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hapi-fhir
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More work on JPA

This commit is contained in:
jamesagnew 2014-05-29 19:00:16 -04:00
parent a0b120f70e
commit be44a2bca2
26 changed files with 2301 additions and 50 deletions
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8
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/Bundle.java
View File

@ -292,4 +292,12 @@ public class Bundle extends BaseBundle /* implements IElement */{
}
public static Bundle withResources(ArrayList<IResource> theUploadBundle, FhirContext theContext, String theServerBase) {
Bundle retVal = new Bundle();
for (IResource next : theUploadBundle) {
retVal.addResource(next, theContext, theServerBase);
}
return retVal;
}
}

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnum.java
View File

@ -164,6 +164,8 @@ public enum ResourceMetadataKeyEnum {
} else {
return (IdDt) retValObj;
}
} else if (retValObj instanceof Number) {
return new IdDt(((Number)retValObj).toString());
}
throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected " + IdDt.class.getCanonicalName());
}

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseHttpClientInvocationWithContents.java
View File

@ -114,7 +114,7 @@ public abstract class BaseHttpClientInvocationWithContents extends BaseHttpClien
if (myTagList != null) {
contents = parser.encodeTagListToString(myTagList);
} else if (myResources != null) {
Bundle bundle = BaseResourceReturningMethodBinding.createBundleFromResourceList(myContext, "", myResources, theEncoding, theUrlBase, "", false, NarrativeModeEnum.NORMAL);
Bundle bundle = BaseResourceReturningMethodBinding.createBundleFromResourceList(myContext, "", myResources, theEncoding, "", "", false, NarrativeModeEnum.NORMAL);
contents = parser.encodeBundleToString(bundle);
} else {
contents = parser.encodeResourceToString(myResource);

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/provider/ServerConformanceProvider.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.rest.server.provider;
*/
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
@ -79,7 +80,14 @@ public class ServerConformanceProvider {
Set<RestfulOperationSystemEnum> systemOps = new HashSet<RestfulOperationSystemEnum>();
for (ResourceBinding next : myRestfulServer.getResourceBindings()) {
List<ResourceBinding> bindings = new ArrayList<ResourceBinding>(myRestfulServer.getResourceBindings());
Collections.sort(bindings, new Comparator<ResourceBinding>() {
@Override
public int compare(ResourceBinding theArg0, ResourceBinding theArg1) {
return theArg0.getResourceName().compareToIgnoreCase(theArg1.getResourceName());
}});
for (ResourceBinding next : bindings) {
Set<RestfulOperationTypeEnum> resourceOps = new HashSet<RestfulOperationTypeEnum>();
RestResource resource = rest.addResource();

2
hapi-fhir-base/src/main/resources/ca/uhn/fhir/rest/server/tester/PublicTester.html
View File

@ -66,7 +66,7 @@ This file is a Thymeleaf template for the
<tr>
<td class="propertyKeyCell">Pretty Printing</td>
<td>
<input type="checkbox" id="configPretty"/>
<input type="checkbox" id="configPretty" checked="checked"/>
</td>
</tr>
</table>

3
hapi-fhir-base/src/main/resources/ca/uhn/fhir/rest/server/tester/PublicTesterResult.html
View File

@ -28,7 +28,8 @@ This file is a Thymeleaf template for the
</tr>
</table>
<div class="bodyHeaderBlock">
Executed invocation against FHIR RESTful Server in ${latencyMs}ms
Executed invocation against FHIR RESTful Server in
<th:block th:text="${latencyMs} + 'ms'"/>
</div>
<table border="0" width="100%" cellpadding="0" cellspacing="0" style="margin-top: 4px;">

10
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/client/TransactionClientTest.java
View File

@ -79,15 +79,15 @@ public class TransactionClientTest {
client.searchWithParam(resources);
assertEquals(HttpPost.class, capt.getValue().getClass());
HttpPost get = (HttpPost) capt.getValue();
assertEquals("http://foo/", get.getURI().toString());
HttpPost post = (HttpPost) capt.getValue();
assertEquals("http://foo/", post.getURI().toString());
Bundle bundle = ctx.newXmlParser().parseBundle(new InputStreamReader(get.getEntity().getContent()));
Bundle bundle = ctx.newXmlParser().parseBundle(new InputStreamReader(post.getEntity().getContent()));
ourLog.info(ctx.newXmlParser().setPrettyPrint(true).encodeBundleToString(bundle));
assertEquals(2, bundle.size());
assertEquals("http://foo/Patient/testPersistWithSimpleLinkP01", bundle.getEntries().get(0).getId().getValue());
assertEquals("http://foo/Patient/testPersistWithSimpleLinkP01", bundle.getEntries().get(0).getLinkSelf().getValue());
assertEquals("Patient/testPersistWithSimpleLinkP01", bundle.getEntries().get(0).getId().getValue());
assertEquals("Patient/testPersistWithSimpleLinkP01", bundle.getEntries().get(0).getLinkSelf().getValue());
assertEquals(null, bundle.getEntries().get(0).getLinkAlternate().getValue());
assertTrue(bundle.getEntries().get(1).getId().isEmpty());

1
hapi-fhir-jpaserver-base/.gitignore vendored
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@ -1,2 +1,3 @@
target/
/bin
nohup.out

6
hapi-fhir-jpaserver-base/pom.xml
View File

@ -21,6 +21,12 @@
<version>0.4-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.1.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>

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

@ -238,6 +238,10 @@ public abstract class BaseFhirDao {
if (nextValue.isEmpty()) {
continue;
}
if (nextValue.getReference().getValue().startsWith("#")) {
// This is a contained resource reference
continue;
}
String typeString = nextValue.getResourceId().getResourceType();
if (isBlank(typeString)) {

75
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDao.java
View File

@ -73,8 +73,15 @@ public class FhirSystemDao extends BaseFhirDao implements IFhirSystemDao {
}
IdDt newId = new IdDt(resourceName + '/' + entity.getId());
ourLog.info("Incoming ID[{}] has been assigned ID[{}]", nextId, newId);
idConversions.put(nextId, newId);
if (nextId.isEmpty()) {
ourLog.info("Transaction resource (with no preexisting ID) has been assigned new ID[{}]", nextId, newId);
} else if (newId.equals(entity.getId())) {
ourLog.info("Transaction resource ID[{}] is being updated", newId);
} else {
ourLog.info("Transaction resource ID[{}] has been assigned new ID[{}]", nextId, newId);
idConversions.put(nextId, newId);
}
persistedResources.add(entity);
}
@ -87,6 +94,8 @@ public class FhirSystemDao extends BaseFhirDao implements IFhirSystemDao {
IdDt newId = idConversions.get(nextId);
ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
nextRef.setResourceId(newId);
} else {
ourLog.info(" * Reference [{}] does not exist in bundle", nextId);
}
}
}
@ -106,38 +115,38 @@ public class FhirSystemDao extends BaseFhirDao implements IFhirSystemDao {
@Override
public TagList getAllTags() {
// CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
// CriteriaQuery<Tuple> cq = builder.createQuery(Tag)
// Root<?> from = cq.from(ResourceTable.class);
// cq.multiselect(from.get("myId").as(Long.class), from.get("myUpdated").as(Date.class));
//
// List<Predicate> predicates = new ArrayList<Predicate>();
// if (theSince != null) {
// Predicate low = builder.greaterThanOrEqualTo(from.<Date> get("myUpdated"), theSince);
// predicates.add(low);
// }
//
// if (theResourceName != null) {
// predicates.add(builder.equal(from.get("myResourceType"), theResourceName));
// }
// if (theId != null) {
// predicates.add(builder.equal(from.get("myId"), theId));
// }
//
// cq.where(builder.and(predicates.toArray(new Predicate[0])));
//
// cq.orderBy(builder.desc(from.get("myUpdated")));
// TypedQuery<Tuple> q = myEntityManager.createQuery(cq);
// if (theLimit > 0) {
// q.setMaxResults(theLimit);
// }
// for (Tuple next : q.getResultList()) {
// long id = (Long) next.get(0);
// Date updated = (Date) next.get(1);
// tuples.add(new HistoryTuple(ResourceTable.class, updated, id));
// }
// CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
// CriteriaQuery<Tuple> cq = builder.createQuery(Tag)
// Root<?> from = cq.from(ResourceTable.class);
// cq.multiselect(from.get("myId").as(Long.class), from.get("myUpdated").as(Date.class));
//
// List<Predicate> predicates = new ArrayList<Predicate>();
// if (theSince != null) {
// Predicate low = builder.greaterThanOrEqualTo(from.<Date> get("myUpdated"), theSince);
// predicates.add(low);
// }
//
// if (theResourceName != null) {
// predicates.add(builder.equal(from.get("myResourceType"), theResourceName));
// }
// if (theId != null) {
// predicates.add(builder.equal(from.get("myId"), theId));
// }
//
// cq.where(builder.and(predicates.toArray(new Predicate[0])));
//
// cq.orderBy(builder.desc(from.get("myUpdated")));
// TypedQuery<Tuple> q = myEntityManager.createQuery(cq);
// if (theLimit > 0) {
// q.setMaxResults(theLimit);
// }
// for (Tuple next : q.getResultList()) {
// long id = (Long) next.get(0);
// Date updated = (Date) next.get(1);
// tuples.add(new HistoryTuple(ResourceTable.class, updated, id));
// }
return null;
return null;
}
}

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

@ -45,8 +45,8 @@ public interface IFhirResourceDao<T extends IResource> {
List<T> history();
List<IResource> history(Date theDate, int theLimit);
List<IResource> history(Date theDate, Integer theLimit);
List<IResource> history(Long theId, Date theSince, int theLimit);
List<IResource> history(Long theId, Date theSince, Integer theLimit);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirSystemDao.java
View File

@ -10,7 +10,7 @@ public interface IFhirSystemDao {
void transaction(List<IResource> theResources);
List<IResource> history(Date theDate, int theLimit);
List<IResource> history(Date theDate, Integer theLimit);
TagList getAllTags();

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

@ -4,6 +4,8 @@ import java.util.Collection;
import java.util.Date;
import javax.persistence.Column;
import javax.persistence.EnumType;
import javax.persistence.Enumerated;
import javax.persistence.Lob;
import javax.persistence.MappedSuperclass;
import javax.persistence.Temporal;
@ -17,7 +19,8 @@ import ca.uhn.fhir.rest.server.EncodingEnum;
@MappedSuperclass
public abstract class BaseHasResource {
@Column(name = "RES_ENCODING", nullable = false)
@Column(name = "RES_ENCODING", nullable = false, length=4)
@Enumerated(EnumType.STRING)
private EncodingEnum myEncoding;
@Temporal(TemporalType.TIMESTAMP)

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

@ -20,7 +20,6 @@ import javax.persistence.Version;
import org.hibernate.annotations.Index;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.server.Constants;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/JpaSystemProvider.java
View File

@ -38,7 +38,7 @@ public class JpaSystemProvider {
}
@History
List<IResource> getHistoryServerWithCriteria(@Since Date theDate, @Count Integer theCount) {
public List<IResource> getHistoryServerWithCriteria(@Since Date theDate, @Count Integer theCount) {
return myDao.history(theDate, theCount);
}
}

15
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoTest.java
View File

@ -3,15 +3,20 @@ package ca.uhn.fhir.jpa.dao;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.springframework.context.support.ClassPathXmlApplicationContext;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
@ -83,6 +88,16 @@ public class FhirSystemDaoTest {
}
@Test
public void testTransactionFromBundle() throws Exception {
InputStream bundleRes = FhirSystemDaoTest.class.getResourceAsStream("/bundle.json");
Bundle bundle = new FhirContext().newJsonParser().parseBundle(new InputStreamReader(bundleRes));
List<IResource> res = bundle.toListOfResources();
ourSystemDao.transaction(res);
}
@Test
public void testPersistWithSimpleLink() {
Patient patient = new Patient();

690
hapi-fhir-jpaserver-base/src/test/resources/bundle.json Normal file
View File

@ -0,0 +1,690 @@
{
"resourceType":"Bundle",
"entry":[
{
"deleted":null,
"title":"Patient http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/Patient/5556918",
"id":"Patient/5556918",
"link":[
{
"rel":"self",
"href":"Patient/5556918"
}
],
"published":"2014-05-29T10:49:32-04:00",
"content":{
"resourceType":"Patient",
"id":"http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/Patient/5556918",
"text":{
"status":"generated",
"div":"<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> Donald null <b>DUCK </b></div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>7000135</td></tr><tr><td>Address</td><td><span>10 Duxon Street </span><br/><span>VICTORIA </span><span>BC </span><span>Can </span></td></tr><tr><td>Date of birth</td><td><span>01 June 1980</span></td></tr></tbody></table></div>"
},
"identifier":[
{
"use":"official",
"label":"University Health Network MRN 7000135",
"system":"urn:oid:2.16.840.1.113883.3.239.18.148",
"value":"7000135",
"assigner":{
"resource":"Organization/1.3.6.1.4.1.12201"
}
}
],
"name":[
{
"family":[
"Duck"
],
"given":[
"Donald"
]
}
],
"telecom":[
{
"system":"phone",
"use":"home"
},
{
"system":"phone",
"use":"work"
},
{
"system":"phone",
"use":"mobile"
},
{
"system":"email",
"use":"home"
}
],
"gender":{
"coding":[
{
"system":"http://hl7.org/fhir/v3/AdministrativeGender",
"code":"M"
}
]
},
"birthDate":"1980-06-01T00:00:00",
"address":[
{
"use":"home",
"line":[
"10 Duxon Street"
],
"city":"VICTORIA",
"state":"BC",
"zip":"V8N 1Y4",
"country":"Can"
}
],
"managingOrganization":{
"resource":"Organization/1.3.6.1.4.1.12201"
}
}
},
{
"deleted":null,
"title":"DiagnosticReport http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/DiagnosticReport/5978827",
"id":"DiagnosticReport/5978827",
"link":[
{
"rel":"self",
"href":"DiagnosticReport/5978827"
}
],
"published":"2014-05-29T10:49:33-04:00",
"content":{
"resourceType":"DiagnosticReport",
"id":"http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/DiagnosticReport/5978827",
"text":{
"status":"generated",
"div":"<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> C&amp;S </div><table class=\"hapiPropertyTable\"><tbody><tr><td>Status</td><td>partial</td></tr><tr><td>Issued</td><td> 29 April 2014 17:21:56 </td></tr></tbody></table><table class=\"hapiTableOfValues\"><thead><tr><td>Name</td><td>Value</td><td>Interpretation</td><td>Reference Range</td><td>Status</td></tr></thead><tbody><tr class=\"hapiTableOfValuesRowEven\"><td> Collection Info </td><td> Spec #102758: 26 Sep 08 1117</td><td/><td/><td>preliminary</td></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Direct Stain </td><td> pus cells</td><td/><td/><td>preliminary</td></tr><tr class=\"hapiTableOfValuesRowEven\"><td> Header </td><td> To view Culture &amp; Sensitivity Results, select</td><td/><td/><td/></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Header </td><td> (Y) Report Query. Do NOT select number beside</td><td/><td/><td/></tr><tr class=\"hapiTableOfValuesRowEven\"><td> Header </td><td> Prelim or Final Result field, as there is</td><td/><td/><td/></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Header </td><td> potential for viewing an incomplete report.</td><td/><td/><td/></tr><tr class=\"hapiTableOfValuesRowEven\"><td> Organism </td><td> Haemophilus influenzae</td><td/><td/><td>final</td></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Qualifier </td><td> =>10 x E6 cfu/L SIGNIFICANT RESULT. Organisms cultured in quantities =>10 x E6 cfu/L are consistent with pneumonia. beta-lactamase positive result suggests resistance to ampicillin but generally susceptible to amoxicillin- clavulanic and cefuroxime.</td><td/><td/><td>final</td></tr><tr class=\"hapiTableOfValuesRowEven\"><td> Sensitivities </td><td> _Beta-lactamase Pos: </td><td/><td/><td>final</td></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Test Comment </td><td> =>10 x E6 cfu/L Commensal flora</td><td/><td/><td>final</td></tr></tbody></table></div>"
},
"contained":[
{
"resourceType":"Observation",
"id":"f816a276-cfad-4eca-a9fa-f1dff844a196",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"146151.1"
}
],
"text":"Collection Info"
},
"valueString":"Spec #102758: 26 Sep 08 1117",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"preliminary"
},
{
"resourceType":"Observation",
"id":"23b55496-1c2a-4d5f-9c24-8ca5042f4027",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"GM.2"
}
],
"text":"Direct Stain"
},
"valueString":"pus cells",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"preliminary"
},
{
"resourceType":"Observation",
"id":"74e6791a-d810-4545-8410-e9eca41e81d6",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H1.3"
}
],
"text":"Header"
},
"valueString":"To view Culture & Sensitivity Results, select",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"cd8c6a6c-7ef5-446f-b07b-47a21bfe28ee",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H2.4"
}
],
"text":"Header"
},
"valueString":"(Y) Report Query. Do NOT select number beside",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"4a3d453d-3a18-432f-8f1f-d7657c50dcd4",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H3.5"
}
],
"text":"Header"
},
"valueString":"Prelim or Final Result field, as there is",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"0dd6cff6-f9db-42cc-89c9-2cd6ba6fe5af",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H4.6"
}
],
"text":"Header"
},
"valueString":"potential for viewing an incomplete report.",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"6d6b0117-220f-4b9a-abf3-5faf772cfa61",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/O.4"
}
],
"text":"Organism"
},
"valueString":"Haemophilus influenzae",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"64068acf-57f4-42c8-b0e6-416247067b16",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/31266.5"
}
],
"text":"Qualifier"
},
"valueString":"=>10 x E6 cfu/L SIGNIFICANT RESULT. Organisms cultured in quantities =>10 x E6 cfu/L are consistent with pneumonia. beta-lactamase positive result suggests resistance to ampicillin but generally susceptible to amoxicillin- clavulanic and cefuroxime.",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"0f9d254f-3ad1-404b-9be9-20258b3c242f",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/31415.6"
}
],
"text":"Sensitivities"
},
"valueString":"_Beta-lactamase Pos: ",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"349bb02b-fbbe-4ce0-b190-3f545240dcc0",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"Q.3"
}
],
"text":"Test Comment"
},
"valueString":"=>10 x E6 cfu/L Commensal flora",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"f816a276-cfad-4eca-a9fa-f1dff844a196",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"146151.1"
}
],
"text":"Collection Info"
},
"valueString":"Spec #102758: 26 Sep 08 1117",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"preliminary"
},
{
"resourceType":"Observation",
"id":"23b55496-1c2a-4d5f-9c24-8ca5042f4027",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"GM.2"
}
],
"text":"Direct Stain"
},
"valueString":"pus cells",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"preliminary"
},
{
"resourceType":"Observation",
"id":"74e6791a-d810-4545-8410-e9eca41e81d6",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H1.3"
}
],
"text":"Header"
},
"valueString":"To view Culture & Sensitivity Results, select",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"cd8c6a6c-7ef5-446f-b07b-47a21bfe28ee",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H2.4"
}
],
"text":"Header"
},
"valueString":"(Y) Report Query. Do NOT select number beside",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"4a3d453d-3a18-432f-8f1f-d7657c50dcd4",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H3.5"
}
],
"text":"Header"
},
"valueString":"Prelim or Final Result field, as there is",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"0dd6cff6-f9db-42cc-89c9-2cd6ba6fe5af",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H4.6"
}
],
"text":"Header"
},
"valueString":"potential for viewing an incomplete report.",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"6d6b0117-220f-4b9a-abf3-5faf772cfa61",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/O.4"
}
],
"text":"Organism"
},
"valueString":"Haemophilus influenzae",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"64068acf-57f4-42c8-b0e6-416247067b16",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/31266.5"
}
],
"text":"Qualifier"
},
"valueString":"=>10 x E6 cfu/L SIGNIFICANT RESULT. Organisms cultured in quantities =>10 x E6 cfu/L are consistent with pneumonia. beta-lactamase positive result suggests resistance to ampicillin but generally susceptible to amoxicillin- clavulanic and cefuroxime.",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"0f9d254f-3ad1-404b-9be9-20258b3c242f",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/31415.6"
}
],
"text":"Sensitivities"
},
"valueString":"_Beta-lactamase Pos: ",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"349bb02b-fbbe-4ce0-b190-3f545240dcc0",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"Q.3"
}
],
"text":"Test Comment"
},
"valueString":"=>10 x E6 cfu/L Commensal flora",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
}
],
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.5",
"code":"4140"
}
],
"text":"C&S"
},
"status":"partial",
"issued":"2014-04-29T17:21:56",
"subject":{
"resource":"Patient/5556918"
},
"identifier":{
"value":"2363922"
},
"diagnosticDateTime":"2014-04-14T00:00:00-04:00",
"result":[
{
"resource":"#f816a276-cfad-4eca-a9fa-f1dff844a196"
},
{
"resource":"#23b55496-1c2a-4d5f-9c24-8ca5042f4027"
},
{
"resource":"#74e6791a-d810-4545-8410-e9eca41e81d6"
},
{
"resource":"#cd8c6a6c-7ef5-446f-b07b-47a21bfe28ee"
},
{
"resource":"#4a3d453d-3a18-432f-8f1f-d7657c50dcd4"
},
{
"resource":"#0dd6cff6-f9db-42cc-89c9-2cd6ba6fe5af"
},
{
"resource":"#6d6b0117-220f-4b9a-abf3-5faf772cfa61"
},
{
"resource":"#64068acf-57f4-42c8-b0e6-416247067b16"
},
{
"resource":"#0f9d254f-3ad1-404b-9be9-20258b3c242f"
},
{
"resource":"#349bb02b-fbbe-4ce0-b190-3f545240dcc0"
}
]
}
},
{
"deleted":null,
"title":"Organization http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/Organization/1.3.6.1.4.1.12201",
"id":"Organization/1.3.6.1.4.1.12201",
"link":[
{
"rel":"self",
"href":"Organization/1.3.6.1.4.1.12201"
}
],
"published":"2014-05-29T10:49:32-04:00",
"content":{
"resourceType":"Organization",
"id":"http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/Organization/1.3.6.1.4.1.12201",
"extension":[
{
"url":"http://fhir.connectinggta.ca/Profile/organization#providerIdPool",
"valueUri":"1.3.6.1.4.1.12201.1"
}
],
"text":{
"status":"empty",
"div":"<div xmlns=\"http://www.w3.org/1999/xhtml\">No narrative template available for resource profile: http://fhir.connectinggta.ca/Profile/organization</div>"
},
"contained":[
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.1",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.1"
},
"name":"Toronto General Hospital"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.2",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.2"
},
"name":"Toronto Western Hospital"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.3",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.3"
},
"name":"Princess Margaret Hospital"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.4",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.4"
},
"name":"Toronto Rehab Institute"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.1",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.1"
},
"name":"Toronto General Hospital"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.2",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.2"
},
"name":"Toronto Western Hospital"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.3",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.3"
},
"name":"Princess Margaret Hospital"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.4",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.4"
},
"name":"Toronto Rehab Institute"
}
],
"name":"University Health Network",
"type":{
"coding":[
{
"code":"HOSPITAL"
}
]
},
"address":[
{
"line":[
"R. Fraser Elliott Building, 1st Floor",
"190 Elizabeth St."
],
"city":"Toronto",
"state":"ON",
"zip":"M5G 2C4"
}
],
"location":[
{
"resource":"#1.3.6.1.4.1.12201.100.1"
},
{
"resource":"#1.3.6.1.4.1.12201.100.2"
},
{
"resource":"#1.3.6.1.4.1.12201.100.3"
},
{
"resource":"#1.3.6.1.4.1.12201.100.4"
}
]
}
}
]
}

112
hapi-fhir-jpaserver-test/src/test/java/ca/uhn/fhir/jpa/test/SystemTest.java Normal file
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@ -0,0 +1,112 @@
package ca.uhn.fhir.jpa.test;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.List;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.springframework.context.support.ClassPathXmlApplicationContext;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.provider.JpaSystemProvider;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu.resource.Observation;
import ca.uhn.fhir.model.dstu.resource.Organization;
import ca.uhn.fhir.model.dstu.resource.Patient;
import ca.uhn.fhir.model.dstu.resource.Questionnaire;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.tester.RestfulServerTesterServlet;
import ca.uhn.test.jpasrv.ObservationResourceProvider;
import ca.uhn.test.jpasrv.OrganizationResourceProvider;
import ca.uhn.test.jpasrv.PatientResourceProvider;
public class SystemTest {
private static Server ourServer;
private static ClassPathXmlApplicationContext ourAppCtx;
private static FhirContext ourCtx;
private static IGenericClient ourClient;
@Test
public void testTransactionFromBundle() throws Exception {
InputStream bundleRes = SystemTest.class.getResourceAsStream("/bundle.json");
Bundle bundle = new FhirContext().newJsonParser().parseBundle(new InputStreamReader(bundleRes));
List<IResource> res = bundle.toListOfResources();
ourClient.transaction(res);
}
@AfterClass
public static void afterClass() throws Exception {
ourServer.stop();
ourAppCtx.stop();
}
@SuppressWarnings("unchecked")
@BeforeClass
public static void beforeClass() throws Exception {
ourAppCtx = new ClassPathXmlApplicationContext("fhir-spring-test-config.xml");
IFhirResourceDao<Patient> patientDao = (IFhirResourceDao<Patient>) ourAppCtx.getBean("myPatientDao", IFhirResourceDao.class);
PatientResourceProvider patientRp = new PatientResourceProvider();
patientRp.setDao(patientDao);
IFhirResourceDao<Questionnaire> questionnaireDao = (IFhirResourceDao<Questionnaire>) ourAppCtx.getBean("myQuestionnaireDao", IFhirResourceDao.class);
QuestionnaireResourceProvider questionnaireRp = new QuestionnaireResourceProvider();
questionnaireRp.setDao(questionnaireDao);
IFhirResourceDao<Observation> observationDao = (IFhirResourceDao<Observation>) ourAppCtx.getBean("myObservationDao", IFhirResourceDao.class);
ObservationResourceProvider observationRp = new ObservationResourceProvider();
observationRp.setDao(observationDao);
IFhirSystemDao systemDao = ourAppCtx.getBean("mySystemDao", IFhirSystemDao.class);
IFhirResourceDao<Organization> organizationDao = (IFhirResourceDao<Organization>) ourAppCtx.getBean("myOrganizationDao", IFhirResourceDao.class);
OrganizationResourceProvider organizationRp = new OrganizationResourceProvider();
organizationRp.setDao(organizationDao);
RestfulServer restServer = new RestfulServer();
restServer.setResourceProviders(patientRp, questionnaireRp, observationRp, organizationRp);
restServer.setPlainProviders(new JpaSystemProvider(systemDao));
int myPort = 8888;
ourServer = new Server(myPort);
ServletContextHandler proxyHandler = new ServletContextHandler();
proxyHandler.setContextPath("/");
RestfulServerTesterServlet testerServlet = new RestfulServerTesterServlet();
String serverBase = "http://localhost:" + myPort + "/fhir/context";
testerServlet.setServerBase(serverBase);
// testerServlet.setServerBase("http://fhir.healthintersections.com.au/open");
ServletHolder handler = new ServletHolder();
handler.setServlet(testerServlet);
proxyHandler.addServlet(handler, "/fhir/tester/*");
ServletHolder servletHolder = new ServletHolder();
servletHolder.setServlet(restServer);
proxyHandler.addServlet(servletHolder, "/fhir/context/*");
ourServer.setHandler(proxyHandler);
ourServer.start();
ourCtx = restServer.getFhirContext();
ourClient = ourCtx.newRestfulGenericClient(serverBase);
ourClient.setLogRequestAndResponse(true);
}
}

690
hapi-fhir-jpaserver-test/src/test/resources/bundle.json Normal file
View File

@ -0,0 +1,690 @@
{
"resourceType":"Bundle",
"entry":[
{
"deleted":null,
"title":"Patient http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/Patient/5556918",
"id":"Patient/5556918",
"link":[
{
"rel":"self",
"href":"Patient/5556918"
}
],
"published":"2014-05-29T10:49:32-04:00",
"content":{
"resourceType":"Patient",
"id":"http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/Patient/5556918",
"text":{
"status":"generated",
"div":"<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> Donald null <b>DUCK </b></div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>7000135</td></tr><tr><td>Address</td><td><span>10 Duxon Street </span><br/><span>VICTORIA </span><span>BC </span><span>Can </span></td></tr><tr><td>Date of birth</td><td><span>01 June 1980</span></td></tr></tbody></table></div>"
},
"identifier":[
{
"use":"official",
"label":"University Health Network MRN 7000135",
"system":"urn:oid:2.16.840.1.113883.3.239.18.148",
"value":"7000135",
"assigner":{
"resource":"Organization/1.3.6.1.4.1.12201"
}
}
],
"name":[
{
"family":[
"Duck"
],
"given":[
"Donald"
]
}
],
"telecom":[
{
"system":"phone",
"use":"home"
},
{
"system":"phone",
"use":"work"
},
{
"system":"phone",
"use":"mobile"
},
{
"system":"email",
"use":"home"
}
],
"gender":{
"coding":[
{
"system":"http://hl7.org/fhir/v3/AdministrativeGender",
"code":"M"
}
]
},
"birthDate":"1980-06-01T00:00:00",
"address":[
{
"use":"home",
"line":[
"10 Duxon Street"
],
"city":"VICTORIA",
"state":"BC",
"zip":"V8N 1Y4",
"country":"Can"
}
],
"managingOrganization":{
"resource":"Organization/1.3.6.1.4.1.12201"
}
}
},
{
"deleted":null,
"title":"DiagnosticReport http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/DiagnosticReport/5978827",
"id":"DiagnosticReport/5978827",
"link":[
{
"rel":"self",
"href":"DiagnosticReport/5978827"
}
],
"published":"2014-05-29T10:49:33-04:00",
"content":{
"resourceType":"DiagnosticReport",
"id":"http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/DiagnosticReport/5978827",
"text":{
"status":"generated",
"div":"<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> C&amp;S </div><table class=\"hapiPropertyTable\"><tbody><tr><td>Status</td><td>partial</td></tr><tr><td>Issued</td><td> 29 April 2014 17:21:56 </td></tr></tbody></table><table class=\"hapiTableOfValues\"><thead><tr><td>Name</td><td>Value</td><td>Interpretation</td><td>Reference Range</td><td>Status</td></tr></thead><tbody><tr class=\"hapiTableOfValuesRowEven\"><td> Collection Info </td><td> Spec #102758: 26 Sep 08 1117</td><td/><td/><td>preliminary</td></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Direct Stain </td><td> pus cells</td><td/><td/><td>preliminary</td></tr><tr class=\"hapiTableOfValuesRowEven\"><td> Header </td><td> To view Culture &amp; Sensitivity Results, select</td><td/><td/><td/></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Header </td><td> (Y) Report Query. Do NOT select number beside</td><td/><td/><td/></tr><tr class=\"hapiTableOfValuesRowEven\"><td> Header </td><td> Prelim or Final Result field, as there is</td><td/><td/><td/></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Header </td><td> potential for viewing an incomplete report.</td><td/><td/><td/></tr><tr class=\"hapiTableOfValuesRowEven\"><td> Organism </td><td> Haemophilus influenzae</td><td/><td/><td>final</td></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Qualifier </td><td> =>10 x E6 cfu/L SIGNIFICANT RESULT. Organisms cultured in quantities =>10 x E6 cfu/L are consistent with pneumonia. beta-lactamase positive result suggests resistance to ampicillin but generally susceptible to amoxicillin- clavulanic and cefuroxime.</td><td/><td/><td>final</td></tr><tr class=\"hapiTableOfValuesRowEven\"><td> Sensitivities </td><td> _Beta-lactamase Pos: </td><td/><td/><td>final</td></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Test Comment </td><td> =>10 x E6 cfu/L Commensal flora</td><td/><td/><td>final</td></tr></tbody></table></div>"
},
"contained":[
{
"resourceType":"Observation",
"id":"f816a276-cfad-4eca-a9fa-f1dff844a196",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"146151.1"
}
],
"text":"Collection Info"
},
"valueString":"Spec #102758: 26 Sep 08 1117",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"preliminary"
},
{
"resourceType":"Observation",
"id":"23b55496-1c2a-4d5f-9c24-8ca5042f4027",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"GM.2"
}
],
"text":"Direct Stain"
},
"valueString":"pus cells",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"preliminary"
},
{
"resourceType":"Observation",
"id":"74e6791a-d810-4545-8410-e9eca41e81d6",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H1.3"
}
],
"text":"Header"
},
"valueString":"To view Culture & Sensitivity Results, select",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"cd8c6a6c-7ef5-446f-b07b-47a21bfe28ee",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H2.4"
}
],
"text":"Header"
},
"valueString":"(Y) Report Query. Do NOT select number beside",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"4a3d453d-3a18-432f-8f1f-d7657c50dcd4",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H3.5"
}
],
"text":"Header"
},
"valueString":"Prelim or Final Result field, as there is",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"0dd6cff6-f9db-42cc-89c9-2cd6ba6fe5af",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H4.6"
}
],
"text":"Header"
},
"valueString":"potential for viewing an incomplete report.",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"6d6b0117-220f-4b9a-abf3-5faf772cfa61",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/O.4"
}
],
"text":"Organism"
},
"valueString":"Haemophilus influenzae",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"64068acf-57f4-42c8-b0e6-416247067b16",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/31266.5"
}
],
"text":"Qualifier"
},
"valueString":"=>10 x E6 cfu/L SIGNIFICANT RESULT. Organisms cultured in quantities =>10 x E6 cfu/L are consistent with pneumonia. beta-lactamase positive result suggests resistance to ampicillin but generally susceptible to amoxicillin- clavulanic and cefuroxime.",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"0f9d254f-3ad1-404b-9be9-20258b3c242f",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/31415.6"
}
],
"text":"Sensitivities"
},
"valueString":"_Beta-lactamase Pos: ",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"349bb02b-fbbe-4ce0-b190-3f545240dcc0",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"Q.3"
}
],
"text":"Test Comment"
},
"valueString":"=>10 x E6 cfu/L Commensal flora",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"f816a276-cfad-4eca-a9fa-f1dff844a196",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"146151.1"
}
],
"text":"Collection Info"
},
"valueString":"Spec #102758: 26 Sep 08 1117",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"preliminary"
},
{
"resourceType":"Observation",
"id":"23b55496-1c2a-4d5f-9c24-8ca5042f4027",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"GM.2"
}
],
"text":"Direct Stain"
},
"valueString":"pus cells",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"preliminary"
},
{
"resourceType":"Observation",
"id":"74e6791a-d810-4545-8410-e9eca41e81d6",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H1.3"
}
],
"text":"Header"
},
"valueString":"To view Culture & Sensitivity Results, select",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"cd8c6a6c-7ef5-446f-b07b-47a21bfe28ee",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H2.4"
}
],
"text":"Header"
},
"valueString":"(Y) Report Query. Do NOT select number beside",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"4a3d453d-3a18-432f-8f1f-d7657c50dcd4",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H3.5"
}
],
"text":"Header"
},
"valueString":"Prelim or Final Result field, as there is",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"0dd6cff6-f9db-42cc-89c9-2cd6ba6fe5af",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H4.6"
}
],
"text":"Header"
},
"valueString":"potential for viewing an incomplete report.",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"6d6b0117-220f-4b9a-abf3-5faf772cfa61",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/O.4"
}
],
"text":"Organism"
},
"valueString":"Haemophilus influenzae",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"64068acf-57f4-42c8-b0e6-416247067b16",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/31266.5"
}
],
"text":"Qualifier"
},
"valueString":"=>10 x E6 cfu/L SIGNIFICANT RESULT. Organisms cultured in quantities =>10 x E6 cfu/L are consistent with pneumonia. beta-lactamase positive result suggests resistance to ampicillin but generally susceptible to amoxicillin- clavulanic and cefuroxime.",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"0f9d254f-3ad1-404b-9be9-20258b3c242f",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/31415.6"
}
],
"text":"Sensitivities"
},
"valueString":"_Beta-lactamase Pos: ",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"349bb02b-fbbe-4ce0-b190-3f545240dcc0",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"Q.3"
}
],
"text":"Test Comment"
},
"valueString":"=>10 x E6 cfu/L Commensal flora",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
}
],
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.5",
"code":"4140"
}
],
"text":"C&S"
},
"status":"partial",
"issued":"2014-04-29T17:21:56",
"subject":{
"resource":"Patient/5556918"
},
"identifier":{
"value":"2363922"
},
"diagnosticDateTime":"2014-04-14T00:00:00-04:00",
"result":[
{
"resource":"#f816a276-cfad-4eca-a9fa-f1dff844a196"
},
{
"resource":"#23b55496-1c2a-4d5f-9c24-8ca5042f4027"
},
{
"resource":"#74e6791a-d810-4545-8410-e9eca41e81d6"
},
{
"resource":"#cd8c6a6c-7ef5-446f-b07b-47a21bfe28ee"
},
{
"resource":"#4a3d453d-3a18-432f-8f1f-d7657c50dcd4"
},
{
"resource":"#0dd6cff6-f9db-42cc-89c9-2cd6ba6fe5af"
},
{
"resource":"#6d6b0117-220f-4b9a-abf3-5faf772cfa61"
},
{
"resource":"#64068acf-57f4-42c8-b0e6-416247067b16"
},
{
"resource":"#0f9d254f-3ad1-404b-9be9-20258b3c242f"
},
{
"resource":"#349bb02b-fbbe-4ce0-b190-3f545240dcc0"
}
]
}
},
{
"deleted":null,
"title":"Organization http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/Organization/1.3.6.1.4.1.12201",
"id":"Organization/1.3.6.1.4.1.12201",
"link":[
{
"rel":"self",
"href":"Organization/1.3.6.1.4.1.12201"
}
],
"published":"2014-05-29T10:49:32-04:00",
"content":{
"resourceType":"Organization",
"id":"http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/Organization/1.3.6.1.4.1.12201",
"extension":[
{
"url":"http://fhir.connectinggta.ca/Profile/organization#providerIdPool",
"valueUri":"1.3.6.1.4.1.12201.1"
}
],
"text":{
"status":"empty",
"div":"<div xmlns=\"http://www.w3.org/1999/xhtml\">No narrative template available for resource profile: http://fhir.connectinggta.ca/Profile/organization</div>"
},
"contained":[
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.1",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.1"
},
"name":"Toronto General Hospital"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.2",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.2"
},
"name":"Toronto Western Hospital"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.3",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.3"
},
"name":"Princess Margaret Hospital"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.4",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.4"
},
"name":"Toronto Rehab Institute"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.1",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.1"
},
"name":"Toronto General Hospital"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.2",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.2"
},
"name":"Toronto Western Hospital"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.3",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.3"
},
"name":"Princess Margaret Hospital"
},
{
"resourceType":"Location",
"id":"1.3.6.1.4.1.12201.100.4",
"identifier":{
"system":"urn:cgta:facility_ids",
"value":"1.3.6.1.4.1.12201.100.4"
},
"name":"Toronto Rehab Institute"
}
],
"name":"University Health Network",
"type":{
"coding":[
{
"code":"HOSPITAL"
}
]
},
"address":[
{
"line":[
"R. Fraser Elliott Building, 1st Floor",
"190 Elizabeth St."
],
"city":"Toronto",
"state":"ON",
"zip":"M5G 2C4"
}
],
"location":[
{
"resource":"#1.3.6.1.4.1.12201.100.1"
},
{
"resource":"#1.3.6.1.4.1.12201.100.2"
},
{
"resource":"#1.3.6.1.4.1.12201.100.3"
},
{
"resource":"#1.3.6.1.4.1.12201.100.4"
}
]
}
}
]
}

3
hapi-fhir-jpaserver-test/src/test/resources/fhir-spring-test-config.xml
View File

@ -29,6 +29,9 @@
<property name="resourceType" value="ca.uhn.fhir.model.dstu.resource.Questionnaire"/>
</bean>
<bean id="mySystemDao" class="ca.uhn.fhir.jpa.dao.FhirSystemDao">
</bean>
<bean id="myPersistenceDataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource" lazy-init="true">
<property name="url" value="jdbc:derby:memory:myUnitTestDB;create=true" />
<!-- <property name="url" value="jdbc:derby:directory:myUnitTestDB;create=true" /> -->

1
hapi-fhir-jpaserver-uhnfhirtest/.gitignore vendored
View File

@ -1,3 +1,4 @@
myUnitTestDB/
target/
/bin
nohup.out

10
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/TestRestfulServer.java
View File

@ -23,9 +23,10 @@ public class TestRestfulServer extends RestfulServer {
super.initialize();
try {
ourLog.info("Creating database");
DriverManager.getConnection("jdbc:derby:directory:" + System.getProperty("fhir.db.location") + ";create=true");
} catch (Exception e) {
ourLog.info("Failed to create database: {}",e.getMessage());
ourLog.error("Failed to create database: {}",e);
}
myAppCtx = new ClassPathXmlApplicationContext("fhir-spring-uhnfhirtest-config.xml", "hapi-jpaserver-springbeans.xml");
@ -46,6 +47,13 @@ public class TestRestfulServer extends RestfulServer {
super.destroy();
myAppCtx.close();
try {
ourLog.info("Shutting down derby");
DriverManager.getConnection("jdbc:derby:directory:" + System.getProperty("fhir.db.location") + ";shutdown=true");
} catch (Exception e) {
ourLog.info("Failed to create database: {}",e.getMessage());
}
}
}

1
hapi-fhir-jpaserver-uhnfhirtest/src/main/resources/META-INF/fhirtest_persistence.xml
View File

@ -15,6 +15,7 @@
<class>ca.uhn.fhir.jpa.entity.ResourceLink</class>
<class>ca.uhn.fhir.jpa.entity.ResourceTable</class>
<class>ca.uhn.fhir.jpa.entity.ResourceTag</class>
<class>ca.uhn.fhir.jpa.entity.TagDefinition</class>
<exclude-unlisted-classes>true</exclude-unlisted-classes>
<properties>

2
hapi-fhir-jpaserver-uhnfhirtest/src/main/resources/fhir-spring-uhnfhirtest-config.xml
View File

@ -20,7 +20,7 @@
<bean id="myPersistenceDataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource" lazy-init="true">
<!-- ;create=true /opt/glassfish/glassfish4/glassfish/nodes/localhost-domain1/fhirtest/fhirdb -->
<property name="url" value="jdbc:derby:directory:#{systemProperties['fhir.db.location']}" />
<property name="url" value="jdbc:derby:directory:#{systemProperties['fhir.db.location']};create=true" />
</bean>
<bean id="myEntityManagerFactory" class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean">

690
hapi-fhir-jpaserver-uhnfhirtest/src/test/resources/bundle.json Normal file
View File

@ -0,0 +1,690 @@
{
"resourceType":"Bundle",
"entry":[
{
"deleted":null,
"title":"Patient http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/Patient/5556918",
"id":"Patient/5556918",
"link":[
{
"rel":"self",
"href":"Patient/5556918"
}
],
"published":"2014-05-29T10:49:32-04:00",
"content":{
"resourceType":"Patient",
"id":"http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/Patient/5556918",
"text":{
"status":"generated",
"div":"<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> Donald null <b>DUCK </b></div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>7000135</td></tr><tr><td>Address</td><td><span>10 Duxon Street </span><br/><span>VICTORIA </span><span>BC </span><span>Can </span></td></tr><tr><td>Date of birth</td><td><span>01 June 1980</span></td></tr></tbody></table></div>"
},
"identifier":[
{
"use":"official",
"label":"University Health Network MRN 7000135",
"system":"urn:oid:2.16.840.1.113883.3.239.18.148",
"value":"7000135",
"assigner":{
"resource":"Organization/1.3.6.1.4.1.12201"
}
}
],
"name":[
{
"family":[
"Duck"
],
"given":[
"Donald"
]
}
],
"telecom":[
{
"system":"phone",
"use":"home"
},
{
"system":"phone",
"use":"work"
},
{
"system":"phone",
"use":"mobile"
},
{
"system":"email",
"use":"home"
}
],
"gender":{
"coding":[
{
"system":"http://hl7.org/fhir/v3/AdministrativeGender",
"code":"M"
}
]
},
"birthDate":"1980-06-01T00:00:00",
"address":[
{
"use":"home",
"line":[
"10 Duxon Street"
],
"city":"VICTORIA",
"state":"BC",
"zip":"V8N 1Y4",
"country":"Can"
}
],
"managingOrganization":{
"resource":"Organization/1.3.6.1.4.1.12201"
}
}
},
{
"deleted":null,
"title":"DiagnosticReport http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/DiagnosticReport/5978827",
"id":"DiagnosticReport/5978827",
"link":[
{
"rel":"self",
"href":"DiagnosticReport/5978827"
}
],
"published":"2014-05-29T10:49:33-04:00",
"content":{
"resourceType":"DiagnosticReport",
"id":"http://uhnvesb01d.uhn.on.ca:25180/uhn-fhir-service-1.0/DiagnosticReport/5978827",
"text":{
"status":"generated",
"div":"<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> C&amp;S </div><table class=\"hapiPropertyTable\"><tbody><tr><td>Status</td><td>partial</td></tr><tr><td>Issued</td><td> 29 April 2014 17:21:56 </td></tr></tbody></table><table class=\"hapiTableOfValues\"><thead><tr><td>Name</td><td>Value</td><td>Interpretation</td><td>Reference Range</td><td>Status</td></tr></thead><tbody><tr class=\"hapiTableOfValuesRowEven\"><td> Collection Info </td><td> Spec #102758: 26 Sep 08 1117</td><td/><td/><td>preliminary</td></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Direct Stain </td><td> pus cells</td><td/><td/><td>preliminary</td></tr><tr class=\"hapiTableOfValuesRowEven\"><td> Header </td><td> To view Culture &amp; Sensitivity Results, select</td><td/><td/><td/></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Header </td><td> (Y) Report Query. Do NOT select number beside</td><td/><td/><td/></tr><tr class=\"hapiTableOfValuesRowEven\"><td> Header </td><td> Prelim or Final Result field, as there is</td><td/><td/><td/></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Header </td><td> potential for viewing an incomplete report.</td><td/><td/><td/></tr><tr class=\"hapiTableOfValuesRowEven\"><td> Organism </td><td> Haemophilus influenzae</td><td/><td/><td>final</td></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Qualifier </td><td> =>10 x E6 cfu/L SIGNIFICANT RESULT. Organisms cultured in quantities =>10 x E6 cfu/L are consistent with pneumonia. beta-lactamase positive result suggests resistance to ampicillin but generally susceptible to amoxicillin- clavulanic and cefuroxime.</td><td/><td/><td>final</td></tr><tr class=\"hapiTableOfValuesRowEven\"><td> Sensitivities </td><td> _Beta-lactamase Pos: </td><td/><td/><td>final</td></tr><tr class=\"hapiTableOfValuesRowOdd\"><td> Test Comment </td><td> =>10 x E6 cfu/L Commensal flora</td><td/><td/><td>final</td></tr></tbody></table></div>"
},
"contained":[
{
"resourceType":"Observation",
"id":"f816a276-cfad-4eca-a9fa-f1dff844a196",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"146151.1"
}
],
"text":"Collection Info"
},
"valueString":"Spec #102758: 26 Sep 08 1117",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"preliminary"
},
{
"resourceType":"Observation",
"id":"23b55496-1c2a-4d5f-9c24-8ca5042f4027",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"GM.2"
}
],
"text":"Direct Stain"
},
"valueString":"pus cells",
"interpretation":{
"coding":[
{
"code":"N"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"preliminary"
},
{
"resourceType":"Observation",
"id":"74e6791a-d810-4545-8410-e9eca41e81d6",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H1.3"
}
],
"text":"Header"
},
"valueString":"To view Culture & Sensitivity Results, select",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"cd8c6a6c-7ef5-446f-b07b-47a21bfe28ee",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H2.4"
}
],
"text":"Header"
},
"valueString":"(Y) Report Query. Do NOT select number beside",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"4a3d453d-3a18-432f-8f1f-d7657c50dcd4",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H3.5"
}
],
"text":"Header"
},
"valueString":"Prelim or Final Result field, as there is",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"0dd6cff6-f9db-42cc-89c9-2cd6ba6fe5af",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"1H4.6"
}
],
"text":"Header"
},
"valueString":"potential for viewing an incomplete report.",
"issued":"2014-04-29T17:21:56"
},
{
"resourceType":"Observation",
"id":"6d6b0117-220f-4b9a-abf3-5faf772cfa61",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/O.4"
}
],
"text":"Organism"
},
"valueString":"Haemophilus influenzae",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"64068acf-57f4-42c8-b0e6-416247067b16",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/31266.5"
}
],
"text":"Qualifier"
},
"valueString":"=>10 x E6 cfu/L SIGNIFICANT RESULT. Organisms cultured in quantities =>10 x E6 cfu/L are consistent with pneumonia. beta-lactamase positive result suggests resistance to ampicillin but generally susceptible to amoxicillin- clavulanic and cefuroxime.",
"interpretation":{
"coding":[
{
"code":"A"
}
]
},
"issued":"2014-04-29T17:21:56",
"status":"final"
},
{
"resourceType":"Observation",
"id":"0f9d254f-3ad1-404b-9be9-20258b3c242f",
"name":{
"coding":[
{
"system":"urn:oid:1.3.6.1.4.1.12201.102.6",
"code":"F/31415.6"
}
],
"text":"Sensitivities"
},
"valueString":"_Beta-lactamase Pos: ",
"interpretation":{
"coding":[
{
"code":"A"
}
]
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