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Merge pull request #215 from hapifhir/gg-work 

R2B fixes
This commit is contained in:
Grahame Grieve 2020-06-03 21:40:28 +10:00 committed by GitHub
parent 1e4dd8c17f 861a0ee706
commit 903eabdfc5
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GPG Key ID: 4AEE18F83AFDEB23
7 changed files with 95 additions and 43 deletions
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69
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertor_14_50.java
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@ -1454,68 +1454,71 @@ public class VersionConvertor_14_50 {
org.hl7.fhir.r5.model.ElementDefinition tgt = new org.hl7.fhir.r5.model.ElementDefinition(); org.hl7.fhir.r5.model.ElementDefinition tgt = new org.hl7.fhir.r5.model.ElementDefinition();
copyElement(src, tgt); copyElement(src, tgt);
if (src.hasPathElement()) if (src.hasPathElement())
tgt.setPathElement(convertString(src.getPathElement())); tgt.setPathElement(convertString(src.getPathElement()));
tgt.setRepresentation(src.getRepresentation().stream() tgt.setRepresentation(src.getRepresentation().stream()
.map(VersionConvertor_14_50::convertPropertyRepresentation) .map(VersionConvertor_14_50::convertPropertyRepresentation)
.collect(Collectors.toList())); .collect(Collectors.toList()));
if (src.hasName()) if (src.hasName())
tgt.setSliceNameElement(convertString(src.getNameElement())); tgt.setSliceNameElement(convertString(src.getNameElement()));
if (src.hasLabel()) if (src.hasLabel())
tgt.setLabelElement(convertString(src.getLabelElement())); tgt.setLabelElement(convertString(src.getLabelElement()));
for (org.hl7.fhir.dstu2016may.model.Coding t : src.getCode()) tgt.addCode(convertCoding(t)); for (org.hl7.fhir.dstu2016may.model.Coding t : src.getCode()) tgt.addCode(convertCoding(t));
if (src.hasSlicing()) if (src.hasSlicing())
tgt.setSlicing(convertElementDefinitionSlicingComponent(src.getSlicing(), context, pos)); tgt.setSlicing(convertElementDefinitionSlicingComponent(src.getSlicing(), context, pos));
if (src.hasShort()) if (src.hasShort())
tgt.setShortElement(convertString(src.getShortElement())); tgt.setShortElement(convertString(src.getShortElement()));
if (src.hasDefinition()) if (src.hasDefinition())
tgt.setDefinitionElement(convertMarkdown(src.getDefinitionElement())); tgt.setDefinitionElement(convertMarkdown(src.getDefinitionElement()));
if (src.hasComments()) if (src.hasComments())
tgt.setCommentElement(convertMarkdown(src.getCommentsElement())); tgt.setCommentElement(convertMarkdown(src.getCommentsElement()));
if (src.hasRequirements()) if (src.hasRequirements())
tgt.setRequirementsElement(convertMarkdown(src.getRequirementsElement())); tgt.setRequirementsElement(convertMarkdown(src.getRequirementsElement()));
for (org.hl7.fhir.dstu2016may.model.StringType t : src.getAlias()) tgt.addAlias(t.getValue()); for (org.hl7.fhir.dstu2016may.model.StringType t : src.getAlias()) tgt.addAlias(t.getValue());
if (src.hasMin()) if (src.hasMin())
tgt.setMin(src.getMin()); tgt.setMin(src.getMin());
if (src.hasMax()) if (src.hasMax())
tgt.setMaxElement(convertString(src.getMaxElement())); tgt.setMaxElement(convertString(src.getMaxElement()));
if (src.hasBase()) if (src.hasBase())
tgt.setBase(convertElementDefinitionBaseComponent(src.getBase())); tgt.setBase(convertElementDefinitionBaseComponent(src.getBase()));
if (src.hasContentReference()) if (src.hasContentReference())
tgt.setContentReferenceElement(convertUri(src.getContentReferenceElement())); tgt.setContentReferenceElement(convertUri(src.getContentReferenceElement()));
for (org.hl7.fhir.dstu2016may.model.ElementDefinition.TypeRefComponent t : src.getType()) convertTypeRefComponent(t, tgt.getType()); // work around for problem in R2B definitions:
if (src.hasDefaultValue()) if (!src.hasContentReference()) {
for (org.hl7.fhir.dstu2016may.model.ElementDefinition.TypeRefComponent t : src.getType()) convertTypeRefComponent(t, tgt.getType());
if (src.hasDefaultValue())
tgt.setDefaultValue(convertType(src.getDefaultValue())); tgt.setDefaultValue(convertType(src.getDefaultValue()));
if (src.hasMeaningWhenMissing()) if (src.hasMeaningWhenMissing())
tgt.setMeaningWhenMissingElement(convertMarkdown(src.getMeaningWhenMissingElement())); tgt.setMeaningWhenMissingElement(convertMarkdown(src.getMeaningWhenMissingElement()));
if (src.hasFixed()) if (src.hasFixed())
tgt.setFixed(convertType(src.getFixed())); tgt.setFixed(convertType(src.getFixed()));
if (src.hasPattern()) if (src.hasPattern())
tgt.setPattern(convertType(src.getPattern())); tgt.setPattern(convertType(src.getPattern()));
if (src.hasExample()) if (src.hasExample())
tgt.addExample().setLabel("General").setValue(convertType(src.getExample())); tgt.addExample().setLabel("General").setValue(convertType(src.getExample()));
if (src.hasMinValue()) if (src.hasMinValue())
tgt.setMinValue(convertType(src.getMinValue())); tgt.setMinValue(convertType(src.getMinValue()));
if (src.hasMaxValue()) if (src.hasMaxValue())
tgt.setMaxValue(convertType(src.getMaxValue())); tgt.setMaxValue(convertType(src.getMaxValue()));
if (src.hasMaxLength()) if (src.hasMaxLength())
tgt.setMaxLengthElement(convertInteger(src.getMaxLengthElement())); tgt.setMaxLengthElement(convertInteger(src.getMaxLengthElement()));
for (org.hl7.fhir.dstu2016may.model.IdType t : src.getCondition()) tgt.addCondition(t.getValue()); for (org.hl7.fhir.dstu2016may.model.IdType t : src.getCondition()) tgt.addCondition(t.getValue());
for (org.hl7.fhir.dstu2016may.model.ElementDefinition.ElementDefinitionConstraintComponent t : src.getConstraint()) tgt.addConstraint(convertElementDefinitionConstraintComponent(t)); for (org.hl7.fhir.dstu2016may.model.ElementDefinition.ElementDefinitionConstraintComponent t : src.getConstraint()) tgt.addConstraint(convertElementDefinitionConstraintComponent(t));
if (src.hasMustSupport()) if (src.hasMustSupport())
tgt.setMustSupportElement(convertBoolean(src.getMustSupportElement())); tgt.setMustSupportElement(convertBoolean(src.getMustSupportElement()));
if (src.hasIsModifier()) if (src.hasIsModifier())
tgt.setIsModifierElement(convertBoolean(src.getIsModifierElement())); tgt.setIsModifierElement(convertBoolean(src.getIsModifierElement()));
if (tgt.getIsModifier()) { if (tgt.getIsModifier()) {
String reason = org.hl7.fhir.dstu2016may.utils.ToolingExtensions.readStringExtension(src, VersionConvertorConstants.MODIFIER_REASON_EXTENSION); String reason = org.hl7.fhir.dstu2016may.utils.ToolingExtensions.readStringExtension(src, VersionConvertorConstants.MODIFIER_REASON_EXTENSION);
if (Utilities.noString(reason)) if (Utilities.noString(reason))
reason = VersionConvertorConstants.MODIFIER_REASON_LEGACY; reason = VersionConvertorConstants.MODIFIER_REASON_LEGACY;
tgt.setIsModifierReason(reason); tgt.setIsModifierReason(reason);
} }
if (src.hasIsSummary()) if (src.hasIsSummary())
tgt.setIsSummaryElement(convertBoolean(src.getIsSummaryElement())); tgt.setIsSummaryElement(convertBoolean(src.getIsSummaryElement()));
if (src.hasBinding()) if (src.hasBinding())
tgt.setBinding(convertElementDefinitionBindingComponent(src.getBinding())); tgt.setBinding(convertElementDefinitionBindingComponent(src.getBinding()));
for (org.hl7.fhir.dstu2016may.model.ElementDefinition.ElementDefinitionMappingComponent t : src.getMapping()) tgt.addMapping(convertElementDefinitionMappingComponent(t)); for (org.hl7.fhir.dstu2016may.model.ElementDefinition.ElementDefinitionMappingComponent t : src.getMapping()) tgt.addMapping(convertElementDefinitionMappingComponent(t));
}
return tgt; return tgt;
} }

37
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
View File

@ -134,7 +134,7 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
cs = findSpecialCodeSystem(system); cs = findSpecialCodeSystem(system);
} }
if (cs == null) { if (cs == null) {
warningMessage = "Unable to resolve system "+system+" - system is not specified or implicit"; warningMessage = "Unable to resolve system "+system;
if (!inExpansion) if (!inExpansion)
throw new FHIRException(warningMessage); throw new FHIRException(warningMessage);
} }
@ -144,8 +144,12 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
throw new FHIRException(warningMessage); throw new FHIRException(warningMessage);
} }
if (cs!=null) if (cs!=null) {
res = validateCode(code, cs); res = validateCode(code, cs);
} else {
// it's in the expansion, but we could find it in a code system
res = findCodeInExpansion(code);
}
} else { } else {
inExpansion = checkExpansion(code); inExpansion = checkExpansion(code);
} }
@ -175,13 +179,38 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
return null; return null;
} }
boolean checkExpansion(Coding code) { private ValidationResult findCodeInExpansion(Coding code) {
if (valueset==null || !valueset.hasExpansion())
return null;
return findCodeInExpansion(code, valueset.getExpansion().getContains());
}
private ValidationResult findCodeInExpansion(Coding code, List<ValueSetExpansionContainsComponent> contains) {
for (ValueSetExpansionContainsComponent containsComponent: contains) {
if (containsComponent.getSystem().equals(code.getSystem()) && containsComponent.getCode().equals(code.getCode())) {
ConceptDefinitionComponent ccd = new ConceptDefinitionComponent();
ccd.setCode(containsComponent.getCode());
ccd.setDisplay(containsComponent.getDisplay());
ValidationResult res = new ValidationResult(ccd);
return res;
}
if (containsComponent.hasContains()) {
ValidationResult res = findCodeInExpansion(code, containsComponent.getContains());
if (res != null) {
return res;
}
}
}
return null;
}
private boolean checkExpansion(Coding code) {
if (valueset==null || !valueset.hasExpansion()) if (valueset==null || !valueset.hasExpansion())
return false; return false;
return checkExpansion(code, valueset.getExpansion().getContains()); return checkExpansion(code, valueset.getExpansion().getContains());
} }
boolean checkExpansion(Coding code, List<ValueSetExpansionContainsComponent> contains) { private boolean checkExpansion(Coding code, List<ValueSetExpansionContainsComponent> contains) {
for (ValueSetExpansionContainsComponent containsComponent: contains) { for (ValueSetExpansionContainsComponent containsComponent: contains) {
if (containsComponent.getSystem().equals(code.getSystem()) && containsComponent.getCode().equals(code.getCode())) if (containsComponent.getSystem().equals(code.getSystem()) && containsComponent.getCode().equals(code.getCode()))
return true; return true;

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/XVerExtensionManager.java
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@ -30,6 +30,8 @@ public class XVerExtensionManager {
BadVersion, Unknown, Invalid, Valid BadVersion, Unknown, Invalid, Valid
} }
public static final String XVER_EXT_MARKER = "XVER_EXT_MARKER";
private Map<String, JsonObject> lists = new HashMap<>(); private Map<String, JsonObject> lists = new HashMap<>();
private IWorkerContext context; private IWorkerContext context;
@ -81,6 +83,7 @@ public class XVerExtensionManager {
JsonObject path = root.getAsJsonObject(e); JsonObject path = root.getAsJsonObject(e);
StructureDefinition sd = new StructureDefinition(); StructureDefinition sd = new StructureDefinition();
sd.setUserData(XVER_EXT_MARKER, "true");
sd.setUrl(url); sd.setUrl(url);
sd.setVersion(context.getVersion()); sd.setVersion(context.getVersion());
sd.setFhirVersion(FHIRVersion.fromCode(context.getVersion())); sd.setFhirVersion(FHIRVersion.fromCode(context.getVersion()));

1
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
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@ -26,6 +26,7 @@ public class I18nConstants {
public final static String CODESYSTEM_CS_VS_MISMATCH = "CodeSystem_CS_VS_MisMatch"; public final static String CODESYSTEM_CS_VS_MISMATCH = "CodeSystem_CS_VS_MisMatch";
public final static String CODESYSTEM_CS_VS_WRONGSYSTEM = "CodeSystem_CS_VS_WrongSystem"; public final static String CODESYSTEM_CS_VS_WRONGSYSTEM = "CodeSystem_CS_VS_WrongSystem";
public final static String EXTENSION_EXT_CONTEXT_WRONG = "Extension_EXT_Context_Wrong"; public final static String EXTENSION_EXT_CONTEXT_WRONG = "Extension_EXT_Context_Wrong";
public final static String EXTENSION_EXT_CONTEXT_WRONG_XVER = "EXTENSION_EXT_CONTEXT_WRONG_XVER";
public final static String EXTENSION_EXT_COUNT_MISMATCH = "Extension_EXT_Count_Mismatch"; public final static String EXTENSION_EXT_COUNT_MISMATCH = "Extension_EXT_Count_Mismatch";
public final static String EXTENSION_EXT_COUNT_NOTFOUND = "Extension_EXT_Count_NotFound"; public final static String EXTENSION_EXT_COUNT_NOTFOUND = "Extension_EXT_Count_NotFound";
public final static String EXTENSION_EXT_FIXED_BANNED = "Extension_EXT_Fixed_Banned"; public final static String EXTENSION_EXT_FIXED_BANNED = "Extension_EXT_Fixed_Banned";

3
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -497,4 +497,5 @@ TYPE_SPECIFIC_CHECKS_DT_BASE64_TOO_LONG = Base64 size is {0} bytes which exceeds
TYPE_SPECIFIC_CHECKS_DT_DECIMAL_CHARS = Found {0} decimal places which exceeds the stated limit of {1} digits TYPE_SPECIFIC_CHECKS_DT_DECIMAL_CHARS = Found {0} decimal places which exceeds the stated limit of {1} digits
Validation_VAL_Profile_WrongType = Specified profile type was "{0}", but found type "{1}" Validation_VAL_Profile_WrongType = Specified profile type was "{0}", but found type "{1}"
Validation_VAL_Profile_WrongType2 = Type mismatch processing profile {0} at path {1}: The element type is {4}, but the profile {3} is for a different type {2} Validation_VAL_Profile_WrongType2 = Type mismatch processing profile {0} at path {1}: The element type is {4}, but the profile {3} is for a different type {2}
VALIDATION_VAL_ILLEGAL_TYPE_CONSTRAINT = Illegal constraint in profile {0} at path {1} - cannot constrain to type {2} from base types {3} VALIDATION_VAL_ILLEGAL_TYPE_CONSTRAINT = Illegal constraint in profile {0} at path {1} - cannot constrain to type {2} from base types {3}
EXTENSION_EXT_CONTEXT_WRONG_XVER = The extension {0} from FHIR version {3} is not allowed to be used at this point (allowed = {1}; this element is [{2}; this is a warning since contexts may be renamed between FHIR versions)

10
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/PackageCacheTests.java
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@ -10,6 +10,7 @@ import org.junit.jupiter.api.Test;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;
import java.util.List;
public class PackageCacheTests { public class PackageCacheTests {
@ -17,7 +18,11 @@ public class PackageCacheTests {
public void testPath() throws IOException { public void testPath() throws IOException {
PackageCacheManager cache = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION); PackageCacheManager cache = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
cache.clear(); cache.clear();
Assertions.assertTrue(cache.listPackages().isEmpty()); List<String> list = cache.listPackages();
if (!list.isEmpty()) {
System.out.println("remaining packages: "+list.toString());
}
Assertions.assertTrue(list.isEmpty());
NpmPackage npm = cache.loadPackage("hl7.fhir.pubpack", "0.0.3"); NpmPackage npm = cache.loadPackage("hl7.fhir.pubpack", "0.0.3");
npm.loadAllFiles(); npm.loadAllFiles();
Assertions.assertNotNull(npm); Assertions.assertNotNull(npm);
@ -30,6 +35,7 @@ public class PackageCacheTests {
npm.save(dir); npm.save(dir);
NpmPackage npm2 = cache.loadPackage("hl7.fhir.pubpack", "file:" + dir.getAbsolutePath()); NpmPackage npm2 = cache.loadPackage("hl7.fhir.pubpack", "file:" + dir.getAbsolutePath());
Assertions.assertNotNull(npm2); Assertions.assertNotNull(npm2);
Assertions.assertFalse(cache.listPackages().isEmpty()); list = cache.listPackages();
Assertions.assertFalse(list.isEmpty());
} }
} }

15
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -1567,14 +1567,23 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} }
} }
if (!ok) { if (!ok) {
rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.getLiteralPath(), false, I18nConstants.EXTENSION_EXT_CONTEXT_WRONG, extUrl, contexts.toString(), plist.toString()); if (definition.hasUserData(XVerExtensionManager.XVER_EXT_MARKER)) {
warning(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.getLiteralPath(), false, I18nConstants.EXTENSION_EXT_CONTEXT_WRONG_XVER, extUrl, contexts.toString(), plist.toString());
} else {
rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.getLiteralPath(), false, I18nConstants.EXTENSION_EXT_CONTEXT_WRONG, extUrl, contexts.toString(), plist.toString());
}
return false; return false;
} else { } else {
if (definition.hasContextInvariant()) { if (definition.hasContextInvariant()) {
for (StringType s : definition.getContextInvariant()) { for (StringType s : definition.getContextInvariant()) {
if (!fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), container, fpe.parse(s.getValue()))) { if (!fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), container, fpe.parse(s.getValue()))) {
rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.getLiteralPath(), false, I18nConstants.PROFILE_EXT_NOT_HERE, extUrl, s.getValue()); if (definition.hasUserData(XVerExtensionManager.XVER_EXT_MARKER)) {
return false; warning(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.getLiteralPath(), false, I18nConstants.PROFILE_EXT_NOT_HERE, extUrl, s.getValue());
return true;
} else {
rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.getLiteralPath(), false, I18nConstants.PROFILE_EXT_NOT_HERE, extUrl, s.getValue());
return false;
}
} }
} }
} }