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hapi-fhir
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Merge branch 'master' into fulltext

This commit is contained in:
jamesagnew 2015-10-09 09:15:48 -04:00
parent b4c86d033e 43f21c0dcf
commit 588016e406
22 changed files with 249 additions and 383 deletions
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259
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/BaseRuntimeDeclaredChildDefinition.java
View File

@ -1,43 +1,17 @@
package ca.uhn.fhir.context;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* 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 static org.apache.commons.lang3.StringUtils.*;
import java.lang.reflect.Field;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import org.apache.commons.lang3.text.WordUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.util.BeanUtils;
public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChildDefinition {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseRuntimeDeclaredChildDefinition.class);
private final IAccessor myAccessor;
private final String myElementName;
private final Field myField;
@ -48,22 +22,13 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
private final IMutator myMutator;
private final String myShortDefinition;
private boolean mySummary;
private Boolean ourUseMethodAccessors;
BaseRuntimeDeclaredChildDefinition(Field theField, Child theChildAnnotation, Description theDescriptionAnnotation, String theElementName) throws ConfigurationException {
super();
if (theField == null) {
throw new IllegalArgumentException("No field speficied");
}
if (theChildAnnotation.min() < 0) {
throw new ConfigurationException("Min must be >= 0");
}
if (theChildAnnotation.max() != -1 && theChildAnnotation.max() < theChildAnnotation.min()) {
throw new ConfigurationException("Max must be >= Min (unless it is -1 / unlimited)");
}
if (isBlank(theElementName)) {
throw new ConfigurationException("Element name must not be blank");
}
Validate.notNull(theField, "No field speficied");
Validate.inclusiveBetween(0, Integer.MAX_VALUE, theChildAnnotation.min(), "Min must be >= 0");
Validate.isTrue(theChildAnnotation.max() == -1 || theChildAnnotation.max() >= theChildAnnotation.min(), "Max must be >= Min (unless it is -1 / unlimited)");
Validate.notBlank(theElementName, "Element name must not be blank");
myField = theField;
myMin = theChildAnnotation.min();
@ -79,69 +44,14 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
myFormalDefinition = null;
}
// TODO: handle lists (max>0), and maybe max=0?
// TODO: finish implementing field level accessors/mutators
if (ourUseMethodAccessors == null) {
try {
myField.setAccessible(true);
ourUseMethodAccessors = false;
} catch (SecurityException e) {
ourLog.info("Can not use field accessors/mutators, going to use methods instead");
ourUseMethodAccessors = true;
}
}
if (ourUseMethodAccessors == false) {
if (List.class.equals(myField.getType())) {
// TODO: verify that generic type is IElement
myAccessor = new FieldListAccessor();
myMutator = new FieldListMutator();
} else {
myAccessor = new FieldPlainAccessor();
myMutator = new FieldPlainMutator();
}
myField.setAccessible(true);
if (List.class.equals(myField.getType())) {
// TODO: verify that generic type is IElement
myAccessor = new FieldListAccessor();
myMutator = new FieldListMutator();
} else {
Class<?> declaringClass = myField.getDeclaringClass();
final Class<?> targetReturnType = myField.getType();
try {
String elementName = myElementName;
if ("class".equals(elementName.toLowerCase())) {
elementName = "classElement"; // because getClass() is reserved
}
final Method accessor = BeanUtils.findAccessor(declaringClass, targetReturnType, elementName);
if (accessor == null) {
StringBuilder b = new StringBuilder();
b.append("Could not find bean accessor/getter for property ");
b.append(elementName);
b.append(" on class ");
b.append(declaringClass.getCanonicalName());
throw new ConfigurationException(b.toString());
}
final Method mutator = findMutator(declaringClass, targetReturnType, elementName);
if (mutator == null) {
StringBuilder b = new StringBuilder();
b.append("Could not find bean mutator/setter for property ");
b.append(elementName);
b.append(" on class ");
b.append(declaringClass.getCanonicalName());
b.append(" (expected return type ");
b.append(targetReturnType.getCanonicalName());
b.append(")");
throw new ConfigurationException(b.toString());
}
if (List.class.isAssignableFrom(targetReturnType)) {
myAccessor = new ListAccessor(accessor);
myMutator = new ListMutator(mutator);
} else {
myAccessor = new PlainAccessor(accessor);
myMutator = new PlainMutator(targetReturnType, mutator);
}
} catch (NoSuchFieldException e) {
throw new ConfigurationException(e);
}
myAccessor = new FieldPlainAccessor();
myMutator = new FieldPlainMutator();
}
}
@ -198,17 +108,6 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
return mySummary;
}
private static Method findMutator(Class<?> theDeclaringClass, Class<?> theTargetReturnType, String theElementName) {
String methodName = "set" + WordUtils.capitalize(theElementName);
try {
return theDeclaringClass.getMethod(methodName, theTargetReturnType);
} catch (NoSuchMethodException e) {
return null;
} catch (SecurityException e) {
throw new ConfigurationException("Failed to scan class '" + theDeclaringClass + "' because of a security exception", e);
}
}
private final class FieldListAccessor implements IAccessor {
@SuppressWarnings("unchecked")
@Override
@ -216,11 +115,10 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
List<IBase> retVal;
try {
retVal = (List<IBase>) myField.get(theTarget);
} catch (IllegalArgumentException e) {
throw new ConfigurationException("Failed to get value", e);
} catch (IllegalAccessException e) {
} catch (Exception e) {
throw new ConfigurationException("Failed to get value", e);
}
if (retVal == null) {
retVal = Collections.emptyList();
}
@ -246,9 +144,7 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
existingList.clear();
}
existingList.add(theValue);
} catch (IllegalArgumentException e) {
throw new ConfigurationException("Failed to set value", e);
} catch (IllegalAccessException e) {
} catch (Exception e) {
throw new ConfigurationException("Failed to set value", e);
}
}
@ -267,11 +163,9 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
if (values == null) {
return Collections.emptyList();
}
List<IBase> retVal = Collections.singletonList((IBase)values);
List<IBase> retVal = Collections.singletonList((IBase) values);
return retVal;
} catch (IllegalArgumentException e) {
throw new ConfigurationException("Failed to get value", e);
} catch (IllegalAccessException e) {
} catch (Exception e) {
throw new ConfigurationException("Failed to get value", e);
}
}
@ -282,125 +176,8 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
public void addValue(Object theTarget, IBase theValue) {
try {
myField.set(theTarget, theValue);
} catch (IllegalArgumentException e) {
} catch (Exception e) {
throw new ConfigurationException("Failed to set value", e);
} catch (IllegalAccessException e) {
throw new ConfigurationException("Failed to set value", e);
}
}
@Override
public void setValue(Object theTarget, IBase theValue) {
addValue(theTarget, theValue);
}
}
private static final class ListAccessor implements IAccessor {
private final Method myAccessorMethod;
private ListAccessor(Method theAccessor) {
myAccessorMethod = theAccessor;
}
@SuppressWarnings("unchecked")
@Override
public List<IBase> getValues(Object theTarget) {
try {
return (List<IBase>) myAccessorMethod.invoke(theTarget);
} catch (IllegalAccessException e) {
throw new ConfigurationException("Failed to get value", e);
} catch (IllegalArgumentException e) {
throw new ConfigurationException("Failed to get value", e);
} catch (InvocationTargetException e) {
throw new ConfigurationException("Failed to get value", e);
}
}
}
private final class ListMutator implements IMutator {
private final Method myMutatorMethod;
private ListMutator(Method theMutator) {
myMutatorMethod = theMutator;
}
private void addValue(Object theTarget, boolean theClear, IBase theValue) {
List<IBase> existingList = myAccessor.getValues(theTarget);
if (existingList == null) {
existingList = new ArrayList<IBase>();
try {
myMutatorMethod.invoke(theTarget, existingList);
} catch (IllegalAccessException e) {
throw new ConfigurationException("Failed to get value", e);
} catch (IllegalArgumentException e) {
throw new ConfigurationException("Failed to get value", e);
} catch (InvocationTargetException e) {
throw new ConfigurationException("Failed to get value", e);
}
}
if (theClear) {
existingList.clear();
}
existingList.add(theValue);
}
@Override
public void addValue(Object theTarget, IBase theValue) {
addValue(theTarget, false, theValue);
}
@Override
public void setValue(Object theTarget, IBase theValue) {
addValue(theTarget, true, theValue);
}
}
private final class PlainAccessor implements IAccessor {
private final Method myAccessorMethod;
private PlainAccessor(Method theAccessor) {
myAccessorMethod = theAccessor;
}
@Override
public List<IBase> getValues(Object theTarget) {
try {
return Collections.singletonList((IBase)myAccessorMethod.invoke(theTarget));
} catch (IllegalAccessException e) {
throw new ConfigurationException("Failed to get value", e);
} catch (IllegalArgumentException e) {
throw new ConfigurationException("Failed to get value", e);
} catch (InvocationTargetException e) {
throw new ConfigurationException("Failed to get value", e);
}
}
}
private final class PlainMutator implements IMutator {
private final Method myMutatorMethod;
private final Class<?> myTargetReturnType;
private PlainMutator(Class<?> theTargetReturnType, Method theMutator) {
assert theTargetReturnType != null;
assert theMutator != null;
myTargetReturnType = theTargetReturnType;
myMutatorMethod = theMutator;
}
@Override
public void addValue(Object theTarget, IBase theValue) {
try {
if (theValue != null && !myTargetReturnType.isAssignableFrom(theValue.getClass())) {
throw new ConfigurationException("Value for field " + myElementName + " expects type " + myTargetReturnType + " but got " + theValue.getClass());
}
myMutatorMethod.invoke(theTarget, theValue);
} catch (IllegalAccessException e) {
throw new ConfigurationException("Failed to get value", e);
} catch (IllegalArgumentException e) {
throw new ConfigurationException("Failed to get value", e);
} catch (InvocationTargetException e) {
throw new ConfigurationException("Failed to get value", e);
}
}

4
hapi-fhir-base/src/main/resources/ca/uhn/fhir/narrative/datatype/SimpleQuantityDt.html Normal file
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@ -0,0 +1,4 @@
<div>
<th:block th:if="${not resource.valueElement.empty}" th:text="${resource.valueElement.valueAsString}"/>
<th:block th:if="${not resource.unitsElement.empty}" th:text="${resource.unitsElement.value}"/>
</div>

3
hapi-fhir-base/src/main/resources/ca/uhn/fhir/narrative/narratives.properties
View File

@ -39,6 +39,9 @@ period.narrative=classpath:ca/uhn/fhir/narrative/datatype/PeriodDt.html
quantity.class=ca.uhn.fhir.model.dstu.composite.QuantityDt
quantity.narrative=classpath:ca/uhn/fhir/narrative/datatype/QuantityDt.html
simplequantity.class=ca.uhn.fhir.model.dstu.composite.SimpleQuantityDt
simplequantity.narrative=classpath:ca/uhn/fhir/narrative/datatype/SimpleQuantityDt.html
################################################
# Resources
################################################

1
hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/App.java
View File

@ -35,6 +35,7 @@ public class App {
ourCommands.add(new RunServerCommand());
ourCommands.add(new ExampleDataUploader());
ourCommands.add(new ValidateCommand());
ourCommands.add(new ValidationDataUploader());
Collections.sort(ourCommands);
}

4
hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/RunServerCommand.java
View File

@ -48,6 +48,8 @@ public class RunServerCommand extends BaseCommand {
public void run(CommandLine theCommandLine) throws ParseException {
myPort = parseOptionInteger(theCommandLine, OPTION_P, DEFAULT_PORT);
// ((ch.qos.logback.classic.Logger)LoggerFactory.getLogger("/")).setLevel(Level.ERROR);
ourLog.info("Preparing HAPI FHIR JPA server");
File tempWarFile;
try {
@ -81,6 +83,8 @@ public class RunServerCommand extends BaseCommand {
ourLog.info("Server started on port {}", myPort);
ourLog.info("Web Testing UI : http://localhost:{}/", myPort);
ourLog.info("Server Base URL: http://localhost:{}/baseDstu2/", myPort);
}
public void run(String[] theArgs) {

179
hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/ValidationDataUploader.java
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@ -1,134 +1,157 @@
package ca.uhn.fhir.cli;
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.ClientProtocolException;
import org.hl7.fhir.instance.model.Bundle;
import org.hl7.fhir.instance.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.instance.model.StructureDefinition;
import org.hl7.fhir.instance.model.ValueSet;
import org.springframework.core.io.Resource;
import org.springframework.core.io.support.PathMatchingResourcePatternResolver;
import org.springframework.core.io.support.ResourcePatternResolver;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
import ca.uhn.fhir.model.dstu2.resource.StructureDefinition;
import ca.uhn.fhir.model.dstu2.resource.ValueSet;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.client.IGenericClient;
public class ValidationDataUploader extends BaseCommand {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValidationDataUploader.class);
public static void main(String[] args) throws Exception {
new ValidationDataUploader().execute();
@Override
public String getCommandDescription() {
return "Uploads the conformance resources (StructureDefinition and ValueSet) from the official FHIR definitions.";
}
private void execute() throws IOException, ClientProtocolException, UnsupportedEncodingException {
ourLog.info("Starting...");
@Override
public String getCommandName() {
return "upload-definitions";
}
FhirContext ctx = FhirContext.forDstu2Hl7Org();
@Override
public Options getOptions() {
Options options = new Options();
Option opt;
IGenericClient client = newClient(ctx,"");
opt = new Option("t", "target", true, "Base URL for the target server (e.g. \"http://example.com/fhir\")");
opt.setRequired(true);
options.addOption(opt);
int total;
int count;
// String vsContents =
// IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/valuesets.xml"),
// "UTF-8");
// Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, vsContents);
//
// int total = bundle.getEntry().size();
// int count = 1;
// for (BundleEntryComponent i : bundle.getEntry()) {
// ValueSet next = (ValueSet) i.getResource();
// next.setId(next.getIdElement().toUnqualifiedVersionless());
//
// ourLog.info("Uploading ValueSet {}/{} : {}", new Object[] {count,total,next.getIdElement().getValue()});
// client.update().resource(next).execute();
//
// count++;
// }
//
// ourLog.info("Finished uploading ValueSets");
return options;
}
// String vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml"), "UTF-8");
// Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, vsContents);
// total = bundle.getEntry().size();
// count = 1;
// for (BundleEntryComponent i : bundle.getEntry()) {
// ValueSet next = (ValueSet) i.getResource();
// next.setId(next.getIdElement().toUnqualifiedVersionless());
//
// ourLog.info("Uploading v3-codesystems ValueSet {}/{} : {}", new Object[] { count, total, next.getIdElement().getValue() });
// client.update().resource(next).execute();
//
// count++;
// }
@Override
public void run(CommandLine theCommandLine) throws ParseException {
String targetServer = theCommandLine.getOptionValue("t");
if (isBlank(targetServer)) {
throw new ParseException("No target server (-t) specified");
} else if (targetServer.startsWith("http") == false) {
throw new ParseException("Invalid target server specified, must begin with 'http'");
}
String vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/v2-tables.xml"), "UTF-8");
FhirContext ctx = FhirContext.forDstu2();
ourLog.info("Uploading definitions to server: " + targetServer);
IGenericClient client = newClient(ctx, targetServer);
long start = System.currentTimeMillis();
String vsContents;
try {
vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/valuesets.xml"), "UTF-8");
} catch (IOException e) {
throw new CommandFailureException(e.toString());
}
Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, vsContents);
int total = bundle.getEntry().size();
int count = 1;
for (Entry i : bundle.getEntry()) {
ValueSet next = (ValueSet) i.getResource();
next.setId(next.getIdElement().toUnqualifiedVersionless());
ourLog.info("Uploading ValueSet {}/{} : {}", new Object[] { count, total, next.getIdElement().getValue() });
client.update().resource(next).execute();
count++;
}
try {
vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml"), "UTF-8");
} catch (IOException e) {
throw new CommandFailureException(e.toString());
}
bundle = ctx.newXmlParser().parseResource(Bundle.class, vsContents);
total = bundle.getEntry().size();
count = 1;
for (BundleEntryComponent i : bundle.getEntry()) {
if (count > 1900) {
for (Entry i : bundle.getEntry()) {
ValueSet next = (ValueSet) i.getResource();
next.setId(next.getIdElement().toUnqualifiedVersionless());
ourLog.info("Uploading v3-codesystems ValueSet {}/{} : {}", new Object[] { count, total, next.getIdElement().getValue() });
client.update().resource(next).execute();
count++;
}
try {
vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/v2-tables.xml"), "UTF-8");
} catch (IOException e) {
throw new CommandFailureException(e.toString());
}
bundle = ctx.newXmlParser().parseResource(Bundle.class, vsContents);
total = bundle.getEntry().size();
count = 1;
for (Entry i : bundle.getEntry()) {
ValueSet next = (ValueSet) i.getResource();
next.setId(next.getIdElement().toUnqualifiedVersionless());
ourLog.info("Uploading v2-tables ValueSet {}/{} : {}", new Object[] { count, total, next.getIdElement().getValue() });
client.update().resource(next).execute();
}
count++;
}
ourLog.info("Finished uploading ValueSets");
ResourcePatternResolver patternResolver = new PathMatchingResourcePatternResolver();
Resource[] mappingLocations = patternResolver.getResources("classpath*:org/hl7/fhir/instance/model/profile/*.profile.xml");
Resource[] mappingLocations;
try {
mappingLocations = patternResolver.getResources("classpath*:org/hl7/fhir/instance/model/profile/*.profile.xml");
} catch (IOException e) {
throw new CommandFailureException(e.toString());
}
total = mappingLocations.length;
count = 1;
for (Resource i : mappingLocations) {
if (count > 140) {
StructureDefinition next = ctx.newXmlParser().parseResource(StructureDefinition.class, IOUtils.toString(i.getInputStream(), "UTF-8"));
StructureDefinition next;
try {
next = ctx.newXmlParser().parseResource(StructureDefinition.class, IOUtils.toString(i.getInputStream(), "UTF-8"));
} catch (Exception e) {
throw new CommandFailureException(e.toString());
}
next.setId(next.getIdElement().toUnqualifiedVersionless());
ourLog.info("Uploading StructureDefinition {}/{} : {}", new Object[] { count, total, next.getIdElement().getValue() });
client.update().resource(next).execute();
try {
client.update().resource(next).execute();
} catch (Exception e) {
ourLog.warn("Failed to upload {} - {}", next.getIdElement().getValue(), e.getMessage());
}
count++;
}
ourLog.info("Finished uploading ValueSets");
}
long delay = System.currentTimeMillis() - start;
@Override
public String getCommandDescription() {
// TODO Auto-generated method stub
return null;
}
@Override
public String getCommandName() {
// TODO Auto-generated method stub
return null;
}
@Override
public Options getOptions() {
// TODO Auto-generated method stub
return null;
}
@Override
public void run(CommandLine theCommandLine) throws ParseException {
// TODO Auto-generated method stub
ourLog.info("Finished uploading definitions to server (took {} ms)", delay);
}
}

31
hapi-fhir-cli/src/main/resources/logback-cli-on.xml
View File

@ -8,38 +8,11 @@
</encoder>
</appender>
<logger name="java.sql" additivity="false" level="warn">
<appender-ref ref="STDOUT" />
</logger>
<logger name="ca.uhn.fhir.jpa" additivity="false" level="info">
<appender-ref ref="STDOUT" />
</logger>
<logger name="ca.uhn.fhir.rest" additivity="false" level="warn">
<appender-ref ref="STDOUT" />
</logger>
<logger name="org.eclipse" additivity="false" level="warn">
<appender-ref ref="STDOUT" />
</logger>
<logger name="org.springframework" additivity="false" level="warn">
<appender-ref ref="STDOUT" />
</logger>
<logger name="org.apache" additivity="false" level="info">
<appender-ref ref="STDOUT" />
</logger>
<logger name="org.thymeleaf" additivity="false" level="warn">
<appender-ref ref="STDOUT" />
</logger>
<logger name="org.hibernate" additivity="false" level="warn">
<logger name="ca.uhn.fhir.cli" additivity="false" level="info">
<appender-ref ref="STDOUT" />
</logger>
<!--
<logger name="ca.uhn.fhir.rest.client" additivity="false" level="trace">
<appender-ref ref="STDOUT" />
</logger>
-->
<root level="info">
<root level="warn">
<appender-ref ref="STDOUT" />
</root>

2
hapi-fhir-cobertura/pom.xml
View File

@ -64,7 +64,7 @@
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.6.0</version>
<version>${slf4j_target_version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSubscriptionDstu2.java
View File

@ -106,16 +106,13 @@ public class FhirResourceDaoSubscriptionDstu2 extends FhirResourceDaoDstu2<Subsc
// SubscriptionCandidateResource
TypedQuery<SubscriptionTable> q = myEntityManager.createNamedQuery("Q_HFJ_SUBSCRIPTION_NEXT_CHECK", SubscriptionTable.class);
q.setParameter("next_check", new Date());
q.setParameter("status", SubscriptionStatusEnum.ACTIVE);
List<SubscriptionTable> subscriptions = q.getResultList();
Collection<Long> subscriptions = mySubscriptionTableDao.finsSubscriptionsWhichNeedToBeChecked(SubscriptionStatusEnum.ACTIVE, new Date());
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
int retVal = 0;
for (final SubscriptionTable nextSubscriptionTable : subscriptions) {
for (final Long nextSubscriptionTablePid : subscriptions) {
retVal += txTemplate.execute(new TransactionCallback<Integer>() {
@Override
public Integer doInTransaction(TransactionStatus theStatus) {

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ISubscriptionTableDao.java
View File

@ -29,6 +29,7 @@ import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import ca.uhn.fhir.jpa.entity.SubscriptionTable;
import ca.uhn.fhir.model.dstu2.valueset.SubscriptionStatusEnum;
public interface ISubscriptionTableDao extends JpaRepository<SubscriptionTable, Long> {
@ -46,4 +47,6 @@ public interface ISubscriptionTableDao extends JpaRepository<SubscriptionTable,
@Query("SELECT t FROM SubscriptionTable t WHERE t.myLastClientPoll < :cutoff OR (t.myLastClientPoll IS NULL AND t.myCreated < :cutoff)")
public Collection<SubscriptionTable> findInactiveBeforeCutoff(@Param("cutoff") Date theCutoff);
@Query("SELECT t.myId FROM SubscriptionTable t WHERE t.myStatus = :status AND t.myNextCheck <= :next_check")
public Collection<Long> finsSubscriptionsWhichNeedToBeChecked(@Param("status") SubscriptionStatusEnum theStatus, @Param("next_check") Date theNextCheck);
}

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/SubscriptionTable.java
View File

@ -52,7 +52,6 @@ import ca.uhn.fhir.model.dstu2.valueset.SubscriptionStatusEnum;
})
@NamedQueries({
@NamedQuery(name="Q_HFJ_SUBSCRIPTION_SET_STATUS", query="UPDATE SubscriptionTable t SET t.myStatus = :status WHERE t.myResId = :res_id"),
@NamedQuery(name="Q_HFJ_SUBSCRIPTION_NEXT_CHECK", query="SELECT t FROM SubscriptionTable t WHERE t.myStatus = :status AND t.myNextCheck <= :next_check"),
@NamedQuery(name="Q_HFJ_SUBSCRIPTION_GET_BY_RES", query="SELECT t FROM SubscriptionTable t WHERE t.myResId = :res_id")
})
//@formatter:on

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SubscriptionsDstu2Test.java
View File

@ -6,6 +6,7 @@ import static org.junit.Assert.fail;
import java.net.URI;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import org.eclipse.jetty.websocket.api.Session;
@ -19,6 +20,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.Test;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptor;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.resource.Subscription;
@ -250,6 +252,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
mySubscriptionDao.read(new IdDt("Subscription", socket.mySubsId));
Observation obs = new Observation();
ResourceMetadataKeyEnum.PROFILES.put(obs, Collections.singletonList(new IdDt("http://foo")));
obs.getSubject().setReference(pId);
obs.setStatus(ObservationStatusEnum.FINAL);
IIdType afterId1 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
@ -301,6 +304,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
IIdType pId = myPatientDao.create(p).getId().toUnqualifiedVersionless();
Subscription subs = new Subscription();
ResourceMetadataKeyEnum.PROFILES.put(subs, Collections.singletonList(new IdDt("http://foo")));
subs.getChannel().setType(SubscriptionChannelTypeEnum.WEBSOCKET);
subs.setCriteria("Observation?subject=Patient/" + pId.getIdPart());
subs.setStatus(SubscriptionStatusEnum.ACTIVE);

8
hapi-fhir-osgi-core/pom.xml
View File

@ -41,6 +41,14 @@
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
<version>1.3-SNAPSHOT</version>
</dependency>
<!-- Don't force OSGi users to use a newer version of SLF4j than we need -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j_target_version}</version>
</dependency>
</dependencies>
<build>

1
hapi-fhir-structures-dstu/src/main/java/ca/uhn/fhir/model/dstu/composite/NarrativeDt.java
View File

@ -90,6 +90,7 @@ public class NarrativeDt extends BaseNarrativeDt<NarrativeStatusEnum> {
return ca.uhn.fhir.util.ElementUtil.allPopulatedChildElements( theType, myStatus, myDiv );
}
/**
* Gets the value(s) for <b>status</b> (generated | extensions | additional).
* creating it if it does

2
hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/client/BearerTokenAuthInterceptorTest.java
View File

@ -39,7 +39,7 @@ public class BearerTokenAuthInterceptorTest {
public void before() {
myHttpClient = mock(HttpClient.class, new ReturnsDeepStubs());
ourCtx.getRestfulClientFactory().setHttpClient(myHttpClient);
ourCtx.getRestfulClientFactory().setServerValidationModeEnum(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
myHttpResponse = mock(HttpResponse.class, new ReturnsDeepStubs());
}

28
hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/model/dstu2/composite/NarrativeDt.java
View File

@ -98,6 +98,20 @@ public class NarrativeDt extends BaseNarrativeDt {
* <p>
* <b>Definition:</b>
* The status of the narrative - whether it's entirely generated (from just the defined data or the extensions too), or whether a human authored it and it may contain additional data
* </p>
*/
public BoundCodeDt<NarrativeStatusEnum> getStatusElement() {
return getStatus();
}
/**
* Gets the value(s) for <b>status</b> (generated | extensions | additional).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* The status of the narrative - whether it's entirely generated (from just the defined data or the extensions too), or whether a human authored it and it may contain additional data
* </p>
*/
public BoundCodeDt<NarrativeStatusEnum> getStatus() {
@ -132,6 +146,20 @@ public class NarrativeDt extends BaseNarrativeDt {
}
/**
* Gets the value(s) for <b>div</b> (Limited xhtml content).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b>
* The actual narrative content, a stripped down version of XHTML
* </p>
*/
public XhtmlDt getDivElement() {
return getDiv();
}
/**
* Gets the value(s) for <b>div</b> (Limited xhtml content).
* creating it if it does

31
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2Test.java
View File

@ -8,9 +8,12 @@ import java.util.ArrayList;
import java.util.List;
import java.util.UUID;
import ca.uhn.fhir.model.dstu2.resource.*;
import ca.uhn.fhir.model.dstu2.valueset.*;
import org.apache.commons.io.IOUtils;
import org.hamcrest.Matchers;
import org.junit.Assert;
import org.junit.Ignore;
import org.junit.Test;
import ca.uhn.fhir.context.ConfigurationException;
@ -26,20 +29,7 @@ import ca.uhn.fhir.model.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.dstu2.resource.Binary;
import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
import ca.uhn.fhir.model.dstu2.resource.Conformance;
import ca.uhn.fhir.model.dstu2.resource.DiagnosticReport;
import ca.uhn.fhir.model.dstu2.resource.Medication;
import ca.uhn.fhir.model.dstu2.resource.MedicationOrder;
import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.resource.QuestionnaireResponse;
import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
import ca.uhn.fhir.model.dstu2.valueset.IdentifierUseEnum;
import ca.uhn.fhir.model.dstu2.valueset.MaritalStatusCodesEnum;
import ca.uhn.fhir.model.dstu2.valueset.ObservationStatusEnum;
import ca.uhn.fhir.model.primitive.DateDt;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.IdDt;
@ -1012,4 +1002,19 @@ public class JsonParserDstu2Test {
Assert.assertThat(message, containsString("contained"));
}
// see #241
@Ignore
@Test
public void testEncodeThenParseShouldNotAddSpuriousId() throws Exception {
Condition condition = new Condition().setVerificationStatus(ConditionVerificationStatusEnum.CONFIRMED);
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
ca.uhn.fhir.model.dstu2.resource.Bundle.Entry entry = new ca.uhn.fhir.model.dstu2.resource.Bundle.Entry();
entry.setFullUrl(IdDt.newRandomUuid());
entry.setResource(condition);
bundle.getEntry().add(entry);
IParser parser = ourCtx.newJsonParser();
String json = parser.encodeResourceToString(bundle);
bundle = (ca.uhn.fhir.model.dstu2.resource.Bundle) parser.parseResource(json);
assertTrue(bundle.getEntry().get(0).getResource().getIdElement().isEmpty());
}
}

14
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/SearchDstu2Test.java
View File

@ -17,6 +17,7 @@ import org.apache.http.HttpResponse;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
@ -163,7 +164,20 @@ public class SearchDstu2Test {
assertEquals("2002", ourLastDateAndList.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(1).getValueAsString());
assertThat(responseContent, containsString("SYSTEM"));
}
@Test
public void testSearchByPut() throws Exception {
HttpPut httpGet = new HttpPut("http://localhost:" + ourPort + "/Patient/_search");
StringEntity entity = new StringEntity("searchDateAndList=2001,2002&searchDateAndList=2003,2004", ContentType.APPLICATION_FORM_URLENCODED);
httpGet.setEntity(entity);
HttpResponse status = ourClient.execute(httpGet);
String responseContent = IOUtils.toString(status.getEntity().getContent());
IOUtils.closeQuietly(status.getEntity().getContent());
ourLog.info(responseContent);
assertEquals(400, status.getStatusLine().getStatusCode());
}
@Test
public void testSearchByPostWithBodyAndUrlParams() throws Exception {

33
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/ServerConformanceProviderDstu2Test.java
View File

@ -1,8 +1,13 @@
package ca.uhn.fhir.rest.server;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.Mockito.*;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import java.util.Collection;
import java.util.List;
@ -282,7 +287,7 @@ public class ServerConformanceProviderDstu2Test {
assertEquals("1", opDef.getParameter().get(2).getMinElement().getValueAsString());
assertEquals("2", opDef.getParameter().get(2).getMaxElement().getValueAsString());
assertEquals("string", opDef.getParameter().get(2).getTypeElement().getValueAsString());
}
}
@Test
public void testProviderWithRequiredAndOptional() throws Exception {
@ -451,7 +456,7 @@ public class ServerConformanceProviderDstu2Test {
}
@Delete
public MethodOutcome delete(@IdParam IdDt theId, @ConditionalUrlParam(supportsMultiple=true) String theConditionalUrl) {
public MethodOutcome delete(@IdParam IdDt theId, @ConditionalUrlParam(supportsMultiple = true) String theConditionalUrl) {
return null;
}
@ -486,7 +491,8 @@ public class ServerConformanceProviderDstu2Test {
public static class MultiOptionalProvider {
@Search(type = Patient.class)
public Patient findPatient(@Description(shortDefinition = "The patient's identifier") @OptionalParam(name = Patient.SP_IDENTIFIER) IdentifierDt theIdentifier, @Description(shortDefinition = "The patient's name") @OptionalParam(name = Patient.SP_NAME) StringDt theName) {
public Patient findPatient(@Description(shortDefinition = "The patient's identifier") @OptionalParam(name = Patient.SP_IDENTIFIER) IdentifierDt theIdentifier,
@Description(shortDefinition = "The patient's name") @OptionalParam(name = Patient.SP_NAME) StringDt theName) {
return null;
}
@ -518,10 +524,9 @@ public class ServerConformanceProviderDstu2Test {
public static class PlainProviderWithExtendedOperationOnNoType {
@Operation(name = "plain", idempotent = true, returnParameters= {
@OperationParam(min=1, max=2, name="out1", type=StringDt.class)
})
public ca.uhn.fhir.rest.server.IBundleProvider everything(javax.servlet.http.HttpServletRequest theServletRequest, @IdParam ca.uhn.fhir.model.primitive.IdDt theId, @OperationParam(name = "start") DateDt theStart, @OperationParam(name = "end") DateDt theEnd) {
@Operation(name = "plain", idempotent = true, returnParameters = { @OperationParam(min = 1, max = 2, name = "out1", type = StringDt.class) })
public ca.uhn.fhir.rest.server.IBundleProvider everything(javax.servlet.http.HttpServletRequest theServletRequest, @IdParam ca.uhn.fhir.model.primitive.IdDt theId,
@OperationParam(name = "start") DateDt theStart, @OperationParam(name = "end") DateDt theEnd) {
return null;
}
@ -530,7 +535,8 @@ public class ServerConformanceProviderDstu2Test {
public static class ProviderWithExtendedOperationReturningBundle implements IResourceProvider {
@Operation(name = "everything", idempotent = true)
public ca.uhn.fhir.rest.server.IBundleProvider everything(javax.servlet.http.HttpServletRequest theServletRequest, @IdParam ca.uhn.fhir.model.primitive.IdDt theId, @OperationParam(name = "start") DateDt theStart, @OperationParam(name = "end") DateDt theEnd) {
public ca.uhn.fhir.rest.server.IBundleProvider everything(javax.servlet.http.HttpServletRequest theServletRequest, @IdParam ca.uhn.fhir.model.primitive.IdDt theId,
@OperationParam(name = "start") DateDt theStart, @OperationParam(name = "end") DateDt theEnd) {
return null;
}
@ -545,8 +551,9 @@ public class ServerConformanceProviderDstu2Test {
@Description(shortDefinition = "This is a search for stuff!")
@Search
public List<DiagnosticReport> findDiagnosticReportsByPatient(@RequiredParam(name = DiagnosticReport.SP_SUBJECT + '.' + Patient.SP_IDENTIFIER) IdentifierDt thePatientId, @OptionalParam(name = DiagnosticReport.SP_CODE) TokenOrListParam theNames,
@OptionalParam(name = DiagnosticReport.SP_DATE) DateRangeParam theDateRange, @IncludeParam(allow = { "DiagnosticReport.result" }) Set<Include> theIncludes) throws Exception {
public List<DiagnosticReport> findDiagnosticReportsByPatient(@RequiredParam(name = DiagnosticReport.SP_SUBJECT + '.' + Patient.SP_IDENTIFIER) IdentifierDt thePatientId,
@OptionalParam(name = DiagnosticReport.SP_CODE) TokenOrListParam theNames, @OptionalParam(name = DiagnosticReport.SP_DATE) DateRangeParam theDateRange,
@IncludeParam(allow = { "DiagnosticReport.result" }) Set<Include> theIncludes) throws Exception {
return null;
}

7
hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/FhirInstanceValidator.java
View File

@ -189,6 +189,13 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
throw new IllegalArgumentException("Unknown encoding: " + theEncoding);
}
for (int i = 0; i < messages.size(); i++) {
ValidationMessage next = messages.get(i);
if ("Binding has no source, so can't be checked".equals(next.getMessage())) {
messages.remove(i);
i--;
}
}
return messages;
}

2
hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/validation/FhirInstanceValidatorTest.java
View File

@ -230,7 +230,7 @@ public class FhirInstanceValidatorTest {
.toString(FhirInstanceValidator.class.getResourceAsStream("/medicationstatement_invalidelement.xml"));
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> res = logResultsAndReturnNonInformationalOnes(output);
List<SingleValidationMessage> res = logResultsAndReturnAll(output);
ourLog.info(res.toString());
for (SingleValidationMessage nextMessage : res) {

8
pom.xml
View File

@ -237,6 +237,14 @@
<thymeleaf-version>2.1.4.RELEASE</thymeleaf-version>
<ebay_cors_filter_version>1.0.1</ebay_cors_filter_version>
<xmlunit_version>1.6</xmlunit_version>
<!--
We are aiming to still work on a very old version of SLF4j even though
we depend on the newest, just to be nice to users of the API. This version
is tested in the hapi-fhir-cobertura.
-->
<slf4j_target_version>1.6.0</slf4j_target_version>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
</properties>