anyURI values containing pipes are not parseable by the org.hl7.fhir.core library

[balhoff]

Turtle filename
allergyintolerance.profile.ttl

That file and other profile files contain lines like this:

fhir:valueSet [
           fhir:v "http://hl7.org/fhir/ValueSet/all-languages|5.0.0"^^xsd:anyURI ;
           fhir:link <http://hl7.org/fhir/ValueSet/all-languages|5.0.0>
         ]

The value "http://hl7.org/fhir/ValueSet/all-languages|5.0.0"^^xsd:anyURI is not parseable by the https://github.com/hapifhir/org.hl7.fhir.core library, which is used to generate the Turtle examples and can also read them back in. Running the test generator gives this error when trying to roundtrip:

org.hl7.fhir.exceptions.FHIRFormatError: Illegal URI http://hl7.org/fhir/ValueSet/all-languages|5.0.0
	at org.hl7.fhir.utilities.turtle.Turtle$TTLURL.setUri(Turtle.java:727)
	at org.hl7.fhir.utilities.turtle.Turtle.parseComplex(Turtle.java:1232)
	at org.hl7.fhir.utilities.turtle.Turtle.parseComplex(Turtle.java:1228)
	at org.hl7.fhir.utilities.turtle.Turtle.parseComplex(Turtle.java:1228)
	at org.hl7.fhir.utilities.turtle.Turtle.parseComplex(Turtle.java:1228)
	at org.hl7.fhir.utilities.turtle.Turtle.parseComplex(Turtle.java:1228)
	at org.hl7.fhir.utilities.turtle.Turtle.parse(Turtle.java:1175)
	at org.hl7.fhir.utilities.turtle.Turtle.parse(Turtle.java:1106)
	at org.hl7.fhir.r5.test.TurtleGeneratorTests.parseGeneratedTurtle(TurtleGeneratorTests.java:120)
	at org.hl7.fhir.r5.test.TurtleGeneratorTests.testInstanceGeneration(TurtleGeneratorTests.java:102)
	at org.hl7.fhir.r5.test.TurtleGeneratorTests.testPublishedExamples(TurtleGeneratorTests.java:87)
	<trimmed>

The error comes from this method (https://github.com/hapifhir/org.hl7.fhir.core/blob/7740b5d857013a905e99d1d82a530d82b58cdf29/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/turtle/Turtle.java#L725) which uses this IRI regex: https://github.com/hapifhir/org.hl7.fhir.core/blob/7740b5d857013a905e99d1d82a530d82b58cdf29/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/turtle/Turtle.java#L54

[balhoff]

Jena riot 5.0.0 gives these warnings:

riot --validate fhir-examples-out-orig/allergyintolerance.profile.ttl
13:49:21 WARN  riot            :: [line: 283, col: 66] Illegal character in IRI (codepoint 0x7C, '|'): <http://hl7.org/fhir/ValueSet/all-languages[|]...>
13:49:21 WARN  riot            :: [line: 283, col: 22] Bad IRI: <http://hl7.org/fhir/ValueSet/all-languages|5.0.0> Code: 4/UNWISE_CHARACTER in PATH: The character matches no grammar rules of URIs/IRIs.
13:49:21 WARN  riot            :: [line: 520, col: 80] Illegal character in IRI (codepoint 0x7C, '|'): <http://hl7.org/fhir/ValueSet/allergyintolerance-clinical[|]...>
13:49:21 WARN  riot            :: [line: 520, col: 22] Bad IRI: <http://hl7.org/fhir/ValueSet/allergyintolerance-clinical|5.0.0> Code: 4/UNWISE_CHARACTER in PATH: The character matches no grammar rules of URIs/IRIs.
13:49:21 WARN  riot            :: [line: 569, col: 84] Illegal character in IRI (codepoint 0x7C, '|'): <http://hl7.org/fhir/ValueSet/allergyintolerance-verification[|]...>
13:49:21 WARN  riot            :: [line: 569, col: 22] Bad IRI: <http://hl7.org/fhir/ValueSet/allergyintolerance-verification|5.0.0> Code: 4/UNWISE_CHARACTER in PATH: The character matches no grammar rules of URIs/IRIs.
13:49:21 WARN  riot            :: [line: 674, col: 81] Illegal character in IRI (codepoint 0x7C, '|'): <http://hl7.org/fhir/ValueSet/allergy-intolerance-category[|]...>
13:49:21 WARN  riot            :: [line: 674, col: 22] Bad IRI: <http://hl7.org/fhir/ValueSet/allergy-intolerance-category|5.0.0> Code: 4/UNWISE_CHARACTER in PATH: The character matches no grammar rules of URIs/IRIs.
13:49:21 WARN  riot            :: [line: 726, col: 84] Illegal character in IRI (codepoint 0x7C, '|'): <http://hl7.org/fhir/ValueSet/allergy-intolerance-criticality[|]...>
13:49:21 WARN  riot            :: [line: 726, col: 22] Bad IRI: <http://hl7.org/fhir/ValueSet/allergy-intolerance-criticality|5.0.0> Code: 4/UNWISE_CHARACTER in PATH: The character matches no grammar rules of URIs/IRIs.
13:49:21 WARN  riot            :: [line: 1624, col: 76] Illegal character in IRI (codepoint 0x7C, '|'): <http://hl7.org/fhir/ValueSet/reaction-event-severity[|]...>
13:49:21 WARN  riot            :: [line: 1624, col: 22] Bad IRI: <http://hl7.org/fhir/ValueSet/reaction-event-severity|5.0.0> Code: 4/UNWISE_CHARACTER in PATH: The character matches no grammar rules of URIs/IRIs.
13:49:21 WARN  riot            :: [line: 1779, col: 80] Illegal character in IRI (codepoint 0x7C, '|'): <http://hl7.org/fhir/ValueSet/allergyintolerance-clinical[|]...>
13:49:21 WARN  riot            :: [line: 1779, col: 22] Bad IRI: <http://hl7.org/fhir/ValueSet/allergyintolerance-clinical|5.0.0> Code: 4/UNWISE_CHARACTER in PATH: The character matches no grammar rules of URIs/IRIs.
13:49:21 WARN  riot            :: [line: 1813, col: 84] Illegal character in IRI (codepoint 0x7C, '|'): <http://hl7.org/fhir/ValueSet/allergyintolerance-verification[|]...>
13:49:21 WARN  riot            :: [line: 1813, col: 22] Bad IRI: <http://hl7.org/fhir/ValueSet/allergyintolerance-verification|5.0.0> Code: 4/UNWISE_CHARACTER in PATH: The character matches no grammar rules of URIs/IRIs.
13:49:21 WARN  riot            :: [line: 1888, col: 81] Illegal character in IRI (codepoint 0x7C, '|'): <http://hl7.org/fhir/ValueSet/allergy-intolerance-category[|]...>
13:49:21 WARN  riot            :: [line: 1888, col: 22] Bad IRI: <http://hl7.org/fhir/ValueSet/allergy-intolerance-category|5.0.0> Code: 4/UNWISE_CHARACTER in PATH: The character matches no grammar rules of URIs/IRIs.
13:49:21 WARN  riot            :: [line: 1925, col: 84] Illegal character in IRI (codepoint 0x7C, '|'): <http://hl7.org/fhir/ValueSet/allergy-intolerance-criticality[|]...>
13:49:21 WARN  riot            :: [line: 1925, col: 22] Bad IRI: <http://hl7.org/fhir/ValueSet/allergy-intolerance-criticality|5.0.0> Code: 4/UNWISE_CHARACTER in PATH: The character matches no grammar rules of URIs/IRIs.
13:49:21 WARN  riot            :: [line: 2357, col: 76] Illegal character in IRI (codepoint 0x7C, '|'): <http://hl7.org/fhir/ValueSet/reaction-event-severity[|]...>
13:49:21 WARN  riot            :: [line: 2357, col: 22] Bad IRI: <http://hl7.org/fhir/ValueSet/reaction-event-severity|5.0.0> Code: 4/UNWISE_CHARACTER in PATH: The character matches no grammar rules of URIs/IRIs.

However, it is not complaining about the xsd:anyURI literals, but about the fhir:link IRIs that are also output, e.g. the second value here:

fhir:valueSet [
  fhir:v "http://hl7.org/fhir/ValueSet/all-languages|5.0.0"^^xsd:anyURI ;
  fhir:link <http://hl7.org/fhir/ValueSet/all-languages|5.0.0>
] ;