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Fox a bunch of JPA bugs

This commit is contained in:
jamesagnew 2014-06-05 16:01:00 -04:00
parent bb86724e12
commit 54078be6e0
28 changed files with 898 additions and 3203 deletions
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9
hapi-fhir-base/src/changes/changes.xml
View File

@ -9,6 +9,15 @@
<release version="0.3" date="2014-May-12" description="This release corrects lots of bugs and introduces the fluent client mode">
</release>
<release version="0.4" date="TBD">
<action type="add">
<![CDATA[<b>BREAKING CHANGE:</b>]]>: IdDt has been modified so that it
contains a partial or complete resource identity. Previously it contained
only the simple alphanumeric id of the resource (the part at the end of the "read" URL for
that resource) but it can now contain a complete URL or even a partial URL (e.g. "Patient/123")
and can optionally contain a version (e.g. "Patient/123/_history/456"). New methods have
been added to this datatype which provide just the numeric portion. See the JavaDoc
for more information.
</action>
<action type="add">
Allow use of QuantityDt as a service parameter to support the "quantity" type. Previously
QuantityDt did not implement IQueryParameterType so it was not valid, and there was no way to

28
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/BaseResourceReference.java
View File

@ -54,30 +54,12 @@ public abstract class BaseResourceReference extends BaseElement {
*/
public BaseResourceReference(IResource theResource) {
myResource = theResource;
setResourceId(theResource.getId());
setReference(theResource.getId());
}
/**
* Gets the value(s) for <b>reference</b> (Relative, internal or absolute URL reference). creating it if it does not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b> A reference to a location at which the other resource is found. The reference may a relative reference, in which case it is relative to the service base URL, or an absolute
* URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be
* version specific. Internal fragment references (start with '#') refer to contained resources
* </p>
*/
public abstract IdDt getResourceId();
/**
* Sets the resource ID
*
* <p>
* <b>Definition:</b> A reference to a location at which the other resource is found. The reference may a relative reference, in which case it is relative to the service base URL, or an absolute
* URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be
* version specific. Internal fragment references (start with '#') refer to contained resources
* </p>
*/
public abstract void setResourceId(IdDt theResourceId);
public abstract BaseResourceReference setReference(IdDt theReference);
/**
* Gets the actual loaded and parsed resource instance, <b>if it is already present</b>. This
@ -107,7 +89,7 @@ public abstract class BaseResourceReference extends BaseElement {
return myResource;
}
IdDt resourceId = getResourceId();
IdDt resourceId = getReference();
if (resourceId == null) {
throw new IllegalStateException("Reference has no resource ID defined");
}
@ -141,6 +123,8 @@ public abstract class BaseResourceReference extends BaseElement {
return myResource;
}
protected abstract IdDt getReference();
public void setResource(IResource theResource) {
myResource = theResource;
}

128
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/composite/ResourceReferenceDt.java
View File

@ -1,24 +1,20 @@
package ca.uhn.fhir.model.dstu.composite;
/*
* #%L
* HAPI FHIR Library
* %%
* Copyright (C) 2014 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.model.dstu.composite;
import java.util.List;
@ -33,10 +29,12 @@ import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.StringDt;
/**
* HAPI/FHIR <b>ResourceReferenceDt</b> Datatype (A reference from one resource to another)
* HAPI/FHIR <b>ResourceReferenceDt</b> Datatype
* (A reference from one resource to another)
*
* <p>
* <b>Definition:</b> A reference from one resource to another
* <b>Definition:</b>
* A reference from one resource to another
* </p>
*
* <p>
@ -45,7 +43,8 @@ import ca.uhn.fhir.model.primitive.StringDt;
* </p>
*/
@DatatypeDef(name="ResourceReferenceDt")
public class ResourceReferenceDt extends BaseResourceReference implements ICompositeDatatype {
public class ResourceReferenceDt
extends BaseResourceReference implements ICompositeDatatype {
/**
* Constructor
@ -78,7 +77,7 @@ public class ResourceReferenceDt extends BaseResourceReference implements ICompo
* The reference itself
*/
public ResourceReferenceDt(String theId) {
setResourceId(new IdDt(theId));
setReference(new IdDt(theId));
}
/**
@ -89,17 +88,24 @@ public class ResourceReferenceDt extends BaseResourceReference implements ICompo
* The reference itself
*/
public ResourceReferenceDt(IdDt theResourceId) {
setResourceId(theResourceId);
setReference(theResourceId);
}
@Child(name = "reference", type = StringDt.class, order = 0, min = 0, max = 1)
@Description(shortDefinition = "Relative, internal or absolute URL reference", formalDefinition = "A reference to a location at which the other resource is found. The reference may a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources")
private StringDt myReference;
@Child(name="reference", type=IdDt.class, order=0, min=0, max=1)
@Description(
shortDefinition="Relative, internal or absolute URL reference",
formalDefinition="A reference to a location at which the other resource is found. The reference may a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources"
)
private IdDt myReference;
@Child(name="display", type=StringDt.class, order=1, min=0, max=1)
@Description(shortDefinition = "Text alternative for the resource", formalDefinition = "Plain text narrative that identifies the resource in addition to the resource reference")
@Description(
shortDefinition="Text alternative for the resource",
formalDefinition="Plain text narrative that identifies the resource in addition to the resource reference"
)
private StringDt myDisplay;
@Override
public boolean isEmpty() {
return super.isBaseEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty( myReference, myDisplay);
@ -111,20 +117,18 @@ public class ResourceReferenceDt extends BaseResourceReference implements ICompo
}
/**
* Gets the value(s) for <b>reference</b> (Relative, internal or absolute URL reference). creating it if it does not
* exist. Will not return <code>null</code>.
* Gets the value(s) for <b>reference</b> (Relative, internal or absolute URL reference).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b> A reference to a location at which the other resource is found. The reference may a relative
* reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location
* where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR
* RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#')
* refer to contained resources
* <b>Definition:</b>
* A reference to a location at which the other resource is found. The reference may a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources
* </p>
*/
public StringDt getReference() {
public IdDt getReference() {
if (myReference == null) {
myReference = new StringDt();
myReference = new IdDt();
}
return myReference;
}
@ -133,14 +137,11 @@ public class ResourceReferenceDt extends BaseResourceReference implements ICompo
* Sets the value(s) for <b>reference</b> (Relative, internal or absolute URL reference)
*
* <p>
* <b>Definition:</b> A reference to a location at which the other resource is found. The reference may a relative
* reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location
* where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR
* RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#')
* refer to contained resources
* <b>Definition:</b>
* A reference to a location at which the other resource is found. The reference may a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources
* </p>
*/
public ResourceReferenceDt setReference(StringDt theValue) {
public ResourceReferenceDt setReference(IdDt theValue) {
myReference = theValue;
return this;
}
@ -149,23 +150,24 @@ public class ResourceReferenceDt extends BaseResourceReference implements ICompo
* Sets the value for <b>reference</b> (Relative, internal or absolute URL reference)
*
* <p>
* <b>Definition:</b> A reference to a location at which the other resource is found. The reference may a relative
* reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location
* where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR
* RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#')
* refer to contained resources
* <b>Definition:</b>
* A reference to a location at which the other resource is found. The reference may a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources
* </p>
*/
public ResourceReferenceDt setReference(String theString) {
return setReference(new StringDt(theString));
public ResourceReferenceDt setReference( String theId) {
myReference = new IdDt(theId);
return this;
}
/**
* Gets the value(s) for <b>display</b> (Text alternative for the resource). creating it if it does not exist. Will
* not return <code>null</code>.
* Gets the value(s) for <b>display</b> (Text alternative for the resource).
* creating it if it does
* not exist. Will not return <code>null</code>.
*
* <p>
* <b>Definition:</b> Plain text narrative that identifies the resource in addition to the resource reference
* <b>Definition:</b>
* Plain text narrative that identifies the resource in addition to the resource reference
* </p>
*/
public StringDt getDisplay() {
@ -179,7 +181,8 @@ public class ResourceReferenceDt extends BaseResourceReference implements ICompo
* Sets the value(s) for <b>display</b> (Text alternative for the resource)
*
* <p>
* <b>Definition:</b> Plain text narrative that identifies the resource in addition to the resource reference
* <b>Definition:</b>
* Plain text narrative that identifies the resource in addition to the resource reference
* </p>
*/
public ResourceReferenceDt setDisplay(StringDt theValue) {
@ -191,7 +194,8 @@ public class ResourceReferenceDt extends BaseResourceReference implements ICompo
* Sets the value for <b>display</b> (Text alternative for the resource)
*
* <p>
* <b>Definition:</b> Plain text narrative that identifies the resource in addition to the resource reference
* <b>Definition:</b>
* Plain text narrative that identifies the resource in addition to the resource reference
* </p>
*/
public ResourceReferenceDt setDisplay( String theString) {
@ -199,17 +203,7 @@ public class ResourceReferenceDt extends BaseResourceReference implements ICompo
return this;
}
@Override
public IdDt getResourceId() {
if (myReference == null) {
return new IdDt();
}
return new IdDt(myReference.getValue());
}
@Override
public void setResourceId(IdDt theResourceId) {
myReference = new StringDt(theResourceId.getValue());
}
}

8
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Binary.java
View File

@ -75,14 +75,6 @@ public class Binary extends BaseResource implements IResource {
return myContentType;
}
/**
* Do not call - throws {@link UnsupportedOperationException}
*/
@Override
public NarrativeDt getText() {
throw new UnsupportedOperationException();
}
@Override
public boolean isEmpty() {
return (myContent.isEmpty()) && StringUtils.isBlank(myContentType);

106
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/dstu/resource/Encounter.java
View File

@ -16,26 +16,6 @@
package ca.uhn.fhir.model.dstu.resource;
/*
* #%L
* HAPI FHIR Library
* %%
* Copyright (C) 2014 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.List;
@ -185,33 +165,6 @@ public class Encounter extends BaseResource implements IResource {
*/
public static final Include INCLUDE_SUBJECT = new Include("Encounter.subject");
/**
* Search parameter constant for <b>!fulfills</b>
* <p>
* Description: <b></b><br/>
* Type: <b>reference</b><br/>
* Path: <b>Encounter.fulfills</b><br/>
* </p>
*/
@SearchParamDefinition(name="!fulfills", path="Encounter.fulfills", description="", type="reference")
public static final String SP_FULFILLS = "!fulfills";
/**
* <b>Fluent Client</b> search parameter constant for <b>!fulfills</b>
* <p>
* Description: <b></b><br/>
* Type: <b>reference</b><br/>
* Path: <b>Encounter.fulfills</b><br/>
* </p>
*/
public static final ReferenceParam FULFILLS = new ReferenceParam(SP_FULFILLS);
/**
* Constant for fluent queries to be used to add include statements. Specifies
* the path value of "<b>Encounter.fulfills</b>".
*/
public static final Include INCLUDE_FULFILLS = new Include("Encounter.fulfills");
/**
* Search parameter constant for <b>length</b>
* <p>
@ -498,11 +451,11 @@ public class Encounter extends BaseResource implements IResource {
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public Encounter addIdentifier( IdentifierUseEnum theUse, String theSystem, String theValue, String theLabel) {
public Encounter addIdentifier( String theSystem, String theValue) {
if (myIdentifier == null) {
myIdentifier = new java.util.ArrayList<IdentifierDt>();
}
myIdentifier.add(new IdentifierDt(theUse, theSystem, theValue, theLabel));
myIdentifier.add(new IdentifierDt(theSystem, theValue));
return this;
}
@ -516,11 +469,11 @@ public class Encounter extends BaseResource implements IResource {
*
* @return Returns a reference to this object, to allow for simple chaining.
*/
public Encounter addIdentifier( String theSystem, String theValue) {
public Encounter addIdentifier( IdentifierUseEnum theUse, String theSystem, String theValue, String theLabel) {
if (myIdentifier == null) {
myIdentifier = new java.util.ArrayList<IdentifierDt>();
}
myIdentifier.add(new IdentifierDt(theSystem, theValue));
myIdentifier.add(new IdentifierDt(theUse, theSystem, theValue, theLabel));
return this;
}
@ -651,8 +604,24 @@ public class Encounter extends BaseResource implements IResource {
* Specific type of encounter (e.g. e-mail consultation, surgical day-care, skilled nursing, rehabilitation)
* </p>
*/
public void addType(EncounterTypeEnum theValue) {
getType().add(new BoundCodeableConceptDt<EncounterTypeEnum>(EncounterTypeEnum.VALUESET_BINDER, theValue));
public BoundCodeableConceptDt<EncounterTypeEnum> addType(EncounterTypeEnum theValue) {
BoundCodeableConceptDt<EncounterTypeEnum> retVal = new BoundCodeableConceptDt<EncounterTypeEnum>(EncounterTypeEnum.VALUESET_BINDER, theValue);
getType().add(retVal);
return retVal;
}
/**
* Add a value for <b>type</b> (Specific type of encounter)
*
* <p>
* <b>Definition:</b>
* Specific type of encounter (e.g. e-mail consultation, surgical day-care, skilled nursing, rehabilitation)
* </p>
*/
public BoundCodeableConceptDt<EncounterTypeEnum> addType() {
BoundCodeableConceptDt<EncounterTypeEnum> retVal = new BoundCodeableConceptDt<EncounterTypeEnum>(EncounterTypeEnum.VALUESET_BINDER);
getType().add(retVal);
return retVal;
}
/**
@ -1157,8 +1126,24 @@ public class Encounter extends BaseResource implements IResource {
*
* </p>
*/
public void addType(ParticipantTypeEnum theValue) {
getType().add(new BoundCodeableConceptDt<ParticipantTypeEnum>(ParticipantTypeEnum.VALUESET_BINDER, theValue));
public BoundCodeableConceptDt<ParticipantTypeEnum> addType(ParticipantTypeEnum theValue) {
BoundCodeableConceptDt<ParticipantTypeEnum> retVal = new BoundCodeableConceptDt<ParticipantTypeEnum>(ParticipantTypeEnum.VALUESET_BINDER, theValue);
getType().add(retVal);
return retVal;
}
/**
* Add a value for <b>type</b> (Role of participant in encounter)
*
* <p>
* <b>Definition:</b>
*
* </p>
*/
public BoundCodeableConceptDt<ParticipantTypeEnum> addType() {
BoundCodeableConceptDt<ParticipantTypeEnum> retVal = new BoundCodeableConceptDt<ParticipantTypeEnum>(ParticipantTypeEnum.VALUESET_BINDER);
getType().add(retVal);
return retVal;
}
/**
@ -1187,6 +1172,9 @@ public class Encounter extends BaseResource implements IResource {
* </p>
*/
public ResourceReferenceDt getIndividual() {
if (myIndividual == null) {
myIndividual = new ResourceReferenceDt();
}
return myIndividual;
}
@ -1355,8 +1343,8 @@ public class Encounter extends BaseResource implements IResource {
*
* </p>
*/
public Hospitalization setPreAdmissionIdentifier( IdentifierUseEnum theUse, String theSystem, String theValue, String theLabel) {
myPreAdmissionIdentifier = new IdentifierDt(theUse, theSystem, theValue, theLabel);
public Hospitalization setPreAdmissionIdentifier( String theSystem, String theValue) {
myPreAdmissionIdentifier = new IdentifierDt(theSystem, theValue);
return this;
}
@ -1368,8 +1356,8 @@ public class Encounter extends BaseResource implements IResource {
*
* </p>
*/
public Hospitalization setPreAdmissionIdentifier( String theSystem, String theValue) {
myPreAdmissionIdentifier = new IdentifierDt(theSystem, theValue);
public Hospitalization setPreAdmissionIdentifier( IdentifierUseEnum theUse, String theSystem, String theValue, String theLabel) {
myPreAdmissionIdentifier = new IdentifierDt(theUse, theSystem, theValue, theLabel);
return this;
}

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -273,7 +273,7 @@ public class JsonParser extends BaseParser implements IParser {
}
case RESOURCE_REF: {
ResourceReferenceDt referenceDt = (ResourceReferenceDt) theValue;
IdDt value = referenceDt.getResourceId();
IdDt value = referenceDt.getReference();
if (theChildName != null) {
theWriter.writeStartObject(theChildName);
} else {

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateRangeParam.java
View File

@ -24,6 +24,8 @@ import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.dstu.valueset.QuantityCompararatorEnum;
@ -184,8 +186,12 @@ public class DateRangeParam implements IQueryParameterAnd {
* "2011-02-22" or "2011-02-22T13:12:00". Will be treated inclusively.
*/
public void setRangeFromDatesInclusive(Date theLowerBound, Date theUpperBound) {
if (theLowerBound != null) {
myLowerBound = new QualifiedDateParam(QuantityCompararatorEnum.GREATERTHAN_OR_EQUALS, theLowerBound);
}
if (theUpperBound != null) {
myUpperBound = new QualifiedDateParam(QuantityCompararatorEnum.LESSTHAN_OR_EQUALS, theUpperBound);
}
validateAndThrowDataFormatExceptionIfInvalid();
}
@ -200,8 +206,12 @@ public class DateRangeParam implements IQueryParameterAnd {
* "2011-02-22" or "2011-02-22T13:12:00". Will be treated inclusively.
*/
public void setRangeFromDatesInclusive(String theLowerBound, String theUpperBound) {
if (StringUtils.isNotBlank(theLowerBound)) {
myLowerBound = new QualifiedDateParam(QuantityCompararatorEnum.GREATERTHAN_OR_EQUALS, theLowerBound);
}
if (StringUtils.isNotBlank(theUpperBound)) {
myUpperBound = new QualifiedDateParam(QuantityCompararatorEnum.LESSTHAN_OR_EQUALS, theUpperBound);
}
validateAndThrowDataFormatExceptionIfInvalid();
}

32
hapi-fhir-base/src/test/java/ca/uhn/fhir/model/primitive/IdDtTest.java
View File

@ -24,8 +24,8 @@ public class IdDtTest {
Patient actual = parseAndEncode(patient);
ResourceReferenceDt ref = actual.getManagingOrganization();
assertEquals("Organization", ref.getResourceId().getResourceType());
assertEquals("123", ref.getResourceId().getUnqualifiedId());
assertEquals("Organization", ref.getReference().getResourceType());
assertEquals("123", ref.getReference().getUnqualifiedId());
}
@ -38,9 +38,9 @@ public class IdDtTest {
Patient actual = parseAndEncode(patient);
ResourceReferenceDt ref = actual.getManagingOrganization();
assertEquals("Organization", ref.getResourceId().getResourceType());
assertEquals("123", ref.getResourceId().getUnqualifiedId());
assertEquals("999", ref.getResourceId().getUnqualifiedVersionId());
assertEquals("Organization", ref.getReference().getResourceType());
assertEquals("123", ref.getReference().getUnqualifiedId());
assertEquals("999", ref.getReference().getUnqualifiedVersionId());
}
@ -53,9 +53,9 @@ public class IdDtTest {
Patient actual = parseAndEncode(patient);
ResourceReferenceDt ref = actual.getManagingOrganization();
assertEquals(null, ref.getResourceId().getResourceType());
assertEquals("123", ref.getResourceId().getUnqualifiedId());
assertEquals("999", ref.getResourceId().getUnqualifiedVersionId());
assertEquals(null, ref.getReference().getResourceType());
assertEquals("123", ref.getReference().getUnqualifiedId());
assertEquals("999", ref.getReference().getUnqualifiedVersionId());
}
@ -69,8 +69,8 @@ public class IdDtTest {
Patient actual = parseAndEncode(patient);
ResourceReferenceDt ref = actual.getManagingOrganization();
assertEquals(null, ref.getResourceId().getResourceType());
assertEquals("123", ref.getResourceId().getUnqualifiedId());
assertEquals(null, ref.getReference().getResourceType());
assertEquals("123", ref.getReference().getUnqualifiedId());
}
@ -83,8 +83,8 @@ public class IdDtTest {
Patient actual = parseAndEncode(patient);
ResourceReferenceDt ref = actual.getManagingOrganization();
assertEquals(null, ref.getResourceId().getResourceType());
assertEquals("123", ref.getResourceId().getUnqualifiedId());
assertEquals(null, ref.getReference().getResourceType());
assertEquals("123", ref.getReference().getUnqualifiedId());
}
@ -97,8 +97,8 @@ public class IdDtTest {
Patient actual = parseAndEncode(patient);
ResourceReferenceDt ref = actual.getManagingOrganization();
assertEquals("Organization", ref.getResourceId().getResourceType());
assertEquals("123", ref.getResourceId().getUnqualifiedId());
assertEquals("Organization", ref.getReference().getResourceType());
assertEquals("123", ref.getReference().getUnqualifiedId());
}
@ -111,8 +111,8 @@ public class IdDtTest {
Patient actual = parseAndEncode(patient);
ResourceReferenceDt ref = actual.getManagingOrganization();
assertEquals("Organization", ref.getResourceId().getResourceType());
assertEquals("123", ref.getResourceId().getUnqualifiedId());
assertEquals("Organization", ref.getReference().getResourceType());
assertEquals("123", ref.getReference().getUnqualifiedId());
}

4
hapi-fhir-base/src/test/java/ca/uhn/fhir/parser/JsonParserTest.java
View File

@ -347,7 +347,7 @@ public class JsonParserTest {
MyPatientWithOneDeclaredExtension actual = parser.parseResource(MyPatientWithOneDeclaredExtension.class, val);
assertEquals(AddressUseEnum.HOME, patient.getAddressFirstRep().getUse().getValueAsEnum());
ResourceReferenceDt ref = actual.getFoo();
assertEquals("Organization/123", ref.getResourceId().getValue());
assertEquals("Organization/123", ref.getReference().getValue());
}
@ -400,7 +400,7 @@ public class JsonParserTest {
try {
p.encodeResourceToString(obs);
} catch (DataFormatException e) {
assertThat(e.getMessage(), StringContains.containsString("PeriodDt"));
assertThat(e.getMessage(), StringContains.containsString("DecimalDt"));
}
}

2
hapi-fhir-base/src/test/java/ca/uhn/fhir/parser/XmlParserTest.java
View File

@ -420,7 +420,7 @@ public class XmlParserTest {
try {
p.encodeResourceToString(obs);
} catch (DataFormatException e) {
assertThat(e.getMessage(), StringContains.containsString("PeriodDt"));
assertThat(e.getMessage(), StringContains.containsString("DecimalDt"));
}
}

54
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseFhirDao.java
View File

@ -1,6 +1,6 @@
package ca.uhn.fhir.jpa.dao;
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.text.Normalizer;
import java.util.ArrayList;
@ -57,6 +57,7 @@ import ca.uhn.fhir.model.dstu.composite.CodingDt;
import ca.uhn.fhir.model.dstu.composite.ContactDt;
import ca.uhn.fhir.model.dstu.composite.HumanNameDt;
import ca.uhn.fhir.model.dstu.composite.IdentifierDt;
import ca.uhn.fhir.model.dstu.composite.PeriodDt;
import ca.uhn.fhir.model.dstu.composite.QuantityDt;
import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.dstu.valueset.SearchParamTypeEnum;
@ -74,6 +75,7 @@ import com.google.common.collect.Lists;
public abstract class BaseFhirDao {
private FhirContext myContext = new FhirContext();
@PersistenceContext(name = "FHIR_UT", type = PersistenceContextType.TRANSACTION, unitName = "FHIR_UT")
private EntityManager myEntityManager;
@Autowired
@ -195,6 +197,8 @@ public abstract class BaseFhirDao {
}
}
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseFhirDao.class);
private void searchHistoryHistory(List<HistoryTuple> theTuples, List<BaseHasResource> theRetVal) {
Collection<HistoryTuple> tuples = Collections2.filter(theTuples, new com.google.common.base.Predicate<HistoryTuple>() {
@Override
@ -212,6 +216,8 @@ public abstract class BaseFhirDao {
return;
}
ourLog.info("Retrieving {} history elements from ResourceHistoryTable", ids.size());
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<ResourceHistoryTable> cq = builder.createQuery(ResourceHistoryTable.class);
Root<ResourceHistoryTable> from = cq.from(ResourceHistoryTable.class);
@ -258,19 +264,19 @@ public abstract class BaseFhirDao {
continue;
}
String typeString = nextValue.getResourceId().getResourceType();
String typeString = nextValue.getReference().getResourceType();
if (isBlank(typeString)) {
throw new InvalidRequestException("Invalid resource reference found at path[" + nextPath + "] - Does not contain resource type - " + nextValue.getReference().getValue());
}
Class<? extends IResource> type = getContext().getResourceDefinition(typeString).getImplementingClass();
String id = nextValue.getResourceId().getUnqualifiedId();
String id = nextValue.getReference().getUnqualifiedId();
if (StringUtils.isBlank(id)) {
continue;
}
IFhirResourceDao<?> dao = getDao(type);
if (dao == null) {
throw new InvalidRequestException("This server is not able to handle resources of type: " + nextValue.getResourceId().getResourceType());
throw new InvalidRequestException("This server is not able to handle resources of type: " + nextValue.getReference().getResourceType());
}
Long valueOf;
try {
@ -333,6 +339,12 @@ public abstract class BaseFhirDao {
continue;
}
nextEntity = new ResourceIndexedSearchParamDate(nextSpDef.getName(), nextValue.getValue(), nextValue.getValue());
} else if (nextObject instanceof PeriodDt) {
PeriodDt nextValue = (PeriodDt) nextObject;
if (nextValue.isEmpty()) {
continue;
}
nextEntity = new ResourceIndexedSearchParamDate(nextSpDef.getName(), nextValue.getStart().getValue(), nextValue.getEnd().getValue());
} else {
if (!multiType) {
throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass());
@ -377,7 +389,8 @@ public abstract class BaseFhirDao {
if (nextObject instanceof QuantityDt) {
QuantityDt nextValue = (QuantityDt) nextObject;
ResourceIndexedSearchParamNumber nextEntity = new ResourceIndexedSearchParamNumber(resourceName, nextValue.getValue().getValue(), nextValue.getSystem().getValueAsString(), nextValue.getUnits().getValue());
ResourceIndexedSearchParamNumber nextEntity = new ResourceIndexedSearchParamNumber(resourceName, nextValue.getValue().getValue(), nextValue.getSystem().getValueAsString(),
nextValue.getUnits().getValue());
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
} else {
@ -460,7 +473,8 @@ public abstract class BaseFhirDao {
} else if (nextObject instanceof ContactDt) {
ContactDt nextContact = (ContactDt) nextObject;
if (nextContact.getValue().isEmpty() == false) {
ResourceIndexedSearchParamString nextEntity = new ResourceIndexedSearchParamString(resourceName, normalizeString(nextContact.getValue().getValueAsString()), nextContact.getValue().getValueAsString());
ResourceIndexedSearchParamString nextEntity = new ResourceIndexedSearchParamString(resourceName, normalizeString(nextContact.getValue().getValueAsString()), nextContact
.getValue().getValueAsString());
nextEntity.setResource(theEntity);
retVal.add(nextEntity);
}
@ -685,11 +699,11 @@ public abstract class BaseFhirDao {
protected String toResourceName(IResource theResource) {
return myContext.getResourceDefinition(theResource).getName();
}
protected String toResourceName(Class<? extends IResource> theResourceType) {
return myContext.getResourceDefinition(theResourceType).getName();
}
protected ResourceTable updateEntity(final IResource theResource, ResourceTable entity, boolean theUpdateHistory) {
if (entity.getPublished() == null) {
entity.setPublished(new Date());
@ -702,6 +716,12 @@ public abstract class BaseFhirDao {
entity.setVersion(entity.getVersion() + 1);
Collection<ResourceIndexedSearchParamString> paramsString = new ArrayList<ResourceIndexedSearchParamString>(entity.getParamsString());
Collection<ResourceIndexedSearchParamToken> paramsToken = new ArrayList<ResourceIndexedSearchParamToken>(entity.getParamsToken());
Collection<ResourceIndexedSearchParamNumber> paramsNumber = new ArrayList<ResourceIndexedSearchParamNumber>(entity.getParamsNumber());
Collection<ResourceIndexedSearchParamDate> paramsDate = new ArrayList<ResourceIndexedSearchParamDate>(entity.getParamsDate());
Collection<ResourceLink> resourceLinks = new ArrayList<ResourceLink>(entity.getResourceLinks());
final List<ResourceIndexedSearchParamString> stringParams = extractSearchParamStrings(entity, theResource);
final List<ResourceIndexedSearchParamToken> tokenParams = extractSearchParamTokens(entity, theResource);
final List<ResourceIndexedSearchParamNumber> numberParams = extractSearchParamNumber(entity, theResource);
@ -711,6 +731,16 @@ public abstract class BaseFhirDao {
populateResourceIntoEntity(theResource, entity);
entity.setUpdated(new Date());
entity.setParamsString(stringParams);
entity.setParamsStringPopulated(stringParams.isEmpty()==false);
entity.setParamsToken(tokenParams);
entity.setParamsTokenPopulated(tokenParams.isEmpty()==false);
entity.setParamsNumber(numberParams);
entity.setParamsNumberPopulated(numberParams.isEmpty()==false);
entity.setParamsDate(dateParams);
entity.setParamsDatePopulated(dateParams.isEmpty()==false);
entity.setResourceLinks(links);
entity.setHasLinks(links.isEmpty()==false);
if (entity.getId() == null) {
myEntityManager.persist(entity);
@ -719,7 +749,7 @@ public abstract class BaseFhirDao {
}
if (entity.isParamsStringPopulated()) {
for (ResourceIndexedSearchParamString next : entity.getParamsString()) {
for (ResourceIndexedSearchParamString next : paramsString) {
myEntityManager.remove(next);
}
}
@ -728,7 +758,7 @@ public abstract class BaseFhirDao {
}
if (entity.isParamsTokenPopulated()) {
for (ResourceIndexedSearchParamToken next : entity.getParamsToken()) {
for (ResourceIndexedSearchParamToken next : paramsToken) {
myEntityManager.remove(next);
}
}
@ -737,7 +767,7 @@ public abstract class BaseFhirDao {
}
if (entity.isParamsNumberPopulated()) {
for (ResourceIndexedSearchParamNumber next : entity.getParamsNumber()) {
for (ResourceIndexedSearchParamNumber next : paramsNumber) {
myEntityManager.remove(next);
}
}
@ -746,7 +776,7 @@ public abstract class BaseFhirDao {
}
if (entity.isParamsDatePopulated()) {
for (ResourceIndexedSearchParamDate next : entity.getParamsDate()) {
for (ResourceIndexedSearchParamDate next : paramsDate) {
myEntityManager.remove(next);
}
}
@ -755,7 +785,7 @@ public abstract class BaseFhirDao {
}
if (entity.isHasLinks()) {
for (ResourceLink next : entity.getResourceLinks()) {
for (ResourceLink next : resourceLinks) {
myEntityManager.remove(next);
}
}

633
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDao.java
View File

@ -67,299 +67,15 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDao.class);
// name = "FHIR_UT", type = PersistenceContextType.TRANSACTION, unitName = "FHIR_UT"
@PersistenceContext()
private EntityManager myEntityManager;
@Autowired
private PlatformTransactionManager myPlatformTransactionManager;
private String myResourceName;
private Class<T> myResourceType;
@Override
public void addTag(IdDt theId, String theScheme, String theTerm, String theLabel) {
BaseHasResource entity = readEntity(theId);
if (entity == null) {
throw new ResourceNotFoundException(theId);
}
for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
if (next.getTag().getScheme().equals(theScheme) && next.getTag().getTerm().equals(theTerm)) {
return;
}
}
TagDefinition def = getTag(theScheme, theTerm, theLabel);
BaseTag newEntity = entity.addTag(def);
myEntityManager.persist(newEntity);
myEntityManager.merge(entity);
}
@Override
public MethodOutcome create(final T theResource) {
ResourceTable entity = new ResourceTable();
entity.setResourceType(toResourceName(theResource));
updateEntity(theResource, entity, false);
MethodOutcome outcome = toMethodOutcome(entity);
return outcome;
}
@Override
public TagList getAllResourceTags() {
return super.getTags(myResourceType, null);
}
public Class<T> getResourceType() {
return myResourceType;
}
@Override
public TagList getTags(IdDt theResourceId) {
return super.getTags(myResourceType, theResourceId);
}
@Override
public List<T> history() {
return null;
}
@Override
public List<IResource> history(Date theSince, Integer theLimit) {
return super.history(myResourceName, null, theSince, theLimit);
}
@Override
public List<T> history(IdDt theId) {
ArrayList<T> retVal = new ArrayList<T>();
String resourceType = getContext().getResourceDefinition(myResourceType).getName();
TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery(ResourceHistoryTable.Q_GETALL, ResourceHistoryTable.class);
q.setParameter("PID", theId.asLong());
q.setParameter("RESTYPE", resourceType);
// TypedQuery<ResourceHistoryTable> query =
// myEntityManager.createQuery(criteriaQuery);
List<ResourceHistoryTable> results = q.getResultList();
for (ResourceHistoryTable next : results) {
retVal.add(toResource(myResourceType, next));
}
try {
retVal.add(read(theId.withoutVersion()));
} catch (ResourceNotFoundException e) {
// ignore
}
if (retVal.isEmpty()) {
throw new ResourceNotFoundException(theId);
}
return retVal;
}
@Override
public List<IResource> history(Long theId, Date theSince, Integer theLimit) {
return super.history(myResourceName, theId, theSince, theLimit);
}
@PostConstruct
public void postConstruct() {
myResourceName = getContext().getResourceDefinition(myResourceType).getName();
}
@Override
public T read(IdDt theId) {
BaseHasResource entity = readEntity(theId);
T retVal = toResource(myResourceType, entity);
return retVal;
}
@Override
public BaseHasResource readEntity(IdDt theId) {
BaseHasResource entity = myEntityManager.find(ResourceTable.class, theId.asLong());
if (theId.hasUnqualifiedVersionId()) {
if (entity.getVersion() != theId.getUnqualifiedVersionIdAsLong()) {
entity = null;
}
}
if (entity == null) {
if (theId.hasUnqualifiedVersionId()) {
entity = myEntityManager.find(ResourceHistoryTable.class, new ResourceHistoryTablePk(myResourceName, theId.asLong(), theId.getUnqualifiedVersionIdAsLong()));
}
if (entity == null) {
throw new ResourceNotFoundException(theId);
}
}
return entity;
}
@Override
public void removeTag(IdDt theId, String theScheme, String theTerm) {
BaseHasResource entity = readEntity(theId);
if (entity == null) {
throw new ResourceNotFoundException(theId);
}
for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
if (next.getTag().getScheme().equals(theScheme) && next.getTag().getTerm().equals(theTerm)) {
myEntityManager.remove(next);
entity.getTags().remove(next);
}
}
myEntityManager.merge(entity);
}
@Override
public List<T> search(Map<String, IQueryParameterType> theParams) {
SearchParameterMap map = new SearchParameterMap();
for (Entry<String, IQueryParameterType> nextEntry : theParams.entrySet()) {
map.put(nextEntry.getKey(), new ArrayList<List<IQueryParameterType>>());
map.get(nextEntry.getKey()).add(Collections.singletonList(nextEntry.getValue()));
}
return search(map);
}
@Override
public List<T> search(SearchParameterMap theParams) {
Set<Long> pids;
if (theParams.isEmpty()) {
pids = null;
} else {
pids = searchForIdsWithAndOr(theParams);
if (pids.isEmpty()) {
return new ArrayList<T>();
}
}
// Execute the query and make sure we return distinct results
{
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<ResourceTable> cq = builder.createQuery(ResourceTable.class);
Root<ResourceTable> from = cq.from(ResourceTable.class);
cq.where(builder.equal(from.get("myResourceType"), getContext().getResourceDefinition(myResourceType).getName()));
if (!theParams.isEmpty()) {
cq.where(from.get("myId").in(pids));
}
TypedQuery<ResourceTable> q = myEntityManager.createQuery(cq);
List<T> retVal = new ArrayList<T>();
for (ResourceTable next : q.getResultList()) {
T resource = toResource(myResourceType, next);
retVal.add(resource);
}
return retVal;
}
}
@Override
public List<T> search(String theParameterName, IQueryParameterType theValue) {
return search(Collections.singletonMap(theParameterName, theValue));
}
@Override
public Set<Long> searchForIds(Map<String, IQueryParameterType> theParams) {
Map<String, List<List<IQueryParameterType>>> map = new HashMap<String, List<List<IQueryParameterType>>>();
for (Entry<String, IQueryParameterType> nextEntry : theParams.entrySet()) {
map.put(nextEntry.getKey(), new ArrayList<List<IQueryParameterType>>());
map.get(nextEntry.getKey()).add(Collections.singletonList(nextEntry.getValue()));
}
return searchForIdsWithAndOr(map);
}
@Override
public Set<Long> searchForIds(String theParameterName, IQueryParameterType theValue) {
return searchForIds(Collections.singletonMap(theParameterName, theValue));
}
@Override
public Set<Long> searchForIdsWithAndOr(Map<String, List<List<IQueryParameterType>>> theParams) {
Map<String, List<List<IQueryParameterType>>> params = theParams;
if (params == null) {
params = Collections.emptyMap();
}
RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(myResourceType);
Set<Long> pids = new HashSet<Long>();
for (Entry<String, List<List<IQueryParameterType>>> nextParamEntry : params.entrySet()) {
String nextParamName = nextParamEntry.getKey();
RuntimeSearchParam nextParamDef = resourceDef.getSearchParam(nextParamName);
if (nextParamDef != null) {
if (nextParamDef.getParamType() == SearchParamTypeEnum.TOKEN) {
for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
pids = addPredicateToken(pids, nextAnd);
if (pids.isEmpty()) {
return new HashSet<Long>();
}
}
} else if (nextParamDef.getParamType() == SearchParamTypeEnum.STRING) {
for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
pids = addPredicateString(pids, nextAnd);
if (pids.isEmpty()) {
return new HashSet<Long>();
}
}
} else if (nextParamDef.getParamType() == SearchParamTypeEnum.QUANTITY) {
for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
pids = addPredicateQuantity(pids, nextAnd);
if (pids.isEmpty()) {
return new HashSet<Long>();
}
}
} else if (nextParamDef.getParamType() == SearchParamTypeEnum.DATE) {
for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
pids = addPredicateDate(pids, nextAnd);
if (pids.isEmpty()) {
return new HashSet<Long>();
}
}
} else if (nextParamDef.getParamType() == SearchParamTypeEnum.REFERENCE) {
for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
pids = addPredicateReference(nextParamName, pids, nextAnd);
if (pids.isEmpty()) {
return new HashSet<Long>();
}
}
} else {
throw new IllegalArgumentException("Don't know how to handle parameter of type: " + nextParamDef.getParamType());
}
}
}
return pids;
}
@SuppressWarnings("unchecked")
@Required
public void setResourceType(Class<? extends IResource> theTableType) {
myResourceType = (Class<T>) theTableType;
}
@Override
public MethodOutcome update(final T theResource, final IdDt theId) {
// TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
// ResourceTable savedEntity = template.execute(new TransactionCallback<ResourceTable>() {
// @Override
// public ResourceTable doInTransaction(TransactionStatus theStatus) {
// final ResourceTable entity = readEntity(theId);
// return updateEntity(theResource, entity,true);
// }
// });
final ResourceTable entity = readEntityLatestVersion(theId);
ResourceTable savedEntity = updateEntity(theResource, entity, true);
return toMethodOutcome(savedEntity);
}
private String mySecondaryPrimaryKeyParamName;
private Set<Long> addPredicateDate(Set<Long> thePids, List<IQueryParameterType> theOrParams) {
if (theOrParams == null || theOrParams.isEmpty()) {
@ -403,21 +119,42 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
}
private void addPredicateDateFromRange(CriteriaBuilder builder, Root<ResourceIndexedSearchParamDate> from, List<Predicate> codePredicates, DateRangeParam range) {
Predicate singleCode;
Date lowerBound = range.getLowerBoundAsInstant();
Date upperBound = range.getUpperBoundAsInstant();
if (lowerBound != null && upperBound != null) {
Predicate low = builder.greaterThanOrEqualTo(from.<Date> get("myValueLow"), lowerBound);
Predicate high = builder.lessThanOrEqualTo(from.<Date> get("myValueHigh"), upperBound);
singleCode = builder.and(low, high);
} else if (lowerBound != null) {
singleCode = builder.greaterThanOrEqualTo(from.<Date> get("myValueLow"), lowerBound);
} else {
singleCode = builder.lessThanOrEqualTo(from.<Date> get("myValueHigh"), upperBound);
Predicate lb = null;
if (lowerBound != null) {
Predicate gt = builder.greaterThanOrEqualTo(from.<Date> get("myValueLow"), lowerBound);
Predicate gin = builder.isNull(from.get("myValueLow"));
Predicate lbo = builder.or(gt, gin);
Predicate lt = builder.greaterThanOrEqualTo(from.<Date> get("myValueHigh"), lowerBound);
Predicate lin = builder.isNull(from.get("myValueHigh"));
Predicate hbo = builder.or(lt, lin);
lb = builder.and(lbo, hbo);
}
codePredicates.add(singleCode);
Predicate ub = null;
if (upperBound != null) {
Predicate gt = builder.lessThanOrEqualTo(from.<Date> get("myValueLow"), upperBound);
Predicate gin = builder.isNull(from.get("myValueLow"));
Predicate lbo = builder.or(gt, gin);
Predicate lt = builder.lessThanOrEqualTo(from.<Date> get("myValueHigh"), upperBound);
Predicate lin = builder.isNull(from.get("myValueHigh"));
Predicate ubo = builder.or(lt, lin);
ub = builder.and(ubo, lbo);
}
if (lb != null && ub != null) {
codePredicates.add(builder.and(lb, ub));
} else if (lb != null) {
codePredicates.add(lb);
} else {
codePredicates.add(ub);
}
}
private Set<Long> addPredicateQuantity(Set<Long> thePids, List<IQueryParameterType> theOrParams) {
@ -696,6 +433,140 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
return new HashSet<Long>(q.getResultList());
}
@Override
public void addTag(IdDt theId, String theScheme, String theTerm, String theLabel) {
BaseHasResource entity = readEntity(theId);
if (entity == null) {
throw new ResourceNotFoundException(theId);
}
for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
if (next.getTag().getScheme().equals(theScheme) && next.getTag().getTerm().equals(theTerm)) {
return;
}
}
TagDefinition def = getTag(theScheme, theTerm, theLabel);
BaseTag newEntity = entity.addTag(def);
myEntityManager.persist(newEntity);
myEntityManager.merge(entity);
}
@Override
public MethodOutcome create(final T theResource) {
ResourceTable entity = new ResourceTable();
entity.setResourceType(toResourceName(theResource));
updateEntity(theResource, entity, false);
MethodOutcome outcome = toMethodOutcome(entity);
return outcome;
}
@Override
public TagList getAllResourceTags() {
return super.getTags(myResourceType, null);
}
public Class<T> getResourceType() {
return myResourceType;
}
@Override
public TagList getTags(IdDt theResourceId) {
return super.getTags(myResourceType, theResourceId);
}
@Override
public List<T> history() {
return null;
}
@Override
public List<IResource> history(Date theSince, Integer theLimit) {
return super.history(myResourceName, null, theSince, theLimit);
}
@Override
public List<T> history(IdDt theId) {
ArrayList<T> retVal = new ArrayList<T>();
String resourceType = getContext().getResourceDefinition(myResourceType).getName();
TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery(ResourceHistoryTable.Q_GETALL, ResourceHistoryTable.class);
q.setParameter("PID", theId.asLong());
q.setParameter("RESTYPE", resourceType);
// TypedQuery<ResourceHistoryTable> query =
// myEntityManager.createQuery(criteriaQuery);
List<ResourceHistoryTable> results = q.getResultList();
for (ResourceHistoryTable next : results) {
retVal.add(toResource(myResourceType, next));
}
try {
retVal.add(read(theId.withoutVersion()));
} catch (ResourceNotFoundException e) {
// ignore
}
if (retVal.isEmpty()) {
throw new ResourceNotFoundException(theId);
}
return retVal;
}
@Override
public List<IResource> history(Long theId, Date theSince, Integer theLimit) {
return super.history(myResourceName, theId, theSince, theLimit);
}
@PostConstruct
public void postConstruct() {
RuntimeResourceDefinition def = getContext().getResourceDefinition(myResourceType);
myResourceName = def.getName();
if (mySecondaryPrimaryKeyParamName != null) {
RuntimeSearchParam sp = def.getSearchParam(mySecondaryPrimaryKeyParamName);
if (sp == null) {
throw new ConfigurationException("Unknown search param on resource[" + myResourceName + "] for secondary key[" + mySecondaryPrimaryKeyParamName + "]");
}
if (sp.getParamType()!=SearchParamTypeEnum.TOKEN) {
throw new ConfigurationException("Search param on resource[" + myResourceName + "] for secondary key[" + mySecondaryPrimaryKeyParamName + "] is not a token type, only token is supported");
}
}
}
@Override
public T read(IdDt theId) {
BaseHasResource entity = readEntity(theId);
T retVal = toResource(myResourceType, entity);
return retVal;
}
@Override
public BaseHasResource readEntity(IdDt theId) {
BaseHasResource entity = myEntityManager.find(ResourceTable.class, theId.asLong());
if (theId.hasUnqualifiedVersionId()) {
if (entity.getVersion() != theId.getUnqualifiedVersionIdAsLong()) {
entity = null;
}
}
if (entity == null) {
if (theId.hasUnqualifiedVersionId()) {
entity = myEntityManager.find(ResourceHistoryTable.class, new ResourceHistoryTablePk(myResourceName, theId.asLong(), theId.getUnqualifiedVersionIdAsLong()));
}
if (entity == null) {
throw new ResourceNotFoundException(theId);
}
}
return entity;
}
private ResourceTable readEntityLatestVersion(IdDt theId) {
ResourceTable entity = myEntityManager.find(ResourceTable.class, theId.asLong());
if (entity == null) {
@ -704,6 +575,158 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
return entity;
}
@Override
public void removeTag(IdDt theId, String theScheme, String theTerm) {
BaseHasResource entity = readEntity(theId);
if (entity == null) {
throw new ResourceNotFoundException(theId);
}
for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
if (next.getTag().getScheme().equals(theScheme) && next.getTag().getTerm().equals(theTerm)) {
myEntityManager.remove(next);
entity.getTags().remove(next);
}
}
myEntityManager.merge(entity);
}
@Override
public List<T> search(Map<String, IQueryParameterType> theParams) {
SearchParameterMap map = new SearchParameterMap();
for (Entry<String, IQueryParameterType> nextEntry : theParams.entrySet()) {
map.put(nextEntry.getKey(), new ArrayList<List<IQueryParameterType>>());
map.get(nextEntry.getKey()).add(Collections.singletonList(nextEntry.getValue()));
}
return search(map);
}
@Override
public List<T> search(SearchParameterMap theParams) {
Set<Long> pids;
if (theParams.isEmpty()) {
pids = null;
} else {
pids = searchForIdsWithAndOr(theParams);
if (pids.isEmpty()) {
return new ArrayList<T>();
}
}
// Execute the query and make sure we return distinct results
{
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<ResourceTable> cq = builder.createQuery(ResourceTable.class);
Root<ResourceTable> from = cq.from(ResourceTable.class);
cq.where(builder.equal(from.get("myResourceType"), getContext().getResourceDefinition(myResourceType).getName()));
if (!theParams.isEmpty()) {
cq.where(from.get("myId").in(pids));
}
TypedQuery<ResourceTable> q = myEntityManager.createQuery(cq);
List<T> retVal = new ArrayList<T>();
for (ResourceTable next : q.getResultList()) {
T resource = toResource(myResourceType, next);
retVal.add(resource);
}
return retVal;
}
}
@Override
public List<T> search(String theParameterName, IQueryParameterType theValue) {
return search(Collections.singletonMap(theParameterName, theValue));
}
@Override
public Set<Long> searchForIds(Map<String, IQueryParameterType> theParams) {
Map<String, List<List<IQueryParameterType>>> map = new HashMap<String, List<List<IQueryParameterType>>>();
for (Entry<String, IQueryParameterType> nextEntry : theParams.entrySet()) {
map.put(nextEntry.getKey(), new ArrayList<List<IQueryParameterType>>());
map.get(nextEntry.getKey()).add(Collections.singletonList(nextEntry.getValue()));
}
return searchForIdsWithAndOr(map);
}
@Override
public Set<Long> searchForIds(String theParameterName, IQueryParameterType theValue) {
return searchForIds(Collections.singletonMap(theParameterName, theValue));
}
@Override
public Set<Long> searchForIdsWithAndOr(Map<String, List<List<IQueryParameterType>>> theParams) {
Map<String, List<List<IQueryParameterType>>> params = theParams;
if (params == null) {
params = Collections.emptyMap();
}
RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(myResourceType);
Set<Long> pids = new HashSet<Long>();
for (Entry<String, List<List<IQueryParameterType>>> nextParamEntry : params.entrySet()) {
String nextParamName = nextParamEntry.getKey();
RuntimeSearchParam nextParamDef = resourceDef.getSearchParam(nextParamName);
if (nextParamDef != null) {
if (nextParamDef.getParamType() == SearchParamTypeEnum.TOKEN) {
for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
pids = addPredicateToken(pids, nextAnd);
if (pids.isEmpty()) {
return new HashSet<Long>();
}
}
} else if (nextParamDef.getParamType() == SearchParamTypeEnum.STRING) {
for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
pids = addPredicateString(pids, nextAnd);
if (pids.isEmpty()) {
return new HashSet<Long>();
}
}
} else if (nextParamDef.getParamType() == SearchParamTypeEnum.QUANTITY) {
for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
pids = addPredicateQuantity(pids, nextAnd);
if (pids.isEmpty()) {
return new HashSet<Long>();
}
}
} else if (nextParamDef.getParamType() == SearchParamTypeEnum.DATE) {
for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
pids = addPredicateDate(pids, nextAnd);
if (pids.isEmpty()) {
return new HashSet<Long>();
}
}
} else if (nextParamDef.getParamType() == SearchParamTypeEnum.REFERENCE) {
for (List<IQueryParameterType> nextAnd : nextParamEntry.getValue()) {
pids = addPredicateReference(nextParamName, pids, nextAnd);
if (pids.isEmpty()) {
return new HashSet<Long>();
}
}
} else {
throw new IllegalArgumentException("Don't know how to handle parameter of type: " + nextParamDef.getParamType());
}
}
}
return pids;
}
@SuppressWarnings("unchecked")
@Required
public void setResourceType(Class<? extends IResource> theTableType) {
myResourceType = (Class<T>) theTableType;
}
/**
* If set, the given param will be treated as a secondary primary key, and multiple resources will not be able to share the same value.
*/
public void setSecondaryPrimaryKeyParamName(String theSecondaryPrimaryKeyParamName) {
mySecondaryPrimaryKeyParamName = theSecondaryPrimaryKeyParamName;
}
private MethodOutcome toMethodOutcome(final ResourceTable entity) {
MethodOutcome outcome = new MethodOutcome();
outcome.setId(new IdDt(entity.getResourceType() + '/' + entity.getId() + '/' + Constants.PARAM_HISTORY + '/' + entity.getVersion()));
@ -738,4 +761,22 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
}
}
@Override
public MethodOutcome update(final T theResource, final IdDt theId) {
// TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
// ResourceTable savedEntity = template.execute(new TransactionCallback<ResourceTable>() {
// @Override
// public ResourceTable doInTransaction(TransactionStatus theStatus) {
// final ResourceTable entity = readEntity(theId);
// return updateEntity(theResource, entity,true);
// }
// });
final ResourceTable entity = readEntityLatestVersion(theId);
ResourceTable savedEntity = updateEntity(theResource, entity, true);
return toMethodOutcome(savedEntity);
}
}

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

@ -91,11 +91,11 @@ public class FhirSystemDao extends BaseFhirDao implements IFhirSystemDao {
for (IResource nextResource : theResources) {
List<ResourceReferenceDt> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, ResourceReferenceDt.class);
for (ResourceReferenceDt nextRef : allRefs) {
IdDt nextId = nextRef.getResourceId();
IdDt nextId = nextRef.getReference();
if (idConversions.containsKey(nextId)) {
IdDt newId = idConversions.get(nextId);
ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
nextRef.setResourceId(newId);
nextRef.setReference(newId);
} else {
ourLog.info(" * Reference [{}] does not exist in bundle", nextId);
}

37
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceHistoryTablePk.java
View File

@ -30,6 +30,43 @@ public class ResourceHistoryTablePk implements Serializable {
myVersion = theVersion;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((myId == null) ? 0 : myId.hashCode());
result = prime * result + ((myResourceType == null) ? 0 : myResourceType.hashCode());
result = prime * result + ((myVersion == null) ? 0 : myVersion.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
ResourceHistoryTablePk other = (ResourceHistoryTablePk) obj;
if (myId == null) {
if (other.myId != null)
return false;
} else if (!myId.equals(other.myId))
return false;
if (myResourceType == null) {
if (other.myResourceType != null)
return false;
} else if (!myResourceType.equals(other.myResourceType))
return false;
if (myVersion == null) {
if (other.myVersion != null)
return false;
} else if (!myVersion.equals(other.myVersion))
return false;
return true;
}
public Long getId() {
return myId;
}

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

@ -23,6 +23,11 @@ public class ResourceIndexedSearchParamDate extends BaseResourceIndexedSearchPar
@Temporal(TemporalType.TIMESTAMP)
public Date myValueLow;
public ResourceIndexedSearchParamDate() {
}
public ResourceIndexedSearchParamDate(String theName, Date theLow, Date theHigh) {
setName(theName);
setValueLow(theLow);

71
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java
View File

@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.entity;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import javax.persistence.CascadeType;
import javax.persistence.Column;
@ -80,23 +81,21 @@ public class ResourceTable extends BaseHasResource implements Serializable {
@Column(name = "RES_VER")
private long myVersion;
public boolean hasTag(String theTerm, String theLabel, String theScheme) {
for (ResourceTag next : getTags()) {
if (next.getTag().getTerm().equals(theTerm)) {
return true;
}
}
return false;
}
public IdDt getIdDt() {
return new IdDt(myResourceType + '/' + myId + '/' + Constants.PARAM_HISTORY + '/' + myVersion);
public ResourceTag addTag(TagDefinition theTag) {
ResourceTag tag = new ResourceTag(this, theTag);
tag.setResourceType(getResourceType());
getTags().add(tag);
return tag;
}
public Long getId() {
return myId;
}
public IdDt getIdDt() {
return new IdDt(myResourceType + '/' + myId + '/' + Constants.PARAM_HISTORY + '/' + myVersion);
}
public Collection<ResourceIndexedSearchParamDate> getParamsDate() {
if (myParamsDate == null) {
myParamsDate = new ArrayList<ResourceIndexedSearchParamDate>();
@ -147,6 +146,15 @@ public class ResourceTable extends BaseHasResource implements Serializable {
return myVersion;
}
public boolean hasTag(String theTerm, String theLabel, String theScheme) {
for (ResourceTag next : getTags()) {
if (next.getTag().getTerm().equals(theTerm)) {
return true;
}
}
return false;
}
public boolean isHasLinks() {
return myHasLinks;
}
@ -176,19 +184,35 @@ public class ResourceTable extends BaseHasResource implements Serializable {
}
public void setParamsDate(Collection<ResourceIndexedSearchParamDate> theParamsDate) {
myParamsDate = theParamsDate;
if (!isParamsDatePopulated() && theParamsDate.isEmpty()) {
return;
}
getParamsDate().clear();
getParamsDate().addAll(theParamsDate);
}
public void setParamsDatePopulated(boolean theParamsDatePopulated) {
myParamsDatePopulated = theParamsDatePopulated;
}
public void setParamsNumber(List<ResourceIndexedSearchParamNumber> theNumberParams) {
if (!isParamsNumberPopulated() && theNumberParams.isEmpty()) {
return;
}
getParamsNumber().clear();
getParamsNumber().addAll(theNumberParams);
}
public void setParamsNumberPopulated(boolean theParamsNumberPopulated) {
myParamsNumberPopulated = theParamsNumberPopulated;
}
public void setParamsString(Collection<ResourceIndexedSearchParamString> theParamsString) {
myParamsString = theParamsString;
if (!isParamsStringPopulated() && theParamsString.isEmpty()) {
return;
}
getParamsString().clear();
getParamsString().addAll(theParamsString);
}
public void setParamsStringPopulated(boolean theParamsStringPopulated) {
@ -196,13 +220,25 @@ public class ResourceTable extends BaseHasResource implements Serializable {
}
public void setParamsToken(Collection<ResourceIndexedSearchParamToken> theParamsToken) {
myParamsToken = theParamsToken;
if (!isParamsTokenPopulated() && theParamsToken.isEmpty()) {
return;
}
getParamsToken().clear();
getParamsToken().addAll(theParamsToken);
}
public void setParamsTokenPopulated(boolean theParamsTokenPopulated) {
myParamsTokenPopulated = theParamsTokenPopulated;
}
public void setResourceLinks(List<ResourceLink> theLinks) {
if (!isHasLinks() && theLinks.isEmpty()) {
return;
}
getResourceLinks().clear();
getResourceLinks().addAll(theLinks);
}
public void setResourceType(String theResourceType) {
myResourceType = theResourceType;
}
@ -231,11 +267,4 @@ public class ResourceTable extends BaseHasResource implements Serializable {
return retVal;
}
public ResourceTag addTag(TagDefinition theTag) {
ResourceTag tag = new ResourceTag(this, theTag);
tag.setResourceType(getResourceType());
getTags().add(tag);
return tag;
}
}

146
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoTest.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.model.dstu.composite.QuantityDt;
import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.dstu.resource.Device;
import ca.uhn.fhir.model.dstu.resource.DiagnosticReport;
import ca.uhn.fhir.model.dstu.resource.Encounter;
import ca.uhn.fhir.model.dstu.resource.Location;
import ca.uhn.fhir.model.dstu.resource.Observation;
import ca.uhn.fhir.model.dstu.resource.Organization;
@ -35,6 +36,7 @@ import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.QualifiedDateParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringParam;
@ -52,6 +54,7 @@ public class FhirResourceDaoTest {
private static IFhirResourceDao<Location> ourLocationDao;
private static Date ourTestStarted;
private static IFhirResourceDao<Encounter> ourEncounterDao;
@Test
public void testPersistAndReadResource() {
@ -379,6 +382,145 @@ public class FhirResourceDaoTest {
}
@Test
public void testDatePeriodParamStartOnly() {
{
Encounter enc = new Encounter();
enc.addIdentifier("testDatePeriodParam", "01");
enc.getPeriod().getStart().setValueAsString("2001-01-02");
ourEncounterDao.create(enc);
}
SearchParameterMap params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam("2001-01-01", "2001-01-03"));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "01"));
List<Encounter> encs = ourEncounterDao.search(params);
assertEquals(1, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam("2001-01-01", null));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "01"));
encs = ourEncounterDao.search(params);
assertEquals(1, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam(null, "2001-01-03"));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "01"));
encs = ourEncounterDao.search(params);
assertEquals(1, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam(null, "2001-01-01"));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "01"));
encs = ourEncounterDao.search(params);
assertEquals(0, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam("2001-01-03",null));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "01"));
encs = ourEncounterDao.search(params);
assertEquals(0, encs.size());
}
@Test
public void testDatePeriodParamEndOnly() {
{
Encounter enc = new Encounter();
enc.addIdentifier("testDatePeriodParam", "02");
enc.getPeriod().getEnd().setValueAsString("2001-01-02");
ourEncounterDao.create(enc);
}
SearchParameterMap params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam("2001-01-01", "2001-01-03"));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "02"));
List<Encounter> encs = ourEncounterDao.search(params);
assertEquals(1, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam("2001-01-01", null));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "02"));
encs = ourEncounterDao.search(params);
assertEquals(1, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam(null, "2001-01-03"));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "02"));
encs = ourEncounterDao.search(params);
assertEquals(1, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam(null, "2001-01-01"));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "02"));
encs = ourEncounterDao.search(params);
assertEquals(0, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam( "2001-01-03",null));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "02"));
encs = ourEncounterDao.search(params);
assertEquals(0, encs.size());
}
@Test
public void testDatePeriodParamStartAndEnd() {
{
Encounter enc = new Encounter();
enc.addIdentifier("testDatePeriodParam", "03");
enc.getPeriod().getStart().setValueAsString("2001-01-02");
enc.getPeriod().getEnd().setValueAsString("2001-01-03");
ourEncounterDao.create(enc);
}
SearchParameterMap params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam("2001-01-01", "2001-01-03"));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "03"));
List<Encounter> encs = ourEncounterDao.search(params);
assertEquals(1, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam("2001-01-02", "2001-01-06"));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "03"));
encs = ourEncounterDao.search(params);
assertEquals(1, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam("2001-01-01", null));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "03"));
encs = ourEncounterDao.search(params);
assertEquals(1, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam(null, "2001-01-03"));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "03"));
encs = ourEncounterDao.search(params);
assertEquals(1, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam(null, "2001-01-05"));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "03"));
encs = ourEncounterDao.search(params);
assertEquals(1, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam(null, "2001-01-01"));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "03"));
encs = ourEncounterDao.search(params);
assertEquals(0, encs.size());
params = new SearchParameterMap();
params.add(Encounter.SP_DATE, new DateRangeParam( "2001-01-05",null));
params.add(Encounter.SP_IDENTIFIER, new IdentifierDt("testDatePeriodParam", "03"));
encs = ourEncounterDao.search(params);
assertEquals(0, encs.size());
}
@Test
public void testSearchStringParamWithNonNormalized() {
{
@ -522,7 +664,8 @@ public class FhirResourceDaoTest {
// Update the name
p1.getNameFirstRep().getGivenFirstRep().setValue("testUpdateMaintainsSearchParamsBBB");
IdDt p1id2 = ourPatientDao.update(p1, p1id).getId();
MethodOutcome update2 = ourPatientDao.update(p1, p1id);
IdDt p1id2 = update2.getId();
ids = ourPatientDao.searchForIds(Patient.SP_GIVEN, new StringDt("testUpdateMaintainsSearchParamsAAA"));
assertEquals(0, ids.size());
@ -555,6 +698,7 @@ public class FhirResourceDaoTest {
ourDeviceDao = ourCtx.getBean("myDeviceDao", IFhirResourceDao.class);
ourOrganizationDao = ourCtx.getBean("myOrganizationDao", IFhirResourceDao.class);
ourLocationDao = ourCtx.getBean("myLocationDao", IFhirResourceDao.class);
ourEncounterDao = ourCtx.getBean("myEncounterDao", IFhirResourceDao.class);
}
}

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

@ -65,7 +65,7 @@ public class FhirSystemDaoTest {
Thread.sleep(10);
IdDt newpid3 = ourPatientDao.update(patient, pid).getId();
List<IResource> values = ourSystemDao.history(start, 1000);
List<IResource> values = ourSystemDao.history(start, null);
assertEquals(4, values.size());
assertEquals(newpid3, values.get(0).getId());
@ -207,7 +207,7 @@ public class FhirSystemDaoTest {
IdDt foundPatientId = patResults.get(0).getId();
ResourceReferenceDt subject = obs.getSubject();
assertEquals(foundPatientId.getUnqualifiedId(), subject.getResourceId().getUnqualifiedId());
assertEquals(foundPatientId.getUnqualifiedId(), subject.getReference().getUnqualifiedId());
// Update

2
hapi-fhir-jpaserver-base/src/test/resources/META-INF/persistence.xml
View File

@ -29,7 +29,7 @@
<property name="hibernate.connection.password" value="" />
<property name="hibernate.jdbc.batch_size" value="0" />
<property name="hibernate.cache.use_minimal_puts" value="false" />
<property name="hibernate.show_sql" value="false" />
<property name="hibernate.show_sql" value="true" />
<property name="hibernate.cache.use_query_cache" value="false" />
<property name="hibernate.cache.use_second_level_cache" value="false" />
<property name="hibernate.cache.use_structured_entries" value="false" />

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

@ -40,6 +40,9 @@
<bean id="myQuestionnaireDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
<property name="resourceType" value="ca.uhn.fhir.model.dstu.resource.Questionnaire"/>
</bean>
<bean id="myEncounterDao" class="ca.uhn.fhir.jpa.dao.FhirResourceDao">
<property name="resourceType" value="ca.uhn.fhir.model.dstu.resource.Encounter"/>
</bean>
<bean id="myPersistenceDataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource" lazy-init="true">
<property name="url" value="jdbc:derby:memory:myUnitTestDB;create=true" />

91
hapi-tinder-plugin/.classpath
View File

@ -1,97 +1,36 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry excluding="**/*.java" kind="src" output="target/test-classes" path="src/test/resources"/>
<classpathentry including="**/*.java" kind="src" path="src/main/java"/>
<classpathentry excluding="**/*.java" kind="src" path="src/main/resources"/>
<classpathentry kind="var" path="M2_REPO/javax/json/javax.json-api/1.0/javax.json-api-1.0.jar" sourcepath="M2_REPO/javax/json/javax.json-api/1.0/javax.json-api-1.0-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/javax/xml/stream/stax-api/1.0-2/stax-api-1.0-2.jar" sourcepath="M2_REPO/javax/xml/stream/stax-api/1.0-2/stax-api-1.0-2-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/javax/servlet/servlet-api/2.3/servlet-api-2.3.jar" sourcepath="M2_REPO/javax/servlet/servlet-api/2.3/servlet-api-2.3-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/javax/enterprise/cdi-api/1.0/cdi-api-1.0.jar" sourcepath="M2_REPO/javax/enterprise/cdi-api/1.0/cdi-api-1.0-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/javax/annotation/jsr250-api/1.0/jsr250-api-1.0.jar" sourcepath="M2_REPO/javax/annotation/jsr250-api/1.0/jsr250-api-1.0-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/javax/inject/javax.inject/1/javax.inject-1.jar" sourcepath="M2_REPO/javax/inject/javax.inject/1/javax.inject-1-sources.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="var" path="M2_REPO/org/glassfish/javax.json/1.0.4/javax.json-1.0.4.jar" sourcepath="M2_REPO/org/glassfish/javax.json/1.0.4/javax.json-1.0.4-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/codehaus/woodstox/woodstox-core-asl/4.2.0/woodstox-core-asl-4.2.0.jar" sourcepath="M2_REPO/org/codehaus/woodstox/woodstox-core-asl/4.2.0/woodstox-core-asl-4.2.0-sources.jar">
<classpathentry kind="src" output="target/classes" path="src/main/java">
<attributes>
<attribute name="javadoc_location" value="jar:file:/home/t3903uhn/.m2/repository/org/codehaus/woodstox/woodstox-core-asl/4.2.0/woodstox-core-asl-4.2.0-javadoc.jar!/"/>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="var" path="M2_REPO/org/codehaus/woodstox/stax2-api/3.1.1/stax2-api-3.1.1.jar" sourcepath="M2_REPO/org/codehaus/woodstox/stax2-api/3.1.1/stax2-api-3.1.1-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/commons/commons-lang3/3.2.1/commons-lang3-3.2.1.jar" sourcepath="M2_REPO/org/apache/commons/commons-lang3/3.2.1/commons-lang3-3.2.1-sources.jar">
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
<attributes>
<attribute name="javadoc_location" value="jar:file:/home/t3903uhn/.m2/repository/org/apache/commons/commons-lang3/3.2.1/commons-lang3-3.2.1-javadoc.jar!/"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
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<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="javadoc_location" value="jar:file:/home/t3903uhn/.m2/repository/ch/qos/logback/logback-classic/1.1.1/logback-classic-1.1.1-javadoc.jar!/"/>
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</classpathentry>
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</classpathentry>
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<attribute name="javadoc_location" value="jar:file:/home/t3903uhn/.m2/repository/junit/junit/4.11/junit-4.11-javadoc.jar!/"/>
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<classpathentry kind="output" path="target/classes"/>
</classpath>

24
hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/TinderStructuresMojo.java
View File

@ -183,24 +183,24 @@ public class TinderStructuresMojo extends AbstractMojo {
public static void main(String[] args) throws Exception {
// ValueSetGenerator vsp = new ValueSetGenerator();
ValueSetGenerator vsp = new ValueSetGenerator();
// vsp.setDirectory("src/test/resources/vs/");
// vsp.parse();
//
// DatatypeGeneratorUsingSpreadsheet dtp = new DatatypeGeneratorUsingSpreadsheet();
// dtp.parse();
// dtp.bindValueSets(vsp);
//
// String dtOutputDir = "target/generated/valuesets/ca/uhn/fhir/model/dstu/composite";
// dtp.writeAll(dtOutputDir);
//
vsp.parse();
DatatypeGeneratorUsingSpreadsheet dtp = new DatatypeGeneratorUsingSpreadsheet();
dtp.parse();
dtp.bindValueSets(vsp);
String dtOutputDir = "target/generated/valuesets/ca/uhn/fhir/model/dstu/composite";
dtp.writeAll(new File(dtOutputDir), "ca.uhn.fhir.model.dstu");
ResourceGeneratorUsingSpreadsheet rp = new ResourceGeneratorUsingSpreadsheet();
rp.setBaseResourceNames(Arrays.asList("list"));
rp.setBaseResourceNames(Arrays.asList("list", "encounter"));
rp.parse();
// rp.bindValueSets(vsp);
String rpOutputDir = "target/generated/valuesets/ca/uhn/fhir/model/dstu/resource";
rp.writeAll(new File(rpOutputDir), "ca.uhn.test");
rp.writeAll(new File(rpOutputDir), "ca.uhn.fhir.model.dstu");
//
// String vsOutputDir = "target/generated/valuesets/ca/uhn/fhir/model/dstu/valueset";
// vsp.writeMarkedValueSets(vsOutputDir);

4
hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/model/BaseElement.java
View File

@ -217,6 +217,10 @@ public abstract class BaseElement {
myShortName = theShortName;
}
public void clearTypes() {
getType().clear();
}
public void setTypeFromString(String theType) {
if (theType == null) {
myType = null;

6
hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/model/Child.java
View File

@ -13,6 +13,12 @@ public abstract class Child extends BaseElement {
private List<SimpleSetter> mySimpleStters = new ArrayList<SimpleSetter>();
@Override
public void clearTypes() {
super.clearTypes();
mySimpleStters.clear();
}
public String getAnnotationType() {
return getSingleType();
}

13
hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/parser/BaseStructureParser.java
View File

@ -334,6 +334,7 @@ public abstract class BaseStructureParser {
for (BaseRootType next : myResources) {
ourLog.info("Writing Resource {}", next.getName());
scanForCorrections(next);
scanForTypeNameConflicts(next);
fixResourceReferenceClassNames(next, thePackageBase);
@ -349,6 +350,18 @@ public abstract class BaseStructureParser {
}
}
private void scanForCorrections(BaseRootType theNext) {
if (theNext.getElementName().equals("ResourceReference")) {
for (BaseElement next : theNext.getChildren()) {
if (next.getElementName().equals("reference")) {
next.clearTypes();
next.setTypeFromString("id");
scanForSimpleSetters((Child) next);
}
}
}
}
private String translateClassName(String theName) {
if ("List".equals(theName)) {
return "ListResource";

17
hapi-tinder-plugin/src/main/resources/vm/dt_composite.vm
View File

@ -256,7 +256,7 @@ public class ${className}
* The reference itself
*/
public ResourceReferenceDt(String theId) {
setResourceId(new IdDt(theId));
setReference(new IdDt(theId));
}
/**
@ -267,7 +267,7 @@ public class ${className}
* The reference itself
*/
public ResourceReferenceDt(IdDt theResourceId) {
setResourceId(theResourceId);
setReference(theResourceId);
}
#end
@ -404,19 +404,6 @@ public class ${className}
return null;
}
#end
#if ( ${className} == "ResourceReferenceDt" )
/** TODO: document */
@Override
public IdDt getResourceId() {
return new IdDt(myReference.getValue());
}
/** TODO: document */
@Override
public void setResourceId(IdDt theResourceId) {
myReference = new StringDt(theResourceId.getValue());
}
#end
#childExtensionTypes( $childExtensionTypes )
}

23
hapi-tinder-plugin/src/main/resources/vm/templates.vm
View File

@ -134,6 +134,23 @@
}
#end
#if ( ${child.boundCode} && ${child.repeatable} )
/**
* Add a value for <b>${child.elementName}</b> (${child.shortName}) using an enumerated type. This
* is intended as a convenience method for situations where the FHIR defined ValueSets are mandatory
* or contain the desirable codes. If you wish to use codes other than those which are built-in,
* you may also use the {@link ${hash}addType()} method.
*
* <p>
* <b>Definition:</b>
* ${child.definition}
* </p>
*/
public ${child.boundDatatype}<${child.bindingClass}> add${child.methodName}(${child.bindingClass} theValue) {
${child.boundDatatype}<${child.bindingClass}> retVal = new ${child.boundDatatype}<${child.bindingClass}>(${child.bindingClass}.VALUESET_BINDER, theValue);
get${child.methodName}().add(retVal);
return retVal;
}
/**
* Add a value for <b>${child.elementName}</b> (${child.shortName})
*
@ -142,8 +159,10 @@
* ${child.definition}
* </p>
*/
public void add${child.methodName}(${child.bindingClass} theValue) {
get${child.methodName}().add(new ${child.boundDatatype}<${child.bindingClass}>(${child.bindingClass}.VALUESET_BINDER, theValue));
public ${child.boundDatatype}<${child.bindingClass}> add${child.methodName}() {
${child.boundDatatype}<${child.bindingClass}> retVal = new ${child.boundDatatype}<${child.bindingClass}>(${child.bindingClass}.VALUESET_BINDER);
get${child.methodName}().add(retVal);
return retVal;
}
/**

2539
hapi-tinder-plugin/tmp/ValueSet.java
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