http://identifiers.org/inchi/'),
CurieNamespace('INCHIKEY', 'http://identifiers.org/inchikey/'),
CurieNamespace('INO', 'http://purl.obolibrary.org/obo/INO_'),
CurieNamespace('INTACT', 'http://identifiers.org/intact/'),
CurieNamespace('IUPHAR_FAMILY',
'http://identifiers.org/iuphar.family/'),
CurieNamespace('KEGG', 'http://identifiers.org/kegg/'),
CurieNamespace('KEGG_BRITE', 'http://www.kegg.jp/entry/'),
CurieNamespace('KEGG_COMPOUND',
'http://identifiers.org/kegg.compound/'),
CurieNamespace('KEGG_DGROUP', 'http://www.kegg.jp/entry/'),
CurieNamespace('KEGG_DISEASE', 'http://identifiers.org/kegg.disease/'),
CurieNamespace('KEGG_DRUG', 'http://identifiers.org/kegg.drug/'),
CurieNamespace('KEGG_ENVIRON', 'http://identifiers.org/kegg.environ/'),
CurieNamespace('KEGG_ENZYME', 'http://www.kegg.jp/entry/'),
CurieNamespace('KEGG_GENE', 'http://www.kegg.jp/entry/'),
CurieNamespace('KEGG_GLYCAN', 'http://identifiers.org/kegg.glycan/'),
CurieNamespace('KEGG_MODULE', 'http://identifiers.org/kegg.module/'),
CurieNamespace('KEGG_ORTHOLOGY',
'http://identifiers.org/kegg.orthology/'),
CurieNamespace('KEGG_RCLASS', 'http://www.kegg.jp/entry/'),
CurieNamespace('KEGG_REACTION',
'http://identifiers.org/kegg.reaction/'),
CurieNamespace('LOINC', 'http://loinc.org/rdf/'),
CurieNamespace('MEDDRA', 'http://identifiers.org/meddra/'),
CurieNamespace('MESH', 'http://identifiers.org/mesh/'),
CurieNamespace('MGI', 'http://identifiers.org/mgi/'),
CurieNamespace('MI', 'http://purl.obolibrary.org/obo/MI_'),
CurieNamespace('MIR', 'http://identifiers.org/mir/'),
CurieNamespace('MONDO', 'http://purl.obolibrary.org/obo/MONDO_'),
CurieNamespace('MP', 'http://purl.obolibrary.org/obo/MP_'),
CurieNamespace('MSigDB', 'https://www.gsea-msigdb.org/gsea/msigdb/'),
CurieNamespace('MetaCyc', 'http://translator.ncats.nih.gov/MetaCyc_'),
CurieNamespace('NCBIGENE', 'http://identifiers.org/ncbigene/'),
CurieNamespace('NCBITaxon',
'http://purl.obolibrary.org/obo/NCBITaxon_'),
CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_'),
CurieNamespace('NDC', 'http://identifiers.org/ndc/'),
CurieNamespace('NDDF', 'http://purl.bioontology.org/ontology/NDDF/'),
CurieNamespace('NLMID',
'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term='),
CurieNamespace('OBAN', 'http://purl.org/oban/'),
CurieNamespace('OBOREL', 'http://purl.obolibrary.org/obo/RO_'),
CurieNamespace('OIO', 'http://www.geneontology.org/formats/oboInOwl#'),
CurieNamespace('OMIM', 'http://purl.obolibrary.org/obo/OMIM_'),
CurieNamespace('ORCID', 'https://orcid.org/'),
CurieNamespace('ORPHA', 'http://www.orpha.net/ORDO/Orphanet_'),
CurieNamespace('ORPHANET', 'http://identifiers.org/orphanet/'),
CurieNamespace('PANTHER_FAMILY',
'http://identifiers.org/panther.family/'),
CurieNamespace('PANTHER_PATHWAY',
'http://identifiers.org/panther.pathway/'),
CurieNamespace('PATO', 'http://purl.obolibrary.org/obo/PATO_'),
CurieNamespace('PATO-PROPERTY',
'http://purl.obolibrary.org/obo/pato#'),
CurieNamespace('PDQ', 'https://www.cancer.gov/publications/pdq#'),
CurieNamespace('PFAM', 'http://identifiers.org/pfam/'),
CurieNamespace('PHARMGKB_DRUG',
'http://identifiers.org/pharmgkb.drug/'),
CurieNamespace('PHARMGKB_PATHWAYS',
'http://identifiers.org/pharmgkb.pathways/'),
CurieNamespace('PHAROS', 'http://pharos.nih.gov'),
CurieNamespace('PIRSF', 'http://identifiers.org/pirsf/'),
CurieNamespace('PMID', 'http://www.ncbi.nlm.nih.gov/pubmed/'),
CurieNamespace('PO', 'http://purl.obolibrary.org/obo/PO_'),
CurieNamespace('POMBASE', 'http://identifiers.org/pombase/'),
CurieNamespace('PR', 'http://purl.obolibrary.org/obo/PR_'),
CurieNamespace('PRINTS', 'http://identifiers.org/prints/'),
CurieNamespace('PRODOM', 'http://identifiers.org/prodom/'),
CurieNamespace('PROSITE', 'http://identifiers.org/prosite/'),
CurieNamespace('PUBCHEM_COMPOUND',
'http://identifiers.org/pubchem.compound/'),
CurieNamespace('PUBCHEM_SUBSTANCE',
'http://identifiers.org/pubchem.substance/'),
CurieNamespace('PathWhiz', 'http://smpdb.ca/pathways/#'),
CurieNamespace('REACT', 'http://www.reactome.org/PathwayBrowser/#/'),
CurieNamespace('REPODB', 'http://apps.chiragjpgroup.org/repoDB/'),
CurieNamespace('RFAM', 'http://identifiers.org/rfam/'),
CurieNamespace('RGD', 'http://identifiers.org/rgd/'),
CurieNamespace('RHEA', 'http://identifiers.org/rhea/'),
CurieNamespace('RNACENTRAL', 'http://identifiers.org/rnacentral/'),
CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_'),
CurieNamespace('RTXKG1', 'http://kg1endpoint.rtx.ai/'),
CurieNamespace(
'RXCUI',
'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm='),
CurieNamespace('RXNORM',
'http://purl.bioontology.org/ontology/RXNORM/'),
CurieNamespace('ResearchID', 'https://publons.com/researcher/'),
CurieNamespace('SEMMEDDB', 'https://skr3.nlm.nih.gov/SemMedDB'),
CurieNamespace('SGD', 'http://identifiers.org/sgd/'),
CurieNamespace('SIDER_DRUG', 'http://identifiers.org/sider.drug/'),
CurieNamespace('SIO', 'http://semanticscience.org/resource/SIO_'),
CurieNamespace('SMART', 'http://identifiers.org/smart/'),
CurieNamespace('SMPDB', 'http://identifiers.org/smpdb/'),
CurieNamespace('SNOMEDCT', 'http://identifiers.org/snomedct/'),
CurieNamespace('SNPEFF', 'http://translator.ncats.nih.gov/SNPEFF_'),
CurieNamespace('SUPFAM', 'http://identifiers.org/supfam/'),
CurieNamespace('ScopusID',
'https://www.scopus.com/authid/detail.uri?authorId='),
CurieNamespace('TAXRANK', 'http://purl.obolibrary.org/obo/TAXRANK_'),
CurieNamespace('TCDB', 'http://identifiers.org/tcdb/'),
CurieNamespace('TIGRFAM', 'http://identifiers.org/tigrfam/'),
CurieNamespace('UBERGRAPH',
'http://translator.renci.org/ubergraph-axioms.ofn#'),
CurieNamespace('UBERON', 'http://purl.obolibrary.org/obo/UBERON_'),
CurieNamespace('UBERON_CORE',
'http://purl.obolibrary.org/obo/uberon/core#'),
CurieNamespace('UMLS', 'http://identifiers.org/umls/'),
CurieNamespace(
'UMLSSC',
'https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt/code#'),
CurieNamespace(
'UMLSSG',
'https://metamap.nlm.nih.gov/Docs/SemGroups_2018.txt/group#'),
CurieNamespace(
'UMLSST',
'https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt/type#'),
CurieNamespace('UNII', 'http://identifiers.org/unii/'),
CurieNamespace('UNIPROT_ISOFORM',
'http://identifiers.org/uniprot.isoform/'),
CurieNamespace('UO', 'http://purl.obolibrary.org/obo/UO_'),
CurieNamespace('UPHENO', 'http://purl.obolibrary.org/obo/UPHENO_'),
CurieNamespace('UniProtKB', 'http://identifiers.org/uniprot/'),
CurieNamespace(
'VANDF',
'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/'
),
CurieNamespace('VMC', 'https://github.com/ga4gh/vr-spec/'),
CurieNamespace('WB', 'http://identifiers.org/wb/'),
CurieNamespace('WBPhenotype',
'http://purl.obolibrary.org/obo/WBPhenotype_'),
CurieNamespace('WBVocab', 'http://bio2rdf.org/wormbase_vocabulary'),
CurieNamespace('WIKIDATA', 'https://www.wikidata.org/wiki/'),
CurieNamespace('WIKIDATA_PROPERTY',
'https://www.wikidata.org/wiki/Property:'),
CurieNamespace('WIKIPATHWAYS', 'http://identifiers.org/wikipathways/'),
CurieNamespace('WormBase', 'https://www.wormbase.org/get?name='),
CurieNamespace('ZFIN', 'http://identifiers.org/zfin/'),
CurieNamespace('ZP', 'http://purl.obolibrary.org/obo/ZP_'),
CurieNamespace('alliancegenome', 'https://www.alliancegenome.org/'),
CurieNamespace('biolink', 'https://w3id.org/biolink/vocab/'),
CurieNamespace('chembio', 'http://translator.ncats.nih.gov/chembio_'),
CurieNamespace('dcat', 'http://www.w3.org/ns/dcat#'),
CurieNamespace('dct', 'http://purl.org/dc/terms/'),
CurieNamespace('dictyBase', 'http://dictybase.org/gene/'),
CurieNamespace('doi', 'https://doi.org/'),
CurieNamespace('fabio', 'http://purl.org/spar/fabio/'),
CurieNamespace('foaf', 'http://xmlns.com/foaf/0.1/'),
CurieNamespace('foodb_compound', 'http://foodb.ca/compounds/'),
CurieNamespace(
'gff3',
'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#'
),
CurieNamespace(
'gpi',
'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#'
),
CurieNamespace('gtpo', 'https://rdf.guidetopharmacology.org/ns/gtpo#'),
CurieNamespace('hetio', 'http://translator.ncats.nih.gov/hetio_'),
CurieNamespace('interpro', 'https://www.ebi.ac.uk/interpro/entry/'),
CurieNamespace('isbn',
'https://www.isbn-international.org/identifier/'),
CurieNamespace('isni', 'https://isni.org/isni/'),
CurieNamespace('issn', 'https://portal.issn.org/resource/ISSN/'),
CurieNamespace('linkml', 'https://w3id.org/linkml/'),
CurieNamespace('medgen', 'https://www.ncbi.nlm.nih.gov/medgen/'),
CurieNamespace('oboformat',
'http://www.geneontology.org/formats/oboInOWL#'),
CurieNamespace('pav', 'http://purl.org/pav/'),
CurieNamespace('prov', 'http://www.w3.org/ns/prov#'),
CurieNamespace('qud', 'http://qudt.org/1.1/schema/qudt#'),
CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'),
CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#'),
CurieNamespace('schema', 'http://schema.org/'),
CurieNamespace('skos', 'https://www.w3.org/TR/skos-reference/#'),
CurieNamespace('wgs', 'http://www.w3.org/2003/01/geo/wgs84_pos'),
CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#'),
]
# class level dictionaries
_prefix_map: Dict[str, CurieNamespace] = {}
@classmethod
def _get_prefix_map(cls):
if not cls._prefix_map:
for ns in cls._namespaces:
# index by upper case for uniformity of search
cls._prefix_map[ns.prefix.upper()] = ns
return cls._prefix_map
@classmethod
def parse_curie(cls, curie: str) -> Tuple[CurieNamespace, str]:
"""
Parse a candidate CURIE
:param curie: candidate curie string
:return: CURIE namespace and object_id
"""
found = CurieNamespace(
"",
""), curie # default value if not a CURIE or unknown XMLNS prefix
if ':' in curie:
part = curie.split(":")
# Normalize retrieval with upper case of prefix for lookup
prefix = part[0].upper()
if prefix in cls._get_prefix_map():
found = cls._prefix_map[prefix], part[1]
return found
@classmethod
def parse_uri(cls, uri: str) -> Tuple[CurieNamespace, str]:
"""
Parse a candidate URI
:param uri: candidate URI string
:return: namespace and object_id
"""
found = CurieNamespace(
"", ""), uri # default value returned if unknown URI namespace
# TODO: is there a more efficient lookup scheme here than a linear search of namespaces?
for ns in cls._namespaces:
base_uri = str(ns)
if uri.startswith(base_uri):
# simple minded deletion of base_uri to give the object_id
object_id = uri.replace(base_uri, "")
found = ns, object_id
break
return found
@classmethod
def parse_identifier(cls, identifier: str) -> Tuple[CurieNamespace, str]:
# trivial case of a null identifier?
if not identifier:
return CurieNamespace("", ""), ""
# check if this is a candidate URI...
if identifier.lower().startswith("http"):
# guess that perhaps it is, so try to parse it
return cls.parse_uri(identifier)
else: # attempt to parse as a CURIE
return cls.parse_curie(identifier)
if sys.version_info < (3, 7, 6):
from linkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from includes.types import String
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
BIOLINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
DEFAULT_ = CurieNamespace('', 'http://example.org/')
# Types
# Enumerations
# Class references
@dataclass
class C(YAMLRoot):
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = URIRef("http://example.org/C")
class_class_curie: ClassVar[str] = None
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml.utils.metamodelcore import URIorCURIE
from linkml_model.types import Uriorcurie
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
IAO = CurieNamespace('IAO', 'http://purl.obolibrary.org/obo/IAO_')
OIO = CurieNamespace('OIO', 'http://www.geneontology.org/formats/oboInOwl#')
LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#')
RDFS = CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#')
SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = LINKML
# Types
# Class references
from linkml.utils.metamodelcore import empty_list, empty_dict, bnode
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml_model.types import String
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
DEFAULT_ = CurieNamespace('', 'https://microbiomedata/schema/')
# Types
# Class references
@dataclass
class Biosample(YAMLRoot):
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = URIRef(
"https://microbiomedata/schema/Biosample")
class_class_curie: ClassVar[str] = None
class_name: ClassVar[str] = "biosample"
from linkml.utils.slot import Slot
from linkml.utils.metamodelcore import empty_list, empty_dict, bnode
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
TCCM = CurieNamespace('tccm', 'https://hotecosystem.org/tccm/')
DEFAULT_ = TCCM
# Types
# Class references
@dataclass
class IterableResolvedValueSet(YAMLRoot):
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = TCCM.IterableResolvedValueSet
class_class_curie: ClassVar[str] = "tccm:IterableResolvedValueSet"
class_name: ClassVar[str] = "IterableResolvedValueSet"
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml.utils.metamodelcore import URIorCURIE
from linkml_model.types import String, Uriorcurie
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
SCT = CurieNamespace('sct', 'http://snomed.info/id/')
DEFAULT_ = SCT
# Types
# Class references
class ContaineeId(URIorCURIE):
pass
@dataclass
class Container(YAMLRoot):
_inherited_slots: ClassVar[List[str]] = []
from linkml.utils.metamodelcore import empty_list, empty_dict, bnode
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml_model.types import String
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
DEFAULT_ = CurieNamespace('', 'https://microbiomedata/schema/')
# Types
# Class references
class NamedThing(YAMLRoot):
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = URIRef(
"https://microbiomedata/schema/NamedThing")
class_class_curie: ClassVar[str] = None
class_name: ClassVar[str] = "named thing"
class_model_uri: ClassVar[URIRef] = URIRef(
from linkml.utils.slot import Slot
from linkml.utils.metamodelcore import empty_list, empty_dict, bnode
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
XSD = CurieNamespace('xsd', 'http://example.org/UNKNOWN/xsd/')
DEFAULT_ = CurieNamespace('', 'http://example.org/tests/issue_260a/')
# Types
class String(str):
""" A character string """
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = URIRef("http://example.org/tests/issue_260a/String")
# Class references
if self._defn.permissible_values[self.text] != self:
raise TypeError(f"Permissible value for code: {self.text} is already assigned")
if self not in self._defn.permissible_values:
if not self._defn.code_set:
# Fixed set of values -- no terminology reference
raise TypeError("{self}: Permissible value not in definition set")
# code_set: Optional[Union[str, URIorCURIE]] = None
# code_set_tag: Optional[str] = None
# code_set_version: Optional[str] = None
# pv_formula: Optional[Union[str, "PvFormulaOptions"]] = None
# This will be imported from the TCCM module when we get everything glued together
RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#')
SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#')
TCCM = CurieNamespace('tccm', 'https://hotecosystem.org/tccm/')
class EntityReferenceCode(extended_str):
pass
@dataclass
class EntityReference(YAMLRoot):
"""
The URI, namespace/name (if known) and a list of code systems that make assertions about the entity.
"""
_inherited_slots: ClassVar[List[str]] = []
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
if sys.version_info < (3, 7, 6):
from linkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
metamodel_version = "1.4.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
ORGDATA = CurieNamespace('ORGDATA',
'http://example.org/sample/organization/data/')
XSD = CurieNamespace('xsd', 'http://example.org/UNKNOWN/xsd/')
DEFAULT_ = CurieNamespace('', 'http://example.org/sample/organization/')
# Types
class YearCount(int):
type_class_uri = XSD.int
type_class_curie = "xsd:int"
type_name = "yearCount"
type_model_uri = URIRef("http://example.org/sample/organization/YearCount")
class String(str):
type_class_uri = XSD.string
type_class_curie = "xsd:string"
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from .issue_260a import C260a, String
from ..issue_260.issue_260b import C260b
from .issue_260c import C260c
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
DEFAULT_ = CurieNamespace('', 'http://example.org/tests/issue_260/')
# Types
# Class references
class C2601(C260a):
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = URIRef(
"http://example.org/tests/issue_260/C2601")
class_class_curie: ClassVar[str] = None
class_name: ClassVar[str] = "c2601"
class_model_uri: ClassVar[URIRef] = URIRef(
"http://example.org/tests/issue_260/C2601")
from linkml.utils.metamodelcore import empty_list, empty_dict, bnode
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml.utils.metamodelcore import Bool, Decimal, ElementIdentifier, NCName, NodeIdentifier, URI, URIorCURIE, XSDDate, XSDDateTime, XSDTime
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
BIOLINKML = CurieNamespace('biolinkml', 'https://w3id.org/biolink/biolinkml/')
SHEX = CurieNamespace('shex', 'http://www.w3.org/ns/shex#')
TYPES = CurieNamespace('types', 'https://example.org/ccdh/datatypes/')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = TYPES
# Types
class Url(String):
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "url"
type_model_uri = TYPES.Url
class String(str):
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml.utils.metamodelcore import URIorCURIE
from linkml_model.extensions import Extension
from linkml_model.types import String, Uriorcurie
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
DEFAULT_ = LINKML
# Types
# Class references
@dataclass
class Annotatable(YAMLRoot):
"""
mixin for classes that support annotations
"""
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = LINKML.Annotatable
if sys.version_info < (3, 7, 6):
from linkml.utils.dataclass_extensions_375 import dataclasses_init_fn_with_kwargs
else:
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml.utils.metamodelcore import URIorCURIE
metamodel_version = "1.5.3"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
TCCM = CurieNamespace('tccm', 'https://hotecosystem.org/tccm/')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = TCCM
# Types
class PersistentURI(URIorCURIE):
""" A Universal Resource Identifier (URI) that persists across service instances. PersistentURIs have enduring
reference and meaning. """
type_class_uri = XSD.anyURI
type_class_curie = "xsd:anyURI"
type_name = "PersistentURI"
type_model_uri = TCCM.PersistentURI
class LocalURI(URIorCURIE):
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml.utils.metamodelcore import URIorCURIE
from linkml_model.types import String, Uriorcurie
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
DEFAULT_ = LINKML
# Types
# Class references
@dataclass
class Extension(YAMLRoot):
"""
a tag/value pair used to add non-model information to an entry
"""
_inherited_slots: ClassVar[List[str]] = []
class_class_uri: ClassVar[URIRef] = LINKML.Extension
from linkml.utils.metamodelcore import empty_list, empty_dict, bnode
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml.utils.metamodelcore import Bool, Decimal, ElementIdentifier, NCName, NodeIdentifier, URI, URIorCURIE, XSDDate, XSDDateTime, XSDTime
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
META = CurieNamespace('meta', 'https://w3id.org/linkml/')
SHEX = CurieNamespace('shex', 'http://www.w3.org/ns/shex#')
XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
DEFAULT_ = CurieNamespace('', 'https://example.com/test14/')
# Types
class String(str):
""" A character string """
type_class_uri = XSD.string
type_class_curie = "xsd:string"
type_name = "string"
type_model_uri = URIRef("https://example.com/test14/String")
class Integer(int):
from linkml.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
from linkml.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
from linkml.utils.formatutils import camelcase, underscore, sfx
from linkml.utils.enumerations import EnumDefinitionImpl
from rdflib import Namespace, URIRef
from linkml.utils.curienamespace import CurieNamespace
from linkml.utils.metamodelcore import ElementIdentifier
from linkml_model.types import Integer, Objectidentifier, String
metamodel_version = "1.7.0"
# Overwrite dataclasses _init_fn to add **kwargs in __init__
dataclasses._init_fn = dataclasses_init_fn_with_kwargs
# Namespaces
BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/vocab/')
EX = CurieNamespace('ex', 'http://example.org/')
LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
MODEL = CurieNamespace('model', 'https://w3id.org/biolink/')
DEFAULT_ = BIOLINK
# Types
# Class references
class PersonId(ElementIdentifier):
pass
@dataclass
class Person(YAMLRoot):
def test_curie_as_curie(self):
""" "curie can't be a local name at the moment" """
BFO = CurieNamespace('bfo', "http://purl.obolibrary.org/obo/BFO_")
self.assertEqual("bfo:curie", BFO.curie)