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Cleanup tests for java config in JPA
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@jamesagnew
jamesagnew committed Oct 20, 2015
1 parent 9c0f6f9 commit 938a251
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Showing 22 changed files with 2,880 additions and 340 deletions.
114 changes: 105 additions & 9 deletions hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
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Original file line number Diff line number Diff line change
Expand Up @@ -81,14 +81,24 @@ public void postConstruct() {

@Override
public ValueSet expand(IIdType theId, String theFilter) {
ValueSet source = loadValueSetForExpansion(theId);
return expand(source, theFilter);

}

private ValueSet loadValueSetForExpansion(IIdType theId) {
if (theId.getValue().startsWith("http://hl7.org/fhir/")) {
org.hl7.fhir.instance.model.ValueSet valueSet = myValidationSupport.fetchResource(myRiCtx, org.hl7.fhir.instance.model.ValueSet.class, theId.getValue());
if (valueSet != null) {
return getContext().newJsonParser().parseResource(ValueSet.class, myRiCtx.newJsonParser().encodeResourceToString(valueSet));
}
}
BaseHasResource sourceEntity = readEntity(theId);
if (sourceEntity == null) {
throw new ResourceNotFoundException(theId);
}
ValueSet source = (ValueSet) toResource(sourceEntity, false);

return expand(source, theFilter);

return source;
}

@Override
Expand Down Expand Up @@ -182,7 +192,7 @@ public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateC
if (!haveCodeableConcept && !haveCoding && !haveCode) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
}
if (!(haveCodeableConcept ^ haveCoding ^ haveCode)) {
if (!multiXor(haveCodeableConcept, haveCoding, haveCode)) {
throw new InvalidRequestException("$validate-code can only validate (system AND code) OR (coding) OR (codeableConcept)");
}

Expand All @@ -199,11 +209,9 @@ public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateC
if (theCode == null || theCode.isEmpty()) {
throw new InvalidRequestException("Either ValueSet ID or ValueSet identifier or system and code must be provided. Unable to validate.");
}
Set<Long> ids = searchForIds(ValueSet.SP_CODE, new TokenParam(toStringOrNull(theSystem), theCode.getValue()));
valueSetIds = new ArrayList<IIdType>();
for (Long next : ids) {
valueSetIds.add(new IdDt("ValueSet", next));
}
String code = theCode.getValue();
String system = toStringOrNull(theSystem);
valueSetIds = findValueSetIdsContainingSystemAndCode(code, system);
}

for (IIdType nextId : valueSetIds) {
Expand All @@ -223,6 +231,30 @@ public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateC
return new ValidateCodeResult(false, "Code not found", null);
}

private List<IIdType> findValueSetIdsContainingSystemAndCode(String theCode, String theSystem) {
if (theSystem != null && theSystem.startsWith("http://hl7.org/fhir/")) {
return Collections.singletonList((IIdType)new IdDt(theSystem));
}

List<IIdType> valueSetIds;
Set<Long> ids = searchForIds(ValueSet.SP_CODE, new TokenParam(theSystem, theCode));
valueSetIds = new ArrayList<IIdType>();
for (Long next : ids) {
valueSetIds.add(new IdDt("ValueSet", next));
}
return valueSetIds;
}

private static boolean multiXor(boolean... theValues) {
int count = 0;
for (int i = 0; i < theValues.length; i++) {
if (theValues[i]) {
count++;
}
}
return count == 1;
}

private String toStringOrNull(IPrimitiveType<String> thePrimitive) {
return thePrimitive != null ? thePrimitive.getValue() : null;
}
Expand Down Expand Up @@ -259,4 +291,68 @@ private ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validate
return null;
}

@Override
public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.LookupCodeResult lookupCode(CodeDt theCode, UriDt theSystem, CodingDt theCoding) {
boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
boolean haveCode = theCode != null && theCode.isEmpty() == false;
boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;

if (!haveCoding && !(haveSystem && haveCode)) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
}
if (!multiXor(haveCoding, (haveSystem && haveCode)) || (haveSystem != haveCode)) {
throw new InvalidRequestException("$lookup can only validate (system AND code) OR (coding.system AND coding.code)");
}

String code;
String system;
if (haveCoding) {
code = theCoding.getCode();
system = theCoding.getSystem();
} else {
code = theCode.getValue();
system = theSystem.getValue();
}

List<IIdType> valueSetIds = findValueSetIdsContainingSystemAndCode(code, system);
for (IIdType nextId : valueSetIds) {
ValueSet expansion = expand(nextId, null);
List<ExpansionContains> contains = expansion.getExpansion().getContains();
ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.LookupCodeResult result = lookup(contains, system, code);
if (result != null) {
return result;
}
}

LookupCodeResult retVal = new LookupCodeResult();
retVal.setFound(false);
retVal.setSearchedForCode(code);
retVal.setSearchedForSystem(system);
return retVal;
}

private ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.LookupCodeResult lookup(List<ExpansionContains> theContains, String theSystem, String theCode) {
for (ExpansionContains nextCode : theContains) {

String system = nextCode.getSystem();
String code = nextCode.getCode();
if (theSystem.equals(system) && theCode.equals(code)) {
ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.LookupCodeResult retVal = new LookupCodeResult();
retVal.setSearchedForCode(code);
retVal.setSearchedForSystem(system);
retVal.setFound(true);
if (nextCode.getAbstract() != null) {
retVal.setCodeIsAbstract(nextCode.getAbstract().booleanValue());
}
retVal.setCodeDisplay(nextCode.getDisplay());
retVal.setCodeSystemVersion(nextCode.getVersion());
retVal.setCodeSystemDisplayName("Unknown"); // TODO: implement
return retVal;
}

}

return null;
}

}
70 changes: 69 additions & 1 deletion hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoValueSet.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,13 +33,81 @@
public interface IFhirResourceDaoValueSet<T extends IBaseResource> extends IFhirResourceDao<T> {

ValueSet expand(IIdType theId, String theFilter);

ValueSet expand(ValueSet theSource, String theFilter);

ValueSet expandByIdentifier(String theUri, String theFilter);

LookupCodeResult lookupCode(CodeDt theCode, UriDt theSystem, CodingDt theCoding);

ValidateCodeResult validateCode(UriDt theValueSetIdentifier, IIdType theId, CodeDt theCode, UriDt theSystem, StringDt theDisplay, CodingDt theCoding, CodeableConceptDt theCodeableConcept);

public class LookupCodeResult {
private String myCodeDisplay;
private boolean myCodeIsAbstract;
private String myCodeSystemDisplayName;
private String myCodeSystemVersion;
private boolean myFound;
private String mySearchedForCode;
private String mySearchedForSystem;

public String getCodeDisplay() {
return myCodeDisplay;
}

public String getCodeSystemDisplayName() {
return myCodeSystemDisplayName;
}

public String getCodeSystemVersion() {
return myCodeSystemVersion;
}

public String getSearchedForCode() {
return mySearchedForCode;
}

public String getSearchedForSystem() {
return mySearchedForSystem;
}

public boolean isCodeIsAbstract() {
return myCodeIsAbstract;
}

public boolean isFound() {
return myFound;
}

public void setCodeDisplay(String theCodeDisplay) {
myCodeDisplay = theCodeDisplay;
}

public void setCodeIsAbstract(boolean theCodeIsAbstract) {
myCodeIsAbstract = theCodeIsAbstract;
}

public void setCodeSystemDisplayName(String theCodeSystemDisplayName) {
myCodeSystemDisplayName = theCodeSystemDisplayName;
}

public void setCodeSystemVersion(String theCodeSystemVersion) {
myCodeSystemVersion = theCodeSystemVersion;
}

public void setFound(boolean theFound) {
myFound = theFound;
}

public void setSearchedForCode(String theSearchedForCode) {
mySearchedForCode = theSearchedForCode;
}

public void setSearchedForSystem(String theSearchedForSystem) {
mySearchedForSystem = theSearchedForSystem;
}
}

public class ValidateCodeResult {
private String myDisplay;
private String myMessage;
Expand Down
40 changes: 40 additions & 0 deletions ...ver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProviderValueSetDstu2.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
import org.apache.commons.lang3.BooleanUtils;

import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
Expand All @@ -41,6 +42,7 @@
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;

public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDstu2<ValueSet> {

Expand Down Expand Up @@ -102,6 +104,42 @@ private String toFilterString(StringDt theFilter) {
return theFilter != null ? theFilter.getValue() : null;
}

//@formatter:off
@Operation(name = "$lookup", idempotent = true, returnParameters= {
@OperationParam(name="name", type=StringDt.class, min=1),
@OperationParam(name="version", type=StringDt.class, min=0),
@OperationParam(name="display", type=StringDt.class, min=1),
@OperationParam(name="abstract", type=BooleanDt.class, min=1),
})
public Parameters lookup(
HttpServletRequest theServletRequest,
@OperationParam(name="code", min=0, max=1) CodeDt theCode,
@OperationParam(name="system", min=0, max=1) UriDt theSystem,
@OperationParam(name="coding", min=0, max=1) CodingDt theCoding
) {
//@formatter:on

startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet> dao = (IFhirResourceDaoValueSet<ValueSet>) getDao();
LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding);
if (result.isFound()==false) {
throw new ResourceNotFoundException("Unable to find code[" + result.getSearchedForCode() + "] in system[" + result.getSearchedForSystem() + "]");
}
Parameters retVal = new Parameters();
retVal.addParameter().setName("name").setValue(new StringDt(result.getCodeSystemDisplayName()));
if (isNotBlank(result.getCodeSystemVersion())) {
retVal.addParameter().setName("version").setValue(new StringDt(result.getCodeSystemVersion()));
}
retVal.addParameter().setName("display").setValue(new StringDt(result.getCodeDisplay()));
retVal.addParameter().setName("abstract").setValue(new BooleanDt(result.isCodeIsAbstract()));
return retVal;
} finally {
endRequest(theServletRequest);
}
}


//@formatter:off
@Operation(name = "$validate-code", idempotent = true, returnParameters= {
@OperationParam(name="result", type=BooleanDt.class, min=1),
Expand Down Expand Up @@ -137,4 +175,6 @@ public Parameters validateCode(
endRequest(theServletRequest);
}
}


}
8 changes: 8 additions & 0 deletions hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/DispatcherServletConfig.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
package ca.uhn.fhir.jpa.config;

import org.springframework.context.annotation.Configuration;

@Configuration
public class DispatcherServletConfig {
//nothing
}
5 changes: 4 additions & 1 deletion ...-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/BaseResourceProviderDstu2Test.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,10 +20,13 @@
import org.junit.Before;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.WebApplicationContext;
import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
import org.springframework.web.context.support.GenericWebApplicationContext;
import org.springframework.web.context.support.WebApplicationContextUtils;
import org.springframework.web.servlet.DispatcherServlet;

import ca.uhn.fhir.jpa.config.DispatcherServletConfig;
import ca.uhn.fhir.jpa.config.TestDstu2Config;
import ca.uhn.fhir.jpa.dao.BaseJpaDstu2Test;
import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
import ca.uhn.fhir.model.api.Bundle;
Expand Down Expand Up @@ -126,7 +129,7 @@ public void before() throws Exception {

DispatcherServlet dispatcherServlet = new DispatcherServlet();
// dispatcherServlet.setApplicationContext(webApplicationContext);
dispatcherServlet.setContextConfigLocation("classpath:/fhir-spring-subscription-config-dstu2.xml");
dispatcherServlet.setContextClass(AnnotationConfigWebApplicationContext.class);
ServletHolder subsServletHolder = new ServletHolder();
subsServletHolder.setServlet(dispatcherServlet);
proxyHandler.addServlet(subsServletHolder, "/*");
Expand Down
15 changes: 10 additions & 5 deletions ...fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu1Test.java
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,11 @@
package ca.uhn.fhir.jpa.provider;

import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;

import java.util.ArrayList;
import java.util.Date;
Expand All @@ -21,9 +25,10 @@
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.springframework.context.support.ClassPathXmlApplicationContext;
import org.springframework.context.annotation.AnnotationConfigApplicationContext;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.TestDstu1Config;
import ca.uhn.fhir.jpa.dao.BaseJpaTest;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
Expand Down Expand Up @@ -60,7 +65,7 @@

public class ResourceProviderDstu1Test extends BaseJpaTest {

private static ClassPathXmlApplicationContext ourAppCtx;
private static AnnotationConfigApplicationContext ourAppCtx;
private static IGenericClient ourClient;
private static DaoConfig ourDaoConfig;
private static FhirContext ourCtx = FhirContext.forDstu1();
Expand Down Expand Up @@ -523,7 +528,7 @@ public static void beforeClass() throws Exception {

ourServerBase = "http://localhost:" + port + "/fhir/context";

ourAppCtx = new ClassPathXmlApplicationContext("hapi-fhir-server-resourceproviders-dstu1.xml", "fhir-jpabase-spring-test-config.xml");
ourAppCtx = new AnnotationConfigApplicationContext(TestDstu1Config.class);

ourDaoConfig = (DaoConfig) ourAppCtx.getBean(DaoConfig.class);

Expand Down

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