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hapi-fhir
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This commit is contained in:
James Agnew 2017-01-24 10:46:56 -05:00
parent 5c752cdace
commit 1ab9b58e9f
4 changed files with 236 additions and 192 deletions
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28
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2Test.java
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@ -67,6 +67,34 @@ public class JsonParserDstu2Test {
private static FhirContext ourCtx = FhirContext.forDstu2(); private static FhirContext ourCtx = FhirContext.forDstu2();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserDstu2Test.class); private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserDstu2Test.class);
/**
* See #544
*/
@Test
public void testBundleStitchReferencesByUuid() throws Exception {
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
DocumentManifest dm = new DocumentManifest();
dm.getSubject().setReference("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
bundle.addEntry().setResource(dm);
Patient patient = new Patient();
patient.addName().addFamily("FAMILY");
bundle.addEntry().setResource(patient).setFullUrl("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle);
ourLog.info(encoded);
bundle = ourCtx.newJsonParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, encoded);
dm = (DocumentManifest) bundle.getEntry().get(0).getResource();
assertEquals("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3", dm.getSubject().getReference());
Patient subject = (Patient) dm.getSubject().getResource();
assertNotNull(subject);
assertEquals("FAMILY", subject.getNameFirstRep().getFamilyAsSingleString());
}
@Test @Test
public void testContainedResourceInExtensionUndeclared() { public void testContainedResourceInExtensionUndeclared() {
Patient p = new Patient(); Patient p = new Patient();

67
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
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@ -34,52 +34,16 @@ import java.util.UUID;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.hamcrest.Matchers; import org.hamcrest.Matchers;
import org.hamcrest.core.StringContains; import org.hamcrest.core.StringContains;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Address.AddressUse; import org.hl7.fhir.dstu3.model.Address.AddressUse;
import org.hl7.fhir.dstu3.model.Address.AddressUseEnumFactory; import org.hl7.fhir.dstu3.model.Address.AddressUseEnumFactory;
import org.hl7.fhir.dstu3.model.Attachment;
import org.hl7.fhir.dstu3.model.AuditEvent;
import org.hl7.fhir.dstu3.model.Basic;
import org.hl7.fhir.dstu3.model.Binary;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent; import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Bundle.BundleType; import org.hl7.fhir.dstu3.model.Bundle.BundleType;
import org.hl7.fhir.dstu3.model.Claim;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.Communication;
import org.hl7.fhir.dstu3.model.Condition;
import org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus; import org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus;
import org.hl7.fhir.dstu3.model.Conformance;
import org.hl7.fhir.dstu3.model.Conformance.UnknownContentCode; import org.hl7.fhir.dstu3.model.Conformance.UnknownContentCode;
import org.hl7.fhir.dstu3.model.Coverage;
import org.hl7.fhir.dstu3.model.DateTimeType;
import org.hl7.fhir.dstu3.model.DateType;
import org.hl7.fhir.dstu3.model.DecimalType;
import org.hl7.fhir.dstu3.model.DiagnosticReport;
import org.hl7.fhir.dstu3.model.EnumFactory;
import org.hl7.fhir.dstu3.model.Enumeration;
import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender; import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.dstu3.model.ExplanationOfBenefit;
import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.dstu3.model.HumanName;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Identifier.IdentifierUse; import org.hl7.fhir.dstu3.model.Identifier.IdentifierUse;
import org.hl7.fhir.dstu3.model.Linkage;
import org.hl7.fhir.dstu3.model.Medication;
import org.hl7.fhir.dstu3.model.MedicationRequest;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus; import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.PrimitiveType;
import org.hl7.fhir.dstu3.model.Quantity;
import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.dstu3.model.RelatedPerson;
import org.hl7.fhir.dstu3.model.SampledData;
import org.hl7.fhir.dstu3.model.SimpleQuantity;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.utilities.xhtml.XhtmlNode; import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.junit.After; import org.junit.After;
import org.junit.AfterClass; import org.junit.AfterClass;
@ -115,6 +79,35 @@ public class JsonParserDstu3Test {
ourCtx.setNarrativeGenerator(null); ourCtx.setNarrativeGenerator(null);
} }
/**
* See #544
*/
@Test
public void testBundleStitchReferencesByUuid() throws Exception {
Bundle bundle = new Bundle();
DocumentManifest dm = new DocumentManifest();
dm.getSubject().setReference("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
bundle.addEntry().setResource(dm);
Patient patient = new Patient();
patient.addName().setFamily("FAMILY");
bundle.addEntry().setResource(patient).setFullUrl("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle);
ourLog.info(encoded);
bundle = ourCtx.newJsonParser().parseResource(Bundle.class, encoded);
dm = (DocumentManifest) bundle.getEntry().get(0).getResource();
assertEquals("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3", dm.getSubject().getReference());
Patient subject = (Patient) dm.getSubject().getResource();
assertNotNull(subject);
assertEquals("FAMILY", subject.getNameFirstRep().getFamily());
}
@Test @Test
public void testIncorrectJsonTypesIdAndArray() { public void testIncorrectJsonTypesIdAndArray() {

322
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java
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@ -81,165 +81,27 @@ public class XmlParserDstu3Test {
*/ */
@Test @Test
public void testBundleStitchReferencesByUuid() throws Exception { public void testBundleStitchReferencesByUuid() throws Exception {
String body = IOUtils.toString(XmlParserDstu3Test.class.getResourceAsStream("/bundle_ref_by_uuid_544.xml"), StandardCharsets.UTF_8); Bundle bundle = new Bundle();
Bundle bundle = ourCtx.newXmlParser().parseResource(Bundle.class, body);
DocumentManifest dm = (DocumentManifest) bundle.getEntry().get(0).getResource(); DocumentManifest dm = new DocumentManifest();
dm.getSubject().setReference("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
bundle.addEntry().setResource(dm);
Patient patient = new Patient();
patient.addName().setFamily("FAMILY");
bundle.addEntry().setResource(patient).setFullUrl("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
ourLog.info(encoded);
bundle = ourCtx.newXmlParser().parseResource(Bundle.class, encoded);
dm = (DocumentManifest) bundle.getEntry().get(0).getResource();
assertEquals("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3", dm.getSubject().getReference()); assertEquals("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3", dm.getSubject().getReference());
Patient subject = (Patient) dm.getSubject().getResource(); Patient subject = (Patient) dm.getSubject().getResource();
assertNotNull(subject); assertNotNull(subject);
} assertEquals("FAMILY", subject.getNameFirstRep().getFamily());
/**
* See #414
*/
@Test
public void testParseXmlExtensionWithoutUrl() {
//@formatter:off
String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
" <extension>\n" +
" <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" +
" </extension>\n" +
"</Patient>";
//@formatter:on
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new LenientErrorHandler());
Patient parsed = (Patient) parser.parseResource(input);
assertEquals(1, parsed.getExtension().size());
assertEquals(null, parsed.getExtension().get(0).getUrl());
assertEquals("2011-01-02T11:13:15", parsed.getExtension().get(0).getValueAsPrimitive().getValueAsString());
try {
parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new StrictErrorHandler());
parser.parseResource(input);
fail();
} catch (DataFormatException e) {
assertEquals("Resource is missing required element 'url' in parent element 'extension'", e.getCause().getMessage());
}
}
/**
* See #414
*/
@Test
public void testParseXmlModifierExtensionWithoutUrl() {
//@formatter:off
String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
" <modifierExtension>\n" +
" <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" +
" </modifierExtension>\n" +
"</Patient>";
//@formatter:on
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new LenientErrorHandler());
Patient parsed = (Patient) parser.parseResource(input);
assertEquals(1, parsed.getModifierExtension().size());
assertEquals(null, parsed.getModifierExtension().get(0).getUrl());
assertEquals("2011-01-02T11:13:15", parsed.getModifierExtension().get(0).getValueAsPrimitive().getValueAsString());
try {
parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new StrictErrorHandler());
parser.parseResource(input);
fail();
} catch (DataFormatException e) {
assertEquals("Resource is missing required element 'url' in parent element 'modifierExtension'", e.getCause().getMessage());
}
}
@Test
public void testEncodeChainedContainedResourcer() {
Organization gp = new Organization();
gp.setName("grandparent");
Organization parent = new Organization();
parent.setName("parent");
parent.getPartOf().setResource(gp);
Organization child = new Organization();
child.setName("child");
child.getPartOf().setResource(parent);
Patient patient = new Patient();
patient.getManagingOrganization().setResource(child);
String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
ourLog.info(encoded);
patient = ourCtx.newXmlParser().parseResource(Patient.class, encoded);
child = (Organization) patient.getManagingOrganization().getResource();
assertEquals("child", child.getName());
parent = (Organization) child.getPartOf().getResource();
assertEquals("parent", parent.getName());
gp = (Organization) parent.getPartOf().getResource();
assertEquals("grandparent", gp.getName());
}
/**
* If a contained resource refers to a contained resource that comes after it, it should still be successfully
* woven together.
*/
@Test
public void testParseWovenContainedResources() throws IOException {
String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_woven_obs.xml"), StandardCharsets.UTF_8);
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new StrictErrorHandler());
org.hl7.fhir.dstu3.model.Bundle bundle = parser.parseResource(Bundle.class, string);
DiagnosticReport resource = (DiagnosticReport) bundle.getEntry().get(0).getResource();
Observation obs = (Observation) resource.getResult().get(1).getResource();
assertEquals("#2", obs.getId());
Reference performerFirstRep = obs.getPerformerFirstRep();
Practitioner performer = (Practitioner) performerFirstRep.getResource();
assertEquals("#3", performer.getId());
}
@Test(expected = DataFormatException.class)
public void testContainedResourceWithNoId() throws IOException {
String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new StrictErrorHandler());
parser.parseResource(Bundle.class, string);
}
@Test()
public void testContainedResourceWithNoIdLenient() throws IOException {
String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new LenientErrorHandler());
parser.parseResource(Bundle.class, string);
}
@Test(expected = DataFormatException.class)
public void testParseWithInvalidLocalRef() throws IOException {
String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new StrictErrorHandler());
parser.parseResource(Bundle.class, string);
}
@Test()
public void testParseWithInvalidLocalRefLenient() throws IOException {
String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new LenientErrorHandler());
parser.parseResource(Bundle.class, string);
} }
@Test @Test
@ -273,6 +135,7 @@ public class XmlParserDstu3Test {
} }
@Test @Test
public void testContainedResourceInExtensionUndeclared() { public void testContainedResourceInExtensionUndeclared() {
Patient p = new Patient(); Patient p = new Patient();
@ -295,6 +158,24 @@ public class XmlParserDstu3Test {
assertEquals("ORG", o.getName()); assertEquals("ORG", o.getName());
} }
@Test(expected = DataFormatException.class)
public void testContainedResourceWithNoId() throws IOException {
String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new StrictErrorHandler());
parser.parseResource(Bundle.class, string);
}
@Test()
public void testContainedResourceWithNoIdLenient() throws IOException {
String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new LenientErrorHandler());
parser.parseResource(Bundle.class, string);
}
@Test @Test
public void testDuration() { public void testDuration() {
Encounter enc = new Encounter(); Encounter enc = new Encounter();
@ -1039,6 +920,37 @@ public class XmlParserDstu3Test {
assertThat(encoded, not(stringContainsInOrder("<DiagnosticReport", "<contained", "<Observation", "<contained", "<Observation", "</DiagnosticReport"))); assertThat(encoded, not(stringContainsInOrder("<DiagnosticReport", "<contained", "<Observation", "<contained", "<Observation", "</DiagnosticReport")));
} }
@Test
public void testEncodeChainedContainedResourcer() {
Organization gp = new Organization();
gp.setName("grandparent");
Organization parent = new Organization();
parent.setName("parent");
parent.getPartOf().setResource(gp);
Organization child = new Organization();
child.setName("child");
child.getPartOf().setResource(parent);
Patient patient = new Patient();
patient.getManagingOrganization().setResource(child);
String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
ourLog.info(encoded);
patient = ourCtx.newXmlParser().parseResource(Patient.class, encoded);
child = (Organization) patient.getManagingOrganization().getResource();
assertEquals("child", child.getName());
parent = (Organization) child.getPartOf().getResource();
assertEquals("parent", parent.getName());
gp = (Organization) parent.getPartOf().getResource();
assertEquals("grandparent", gp.getName());
}
/** /**
* See #326 * See #326
*/ */
@ -1945,8 +1857,6 @@ public class XmlParserDstu3Test {
assertThat(output, containsString("<text><status value=\"generated\"/><div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">John <b>SMITH </b>")); assertThat(output, containsString("<text><status value=\"generated\"/><div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">John <b>SMITH </b>"));
} }
@Test @Test
public void testMoreExtensions() throws Exception { public void testMoreExtensions() throws Exception {
@ -2192,6 +2102,8 @@ public class XmlParserDstu3Test {
} }
@Test @Test
public void testParseAndEncodeCommentsOnExtensions() { public void testParseAndEncodeCommentsOnExtensions() {
//@formatter:off //@formatter:off
@ -3121,6 +3033,106 @@ public class XmlParserDstu3Test {
} }
} }
@Test(expected = DataFormatException.class)
public void testParseWithInvalidLocalRef() throws IOException {
String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new StrictErrorHandler());
parser.parseResource(Bundle.class, string);
}
@Test()
public void testParseWithInvalidLocalRefLenient() throws IOException {
String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new LenientErrorHandler());
parser.parseResource(Bundle.class, string);
}
/**
* If a contained resource refers to a contained resource that comes after it, it should still be successfully
* woven together.
*/
@Test
public void testParseWovenContainedResources() throws IOException {
String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_woven_obs.xml"), StandardCharsets.UTF_8);
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new StrictErrorHandler());
org.hl7.fhir.dstu3.model.Bundle bundle = parser.parseResource(Bundle.class, string);
DiagnosticReport resource = (DiagnosticReport) bundle.getEntry().get(0).getResource();
Observation obs = (Observation) resource.getResult().get(1).getResource();
assertEquals("#2", obs.getId());
Reference performerFirstRep = obs.getPerformerFirstRep();
Practitioner performer = (Practitioner) performerFirstRep.getResource();
assertEquals("#3", performer.getId());
}
/**
* See #414
*/
@Test
public void testParseXmlExtensionWithoutUrl() {
//@formatter:off
String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
" <extension>\n" +
" <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" +
" </extension>\n" +
"</Patient>";
//@formatter:on
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new LenientErrorHandler());
Patient parsed = (Patient) parser.parseResource(input);
assertEquals(1, parsed.getExtension().size());
assertEquals(null, parsed.getExtension().get(0).getUrl());
assertEquals("2011-01-02T11:13:15", parsed.getExtension().get(0).getValueAsPrimitive().getValueAsString());
try {
parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new StrictErrorHandler());
parser.parseResource(input);
fail();
} catch (DataFormatException e) {
assertEquals("Resource is missing required element 'url' in parent element 'extension'", e.getCause().getMessage());
}
}
/**
* See #414
*/
@Test
public void testParseXmlModifierExtensionWithoutUrl() {
//@formatter:off
String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
" <modifierExtension>\n" +
" <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" +
" </modifierExtension>\n" +
"</Patient>";
//@formatter:on
IParser parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new LenientErrorHandler());
Patient parsed = (Patient) parser.parseResource(input);
assertEquals(1, parsed.getModifierExtension().size());
assertEquals(null, parsed.getModifierExtension().get(0).getUrl());
assertEquals("2011-01-02T11:13:15", parsed.getModifierExtension().get(0).getValueAsPrimitive().getValueAsString());
try {
parser = ourCtx.newXmlParser();
parser.setParserErrorHandler(new StrictErrorHandler());
parser.parseResource(input);
fail();
} catch (DataFormatException e) {
assertEquals("Resource is missing required element 'url' in parent element 'modifierExtension'", e.getCause().getMessage());
}
}
/** /**
* See #339 * See #339
* *

11
src/changes/changes.xml
View File

@ -222,6 +222,17 @@
return an HTTP 404 and not a 400, per the HTTP spec. Thanks to return an HTTP 404 and not a 400, per the HTTP spec. Thanks to
GitHub user @CarthageKing for the pull request! GitHub user @CarthageKing for the pull request!
</action> </action>
<action type="fix" issue="544">
When parsing a Bundle containing placeholder fullUrls and references
(e.g. "urn:uuid:0000-0000") the resource reference targets did not get
populated with the given resources. Note that as a part of this
change, <![CDATA[<code>IdType</code> and <code>IdDt</code>]]> have been modified
so that when parsing a placeholder ID, the complete placeholder including the
"urn:uuid:" or "urn:oid:" prefix will be placed into the ID part. Previously,
the prefix was treated as the base URL, which led to strange behaviour
like the placeholder being treated as a real IDs. Thanks to GitHub
user @jodue for reporting!
</action>
</release> </release>
<release version="2.1" date="2016-11-11"> <release version="2.1" date="2016-11-11">
<action type="add"> <action type="add">