Transformation from DHIS to FHIR for tracked entities.

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/model/ImmutableDataElement.java

@@ -45,7 +45,7 @@
  * @author volsch
  */
 @Scriptable
-public class ImmutableDataElement implements DataElement, Serializable
+public class ImmutableDataElement implements DataElement, ImmutableDhisObject, Serializable
 {
     private static final long serialVersionUID = -7040983692879273412L;
 

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/model/ImmutableDataValue.java

@@ -43,7 +43,7 @@
  *
  * @author volsch
  */
-public class ImmutableDataValue implements DataValue, Serializable
+public class ImmutableDataValue implements DataValue, ImmutableDhisObject, Serializable
 {
     private static final long serialVersionUID = 5577400306112844124L;
 

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/model/ImmutableDhisObject.java

@@ -0,0 +1,38 @@
+package org.dhis2.fhir.adapter.dhis.model;
+
+/*
+ * Copyright (c) 2004-2018, University of Oslo
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * Neither the name of the HISP project nor the names of its contributors may
+ * be used to endorse or promote products derived from this software without
+ * specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+/**
+ * Marker interface that marks immutable DHIS objects.
+ *
+ * @author volsch
+ */
+public interface ImmutableDhisObject
+{
+}

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/model/ImmutableOption.java

@@ -42,7 +42,7 @@
  *
  * @author volsch
  */
-public class ImmutableOption implements Option, Serializable
+public class ImmutableOption implements Option, ImmutableDhisObject, Serializable
 {
     private static final long serialVersionUID = -4836329163657710844L;
 

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/model/ImmutableOptionSet.java

@@ -44,7 +44,7 @@
  *
  * @author volsch
  */
-public class ImmutableOptionSet implements OptionSet, Serializable
+public class ImmutableOptionSet implements OptionSet, ImmutableDhisObject, Serializable
 {
     private static final long serialVersionUID = -5542523378884979052L;
 

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/sync/DhisResourceQueueItem.java

@@ -28,7 +28,6 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
 import org.dhis2.fhir.adapter.data.model.ProcessedItemInfo;
 import org.dhis2.fhir.adapter.data.model.UuidDataGroupId;
 import org.dhis2.fhir.adapter.data.processor.DataItemQueueItem;
@@ -55,17 +54,4 @@ public DhisResourceQueueItem( @Nonnull UuidDataGroupId dataGroupId, @Nonnull Pro
     {
         super( dataGroupId, processedItemInfo );
     }
-
-    @JsonIgnore
-    @Override
-    public UuidDataGroupId getDataGroupId()
-    {
-        return super.getDataGroupId();
-    }
-
-    @Override
-    public void setDataGroupId( UuidDataGroupId dataGroupId )
-    {
-        super.setDataGroupId( dataGroupId );
-    }
 }

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/program/Enrollment.java

@@ -62,7 +62,8 @@ public class Enrollment implements DhisResource, Serializable
     @JsonInclude( JsonInclude.Include.NON_NULL )
     private String id;
 
-    @JsonProperty( access = JsonProperty.Access.READ_ONLY )
+    @JsonProperty
+    @JsonInclude( JsonInclude.Include.NON_NULL )
     private ZonedDateTime lastUpdated;
 
     @JsonProperty( "orgUnit" )

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/program/Event.java

@@ -60,7 +60,8 @@ public class Event implements DhisResource, Serializable, Comparable<Event>
     @JsonInclude( JsonInclude.Include.NON_NULL )
     private String id;
 
-    @JsonProperty( access = JsonProperty.Access.READ_ONLY )
+    @JsonProperty
+    @JsonInclude( JsonInclude.Include.NON_NULL )
     private ZonedDateTime lastUpdated;
 
     @JsonProperty( "orgUnit" )

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/program/ImmutableProgram.java

@@ -31,6 +31,7 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import org.dhis2.fhir.adapter.dhis.model.ImmutableDhisObject;
 import org.dhis2.fhir.adapter.dhis.model.Reference;
 
 import javax.annotation.Nonnull;
@@ -41,7 +42,7 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
-public class ImmutableProgram implements Program, Serializable
+public class ImmutableProgram implements Program, ImmutableDhisObject, Serializable
 {
     private static final long serialVersionUID = 4157706296470781519L;
 

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/program/ImmutableProgramStage.java

@@ -31,6 +31,7 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import org.dhis2.fhir.adapter.dhis.model.ImmutableDhisObject;
 import org.dhis2.fhir.adapter.dhis.model.Reference;
 
 import javax.annotation.Nonnull;
@@ -41,7 +42,7 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
-public class ImmutableProgramStage implements ProgramStage, Serializable
+public class ImmutableProgramStage implements ProgramStage, ImmutableDhisObject, Serializable
 {
     private static final long serialVersionUID = 6563663856499434307L;
 

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/program/ImmutableProgramStageDataElement.java

@@ -31,12 +31,13 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import org.dhis2.fhir.adapter.dhis.model.ImmutableDhisObject;
 import org.dhis2.fhir.adapter.dhis.model.WritableDataElement;
 
 import javax.annotation.Nonnull;
 import java.io.Serializable;
 
-public class ImmutableProgramStageDataElement implements ProgramStageDataElement, Serializable
+public class ImmutableProgramStageDataElement implements ProgramStageDataElement, ImmutableDhisObject, Serializable
 {
     private static final long serialVersionUID = -5845301607041878968L;
 

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/program/ImmutableProgramTrackedEntityAttribute.java

@@ -31,14 +31,15 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import org.dhis2.fhir.adapter.dhis.model.ImmutableDhisObject;
 import org.dhis2.fhir.adapter.dhis.tracker.trackedentity.ImmutableTrackedEntityAttribute;
 import org.dhis2.fhir.adapter.dhis.tracker.trackedentity.TrackedEntityAttribute;
 import org.dhis2.fhir.adapter.model.ValueType;
 
 import javax.annotation.Nonnull;
 import java.io.Serializable;
 
-public class ImmutableProgramTrackedEntityAttribute implements ProgramTrackedEntityAttribute, Serializable
+public class ImmutableProgramTrackedEntityAttribute implements ProgramTrackedEntityAttribute, ImmutableDhisObject, Serializable
 {
     private static final long serialVersionUID = -6094500152005916960L;
 

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/program/ProgramMetadataService.java

@@ -36,5 +36,5 @@
 public interface ProgramMetadataService
 {
     @Nonnull
-    Optional<? extends Program> findOneByReference( @Nonnull Reference reference );
+    Optional<? extends Program> findProgramByReference( @Nonnull Reference reference );
 }

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/program/impl/ProgramMetadataServiceImpl.java

@@ -84,7 +84,7 @@ public ProgramMetadataServiceImpl( @Nonnull @Qualifier( "systemDhis2RestTemplate
     @Cacheable
     @Nonnull
     @Override
-    public Optional<? extends Program> findOneByReference( @Nonnull Reference reference )
+    public Optional<? extends Program> findProgramByReference( @Nonnull Reference reference )
     {
         final ResponseEntity<DhisPrograms> result;
         switch ( reference.getType() )

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/trackedentity/ImmutableTrackedEntityAttribute.java

@@ -31,14 +31,15 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import org.dhis2.fhir.adapter.dhis.model.ImmutableDhisObject;
 import org.dhis2.fhir.adapter.dhis.model.ImmutableOptionSet;
 import org.dhis2.fhir.adapter.dhis.model.OptionSet;
 import org.dhis2.fhir.adapter.model.ValueType;
 
 import javax.annotation.Nonnull;
 import java.io.Serializable;
 
-public class ImmutableTrackedEntityAttribute implements TrackedEntityAttribute, Serializable
+public class ImmutableTrackedEntityAttribute implements TrackedEntityAttribute, ImmutableDhisObject, Serializable
 {
     private static final long serialVersionUID = -6135628541438060211L;
 

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/trackedentity/ImmutableTrackedEntityType.java

@@ -31,6 +31,7 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import org.dhis2.fhir.adapter.dhis.model.ImmutableDhisObject;
 import org.dhis2.fhir.adapter.dhis.model.Reference;
 import org.dhis2.fhir.adapter.scriptable.Scriptable;
 
@@ -43,7 +44,7 @@
 import java.util.stream.Collectors;
 
 @Scriptable
-public class ImmutableTrackedEntityType implements TrackedEntityType, Serializable
+public class ImmutableTrackedEntityType implements TrackedEntityType, ImmutableDhisObject, Serializable
 {
     private static final long serialVersionUID = 797154293863611491L;
 

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/trackedentity/ImmutableTrackedEntityTypeAttribute.java

@@ -31,12 +31,13 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import org.dhis2.fhir.adapter.dhis.model.ImmutableDhisObject;
 import org.dhis2.fhir.adapter.model.ValueType;
 
 import javax.annotation.Nonnull;
 import java.io.Serializable;
 
-public class ImmutableTrackedEntityTypeAttribute implements TrackedEntityTypeAttribute, Serializable
+public class ImmutableTrackedEntityTypeAttribute implements TrackedEntityTypeAttribute, ImmutableDhisObject, Serializable
 {
     private static final long serialVersionUID = -6094500152005916960L;
 

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/trackedentity/TrackedEntityAttributes.java

@@ -89,7 +89,8 @@ public Optional<TrackedEntityAttribute> getOptionalById( @Nonnull String id )
         Map<String, TrackedEntityAttribute> attributesById = this.attributesById;
         if ( attributesById == null )
         {
-            this.attributesById = attributesById = attributes.stream().collect( Collectors.toMap( TrackedEntityAttribute::getId, a -> a ) );
+            this.attributesById = attributesById = attributes.stream().map( ImmutableTrackedEntityAttribute::new )
+                .collect( Collectors.toMap( TrackedEntityAttribute::getId, a -> a ) );
         }
         return Optional.ofNullable( attributesById.get( id ) );
     }
@@ -100,7 +101,8 @@ public Optional<TrackedEntityAttribute> getOptionalByCode( @Nonnull String code
         Map<String, TrackedEntityAttribute> attributesByCode = this.attributesByCode;
         if ( attributesByCode == null )
         {
-            this.attributesByCode = attributesByCode = attributes.stream().filter( a -> StringUtils.isNotBlank( a.getCode() ) ).collect( Collectors.toMap( TrackedEntityAttribute::getCode, a -> a ) );
+            this.attributesByCode = attributesByCode = attributes.stream().filter( a -> StringUtils.isNotBlank( a.getCode() ) )
+                .map( ImmutableTrackedEntityAttribute::new ).collect( Collectors.toMap( TrackedEntityAttribute::getCode, a -> a ) );
         }
         return Optional.ofNullable( attributesByCode.get( code ) );
     }
@@ -111,7 +113,8 @@ public Optional<TrackedEntityAttribute> getOptionalByName( @Nonnull String name
         Map<String, TrackedEntityAttribute> attributesByName = this.attributesByName;
         if ( attributesByName == null )
         {
-            this.attributesByName = attributesByName = attributes.stream().collect( Collectors.toMap( TrackedEntityAttribute::getName, a -> a ) );
+            this.attributesByName = attributesByName = attributes.stream().map( ImmutableTrackedEntityAttribute::new )
+                .collect( Collectors.toMap( TrackedEntityAttribute::getName, a -> a ) );
         }
         return Optional.ofNullable( attributesByName.get( name ) );
     }

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/trackedentity/TrackedEntityInstance.java

@@ -54,7 +54,8 @@ public class TrackedEntityInstance implements DhisResource, Serializable
     @JsonInclude( JsonInclude.Include.NON_NULL )
     private String id;
 
-    @JsonProperty( access = JsonProperty.Access.READ_ONLY )
+    @JsonProperty
+    @JsonInclude( JsonInclude.Include.NON_NULL )
     private ZonedDateTime lastUpdated;
 
     @JsonIgnore

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/trackedentity/TrackedEntityMetadataService.java

@@ -37,7 +37,7 @@
 public interface TrackedEntityMetadataService
 {
     @Nonnull
-    Optional<? extends TrackedEntityType> getType( @Nonnull Reference reference );
+    Optional<? extends TrackedEntityType> findTypeByReference( @Nonnull Reference reference );
 
     @Nonnull
     TrackedEntityAttributes getAttributes();

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/tracker/trackedentity/impl/TrackedEntityMetadataServiceImpl.java

@@ -77,7 +77,7 @@ public TrackedEntityMetadataServiceImpl( @Nonnull @Qualifier( "systemDhis2RestTe
     @Cacheable( value = "trackedEntityTypes", cacheManager = "dhisCacheManager" )
     @Nonnull
     @Override
-    public Optional<? extends TrackedEntityType> getType( @Nonnull Reference reference )
+    public Optional<? extends TrackedEntityType> findTypeByReference( @Nonnull Reference reference )
     {
         switch ( reference.getType() )
         {

dhis/src/test/java/org/dhis2/fhir/adapter/dhis/tracker/program/impl/ProgramMetadataServiceImplTest.java

@@ -83,7 +83,7 @@ public void findOneByReferenceId() throws IOException
             "generatedByEnrollmentDate,minDaysFromStart,programStageDataElements%5Bid,compulsory,allowProvidedElsewhere,dataElement%5Bid,name,code,valueType,optionSetValue,optionSet%5Bid,name,options%5Bcode,name%5D%5D%5D%5D%5D" ) )
             .andExpect( method( HttpMethod.GET ) ).andRespond( withSuccess( IOUtils.resourceToByteArray( "/org/dhis2/fhir/adapter/dhis/tracker/program/impl/program.json" ), MediaType.APPLICATION_JSON ) );
 
-        Optional<? extends Program> ou = service.findOneByReference( new Reference( "93783", ReferenceType.ID ) );
+        Optional<? extends Program> ou = service.findProgramByReference( new Reference( "93783", ReferenceType.ID ) );
         Assert.assertTrue( ou.isPresent() );
         assertProgram( ou.get() );
     }
@@ -96,7 +96,7 @@ public void findOneByReferenceIdNotFound()
             "generatedByEnrollmentDate,minDaysFromStart,programStageDataElements%5Bid,compulsory,allowProvidedElsewhere,dataElement%5Bid,name,code,valueType,optionSetValue,optionSet%5Bid,name,options%5Bcode,name%5D%5D%5D%5D%5D" ) ).andExpect( method( HttpMethod.GET ) )
             .andRespond( MockRestResponseCreators.withStatus( HttpStatus.NOT_FOUND ).body( "{}" ).contentType( MediaType.APPLICATION_JSON ) );
 
-        Optional<? extends Program> ou = service.findOneByReference( new Reference( "93783", ReferenceType.ID ) );
+        Optional<? extends Program> ou = service.findProgramByReference( new Reference( "93783", ReferenceType.ID ) );
         Assert.assertFalse( ou.isPresent() );
     }
 
@@ -107,7 +107,7 @@ public void findOneByReferenceIdServerError()
             "trackedEntityType%5Bid%5D,programTrackedEntityAttributes%5Bid,name,valueType,mandatory,allowFutureDate,trackedEntityAttribute%5Bid,name,code,valueType,generated%5D%5D,programStages%5Bid,name,repeatable,captureCoordinates," +
             "generatedByEnrollmentDate,minDaysFromStart,programStageDataElements%5Bid,compulsory,allowProvidedElsewhere,dataElement%5Bid,name,code,valueType,optionSetValue,optionSet%5Bid,name,options%5Bcode,name%5D%5D%5D%5D%5D" ) ).andExpect( method( HttpMethod.GET ) )
             .andRespond( MockRestResponseCreators.withServerError() );
-        service.findOneByReference( new Reference( "93783", ReferenceType.ID ) );
+        service.findProgramByReference( new Reference( "93783", ReferenceType.ID ) );
     }
 
     @Test
@@ -118,7 +118,7 @@ public void findOneByReferenceCode() throws IOException
             "generatedByEnrollmentDate,minDaysFromStart,programStageDataElements%5Bid,compulsory,allowProvidedElsewhere,dataElement%5Bid,name,code,valueType,optionSetValue,optionSet%5Bid,name,options%5Bcode,name%5D%5D%5D%5D%5D&filter=code:eq:OU_3783" ) ).andExpect( method( HttpMethod.GET ) )
             .andRespond( withSuccess( IOUtils.resourceToByteArray( "/org/dhis2/fhir/adapter/dhis/tracker/program/impl/programs.json" ), MediaType.APPLICATION_JSON ) );
 
-        Optional<? extends Program> ou = service.findOneByReference( new Reference( "OU_3783", ReferenceType.CODE ) );
+        Optional<? extends Program> ou = service.findProgramByReference( new Reference( "OU_3783", ReferenceType.CODE ) );
         Assert.assertTrue( ou.isPresent() );
         assertProgram( ou.get() );
     }
@@ -131,7 +131,7 @@ public void findOneByReferenceCodeNotFound() throws IOException
             "generatedByEnrollmentDate,minDaysFromStart,programStageDataElements%5Bid,compulsory,allowProvidedElsewhere,dataElement%5Bid,name,code,valueType,optionSetValue,optionSet%5Bid,name,options%5Bcode,name%5D%5D%5D%5D%5D&filter=code:eq:OU_3783" ) ).andExpect( method( HttpMethod.GET ) )
             .andRespond( withSuccess( IOUtils.resourceToByteArray( "/org/dhis2/fhir/adapter/dhis/tracker/program/impl/emptyPrograms.json" ), MediaType.APPLICATION_JSON ) );
 
-        Optional<? extends Program> ou = service.findOneByReference( new Reference( "OU_3783", ReferenceType.CODE ) );
+        Optional<? extends Program> ou = service.findProgramByReference( new Reference( "OU_3783", ReferenceType.CODE ) );
         Assert.assertFalse( ou.isPresent() );
     }
 
@@ -143,7 +143,7 @@ public void findOneByReferenceName() throws IOException
             "generatedByEnrollmentDate,minDaysFromStart,programStageDataElements%5Bid,compulsory,allowProvidedElsewhere,dataElement%5Bid,name,code,valueType,optionSetValue,optionSet%5Bid,name,options%5Bcode,name%5D%5D%5D%5D%5D&filter=name:eq:Freetown" ) ).andExpect( method( HttpMethod.GET ) )
             .andRespond( withSuccess( IOUtils.resourceToByteArray( "/org/dhis2/fhir/adapter/dhis/tracker/program/impl/programs.json" ), MediaType.APPLICATION_JSON ) );
 
-        Optional<? extends Program> ou = service.findOneByReference( new Reference( "Freetown", ReferenceType.NAME ) );
+        Optional<? extends Program> ou = service.findProgramByReference( new Reference( "Freetown", ReferenceType.NAME ) );
         Assert.assertTrue( ou.isPresent() );
         assertProgram( ou.get() );
     }
@@ -156,7 +156,7 @@ public void findOneByReferenceNameNotFound() throws IOException
             "generatedByEnrollmentDate,minDaysFromStart,programStageDataElements%5Bid,compulsory,allowProvidedElsewhere,dataElement%5Bid,name,code,valueType,optionSetValue,optionSet%5Bid,name,options%5Bcode,name%5D%5D%5D%5D%5D&filter=name:eq:Freetown" ) ).andExpect( method( HttpMethod.GET ) )
             .andRespond( withSuccess( IOUtils.resourceToByteArray( "/org/dhis2/fhir/adapter/dhis/tracker/program/impl/emptyPrograms.json" ), MediaType.APPLICATION_JSON ) );
 
-        Optional<? extends Program> ou = service.findOneByReference( new Reference( "Freetown", ReferenceType.NAME ) );
+        Optional<? extends Program> ou = service.findProgramByReference( new Reference( "Freetown", ReferenceType.NAME ) );
         Assert.assertFalse( ou.isPresent() );
     }