Add ValueSet expansion support, fix profile bugs
HapiWorkerContext needed ValueSet expansion support for validation, now that resources are found and loaded. ParserBase had a bug when comparing names (was not looking at IdPart) Profiles had errors in FHIRPaths using invalid $context name
This commit is contained in:
Michael Lawley
parent
3623bbca16
commit
884bfbeed5
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@ -31,13 +31,18 @@ import org.hl7.fhir.dstu2016may.model.ValueSet.ConceptReferenceComponent;
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import org.hl7.fhir.dstu2016may.model.ValueSet.ConceptSetComponent;
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import org.hl7.fhir.dstu2016may.model.ValueSet.ValueSetExpansionComponent;
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import org.hl7.fhir.dstu2016may.model.ValueSet.ValueSetExpansionContainsComponent;
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import org.hl7.fhir.dstu2016may.terminologies.ValueSetExpander;
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import org.hl7.fhir.dstu2016may.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
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import org.hl7.fhir.dstu2016may.terminologies.ValueSetExpanderFactory;
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import org.hl7.fhir.dstu2016may.terminologies.ValueSetExpanderSimple;
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import org.hl7.fhir.dstu2016may.utils.IWorkerContext;
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import org.hl7.fhir.dstu2016may.validation.IResourceValidator;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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public final class HapiWorkerContext implements IWorkerContext {
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public final class HapiWorkerContext implements IWorkerContext, ValueSetExpanderFactory {
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private final FhirContext myCtx;
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private Map<String, Resource> myFetchedResourceCache = new HashMap<String, Resource>();
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private IValidationSupport myValidationSupport;
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@ -201,8 +206,8 @@ public final class HapiWorkerContext implements IWorkerContext {
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}
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}
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}
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boolean caseSensitive = true;
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if (isNotBlank(theSystem)) {
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CodeSystem system = fetchCodeSystem(theSystem);
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@ -259,10 +264,27 @@ public final class HapiWorkerContext implements IWorkerContext {
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return new ValidationResult(IssueSeverity.ERROR, "Unknown code[" + theCode + "] in system[" + theSystem + "]");
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}
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@Override
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public ValueSetExpander getExpander() {
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ValueSetExpanderSimple retVal = new ValueSetExpanderSimple(this, this);
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return retVal;
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}
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@Override
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public ValueSetExpansionOutcome expandVS(ValueSet theSource, boolean theCacheOk) {
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throw new UnsupportedOperationException();
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ValueSetExpansionOutcome vso;
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try {
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vso = getExpander().expand(theSource);
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} catch (InvalidRequestException e) {
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throw e;
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} catch (Exception e) {
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throw new InternalErrorException(e);
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}
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if (vso.getError() != null) {
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throw new InvalidRequestException(vso.getError());
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} else {
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return vso;
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}
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}
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@Override
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@ -25,13 +25,13 @@ import org.hl7.fhir.utilities.Utilities;
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public abstract class ParserBase {
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interface IErrorNotifier {
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}
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public enum ValidationPolicy { NONE, QUICK, EVERYTHING }
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public static boolean isPrimitive(String code) {
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return Utilities.existsInList(code,
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"xhtml", "boolean", "integer", "string", "decimal", "uri", "base64Binary", "instant", "date", "dateTime",
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return Utilities.existsInList(code,
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"xhtml", "boolean", "integer", "string", "decimal", "uri", "base64Binary", "instant", "date", "dateTime",
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"time", "code", "oid", "id", "markdown", "unsignedInt", "positiveInt", "xhtml", "base64Binary");
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}
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@ -49,12 +49,12 @@ public abstract class ParserBase {
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this.policy = policy;
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this.errors = errors;
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}
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public abstract Element parse(InputStream stream) throws Exception;
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public abstract void compose(Element e, OutputStream destination, OutputStyle style, String base) throws Exception;
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public void logError(int line, int col, String path, IssueType type, String message, IssueSeverity level) throws FHIRFormatError {
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if (policy == ValidationPolicy.EVERYTHING) {
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ValidationMessage msg = new ValidationMessage(Source.InstanceValidator, type, line, col, path, message, level);
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@ -62,8 +62,8 @@ public abstract class ParserBase {
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} else if (level == IssueSeverity.FATAL || (level == IssueSeverity.ERROR && policy == ValidationPolicy.QUICK))
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throw new FHIRFormatError(message+String.format(" at line %d col %d", line, col));
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}
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protected StructureDefinition getDefinition(int line, int col, String ns, String name) throws FHIRFormatError {
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if (ns == null) {
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logError(line, col, name, IssueType.STRUCTURE, "This cannot be parsed as a FHIR object (no namespace)", IssueSeverity.FATAL);
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@ -74,7 +74,7 @@ public abstract class ParserBase {
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return null;
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}
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for (StructureDefinition sd : context.allStructures()) {
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if (name.equals(sd.getId())) {
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if (name.equals(sd.getIdElement().getIdPart())) {
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if((ns == null || ns.equals(FormatUtilities.FHIR_NS)) && !ToolingExtensions.hasExtension(sd, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace"))
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return sd;
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String sns = ToolingExtensions.readStringExtension(sd, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace");
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@ -92,7 +92,7 @@ public abstract class ParserBase {
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return null;
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}
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for (StructureDefinition sd : context.allStructures()) {
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if (name.equals(sd.getId())) {
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if (name.equals(sd.getIdElement().getIdPart())) {
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return sd;
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}
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}
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@ -100,7 +100,7 @@ public abstract class ParserBase {
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return null;
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}
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protected List<Property> getChildProperties(Property property, String elementName, String statedType) throws DefinitionException {
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ElementDefinition ed = property.getDefinition();
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StructureDefinition sd = property.getStructure();
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@ -128,12 +128,12 @@ public abstract class ParserBase {
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if (t == null && ToolingExtensions.hasExtension(ed, "http://hl7.org/fhir/StructureDefinition/elementdefinition-defaultype"))
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t = ToolingExtensions.readStringExtension(ed, "http://hl7.org/fhir/StructureDefinition/elementdefinition-defaultype");
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boolean ok = false;
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for (TypeRefComponent tr : ed.getType())
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if (tr.getCode().equals(t))
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for (TypeRefComponent tr : ed.getType())
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if (tr.getCode().equals(t))
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ok = true;
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if (!ok)
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throw new DefinitionException("Type '"+t+"' is not an acceptable type for '"+elementName+"' on property "+property.getDefinition().getPath());
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} else {
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t = elementName.substring(tail(ed.getPath()).length() - 3);
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if (isPrimitive(lowFirst(t)))
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@ -20460,7 +20460,7 @@
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<key value="dom-3"/>
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<severity value="error"/>
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<human value="If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource"/>
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<expression value="contained.select(('#'+id in $context.descendents().reference).not()).empty()"/>
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<expression value="contained.select(('#'+id in %resource.descendents().reference).not()).empty()"/>
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<xpath value="not(exists(for $id in f:contained/*/@id return $id[not(ancestor::f:contained/parent::*/descendant::f:reference/@value=concat('#', $id))]))"/>
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</constraint>
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<constraint>
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@ -20649,7 +20649,7 @@
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<key value="dom-3"/>
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<severity value="error"/>
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<human value="If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource"/>
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<expression value="contained.select(('#'+id in $context.descendents().reference).not()).empty()"/>
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<expression value="contained.select(('#'+id in %resource.descendents().reference).not()).empty()"/>
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<xpath value="not(exists(for $id in f:contained/*/@id return $id[not(ancestor::f:contained/parent::*/descendant::f:reference/@value=concat('#', $id))]))"/>
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</constraint>
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<constraint>
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@ -121071,7 +121071,7 @@
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<key value="obs-7"/>
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<severity value="error"/>
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<human value="Component code SHALL not be same as observation code"/>
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<expression value="component.where(code = $context.code).empty()"/>
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<expression value="component.where(code = %resource.code).empty()"/>
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<xpath value="not(exists(f:component/f:code)) or count(for $coding in f:code/f:coding return parent::*/f:component/f:code/f:coding[f:code/@value=$coding/f:code/@value and f:system/@value=$coding/f:system/@value])=0"/>
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</constraint>
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<mapping>
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@ -122307,7 +122307,7 @@
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<key value="obs-7"/>
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<severity value="error"/>
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<human value="Component code SHALL not be same as observation code"/>
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<expression value="component.where(code = $context.code).empty()"/>
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<expression value="component.where(code = %resource.code).empty()"/>
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<xpath value="not(exists(f:component/f:code)) or count(for $coding in f:code/f:coding return parent::*/f:component/f:code/f:coding[f:code/@value=$coding/f:code/@value and f:system/@value=$coding/f:system/@value])=0"/>
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</constraint>
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<mapping>
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@ -154515,7 +154515,7 @@
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<key value="sdf-8"/>
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<severity value="error"/>
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<human value="In any snapshot or differential, all the elements except the first have to have a path that starts with the path of the first + ".""/>
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<expression value="snapshot.element.tail().all(path.startsWith($context.snapshot.element.first().path+'.')) and differential.element.tail().all(path.startsWith($context.differential.element.first().path+'.'))"/>
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<expression value="snapshot.element.tail().all(path.startsWith(%resource.snapshot.element.first().path+'.')) and differential.element.tail().all(path.startsWith(%resource.differential.element.first().path+'.'))"/>
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<xpath value="string-join(for $elementName in f:*[self::f:snapshot or self::f:differential]/f:element[position()>1]/f:path/@value return if (starts-with($elementName, concat($elementName/ancestor::f:element/parent::f:*/f:element[1]/f:path/@value, '.'))) then '' else $elementName,'')=''"/>
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</constraint>
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<constraint>
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@ -155580,7 +155580,7 @@
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<key value="sdf-8"/>
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<severity value="error"/>
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<human value="In any snapshot or differential, all the elements except the first have to have a path that starts with the path of the first + ".""/>
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<expression value="snapshot.element.tail().all(path.startsWith($context.snapshot.element.first().path+'.')) and differential.element.tail().all(path.startsWith($context.differential.element.first().path+'.'))"/>
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<expression value="snapshot.element.tail().all(path.startsWith(%resource.snapshot.element.first().path+'.')) and differential.element.tail().all(path.startsWith(%resource.differential.element.first().path+'.'))"/>
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<xpath value="string-join(for $elementName in f:*[self::f:snapshot or self::f:differential]/f:element[position()>1]/f:path/@value return if (starts-with($elementName, concat($elementName/ancestor::f:element/parent::f:*/f:element[1]/f:path/@value, '.'))) then '' else $elementName,'')=''"/>
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</constraint>
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<constraint>
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@ -4681,7 +4681,7 @@
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<key value="ref-1"/>
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<severity value="error"/>
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<human value="SHALL have a local reference if the resource is provided inline"/>
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<expression value="reference.startsWith('#').not() or ($context.reference.substring(1).trace('url') in $resource.contained.id.trace('ids'))"/>
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<expression value="reference.startsWith('#').not() or (reference.substring(1).trace('url') in %resource.contained.id.trace('ids'))"/>
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<xpath value="not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])"/>
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</constraint>
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<mapping>
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@ -4779,7 +4779,7 @@
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<key value="ref-1"/>
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<severity value="error"/>
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<human value="SHALL have a local reference if the resource is provided inline"/>
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<expression value="reference.startsWith('#').not() or ($context.reference.substring(1).trace('url') in $resource.contained.id.trace('ids'))"/>
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<expression value="reference.startsWith('#').not() or (reference.substring(1).trace('url') in %resource.contained.id.trace('ids'))"/>
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<xpath value="not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])"/>
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</constraint>
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<mapping>
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