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refactor: move modules from utils to types #396

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2 changes: 1 addition & 1 deletion linkml_runtime/__init__.py
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from pathlib import Path
from linkml_runtime.utils.curienamespace import CurieNamespace
from linkml_runtime.types.curienamespace import CurieNamespace
from linkml_runtime.utils.schemaview import SchemaView
from rdflib import RDF, RDFS, SKOS, XSD, OWL

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6 changes: 3 additions & 3 deletions linkml_runtime/linkml_model/annotations.py
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from typing import Optional, Union, ClassVar, Any
from dataclasses import dataclass

from linkml_runtime.utils.slot import Slot
from linkml_runtime.utils.metamodelcore import empty_dict
from linkml_runtime.types.slot import Slot
from linkml_runtime.types.metamodelcore import empty_dict
from linkml_runtime.utils.yamlutils import YAMLRoot
from rdflib import URIRef
from linkml_runtime.utils.curienamespace import CurieNamespace
from linkml_runtime.types.curienamespace import CurieNamespace
from .extensions import AnyValue, Extension, ExtensionTag

metamodel_version = "1.7.0"
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10 changes: 5 additions & 5 deletions linkml_runtime/linkml_model/datasets.py
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from typing import Optional, Union, ClassVar, Any
from dataclasses import dataclass

from linkml_runtime.utils.slot import Slot
from linkml_runtime.utils.metamodelcore import empty_list
from linkml_runtime.types.slot import Slot
from linkml_runtime.types.metamodelcore import empty_list

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from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str
from linkml_runtime.utils.enumerations import EnumDefinitionImpl
from linkml_runtime.types.enum import EnumDefinitionImpl

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from rdflib import URIRef
from linkml_runtime.utils.curienamespace import CurieNamespace
from linkml_runtime.utils.metamodelcore import URI, URIorCURIE, XSDDateTime
from linkml_runtime.types.curienamespace import CurieNamespace
from linkml_runtime.types.metamodelcore import URI, URIorCURIE, XSDDateTime

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metamodel_version = "1.7.0"
version = None
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8 changes: 4 additions & 4 deletions linkml_runtime/linkml_model/extensions.py
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from typing import Optional, Union, ClassVar, Any
from dataclasses import dataclass

from linkml_runtime.utils.slot import Slot
from linkml_runtime.utils.metamodelcore import empty_dict
from linkml_runtime.types.slot import Slot
from linkml_runtime.types.metamodelcore import empty_dict
from linkml_runtime.utils.yamlutils import YAMLRoot
from rdflib import URIRef
from linkml_runtime.utils.curienamespace import CurieNamespace
from linkml_runtime.utils.metamodelcore import URIorCURIE
from linkml_runtime.types.curienamespace import CurieNamespace
from linkml_runtime.types.metamodelcore import URIorCURIE

metamodel_version = "1.7.0"
version = "2.0.0"
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6 changes: 3 additions & 3 deletions linkml_runtime/linkml_model/mappings.py
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from typing import Optional, Union

from linkml_runtime.utils.slot import Slot
from linkml_runtime.utils.curienamespace import CurieNamespace
from linkml_runtime.utils.metamodelcore import URIorCURIE
from linkml_runtime.types.slot import Slot
from linkml_runtime.types.curienamespace import CurieNamespace
from linkml_runtime.types.metamodelcore import URIorCURIE

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metamodel_version = "1.7.0"
version = "2.0.0"
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10 changes: 5 additions & 5 deletions linkml_runtime/linkml_model/meta.py
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from typing import Optional, Union, ClassVar, Any
from dataclasses import dataclass

from linkml_runtime.utils.slot import Slot
from linkml_runtime.utils.metamodelcore import empty_list, empty_dict
from linkml_runtime.types.slot import Slot
from linkml_runtime.types.metamodelcore import empty_list, empty_dict
from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str
from linkml_runtime.utils.formatutils import sfx
from linkml_runtime.utils.enumerations import EnumDefinitionImpl
from linkml_runtime.types.enum import EnumDefinitionImpl
from rdflib import URIRef
from linkml_runtime.utils.curienamespace import CurieNamespace
from linkml_runtime.types.curienamespace import CurieNamespace
from .annotations import Annotation, AnnotationTag
from .extensions import Extension, ExtensionTag
from .units import UnitOfMeasure
from linkml_runtime.utils.metamodelcore import Bool, NCName, URI, URIorCURIE, XSDDateTime
from linkml_runtime.types.metamodelcore import Bool, NCName, URI, URIorCURIE, XSDDateTime

metamodel_version = "1.7.0"
version = None
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4 changes: 2 additions & 2 deletions linkml_runtime/linkml_model/types.py
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# license: https://creativecommons.org/publicdomain/zero/1.0/


from linkml_runtime.utils.curienamespace import CurieNamespace
from linkml_runtime.utils.metamodelcore import Bool, Curie, Decimal, ElementIdentifier, NCName, NodeIdentifier, URI, URIorCURIE, XSDDate, XSDDateTime, XSDTime
from linkml_runtime.types.curienamespace import CurieNamespace
from linkml_runtime.types.metamodelcore import Bool, Curie, Decimal, ElementIdentifier, NCName, NodeIdentifier, URI, URIorCURIE, XSDDate, XSDDateTime, XSDTime

metamodel_version = "1.7.0"
version = None
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8 changes: 4 additions & 4 deletions linkml_runtime/linkml_model/units.py
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from typing import Optional, Union, ClassVar, Any
from dataclasses import dataclass

from linkml_runtime.utils.slot import Slot
from linkml_runtime.utils.metamodelcore import empty_list
from linkml_runtime.types.slot import Slot
from linkml_runtime.types.metamodelcore import empty_list
from linkml_runtime.utils.yamlutils import YAMLRoot
from rdflib import URIRef
from linkml_runtime.utils.curienamespace import CurieNamespace
from linkml_runtime.utils.metamodelcore import URIorCURIE
from linkml_runtime.types.curienamespace import CurieNamespace
from linkml_runtime.types.metamodelcore import URIorCURIE

metamodel_version = "1.7.0"
version = None
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10 changes: 5 additions & 5 deletions linkml_runtime/linkml_model/validation.py
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from typing import Optional, Union, ClassVar, Any
from dataclasses import dataclass

from linkml_runtime.utils.slot import Slot
from linkml_runtime.utils.metamodelcore import empty_list
from linkml_runtime.types.slot import Slot
from linkml_runtime.types.metamodelcore import empty_list

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from linkml_runtime.utils.yamlutils import YAMLRoot
from linkml_runtime.utils.enumerations import EnumDefinitionImpl
from linkml_runtime.types.enum import EnumDefinitionImpl

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from rdflib import URIRef
from linkml_runtime.utils.curienamespace import CurieNamespace
from linkml_runtime.utils.metamodelcore import NodeIdentifier
from linkml_runtime.types.curienamespace import CurieNamespace
from linkml_runtime.types.metamodelcore import NodeIdentifier

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metamodel_version = "1.7.0"
version = None
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2 changes: 1 addition & 1 deletion linkml_runtime/processing/referencevalidator.py
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)
from linkml_runtime.utils import yamlutils
from linkml_runtime.utils.eval_utils import eval_expr
from linkml_runtime.utils.metamodelcore import (
from linkml_runtime.types.metamodelcore import (
XSDTime,
Bool,
XSDDate,
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10 changes: 5 additions & 5 deletions linkml_runtime/processing/validation_datamodel.py
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PermissibleValue,
)

from linkml_runtime.utils.slot import Slot
from linkml_runtime.utils.metamodelcore import empty_list, empty_dict
from linkml_runtime.types.slot import Slot
from linkml_runtime.types.metamodelcore import empty_list, empty_dict
from linkml_runtime.utils.yamlutils import (
YAMLRoot,
)
from linkml_runtime.utils.enumerations import EnumDefinitionImpl
from linkml_runtime.types.enum import EnumDefinitionImpl
from rdflib import URIRef
from linkml_runtime.utils.curienamespace import CurieNamespace
from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE
from linkml_runtime.types.curienamespace import CurieNamespace
from linkml_runtime.types.metamodelcore import Bool, URIorCURIE

metamodel_version = "1.7.0"
version = None
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0 linkml_runtime/utils/curienamespace.py → linkml_runtime/types/curienamespace.py
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2 changes: 1 addition & 1 deletion linkml_runtime/utils/enumerations.py → linkml_runtime/types/enum.py
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from dataclasses import fields
from typing import Union, Optional

from linkml_runtime.utils.metamodelcore import Curie
from linkml_runtime.types.metamodelcore import Curie
from linkml_runtime.utils.yamlutils import YAMLRoot


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210 changes: 210 additions & 0 deletions linkml_runtime/utils/curie_validator.py
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import re

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"""

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Regex for CURIEs

These regex are directly derived from the collected ABNF in RFC3986
(except for DIGIT, ALPHA and HEXDIG, defined by RFC2234).

They should be processed with re.VERBOSE.
"""


### basics

DIGIT = r"[0-9]"

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ALPHA = r"[A-Za-z]"

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HEXDIG = r"[0-9ABCDEF]"

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# pct-encoded = "%" HEXDIG HEXDIG
pct_encoded = r" %% %(HEXDIG)s %(HEXDIG)s" % locals()

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ucschar = "(?: \u00a0-\ud7ff | \uf900-\ufdcf | \ufdf0-\uffef | \u10000-\u1fffD | \u20000-\u2fffD | \u30000-\u3fffD | \u40000-\u4fffD | \u50000-\u5fffD | \u60000-\u6fffD | \u70000-\u7fffD | \u80000-\u8fffD | \u90000-\u9fffD | \ua0000-\uafffD | \ub0000-\ubfffD | \uc0000-\ucfffD | \ud0000-\udfffD | \ue1000-\uefff )"

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# iunreserved = ALPHA / DIGIT / "-" / "." / "_" / "~"
iunreserved = r"(?: %(ALPHA)s | %(DIGIT)s | \- | \. | _ | ~ | %(ucschar)s )" % locals()

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# gen-delims = ":" / "/" / "?" / "#" / "[" / "]" / "@"
gen_delims = r"(?: : | / | \? | \# | \[ | \] | @ )"

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# sub-delims = "!" / "$" / "&" / "'" / "("
sub_delims = r"(?: ! | \$ | & | ' | \( | \) | \* | \+ | , | ; | = )"

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# ipchar = iunreserved / pct-encoded / sub-delims / ":" / "@"
ipchar = r"(?: %(iunreserved)s | %(pct_encoded)s | %(sub_delims)s | : | @ )" % locals()

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# reserved = gen-delims / sub-delims
reserved = r"(?: %(gen_delims)s | %(sub_delims)s )" % locals()

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CombiningChar = "[\u0300-\u0345] | [\u0360-\u0361] | [\u0483-\u0486] | [\u0591-\u05a1] | [\u05a3-\u05b9] | [\u05bb-\u05bd] | \u05bf | [\u05c1-\u05c2] | \u05c4 | [\u064b-\u0652] | \u0670 | [\u06d6-\u06dc] | [\u06dd-\u06df] | [\u06e0-\u06e4] | [\u06e7-\u06e8] | [\u06ea-\u06ed] | [\u0901-\u0903] | \u093c | [\u093e-\u094c] | \u094d | [\u0951-\u0954] | [\u0962-\u0963] | [\u0981-\u0983] | \u09bc | \u09be | \u09bf | [\u09c0-\u09c4] | [\u09c7-\u09c8] | [\u09cb-\u09cd] | \u09d7 | [\u09e2-\u09e3] | \u0a02 | \u0a3c | \u0a3e | \u0a3f | [\u0a40-\u0a42] | [\u0a47-\u0a48] | [\u0a4b-\u0a4d] | [\u0a70-\u0a71] | [\u0a81-\u0a83] | \u0abc | [\u0abe-\u0ac5] | [\u0ac7-\u0ac9] | [\u0acb-\u0acd] | [\u0b01-\u0b03] | \u0b3c | [\u0b3e-\u0b43] | [\u0b47-\u0b48] | [\u0b4b-\u0b4d] | [\u0b56-\u0b57] | [\u0b82-\u0b83] | [\u0bbe-\u0bc2] | [\u0bc6-\u0bc8] | [\u0bca-\u0bcd] | \u0bd7 | [\u0c01-\u0c03] | [\u0c3e-\u0c44] | [\u0c46-\u0c48] | [\u0c4a-\u0c4d] | [\u0c55-\u0c56] | [\u0c82-\u0c83] | [\u0cbe-\u0cc4] | [\u0cc6-\u0cc8] | [\u0cca-\u0ccd] | [\u0cd5-\u0cd6] | [\u0d02-\u0d03] | [\u0d3e-\u0d43] | [\u0d46-\u0d48] | [\u0d4a-\u0d4d] | \u0d57 | \u0e31 | [\u0e34-\u0e3a] | [\u0e47-\u0e4e] | \u0eb1 | [\u0eb4-\u0eb9] | [\u0ebb-\u0ebc] | [\u0ec8-\u0ecd] | [\u0f18-\u0f19] | \u0f35 | \u0f37 | \u0f39 | \u0f3e | \u0f3f | [\u0f71-\u0f84] | [\u0f86-\u0f8b] | [\u0f90-\u0f95] | \u0f97 | [\u0f99-\u0fad] | [\u0fb1-\u0fb7] | \u0fb9 | [\u20d0-\u20dc] | \u20e1 | [\u302a-\u302f] | \u3099 | \u309a"

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Extender = "\u00b7 | \u02d0 | \u02d1 | \u0387 | \u0640 | \u0e46 | \u0ec6 | \u3005 | [\u3031-\u3035] | [\u309d-\u309e] | [\u30fc-\u30fe]"

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NCNameChar = r"(?: %(ALPHA)s | %(DIGIT)s | \. | \- | _ | %(CombiningChar)s | %(Extender)s )" % locals()

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prefix = r"(?: %(ALPHA)s | _ ) (?: %(NCNameChar)s )*" % locals()

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### iauthority

# dec-octet = DIGIT ; 0-9
# / %x31-39 DIGIT ; 10-99
# / "1" 2DIGIT ; 100-199
# / "2" %x30-34 DIGIT ; 200-249
# / "25" %x30-35 ; 250-255
dec_octet = (

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r"""(?: %(DIGIT)s |
[1-9] %(DIGIT)s |
1 %(DIGIT)s{2} |
2 [0-4] %(DIGIT)s |
25 [0-5]
)
"""
% locals()
)

# IPv4address = dec-octet "." dec-octet "." dec-octet "." dec-octet
IPv4address = r"%(dec_octet)s \. %(dec_octet)s \. %(dec_octet)s \. %(dec_octet)s" % locals()

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# h16 = 1*4HEXDIG
h16 = r"(?: %(HEXDIG)s ){1,4}" % locals()

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# ls32 = ( h16 ":" h16 ) / IPv4address
ls32 = r"(?: (?: %(h16)s : %(h16)s ) | %(IPv4address)s )" % locals()

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# IPv6address = 6( h16 ":" ) ls32
# / "::" 5( h16 ":" ) ls32
# / [ h16 ] "::" 4( h16 ":" ) ls32
# / [ *1( h16 ":" ) h16 ] "::" 3( h16 ":" ) ls32
# / [ *2( h16 ":" ) h16 ] "::" 2( h16 ":" ) ls32
# / [ *3( h16 ":" ) h16 ] "::" h16 ":" ls32
# / [ *4( h16 ":" ) h16 ] "::" ls32
# / [ *5( h16 ":" ) h16 ] "::" h16
# / [ *6( h16 ":" ) h16 ] "::"
IPv6address = (

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r"""(?: (?: %(h16)s : ){6} %(ls32)s |
:: (?: %(h16)s : ){5} %(ls32)s |
%(h16)s :: (?: %(h16)s : ){4} %(ls32)s |
(?: %(h16)s : ) %(h16)s :: (?: %(h16)s : ){3} %(ls32)s |
(?: %(h16)s : ){2} %(h16)s :: (?: %(h16)s : ){2} %(ls32)s |
(?: %(h16)s : ){3} %(h16)s :: %(h16)s : %(ls32)s |
(?: %(h16)s : ){4} %(h16)s :: %(ls32)s |
(?: %(h16)s : ){5} %(h16)s :: %(h16)s |
(?: %(h16)s : ){6} %(h16)s ::
)
"""
% locals()
)

# IPvFuture = "v" 1*HEXDIG "." 1*( iunreserved / sub-delims / ":" )
IPvFuture = r"v %(HEXDIG)s+ \. (?: %(iunreserved)s | %(sub_delims)s | : )+" % locals()

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# IP-literal = "[" ( IPv6address / IPvFuture ) "]"
IP_literal = r"\[ (?: %(IPv6address)s | %(IPvFuture)s ) \]" % locals()

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# ireg-name = *( iunreserved / pct-encoded / sub-delims )
ireg_name = r"(?: %(iunreserved)s | %(pct_encoded)s | %(sub_delims)s )*" % locals()

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# iuserinfo = *( iunreserved / pct-encoded / sub-delims / ":" )
iuserinfo = r"(?: %(iunreserved)s | %(pct_encoded)s | %(sub_delims)s | : )" % locals()

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# ihost = IP-literal / IPv4address / ireg-name
ihost = r"(?: %(IP_literal)s | %(IPv4address)s | %(ireg_name)s )" % locals()

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# iport = *DIGIT
iport = r"(?: %(DIGIT)s )*" % locals()

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# iauthority = [ iuserinfo "@" ] ihost [ ":" iport ]
iauthority = r"(?: %(iuserinfo)s @)? %(ihost)s (?: : %(iport)s)?" % locals()

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### Path

# isegment = *ipchar
isegment = r"%(ipchar)s*" % locals()

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# isegment-nz = 1*ipchar
isegment_nz = r"%(ipchar)s+" % locals()

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# isegment-nz-nc = 1*( iunreserved / pct-encoded / sub-delims / "@" )
# ; non-zero-length segment without any colon ":"
isegment_nz_nc = r"(?: %(iunreserved)s | %(pct_encoded)s | %(sub_delims)s | @ )+" % locals()

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# ipath-abempty = *( "/" isegment )
ipath_abempty = r"(?: / %(isegment)s )*" % locals()

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# path-absolute = "/" [ isegment-nz *( "/" isegment ) ]
ipath_absolute = r"/ (?: %(isegment_nz)s (?: / %(isegment)s )* )?" % locals()

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# ipath-noscheme = isegment-nz-nc *( "/" isegment )
ipath_noscheme = r"%(isegment_nz_nc)s (?: / %(isegment)s )*" % locals()

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# ipath-rootless = isegment-nz *( "/" isegment )
ipath_rootless = r"%(isegment_nz)s (?: / %(isegment)s )*" % locals()

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# path-empty = 0<ipchar>
ipath_empty = r"" ### FIXME

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# path = path-abempty ; begins with "/" or is empty
# / path-absolute ; begins with "/" but not "//"
# / path-noscheme ; begins with a non-colon segment
# / path-rootless ; begins with a segment
# / path-empty ; zero characters
path = (

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r"""(?: %(ipath_abempty)s |
%(ipath_absolute)s |
%(ipath_noscheme)s |
%(ipath_rootless)s |
%(ipath_empty)s
)
"""
% locals()
)

iprivate = r"[\uE000-\uF8FF] | [\uF0000-\uFFFFD] | [\u100000-\u10FFFD]"

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### Query and Fragment

# iquery = *( ipchar / "/" / "?" )
iquery = r"(?: %(ipchar)s | %(iprivate)s | / | \? )*" % locals()

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# ifragment = *( ipchar / "/" / "?" )
ifragment = r"(?: %(ipchar)s | / | \? )*" % locals()

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### URIs


# irelative-part = "//" iauthority ipath-abempty
# / ipath-absolute
# / path-noscheme
# / path-empty
irelative_part = (

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r"""(?: (?: // %(iauthority)s %(ipath_abempty)s ) |
%(ipath_absolute)s |
%(ipath_noscheme)s |
%(ipath_empty)s
)
"""
% locals()
)

# irelative-ref = irelative-part [ "?" iquery ] [ "#" ifragment ]
irelative_ref = r"%(irelative_part)s (?: \? %(iquery)s)? (?: \# %(ifragment)s)?" % locals()

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CURIE = r"(?: (?: (?: %(prefix)s )? : )? %(irelative_ref)s )" % locals()
curie_validator = re.compile(f"^{CURIE}$", re.VERBOSE)

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# URI-reference = URI / relative-ref
safe_CURIE = r"(?: \[ %(CURIE)s \] )" % locals()
safe_curie_validator = re.compile(f"^{safe_CURIE}$", re.VERBOSE)

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def validate_curie(input):
print(CURIE)
return curie_validator.match(input)

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def validate_safe_curie(input):
return safe_curie_validator.match(input)

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2 changes: 1 addition & 1 deletion linkml_runtime/utils/inference_utils.py
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Expand Up @@ -6,7 +6,7 @@

from linkml_runtime.utils.schemaview import SchemaView
from linkml_runtime.linkml_model import SlotDefinitionName, PermissibleValue, ClassDefinitionName
from linkml_runtime.utils.enumerations import EnumDefinitionImpl
from linkml_runtime.types.enum import EnumDefinitionImpl
from linkml_runtime.utils.eval_utils import eval_expr
from linkml_runtime.utils.walker_utils import traverse_object_tree
from linkml_runtime.utils.yamlutils import YAMLRoot
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