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Correctly handle Bundle.entry.base

This commit is contained in:
jamesagnew 2015-06-12 08:27:03 -04:00
parent e536486638
commit 0479a48a41
6 changed files with 1421 additions and 1261 deletions
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14
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
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@ -328,7 +328,19 @@ public abstract class BaseParser implements IParser {
versionIdPart = ResourceMetadataKeyEnum.VERSION.get((IResource) res);
}
res.setId(new IdDt(baseType.getValueAsString(), resDef.getName(), res.getIdElement().getIdPart(), versionIdPart));
String baseUrl = baseType.getValueAsString();
String idPart = res.getIdElement().getIdPart();
String resourceName = resDef.getName();
if (!baseUrl.startsWith("cid:") && !baseUrl.startsWith("urn:")) {
res.setId(new IdDt(baseUrl, resourceName, idPart, versionIdPart));
} else {
if (baseUrl.endsWith(":")) {
res.setId(new IdDt(baseUrl + idPart));
} else {
res.setId(new IdDt(baseUrl + ':' + idPart));
}
}
}
}

28
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java
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@ -1059,8 +1059,6 @@ class ParserState<T> {
} else {
throw new DataFormatException("Unexpected element in entry: " + theLocalPart);
}
// TODO: handle category
}
protected BundleEntry getEntry() {
@ -1317,10 +1315,20 @@ class ParserState<T> {
String resourceName = myContext.getResourceDefinition(nextResource).getName();
String bundleIdPart = nextResource.getId().getIdPart();
if (isNotBlank(bundleIdPart)) {
String baseUrl;
if (isNotBlank(entryBaseUrl)) {
nextResource.setId(new IdDt(entryBaseUrl, resourceName, bundleIdPart, version));
baseUrl = entryBaseUrl;
} else {
nextResource.setId(new IdDt(bundleBaseUrl, resourceName, bundleIdPart, version));
baseUrl = bundleBaseUrl;
}
if (!baseUrl.startsWith("cid:") && !baseUrl.startsWith("urn:")) {
nextResource.setId(new IdDt(baseUrl, resourceName, bundleIdPart, version));
} else {
if (baseUrl.endsWith(":")) {
nextResource.setId(new IdDt(baseUrl + bundleIdPart));
} else {
nextResource.setId(new IdDt(baseUrl + ':' + bundleIdPart));
}
}
}
}
@ -1535,9 +1543,9 @@ class ParserState<T> {
try {
child = myDefinition.getChildByNameOrThrowDataFormatException(theChildName);
} catch (DataFormatException e) {
/* This means we've found an element that doesn't exist on the structure.
* If the error handler doesn't throw an exception, swallow the element silently along
* with any child elements
/*
* This means we've found an element that doesn't exist on the structure. If the error handler doesn't
* throw an exception, swallow the element silently along with any child elements
*/
myErrorHandler.unknownElement(null, theChildName);
push(new SwallowChildrenWholeState(getPreResourceState()));
@ -2093,7 +2101,7 @@ class ParserState<T> {
}
}
}
}else if (theElement instanceof IBaseReference) {
} else if (theElement instanceof IBaseReference) {
IBaseReference nextRef = (IBaseReference) theElement;
String ref = nextRef.getReferenceElement().getValue();
if (isNotBlank(ref)) {
@ -2589,7 +2597,7 @@ class ParserState<T> {
@Override
public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
// IGNORE - don't handle this as an error, we process these as XML events
// IGNORE - don't handle this as an error, we process these as XML events
}
@Override
@ -2598,7 +2606,7 @@ class ParserState<T> {
myDt.setValueAsString(theValue);
return;
} else {
// IGNORE - don't handle this as an error, we process these as XML events
// IGNORE - don't handle this as an error, we process these as XML events
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java
View File

@ -25,6 +25,7 @@ import static org.apache.commons.lang3.StringUtils.*;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
@ -128,7 +129,7 @@ public class FhirSystemDaoDstu2 extends BaseFhirSystemDao<Bundle> {
ourLog.info("Beginning transaction with {} resources", theResources.getEntry().size());
long start = System.currentTimeMillis();
Set<IdDt> allIds = new HashSet<IdDt>();
Set<IdDt> allIds = new LinkedHashSet<IdDt>();
Map<IdDt, IdDt> idSubstitutions = new HashMap<IdDt, IdDt>();
Map<IdDt, DaoMethodOutcome> idToPersistedOutcome = new HashMap<IdDt, DaoMethodOutcome>();

672
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2Test.java
View File

@ -50,9 +50,103 @@ public class FhirSystemDaoDstu2Test {
private static ClassPathXmlApplicationContext ourCtx;
private static FhirContext ourFhirContext;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu2Test.class);
private static IFhirResourceDao<Observation> ourObservationDao;
private static IFhirResourceDao<Patient> ourPatientDao;
private static IFhirSystemDao<Bundle> ourSystemDao;
private static IFhirResourceDao<Observation> ourObservationDao;
private void deleteEverything() {
FhirSystemDaoDstu2Test.doDeleteEverything(ourSystemDao);
}
@Test
public void testSystemMetaOperation() {
deleteEverything();
MetaDt meta = ourSystemDao.metaGetOperation();
List<CodingDt> published = meta.getTag();
assertEquals(0, published.size());
String methodName = "testSystemMetaOperation";
IdDt id1;
{
Patient patient = new Patient();
patient.addIdentifier().setSystem("urn:system").setValue(methodName);
patient.addName().addFamily("Tester").addGiven("Joe");
TagList tagList = new TagList();
tagList.addTag(null, "Dog", "Puppies");
ResourceMetadataKeyEnum.TAG_LIST.put(patient, tagList);
List<BaseCodingDt> securityLabels = new ArrayList<BaseCodingDt>();
securityLabels.add(new CodingDt().setSystem("seclabel:sys:1").setCode("seclabel:code:1").setDisplay("seclabel:dis:1"));
ResourceMetadataKeyEnum.SECURITY_LABELS.put(patient, securityLabels);
ArrayList<IdDt> profiles = new ArrayList<IdDt>();
profiles.add(new IdDt("http://profile/1"));
ResourceMetadataKeyEnum.PROFILES.put(patient, profiles);
id1 = ourPatientDao.create(patient).getId();
}
{
Patient patient = new Patient();
patient.addIdentifier().setSystem("urn:system").setValue(methodName);
patient.addName().addFamily("Tester").addGiven("Joe");
TagList tagList = new TagList();
tagList.addTag("http://foo", "Cat", "Kittens");
ResourceMetadataKeyEnum.TAG_LIST.put(patient, tagList);
List<BaseCodingDt> securityLabels = new ArrayList<BaseCodingDt>();
securityLabels.add(new CodingDt().setSystem("seclabel:sys:2").setCode("seclabel:code:2").setDisplay("seclabel:dis:2"));
ResourceMetadataKeyEnum.SECURITY_LABELS.put(patient, securityLabels);
ArrayList<IdDt> profiles = new ArrayList<IdDt>();
profiles.add(new IdDt("http://profile/2"));
ResourceMetadataKeyEnum.PROFILES.put(patient, profiles);
ourPatientDao.create(patient);
}
meta = ourSystemDao.metaGetOperation();
published = meta.getTag();
assertEquals(2, published.size());
assertEquals(null, published.get(0).getSystem());
assertEquals("Dog", published.get(0).getCode());
assertEquals("Puppies", published.get(0).getDisplay());
assertEquals("http://foo", published.get(1).getSystem());
assertEquals("Cat", published.get(1).getCode());
assertEquals("Kittens", published.get(1).getDisplay());
List<CodingDt> secLabels = meta.getSecurity();
assertEquals(2, secLabels.size());
assertEquals("seclabel:sys:1", secLabels.get(0).getSystemElement().getValue());
assertEquals("seclabel:code:1", secLabels.get(0).getCodeElement().getValue());
assertEquals("seclabel:dis:1", secLabels.get(0).getDisplayElement().getValue());
assertEquals("seclabel:sys:2", secLabels.get(1).getSystemElement().getValue());
assertEquals("seclabel:code:2", secLabels.get(1).getCodeElement().getValue());
assertEquals("seclabel:dis:2", secLabels.get(1).getDisplayElement().getValue());
List<UriDt> profiles = meta.getProfile();
assertEquals(2, profiles.size());
assertEquals("http://profile/1", profiles.get(0).getValue());
assertEquals("http://profile/2", profiles.get(1).getValue());
ourPatientDao.removeTag(id1, TagTypeEnum.TAG, null, "Dog");
ourPatientDao.removeTag(id1, TagTypeEnum.SECURITY_LABEL, "seclabel:sys:1", "seclabel:code:1");
ourPatientDao.removeTag(id1, TagTypeEnum.PROFILE, BaseFhirDao.NS_JPA_PROFILE, "http://profile/1");
meta = ourSystemDao.metaGetOperation();
published = meta.getTag();
assertEquals(1, published.size());
assertEquals("http://foo", published.get(0).getSystem());
assertEquals("Cat", published.get(0).getCode());
assertEquals("Kittens", published.get(0).getDisplay());
secLabels = meta.getSecurity();
assertEquals(1, secLabels.size());
assertEquals("seclabel:sys:2", secLabels.get(0).getSystemElement().getValue());
assertEquals("seclabel:code:2", secLabels.get(0).getCodeElement().getValue());
assertEquals("seclabel:dis:2", secLabels.get(0).getDisplayElement().getValue());
profiles = meta.getProfile();
assertEquals(1, profiles.size());
assertEquals("http://profile/2", profiles.get(0).getValue());
}
@Test
public void testTransactionCreateMatchUrlWithOneMatch() {
@ -96,109 +190,6 @@ public class FhirSystemDaoDstu2Test {
}
@Test
public void testTransactionCreateWithInvalidReferenceNumeric() {
String methodName = "testTransactionCreateWithInvalidReferenceNumeric";
Bundle request = new Bundle();
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.addName().addFamily("Hello");
p.getManagingOrganization().setReference("Organization/9999999999999999");
request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.POST);
try {
ourSystemDao.transaction(request);
fail();
} catch (InvalidRequestException e) {
assertThat(e.getMessage(), containsString("Resource Organization/9999999999999999 not found, specified in path: Patient.managingOrganization"));
}
}
@Test
public void testTransactionCreateWithInvalidReferenceTextual() {
String methodName = "testTransactionCreateWithInvalidReferenceTextual";
Bundle request = new Bundle();
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.addName().addFamily("Hello");
p.getManagingOrganization().setReference("Organization/" + methodName);
request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.POST);
try {
ourSystemDao.transaction(request);
fail();
} catch (InvalidRequestException e) {
assertThat(e.getMessage(), containsString("Resource Organization/" + methodName + " not found, specified in path: Patient.managingOrganization"));
}
}
@Test
public void testTransactionFromBundle() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve.xml");
String bundleStr = IOUtils.toString(bundleRes);
Bundle bundle = ourFhirContext.newXmlParser().parseResource(Bundle.class, bundleStr);
Bundle resp = ourSystemDao.transaction(bundle);
ourLog.info(ourFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
OperationOutcome oo = (OperationOutcome) resp.getEntry().get(0).getResource();
assertThat(oo.getIssue().get(0).getDetailsElement().getValue(), containsString("Transaction completed"));
assertThat(resp.getEntry().get(1).getTransactionResponse().getLocation(), startsWith("Patient/a555-44-4444/_history/"));
assertThat(resp.getEntry().get(2).getTransactionResponse().getLocation(), startsWith("Patient/temp6789/_history/"));
assertThat(resp.getEntry().get(3).getTransactionResponse().getLocation(), startsWith("Organization/GHH/_history/"));
Patient p = ourPatientDao.read(new IdDt("Patient/a555-44-4444/_history/1"));
assertEquals("Patient/temp6789", p.getLink().get(0).getOther().getReference().getValue());
}
@Test
public void testTransactionReadAndSearch() {
String methodName = "testTransactionReadAndSearch";
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.setId("Patient/" + methodName);
IdDt idv1 = ourPatientDao.update(p).getId();
ourLog.info("Created patient, got id: {}", idv1);
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.addName().addFamily("Family Name");
p.setId("Patient/" + methodName);
IdDt idv2 = ourPatientDao.update(p).getId();
ourLog.info("Updated patient, got id: {}", idv2);
Bundle request = new Bundle();
request.addEntry().getTransaction().setMethod(HTTPVerbEnum.GET).setUrl(idv1.toUnqualifiedVersionless().getValue());
request.addEntry().getTransaction().setMethod(HTTPVerbEnum.GET).setUrl(idv1.toUnqualified().getValue());
request.addEntry().getTransaction().setMethod(HTTPVerbEnum.GET).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
Bundle resp = ourSystemDao.transaction(request);
assertEquals(4, resp.getEntry().size());
Entry nextEntry;
nextEntry = resp.getEntry().get(1);
assertEquals(Patient.class, nextEntry.getResource().getClass());
assertEquals(idv2.toUnqualified(), nextEntry.getResource().getId().toUnqualified());
nextEntry = resp.getEntry().get(2);
assertEquals(Patient.class, nextEntry.getResource().getClass());
assertEquals(idv1.toUnqualified(), nextEntry.getResource().getId().toUnqualified());
nextEntry = resp.getEntry().get(3);
assertEquals(Bundle.class, nextEntry.getResource().getClass());
Bundle respBundle = (Bundle) nextEntry.getResource();
assertEquals(1, respBundle.getTotal().intValue());
}
@Test
public void testTransactionCreateMatchUrlWithTwoMatch() {
String methodName = "testTransactionCreateMatchUrlWithTwoMatch";
@ -289,6 +280,89 @@ public class FhirSystemDaoDstu2Test {
assertThat(patientId, not(containsString("test")));
}
@Test
public void testTransactionCreateWithInvalidReferenceNumeric() {
String methodName = "testTransactionCreateWithInvalidReferenceNumeric";
Bundle request = new Bundle();
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.addName().addFamily("Hello");
p.getManagingOrganization().setReference("Organization/9999999999999999");
request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.POST);
try {
ourSystemDao.transaction(request);
fail();
} catch (InvalidRequestException e) {
assertThat(e.getMessage(), containsString("Resource Organization/9999999999999999 not found, specified in path: Patient.managingOrganization"));
}
}
@Test
public void testTransactionCreateWithInvalidReferenceTextual() {
String methodName = "testTransactionCreateWithInvalidReferenceTextual";
Bundle request = new Bundle();
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.addName().addFamily("Hello");
p.getManagingOrganization().setReference("Organization/" + methodName);
request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.POST);
try {
ourSystemDao.transaction(request);
fail();
} catch (InvalidRequestException e) {
assertThat(e.getMessage(), containsString("Resource Organization/" + methodName + " not found, specified in path: Patient.managingOrganization"));
}
}
@Test
public void testTransactionDeleteByResourceId() {
String methodName = "testTransactionDeleteByResourceId";
Patient p1 = new Patient();
p1.addIdentifier().setSystem("urn:system").setValue(methodName);
IdDt id1 = ourPatientDao.create(p1).getId();
ourLog.info("Created patient, got it: {}", id1);
Patient p2 = new Patient();
p2.addIdentifier().setSystem("urn:system").setValue(methodName);
p2.setId("Patient/" + methodName);
IdDt id2 = ourPatientDao.update(p2).getId();
ourLog.info("Created patient, got it: {}", id2);
Bundle request = new Bundle();
request.addEntry().getTransaction().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient/" + id1.getIdPart());
request.addEntry().getTransaction().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient/" + id2.getIdPart());
ourPatientDao.read(id1.toVersionless());
ourPatientDao.read(id2.toVersionless());
Bundle resp = ourSystemDao.transaction(request);
assertEquals(3, resp.getEntry().size());
assertEquals("204", resp.getEntry().get(1).getTransactionResponse().getStatus());
assertEquals("204", resp.getEntry().get(2).getTransactionResponse().getStatus());
try {
ourPatientDao.read(id1.toVersionless());
fail();
} catch (ResourceGoneException e) {
// good
}
try {
ourPatientDao.read(id2.toVersionless());
fail();
} catch (ResourceGoneException e) {
// good
}
}
@Test
public void testTransactionDeleteMatchUrlWithOneMatch() {
String methodName = "testTransactionDeleteMatchUrlWithOneMatch";
@ -360,51 +434,6 @@ public class FhirSystemDaoDstu2Test {
}
}
@Test
public void testTransactionDeleteByResourceId() {
String methodName = "testTransactionDeleteByResourceId";
Patient p1 = new Patient();
p1.addIdentifier().setSystem("urn:system").setValue(methodName);
IdDt id1 = ourPatientDao.create(p1).getId();
ourLog.info("Created patient, got it: {}", id1);
Patient p2 = new Patient();
p2.addIdentifier().setSystem("urn:system").setValue(methodName);
p2.setId("Patient/" + methodName);
IdDt id2 = ourPatientDao.update(p2).getId();
ourLog.info("Created patient, got it: {}", id2);
Bundle request = new Bundle();
request.addEntry().getTransaction().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient/" + id1.getIdPart());
request.addEntry().getTransaction().setMethod(HTTPVerbEnum.DELETE).setUrl("Patient/" + id2.getIdPart());
ourPatientDao.read(id1.toVersionless());
ourPatientDao.read(id2.toVersionless());
Bundle resp = ourSystemDao.transaction(request);
assertEquals(3, resp.getEntry().size());
assertEquals("204", resp.getEntry().get(1).getTransactionResponse().getStatus());
assertEquals("204", resp.getEntry().get(2).getTransactionResponse().getStatus());
try {
ourPatientDao.read(id1.toVersionless());
fail();
} catch (ResourceGoneException e) {
// good
}
try {
ourPatientDao.read(id2.toVersionless());
fail();
} catch (ResourceGoneException e) {
// good
}
}
@Test
public void testTransactionDeleteMatchUrlWithZeroMatch() {
String methodName = "testTransactionDeleteMatchUrlWithZeroMatch";
@ -463,6 +492,71 @@ public class FhirSystemDaoDstu2Test {
ourSystemDao.transaction(request);
}
@Test
public void testTransactionFromBundle() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve.xml");
String bundleStr = IOUtils.toString(bundleRes);
Bundle bundle = ourFhirContext.newXmlParser().parseResource(Bundle.class, bundleStr);
Bundle resp = ourSystemDao.transaction(bundle);
ourLog.info(ourFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
OperationOutcome oo = (OperationOutcome) resp.getEntry().get(0).getResource();
assertThat(oo.getIssue().get(0).getDetailsElement().getValue(), containsString("Transaction completed"));
assertThat(resp.getEntry().get(1).getTransactionResponse().getLocation(), startsWith("Patient/a555-44-4444/_history/"));
assertThat(resp.getEntry().get(2).getTransactionResponse().getLocation(), startsWith("Patient/temp6789/_history/"));
assertThat(resp.getEntry().get(3).getTransactionResponse().getLocation(), startsWith("Organization/GHH/_history/"));
Patient p = ourPatientDao.read(new IdDt("Patient/a555-44-4444/_history/1"));
assertEquals("Patient/temp6789", p.getLink().get(0).getOther().getReference().getValue());
}
@Test
public void testTransactionReadAndSearch() {
String methodName = "testTransactionReadAndSearch";
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.setId("Patient/" + methodName);
IdDt idv1 = ourPatientDao.update(p).getId();
ourLog.info("Created patient, got id: {}", idv1);
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.addName().addFamily("Family Name");
p.setId("Patient/" + methodName);
IdDt idv2 = ourPatientDao.update(p).getId();
ourLog.info("Updated patient, got id: {}", idv2);
Bundle request = new Bundle();
request.addEntry().getTransaction().setMethod(HTTPVerbEnum.GET).setUrl(idv1.toUnqualifiedVersionless().getValue());
request.addEntry().getTransaction().setMethod(HTTPVerbEnum.GET).setUrl(idv1.toUnqualified().getValue());
request.addEntry().getTransaction().setMethod(HTTPVerbEnum.GET).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
Bundle resp = ourSystemDao.transaction(request);
assertEquals(4, resp.getEntry().size());
Entry nextEntry;
nextEntry = resp.getEntry().get(1);
assertEquals(Patient.class, nextEntry.getResource().getClass());
assertEquals(idv2.toUnqualified(), nextEntry.getResource().getId().toUnqualified());
nextEntry = resp.getEntry().get(2);
assertEquals(Patient.class, nextEntry.getResource().getClass());
assertEquals(idv1.toUnqualified(), nextEntry.getResource().getId().toUnqualified());
nextEntry = resp.getEntry().get(3);
assertEquals(Bundle.class, nextEntry.getResource().getClass());
Bundle respBundle = (Bundle) nextEntry.getResource();
assertEquals(1, respBundle.getTotal().intValue());
}
@Test
public void testTransactionUpdateMatchUrlWithOneMatch() {
String methodName = "testTransactionUpdateMatchUrlWithOneMatch";
@ -617,99 +711,6 @@ public class FhirSystemDaoDstu2Test {
}
@Test
public void testTransactionWithRelativeOidIds() throws Exception {
Bundle res = new Bundle();
res.setType(BundleTypeEnum.TRANSACTION);
Patient p1 = new Patient();
p1.setId("urn:oid:0.1.2.3");
p1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds01");
res.addEntry().setResource(p1).getTransaction().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
Observation o1 = new Observation();
o1.setId("cid:observation1");
o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
o1.setSubject(new ResourceReferenceDt("urn:oid:0.1.2.3"));
res.addEntry().setResource(o1).getTransaction().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
Observation o2 = new Observation();
o2.setId("cid:observation2");
o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03");
o2.setSubject(new ResourceReferenceDt("urn:oid:0.1.2.3"));
res.addEntry().setResource(o2).getTransaction().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
Bundle resp = ourSystemDao.transaction(res);
ourLog.info(ourFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(BundleTypeEnum.TRANSACTION_RESPONSE, resp.getTypeElement().getValueAsEnum());
assertEquals(4, resp.getEntry().size());
assertEquals(OperationOutcome.class, resp.getEntry().get(0).getResource().getClass());
OperationOutcome outcome = (OperationOutcome) resp.getEntry().get(0).getResource();
assertThat(outcome.getIssue().get(1).getDetails(), containsString("Placeholder resource ID \"Patient/urn:oid:0.1.2.3\" was replaced with permanent ID \"Patient/"));
assertTrue(resp.getEntry().get(1).getTransactionResponse().getLocation(), new IdDt(resp.getEntry().get(1).getTransactionResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
assertTrue(resp.getEntry().get(2).getTransactionResponse().getLocation(), new IdDt(resp.getEntry().get(2).getTransactionResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
assertTrue(resp.getEntry().get(3).getTransactionResponse().getLocation(), new IdDt(resp.getEntry().get(3).getTransactionResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
o1 = ourObservationDao.read(new IdDt(resp.getEntry().get(2).getTransactionResponse().getLocation()));
o2 = ourObservationDao.read(new IdDt(resp.getEntry().get(3).getTransactionResponse().getLocation()));
assertThat(o1.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
assertThat(o2.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
}
/**
* This is not the correct way to do it, but we'll allow it to be lenient
*/
@Test
public void testTransactionWithRelativeOidIdsQualified() throws Exception {
Bundle res = new Bundle();
res.setType(BundleTypeEnum.TRANSACTION);
Patient p1 = new Patient();
p1.setId("urn:oid:0.1.2.3");
p1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds01");
res.addEntry().setResource(p1).getTransaction().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
Observation o1 = new Observation();
o1.setId("cid:observation1");
o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
o1.setSubject(new ResourceReferenceDt("Patient/urn:oid:0.1.2.3"));
res.addEntry().setResource(o1).getTransaction().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
Observation o2 = new Observation();
o2.setId("cid:observation2");
o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03");
o2.setSubject(new ResourceReferenceDt("Patient/urn:oid:0.1.2.3"));
res.addEntry().setResource(o2).getTransaction().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
Bundle resp = ourSystemDao.transaction(res);
ourLog.info(ourFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(BundleTypeEnum.TRANSACTION_RESPONSE, resp.getTypeElement().getValueAsEnum());
assertEquals(4, resp.getEntry().size());
assertEquals(OperationOutcome.class, resp.getEntry().get(0).getResource().getClass());
OperationOutcome outcome = (OperationOutcome) resp.getEntry().get(0).getResource();
assertThat(outcome.getIssue().get(1).getDetails(), containsString("Placeholder resource ID \"Patient/urn:oid:0.1.2.3\" was replaced with permanent ID \"Patient/"));
assertTrue(resp.getEntry().get(1).getTransactionResponse().getLocation(), new IdDt(resp.getEntry().get(1).getTransactionResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
assertTrue(resp.getEntry().get(2).getTransactionResponse().getLocation(), new IdDt(resp.getEntry().get(2).getTransactionResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
assertTrue(resp.getEntry().get(3).getTransactionResponse().getLocation(), new IdDt(resp.getEntry().get(3).getTransactionResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
o1 = ourObservationDao.read(new IdDt(resp.getEntry().get(2).getTransactionResponse().getLocation()));
o2 = ourObservationDao.read(new IdDt(resp.getEntry().get(3).getTransactionResponse().getLocation()));
assertThat(o1.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
assertThat(o2.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
}
//
//
// /**
@ -812,6 +813,99 @@ public class FhirSystemDaoDstu2Test {
//
// }
@Test
public void testTransactionWithRelativeOidIds() throws Exception {
Bundle res = new Bundle();
res.setType(BundleTypeEnum.TRANSACTION);
Patient p1 = new Patient();
p1.setId("urn:oid:0.1.2.3");
p1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds01");
res.addEntry().setResource(p1).getTransaction().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
Observation o1 = new Observation();
o1.setId("cid:observation1");
o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
o1.setSubject(new ResourceReferenceDt("urn:oid:0.1.2.3"));
res.addEntry().setResource(o1).getTransaction().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
Observation o2 = new Observation();
o2.setId("cid:observation2");
o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03");
o2.setSubject(new ResourceReferenceDt("urn:oid:0.1.2.3"));
res.addEntry().setResource(o2).getTransaction().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
Bundle resp = ourSystemDao.transaction(res);
ourLog.info(ourFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(BundleTypeEnum.TRANSACTION_RESPONSE, resp.getTypeElement().getValueAsEnum());
assertEquals(4, resp.getEntry().size());
assertEquals(OperationOutcome.class, resp.getEntry().get(0).getResource().getClass());
OperationOutcome outcome = (OperationOutcome) resp.getEntry().get(0).getResource();
assertThat(outcome.getIssue().get(1).getDetails(), containsString("Placeholder resource ID \"Patient/urn:oid:0.1.2.3\" was replaced with permanent ID \"Patient/"));
assertTrue(resp.getEntry().get(1).getTransactionResponse().getLocation(), new IdDt(resp.getEntry().get(1).getTransactionResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
assertTrue(resp.getEntry().get(2).getTransactionResponse().getLocation(), new IdDt(resp.getEntry().get(2).getTransactionResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
assertTrue(resp.getEntry().get(3).getTransactionResponse().getLocation(), new IdDt(resp.getEntry().get(3).getTransactionResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
o1 = ourObservationDao.read(new IdDt(resp.getEntry().get(2).getTransactionResponse().getLocation()));
o2 = ourObservationDao.read(new IdDt(resp.getEntry().get(3).getTransactionResponse().getLocation()));
assertThat(o1.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
assertThat(o2.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
}
/**
* This is not the correct way to do it, but we'll allow it to be lenient
*/
@Test
public void testTransactionWithRelativeOidIdsQualified() throws Exception {
Bundle res = new Bundle();
res.setType(BundleTypeEnum.TRANSACTION);
Patient p1 = new Patient();
p1.setId("urn:oid:0.1.2.3");
p1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds01");
res.addEntry().setResource(p1).getTransaction().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
Observation o1 = new Observation();
o1.setId("cid:observation1");
o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
o1.setSubject(new ResourceReferenceDt("Patient/urn:oid:0.1.2.3"));
res.addEntry().setResource(o1).getTransaction().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
Observation o2 = new Observation();
o2.setId("cid:observation2");
o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03");
o2.setSubject(new ResourceReferenceDt("Patient/urn:oid:0.1.2.3"));
res.addEntry().setResource(o2).getTransaction().setMethod(HTTPVerbEnum.POST).setUrl("Observation");
Bundle resp = ourSystemDao.transaction(res);
ourLog.info(ourFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(BundleTypeEnum.TRANSACTION_RESPONSE, resp.getTypeElement().getValueAsEnum());
assertEquals(4, resp.getEntry().size());
assertEquals(OperationOutcome.class, resp.getEntry().get(0).getResource().getClass());
OperationOutcome outcome = (OperationOutcome) resp.getEntry().get(0).getResource();
assertThat(outcome.getIssue().get(1).getDetails(), containsString("Placeholder resource ID \"Patient/urn:oid:0.1.2.3\" was replaced with permanent ID \"Patient/"));
assertTrue(resp.getEntry().get(1).getTransactionResponse().getLocation(), new IdDt(resp.getEntry().get(1).getTransactionResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
assertTrue(resp.getEntry().get(2).getTransactionResponse().getLocation(), new IdDt(resp.getEntry().get(2).getTransactionResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
assertTrue(resp.getEntry().get(3).getTransactionResponse().getLocation(), new IdDt(resp.getEntry().get(3).getTransactionResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
o1 = ourObservationDao.read(new IdDt(resp.getEntry().get(2).getTransactionResponse().getLocation()));
o2 = ourObservationDao.read(new IdDt(resp.getEntry().get(3).getTransactionResponse().getLocation()));
assertThat(o1.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
assertThat(o2.getSubject().getReference().getValue(), endsWith("Patient/" + p1.getId().getIdPart()));
}
@AfterClass
public static void afterClass() {
ourCtx.close();
@ -828,100 +922,6 @@ public class FhirSystemDaoDstu2Test {
ourSystemDao = ourCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
}
@Test
public void testSystemMetaOperation() {
deleteEverything();
MetaDt meta = ourSystemDao.metaGetOperation();
List<CodingDt> published = meta.getTag();
assertEquals(0, published.size());
String methodName = "testSystemMetaOperation";
IdDt id1;
{
Patient patient = new Patient();
patient.addIdentifier().setSystem("urn:system").setValue(methodName);
patient.addName().addFamily("Tester").addGiven("Joe");
TagList tagList = new TagList();
tagList.addTag(null, "Dog", "Puppies");
ResourceMetadataKeyEnum.TAG_LIST.put(patient, tagList);
List<BaseCodingDt> securityLabels = new ArrayList<BaseCodingDt>();
securityLabels.add(new CodingDt().setSystem("seclabel:sys:1").setCode("seclabel:code:1").setDisplay("seclabel:dis:1"));
ResourceMetadataKeyEnum.SECURITY_LABELS.put(patient, securityLabels);
ArrayList<IdDt> profiles = new ArrayList<IdDt>();
profiles.add(new IdDt("http://profile/1"));
ResourceMetadataKeyEnum.PROFILES.put(patient, profiles);
id1 = ourPatientDao.create(patient).getId();
}
{
Patient patient = new Patient();
patient.addIdentifier().setSystem("urn:system").setValue(methodName);
patient.addName().addFamily("Tester").addGiven("Joe");
TagList tagList = new TagList();
tagList.addTag("http://foo", "Cat", "Kittens");
ResourceMetadataKeyEnum.TAG_LIST.put(patient, tagList);
List<BaseCodingDt> securityLabels = new ArrayList<BaseCodingDt>();
securityLabels.add(new CodingDt().setSystem("seclabel:sys:2").setCode("seclabel:code:2").setDisplay("seclabel:dis:2"));
ResourceMetadataKeyEnum.SECURITY_LABELS.put(patient, securityLabels);
ArrayList<IdDt> profiles = new ArrayList<IdDt>();
profiles.add(new IdDt("http://profile/2"));
ResourceMetadataKeyEnum.PROFILES.put(patient, profiles);
ourPatientDao.create(patient);
}
meta = ourSystemDao.metaGetOperation();
published = meta.getTag();
assertEquals(2, published.size());
assertEquals(null, published.get(0).getSystem());
assertEquals("Dog", published.get(0).getCode());
assertEquals("Puppies", published.get(0).getDisplay());
assertEquals("http://foo", published.get(1).getSystem());
assertEquals("Cat", published.get(1).getCode());
assertEquals("Kittens", published.get(1).getDisplay());
List<CodingDt> secLabels = meta.getSecurity();
assertEquals(2, secLabels.size());
assertEquals("seclabel:sys:1", secLabels.get(0).getSystemElement().getValue());
assertEquals("seclabel:code:1", secLabels.get(0).getCodeElement().getValue());
assertEquals("seclabel:dis:1", secLabels.get(0).getDisplayElement().getValue());
assertEquals("seclabel:sys:2", secLabels.get(1).getSystemElement().getValue());
assertEquals("seclabel:code:2", secLabels.get(1).getCodeElement().getValue());
assertEquals("seclabel:dis:2", secLabels.get(1).getDisplayElement().getValue());
List<UriDt> profiles = meta.getProfile();
assertEquals(2, profiles.size());
assertEquals("http://profile/1", profiles.get(0).getValue());
assertEquals("http://profile/2", profiles.get(1).getValue());
ourPatientDao.removeTag(id1, TagTypeEnum.TAG, null, "Dog");
ourPatientDao.removeTag(id1, TagTypeEnum.SECURITY_LABEL, "seclabel:sys:1", "seclabel:code:1");
ourPatientDao.removeTag(id1, TagTypeEnum.PROFILE, BaseFhirDao.NS_JPA_PROFILE, "http://profile/1");
meta = ourSystemDao.metaGetOperation();
published = meta.getTag();
assertEquals(1, published.size());
assertEquals("http://foo", published.get(0).getSystem());
assertEquals("Cat", published.get(0).getCode());
assertEquals("Kittens", published.get(0).getDisplay());
secLabels = meta.getSecurity();
assertEquals(1, secLabels.size());
assertEquals("seclabel:sys:2", secLabels.get(0).getSystemElement().getValue());
assertEquals("seclabel:code:2", secLabels.get(0).getCodeElement().getValue());
assertEquals("seclabel:dis:2", secLabels.get(0).getDisplayElement().getValue());
profiles = meta.getProfile();
assertEquals(1, profiles.size());
assertEquals("http://profile/2", profiles.get(0).getValue());
}
private void deleteEverything() {
FhirSystemDaoDstu2Test.doDeleteEverything(ourSystemDao);
}
static void doDeleteEverything(IFhirSystemDao<Bundle> systemDao) {
IBundleProvider all = systemDao.history(null);
List<IBaseResource> allRes = all.getResources(0, all.size());

1960
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java
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5
src/changes/changes.xml
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@ -84,6 +84,11 @@
now work, in order to be lenient. Thanks to Bill De Beaubien for
reporting!
</action>
<action type="fix">
When parsing Bundles, if Bundle.entry.base is set to "cid:" (for DSTU1)
or "urn:uuid:" / "urn:oid:" (for DSTU2) this is now correctly passed as
the base in resource.getId()
</action>
</release>
<release version="1.0" date="2015-May-8">
<action type="add">