More work on QA validator
This commit is contained in:
James Agnew
parent
ab2129d651
commit
c49941060b
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@ -37,12 +37,31 @@ import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.instance.model.annotations.Child;
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import org.hl7.fhir.instance.model.annotations.Description;
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import org.hl7.fhir.instance.model.annotations.DatatypeDef;
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import org.apache.commons.lang3.Validate;
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import org.hl7.fhir.instance.model.annotations.Block;
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import org.hl7.fhir.instance.model.api.*;
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/**
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* Base definition for all elements in a resource.
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*/
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public abstract class Element extends Base implements IBaseHasExtensions {
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/**
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* Returns an unmodifiable list containing all extensions on this element which
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* match the given URL.
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*
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* @param theUrl The URL. Must not be blank or null.
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* @return an unmodifiable list containing all extensions on this element which
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* match the given URL
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*/
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public List<Extension> getExtensionsByUrl(String theUrl) {
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Validate.notBlank(theUrl, "theUrl must not be blank or null");
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ArrayList<Extension> retVal = new ArrayList<Extension>();
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for (Extension next : getExtension()) {
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if (theUrl.equals(next.getUrl())) {
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retVal.add(next);
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}
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}
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return Collections.unmodifiableList(retVal);
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}
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/**
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* unique id for the element within a resource (for internal references).
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@ -14,6 +14,7 @@ import org.hl7.fhir.instance.client.ResourceFormat;
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import org.hl7.fhir.instance.model.Bundle;
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import org.hl7.fhir.instance.model.ConceptMap;
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import org.hl7.fhir.instance.model.Conformance;
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import org.hl7.fhir.instance.model.DataElement;
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import org.hl7.fhir.instance.model.ElementDefinition.TypeRefComponent;
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import org.hl7.fhir.instance.model.OperationOutcome;
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import org.hl7.fhir.instance.model.Parameters;
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@ -52,6 +53,7 @@ public class WorkerContext implements NameResolver {
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private ITerminologyServices terminologyServices = new NullTerminologyServices();
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private IFHIRClient client = new NullClient();
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private Map<String, ValueSet> codeSystems = new HashMap<String, ValueSet>();
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private Map<String, DataElement> dataElements = new HashMap<String, DataElement>();
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private Map<String, ValueSet> valueSets = new HashMap<String, ValueSet>();
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private Map<String, ConceptMap> maps = new HashMap<String, ConceptMap>();
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private Map<String, StructureDefinition> profiles = new HashMap<String, StructureDefinition>();
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@ -97,6 +99,10 @@ public class WorkerContext implements NameResolver {
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return codeSystems;
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}
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public Map<String, DataElement> getDataElements() {
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return dataElements;
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}
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public Map<String, ValueSet> getValueSets() {
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return valueSets;
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}
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@ -302,4 +302,20 @@ public class BaseValidator {
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return thePass;
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}
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/**
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* Test a rule and add a {@link IssueSeverity#WARNING} validation message if the validation fails
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*
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* @param thePass
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* Set this parameter to <code>false</code> if the validation does not pass
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* @return Returns <code>thePass</code> (in other words, returns <code>true</code> if the rule did not fail validation)
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*/
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protected boolean warning(List<ValidationMessage> errors, IssueType type, List<String> pathParts, boolean thePass, String theMessage, Object... theMessageArguments) {
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if (!thePass) {
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String path = toPath(pathParts);
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String message = formatMessage(theMessage, theMessageArguments);
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errors.add(new ValidationMessage(source, type, -1, -1, path, message, IssueSeverity.WARNING));
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}
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return thePass;
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}
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}
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@ -15,9 +15,12 @@ import org.apache.commons.lang3.Validate;
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import org.hl7.fhir.instance.model.Attachment;
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import org.hl7.fhir.instance.model.BooleanType;
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import org.hl7.fhir.instance.model.Coding;
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import org.hl7.fhir.instance.model.DataElement;
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import org.hl7.fhir.instance.model.DateTimeType;
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import org.hl7.fhir.instance.model.DateType;
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import org.hl7.fhir.instance.model.DecimalType;
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import org.hl7.fhir.instance.model.ElementDefinition;
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import org.hl7.fhir.instance.model.Extension;
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import org.hl7.fhir.instance.model.InstantType;
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import org.hl7.fhir.instance.model.IntegerType;
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import org.hl7.fhir.instance.model.OperationOutcome.IssueSeverity;
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@ -42,8 +45,6 @@ import org.hl7.fhir.instance.model.ValueSet.ConceptSetComponent;
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import org.hl7.fhir.instance.model.valuesets.IssueType;
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import org.hl7.fhir.instance.utils.WorkerContext;
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import ca.uhn.fhir.context.FhirContext;
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/**
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* Validates that an instance of {@link QuestionnaireAnswers} is valid against the {@link Questionnaire} that it claims to conform to.
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*
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@ -58,6 +59,7 @@ public class QuestionnaireAnswersValidator extends BaseValidator {
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* ****************************************************************
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*/
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private static final List<String> EMPTY_PATH = Collections.emptyList();
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private WorkerContext myWorkerCtx;
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public QuestionnaireAnswersValidator(WorkerContext theWorkerCtx) {
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@ -192,29 +194,54 @@ public class QuestionnaireAnswersValidator extends BaseValidator {
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private void validateQuestion(List<ValidationMessage> theErrors, QuestionComponent theQuestion, org.hl7.fhir.instance.model.QuestionnaireAnswers.GroupComponent theAnsGroup,
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LinkedList<String> thePathStack, QuestionnaireAnswers theAnswers, boolean theValidateRequired) {
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String linkId = theQuestion.getLinkId();
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QuestionComponent question = theQuestion;
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String linkId = question.getLinkId();
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if (!fail(theErrors, IssueType.INVALID, thePathStack, isNotBlank(linkId), "Questionnaire is invalid, question found with no link ID")) {
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return;
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}
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AnswerFormat type = theQuestion.getType();
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AnswerFormat type = question.getType();
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if (type == null) {
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if (theQuestion.getGroup().isEmpty()) {
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rule(theErrors, IssueType.INVALID, thePathStack, false, "Questionnaire in invalid, no type and no groups specified for question with link ID[{0}]", linkId);
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return;
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// Support old format/casing and new
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List<Extension> extensions = question.getExtensionsByUrl("http://hl7.org/fhir/StructureDefinition/questionnaire-deReference");
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if (extensions.isEmpty()) {
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extensions = question.getExtensionsByUrl("http://hl7.org/fhir/StructureDefinition/questionnaire-dereference");
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}
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if (extensions.isEmpty() == false) {
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if (extensions.size() > 1) {
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warning(theErrors, IssueType.BUSINESSRULE, thePathStack, false, "Questionnaire is invalid, element contains multiple extensions with URL 'questionnaire-dereference', maximum one may be contained in a single element");
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}
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return;
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/*
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* Hopefully we will implement this soon...
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*/
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// Extension ext = extensions.get(0);
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// Reference ref = (Reference) ext.getValue();
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// DataElement de = myWorkerCtx.getDataElements().get(ref.getReference());
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// if (de.getElement().size() != 1) {
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// warning(theErrors, IssueType.BUSINESSRULE, EMPTY_PATH, false, "DataElement {0} has wrong number of elements: {1}", ref.getReference(), de.getElement().size());
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// }
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// ElementDefinition element = de.getElement().get(0);
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// question = toQuestion(element);
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} else {
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if (question.getGroup().isEmpty()) {
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rule(theErrors, IssueType.INVALID, thePathStack, false, "Questionnaire is invalid, no type and no groups specified for question with link ID[{0}]", linkId);
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return;
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}
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type = AnswerFormat.NULL;
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}
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type = AnswerFormat.NULL;
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}
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List<org.hl7.fhir.instance.model.QuestionnaireAnswers.QuestionComponent> answers = findAnswersByLinkId(theAnsGroup.getQuestion(), linkId);
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if (answers.size() > 1) {
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rule(theErrors, IssueType.BUSINESSRULE, thePathStack, !theQuestion.getRequired(), "Multiple answers repetitions found with linkId[{0}]", linkId);
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rule(theErrors, IssueType.BUSINESSRULE, thePathStack, !question.getRequired(), "Multiple answers repetitions found with linkId[{0}]", linkId);
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}
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if (answers.size() == 0) {
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if (theValidateRequired) {
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rule(theErrors, IssueType.BUSINESSRULE, thePathStack, !theQuestion.getRequired(), "Missing answer to required question with linkId[{0}]", linkId);
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rule(theErrors, IssueType.BUSINESSRULE, thePathStack, !question.getRequired(), "Missing answer to required question with linkId[{0}]", linkId);
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} else {
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hint(theErrors, IssueType.BUSINESSRULE, thePathStack, !theQuestion.getRequired(), "Missing answer to required question with linkId[{0}]", linkId);
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hint(theErrors, IssueType.BUSINESSRULE, thePathStack, !question.getRequired(), "Missing answer to required question with linkId[{0}]", linkId);
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}
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return;
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}
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@ -222,13 +249,14 @@ public class QuestionnaireAnswersValidator extends BaseValidator {
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org.hl7.fhir.instance.model.QuestionnaireAnswers.QuestionComponent answerQuestion = answers.get(0);
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try {
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thePathStack.add("question[" + answers.indexOf(answerQuestion) + "]");
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validateQuestionAnswers(theErrors, theQuestion, thePathStack, type, answerQuestion, theAnswers, theValidateRequired);
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validateQuestionGroups(theErrors, theQuestion, answerQuestion, thePathStack, theAnswers, theValidateRequired);
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validateQuestionAnswers(theErrors, question, thePathStack, type, answerQuestion, theAnswers, theValidateRequired);
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validateQuestionGroups(theErrors, question, answerQuestion, thePathStack, theAnswers, theValidateRequired);
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} finally {
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thePathStack.removeLast();
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}
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}
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private void validateQuestionGroups(List<ValidationMessage> theErrors, QuestionComponent theQuestion, org.hl7.fhir.instance.model.QuestionnaireAnswers.QuestionComponent theAnswerQuestion,
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LinkedList<String> thePathSpec, QuestionnaireAnswers theAnswers, boolean theValidateRequired) {
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validateGroups(theErrors, theQuestion.getGroup(), theAnswerQuestion.getGroup(), thePathSpec, theAnswers, theValidateRequired);
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@ -4,11 +4,13 @@ import static org.hamcrest.Matchers.containsString;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertThat;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.instance.model.Coding;
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import org.hl7.fhir.instance.model.DataElement;
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import org.hl7.fhir.instance.model.Questionnaire;
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import org.hl7.fhir.instance.model.Questionnaire.AnswerFormat;
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import org.hl7.fhir.instance.model.Questionnaire.GroupComponent;
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@ -24,6 +26,7 @@ import org.junit.Before;
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import org.junit.Test;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.parser.DataFormatException;
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public class QuestionnaireAnswersValidatorTest {
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private static final FhirContext ourCtx = FhirContext.forDstu2Hl7Org();
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@ -56,6 +59,20 @@ public class QuestionnaireAnswersValidatorTest {
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assertThat(errors.toString(), containsString("Answer to question with linkId[link0] found of type [StringType] but this is invalid for question of type [boolean]"));
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}
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@Test
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public void testExtensionDereference() throws Exception {
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Questionnaire q = ourCtx.newJsonParser().parseResource(Questionnaire.class, IOUtils.toString(getClass().getResourceAsStream("/dereference-q.json")));
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QuestionnaireAnswers qa = ourCtx.newXmlParser().parseResource(QuestionnaireAnswers.class, IOUtils.toString(getClass().getResourceAsStream("/dereference-qa.xml")));
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DataElement de = ourCtx.newJsonParser().parseResource(DataElement.class, IOUtils.toString(getClass().getResourceAsStream("/dereference-de.json")));
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myWorkerCtx.getQuestionnaires().put(qa.getQuestionnaire().getReference(), q);
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myWorkerCtx.getDataElements().put("DataElement/4771", de);
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List<ValidationMessage> errors = new ArrayList<ValidationMessage>();
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myVal.validate(errors, qa);
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ourLog.info(errors.toString());
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assertEquals(errors.toString(), errors.size(), 0);
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}
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@Test
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public void testGroupWithNoLinkIdInQuestionnaireAnswers() {
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@ -0,0 +1,30 @@
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{
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"resourceType":"DataElement",
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"id":"4770",
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"meta":{
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"versionId":"1",
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"lastUpdated":"2015-07-09T03:28:33.831-04:00"
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},
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"text":{
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"status":"generated",
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"div":"<div xmlns=\"http://www.w3.org/1999/xhtml\"><!-- Snipped for brevity --></div>"
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},
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"identifier":{
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"value":"Age Question"
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},
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"version":"1.0",
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"name":"QuestionSample",
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"status":"active",
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"publisher":"EDIFECS",
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"element":[
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{
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"path":"DataElement.question",
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"label":"What is your age?",
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"type":[
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{
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"code":"positiveInt"
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}
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]
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}
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]
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}
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@ -0,0 +1,63 @@
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{
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"resourceType":"Questionnaire",
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"id":"4772",
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"meta":{
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"versionId":"1",
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"lastUpdated":"2015-07-09T03:30:29.589-04:00"
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},
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"identifier":[
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{
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"value":"My First Questionnaire"
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}
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],
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"date":"2015-07-09T11:32:03+04:00",
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"publisher":"Edifecs",
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"group":{
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"title":"Main Group",
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"group":[
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{
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"text":"Common",
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"question":[
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{
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"linkId":"Link0",
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"text":"What is your name?",
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"type":"string"
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},
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{
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"linkId":"Link1",
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"text":"What is your age?",
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"type":"integer"
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},
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{
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"linkId":"Link2",
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"text":"Do you smoke?",
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"type":"boolean"
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},
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{
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"extension":[
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{
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"url":"http://hl7.org/fhir/StructureDefinition/questionnaire-deReference",
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"valueReference":{
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"reference":"DataElement/4770"
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}
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}
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],
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"linkId":"Link3"
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},
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{
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"extension":[
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{
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"url":"http://hl7.org/fhir/StructureDefinition/questionnaire-deReference",
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"valueReference":{
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"reference":"DataElement/4771"
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}
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}
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],
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"linkId":"Link4"
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}
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]
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}
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]
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}
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}
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@ -0,0 +1,53 @@
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<QuestionnaireAnswers xmlns="http://hl7.org/fhir">
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<identifier>
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<value value="4772"/>
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</identifier>
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<questionnaire>
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<reference value="Questionnaire/4772"/>
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</questionnaire>
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<subject>
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<reference value="Organization/4769"/>
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</subject>
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<authored value="2015-07-29T20:39:17+04:00"/>
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<group>
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<title value="Main Group"/>
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<group>
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<text value="Common"/>
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<question>
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<linkId value="Link0"/>
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<text value="What is your name?"/>
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<answer>
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<valueString value="swewe"/>
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</answer>
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</question>
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<question>
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<linkId value="Link1"/>
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<text value="What is your age?"/>
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<answer>
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<valueInteger value="1"/>
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</answer>
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</question>
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<question>
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<linkId value="Link2"/>
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<text value="Do you smoke?"/>
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<answer>
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<valueBoolean value="false"/>
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</answer>
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</question>
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<question>
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<linkId value="Link3"/>
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<text value="What is your age?"/>
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<answer>
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<valueInteger value="23"/>
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</answer>
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</question>
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<question>
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<linkId value="Link4"/>
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<text value="Do you smoke?"/>
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<answer>
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<valueBoolean value="false"/>
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</answer>
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</question>
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</group>
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</group>
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</QuestionnaireAnswers>
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