Add validation module for QuestionnaireAnswers
This commit is contained in:
James Agnew
parent
818c40498c
commit
3bba0c0425
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@ -0,0 +1,22 @@
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package ca.uhn.fhir.validation;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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public interface IResourceLoader {
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/**
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* Load the latest version of a given resource
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*
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* @param theType
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* The type of the resource to load
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* @param theId
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* The ID of the resource to load
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* @throws ResourceNotFoundException
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* If the resource is not known
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*/
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public <T extends IBaseResource> T load(Class<T> theType, IIdType theId) throws ResourceNotFoundException;
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}
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@ -23,7 +23,7 @@ package ca.uhn.fhir.validation;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.rest.server.EncodingEnum;
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interface IValidationContext<T> {
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public interface IValidationContext<T> {
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FhirContext getFhirContext();
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@ -218,7 +218,6 @@
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<artifactId>maven-compiler-plugin</artifactId>
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<configuration>
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<fork>true</fork>
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<verbose>true</verbose>
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</configuration>
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</plugin>
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</plugins>
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@ -0,0 +1,51 @@
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package ca.uhn.fhir.validation;
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import java.util.List;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.validation.ValidationMessage;
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import ca.uhn.fhir.model.api.Bundle;
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/**
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* Base class for a bridge between the RI validation tools and HAPI
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*/
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abstract class BaseValidatorBridge implements IValidator {
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public BaseValidatorBridge() {
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super();
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}
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private void doValidate(IValidationContext<?> theCtx) {
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List<ValidationMessage> messages = validate(theCtx);
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for (ValidationMessage riMessage : messages) {
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SingleValidationMessage hapiMessage = new SingleValidationMessage();
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if (riMessage.getCol() != -1) {
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hapiMessage.setLocationCol(riMessage.getCol());
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}
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if (riMessage.getLine() != -1) {
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hapiMessage.setLocationLine(riMessage.getLine());
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}
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hapiMessage.setLocationString(riMessage.getLocation());
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hapiMessage.setMessage(riMessage.getMessage());
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if (riMessage.getLevel() != null) {
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hapiMessage.setSeverity(ResultSeverityEnum.fromCode(riMessage.getLevel().toCode()));
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}
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theCtx.addValidationMessage(hapiMessage);
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}
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}
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protected abstract List<ValidationMessage> validate(IValidationContext<?> theCtx);
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@Override
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public void validateBundle(IValidationContext<Bundle> theCtx) {
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doValidate(theCtx);
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}
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@Override
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public void validateResource(IValidationContext<IBaseResource> theCtx) {
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doValidate(theCtx);
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}
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}
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@ -14,7 +14,6 @@ import javax.xml.parsers.DocumentBuilderFactory;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.instance.model.OperationOutcome.IssueSeverity;
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import org.hl7.fhir.instance.model.StructureDefinition;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.utils.WorkerContext;
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import org.hl7.fhir.instance.validation.ValidationMessage;
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import org.w3c.dom.Document;
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@ -24,7 +23,6 @@ import org.xml.sax.InputSource;
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import ca.uhn.fhir.context.ConfigurationException;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.model.api.Bundle;
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import ca.uhn.fhir.rest.server.EncodingEnum;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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@ -32,9 +30,9 @@ import com.google.gson.Gson;
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import com.google.gson.GsonBuilder;
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import com.google.gson.JsonObject;
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public class FhirInstanceValidator implements IValidator {
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public class FhirInstanceValidator extends BaseValidatorBridge implements IValidator {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidator.class);
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static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidator.class);
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private DocumentBuilderFactory myDocBuilderFactory;
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@ -43,7 +41,39 @@ public class FhirInstanceValidator implements IValidator {
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myDocBuilderFactory.setNamespaceAware(true);
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}
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List<ValidationMessage> validate(FhirContext theCtx, String theInput, EncodingEnum theEncoding) {
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private String determineResourceName(Document theDocument) {
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Element root = null;
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NodeList list = theDocument.getChildNodes();
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for (int i = 0; i < list.getLength(); i++) {
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if (list.item(i) instanceof Element) {
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root = (Element) list.item(i);
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break;
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}
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}
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root = theDocument.getDocumentElement();
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return root.getLocalName();
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}
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private StructureDefinition loadProfileOrReturnNull(List<ValidationMessage> theMessages, FhirContext theCtx, String theResourceName) {
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if (isBlank(theResourceName)) {
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theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL).setMessage("Could not determine resource type from request. Content appears invalid."));
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return null;
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}
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String profileCpName = "/org/hl7/fhir/instance/model/profile/" + theResourceName.toLowerCase() + ".profile.xml";
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String profileText;
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try {
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profileText = IOUtils.toString(FhirInstanceValidator.class.getResourceAsStream(profileCpName), "UTF-8");
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} catch (IOException e1) {
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theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL).setMessage("No profile found for resource type " + theResourceName));
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return null;
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}
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StructureDefinition profile = theCtx.newXmlParser().parseResource(StructureDefinition.class, profileText);
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return profile;
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}
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protected List<ValidationMessage> validate(FhirContext theCtx, String theInput, EncodingEnum theEncoding) {
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WorkerContext workerContext = new WorkerContext();
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org.hl7.fhir.instance.validation.InstanceValidator v;
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try {
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@ -97,61 +127,9 @@ public class FhirInstanceValidator implements IValidator {
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return messages;
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}
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private StructureDefinition loadProfileOrReturnNull(List<ValidationMessage> theMessages, FhirContext theCtx, String theResourceName) {
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if (isBlank(theResourceName)) {
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theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL).setMessage("Could not determine resource type from request. Content appears invalid."));
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return null;
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}
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String profileCpName = "/org/hl7/fhir/instance/model/profile/" + theResourceName.toLowerCase() + ".profile.xml";
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String profileText;
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try {
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profileText = IOUtils.toString(FhirInstanceValidator.class.getResourceAsStream(profileCpName), "UTF-8");
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} catch (IOException e1) {
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theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL).setMessage("No profile found for resource type " + theResourceName));
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return null;
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}
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StructureDefinition profile = theCtx.newXmlParser().parseResource(StructureDefinition.class, profileText);
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return profile;
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}
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private String determineResourceName(Document theDocument) {
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Element root = null;
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NodeList list = theDocument.getChildNodes();
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for (int i = 0; i < list.getLength(); i++) {
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if (list.item(i) instanceof Element) {
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root = (Element) list.item(i);
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break;
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}
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}
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root = theDocument.getDocumentElement();
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return root.getLocalName();
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}
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@Override
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public void validateResource(IValidationContext<IBaseResource> theCtx) {
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List<ValidationMessage> messages = validate(theCtx.getFhirContext(), theCtx.getResourceAsString(), theCtx.getResourceAsStringEncoding());
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for (ValidationMessage riMessage : messages) {
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SingleValidationMessage hapiMessage = new SingleValidationMessage();
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if (riMessage.getCol() != -1) {
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hapiMessage.setLocationCol(riMessage.getCol());
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}
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if (riMessage.getLine() != -1) {
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hapiMessage.setLocationLine(riMessage.getLine());
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}
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hapiMessage.setLocationString(riMessage.getLocation());
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hapiMessage.setMessage(riMessage.getMessage());
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if (riMessage.getLevel() != null) {
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hapiMessage.setSeverity(ResultSeverityEnum.fromCode(riMessage.getLevel().toCode()));
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}
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theCtx.addValidationMessage(hapiMessage);
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}
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}
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@Override
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public void validateBundle(IValidationContext<Bundle> theContext) {
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// nothing for now
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protected List<ValidationMessage> validate(IValidationContext<?> theCtx) {
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return validate(theCtx.getFhirContext(), theCtx.getResourceAsString(), theCtx.getResourceAsStringEncoding());
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}
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}
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@ -0,0 +1,139 @@
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package ca.uhn.fhir.validation;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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import org.hl7.fhir.instance.model.OperationOutcome.IssueSeverity;
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import org.hl7.fhir.instance.model.Questionnaire;
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import org.hl7.fhir.instance.model.QuestionnaireAnswers;
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import org.hl7.fhir.instance.model.ValueSet;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.instance.utils.WorkerContext;
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import org.hl7.fhir.instance.validation.QuestionnaireAnswersValidator;
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import org.hl7.fhir.instance.validation.ValidationMessage;
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import ca.uhn.fhir.context.RuntimeResourceDefinition;
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import ca.uhn.fhir.parser.IParser;
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import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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import ca.uhn.fhir.util.ResourceReferenceInfo;
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public class FhirQuestionnaireAnswersValidator extends BaseValidatorBridge {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirQuestionnaireAnswersValidator.class);
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private IResourceLoader myResourceLoader;
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/**
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* Set the class which will be used to load linked resources from the <code>QuestionnaireAnswers</code>. Specifically, if the <code>QuestionnaireAnswers</code> refers to an external (non-contained)
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* <code>Questionnaire</code>, or to any external (non-contained) <code>ValueSet</code>, the resource loader will be used to fetch those resources during the validation.
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*
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* @param theResourceLoader
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* The resourceloader to use. May be <code>null</code> if no resource loader should be used (in which case any <code>QuestionaireAnswers</code> with external references will fail to
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* validate.)
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*/
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public void setResourceLoader(IResourceLoader theResourceLoader) {
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myResourceLoader = theResourceLoader;
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}
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@Override
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protected List<ValidationMessage> validate(IValidationContext<?> theCtx) {
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Object resource = theCtx.getResource();
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if (!(theCtx.getResource() instanceof IBaseResource)) {
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ourLog.debug("Not validating object of type {}", theCtx.getResource().getClass());
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return Collections.emptyList();
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}
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if (resource instanceof QuestionnaireAnswers) {
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return doValidate(theCtx, (QuestionnaireAnswers) resource);
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}
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RuntimeResourceDefinition def = theCtx.getFhirContext().getResourceDefinition((IBaseResource) resource);
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if ("QuestionnaireAnswers".equals(def.getName()) == false) {
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return Collections.emptyList();
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}
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/*
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* If we have a non-RI structure, convert it
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*/
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IParser p = theCtx.getFhirContext().newJsonParser();
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String string = p.encodeResourceToString((IBaseResource) resource);
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QuestionnaireAnswers qa = p.parseResource(QuestionnaireAnswers.class, string);
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return doValidate(theCtx, qa);
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}
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private List<ValidationMessage> doValidate(IValidationContext<?> theValCtx, QuestionnaireAnswers theResource) {
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WorkerContext workerCtx = new WorkerContext();
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ArrayList<ValidationMessage> retVal = new ArrayList<ValidationMessage>();
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if (!loadReferences(theResource, workerCtx, theValCtx, retVal)) {
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return retVal;
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}
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QuestionnaireAnswersValidator val = new QuestionnaireAnswersValidator(workerCtx);
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val.validate(retVal, theResource);
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return retVal;
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}
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private boolean loadReferences(IBaseResource theResource, WorkerContext theWorkerCtx, IValidationContext<?> theValCtx, ArrayList<ValidationMessage> theMessages) {
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List<ResourceReferenceInfo> refs = theValCtx.getFhirContext().newTerser().getAllResourceReferences(theResource);
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List<IBaseResource> newResources = new ArrayList<IBaseResource>();
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for (ResourceReferenceInfo nextRefInfo : refs) {
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IIdType nextRef = nextRefInfo.getResourceReference().getReferenceElement();
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String resourceType = nextRef.getResourceType();
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if ("ValueSet".equals(resourceType)) {
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if (!theWorkerCtx.getValueSets().containsKey(nextRef.getValue())) {
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ValueSet resource = tryToLoad(ValueSet.class, nextRef, theMessages);
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if (resource == null) {
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return false;
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}
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theWorkerCtx.getValueSets().put(nextRef.getValue(), resource);
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newResources.add(resource);
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}
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} else if ("Questionnaire".equals(resourceType)) {
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if (!theWorkerCtx.getQuestionnaires().containsKey(nextRef.getValue())) {
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Questionnaire resource = tryToLoad(Questionnaire.class, nextRef, theMessages);
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if (resource == null) {
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return false;
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}
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theWorkerCtx.getQuestionnaires().put(nextRef.getValue(), resource);
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newResources.add(resource);
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}
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}
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}
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for (IBaseResource nextAddedResource : newResources) {
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boolean outcome = loadReferences(nextAddedResource, theWorkerCtx, theValCtx, theMessages);
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if (!outcome) {
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return false;
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}
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}
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return true;
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}
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private <T extends IBaseResource> T tryToLoad(Class<T> theType, IIdType theReference, List<ValidationMessage> theMessages) {
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if (myResourceLoader == null) {
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theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL).setMessage("No resource loader present, could not load " + theReference));
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return null;
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}
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try {
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T retVal = myResourceLoader.load(theType, theReference);
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if (retVal == null) {
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throw new IllegalStateException("ResourceLoader returned null. This is a bug with the resourceloader. Reference was: " + theReference);
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}
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return retVal;
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} catch (ResourceNotFoundException e) {
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theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL).setMessage("Reference could not be found: " + theReference));
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return null;
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}
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}
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}
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@ -0,0 +1,124 @@
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package ca.uhn.fhir.validation;
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import static org.hamcrest.Matchers.containsString;
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import static org.junit.Assert.*;
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import static org.mockito.Mockito.mock;
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import static org.mockito.Mockito.when;
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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.IdType;
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import org.hl7.fhir.instance.model.Questionnaire;
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import org.hl7.fhir.instance.model.QuestionnaireAnswers;
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import org.hl7.fhir.instance.model.Reference;
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import org.hl7.fhir.instance.model.StringType;
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import org.hl7.fhir.instance.model.ValueSet;
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import org.hl7.fhir.instance.model.Questionnaire.AnswerFormat;
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import org.hl7.fhir.instance.utils.WorkerContext;
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import org.hl7.fhir.instance.validation.QuestionnaireAnswersValidator;
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import org.hl7.fhir.instance.validation.ValidationMessage;
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import org.junit.Before;
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import org.junit.Test;
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import org.mockito.Mockito;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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public class QuestionnaireAnswersValidatorIntegrationTest {
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private static final FhirContext ourCtx = FhirContext.forDstu2Hl7Org();
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(QuestionnaireAnswersValidatorIntegrationTest.class);
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private IResourceLoader myResourceLoaderMock;
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private FhirValidator myVal;
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@Before
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public void before() {
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myResourceLoaderMock = mock(IResourceLoader.class);
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FhirQuestionnaireAnswersValidator qaVal = new FhirQuestionnaireAnswersValidator();
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qaVal.setResourceLoader(myResourceLoaderMock);
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myVal = ourCtx.newValidator();
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myVal.setValidateAgainstStandardSchema(false);
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myVal.setValidateAgainstStandardSchematron(false);
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myVal.registerValidator(qaVal);
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}
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@Test
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public void testAnswerWithWrongType() {
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Questionnaire q = new Questionnaire();
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q.getGroup().addQuestion().setLinkId("link0").setRequired(true).setType(AnswerFormat.BOOLEAN);
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when(myResourceLoaderMock.load(Mockito.eq(Questionnaire.class), Mockito.eq(new IdType("http://example.com/Questionnaire/q1")))).thenReturn(q);
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QuestionnaireAnswers qa = new QuestionnaireAnswers();
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qa.getQuestionnaire().setReference("http://example.com/Questionnaire/q1");
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qa.getGroup().addQuestion().setLinkId("link0").addAnswer().setValue(new StringType("FOO"));
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ValidationResult result = myVal.validateWithResult(qa);
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ourLog.info(result.getMessages().toString());
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assertThat(result.getMessages().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 testCodedAnswer() {
|
||||
String questionnaireRef = "http://example.com/Questionnaire/q1";
|
||||
|
||||
Questionnaire q = new Questionnaire();
|
||||
q.getGroup().addQuestion().setLinkId("link0").setRequired(false).setType(AnswerFormat.CHOICE).setOptions(new Reference("http://somevalueset/ValueSet/123"));
|
||||
when(myResourceLoaderMock.load(Mockito.eq(Questionnaire.class), Mockito.eq(new IdType("http://example.com/Questionnaire/q1")))).thenReturn(q);
|
||||
|
||||
ValueSet options = new ValueSet();
|
||||
options.getDefine().setSystem("urn:system").addConcept().setCode("code0");
|
||||
when(myResourceLoaderMock.load(Mockito.eq(ValueSet.class), Mockito.eq(new IdType("http://somevalueset/ValueSet/123")))).thenReturn(options);
|
||||
|
||||
QuestionnaireAnswers qa;
|
||||
|
||||
// Good code
|
||||
|
||||
qa = new QuestionnaireAnswers();
|
||||
qa.getQuestionnaire().setReference(questionnaireRef);
|
||||
qa.getGroup().addQuestion().setLinkId("link0").addAnswer().setValue(new Coding().setSystem("urn:system").setCode("code0"));
|
||||
ValidationResult result = myVal.validateWithResult(qa);
|
||||
assertEquals(result.getMessages().toString(), 0, result.getMessages().size());
|
||||
|
||||
// Bad code
|
||||
|
||||
qa = new QuestionnaireAnswers();
|
||||
qa.getQuestionnaire().setReference(questionnaireRef);
|
||||
qa.getGroup().addQuestion().setLinkId("link0").addAnswer().setValue(new Coding().setSystem("urn:system").setCode("code1"));
|
||||
result = myVal.validateWithResult(qa);
|
||||
ourLog.info(result.getMessages().toString());
|
||||
assertThat(result.getMessages().toString(), containsString("myLocationString=QuestionnaireAnswers.group(0).question(0).answer(0)"));
|
||||
assertThat(result.getMessages().toString(), containsString("myMessage=Question with linkId[link0] has answer with system[urn:system] and code[code1] but this is not a valid answer for ValueSet[http://somevalueset/ValueSet/123]"));
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testUnknownValueSet() {
|
||||
String questionnaireRef = "http://example.com/Questionnaire/q1";
|
||||
|
||||
Questionnaire q = new Questionnaire();
|
||||
q.getGroup().addQuestion().setLinkId("link0").setRequired(false).setType(AnswerFormat.CHOICE).setOptions(new Reference("http://somevalueset/ValueSet/123"));
|
||||
when(myResourceLoaderMock.load(Mockito.eq(Questionnaire.class), Mockito.eq(new IdType("http://example.com/Questionnaire/q1")))).thenReturn(q);
|
||||
|
||||
when(myResourceLoaderMock.load(Mockito.eq(ValueSet.class), Mockito.eq(new IdType("http://somevalueset/ValueSet/123")))).thenThrow(new ResourceNotFoundException("Unknown"));
|
||||
|
||||
QuestionnaireAnswers qa;
|
||||
|
||||
// Bad code
|
||||
|
||||
qa = new QuestionnaireAnswers();
|
||||
qa.getQuestionnaire().setReference(questionnaireRef);
|
||||
qa.getGroup().addQuestion().setLinkId("link0").addAnswer().setValue(new Coding().setSystem("urn:system").setCode("code1"));
|
||||
ValidationResult result = myVal.validateWithResult(qa);
|
||||
assertThat(result.getMessages().toString(), containsString("myMessage=Reference could not be found: http://some"));
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue