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hapi-fhir
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Merge remote-tracking branch 'upstream/master'

This commit is contained in:
Thomas Andersen 2015-09-30 23:16:40 +02:00
parent 74557d6e85 9664174b6a
commit 4b2a3e6882
51 changed files with 2113 additions and 1139 deletions
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7
.project
View File

@ -11,8 +11,13 @@
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name>
<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
<triggers>full,incremental,</triggers>
<arguments>
<dictionary>
<key>LaunchConfigHandle</key>
<value>&lt;project&gt;/.externalToolBuilders/org.eclipse.m2e.core.maven2Builder.launch</value>
</dictionary>
</arguments>
</buildCommand>
</buildSpec>

8
examples/src/main/java/example/ValidatorExamples.java
View File

@ -176,13 +176,13 @@ public class ValidatorExamples {
IValidationSupport valSupport = new IValidationSupport() {
@Override
public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
// TODO: Implement
return null;
}
@Override
public boolean isCodeSystemSupported(String theSystem) {
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
// TODO: Implement
return false;
}
@ -194,13 +194,13 @@ public class ValidatorExamples {
}
@Override
public ValueSet fetchCodeSystem(String theSystem) {
public ValueSet fetchCodeSystem(FhirContext theContext, String theSystem) {
// TODO: Implement
return null;
}
@Override
public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
// TODO: Implement
return null;
}

14
hapi-fhir-base/.project
View File

@ -16,13 +16,23 @@
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.wst.validation.validationbuilder</name>
<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
<triggers>full,incremental,</triggers>
<arguments>
<dictionary>
<key>LaunchConfigHandle</key>
<value>&lt;project&gt;/.externalToolBuilders/org.eclipse.wst.validation.validationbuilder.launch</value>
</dictionary>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name>
<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
<triggers>full,incremental,</triggers>
<arguments>
<dictionary>
<key>LaunchConfigHandle</key>
<value>&lt;project&gt;/.externalToolBuilders/org.eclipse.m2e.core.maven2Builder (1).launch</value>
</dictionary>
</arguments>
</buildCommand>
</buildSpec>

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/IRuntimeDatatypeDefinition.java
View File

@ -27,7 +27,7 @@ public interface IRuntimeDatatypeDefinition {
boolean isSpecialization();
public BaseRuntimeElementDefinition<?> getProfileOf();
public Class<? extends IBaseDatatype> getProfileOf();
boolean isProfileOf(Class<? extends IBaseDatatype> theType);

63
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeChildChoiceDefinition.java
View File

@ -30,6 +30,8 @@ import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.model.api.annotation.Child;
@ -41,6 +43,7 @@ public class RuntimeChildChoiceDefinition extends BaseRuntimeDeclaredChildDefini
private Map<String, BaseRuntimeElementDefinition<?>> myNameToChildDefinition;
private Map<Class<? extends IBase>, String> myDatatypeToElementName;
private Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myDatatypeToElementDefinition;
private String myReferenceSuffix;
public RuntimeChildChoiceDefinition(Field theField, String theElementName, Child theChildAnnotation, Description theDescriptionAnnotation, List<Class<? extends IBase>> theChoiceTypes) {
super(theField, theChildAnnotation, theDescriptionAnnotation, theElementName);
@ -82,9 +85,15 @@ public class RuntimeChildChoiceDefinition extends BaseRuntimeDeclaredChildDefini
myDatatypeToElementName = new HashMap<Class<? extends IBase>, String>();
myDatatypeToElementDefinition = new HashMap<Class<? extends IBase>, BaseRuntimeElementDefinition<?>>();
if (theContext.getVersion().getVersion().equals(FhirVersionEnum.DSTU1)) {
myReferenceSuffix = "Resource";
} else {
myReferenceSuffix = "Reference";
}
for (Class<? extends IBase> next : myChoiceTypes) {
String elementName;
String elementName = null;
BaseRuntimeElementDefinition<?> nextDef;
boolean nonPreferred = false;
if (IBaseResource.class.isAssignableFrom(next)) {
@ -109,32 +118,43 @@ public class RuntimeChildChoiceDefinition extends BaseRuntimeDeclaredChildDefini
* element fooString when encoded, because markdown is a profile of string. This is according to the
* FHIR spec
*/
nextDefForChoice = nextDefDatatype.getProfileOf();
nextDefForChoice = null;
nonPreferred = true;
Class<? extends IBaseDatatype> profileType = nextDefDatatype.getProfileOf();
BaseRuntimeElementDefinition<?> elementDef = theClassToElementDefinitions.get(profileType);
elementName = getElementName() + StringUtils.capitalize(elementDef.getName());
}
}
elementName = getElementName() + StringUtils.capitalize(nextDefForChoice.getName());
}
if (myNameToChildDefinition.containsKey(elementName) == false || !nonPreferred) {
myNameToChildDefinition.put(elementName, nextDef);
}
if (IBaseResource.class.isAssignableFrom(next)) {
Class<? extends IBase> refType = theContext.getVersion().getResourceReferenceType();
myDatatypeToElementDefinition.put(refType, nextDef);
String alternateElementName;
if (theContext.getVersion().getVersion().equals(FhirVersionEnum.DSTU1)) {
alternateElementName = getElementName() + "Resource";
} else {
alternateElementName = getElementName() + "Reference";
if (nextDefForChoice != null) {
elementName = getElementName() + StringUtils.capitalize(nextDefForChoice.getName());
}
myDatatypeToElementName.put(refType, alternateElementName);
}
// I don't see how elementName could be null here, but eclipse complains..
if (elementName != null) {
if (myNameToChildDefinition.containsKey(elementName) == false || !nonPreferred) {
myNameToChildDefinition.put(elementName, nextDef);
}
}
/*
* If this is a resource reference, the element name is "fooNameReference"
*/
if (IBaseResource.class.isAssignableFrom(next) || IBaseReference.class.isAssignableFrom(next)) {
next = theContext.getVersion().getResourceReferenceType();
elementName = getElementName() + myReferenceSuffix;
}
myDatatypeToElementDefinition.put(next, nextDef);
myDatatypeToElementName.put(next, elementName);
if (myDatatypeToElementName.containsKey(next)) {
String existing = myDatatypeToElementName.get(next);
if (!existing.equals(elementName)) {
throw new ConfigurationException("Already have element name " + existing + " for datatype " + next.getClass().getSimpleName() + " in " + getElementName() + ", cannot add " + elementName);
}
} else {
myDatatypeToElementName.put(next, elementName);
}
}
myNameToChildDefinition = Collections.unmodifiableMap(myNameToChildDefinition);
@ -145,7 +165,8 @@ public class RuntimeChildChoiceDefinition extends BaseRuntimeDeclaredChildDefini
@Override
public String getChildNameByDatatype(Class<? extends IBase> theDatatype) {
return myDatatypeToElementName.get(theDatatype);
String retVal = myDatatypeToElementName.get(theDatatype);
return retVal;
}
@Override

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeCompositeDatatypeDefinition.java
View File

@ -65,8 +65,8 @@ public class RuntimeCompositeDatatypeDefinition extends BaseRuntimeElementCompos
}
@Override
public BaseRuntimeElementDefinition<?> getProfileOf() {
return myProfileOf;
public Class<? extends IBaseDatatype> getProfileOf() {
return myProfileOfType;
}
@Override

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimePrimitiveDatatypeDefinition.java
View File

@ -58,8 +58,8 @@ public class RuntimePrimitiveDatatypeDefinition extends BaseRuntimeElementDefini
}
@Override
public BaseRuntimeElementDefinition<?> getProfileOf() {
return myProfileOf;
public Class<? extends IBaseDatatype> getProfileOf() {
return myProfileOfType;
}
@Override

35
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/OperationParameter.java
View File

@ -24,6 +24,7 @@ import java.lang.reflect.Method;
import java.lang.reflect.Modifier;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
import java.util.List;
import java.util.Map;
@ -47,6 +48,7 @@ import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.param.CollectionBinder;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ResourceParameter;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -66,6 +68,7 @@ public class OperationParameter implements IParameter {
private Class<?> myParameterType;
private String myParamType;
private FhirContext myContext;
private boolean myAllowGet;
public OperationParameter(FhirContext theCtx, String theOperationName, OperationParam theOperationParam) {
this(theCtx, theOperationName, theOperationParam.name(), theOperationParam.min(), theOperationParam.max());
@ -107,6 +110,8 @@ public class OperationParameter implements IParameter {
myMax = 1;
}
myAllowGet = IPrimitiveType.class.isAssignableFrom(myParameterType);
/*
* The parameter can be of type string for validation methods - This is a bit
* weird. See ValidateDstu2Test. We should probably clean this up..
@ -114,6 +119,10 @@ public class OperationParameter implements IParameter {
if (!myParameterType.equals(IBase.class) && !myParameterType.equals(String.class)) {
if (IBaseResource.class.isAssignableFrom(myParameterType) && myParameterType.isInterface()) {
myParamType = "Resource";
} else if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
myParamType = "date";
myMax = 2;
myAllowGet = true;
} else if (!IBase.class.isAssignableFrom(myParameterType) || myParameterType.isInterface() || Modifier.isAbstract(myParameterType.getModifiers())) {
throw new ConfigurationException("Invalid type for @OperationParam: " + myParameterType.getName());
} else if (myParameterType.equals(ValidationModeEnum.class)) {
@ -153,13 +162,25 @@ public class OperationParameter implements IParameter {
if (theRequest.getRequestType() == RequestTypeEnum.GET) {
String[] paramValues = theRequest.getParameters().get(myName);
if (paramValues != null && paramValues.length > 0) {
if (IPrimitiveType.class.isAssignableFrom(myParameterType)) {
for (String nextValue : paramValues) {
FhirContext ctx = theRequest.getServer().getFhirContext();
RuntimePrimitiveDatatypeDefinition def = (RuntimePrimitiveDatatypeDefinition) ctx.getElementDefinition((Class<? extends IBase>) myParameterType);
IPrimitiveType<?> instance = def.newInstance();
instance.setValueAsString(nextValue);
matchingParamValues.add(instance);
if (myAllowGet) {
if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
List<QualifiedParamList> parameters = new ArrayList<QualifiedParamList>();
parameters.add(QualifiedParamList.singleton(paramValues[0]));
if (paramValues.length > 1) {
parameters.add(QualifiedParamList.singleton(paramValues[1]));
}
DateRangeParam dateRangeParam = new DateRangeParam();
dateRangeParam.setValuesAsQueryTokens(parameters);
matchingParamValues.add(dateRangeParam);
} else {
for (String nextValue : paramValues) {
FhirContext ctx = theRequest.getServer().getFhirContext();
RuntimePrimitiveDatatypeDefinition def = (RuntimePrimitiveDatatypeDefinition) ctx.getElementDefinition((Class<? extends IBase>) myParameterType);
IPrimitiveType<?> instance = def.newInstance();
instance.setValueAsString(nextValue);
matchingParamValues.add(instance);
}
}
} else {
HapiLocalizer localizer = theRequest.getServer().getFhirContext().getLocalizer();

9
hapi-fhir-base/src/main/resources/ca/uhn/fhir/narrative/Medication.html
View File

@ -11,7 +11,14 @@ a browser.
<!--*/-->
<div>
<div class="hapiHeaderText" th:if="${not resource.nameElement.empty}" th:narrative="${resource.name}"></div>
<th:block th:switch="${fhirVersion}">
<th:block th:case="'DSTU1'">
<div class="hapiHeaderText" th:if="${not resource.nameElement.empty}" th:narrative="${resource.name}"></div>
</th:block>
<th:block th:case="*">
<div class="hapiHeaderText" th:if="${not resource.code.empty}" th:narrative="${resource.code}"></div>
</th:block>
</th:block>
</div>
<!--/*-->

8
hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupport.java
View File

@ -16,12 +16,12 @@ public class LoadingValidationSupport implements IValidationSupport {
private static FhirContext myCtx = FhirContext.forDstu2Hl7Org();
@Override
public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
return null;
}
@Override
public ValueSet fetchCodeSystem(String theSystem) {
public ValueSet fetchCodeSystem(FhirContext theContext, String theSystem) {
return null;
}
@ -46,12 +46,12 @@ public class LoadingValidationSupport implements IValidationSupport {
}
@Override
public boolean isCodeSystemSupported(String theSystem) {
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
return false;
}
@Override
public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
return null;
}

14
hapi-fhir-jpaserver-base/.classpath
View File

@ -1,21 +1,21 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" output="target/test-classes" path="src/test/java">
<classpathentry kind="src" path="src/test/java">
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**/*.java" including="**/*.java" kind="src" output="target/test-classes" path="src/test/resources"/>
<classpathentry kind="src" output="target/classes" path="src/main/java">
<classpathentry kind="src" path="src/test/resources"/>
<classpathentry kind="src" path="src/main/java">
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**/*.java" including="**/*.java" kind="src" path="src/main/resources"/>
<classpathentry including="**/*.java" kind="src" path="target/generated-sources/tinder"/>
<classpathentry excluding="**" kind="src" output="target/classes" path="target/generated-resources/tinder">
<classpathentry kind="src" path="src/main/resources"/>
<classpathentry kind="src" path="target/generated-sources/tinder"/>
<classpathentry kind="src" path="target/generated-resources/tinder">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
@ -32,5 +32,5 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="output" path="target/classes"/>
<classpathentry kind="output" path="bin"/>
</classpath>

14
hapi-fhir-jpaserver-base/.project
View File

@ -17,13 +17,23 @@
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.wst.validation.validationbuilder</name>
<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
<triggers>full,incremental,</triggers>
<arguments>
<dictionary>
<key>LaunchConfigHandle</key>
<value>&lt;project&gt;/.externalToolBuilders/org.eclipse.wst.validation.validationbuilder (1).launch</value>
</dictionary>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name>
<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
<triggers>full,incremental,</triggers>
<arguments>
<dictionary>
<key>LaunchConfigHandle</key>
<value>&lt;project&gt;/.externalToolBuilders/org.eclipse.m2e.core.maven2Builder (2).launch</value>
</dictionary>
</arguments>
</buildCommand>
</buildSpec>

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -111,6 +111,7 @@ import ca.uhn.fhir.rest.method.QualifiedParamList;
import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -715,7 +716,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
return ids;
}
static SearchParameterMap translateMatchUrl(String theMatchUrl, RuntimeResourceDefinition resourceDef) {
public static SearchParameterMap translateMatchUrl(String theMatchUrl, RuntimeResourceDefinition resourceDef) {
SearchParameterMap paramMap = new SearchParameterMap();
List<NameValuePair> parameters;
try {
@ -778,7 +779,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
}
continue;
}
if (nextParamName.startsWith("_")) {
continue;
}
RuntimeSearchParam paramDef = resourceDef.getSearchParam(nextParamName);
if (paramDef == null) {
throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Resource type " + resourceDef.getName() + " does not have a parameter with name: " + nextParamName);

115
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -1227,11 +1227,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
} else {
theOrders.add(theBuilder.desc(theFrom.get("myUpdated")));
}
createSort(theBuilder, theFrom, theSort.getChain(), theOrders, thePredicates);
return;
}
RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(myResourceType);
RuntimeSearchParam param = resourceDef.getSearchParam(theSort.getParamName());
if (param == null) {
@ -1615,7 +1615,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
/**
* THIS SHOULD RETURN HASHSET and not jsut Set because we add to it later (so it can't be Collections.emptySet())
*/
private HashSet<Long> loadReverseIncludes(List<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode) {
private HashSet<Long> loadReverseIncludes(Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode) {
if (theMatches.size() == 0) {
return new HashSet<Long>();
}
@ -1902,7 +1902,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
Long pid = translateForcedIdToPid(theId);
BaseHasResource entity = myEntityManager.find(ResourceTable.class, pid);
if (entity == null) {
throw new ResourceNotFoundException(theId);
}
@ -2013,6 +2013,9 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
for (Tuple next : query.getResultList()) {
loadPids.add(next.get(0, Long.class));
}
if (loadPids.isEmpty()) {
return new SimpleBundleProvider();
}
} else {
loadPids = searchForIdsWithAndOr(theParams);
if (loadPids.isEmpty()) {
@ -2020,6 +2023,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
}
}
// Load _include and _revinclude before filter and sort in everything mode
if (theParams.isEverythingMode() == true) {
if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
loadPids.addAll(loadReverseIncludes(loadPids, theParams.getRevIncludes(), true));
loadPids.addAll(loadReverseIncludes(loadPids, theParams.getIncludes(), false));
}
}
// Handle _lastUpdated
DateRangeParam lu = theParams.getLastUpdated();
if (lu != null && (lu.getLowerBoundAsInstant() != null || lu.getUpperBoundAsInstant() != null)) {
@ -2028,7 +2039,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
CriteriaQuery<Long> cq = builder.createQuery(Long.class);
Root<ResourceTable> from = cq.from(ResourceTable.class);
cq.select(from.get("myId").as(Long.class));
Predicate predicateIds = (from.get("myId").in(loadPids));
Predicate predicateLower = lu.getLowerBoundAsInstant() != null ? builder.greaterThanOrEqualTo(from.<Date> get("myUpdated"), lu.getLowerBoundAsInstant()) : null;
Predicate predicateUpper = lu.getUpperBoundAsInstant() != null ? builder.lessThanOrEqualTo(from.<Date> get("myUpdated"), lu.getUpperBoundAsInstant()) : null;
@ -2044,59 +2055,22 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
for (Long next : query.getResultList()) {
loadPids.add(next);
}
if (loadPids.isEmpty()) {
return new SimpleBundleProvider();
}
}
// Handle sorting if any was provided
final List<Long> pids;
if (theParams.getSort() != null && isNotBlank(theParams.getSort().getParamName())) {
List<Order> orders = new ArrayList<Order>();
List<Predicate> predicates = new ArrayList<Predicate>();
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<Tuple> cq = builder.createTupleQuery();
Root<ResourceTable> from = cq.from(ResourceTable.class);
predicates.add(from.get("myId").in(loadPids));
createSort(builder, from, theParams.getSort(), orders, predicates);
if (orders.size() > 0) {
Set<Long> originalPids = loadPids;
loadPids = new LinkedHashSet<Long>();
cq.multiselect(from.get("myId").as(Long.class));
cq.where(predicates.toArray(new Predicate[0]));
cq.orderBy(orders);
TypedQuery<Tuple> query = myEntityManager.createQuery(cq);
for (Tuple next : query.getResultList()) {
loadPids.add(next.get(0, Long.class));
}
ourLog.debug("Sort PID order is now: {}", loadPids);
pids = new ArrayList<Long>(loadPids);
// Any ressources which weren't matched by the sort get added to the bottom
for (Long next : originalPids) {
if (loadPids.contains(next) == false) {
pids.add(next);
}
}
} else {
pids = new ArrayList<Long>(loadPids);
}
} else {
pids = new ArrayList<Long>(loadPids);
}
final List<Long> pids = processSort(theParams, loadPids);
// Load _revinclude resources
final Set<Long> revIncludedPids;
if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true);
if (theParams.isEverythingMode()) {
revIncludedPids.addAll(loadReverseIncludes(pids, theParams.getIncludes(), false));
if (theParams.isEverythingMode() == false) {
if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true);
} else {
revIncludedPids = new HashSet<Long>();
}
} else {
revIncludedPids = new HashSet<Long>();
@ -2152,6 +2126,49 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
return retVal;
}
private List<Long> processSort(final SearchParameterMap theParams, Set<Long> loadPids) {
final List<Long> pids;
if (theParams.getSort() != null && isNotBlank(theParams.getSort().getParamName())) {
List<Order> orders = new ArrayList<Order>();
List<Predicate> predicates = new ArrayList<Predicate>();
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<Tuple> cq = builder.createTupleQuery();
Root<ResourceTable> from = cq.from(ResourceTable.class);
predicates.add(from.get("myId").in(loadPids));
createSort(builder, from, theParams.getSort(), orders, predicates);
if (orders.size() > 0) {
Set<Long> originalPids = loadPids;
loadPids = new LinkedHashSet<Long>();
cq.multiselect(from.get("myId").as(Long.class));
cq.where(predicates.toArray(new Predicate[0]));
cq.orderBy(orders);
TypedQuery<Tuple> query = myEntityManager.createQuery(cq);
for (Tuple next : query.getResultList()) {
loadPids.add(next.get(0, Long.class));
}
ourLog.debug("Sort PID order is now: {}", loadPids);
pids = new ArrayList<Long>(loadPids);
// Any ressources which weren't matched by the sort get added to the bottom
for (Long next : originalPids) {
if (loadPids.contains(next) == false) {
pids.add(next);
}
}
} else {
pids = new ArrayList<Long>(loadPids);
}
} else {
pids = new ArrayList<Long>(loadPids);
}
return pids;
}
@Override
public IBundleProvider search(String theParameterName, IQueryParameterType theValue) {
return search(Collections.singletonMap(theParameterName, theValue));

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoPatientDstu2.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.dao;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2015 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.Collections;
import javax.servlet.http.HttpServletRequest;
@ -8,13 +28,15 @@ import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.UnsignedIntDt;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>implements IFhirResourceDaoPatient<Patient> {
@Override
public IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount) {
public IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount, DateRangeParam theLastUpdated, SortSpec theSort) {
SearchParameterMap paramMap = new SearchParameterMap();
if (theCount != null) {
paramMap.setCount(theCount.getValue());
@ -23,6 +45,8 @@ public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>im
paramMap.setRevIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
paramMap.setIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
paramMap.setEverythingMode(true);
paramMap.setSort(theSort);
paramMap.setLastUpdated(theLastUpdated);
paramMap.add("_id", new StringParam(theId.getIdPart()));
ca.uhn.fhir.rest.server.IBundleProvider retVal = search(paramMap);
return retVal;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoPatient.java
View File

@ -26,10 +26,12 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.UnsignedIntDt;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
public interface IFhirResourceDaoPatient<T extends IBaseResource> extends IFhirResourceDao<T> {
IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount);
IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount, DateRangeParam theLastUpdate, SortSpec theSort);
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaValidationSupportDstu2.java
View File

@ -51,12 +51,12 @@ public class JpaValidationSupportDstu2 implements IValidationSupport {
private FhirContext myDstu2Ctx;
@Override
public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
return null;
}
@Override
public ValueSet fetchCodeSystem(String theSystem) {
public ValueSet fetchCodeSystem(FhirContext theCtx, String theSystem) {
return null;
}
@ -85,20 +85,19 @@ public class JpaValidationSupportDstu2 implements IValidationSupport {
/*
* Validator wants RI structures and not HAPI ones, so convert
*
* TODO: we really need a more efficient way of converting.. Or maybe this will
* just go away when we move to RI structures
* TODO: we really need a more efficient way of converting.. Or maybe this will just go away when we move to RI structures
*/
String encoded = myDstu2Ctx.newJsonParser().encodeResourceToString(res);
return myRiCtx.newJsonParser().parseResource(theClass, encoded);
}
@Override
public boolean isCodeSystemSupported(String theSystem) {
public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
return false;
}
@Override
public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
return null;
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParameterMap.java
View File

@ -46,6 +46,7 @@ public class SearchParameterMap extends LinkedHashMap<String, List<List<? extend
private Set<Include> myIncludes;
private DateRangeParam myLastUpdated;
private Set<Include> myRevIncludes;
private SortSpec mySort;
public void add(String theName, IQueryParameterAnd<?> theAnd) {
@ -76,8 +77,8 @@ public class SearchParameterMap extends LinkedHashMap<String, List<List<? extend
}
public void add(String theName, IQueryParameterType theParam) {
assert !Constants.PARAM_LASTUPDATED.equals(theName); // this has it's own field in the map
assert!Constants.PARAM_LASTUPDATED.equals(theName); // this has it's own field in the map
if (theParam == null) {
return;
}

39
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProviderPatientDstu2.java
View File

@ -1,11 +1,35 @@
package ca.uhn.fhir.jpa.provider;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2015 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoPatient;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.Sort;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.Constants;
public class BaseJpaResourceProviderPatientDstu2 extends JpaResourceProviderDstu2<Patient> {
@ -18,12 +42,21 @@ public class BaseJpaResourceProviderPatientDstu2 extends JpaResourceProviderDstu
ca.uhn.fhir.model.primitive.IdDt theId,
@Description(formalDefinition="Results from this method are returned across multiple pages. This parameter controls the size of those pages.")
@OperationParam(name = "_count")
ca.uhn.fhir.model.primitive.UnsignedIntDt theCount) {
@OperationParam(name = Constants.PARAM_COUNT)
ca.uhn.fhir.model.primitive.UnsignedIntDt theCount,
@Description(shortDefinition="Only return resources which were last updated as specified by the given range")
@OperationParam(name = Constants.PARAM_LASTUPDATED, min=0, max=1)
DateRangeParam theLastUpdated,
// @OperationParam(name = Constants.PARAM_SORT, min=0, max=1)
@Sort
SortSpec theSortSpec
) {
startRequest(theServletRequest);
try {
return ((IFhirResourceDaoPatient<Patient>)getDao()).everything(theServletRequest, theId, theCount);
return ((IFhirResourceDaoPatient<Patient>)getDao()).everything(theServletRequest, theId, theCount, theLastUpdated, theSortSpec);
} finally {
endRequest(theServletRequest);
}

234
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/SubscriptionWebsocketHandler.java
View File

@ -27,36 +27,49 @@ import java.util.concurrent.ScheduledFuture;
import javax.annotation.PostConstruct;
import javax.annotation.PreDestroy;
import org.apache.http.NameValuePair;
import org.apache.http.client.utils.URLEncodedUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.scheduling.TaskScheduler;
import org.springframework.web.socket.CloseStatus;
import org.springframework.web.socket.TextMessage;
import org.springframework.web.socket.WebSocketSession;
import org.springframework.web.socket.handler.TextWebSocketHandler;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSubscription;
import ca.uhn.fhir.model.dstu2.resource.Subscription;
import ca.uhn.fhir.model.dstu2.valueset.SubscriptionChannelTypeEnum;
import ca.uhn.fhir.model.dstu2.valueset.SubscriptionStatusEnum;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
public class SubscriptionWebsocketHandler extends TextWebSocketHandler implements ISubscriptionWebsocketHandler, Runnable {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SubscriptionWebsocketHandler.class);
@Autowired
@Qualifier("myFhirContextDstu2")
private FhirContext myCtx;
private ScheduledFuture<?> myScheduleFuture;
private IState myState = new InitialState();
@Autowired
private IFhirResourceDaoSubscription<Subscription> mySubscriptionDao;
private IIdType mySubscriptionId;
private Long mySubscriptionPid;
@Autowired
private TaskScheduler myTaskScheduler;
@Override
public void afterConnectionClosed(WebSocketSession theSession, CloseStatus theStatus) throws Exception {
super.afterConnectionClosed(theSession, theStatus);
@ -68,53 +81,113 @@ public class SubscriptionWebsocketHandler extends TextWebSocketHandler implement
super.afterConnectionEstablished(theSession);
ourLog.info("Incoming WebSocket connection from {}", theSession.getRemoteAddress());
}
protected void handleFailure(Exception theE) {
ourLog.error("Failure during communication", theE);
}
@Override
protected void handleTextMessage(WebSocketSession theSession, TextMessage theMessage) throws Exception {
ourLog.info("Textmessage: " + theMessage.getPayload());
myState.handleTextMessage(theSession, theMessage);
}
@Override
public void handleTransportError(WebSocketSession theSession, Throwable theException) throws Exception {
super.handleTransportError(theSession, theException);
ourLog.error("Transport error", theException);
}
@PostConstruct
public void postConstruct() {
ourLog.info("Creating scheduled task for subscription websocket connection");
myScheduleFuture = myTaskScheduler.scheduleWithFixedDelay(this, 1000);
}
@PreDestroy
public void preDescroy() {
ourLog.info("Cancelling scheduled task for subscription websocket connection");
myScheduleFuture.cancel(true);
IState state = myState;
if (state != null) {
state.closing();
}
}
@Override
public void run() {
Long subscriptionPid = mySubscriptionPid;
if (subscriptionPid == null) {
return;
}
ourLog.debug("Subscription {} websocket handler polling", subscriptionPid);
List<IBaseResource> results = mySubscriptionDao.getUndeliveredResourcesAndPurge(subscriptionPid);
if (results.isEmpty() == false) {
myState.deliver(results);
}
}
private class SimpleBoundState implements IState {
private class BoundDynamicSubscriptionState implements IState {
private EncodingEnum myEncoding;
private WebSocketSession mySession;
public BoundDynamicSubscriptionState(WebSocketSession theSession, EncodingEnum theEncoding) {
mySession = theSession;
myEncoding = theEncoding;
}
@Override
public void closing() {
ourLog.info("Deleting subscription {}", mySubscriptionId);
try {
mySubscriptionDao.delete(mySubscriptionId);
} catch (Exception e) {
handleFailure(e);
}
}
@Override
public void deliver(List<IBaseResource> theResults) {
try {
for (IBaseResource nextResource : theResults) {
ourLog.info("Sending WebSocket message for resource: {}", nextResource.getIdElement());
String encoded = myEncoding.newParser(myCtx).encodeResourceToString(nextResource);
String payload = "add " + mySubscriptionId.getIdPart() + '\n' + encoded;
mySession.sendMessage(new TextMessage(payload));
}
} catch (IOException e) {
handleFailure(e);
}
}
@Override
public void handleTextMessage(WebSocketSession theSession, TextMessage theMessage) {
try {
theSession.sendMessage(new TextMessage("Unexpected client message: " + theMessage.getPayload()));
} catch (IOException e) {
handleFailure(e);
}
}
}
private class BoundStaticSubscipriptionState implements IState {
private WebSocketSession mySession;
public SimpleBoundState(WebSocketSession theSession) {
public BoundStaticSubscipriptionState(WebSocketSession theSession) {
mySession = theSession;
}
@Override
public void closing() {
// nothing
}
@Override
public void deliver(List<IBaseResource> theResults) {
try {
@ -134,11 +207,93 @@ public class SubscriptionWebsocketHandler extends TextWebSocketHandler implement
handleFailure(e);
}
}
}
private class InitialState implements IState {
private IIdType bindSimple(WebSocketSession theSession, String theBindString) {
IdDt id = new IdDt(theBindString);
if (!id.hasIdPart() || !id.isIdPartValid()) {
try {
theSession.close(new CloseStatus(CloseStatus.PROTOCOL_ERROR.getCode(), "Invalid bind request - No ID included"));
} catch (IOException e) {
handleFailure(e);
}
return null;
}
if (id.hasResourceType() == false) {
id = id.withResourceType("Subscription");
}
try {
Subscription subscription = mySubscriptionDao.read(id);
mySubscriptionPid = mySubscriptionDao.getSubscriptionTablePidForSubscriptionResource(id);
mySubscriptionId = subscription.getIdElement();
myState = new BoundStaticSubscipriptionState(theSession);
} catch (ResourceNotFoundException e) {
try {
theSession.close(new CloseStatus(CloseStatus.PROTOCOL_ERROR.getCode(), "Invalid bind request - Unknown subscription: " + id.getValue()));
} catch (IOException e1) {
handleFailure(e);
}
return null;
}
return id;
}
private IIdType bingSearch(WebSocketSession theSession, String theRemaining) {
Subscription subscription = new Subscription();
subscription.getChannel().setType(SubscriptionChannelTypeEnum.WEBSOCKET);
subscription.setStatus(SubscriptionStatusEnum.ACTIVE);
subscription.setCriteria(theRemaining);
try {
String params = theRemaining.substring(theRemaining.indexOf('?')+1);
List<NameValuePair> paramValues = URLEncodedUtils.parse(params, Constants.CHARSET_UTF8, '&');
EncodingEnum encoding = EncodingEnum.JSON;
for (NameValuePair nameValuePair : paramValues) {
if (Constants.PARAM_FORMAT.equals(nameValuePair.getName())) {
EncodingEnum nextEncoding = Constants.FORMAT_VAL_TO_ENCODING.get(nameValuePair.getValue());
if (nextEncoding != null) {
encoding = nextEncoding;
}
}
}
IIdType id = mySubscriptionDao.create(subscription).getId();
mySubscriptionPid = mySubscriptionDao.getSubscriptionTablePidForSubscriptionResource(id);
mySubscriptionId = subscription.getIdElement();
myState = new BoundDynamicSubscriptionState(theSession, encoding);
return id;
} catch (UnprocessableEntityException e) {
ourLog.warn("Failed to bind subscription: " + e.getMessage());
try {
theSession.close(new CloseStatus(CloseStatus.PROTOCOL_ERROR.getCode(), "Invalid bind request - " + e.getMessage()));
} catch (IOException e2) {
handleFailure(e2);
}
} catch (Exception e) {
handleFailure(e);
try {
theSession.close(new CloseStatus(CloseStatus.PROTOCOL_ERROR.getCode(), "Invalid bind request - No ID included"));
} catch (IOException e2) {
handleFailure(e2);
}
}
return null;
}
@Override
public void closing() {
// nothing
}
@Override
public void deliver(List<IBaseResource> theResults) {
throw new IllegalStateException();
@ -148,52 +303,37 @@ public class SubscriptionWebsocketHandler extends TextWebSocketHandler implement
public void handleTextMessage(WebSocketSession theSession, TextMessage theMessage) {
String message = theMessage.getPayload();
if (message.startsWith("bind ")) {
IdDt id = new IdDt(message.substring("bind ".length()));
if (!id.hasIdPart() || !id.isIdPartValid()) {
try {
theSession.close(new CloseStatus(CloseStatus.PROTOCOL_ERROR.getCode(), "Invalid bind request - No ID included"));
} catch (IOException e) {
handleFailure(e);
String remaining = message.substring("bind ".length());
IIdType subscriptionId;
if (remaining.contains("?")) {
subscriptionId = bingSearch(theSession, remaining);
} else {
subscriptionId = bindSimple(theSession, remaining);
if (subscriptionId == null) {
return;
}
return;
}
if (id.hasResourceType()==false) {
id = id.withResourceType("Subscription");
}
try {
Subscription subscription = mySubscriptionDao.read(id);
mySubscriptionPid = mySubscriptionDao.getSubscriptionTablePidForSubscriptionResource(id);
mySubscriptionId = subscription.getIdElement();
myState = new SimpleBoundState(theSession);
} catch (ResourceNotFoundException e) {
try {
theSession.close(new CloseStatus(CloseStatus.PROTOCOL_ERROR.getCode(), "Invalid bind request - Unknown subscription: " + id.getValue()));
} catch (IOException e1) {
handleFailure(e);
}
return;
}
try {
theSession.sendMessage(new TextMessage("bound " + id.getIdPart()));
theSession.sendMessage(new TextMessage("bound " + subscriptionId.getIdPart()));
} catch (IOException e) {
handleFailure(e);
}
}
}
}
private interface IState{
private interface IState {
void closing();
void deliver(List<IBaseResource> theResults);
void handleTextMessage(WebSocketSession theSession, TextMessage theMessage);
}
}
}

6
hapi-fhir-jpaserver-base/src/main/resources/fhir-spring-subscription-config-dstu2.xml
View File

@ -4,16 +4,18 @@
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:websocket="http://www.springframework.org/schema/websocket"
xmlns:task="http://www.springframework.org/schema/task"
xmlns:tx="http://www.springframework.org/schema/tx"
xsi:schemaLocation="
http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context-3.0.xsd
http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
http://www.springframework.org/schema/websocket http://www.springframework.org/schema/websocket/spring-websocket.xsd
http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx.xsd
http://www.springframework.org/schema/task http://www.springframework.org/schema/task/spring-task.xsd">
<context:annotation-config />
<websocket:handlers>
<websocket:mapping path="/baseDstu2/websocket" handler="mySubscriptionWebsocketHandler" />
<websocket:mapping path="/websocket/dstu2" handler="mySubscriptionWebsocketHandler" />
</websocket:handlers>
<!--
@ -26,4 +28,6 @@
<bean id="mySubscriptionSecurityInterceptor" class="ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptor"/>
<tx:annotation-driven transaction-manager="myTxManagerDstu2" />
</beans>

16
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2SearchTest.java
View File

@ -65,6 +65,8 @@ import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.CompositeParam;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
@ -78,6 +80,7 @@ import ca.uhn.fhir.rest.param.TokenAndListParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@ -85,6 +88,19 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
public class FhirResourceDaoDstu2SearchTest extends BaseJpaDstu2Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2SearchTest.class);
@Test
public void testSearchWithEmptySort() {
SearchParameterMap criteriaUrl = new SearchParameterMap();
DateRangeParam range = new DateRangeParam();
range.setLowerBound(new DateParam(QuantityCompararatorEnum.GREATERTHAN, 1000000));
range.setUpperBound(new DateParam(QuantityCompararatorEnum.LESSTHAN, 2000000));
criteriaUrl.setLastUpdated(range);
criteriaUrl.setSort(new SortSpec(Constants.PARAM_LASTUPDATED, SortOrderEnum.ASC));
IBundleProvider results = myObservationDao.search(criteriaUrl);
assertEquals(0, results.size());
}
@Test
public void testIndexNoDuplicatesString() {
Patient p = new Patient();

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2Test.java
View File

@ -1919,6 +1919,10 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
@Test()
public void testSortByComposite() {
Observation o = new Observation();
o.getCode().setText("testSortByComposite");
myObservationDao.create(o);
SearchParameterMap pm = new SearchParameterMap();
pm.setSort(new SortSpec(Observation.SP_CODE_VALUE_CONCEPT));
try {

93
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java
View File

@ -602,6 +602,96 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
}
}
@Test
public void testEverythingWithLastUpdatedAndSort() throws Exception {
String methodName = "testEverythingWithLastUpdatedAndSort";
long time0 = System.currentTimeMillis();
Thread.sleep(10);
Organization org = new Organization();
org.setName(methodName);
IIdType oId = ourClient.create().resource(org).execute().getId().toUnqualifiedVersionless();
long time1 = System.currentTimeMillis();
Thread.sleep(10);
Patient p = new Patient();
p.addName().addFamily(methodName);
p.getManagingOrganization().setReference(oId);
IIdType pId = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
long time2 = System.currentTimeMillis();
Thread.sleep(10);
Condition c = new Condition();
c.getCode().setText(methodName);
c.getPatient().setReference(pId);
IIdType cId = ourClient.create().resource(c).execute().getId().toUnqualifiedVersionless();
Thread.sleep(10);
long time3 = System.currentTimeMillis();
// %3E=> %3C=<
HttpGet get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantDt(new Date(time1)).getValueAsString());
CloseableHttpResponse response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String output = IOUtils.toString(response.getEntity().getContent());
IOUtils.closeQuietly(response.getEntity().getContent());
ourLog.info(output);
List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
ourLog.info(ids.toString());
assertThat(ids, containsInAnyOrder(pId, cId));
} finally {
response.close();
}
get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantDt(new Date(time2)).getValueAsString() + "&_lastUpdated=%3C" + new InstantDt(new Date(time3)).getValueAsString());
response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String output = IOUtils.toString(response.getEntity().getContent());
IOUtils.closeQuietly(response.getEntity().getContent());
ourLog.info(output);
List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
ourLog.info(ids.toString());
assertThat(ids, containsInAnyOrder(cId));
} finally {
response.close();
}
get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantDt(new Date(time1)).getValueAsString() + "&_sort=_lastUpdated");
response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String output = IOUtils.toString(response.getEntity().getContent());
IOUtils.closeQuietly(response.getEntity().getContent());
ourLog.info(output);
List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
ourLog.info(ids.toString());
assertThat(ids, contains(pId, cId));
} finally {
response.close();
}
get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_sort:desc=_lastUpdated");
response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String output = IOUtils.toString(response.getEntity().getContent());
IOUtils.closeQuietly(response.getEntity().getContent());
ourLog.info(output);
List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
ourLog.info(ids.toString());
assertThat(ids, contains(cId, pId, oId));
} finally {
response.close();
}
}
/**
* See #148
*/
@ -1203,6 +1293,9 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
@Test(expected = InvalidRequestException.class)
public void testSearchWithInvalidSort() throws Exception {
Observation o = new Observation();
o.getCode().setText("testSearchWithInvalidSort");
myObservationDao.create(o);
//@formatter:off
Bundle found = ourClient
.search()

225
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SubscriptionsDstu2Test.java
View File

@ -5,6 +5,8 @@ import static org.junit.Assert.assertNull;
import static org.junit.Assert.fail;
import java.net.URI;
import java.util.ArrayList;
import java.util.List;
import org.eclipse.jetty.websocket.api.Session;
import org.eclipse.jetty.websocket.api.annotations.OnWebSocketConnect;
@ -12,6 +14,7 @@ import org.eclipse.jetty.websocket.api.annotations.OnWebSocketMessage;
import org.eclipse.jetty.websocket.api.annotations.WebSocket;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
import org.eclipse.jetty.websocket.client.WebSocketClient;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.Test;
@ -22,10 +25,20 @@ import ca.uhn.fhir.model.dstu2.resource.Subscription;
import ca.uhn.fhir.model.dstu2.valueset.ObservationStatusEnum;
import ca.uhn.fhir.model.dstu2.valueset.SubscriptionChannelTypeEnum;
import ca.uhn.fhir.model.dstu2.valueset.SubscriptionStatusEnum;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
public class BaseSocket {
protected String myError;
protected boolean myGotBound;
protected int myPingCount;
protected String mySubsId;
}
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SubscriptionsDstu2Test.class);
@Override
@ -37,7 +50,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
myDaoConfig.getInterceptors().add(interceptor);
}
private void sleepUntilPingCount(SimpleEchoSocket socket, int wantPingCount) throws InterruptedException {
private void sleepUntilPingCount(BaseSocket socket, int wantPingCount) throws InterruptedException {
ourLog.info("Entering loop");
for (long start = System.currentTimeMillis(), now = System.currentTimeMillis(); now - start <= 20000; now = System.currentTimeMillis()) {
ourLog.debug("Starting");
@ -90,7 +103,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
subs.setStatus(SubscriptionStatusEnum.REQUESTED);
IIdType id = ourClient.create().resource(subs).execute().getId();
subs.setId(id);
try {
subs.setStatus(SubscriptionStatusEnum.ACTIVE);
ourClient.update().resource(subs).execute();
@ -100,7 +113,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
}
try {
subs.setStatus((SubscriptionStatusEnum)null);
subs.setStatus((SubscriptionStatusEnum) null);
ourClient.update().resource(subs).execute();
fail();
} catch (UnprocessableEntityException e) {
@ -111,14 +124,13 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
ourClient.update().resource(subs).execute();
}
@Test
public void testCreateWithPopulatedButInvalidStatue() {
Subscription subs = new Subscription();
subs.getChannel().setType(SubscriptionChannelTypeEnum.WEBSOCKET);
subs.setCriteria("Observation?identifier=123");
subs.getStatusElement().setValue("aaaaa");
try {
ourClient.create().resource(subs).execute();
fail();
@ -149,6 +161,135 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
}
}
@Test
public void testSubscriptionDynamic() throws Exception {
myDaoConfig.setSubscriptionEnabled(true);
myDaoConfig.setSubscriptionPollDelay(0);
String methodName = "testSubscriptionDynamic";
Patient p = new Patient();
p.addName().addFamily(methodName);
IIdType pId = myPatientDao.create(p).getId().toUnqualifiedVersionless();
String criteria = "Observation?subject=Patient/" + pId.getIdPart();
DynamicEchoSocket socket = new DynamicEchoSocket(criteria, EncodingEnum.JSON);
WebSocketClient client = new WebSocketClient();
try {
client.start();
URI echoUri = new URI("ws://localhost:" + ourPort + "/websocket/dstu2");
client.connect(socket, echoUri, new ClientUpgradeRequest());
ourLog.info("Connecting to : {}", echoUri);
sleepUntilPingCount(socket, 1);
mySubscriptionDao.read(new IdDt("Subscription", socket.mySubsId));
Observation obs = new Observation();
obs.getSubject().setReference(pId);
obs.setStatus(ObservationStatusEnum.FINAL);
IIdType afterId1 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
obs = new Observation();
obs.getSubject().setReference(pId);
obs.setStatus(ObservationStatusEnum.FINAL);
IIdType afterId2 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
Thread.sleep(100);
sleepUntilPingCount(socket, 3);
obs = (Observation) socket.myReceived.get(0);
assertEquals(afterId1.getValue(), obs.getIdElement().toUnqualifiedVersionless().getValue());
obs = (Observation) socket.myReceived.get(1);
assertEquals(afterId2.getValue(), obs.getIdElement().toUnqualifiedVersionless().getValue());
obs = new Observation();
obs.getSubject().setReference(pId);
obs.setStatus(ObservationStatusEnum.FINAL);
IIdType afterId3 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
sleepUntilPingCount(socket, 4);
obs = (Observation) socket.myReceived.get(2);
assertEquals(afterId3.getValue(), obs.getIdElement().toUnqualifiedVersionless().getValue());
} finally {
try {
client.stop();
} catch (Exception e) {
ourLog.error("Failure", e);
fail(e.getMessage());
}
}
}
@Test
public void testSubscriptionDynamicXml() throws Exception {
myDaoConfig.setSubscriptionEnabled(true);
myDaoConfig.setSubscriptionPollDelay(0);
String methodName = "testSubscriptionDynamic";
Patient p = new Patient();
p.addName().addFamily(methodName);
IIdType pId = myPatientDao.create(p).getId().toUnqualifiedVersionless();
String criteria = "Observation?subject=Patient/" + pId.getIdPart() + "&_format=xml";
DynamicEchoSocket socket = new DynamicEchoSocket(criteria, EncodingEnum.XML);
WebSocketClient client = new WebSocketClient();
try {
client.start();
URI echoUri = new URI("ws://localhost:" + ourPort + "/websocket/dstu2");
client.connect(socket, echoUri, new ClientUpgradeRequest());
ourLog.info("Connecting to : {}", echoUri);
sleepUntilPingCount(socket, 1);
mySubscriptionDao.read(new IdDt("Subscription", socket.mySubsId));
Observation obs = new Observation();
obs.getSubject().setReference(pId);
obs.setStatus(ObservationStatusEnum.FINAL);
IIdType afterId1 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
obs = new Observation();
obs.getSubject().setReference(pId);
obs.setStatus(ObservationStatusEnum.FINAL);
IIdType afterId2 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
Thread.sleep(100);
sleepUntilPingCount(socket, 3);
obs = (Observation) socket.myReceived.get(0);
assertEquals(afterId1.getValue(), obs.getIdElement().toUnqualifiedVersionless().getValue());
obs = (Observation) socket.myReceived.get(1);
assertEquals(afterId2.getValue(), obs.getIdElement().toUnqualifiedVersionless().getValue());
obs = new Observation();
obs.getSubject().setReference(pId);
obs.setStatus(ObservationStatusEnum.FINAL);
IIdType afterId3 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
sleepUntilPingCount(socket, 4);
obs = (Observation) socket.myReceived.get(2);
assertEquals(afterId3.getValue(), obs.getIdElement().toUnqualifiedVersionless().getValue());
} finally {
try {
client.stop();
} catch (Exception e) {
ourLog.error("Failure", e);
fail(e.getMessage());
}
}
}
@Test
public void testSubscriptionSimple() throws Exception {
myDaoConfig.setSubscriptionEnabled(true);
@ -183,7 +324,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
SimpleEchoSocket socket = new SimpleEchoSocket(subsId);
try {
client.start();
URI echoUri = new URI("ws://localhost:" + ourPort + "/baseDstu2/websocket");
URI echoUri = new URI("ws://localhost:" + ourPort + "/websocket/dstu2");
ClientUpgradeRequest request = new ClientUpgradeRequest();
client.connect(socket, echoUri, request);
ourLog.info("Connecting to : {}", echoUri);
@ -196,7 +337,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
IIdType afterId3 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
sleepUntilPingCount(socket, 2);
} finally {
try {
client.stop();
@ -241,28 +382,15 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
* Basic Echo Client Socket
*/
@WebSocket(maxTextMessageSize = 64 * 1024)
public static class SimpleEchoSocket {
private String myError;
private boolean myGotBound;
private int myPingCount;
// @OnWebSocketClose
// public void onClose(int statusCode, String reason) {
// ourLog.info("Connection closed: {} - {}", statusCode, reason);
// this.session = null;
// this.closeLatch.countDown();
// }
private String mySubsId;
public class SimpleEchoSocket extends BaseSocket {
@SuppressWarnings("unused")
private Session session;
public SimpleEchoSocket(String theSubsId) {
mySubsId = theSubsId;
}
@OnWebSocketConnect
public void onConnect(Session session) {
ourLog.info("Got connect: {}", session);
@ -275,13 +403,13 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
ourLog.error("Failure", t);
}
}
@OnWebSocketMessage
public void onMessage(String theMsg) {
ourLog.info("Got msg: {}", theMsg);
if (theMsg.equals("bound " + mySubsId)) {
myGotBound = true;
} else if (myGotBound && theMsg.startsWith("ping " + mySubsId)){
} else if (myGotBound && theMsg.startsWith("ping " + mySubsId)) {
myPingCount++;
} else {
myError = "Unexpected message: " + theMsg;
@ -289,4 +417,51 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
}
}
/**
* Basic Echo Client Socket
*/
@WebSocket(maxTextMessageSize = 64 * 1024)
public class DynamicEchoSocket extends BaseSocket {
private List<IBaseResource> myReceived = new ArrayList<IBaseResource>();
@SuppressWarnings("unused")
private Session session;
private String myCriteria;
private EncodingEnum myEncoding;
public DynamicEchoSocket(String theCriteria, EncodingEnum theEncoding) {
myCriteria = theCriteria;
myEncoding = theEncoding;
}
@OnWebSocketConnect
public void onConnect(Session session) {
ourLog.info("Got connect: {}", session);
this.session = session;
try {
String sending = "bind " + myCriteria;
ourLog.info("Sending: {}", sending);
session.getRemote().sendString(sending);
} catch (Throwable t) {
ourLog.error("Failure", t);
}
}
@OnWebSocketMessage
public void onMessage(String theMsg) {
ourLog.info("Got msg: {}", theMsg);
if (theMsg.startsWith("bound ")) {
myGotBound = true;
mySubsId = (theMsg.substring("bound ".length()));
myPingCount++;
} else if (myGotBound && theMsg.startsWith("add " + mySubsId + "\n")) {
String text = theMsg.substring(("add " + mySubsId + "\n").length());
IBaseResource res = myEncoding.newParser(myFhirCtx).parseResource(text);
myReceived.add(res);
myPingCount++;
} else {
myError = "Unexpected message: " + theMsg;
}
}
}
}

7
hapi-fhir-jpaserver-uhnfhirtest/pom.xml
View File

@ -42,6 +42,13 @@
<type>war</type>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>1.3-SNAPSHOT</version>
<classifier>classes</classifier>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.phloc</groupId>

29
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/DerbyNetworkServer.java
View File

@ -1,5 +1,9 @@
package ca.uhn.fhirtest;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.Writer;
import org.apache.derby.drda.NetworkServerControl;
import org.springframework.beans.factory.DisposableBean;
import org.springframework.beans.factory.InitializingBean;
@ -22,7 +26,30 @@ public class DerbyNetworkServer implements InitializingBean, DisposableBean {
@Override
public void afterPropertiesSet() throws Exception {
server = new NetworkServerControl();
server.start (null);
Writer w = new Writer() {
@Override
public void write(char[] theCbuf, int theOff, int theLen) throws IOException {
ourLog.info("[DERBY] " + new String(theCbuf, theOff, theLen));
}
@Override
public void flush() throws IOException {
// nothing
}
@Override
public void close() throws IOException {
// nothing
}};
server.start (new PrintWriter(w));
}
public static void main(String[] args) throws Exception {
DerbyNetworkServer s = new DerbyNetworkServer();
s.afterPropertiesSet();
s.destroy();
}
}

12
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/TestRestfulServer.java
View File

@ -8,6 +8,7 @@ import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.lang3.StringUtils;
import org.springframework.context.ApplicationContext;
import org.springframework.context.support.ClassPathXmlApplicationContext;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.WebApplicationContext;
@ -35,7 +36,7 @@ public class TestRestfulServer extends RestfulServer {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestRestfulServer.class);
private ClassPathXmlApplicationContext myAppCtx;
private ApplicationContext myAppCtx;
@SuppressWarnings("unchecked")
@Override
@ -44,6 +45,7 @@ public class TestRestfulServer extends RestfulServer {
// Get the spring context from the web container (it's declared in web.xml)
WebApplicationContext parentAppCtx = ContextLoaderListener.getCurrentWebApplicationContext();
myAppCtx = (parentAppCtx);
// These two parmeters are also declared in web.xml
String implDesc = getInitParameter("ImplementationDescription");
@ -64,9 +66,6 @@ public class TestRestfulServer extends RestfulServer {
String baseUrlProperty;
switch (fhirVersionParam.trim().toUpperCase()) {
case "DSTU1": {
myAppCtx = new ClassPathXmlApplicationContext(new String[] {
"hapi-fhir-server-database-config-dstu1.xml",
"hapi-fhir-server-resourceproviders-dstu1.xml"}, parentAppCtx);
setFhirContext(FhirContext.forDstu1());
beans = myAppCtx.getBean("myResourceProvidersDstu1", List.class);
systemProviderDstu1 = myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class);
@ -79,11 +78,6 @@ public class TestRestfulServer extends RestfulServer {
break;
}
case "DSTU2": {
myAppCtx = new ClassPathXmlApplicationContext(new String[] {
"hapi-fhir-server-database-config-dstu2.xml",
"hapi-fhir-server-resourceproviders-dstu2.xml",
"fhir-spring-subscription-config-dstu2.xml"
}, parentAppCtx);
setFhirContext(FhirContext.forDstu2());
beans = myAppCtx.getBean("myResourceProvidersDstu2", List.class);
systemProviderDstu2 = myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);

27
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/mvc/SubscriptionPlaygroundController.java Normal file
View File

@ -0,0 +1,27 @@
package ca.uhn.fhirtest.mvc;
import javax.servlet.http.HttpServletRequest;
import org.springframework.ui.ModelMap;
import org.springframework.web.bind.annotation.RequestMapping;
import ca.uhn.fhir.to.BaseController;
import ca.uhn.fhir.to.model.HomeRequest;
@org.springframework.stereotype.Controller()
public class SubscriptionPlaygroundController extends BaseController {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SubscriptionPlaygroundController.class);
@RequestMapping(value = { "/subscriptions" })
public String subscriptionsHome(final HttpServletRequest theServletRequest, HomeRequest theRequest, final ModelMap theModel) {
addCommonParams(theServletRequest, theRequest, theModel);
theModel.put("notHome", true);
theModel.put("extraBreadcrumb", "Subscriptions");
ourLog.info(logPrefix(theModel) + "Displayed subscriptions playground page");
return "subscriptions";
}
}

4
hapi-fhir-jpaserver-uhnfhirtest/src/main/resources/hapi-fhir-server-database-config-dstu1.xml
View File

@ -51,9 +51,9 @@
</property>
</bean>
<bean id="myTxManager" class="org.springframework.orm.jpa.JpaTransactionManager">
<bean id="transactionManager" class="org.springframework.orm.jpa.JpaTransactionManager">
<property name="entityManagerFactory" ref="entityManagerFactory" />
</bean>
<tx:annotation-driven transaction-manager="myTxManager" />
<tx:annotation-driven transaction-manager="transactionManager" />
</beans>

4
hapi-fhir-jpaserver-uhnfhirtest/src/main/resources/hapi-fhir-server-database-config-dstu2.xml
View File

@ -38,9 +38,9 @@
</property>
</bean>
<bean id="myTxManager" class="org.springframework.orm.jpa.JpaTransactionManager">
<bean id="transactionManager" class="org.springframework.orm.jpa.JpaTransactionManager">
<property name="entityManagerFactory" ref="entityManagerFactory" />
</bean>
<tx:annotation-driven transaction-manager="myTxManager" />
<tx:annotation-driven transaction-manager="transactionManager" />
</beans>

7
hapi-fhir-jpaserver-uhnfhirtest/src/main/resources/logback.xml
View File

@ -43,6 +43,13 @@
<appender-ref ref="ACCESS" />
</logger>
<logger name="org.springframework.web.socket.handler.ExceptionWebSocketHandlerDecorator" additivity="false" level="debug">
<appender-ref ref="STDOUT" />
<appender-ref ref="FILE" />
</logger>
</appender>
<root level="INFO">
<appender-ref ref="FILE" />
</root>

16
hapi-fhir-jpaserver-uhnfhirtest/src/main/webapp/WEB-INF/hapi-fhir-tester-config-extracontrollers.xml Normal file
View File

@ -0,0 +1,16 @@
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:mvc="http://www.springframework.org/schema/mvc" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:tx="http://www.springframework.org/schema/tx" xmlns:context="http://www.springframework.org/schema/context" xmlns:security="http://www.springframework.org/schema/security"
xmlns:oauth="http://www.springframework.org/schema/security/oauth2"
xsi:schemaLocation="http://www.springframework.org/schema/security/oauth2 http://www.springframework.org/schema/security/spring-security-oauth2-2.0.xsd
http://www.springframework.org/schema/mvc http://www.springframework.org/schema/mvc/spring-mvc-3.2.xsd
http://www.springframework.org/schema/security http://www.springframework.org/schema/security/spring-security-3.1.xsd
http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-3.2.xsd
http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-3.2.xsd
http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context-3.2.xsd">
<context:component-scan base-package="ca.uhn.fhirtest.mvc" />
<mvc:annotation-driven />
</beans>

2
hapi-fhir-jpaserver-uhnfhirtest/src/main/webapp/WEB-INF/hapi-fhir-tester-config.xml
View File

@ -34,6 +34,8 @@
<property name="socketTimeout" value="10000"/>
</bean>
<context:component-scan base-package="ca.uhn.fhirtest.mvc" />
<mvc:interceptors>
<mvc:interceptor>
<mvc:mapping path="/**"/>

133
hapi-fhir-jpaserver-uhnfhirtest/src/main/webapp/WEB-INF/templates/subscriptions.html Normal file
View File

@ -0,0 +1,133 @@
<!DOCTYPE html>
<html lang="en">
<head th:include="tmpl-head :: head">
<title>RESTful Tester</title>
</head>
<body>
<form action="" method="get" id="outerForm">
<input type="hidden" id="serverId" name="serverId"
th:value="${serverId}" />
<div th:replace="tmpl-navbar-top :: top"></div>
<div class="container-fluid">
<div class="row">
<div th:replace="tmpl-navbar-left :: left"></div>
<div class="col-sm-9 col-sm-offset-3 col-md-9 col-md-offset-3 main">
<div th:replace="tmpl-banner :: banner"></div>
<!-- ********************************************************** -->
<!-- ** Subscriptions Playground ** -->
<!-- ********************************************************** -->
<div class="panel panel-default" th:if="${resourceName.empty}">
<div class="panel-heading">
<h3 class="panel-title">Subscriptions Playground</h3>
</div>
<div class="panel-body">
<div class="container-fluid">
<p>
This page is a test playground for WebSocket Subscriptions
</p>
</div>
</div>
</div>
<!-- Nav tabs -->
<ul class="nav nav-tabs" role="tablist">
<li role="presentation" class="active"><a href="#wss"
aria-controls="wss" role="tab" data-toggle="tab">Static
Websocket</a></li>
<li role="presentation"><a href="#wsd" aria-controls="wsd"
role="tab" data-toggle="tab">Dynamic Websocket</a></li>
</ul>
<!-- Tab panes -->
<div class="tab-content">
<div role="tabpanel" class="tab-pane active" id="wss">...1</div>
<!-- Dynamic WebSocket -->
<div role="tabpanel" class="tab-pane" id="wsd">
<script type="text/javascript">
function dwsCreate() {
try {
var socket = new WebSocket("ws://localhost:8888/websocket/dstu2");
alert('Socket Status: '+socket.readyState);
socket.onopen = function() {
alert("Opening Socket: " + socket.readyState);
socket.send("bind Observation?");
}
socket.onmessage = function(msg) {
alert("New message: " + msg);
}
socket.onerror = function(error) {
alert("error: " + error);
}
} catch (exception) {
alert('Error'+exception);
}
return false;
}
</script>
<div class="row">
<div class="col-sm-12">
Enter a criteria in the text box below and then click subscribe to
create a dynamic subscription and then display the results as they
arrive.
</div>
</div>
<div class="row" style="boorder-top: 10px;">
<div class="col-sm-7">
<div class="input-group">
<div class="input-group-addon">
Criteria
</div>
<input class="form-control" placeholder="e.g: Observation?patient=123" id="dws_criteria"/>
</div>
</div>
<div class="col-sm-3">
<button type="button" class="btn btn-default btn-primary btn-block" id="dws_create" onclick="dwsCreate();"><i class="glyphicon glyphicon-cog"></i> Subscribe</button>
</div>
</div>
</div>
</div>
<!-- Dynamic Subscription Results -->
<div class="panel panel-default">
<div class="panel-heading">Subscription Results</div>
<div class="panel-body">
<p>
This will be status...
</p>
</div>
<!-- List group -->
<ul class="list-group">
<li class="list-group-item">Cras justo odio</li>
<li class="list-group-item">Dapibus ac facilisis in</li>
<li class="list-group-item">Morbi leo risus</li>
<li class="list-group-item">Porta ac consectetur ac</li>
<li class="list-group-item">Vestibulum at eros</li>
</ul>
</div>
</div>
</div>
</div>
</div>
</form>
<div th:replace="tmpl-footer :: footer"></div>
</body>
</html>

6
hapi-fhir-jpaserver-uhnfhirtest/src/main/webapp/WEB-INF/web.xml
View File

@ -12,6 +12,11 @@
/WEB-INF/hapi-fhir-server-config.xml
/WEB-INF/hapi-fhir-tester-application-context.xml
/WEB-INF/hapi-fhir-tester-config.xml
classpath:/hapi-fhir-server-database-config-dstu1.xml
classpath:/hapi-fhir-server-database-config-dstu2.xml
classpath:hapi-fhir-server-resourceproviders-dstu1.xml
classpath:hapi-fhir-server-resourceproviders-dstu2.xml
classpath:fhir-spring-subscription-config-dstu2.xml
</param-value>
</context-param>
@ -25,6 +30,7 @@
<param-value>
/WEB-INF/hapi-fhir-tester-application-context.xml
/WEB-INF/hapi-fhir-tester-config.xml
classpath:fhir-spring-subscription-config-dstu2.xml
</param-value>
</init-param>
<load-on-startup>2</load-on-startup>

2
hapi-fhir-jpaserver-uhnfhirtest/src/test/java/ca/uhn/fhirtest/UhnFhirTestApp.java
View File

@ -67,7 +67,7 @@ public class UhnFhirTestApp {
client.create(p1);
List<IResource> resources = ctx.newJsonParser().parseBundle(IOUtils.toString(UhnFhirTestApp.class.getResourceAsStream("/bundle.json"))).toListOfResources();
client.transaction().withResources(resources).execute();
// client.transaction().withResources(resources).execute();
// for (int i = 0; i < 1000; i++) {
//

60
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/narrative/DefaultThymeleafNarrativeGeneratorTestDstu2.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.narrative;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
@ -53,7 +54,7 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
Patient value = new Patient();
value.addIdentifier().setSystem("urn:names").setValue("123456");
value.addName().addFamily("blow").addGiven("joe").addGiven((String)null).addGiven("john");
value.addName().addFamily("blow").addGiven("joe").addGiven((String) null).addGiven("john");
value.getAddressFirstRep().addLine("123 Fake Street").addLine("Unit 1");
value.getAddressFirstRep().setCity("Toronto").setState("ON").setCountry("Canada");
@ -67,12 +68,12 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
String title = myGen.generateTitle(value);
assertEquals("joe john BLOW (123456)", title);
// ourLog.info(title);
// ourLog.info(title);
value.getIdentifierFirstRep().setValue("FOO MRN 123");
title = myGen.generateTitle(value);
assertEquals("joe john BLOW (FOO MRN 123)", title);
// ourLog.info(title);
// ourLog.info(title);
}
@ -80,7 +81,7 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
public void testGenerateEncounter() throws DataFormatException {
Encounter enc = new Encounter();
enc.addIdentifier().setSystem("urn:visits").setValue( "1234567");
enc.addIdentifier().setSystem("urn:visits").setValue("1234567");
enc.setClassElement(EncounterClassEnum.AMBULATORY);
enc.setPeriod(new PeriodDt().setStart(new DateTimeDt("2001-01-02T11:11:00")));
enc.setType(ca.uhn.fhir.model.dstu2.valueset.EncounterTypeEnum.ANNUAL_DIABETES_MELLITUS_SCREENING);
@ -92,7 +93,6 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
}
@Test
public void testGenerateDiagnosticReport() throws DataFormatException {
DiagnosticReport value = new DiagnosticReport();
@ -127,9 +127,9 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
OperationOutcome oo = ourCtx.newXmlParser().parseResource(OperationOutcome.class, parse);
// String output = gen.generateTitle(oo);
// ourLog.info(output);
// assertEquals("Operation Outcome (2 issues)", output);
// String output = gen.generateTitle(oo);
// ourLog.info(output);
// assertEquals("Operation Outcome (2 issues)", output);
NarrativeDt narrative = new NarrativeDt();
myGen.generateNarrative(null, oo, narrative);
@ -137,11 +137,11 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
ourLog.info(output);
// oo = new OperationOutcome();
// oo.addIssue().setSeverity(IssueSeverityEnum.FATAL).setDetails("AA");
// output = gen.generateTitle(oo);
// ourLog.info(output);
// assertEquals("Operation Outcome (fatal)", output);
// oo = new OperationOutcome();
// oo.addIssue().setSeverity(IssueSeverityEnum.FATAL).setDetails("AA");
// output = gen.generateTitle(oo);
// ourLog.info(output);
// assertEquals("Operation Outcome (fatal)", output);
}
@ -193,27 +193,43 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
assertThat(output, StringContains.containsString("<div class=\"hapiHeaderText\"> Some &amp; Diagnostic Report </div>"));
}
@Test
public void testGenerateMedicationPrescription(){
public void testGenerateMedicationPrescription() {
MedicationOrder mp = new MedicationOrder();
mp.setId("12345");
Medication med = new Medication();
med.getCode().setText("ciproflaxin");
ResourceReferenceDt medRef = new ResourceReferenceDt(med);
mp.setMedication(medRef );
mp.setMedication(medRef);
mp.setStatus(MedicationOrderStatusEnum.ACTIVE);
mp.setDateWritten(new DateTimeDt("2014-09-01"));
NarrativeDt narrative = new NarrativeDt();
myGen.generateNarrative(mp, narrative);
assertTrue("Expected medication name of ciprofloaxin within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ciprofloaxin")>-1);
assertTrue("Expected string status of ACTIVE within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ACTIVE")>-1);
assertTrue("Expected medication name of ciprofloaxin within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ciprofloaxin") > -1);
assertTrue("Expected string status of ACTIVE within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ACTIVE") > -1);
String title = myGen.generateTitle(mp);
assertEquals("ciprofloaxin", title);
}
@Test
public void testGenerateMedication() {
Medication med = new Medication();
med.getCode().setText("ciproflaxin");
NarrativeDt narrative = new NarrativeDt();
myGen.generateNarrative(med, narrative);
String string = narrative.getDiv().toString();
assertThat(string, containsString("ciproflaxin"));
String title = myGen.generateTitle(med);
assertEquals("ciproflaxin", title);
}
}

428
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java
View File

@ -92,63 +92,6 @@ public class XmlParserDstu2Test {
private static final FhirContext ourCtx = FhirContext.forDstu2();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserDstu2Test.class);
@Test
public void testParseBundleWithResourceId() {
//@formatter:off
String input = "<Bundle xmlns=\"http://hl7.org/fhir\">"
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"3\"/><lastUpdated value=\"2015-09-11T23:35:43.273-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"2\"/><lastUpdated value=\"2015-09-11T23:35:42.849-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"1\"/><lastUpdated value=\"2015-09-11T23:35:42.295-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+ "</Bundle>\n";
//@formatter:on
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, input);
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/3", bundle.getEntry().get(0).getResource().getId().getValue());
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/2", bundle.getEntry().get(1).getResource().getId().getValue());
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/1", bundle.getEntry().get(2).getResource().getId().getValue());
}
@Test
public void testEncodeReferenceUsingUnqualifiedResourceWorksCorrectly() {
Patient patient = new Patient();
patient.setId("phitcc_pat_normal");
patient.addName().addGiven("Patty").setUse(NameUseEnum.NICKNAME);
patient.addTelecom().setSystem(ContactPointSystemEnum.EMAIL).setValue("patpain@ehealthinnovation.org");
patient.setGender(AdministrativeGenderEnum.FEMALE);
patient.setBirthDate(new DateDt("2001-10-13"));
DateTimeDt obsEffectiveTime = new DateTimeDt("2015-04-11T12:22:01-04:00");
Observation obsParent = new Observation();
obsParent.setId("phitcc_obs_bp_parent");
obsParent.getSubject().setResource(patient);
obsParent.setStatus(ObservationStatusEnum.FINAL);
obsParent.setEffective(obsEffectiveTime);
Observation obsSystolic = new Observation();
obsSystolic.setId("phitcc_obs_bp_dia");
obsSystolic.getSubject().setResource(patient);
obsSystolic.setEffective(obsEffectiveTime);
obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsSystolic));
Observation obsDiastolic = new Observation();
obsDiastolic.setId("phitcc_obs_bp_dia");
obsDiastolic.getSubject().setResource(patient);
obsDiastolic.setEffective(obsEffectiveTime);
obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsDiastolic));
String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(obsParent);
ourLog.info(str);
assertThat(str, containsString("<reference value=\"Patient/phitcc_pat_normal\"/>"));
assertThat(str, containsString("<reference value=\"Observation/phitcc_obs_bp_dia\"/>"));
}
@Test
public void testBundleWithBinary() {
//@formatter:off
@ -231,86 +174,6 @@ public class XmlParserDstu2Test {
assertTrue(parsed.getEntries().get(0).getResource().getId().isEmpty());
}
/**
* See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
*/
@Test
public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
IParser xmlParser = ourCtx.newXmlParser();
String input = IOUtils.toString(XmlParser.class.getResourceAsStream("/medicationstatement_invalidelement.xml"));
MedicationStatement ms = xmlParser.parseResource(MedicationStatement.class, input);
SimpleQuantityDt q = (SimpleQuantityDt) ms.getDosage().get(0).getQuantity();
assertEquals("1", q.getValueElement().getValueAsString());
String output = xmlParser.encodeResourceToString(ms);
assertThat(output, containsString("<quantityQuantity><value value=\"1\"/></quantityQuantity>"));
}
/**
* See #216
*/
@Test
public void testEncodeAndParseIdentifierDstu2() {
IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
Patient patient = new Patient();
patient.addIdentifier().setSystem("SYS").setValue("VAL").setType(IdentifierTypeCodesEnum.MR);
String out = xmlParser.encodeResourceToString(patient);
ourLog.info(out);
//@formatter:off
assertThat(out, stringContainsInOrder("<identifier>",
"<type>",
"<coding>",
"<system value=\"http://hl7.org/fhir/v2/0203\"/>",
"<code value=\"MR\"/>",
"</coding>",
"</type>",
"<system value=\"SYS\"/>",
"<value value=\"VAL\"/>",
"</identifier>"));
//@formatter:on
patient = ourCtx.newXmlParser().parseResource(Patient.class, out);
assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), contains(IdentifierTypeCodesEnum.MR));
assertEquals("http://hl7.org/fhir/v2/0203", patient.getIdentifier().get(0).getType().getCoding().get(0).getSystem());
assertEquals("MR", patient.getIdentifier().get(0).getType().getCoding().get(0).getCode());
}
/**
* See #216
*/
@Test
public void testParseMalformedIdentifierDstu2() {
// This was changed from 0.5 to 1.0.0
//@formatter:off
String out = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
" <identifier>\n" +
" <type value=\"MRN\"/>\n" +
" <system value=\"SYS\"/>\n" +
" <value value=\"VAL\"/>\n" +
" </identifier>\n" +
"</Patient>";
//@formatter:on
IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
IParser p = ourCtx.newXmlParser();
p.setParserErrorHandler(errorHandler);
Patient patient = p.parseResource(Patient.class, out);
assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), IsEmptyCollection.empty());
ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
verify(errorHandler, times(1)).unknownAttribute(any(IParseLocation.class), capt.capture());
assertEquals("value", capt.getValue());
}
@Test
public void testEncodeAndParseContained() {
IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
@ -448,9 +311,11 @@ public class XmlParserDstu2Test {
String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
assertThat(enc, containsString("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://example.com/extensions#someext\"><valueDateTime value=\"2011-01-02T11:13:15\"/></extension>"));
assertThat(enc, containsString("<modifierExtension url=\"http://example.com/extensions#modext\"><valueDate value=\"1995-01-02\"/></modifierExtension>"));
assertThat(enc, containsString("<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value2\"/></extension></extension>"));
assertThat(enc, containsString(
"<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value2\"/></extension></extension>"));
assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
assertThat(enc, containsString("<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
assertThat(enc, containsString(
"<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
/*
* Now parse this back
@ -490,6 +355,38 @@ public class XmlParserDstu2Test {
}
/**
* See #216
*/
@Test
public void testEncodeAndParseIdentifierDstu2() {
IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
Patient patient = new Patient();
patient.addIdentifier().setSystem("SYS").setValue("VAL").setType(IdentifierTypeCodesEnum.MR);
String out = xmlParser.encodeResourceToString(patient);
ourLog.info(out);
//@formatter:off
assertThat(out, stringContainsInOrder("<identifier>",
"<type>",
"<coding>",
"<system value=\"http://hl7.org/fhir/v2/0203\"/>",
"<code value=\"MR\"/>",
"</coding>",
"</type>",
"<system value=\"SYS\"/>",
"<value value=\"VAL\"/>",
"</identifier>"));
//@formatter:on
patient = ourCtx.newXmlParser().parseResource(Patient.class, out);
assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), contains(IdentifierTypeCodesEnum.MR));
assertEquals("http://hl7.org/fhir/v2/0203", patient.getIdentifier().get(0).getType().getCoding().get(0).getSystem());
assertEquals("MR", patient.getIdentifier().get(0).getType().getCoding().get(0).getCode());
}
@Test
public void testEncodeAndParseMetaProfileAndTags() {
Patient p = new Patient();
@ -595,6 +492,38 @@ public class XmlParserDstu2Test {
assertEquals(new Tag("scheme2", "term2", "label2"), tagList.get(1));
}
/**
* Test for #233
*/
@Test
public void testEncodeAndParseProfiledDatatype() {
MedicationOrder mo = new MedicationOrder();
mo.addDosageInstruction().getTiming().getRepeat().setBounds(new DurationDt().setCode("code"));
String out = ourCtx.newXmlParser().encodeResourceToString(mo);
ourLog.info(out);
assertThat(out, containsString("</boundsQuantity>"));
mo = ourCtx.newXmlParser().parseResource(MedicationOrder.class, out);
DurationDt duration = (DurationDt) mo.getDosageInstruction().get(0).getTiming().getRepeat().getBounds();
assertEquals("code", duration.getCode());
}
/**
* See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
*/
@Test
public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
IParser xmlParser = ourCtx.newXmlParser();
String input = IOUtils.toString(XmlParser.class.getResourceAsStream("/medicationstatement_invalidelement.xml"));
MedicationStatement ms = xmlParser.parseResource(MedicationStatement.class, input);
SimpleQuantityDt q = (SimpleQuantityDt) ms.getDosage().get(0).getQuantity();
assertEquals("1", q.getValueElement().getValueAsString());
String output = xmlParser.encodeResourceToString(ms);
assertThat(output, containsString("<quantityQuantity><value value=\"1\"/></quantityQuantity>"));
}
@Test
public void testEncodeAndParseSecurityLabels() {
Patient p = new Patient();
@ -791,12 +720,14 @@ public class XmlParserDstu2Test {
ourLog.info(encoded);
// @formatter:on
assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
assertThat(encoded,
stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
//@formatter:off
}
/**
* See #113
*/
@ -824,12 +755,13 @@ public class XmlParserDstu2Test {
ourLog.info(encoded);
//@formatter:on
assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"1\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#1\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
assertThat(encoded,
stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"1\"/>", "<code>", "<coding>",
"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#1\"/>",
"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
//@formatter:off
}
/**
* See #113
*/
@ -861,8 +793,10 @@ public class XmlParserDstu2Test {
ourLog.info(encoded);
//@formatter:on
assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
assertThat(encoded,
stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
//@formatter:off
}
@ -893,7 +827,6 @@ public class XmlParserDstu2Test {
assertThat(encoded, (containsString("BARFOO")));
}
/**
* #158
@ -911,6 +844,7 @@ public class XmlParserDstu2Test {
assertThat(encoded, not(containsString("tag")));
}
/**
* #158
*/
@ -929,7 +863,6 @@ public class XmlParserDstu2Test {
assertThat(encoded, not(containsString("Label")));
}
@Test
public void testEncodeExtensionWithResourceContent() {
IParser parser = ourCtx.newXmlParser();
@ -951,6 +884,7 @@ public class XmlParserDstu2Test {
}
@Test
public void testEncodeNarrativeSuppressed() {
Patient patient = new Patient();
@ -1010,7 +944,44 @@ public class XmlParserDstu2Test {
}
@Test
public void testEncodeReferenceUsingUnqualifiedResourceWorksCorrectly() {
Patient patient = new Patient();
patient.setId("phitcc_pat_normal");
patient.addName().addGiven("Patty").setUse(NameUseEnum.NICKNAME);
patient.addTelecom().setSystem(ContactPointSystemEnum.EMAIL).setValue("patpain@ehealthinnovation.org");
patient.setGender(AdministrativeGenderEnum.FEMALE);
patient.setBirthDate(new DateDt("2001-10-13"));
DateTimeDt obsEffectiveTime = new DateTimeDt("2015-04-11T12:22:01-04:00");
Observation obsParent = new Observation();
obsParent.setId("phitcc_obs_bp_parent");
obsParent.getSubject().setResource(patient);
obsParent.setStatus(ObservationStatusEnum.FINAL);
obsParent.setEffective(obsEffectiveTime);
Observation obsSystolic = new Observation();
obsSystolic.setId("phitcc_obs_bp_dia");
obsSystolic.getSubject().setResource(patient);
obsSystolic.setEffective(obsEffectiveTime);
obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsSystolic));
Observation obsDiastolic = new Observation();
obsDiastolic.setId("phitcc_obs_bp_dia");
obsDiastolic.getSubject().setResource(patient);
obsDiastolic.setEffective(obsEffectiveTime);
obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsDiastolic));
String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(obsParent);
ourLog.info(str);
assertThat(str, containsString("<reference value=\"Patient/phitcc_pat_normal\"/>"));
assertThat(str, containsString("<reference value=\"Observation/phitcc_obs_bp_dia\"/>"));
}
@Test
public void testEncodeSummary() {
Patient patient = new Patient();
@ -1052,6 +1023,57 @@ public class XmlParserDstu2Test {
assertThat(encoded, not(containsString("maritalStatus")));
}
@Test
public void testEncodeWithEncodeElements() throws Exception {
String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
Patient patient = new Patient();
patient.addName().addFamily("FAMILY");
patient.addAddress().addLine("LINE1");
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
bundle.setTotal(100);
bundle.addEntry().setResource(patient);
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, not(containsString("total")));
assertThat(out, (containsString("Patient")));
assertThat(out, (containsString("name")));
assertThat(out, not(containsString("address")));
}
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, (containsString("total")));
assertThat(out, (containsString("Patient")));
assertThat(out, (containsString("name")));
assertThat(out, not(containsString("address")));
}
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, (containsString("total")));
assertThat(out, (containsString("Patient")));
assertThat(out, (containsString("name")));
assertThat(out, (containsString("address")));
}
}
@Test
public void testMoreExtensions() throws Exception {
@ -1105,7 +1127,7 @@ public class XmlParserDstu2Test {
assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
assertThat(enc, containsString("<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
}
@Test
public void testOmitResourceId() {
Patient p = new Patient();
@ -1116,57 +1138,6 @@ public class XmlParserDstu2Test {
assertThat(ourCtx.newXmlParser().setOmitResourceId(true).encodeResourceToString(p), containsString("ABC"));
assertThat(ourCtx.newXmlParser().setOmitResourceId(true).encodeResourceToString(p), not(containsString("123")));
}
@Test
public void testEncodeWithEncodeElements() throws Exception {
String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
Patient patient = new Patient();
patient.addName().addFamily("FAMILY");
patient.addAddress().addLine("LINE1");
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
bundle.setTotal(100);
bundle.addEntry().setResource(patient);
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, not(containsString("total")));
assertThat(out, (containsString("Patient")));
assertThat(out, (containsString("name")));
assertThat(out, not(containsString("address")));
}
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, (containsString("total")));
assertThat(out, (containsString("Patient")));
assertThat(out, (containsString("name")));
assertThat(out, not(containsString("address")));
}
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, (containsString("total")));
assertThat(out, (containsString("Patient")));
assertThat(out, (containsString("name")));
assertThat(out, (containsString("address")));
}
}
@Test
public void testParseAndEncodeBundle() throws Exception {
@ -1202,7 +1173,7 @@ public class XmlParserDstu2Test {
assertTrue(d.toString(), d.identical());
}
@Test
public void testParseAndEncodeBundleNewStyle() throws Exception {
String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
@ -1239,7 +1210,8 @@ public class XmlParserDstu2Test {
assertTrue(d.toString(), d.identical());
}
@Test
public void testParseAndEncodeExtensionOnResourceReference() {
//@formatter:off
@ -1642,6 +1614,22 @@ public class XmlParserDstu2Test {
assertEquals("Observation", link.getUrl());
}
@Test
public void testParseBundleWithResourceId() {
//@formatter:off
String input = "<Bundle xmlns=\"http://hl7.org/fhir\">"
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"3\"/><lastUpdated value=\"2015-09-11T23:35:43.273-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"2\"/><lastUpdated value=\"2015-09-11T23:35:42.849-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"1\"/><lastUpdated value=\"2015-09-11T23:35:42.295-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+ "</Bundle>\n";
//@formatter:on
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, input);
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/3", bundle.getEntry().get(0).getResource().getId().getValue());
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/2", bundle.getEntry().get(1).getResource().getId().getValue());
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/1", bundle.getEntry().get(2).getResource().getId().getValue());
}
/**
* see #144 and #146
*/
@ -1710,6 +1698,38 @@ public class XmlParserDstu2Test {
}
/**
* See #216
*/
@Test
public void testParseMalformedIdentifierDstu2() {
// This was changed from 0.5 to 1.0.0
//@formatter:off
String out = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
" <identifier>\n" +
" <type value=\"MRN\"/>\n" +
" <system value=\"SYS\"/>\n" +
" <value value=\"VAL\"/>\n" +
" </identifier>\n" +
"</Patient>";
//@formatter:on
IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
IParser p = ourCtx.newXmlParser();
p.setParserErrorHandler(errorHandler);
Patient patient = p.parseResource(Patient.class, out);
assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), IsEmptyCollection.empty());
ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
verify(errorHandler, times(1)).unknownAttribute(any(IParseLocation.class), capt.capture());
assertEquals("value", capt.getValue());
}
@Test
public void testParseMetadata() throws Exception {
//@formatter:off

141
hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/DefaultProfileValidationSupport.java
View File

@ -1,5 +1,7 @@
package ca.uhn.fhir.validation;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
@ -20,67 +22,102 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
public class DefaultProfileValidationSupport implements IValidationSupport {
private Map<String, ValueSet> myDefaultValueSets;
@Override
public boolean isCodeSystemSupported(String theSystem) {
return false;
}
@SuppressWarnings("unchecked")
@Override
public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
if (theUri.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
return (T) FhirInstanceValidator.loadProfileOrReturnNull(null, FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext), theUri.substring("http://hl7.org/fhir/StructureDefinition/".length()));
}
if (theUri.startsWith("http://hl7.org/fhir/ValueSet/")) {
Map<String, ValueSet> defaultValueSets = myDefaultValueSets;
if (defaultValueSets == null) {
InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/valuesets.xml");
if (valuesetText == null) {
return null;
}
InputStreamReader reader;
try {
reader = new InputStreamReader(valuesetText, "UTF-8");
} catch (UnsupportedEncodingException e) {
// Shouldn't happen!
throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
}
defaultValueSets = new HashMap<String, ValueSet>();
FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
for (BundleEntryComponent next : bundle.getEntry()) {
IdType nextId = new IdType(next.getFullUrl());
if (nextId.isEmpty() || !nextId.getValue().startsWith("http://hl7.org/fhir/ValueSet/")) {
continue;
}
defaultValueSets.put(nextId.toVersionless().getValue(), (ValueSet) next.getResource());
}
myDefaultValueSets = defaultValueSets;
}
return (T) defaultValueSets.get(theUri);
}
return null;
}
private Map<String, ValueSet> myDefaultValueSets;
private Map<String, ValueSet> myCodeSystems;
@Override
public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
return false;
}
@SuppressWarnings("unchecked")
@Override
public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
if (theUri.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
return (T) FhirInstanceValidator.loadProfileOrReturnNull(null, FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext), theUri.substring("http://hl7.org/fhir/StructureDefinition/".length()));
}
if (theUri.startsWith("http://hl7.org/fhir/ValueSet/")) {
Map<String, ValueSet> defaultValueSets = myDefaultValueSets;
if (defaultValueSets == null) {
InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/valuesets.xml");
if (valuesetText == null) {
return null;
}
InputStreamReader reader;
try {
reader = new InputStreamReader(valuesetText, "UTF-8");
} catch (UnsupportedEncodingException e) {
// Shouldn't happen!
throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
}
defaultValueSets = new HashMap<String, ValueSet>();
FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
for (BundleEntryComponent next : bundle.getEntry()) {
IdType nextId = new IdType(next.getFullUrl());
if (nextId.isEmpty() || !nextId.getValue().startsWith("http://hl7.org/fhir/ValueSet/")) {
continue;
}
defaultValueSets.put(nextId.toVersionless().getValue(), (ValueSet) next.getResource());
}
myDefaultValueSets = defaultValueSets;
}
return (T) defaultValueSets.get(theUri);
}
return null;
}
@Override
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
return new CodeValidationResult(IssueSeverity.INFORMATION, "Unknown code: " + theCodeSystem + " / " + theCode);
}
@Override
public ValueSet fetchCodeSystem(String theSystem) {
return null;
public ValueSet fetchCodeSystem(FhirContext theContext, String theSystem) {
Map<String, ValueSet> codeSystems = myCodeSystems;
if (codeSystems == null) {
codeSystems = new HashMap<String, ValueSet>();
loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/valuesets.xml");
loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/v2-tables.xml");
loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml");
myCodeSystems = codeSystems;
}
return codeSystems.get(theSystem);
}
private void loadCodeSystems(FhirContext theContext, Map<String, ValueSet> codeSystems, String file) {
InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(file);
if (valuesetText != null) {
InputStreamReader reader;
try {
reader = new InputStreamReader(valuesetText, "UTF-8");
} catch (UnsupportedEncodingException e) {
// Shouldn't happen!
throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
}
FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
for (BundleEntryComponent next : bundle.getEntry()) {
ValueSet nextValueSet = (ValueSet) next.getResource();
String system = nextValueSet.getCodeSystem().getSystem();
if (isNotBlank(system)) {
codeSystems.put(system, nextValueSet);
}
}
}
}
@Override
public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
return null;
}

8
hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/FhirInstanceValidator.java
View File

@ -269,7 +269,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
@Override
public ValueSetExpansionComponent expandVS(ConceptSetComponent theInc) {
return myValidationSupport.expandValueSet(theInc);
return myValidationSupport.expandValueSet(myCtx, theInc);
}
@Override
@ -282,7 +282,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
if (myValidationSupport == null) {
return null;
} else {
return myValidationSupport.fetchCodeSystem(theSystem);
return myValidationSupport.fetchCodeSystem(myCtx, theSystem);
}
}
@ -335,13 +335,13 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
if (myValidationSupport == null) {
return false;
} else {
return myValidationSupport.isCodeSystemSupported(theSystem);
return myValidationSupport.isCodeSystemSupported(myCtx, theSystem);
}
}
@Override
public ValidationResult validateCode(String theSystem, String theCode, String theDisplay) {
CodeValidationResult result = myValidationSupport.validateCode(theSystem, theCode, theDisplay);
CodeValidationResult result = myValidationSupport.validateCode(myCtx, theSystem, theCode, theDisplay);
if (result == null) {
return null;
}

8
hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/IValidationSupport.java
View File

@ -18,7 +18,7 @@ public interface IValidationSupport {
* The portion to include
* @return The expansion
*/
ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude);
ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude);
/**
* Fetch a code system by ID
@ -27,7 +27,7 @@ public interface IValidationSupport {
* The code system
* @return The valueset (must not be null, but can be an empty ValueSet)
*/
ValueSet fetchCodeSystem(String theSystem);
ValueSet fetchCodeSystem(FhirContext theContext, String theSystem);
/**
* Loads a resource needed by the validation (a StructureDefinition, or a
@ -53,7 +53,7 @@ public interface IValidationSupport {
* @return Returns <code>true</code> if codes in the given code system can be
* validated
*/
boolean isCodeSystemSupported(String theSystem);
boolean isCodeSystemSupported(FhirContext theContext, String theSystem);
/**
* Validates that the given code exists and if possible returns a display
@ -68,7 +68,7 @@ public interface IValidationSupport {
* The display name, if it should also be validated
* @return Returns a validation result object
*/
CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay);
CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay);
public class CodeValidationResult {
private ConceptDefinitionComponent definition;

24
hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/ValidationSupportChain.java
View File

@ -24,19 +24,19 @@ public class ValidationSupportChain implements IValidationSupport {
}
@Override
public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
for (IValidationSupport next : myChain) {
if (next.isCodeSystemSupported(theInclude.getSystem())) {
return next.expandValueSet(theInclude);
if (next.isCodeSystemSupported(theCtx, theInclude.getSystem())) {
return next.expandValueSet(theCtx, theInclude);
}
}
return myChain.get(0).expandValueSet(theInclude);
return myChain.get(0).expandValueSet(theCtx, theInclude);
}
@Override
public ValueSet fetchCodeSystem(String theSystem) {
public ValueSet fetchCodeSystem(FhirContext theCtx, String theSystem) {
for (IValidationSupport next : myChain) {
ValueSet retVal = next.fetchCodeSystem(theSystem);
ValueSet retVal = next.fetchCodeSystem(theCtx, theSystem);
if (retVal != null) {
return retVal;
}
@ -56,9 +56,9 @@ public class ValidationSupportChain implements IValidationSupport {
}
@Override
public boolean isCodeSystemSupported(String theSystem) {
public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
for (IValidationSupport next : myChain) {
if (next.isCodeSystemSupported(theSystem)) {
if (next.isCodeSystemSupported(theCtx, theSystem)) {
return true;
}
}
@ -66,13 +66,13 @@ public class ValidationSupportChain implements IValidationSupport {
}
@Override
public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
for (IValidationSupport next : myChain) {
if (next.isCodeSystemSupported(theCodeSystem)) {
return next.validateCode(theCodeSystem, theCode, theDisplay);
if (next.isCodeSystemSupported(theCtx, theCodeSystem)) {
return next.validateCode(theCtx, theCodeSystem, theCode, theDisplay);
}
}
return myChain.get(0).validateCode(theCodeSystem, theCode, theDisplay);
return myChain.get(0).validateCode(theCtx, theCodeSystem, theCode, theDisplay);
}
}

55
hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/validation/FhirInstanceValidatorTest.java
View File

@ -2,7 +2,9 @@ package ca.uhn.fhir.validation;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.greaterThan;
import static org.junit.Assert.*;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
@ -16,6 +18,7 @@ import org.apache.commons.io.IOUtils;
import org.hl7.fhir.instance.model.CodeType;
import org.hl7.fhir.instance.model.Observation;
import org.hl7.fhir.instance.model.Observation.ObservationStatus;
import org.hl7.fhir.instance.model.Patient;
import org.hl7.fhir.instance.model.StringType;
import org.hl7.fhir.instance.model.ValueSet;
import org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent;
@ -61,19 +64,19 @@ public class FhirInstanceValidatorTest {
myValidConcepts = new ArrayList<String>();
myMockSupport = mock(IValidationSupport.class);
when(myMockSupport.expandValueSet(any(ConceptSetComponent.class))).thenAnswer(new Answer<ValueSetExpansionComponent>() {
when(myMockSupport.expandValueSet(any(FhirContext.class), any(ConceptSetComponent.class))).thenAnswer(new Answer<ValueSetExpansionComponent>() {
@Override
public ValueSetExpansionComponent answer(InvocationOnMock theInvocation) throws Throwable {
ConceptSetComponent arg = (ConceptSetComponent)theInvocation.getArguments()[0];
ValueSetExpansionComponent retVal = mySupportedCodeSystemsForExpansion.get(arg.getSystem());
if (retVal == null) {
retVal = myDefaultValidationSupport.expandValueSet(arg);
retVal = myDefaultValidationSupport.expandValueSet(any(FhirContext.class), arg);
}
ourLog.info("expandValueSet({}) : {}", new Object[] { theInvocation.getArguments()[0], retVal });
return retVal;
}
});
when(myMockSupport.isCodeSystemSupported(any(String.class))).thenAnswer(new Answer<Boolean>() {
when(myMockSupport.isCodeSystemSupported(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<Boolean>() {
@Override
public Boolean answer(InvocationOnMock theInvocation) throws Throwable {
boolean retVal = mySupportedCodeSystemsForExpansion.containsKey(theInvocation.getArguments()[0]);
@ -93,28 +96,29 @@ public class FhirInstanceValidatorTest {
return retVal;
}
});
when(myMockSupport.validateCode(any(String.class), any(String.class), any(String.class)))
when(myMockSupport.validateCode(any(FhirContext.class), any(String.class), any(String.class), any(String.class)))
.thenAnswer(new Answer<CodeValidationResult>() {
@Override
public CodeValidationResult answer(InvocationOnMock theInvocation) throws Throwable {
String system = (String) theInvocation.getArguments()[0];
String code = (String) theInvocation.getArguments()[1];
FhirContext ctx = (FhirContext) theInvocation.getArguments()[0];
String system = (String) theInvocation.getArguments()[1];
String code = (String) theInvocation.getArguments()[2];
CodeValidationResult retVal;
if (myValidConcepts.contains(system + "___" + code)) {
retVal = new CodeValidationResult(new ConceptDefinitionComponent(new CodeType(code)));
} else {
retVal = myDefaultValidationSupport.validateCode(system, code, (String) theInvocation.getArguments()[2]);
retVal = myDefaultValidationSupport.validateCode(ctx, system, code, (String) theInvocation.getArguments()[2]);
}
ourLog.info("validateCode({}, {}, {}) : {}",
new Object[] { system, code, (String) theInvocation.getArguments()[2], retVal });
return retVal;
}
});
when(myMockSupport.fetchCodeSystem(any(String.class))).thenAnswer(new Answer<ValueSet>() {
when(myMockSupport.fetchCodeSystem(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<ValueSet>() {
@Override
public ValueSet answer(InvocationOnMock theInvocation) throws Throwable {
ValueSet retVal = myDefaultValidationSupport.fetchCodeSystem((String) theInvocation.getArguments()[0]);
ourLog.info("fetchCodeSystem({}) : {}", new Object[] { (String) theInvocation.getArguments()[0], retVal });
ValueSet retVal = myDefaultValidationSupport.fetchCodeSystem((FhirContext) theInvocation.getArguments()[0],(String) theInvocation.getArguments()[1]);
ourLog.info("fetchCodeSystem({}) : {}", new Object[] { (String) theInvocation.getArguments()[1], retVal });
return retVal;
}
});
@ -306,6 +310,29 @@ public class FhirInstanceValidatorTest {
output.getMessages().get(0).getMessage());
}
@Test
public void testValidateResourceWithValuesetExpansion() {
Patient patient = new Patient();
patient.addIdentifier().setSystem("http://system").setValue("12345").getType().addCoding().setSystem("foo").setCode("bar");
ValidationResult output = myVal.validateWithResult(patient);
List<SingleValidationMessage> all = logResultsAndReturnAll(output);
assertEquals(1, all.size());
assertEquals("/f:Patient/f:identifier/f:type", all.get(0).getLocationString());
assertEquals("None of the codes are in the expected value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type)", all.get(0).getMessage());
assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
patient = new Patient();
patient.addIdentifier().setSystem("http://system").setValue("12345").getType().addCoding().setSystem("http://hl7.org/fhir/v2/0203").setCode("MR");
output = myVal.validateWithResult(patient);
all = logResultsAndReturnAll(output);
assertEquals(0, all.size());
}
@Test
public void testValidateResourceWithExampleBindingCodeValidationFailing() {
Observation input = new Observation();
@ -353,7 +380,11 @@ public class FhirInstanceValidatorTest {
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertEquals(errors.toString(), 0, errors.size());
assertEquals(errors.toString(), 1, errors.size());
assertEquals("Unable to validate code \"1234\" in code system \"http://loinc.org\"", errors.get(0).getMessage());
assertEquals(ResultSeverityEnum.WARNING, errors.get(0).getSeverity());
}
@Test

15
hapi-fhir-testpage-overlay/pom.xml
View File

@ -44,11 +44,7 @@
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>1.3-SNAPSHOT</version>
</dependency>
<!--<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dev</artifactId>
<version>0.9</version>
</dependency>-->
<!--<dependency> <groupId>ca.uhn.hapi.fhir</groupId> <artifactId>hapi-fhir-structures-dev</artifactId> <version>0.9</version> </dependency> -->
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
@ -71,7 +67,7 @@
<artifactId>logback-classic</artifactId>
<scope>test</scope>
</dependency>
<!-- Database -->
<dependency>
<groupId>commons-dbcp</groupId>
@ -202,6 +198,13 @@
<skip>false</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<attachClasses>true</attachClasses>
</configuration>
</plugin>
</plugins>
</build>

637
hapi-fhir-testpage-overlay/src/main/java/ca/uhn/fhir/to/BaseController.java Normal file
View File

@ -0,0 +1,637 @@
package ca.uhn.fhir.to;
import static org.apache.commons.lang3.StringUtils.defaultString;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.Header;
import org.apache.http.HttpEntity;
import org.apache.http.HttpEntityEnclosingRequest;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpRequestBase;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.HttpEntityWrapper;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.ui.ModelMap;
import org.thymeleaf.TemplateEngine;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.BundleEntry;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu.resource.Conformance;
import ca.uhn.fhir.model.dstu.resource.Conformance.Rest;
import ca.uhn.fhir.model.primitive.DecimalDt;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.rest.client.GenericClient;
import ca.uhn.fhir.rest.client.IClientInterceptor;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.to.model.HomeRequest;
import ca.uhn.fhir.util.ExtensionConstants;
public class BaseController {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseController.class);
static final String PARAM_RESOURCE = "resource";
static final String RESOURCE_COUNT_EXT_URL = "http://hl7api.sourceforge.net/hapi-fhir/res/extdefs.html#resourceCount";
@Autowired
protected TesterConfig myConfig;
private Map<FhirVersionEnum, FhirContext> myContexts = new HashMap<FhirVersionEnum, FhirContext>();
private List<String> myFilterHeaders;
@Autowired
private TemplateEngine myTemplateEngine;
public BaseController() {
super();
}
protected IResource addCommonParams(HttpServletRequest theServletRequest, final HomeRequest theRequest, final ModelMap theModel) {
if (myConfig.getDebugTemplatesMode()) {
myTemplateEngine.getCacheManager().clearAllCaches();
}
final String serverId = theRequest.getServerIdWithDefault(myConfig);
final String serverBase = theRequest.getServerBase(theServletRequest, myConfig);
final String serverName = theRequest.getServerName(myConfig);
theModel.put("serverId", serverId);
theModel.put("base", serverBase);
theModel.put("baseName", serverName);
theModel.put("resourceName", defaultString(theRequest.getResource()));
theModel.put("encoding", theRequest.getEncoding());
theModel.put("pretty", theRequest.getPretty());
theModel.put("_summary", theRequest.get_summary());
theModel.put("serverEntries", myConfig.getIdToServerName());
return loadAndAddConf(theServletRequest, theRequest, theModel);
}
private Header[] applyHeaderFilters(Header[] theAllHeaders) {
if (myFilterHeaders == null || myFilterHeaders.isEmpty()) {
return theAllHeaders;
}
ArrayList<Header> retVal = new ArrayList<Header>();
for (Header next : theAllHeaders) {
if (!myFilterHeaders.contains(next.getName().toLowerCase())) {
retVal.add(next);
}
}
return retVal.toArray(new Header[retVal.size()]);
}
private String format(String theResultBody, EncodingEnum theEncodingEnum) {
String str = StringEscapeUtils.escapeHtml4(theResultBody);
if (str == null || theEncodingEnum == null) {
return str;
}
StringBuilder b = new StringBuilder();
if (theEncodingEnum == EncodingEnum.JSON) {
boolean inValue = false;
boolean inQuote = false;
for (int i = 0; i < str.length(); i++) {
char prevChar = (i > 0) ? str.charAt(i - 1) : ' ';
char nextChar = str.charAt(i);
char nextChar2 = (i + 1) < str.length() ? str.charAt(i + 1) : ' ';
char nextChar3 = (i + 2) < str.length() ? str.charAt(i + 2) : ' ';
char nextChar4 = (i + 3) < str.length() ? str.charAt(i + 3) : ' ';
char nextChar5 = (i + 4) < str.length() ? str.charAt(i + 4) : ' ';
char nextChar6 = (i + 5) < str.length() ? str.charAt(i + 5) : ' ';
if (inQuote) {
b.append(nextChar);
if (prevChar != '\\' && nextChar == '&' && nextChar2 == 'q' && nextChar3 == 'u' && nextChar4 == 'o' && nextChar5 == 't' && nextChar6 == ';') {
b.append("quot;</span>");
i += 5;
inQuote = false;
} else if (nextChar == '\\' && nextChar2 == '"') {
b.append("quot;</span>");
i += 5;
inQuote = false;
}
} else {
if (nextChar == ':') {
inValue = true;
b.append(nextChar);
} else if (nextChar == '[' || nextChar == '{') {
b.append("<span class='hlControl'>");
b.append(nextChar);
b.append("</span>");
inValue = false;
} else if (nextChar == '}' || nextChar == '}' || nextChar == ',') {
b.append("<span class='hlControl'>");
b.append(nextChar);
b.append("</span>");
inValue = false;
} else if (nextChar == '&' && nextChar2 == 'q' && nextChar3 == 'u' && nextChar4 == 'o' && nextChar5 == 't' && nextChar6 == ';') {
if (inValue) {
b.append("<span class='hlQuot'>&quot;");
} else {
b.append("<span class='hlTagName'>&quot;");
}
inQuote = true;
i += 5;
} else if (nextChar == ':') {
b.append("<span class='hlControl'>");
b.append(nextChar);
b.append("</span>");
inValue = true;
} else {
b.append(nextChar);
}
}
}
} else {
boolean inQuote = false;
boolean inTag = false;
for (int i = 0; i < str.length(); i++) {
char nextChar = str.charAt(i);
char nextChar2 = (i + 1) < str.length() ? str.charAt(i + 1) : ' ';
char nextChar3 = (i + 2) < str.length() ? str.charAt(i + 2) : ' ';
char nextChar4 = (i + 3) < str.length() ? str.charAt(i + 3) : ' ';
char nextChar5 = (i + 4) < str.length() ? str.charAt(i + 4) : ' ';
char nextChar6 = (i + 5) < str.length() ? str.charAt(i + 5) : ' ';
if (inQuote) {
b.append(nextChar);
if (nextChar == '&' && nextChar2 == 'q' && nextChar3 == 'u' && nextChar4 == 'o' && nextChar5 == 't' && nextChar6 == ';') {
b.append("quot;</span>");
i += 5;
inQuote = false;
}
} else if (inTag) {
if (nextChar == '&' && nextChar2 == 'g' && nextChar3 == 't' && nextChar4 == ';') {
b.append("</span><span class='hlControl'>&gt;</span>");
inTag = false;
i += 3;
} else if (nextChar == ' ') {
b.append("</span><span class='hlAttr'>");
b.append(nextChar);
} else if (nextChar == '&' && nextChar2 == 'q' && nextChar3 == 'u' && nextChar4 == 'o' && nextChar5 == 't' && nextChar6 == ';') {
b.append("<span class='hlQuot'>&quot;");
inQuote = true;
i += 5;
} else {
b.append(nextChar);
}
} else {
if (nextChar == '&' && nextChar2 == 'l' && nextChar3 == 't' && nextChar4 == ';') {
b.append("<span class='hlControl'>&lt;</span><span class='hlTagName'>");
inTag = true;
i += 3;
} else {
b.append(nextChar);
}
}
}
}
return b.toString();
}
private String formatUrl(String theUrlBase, String theResultBody) {
String str = theResultBody;
if (str == null) {
return str;
}
try {
str = URLDecoder.decode(str, "UTF-8");
} catch (UnsupportedEncodingException e) {
ourLog.error("Should not happen", e);
}
StringBuilder b = new StringBuilder();
b.append("<span class='hlUrlBase'>");
boolean inParams = false;
for (int i = 0; i < str.length(); i++) {
char nextChar = str.charAt(i);
// char nextChar2 = i < str.length()-2 ? str.charAt(i+1):' ';
// char nextChar3 = i < str.length()-2 ? str.charAt(i+2):' ';
if (!inParams) {
if (nextChar == '?') {
inParams = true;
b.append("</span><wbr /><span class='hlControl'>?</span><span class='hlTagName'>");
} else {
if (i == theUrlBase.length()) {
b.append("</span><wbr /><span class='hlText'>");
}
b.append(nextChar);
}
} else {
if (nextChar == '&') {
b.append("</span><wbr /><span class='hlControl'>&amp;</span><span class='hlTagName'>");
} else if (nextChar == '=') {
b.append("</span><span class='hlControl'>=</span><span class='hlAttr'>");
// }else if (nextChar=='%' && Character.isLetterOrDigit(nextChar2)&& Character.isLetterOrDigit(nextChar3)) {
// URLDecoder.decode(s, enc)
} else {
b.append(nextChar);
}
}
}
if (inParams) {
b.append("</span>");
}
return b.toString();
}
protected FhirContext getContext(HomeRequest theRequest) {
FhirVersionEnum version = theRequest.getFhirVersion(myConfig);
FhirContext retVal = myContexts.get(version);
if (retVal == null) {
retVal = new FhirContext(version);
myContexts.put(version, retVal);
}
return retVal;
}
protected RuntimeResourceDefinition getResourceType(HomeRequest theRequest, HttpServletRequest theReq) throws ServletException {
String resourceName = StringUtils.defaultString(theReq.getParameter(PARAM_RESOURCE));
RuntimeResourceDefinition def = getContext(theRequest).getResourceDefinition(resourceName);
if (def == null) {
throw new ServletException("Invalid resourceName: " + resourceName);
}
return def;
}
protected ResultType handleClientException(GenericClient theClient, Exception e, ModelMap theModel) {
ResultType returnsResource;
returnsResource = ResultType.NONE;
ourLog.warn("Failed to invoke server", e);
if (theClient.getLastResponse() == null) {
theModel.put("errorMsg", "Error: " + e.getMessage());
}
return returnsResource;
}
private IResource loadAndAddConf(HttpServletRequest theServletRequest, final HomeRequest theRequest, final ModelMap theModel) {
switch (theRequest.getFhirVersion(myConfig)) {
case DEV:
return loadAndAddConfDstu2(theServletRequest, theRequest, theModel);
case DSTU1:
return loadAndAddConfDstu1(theServletRequest, theRequest, theModel);
case DSTU2:
return loadAndAddConfDstu2(theServletRequest, theRequest, theModel);
}
throw new IllegalStateException("Unknown version: " + theRequest.getFhirVersion(myConfig));
}
private Conformance loadAndAddConfDstu1(HttpServletRequest theServletRequest, final HomeRequest theRequest, final ModelMap theModel) {
CaptureInterceptor interceptor = new CaptureInterceptor();
GenericClient client = theRequest.newClient(theServletRequest, getContext(theRequest), myConfig, interceptor);
Conformance conformance;
try {
conformance = (Conformance) client.conformance();
} catch (Exception e) {
ourLog.warn("Failed to load conformance statement", e);
theModel.put("errorMsg", "Failed to load conformance statement, error was: " + e.toString());
conformance = new Conformance();
}
theModel.put("jsonEncodedConf", getContext(theRequest).newJsonParser().encodeResourceToString(conformance));
Map<String, Number> resourceCounts = new HashMap<String, Number>();
long total = 0;
for (Rest nextRest : conformance.getRest()) {
for (ca.uhn.fhir.model.dstu.resource.Conformance.RestResource nextResource : nextRest.getResource()) {
List<ExtensionDt> exts = nextResource.getUndeclaredExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (exts != null && exts.size() > 0) {
Number nextCount = ((DecimalDt) (exts.get(0).getValue())).getValueAsNumber();
resourceCounts.put(nextResource.getType().getValue(), nextCount);
total += nextCount.longValue();
}
}
}
theModel.put("resourceCounts", resourceCounts);
if (total > 0) {
for (Rest nextRest : conformance.getRest()) {
Collections.sort(nextRest.getResource(), new Comparator<ca.uhn.fhir.model.dstu.resource.Conformance.RestResource>() {
@Override
public int compare(ca.uhn.fhir.model.dstu.resource.Conformance.RestResource theO1, ca.uhn.fhir.model.dstu.resource.Conformance.RestResource theO2) {
DecimalDt count1 = new DecimalDt();
List<ExtensionDt> count1exts = theO1.getUndeclaredExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (count1exts != null && count1exts.size() > 0) {
count1 = (DecimalDt) count1exts.get(0).getValue();
}
DecimalDt count2 = new DecimalDt();
List<ExtensionDt> count2exts = theO2.getUndeclaredExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (count2exts != null && count2exts.size() > 0) {
count2 = (DecimalDt) count2exts.get(0).getValue();
}
int retVal = count2.compareTo(count1);
if (retVal == 0) {
retVal = theO1.getType().getValue().compareTo(theO2.getType().getValue());
}
return retVal;
}
});
}
}
theModel.put("conf", conformance);
theModel.put("requiredParamExtension", ExtensionConstants.PARAM_IS_REQUIRED);
return conformance;
}
private IResource loadAndAddConfDstu2(HttpServletRequest theServletRequest, final HomeRequest theRequest, final ModelMap theModel) {
CaptureInterceptor interceptor = new CaptureInterceptor();
GenericClient client = theRequest.newClient(theServletRequest, getContext(theRequest), myConfig, interceptor);
ca.uhn.fhir.model.dstu2.resource.Conformance conformance;
try {
conformance = (ca.uhn.fhir.model.dstu2.resource.Conformance) client.conformance();
} catch (Exception e) {
ourLog.warn("Failed to load conformance statement", e);
theModel.put("errorMsg", "Failed to load conformance statement, error was: " + e.toString());
conformance = new ca.uhn.fhir.model.dstu2.resource.Conformance();
}
theModel.put("jsonEncodedConf", getContext(theRequest).newJsonParser().encodeResourceToString(conformance));
Map<String, Number> resourceCounts = new HashMap<String, Number>();
long total = 0;
for (ca.uhn.fhir.model.dstu2.resource.Conformance.Rest nextRest : conformance.getRest()) {
for (ca.uhn.fhir.model.dstu2.resource.Conformance.RestResource nextResource : nextRest.getResource()) {
List<ExtensionDt> exts = nextResource.getUndeclaredExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (exts != null && exts.size() > 0) {
Number nextCount = ((DecimalDt) (exts.get(0).getValue())).getValueAsNumber();
resourceCounts.put(nextResource.getTypeElement().getValue(), nextCount);
total += nextCount.longValue();
}
}
}
theModel.put("resourceCounts", resourceCounts);
if (total > 0) {
for (ca.uhn.fhir.model.dstu2.resource.Conformance.Rest nextRest : conformance.getRest()) {
Collections.sort(nextRest.getResource(), new Comparator<ca.uhn.fhir.model.dstu2.resource.Conformance.RestResource>() {
@Override
public int compare(ca.uhn.fhir.model.dstu2.resource.Conformance.RestResource theO1, ca.uhn.fhir.model.dstu2.resource.Conformance.RestResource theO2) {
DecimalDt count1 = new DecimalDt();
List<ExtensionDt> count1exts = theO1.getUndeclaredExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (count1exts != null && count1exts.size() > 0) {
count1 = (DecimalDt) count1exts.get(0).getValue();
}
DecimalDt count2 = new DecimalDt();
List<ExtensionDt> count2exts = theO2.getUndeclaredExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (count2exts != null && count2exts.size() > 0) {
count2 = (DecimalDt) count2exts.get(0).getValue();
}
int retVal = count2.compareTo(count1);
if (retVal == 0) {
retVal = theO1.getTypeElement().getValue().compareTo(theO2.getTypeElement().getValue());
}
return retVal;
}
});
}
}
theModel.put("conf", conformance);
theModel.put("requiredParamExtension", ExtensionConstants.PARAM_IS_REQUIRED);
return conformance;
}
protected String logPrefix(ModelMap theModel) {
return "[server=" + theModel.get("serverId") + "] - ";
}
private String parseNarrative(HomeRequest theRequest, EncodingEnum theCtEnum, String theResultBody) {
try {
IResource resource = (IResource) theCtEnum.newParser(getContext(theRequest)).parseResource(theResultBody);
String retVal = resource.getText().getDiv().getValueAsString();
return StringUtils.defaultString(retVal);
} catch (Exception e) {
ourLog.error("Failed to parse resource", e);
return "";
}
}
protected String preProcessMessageBody(String theBody) {
if (theBody == null) {
return "";
}
String retVal = theBody.trim();
StringBuilder b = new StringBuilder();
for (int i = 0; i < retVal.length(); i++) {
char nextChar = retVal.charAt(i);
int nextCharI = nextChar;
if (nextCharI == 65533) {
b.append(' ');
continue;
}
if (nextCharI == 160) {
b.append(' ');
continue;
}
if (nextCharI == 194) {
b.append(' ');
continue;
}
b.append(nextChar);
}
retVal = b.toString();
return retVal;
}
protected void processAndAddLastClientInvocation(GenericClient theClient, ResultType theResultType, ModelMap theModelMap, long theLatency, String outcomeDescription, CaptureInterceptor theInterceptor, HomeRequest theRequest) {
try {
HttpRequestBase lastRequest = theInterceptor.getLastRequest();
HttpResponse lastResponse = theInterceptor.getLastResponse();
String requestBody = null;
String requestUrl = lastRequest != null ? lastRequest.getURI().toASCIIString() : null;
String action = lastRequest != null ? lastRequest.getMethod() : null;
String resultStatus = lastResponse != null ? lastResponse.getStatusLine().toString() : null;
String resultBody = StringUtils.defaultString(theInterceptor.getLastResponseBody());
if (lastRequest instanceof HttpEntityEnclosingRequest) {
HttpEntity entity = ((HttpEntityEnclosingRequest) lastRequest).getEntity();
if (entity.isRepeatable()) {
requestBody = IOUtils.toString(entity.getContent());
}
}
ContentType ct = lastResponse != null ? ContentType.get(lastResponse.getEntity()) : null;
String mimeType = ct != null ? ct.getMimeType() : null;
EncodingEnum ctEnum = EncodingEnum.forContentType(mimeType);
String narrativeString = "";
StringBuilder resultDescription = new StringBuilder();
Bundle bundle = null;
if (ctEnum == null) {
resultDescription.append("Non-FHIR response");
} else {
switch (ctEnum) {
case JSON:
if (theResultType == ResultType.RESOURCE) {
narrativeString = parseNarrative(theRequest, ctEnum, resultBody);
resultDescription.append("JSON resource");
} else if (theResultType == ResultType.BUNDLE) {
resultDescription.append("JSON bundle");
bundle = getContext(theRequest).newJsonParser().parseBundle(resultBody);
}
break;
case XML:
default:
if (theResultType == ResultType.RESOURCE) {
narrativeString = parseNarrative(theRequest, ctEnum, resultBody);
resultDescription.append("XML resource");
} else if (theResultType == ResultType.BUNDLE) {
resultDescription.append("XML bundle");
bundle = getContext(theRequest).newXmlParser().parseBundle(resultBody);
}
break;
}
}
/*
* DSTU2 no longer has a title in the bundle format, but it's still useful here..
*/
if (bundle != null) {
INarrativeGenerator gen = getContext(theRequest).getNarrativeGenerator();
if (gen != null) {
for (BundleEntry next : bundle.getEntries()) {
if (next.getTitle().isEmpty() && next.getResource() != null) {
String title = gen.generateTitle(next.getResource());
next.getTitle().setValue(title);
}
}
}
}
resultDescription.append(" (").append(resultBody.length() + " bytes)");
Header[] requestHeaders = lastRequest != null ? applyHeaderFilters(lastRequest.getAllHeaders()) : new Header[0];
Header[] responseHeaders = lastResponse != null ? applyHeaderFilters(lastResponse.getAllHeaders()) : new Header[0];
theModelMap.put("outcomeDescription", outcomeDescription);
theModelMap.put("resultDescription", resultDescription.toString());
theModelMap.put("action", action);
theModelMap.put("bundle", bundle);
theModelMap.put("resultStatus", resultStatus);
theModelMap.put("requestUrl", requestUrl);
theModelMap.put("requestUrlText", formatUrl(theClient.getUrlBase(), requestUrl));
String requestBodyText = format(requestBody, ctEnum);
theModelMap.put("requestBody", requestBodyText);
String resultBodyText = format(resultBody, ctEnum);
theModelMap.put("resultBody", resultBodyText);
theModelMap.put("resultBodyIsLong", resultBodyText.length() > 1000);
theModelMap.put("requestHeaders", requestHeaders);
theModelMap.put("responseHeaders", responseHeaders);
theModelMap.put("narrative", narrativeString);
theModelMap.put("latencyMs", theLatency);
} catch (Exception e) {
ourLog.error("Failure during processing", e);
theModelMap.put("errorMsg", "Error during processing: " + e.getMessage());
}
}
public static class CaptureInterceptor implements IClientInterceptor {
private HttpRequestBase myLastRequest;
private HttpResponse myLastResponse;
private String myResponseBody;
public HttpRequestBase getLastRequest() {
return myLastRequest;
}
public HttpResponse getLastResponse() {
return myLastResponse;
}
public String getLastResponseBody() {
return myResponseBody;
}
@Override
public void interceptRequest(HttpRequestBase theRequest) {
assert myLastRequest == null;
myLastRequest = theRequest;
}
@Override
public void interceptResponse(HttpResponse theResponse) throws IOException {
assert myLastResponse == null;
myLastResponse = theResponse;
HttpEntity respEntity = theResponse.getEntity();
if (respEntity != null) {
final byte[] bytes;
try {
bytes = IOUtils.toByteArray(respEntity.getContent());
} catch (IllegalStateException e) {
throw new InternalErrorException(e);
}
myResponseBody = new String(bytes, "UTF-8");
theResponse.setEntity(new MyEntityWrapper(respEntity, bytes));
}
}
private static class MyEntityWrapper extends HttpEntityWrapper {
private byte[] myBytes;
public MyEntityWrapper(HttpEntity theWrappedEntity, byte[] theBytes) {
super(theWrappedEntity);
myBytes = theBytes;
}
@Override
public InputStream getContent() throws IOException {
return new ByteArrayInputStream(myBytes);
}
@Override
public void writeTo(OutputStream theOutstream) throws IOException {
theOutstream.write(myBytes);
}
}
}
protected enum ResultType {
BUNDLE, NONE, RESOURCE, TAGLIST
}
}

612
hapi-fhir-testpage-overlay/src/main/java/ca/uhn/fhir/to/Controller.java
View File

@ -2,19 +2,10 @@ package ca.uhn.fhir.to;
import static org.apache.commons.lang3.StringUtils.*;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.TreeSet;
import javax.json.Json;
@ -22,27 +13,13 @@ import javax.json.stream.JsonGenerator;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.Header;
import org.apache.http.HttpEntity;
import org.apache.http.HttpEntityEnclosingRequest;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpRequestBase;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.HttpEntityWrapper;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.ui.ModelMap;
import org.springframework.validation.BindingResult;
import org.springframework.web.bind.annotation.RequestMapping;
import org.thymeleaf.TemplateEngine;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.BundleEntry;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.Include;
@ -55,13 +32,10 @@ import ca.uhn.fhir.model.dstu.valueset.SearchParamTypeEnum;
import ca.uhn.fhir.model.dstu2.valueset.ResourceTypeEnum;
import ca.uhn.fhir.model.primitive.BoundCodeDt;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.DecimalDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.client.GenericClient;
import ca.uhn.fhir.rest.client.IClientInterceptor;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.gclient.ICreateTyped;
import ca.uhn.fhir.rest.gclient.IQuery;
@ -73,27 +47,14 @@ import ca.uhn.fhir.rest.gclient.StringClientParam;
import ca.uhn.fhir.rest.gclient.TokenClientParam;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.to.model.HomeRequest;
import ca.uhn.fhir.to.model.ResourceRequest;
import ca.uhn.fhir.to.model.TransactionRequest;
import ca.uhn.fhir.util.ExtensionConstants;
@org.springframework.stereotype.Controller()
public class Controller {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Controller.class);
private static final String PARAM_RESOURCE = "resource";
private static final String RESOURCE_COUNT_EXT_URL = "http://hl7api.sourceforge.net/hapi-fhir/res/extdefs.html#resourceCount";
@Autowired
private TesterConfig myConfig;
private Map<FhirVersionEnum, FhirContext> myContexts = new HashMap<FhirVersionEnum, FhirContext>();
private List<String> myFilterHeaders;
@Autowired
private TemplateEngine myTemplateEngine;
public class Controller extends BaseController {
static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Controller.class);
@RequestMapping(value = { "/about" })
public String actionAbout(HttpServletRequest theServletRequest, final HomeRequest theRequest, final ModelMap theModel) {
@ -558,39 +519,6 @@ public class Controller {
return "result";
}
private IResource addCommonParams(HttpServletRequest theServletRequest, final HomeRequest theRequest, final ModelMap theModel) {
if (myConfig.getDebugTemplatesMode()) {
myTemplateEngine.getCacheManager().clearAllCaches();
}
final String serverId = theRequest.getServerIdWithDefault(myConfig);
final String serverBase = theRequest.getServerBase(theServletRequest, myConfig);
final String serverName = theRequest.getServerName(myConfig);
theModel.put("serverId", serverId);
theModel.put("base", serverBase);
theModel.put("baseName", serverName);
theModel.put("resourceName", defaultString(theRequest.getResource()));
theModel.put("encoding", theRequest.getEncoding());
theModel.put("pretty", theRequest.getPretty());
theModel.put("_summary", theRequest.get_summary());
theModel.put("serverEntries", myConfig.getIdToServerName());
return loadAndAddConf(theServletRequest, theRequest, theModel);
}
private Header[] applyHeaderFilters(Header[] theAllHeaders) {
if (myFilterHeaders == null || myFilterHeaders.isEmpty()) {
return theAllHeaders;
}
ArrayList<Header> retVal = new ArrayList<Header>();
for (Header next : theAllHeaders) {
if (!myFilterHeaders.contains(next.getName().toLowerCase())) {
retVal.add(next);
}
}
return retVal.toArray(new Header[retVal.size()]);
}
private void doActionCreateOrValidate(HttpServletRequest theReq, HomeRequest theRequest, BindingResult theBindingResult, ModelMap theModel, String theMethod) {
boolean validate = "validate".equals(theMethod);
@ -805,197 +733,6 @@ public class Controller {
return haveSearchParams;
}
private String format(String theResultBody, EncodingEnum theEncodingEnum) {
String str = StringEscapeUtils.escapeHtml4(theResultBody);
if (str == null || theEncodingEnum == null) {
return str;
}
StringBuilder b = new StringBuilder();
if (theEncodingEnum == EncodingEnum.JSON) {
boolean inValue = false;
boolean inQuote = false;
for (int i = 0; i < str.length(); i++) {
char prevChar = (i > 0) ? str.charAt(i - 1) : ' ';
char nextChar = str.charAt(i);
char nextChar2 = (i + 1) < str.length() ? str.charAt(i + 1) : ' ';
char nextChar3 = (i + 2) < str.length() ? str.charAt(i + 2) : ' ';
char nextChar4 = (i + 3) < str.length() ? str.charAt(i + 3) : ' ';
char nextChar5 = (i + 4) < str.length() ? str.charAt(i + 4) : ' ';
char nextChar6 = (i + 5) < str.length() ? str.charAt(i + 5) : ' ';
if (inQuote) {
b.append(nextChar);
if (prevChar != '\\' && nextChar == '&' && nextChar2 == 'q' && nextChar3 == 'u' && nextChar4 == 'o' && nextChar5 == 't' && nextChar6 == ';') {
b.append("quot;</span>");
i += 5;
inQuote = false;
} else if (nextChar == '\\' && nextChar2 == '"') {
b.append("quot;</span>");
i += 5;
inQuote = false;
}
} else {
if (nextChar == ':') {
inValue = true;
b.append(nextChar);
} else if (nextChar == '[' || nextChar == '{') {
b.append("<span class='hlControl'>");
b.append(nextChar);
b.append("</span>");
inValue = false;
} else if (nextChar == '}' || nextChar == '}' || nextChar == ',') {
b.append("<span class='hlControl'>");
b.append(nextChar);
b.append("</span>");
inValue = false;
} else if (nextChar == '&' && nextChar2 == 'q' && nextChar3 == 'u' && nextChar4 == 'o' && nextChar5 == 't' && nextChar6 == ';') {
if (inValue) {
b.append("<span class='hlQuot'>&quot;");
} else {
b.append("<span class='hlTagName'>&quot;");
}
inQuote = true;
i += 5;
} else if (nextChar == ':') {
b.append("<span class='hlControl'>");
b.append(nextChar);
b.append("</span>");
inValue = true;
} else {
b.append(nextChar);
}
}
}
} else {
boolean inQuote = false;
boolean inTag = false;
for (int i = 0; i < str.length(); i++) {
char nextChar = str.charAt(i);
char nextChar2 = (i + 1) < str.length() ? str.charAt(i + 1) : ' ';
char nextChar3 = (i + 2) < str.length() ? str.charAt(i + 2) : ' ';
char nextChar4 = (i + 3) < str.length() ? str.charAt(i + 3) : ' ';
char nextChar5 = (i + 4) < str.length() ? str.charAt(i + 4) : ' ';
char nextChar6 = (i + 5) < str.length() ? str.charAt(i + 5) : ' ';
if (inQuote) {
b.append(nextChar);
if (nextChar == '&' && nextChar2 == 'q' && nextChar3 == 'u' && nextChar4 == 'o' && nextChar5 == 't' && nextChar6 == ';') {
b.append("quot;</span>");
i += 5;
inQuote = false;
}
} else if (inTag) {
if (nextChar == '&' && nextChar2 == 'g' && nextChar3 == 't' && nextChar4 == ';') {
b.append("</span><span class='hlControl'>&gt;</span>");
inTag = false;
i += 3;
} else if (nextChar == ' ') {
b.append("</span><span class='hlAttr'>");
b.append(nextChar);
} else if (nextChar == '&' && nextChar2 == 'q' && nextChar3 == 'u' && nextChar4 == 'o' && nextChar5 == 't' && nextChar6 == ';') {
b.append("<span class='hlQuot'>&quot;");
inQuote = true;
i += 5;
} else {
b.append(nextChar);
}
} else {
if (nextChar == '&' && nextChar2 == 'l' && nextChar3 == 't' && nextChar4 == ';') {
b.append("<span class='hlControl'>&lt;</span><span class='hlTagName'>");
inTag = true;
i += 3;
} else {
b.append(nextChar);
}
}
}
}
return b.toString();
}
private String formatUrl(String theUrlBase, String theResultBody) {
String str = theResultBody;
if (str == null) {
return str;
}
try {
str = URLDecoder.decode(str, "UTF-8");
} catch (UnsupportedEncodingException e) {
ourLog.error("Should not happen", e);
}
StringBuilder b = new StringBuilder();
b.append("<span class='hlUrlBase'>");
boolean inParams = false;
for (int i = 0; i < str.length(); i++) {
char nextChar = str.charAt(i);
// char nextChar2 = i < str.length()-2 ? str.charAt(i+1):' ';
// char nextChar3 = i < str.length()-2 ? str.charAt(i+2):' ';
if (!inParams) {
if (nextChar == '?') {
inParams = true;
b.append("</span><wbr /><span class='hlControl'>?</span><span class='hlTagName'>");
} else {
if (i == theUrlBase.length()) {
b.append("</span><wbr /><span class='hlText'>");
}
b.append(nextChar);
}
} else {
if (nextChar == '&') {
b.append("</span><wbr /><span class='hlControl'>&amp;</span><span class='hlTagName'>");
} else if (nextChar == '=') {
b.append("</span><span class='hlControl'>=</span><span class='hlAttr'>");
// }else if (nextChar=='%' && Character.isLetterOrDigit(nextChar2)&& Character.isLetterOrDigit(nextChar3)) {
// URLDecoder.decode(s, enc)
} else {
b.append(nextChar);
}
}
}
if (inParams) {
b.append("</span>");
}
return b.toString();
}
private FhirContext getContext(HomeRequest theRequest) {
FhirVersionEnum version = theRequest.getFhirVersion(myConfig);
FhirContext retVal = myContexts.get(version);
if (retVal == null) {
retVal = new FhirContext(version);
myContexts.put(version, retVal);
}
return retVal;
}
private RuntimeResourceDefinition getResourceType(HomeRequest theRequest, HttpServletRequest theReq) throws ServletException {
String resourceName = StringUtils.defaultString(theReq.getParameter(PARAM_RESOURCE));
RuntimeResourceDefinition def = getContext(theRequest).getResourceDefinition(resourceName);
if (def == null) {
throw new ServletException("Invalid resourceName: " + resourceName);
}
return def;
}
private ResultType handleClientException(GenericClient theClient, Exception e, ModelMap theModel) {
ResultType returnsResource;
returnsResource = ResultType.NONE;
ourLog.warn("Failed to invoke server", e);
if (theClient.getLastResponse() == null) {
theModel.put("errorMsg", "Error: " + e.getMessage());
}
return returnsResource;
}
private boolean handleSearchParam(String paramIdxString, HttpServletRequest theReq, IQuery theQuery, JsonGenerator theClientCodeJsonWriter) {
String nextName = theReq.getParameter("param." + paramIdxString + ".name");
if (isBlank(nextName)) {
@ -1099,349 +836,4 @@ public class Controller {
return true;
}
private IResource loadAndAddConf(HttpServletRequest theServletRequest, final HomeRequest theRequest, final ModelMap theModel) {
switch (theRequest.getFhirVersion(myConfig)) {
case DEV:
return loadAndAddConfDstu2(theServletRequest, theRequest, theModel);
case DSTU1:
return loadAndAddConfDstu1(theServletRequest, theRequest, theModel);
case DSTU2:
return loadAndAddConfDstu2(theServletRequest, theRequest, theModel);
}
throw new IllegalStateException("Unknown version: " + theRequest.getFhirVersion(myConfig));
}
private Conformance loadAndAddConfDstu1(HttpServletRequest theServletRequest, final HomeRequest theRequest, final ModelMap theModel) {
CaptureInterceptor interceptor = new CaptureInterceptor();
GenericClient client = theRequest.newClient(theServletRequest, getContext(theRequest), myConfig, interceptor);
Conformance conformance;
try {
conformance = (Conformance) client.conformance();
} catch (Exception e) {
ourLog.warn("Failed to load conformance statement", e);
theModel.put("errorMsg", "Failed to load conformance statement, error was: " + e.toString());
conformance = new Conformance();
}
theModel.put("jsonEncodedConf", getContext(theRequest).newJsonParser().encodeResourceToString(conformance));
Map<String, Number> resourceCounts = new HashMap<String, Number>();
long total = 0;
for (Rest nextRest : conformance.getRest()) {
for (RestResource nextResource : nextRest.getResource()) {
List<ExtensionDt> exts = nextResource.getUndeclaredExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (exts != null && exts.size() > 0) {
Number nextCount = ((DecimalDt) (exts.get(0).getValue())).getValueAsNumber();
resourceCounts.put(nextResource.getType().getValue(), nextCount);
total += nextCount.longValue();
}
}
}
theModel.put("resourceCounts", resourceCounts);
if (total > 0) {
for (Rest nextRest : conformance.getRest()) {
Collections.sort(nextRest.getResource(), new Comparator<RestResource>() {
@Override
public int compare(RestResource theO1, RestResource theO2) {
DecimalDt count1 = new DecimalDt();
List<ExtensionDt> count1exts = theO1.getUndeclaredExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (count1exts != null && count1exts.size() > 0) {
count1 = (DecimalDt) count1exts.get(0).getValue();
}
DecimalDt count2 = new DecimalDt();
List<ExtensionDt> count2exts = theO2.getUndeclaredExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (count2exts != null && count2exts.size() > 0) {
count2 = (DecimalDt) count2exts.get(0).getValue();
}
int retVal = count2.compareTo(count1);
if (retVal == 0) {
retVal = theO1.getType().getValue().compareTo(theO2.getType().getValue());
}
return retVal;
}
});
}
}
theModel.put("conf", conformance);
theModel.put("requiredParamExtension", ExtensionConstants.PARAM_IS_REQUIRED);
return conformance;
}
private IResource loadAndAddConfDstu2(HttpServletRequest theServletRequest, final HomeRequest theRequest, final ModelMap theModel) {
CaptureInterceptor interceptor = new CaptureInterceptor();
GenericClient client = theRequest.newClient(theServletRequest, getContext(theRequest), myConfig, interceptor);
ca.uhn.fhir.model.dstu2.resource.Conformance conformance;
try {
conformance = (ca.uhn.fhir.model.dstu2.resource.Conformance) client.conformance();
} catch (Exception e) {
ourLog.warn("Failed to load conformance statement", e);
theModel.put("errorMsg", "Failed to load conformance statement, error was: " + e.toString());
conformance = new ca.uhn.fhir.model.dstu2.resource.Conformance();
}
theModel.put("jsonEncodedConf", getContext(theRequest).newJsonParser().encodeResourceToString(conformance));
Map<String, Number> resourceCounts = new HashMap<String, Number>();
long total = 0;
for (ca.uhn.fhir.model.dstu2.resource.Conformance.Rest nextRest : conformance.getRest()) {
for (ca.uhn.fhir.model.dstu2.resource.Conformance.RestResource nextResource : nextRest.getResource()) {
List<ExtensionDt> exts = nextResource.getUndeclaredExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (exts != null && exts.size() > 0) {
Number nextCount = ((DecimalDt) (exts.get(0).getValue())).getValueAsNumber();
resourceCounts.put(nextResource.getTypeElement().getValue(), nextCount);
total += nextCount.longValue();
}
}
}
theModel.put("resourceCounts", resourceCounts);
if (total > 0) {
for (ca.uhn.fhir.model.dstu2.resource.Conformance.Rest nextRest : conformance.getRest()) {
Collections.sort(nextRest.getResource(), new Comparator<ca.uhn.fhir.model.dstu2.resource.Conformance.RestResource>() {
@Override
public int compare(ca.uhn.fhir.model.dstu2.resource.Conformance.RestResource theO1, ca.uhn.fhir.model.dstu2.resource.Conformance.RestResource theO2) {
DecimalDt count1 = new DecimalDt();
List<ExtensionDt> count1exts = theO1.getUndeclaredExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (count1exts != null && count1exts.size() > 0) {
count1 = (DecimalDt) count1exts.get(0).getValue();
}
DecimalDt count2 = new DecimalDt();
List<ExtensionDt> count2exts = theO2.getUndeclaredExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (count2exts != null && count2exts.size() > 0) {
count2 = (DecimalDt) count2exts.get(0).getValue();
}
int retVal = count2.compareTo(count1);
if (retVal == 0) {
retVal = theO1.getTypeElement().getValue().compareTo(theO2.getTypeElement().getValue());
}
return retVal;
}
});
}
}
theModel.put("conf", conformance);
theModel.put("requiredParamExtension", ExtensionConstants.PARAM_IS_REQUIRED);
return conformance;
}
private String logPrefix(ModelMap theModel) {
return "[server=" + theModel.get("serverId") + "] - ";
}
private String parseNarrative(HomeRequest theRequest, EncodingEnum theCtEnum, String theResultBody) {
try {
IResource resource = (IResource) theCtEnum.newParser(getContext(theRequest)).parseResource(theResultBody);
String retVal = resource.getText().getDiv().getValueAsString();
return StringUtils.defaultString(retVal);
} catch (Exception e) {
ourLog.error("Failed to parse resource", e);
return "";
}
}
private String preProcessMessageBody(String theBody) {
if (theBody == null) {
return "";
}
String retVal = theBody.trim();
StringBuilder b = new StringBuilder();
for (int i = 0; i < retVal.length(); i++) {
char nextChar = retVal.charAt(i);
int nextCharI = nextChar;
if (nextCharI == 65533) {
b.append(' ');
continue;
}
if (nextCharI == 160) {
b.append(' ');
continue;
}
if (nextCharI == 194) {
b.append(' ');
continue;
}
b.append(nextChar);
}
retVal = b.toString();
return retVal;
}
private void processAndAddLastClientInvocation(GenericClient theClient, ResultType theResultType, ModelMap theModelMap, long theLatency, String outcomeDescription,
CaptureInterceptor theInterceptor, HomeRequest theRequest) {
try {
HttpRequestBase lastRequest = theInterceptor.getLastRequest();
HttpResponse lastResponse = theInterceptor.getLastResponse();
String requestBody = null;
String requestUrl = lastRequest != null ? lastRequest.getURI().toASCIIString() : null;
String action = lastRequest != null ? lastRequest.getMethod() : null;
String resultStatus = lastResponse != null ? lastResponse.getStatusLine().toString() : null;
String resultBody = StringUtils.defaultString(theInterceptor.getLastResponseBody());
if (lastRequest instanceof HttpEntityEnclosingRequest) {
HttpEntity entity = ((HttpEntityEnclosingRequest) lastRequest).getEntity();
if (entity.isRepeatable()) {
requestBody = IOUtils.toString(entity.getContent());
}
}
ContentType ct = lastResponse != null ? ContentType.get(lastResponse.getEntity()) : null;
String mimeType = ct != null ? ct.getMimeType() : null;
EncodingEnum ctEnum = EncodingEnum.forContentType(mimeType);
String narrativeString = "";
StringBuilder resultDescription = new StringBuilder();
Bundle bundle = null;
if (ctEnum == null) {
resultDescription.append("Non-FHIR response");
} else {
switch (ctEnum) {
case JSON:
if (theResultType == ResultType.RESOURCE) {
narrativeString = parseNarrative(theRequest, ctEnum, resultBody);
resultDescription.append("JSON resource");
} else if (theResultType == ResultType.BUNDLE) {
resultDescription.append("JSON bundle");
bundle = getContext(theRequest).newJsonParser().parseBundle(resultBody);
}
break;
case XML:
default:
if (theResultType == ResultType.RESOURCE) {
narrativeString = parseNarrative(theRequest, ctEnum, resultBody);
resultDescription.append("XML resource");
} else if (theResultType == ResultType.BUNDLE) {
resultDescription.append("XML bundle");
bundle = getContext(theRequest).newXmlParser().parseBundle(resultBody);
}
break;
}
}
/*
* DSTU2 no longer has a title in the bundle format, but it's still useful here..
*/
if (bundle != null) {
INarrativeGenerator gen = getContext(theRequest).getNarrativeGenerator();
if (gen != null) {
for (BundleEntry next : bundle.getEntries()) {
if (next.getTitle().isEmpty() && next.getResource() != null) {
String title = gen.generateTitle(next.getResource());
next.getTitle().setValue(title);
}
}
}
}
resultDescription.append(" (").append(resultBody.length() + " bytes)");
Header[] requestHeaders = lastRequest != null ? applyHeaderFilters(lastRequest.getAllHeaders()) : new Header[0];
Header[] responseHeaders = lastResponse != null ? applyHeaderFilters(lastResponse.getAllHeaders()) : new Header[0];
theModelMap.put("outcomeDescription", outcomeDescription);
theModelMap.put("resultDescription", resultDescription.toString());
theModelMap.put("action", action);
theModelMap.put("bundle", bundle);
theModelMap.put("resultStatus", resultStatus);
theModelMap.put("requestUrl", requestUrl);
theModelMap.put("requestUrlText", formatUrl(theClient.getUrlBase(), requestUrl));
String requestBodyText = format(requestBody, ctEnum);
theModelMap.put("requestBody", requestBodyText);
String resultBodyText = format(resultBody, ctEnum);
theModelMap.put("resultBody", resultBodyText);
theModelMap.put("resultBodyIsLong", resultBodyText.length() > 1000);
theModelMap.put("requestHeaders", requestHeaders);
theModelMap.put("responseHeaders", responseHeaders);
theModelMap.put("narrative", narrativeString);
theModelMap.put("latencyMs", theLatency);
} catch (Exception e) {
ourLog.error("Failure during processing", e);
theModelMap.put("errorMsg", "Error during processing: " + e.getMessage());
}
}
public static class CaptureInterceptor implements IClientInterceptor {
private HttpRequestBase myLastRequest;
private HttpResponse myLastResponse;
private String myResponseBody;
public HttpRequestBase getLastRequest() {
return myLastRequest;
}
public HttpResponse getLastResponse() {
return myLastResponse;
}
public String getLastResponseBody() {
return myResponseBody;
}
@Override
public void interceptRequest(HttpRequestBase theRequest) {
assert myLastRequest == null;
myLastRequest = theRequest;
}
@Override
public void interceptResponse(HttpResponse theResponse) throws IOException {
assert myLastResponse == null;
myLastResponse = theResponse;
HttpEntity respEntity = theResponse.getEntity();
if (respEntity != null) {
final byte[] bytes;
try {
bytes = IOUtils.toByteArray(respEntity.getContent());
} catch (IllegalStateException e) {
throw new InternalErrorException(e);
}
myResponseBody = new String(bytes, "UTF-8");
theResponse.setEntity(new MyEntityWrapper(respEntity, bytes));
}
}
private static class MyEntityWrapper extends HttpEntityWrapper {
private byte[] myBytes;
public MyEntityWrapper(HttpEntity theWrappedEntity, byte[] theBytes) {
super(theWrappedEntity);
myBytes = theBytes;
}
@Override
public InputStream getContent() throws IOException {
return new ByteArrayInputStream(myBytes);
}
@Override
public void writeTo(OutputStream theOutstream) throws IOException {
theOutstream.write(myBytes);
}
}
}
private enum ResultType {
BUNDLE, NONE, RESOURCE, TAGLIST
}
}

11
hapi-tinder-plugin/pom.xml
View File

@ -31,17 +31,22 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu</artifactId>
<version>1.1</version>
<version>1.2</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>1.1</version>
<version>1.2</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>1.1</version>
<version>1.2</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
<version>1.2</version>
</dependency>
<dependency>

7
hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/TinderStructuresMojo.java
View File

@ -228,7 +228,7 @@ public class TinderStructuresMojo extends AbstractMojo {
String dtOutputDir = "target/generated-sources/tinder/ca/uhn/fhir/model/dev/composite";
ResourceGeneratorUsingSpreadsheet rp = new ResourceGeneratorUsingSpreadsheet("dstu2", ".");
rp.setBaseResourceNames(Arrays.asList( "bundle"
rp.setBaseResourceNames(Arrays.asList( "careplan"
// //, "contract"
// "valueset", "organization", "location"
// , "observation", "conformance"
@ -252,11 +252,12 @@ public class TinderStructuresMojo extends AbstractMojo {
rp.getLocalImports().putAll(datatypeLocalImports);
datatypeLocalImports.putAll(rp.getLocalImports());
String vsOutputDir = "target/generated-sources/tinder/ca/uhn/fhir/model/dev/valueset";
vsp.writeMarkedValueSets(new File(vsOutputDir), "ca.uhn.fhir.model.dev");
dtp.writeAll(new File(dtOutputDir), null, "ca.uhn.fhir.model.dev");
rp.writeAll(new File(rpOutputDir), new File(rpSOutputDir), "ca.uhn.fhir.model.dev");
String vsOutputDir = "target/generated-sources/tinder/ca/uhn/fhir/model/dev/valueset";
vsp.writeMarkedValueSets(new File(vsOutputDir), "ca.uhn.fhir.model.dev");
}
public static class ProfileFileDefinition {

6
hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ValueSetGenerator.java
View File

@ -79,7 +79,11 @@ public class ValueSetGenerator {
version = "dstu2";
}
String vs = IOUtils.toString(ValueSetGenerator.class.getResourceAsStream("/vs/" + version + "/all-valuesets-bundle.xml"));
String name = "/vs/" + version + "/all-valuesets-bundle.xml";
if (version.equals("dstu2")) {
name = "/org/hl7/fhir/instance/model/valueset/valuesets.xml";
}
String vs = IOUtils.toString(ValueSetGenerator.class.getResourceAsStream(name));
if ("dstu".equals(myVersion)) {
Bundle bundle = newXmlParser.parseBundle(vs);
for (BundleEntry next : bundle.getEntries()) {

22
src/changes/changes.xml
View File

@ -84,6 +84,28 @@
a more appropriate 400/404 in the JPA server (vread on invalid version,
delete with no ID, etc.)
</action>
<action type="fix">
Fix narrative generation for DSTU2 Medication resource
</action>
<action type="fix">
Profile validator now works for valuesets which use
v2 tables
</action>
<action type="add">
JPA server Patient/[id]/$everything operation now supports
_lastUpdated filtering and _sort'ing of results.
</action>
<action type="fix" issue="233">
Fix parser issue where profiled choice element datatypes (e.g. value[x] where one allowable
type is Duration, which is a profile of Quantity) get incorrectly encoded using the
profiled datatype name instead of the base datatype name as required by the FHIR
spec. Thanks to Nehashri Puttu Lokesh for reporting!
</action>
<action type="fix">
Some generated Enum types in DSTU2 HAPI structures
did not have latest valueset definitions applied. Thanks
to Bill de Beaubien for reporting!
</action>
</release>
<release version="1.2" date="2015-09-18">
<action type="add">