Adds support for FHIR ID to DHIS2 Code mapping.

opensrp · Aug 13, 2019 · 15d0535 · 15d0535
1 parent d1967f6
commit 15d0535
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Showing 23 changed files with 179 additions and 52 deletions.
diff --git a/.../adapter/fhir/transform/dhis/impl/util/dstu3/Dstu3CodeDhisToFhirTransformerUtilsTest.java b/.../adapter/fhir/transform/dhis/impl/util/dstu3/Dstu3CodeDhisToFhirTransformerUtilsTest.java
@@ -191,7 +191,7 @@ public void getByMappedCodeNull()
     @Test
     public void getByMappedCode()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", null, null, null, false );
         final SystemCode systemCode = new SystemCode();
         systemCode.setSystemCode( "837232" );
 
@@ -215,7 +215,7 @@ public void getByMappedCode()
     @Test
     public void getByMappedCodeNotFound()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", null, null, null, false );
 
         final Map<String, Object> variables = new HashMap<>();
         variables.put( ScriptVariable.CONTEXT.getVariableName(), context );
@@ -237,7 +237,7 @@ public void getByMappedCodeNotFound()
     @Test
     public void getCodeWithoutPrefixPrefix()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", "SE_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", "SE_", null, null, false );
 
         final Map<String, Object> variables = new HashMap<>();
         variables.put( ScriptVariable.CONTEXT.getVariableName(), context );
@@ -253,7 +253,7 @@ public void getCodeWithoutPrefixPrefix()
     @Test
     public void getCodeWithoutPrefixNoPrefix()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", "SE_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", "SE_", null, null, false );
 
         final Map<String, Object> variables = new HashMap<>();
         variables.put( ScriptVariable.CONTEXT.getVariableName(), context );
@@ -269,7 +269,7 @@ public void getCodeWithoutPrefixNoPrefix()
     @Test
     public void getCodeWithoutPrefixNoPrefixSystem()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", null, null, null, false );
 
         final Map<String, Object> variables = new HashMap<>();
         variables.put( ScriptVariable.CONTEXT.getVariableName(), context );

diff --git a/...2/fhir/adapter/fhir/transform/fhir/impl/util/ReferenceFhirToDhisTransformerUtilsTest.java b/...2/fhir/adapter/fhir/transform/fhir/impl/util/ReferenceFhirToDhisTransformerUtilsTest.java
@@ -144,7 +144,7 @@ public void getResource()
         final FhirClientResource fhirClientResource = new FhirClientResource();
         fhirClientResource.setId( fhirClientResourceId );
         fhirClientResource.setFhirClient( fhirClient );
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );
@@ -187,7 +187,7 @@ public void getResourceRefreshed()
         final FhirClientResource fhirClientResource = new FhirClientResource();
         fhirClientResource.setId( fhirClientResourceId );
         fhirClientResource.setFhirClient( fhirClient );
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );
@@ -230,7 +230,7 @@ public void initReference()
         final FhirClientResource fhirClientResource = new FhirClientResource();
         fhirClientResource.setId( fhirClientResourceId );
         fhirClientResource.setFhirClient( fhirClient );
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );

diff --git a/.../adapter/fhir/transform/fhir/impl/util/dstu3/Dstu3CodeFhirToDhisTransformerUtilsTest.java b/.../adapter/fhir/transform/fhir/impl/util/dstu3/Dstu3CodeFhirToDhisTransformerUtilsTest.java
@@ -335,7 +335,7 @@ public void getResourceCodes()
     @Test
     public void getMappedCodeNotFound()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com/2", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com/2", null, null, null, false );
 
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
@@ -349,7 +349,7 @@ public void getMappedCodeNotFound()
     @Test
     public void getMappedCodeFound()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com/2", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com/2", null, null, null, false );
 
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
@@ -367,7 +367,7 @@ public void getMappedCodeFound()
     @Test
     public void getMappedCodeFoundMapped()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com/2", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com/2", null, null, null, false );
 
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();

diff --git a/.../fhir/transform/fhir/impl/util/dstu3/Dstu3FhirResourceFhirToDhisTransformerUtilsTest.java b/.../fhir/transform/fhir/impl/util/dstu3/Dstu3FhirResourceFhirToDhisTransformerUtilsTest.java
@@ -111,6 +111,8 @@ public void getIdentifierReferenceNull()
     @Test
     public void getCanonicalReferenceNull()
     {
+        Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
+        Mockito.doReturn( Collections.singletonMap( ScriptVariable.CONTEXT.getVariableName(), context ) ).when( scriptExecution ).getVariables();
         Assert.assertNull( utils.getCanonicalAdapterReference( null, "MEASURE" ) );
     }
 
@@ -424,6 +426,22 @@ public void getAdapterReferenceDhisFhirIdentifierCode()
         Assert.assertEquals( new org.dhis2.fhir.adapter.dhis.model.Reference( "5678", ReferenceType.CODE ), adapterReference );
     }
 
+    @Test
+    public void getAdapterReferenceDhisFhirIdCode()
+    {
+        Mockito.doReturn( request ).when( context ).getFhirRequest();
+        Mockito.doReturn( true ).when( request ).isDhisFhirId();
+        Mockito.doReturn( new ResourceSystem( FhirResourceType.PATIENT, "National ID", null, null, null, true ) )
+            .when( request ).getResourceSystem( Mockito.eq( FhirResourceType.PATIENT ) );
+        Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
+        Mockito.doReturn( Collections.singletonMap( ScriptVariable.CONTEXT.getVariableName(), context ) ).when( scriptExecution ).getVariables();
+
+        final org.dhis2.fhir.adapter.dhis.model.Reference adapterReference = utils.getAdapterReference( new Reference( "Patient/5678" ), "PATIENT" );
+
+        Assert.assertNotNull( adapterReference );
+        Assert.assertEquals( new org.dhis2.fhir.adapter.dhis.model.Reference( "5678", ReferenceType.CODE ), adapterReference );
+    }
+
     @Test
     public void getAdapterReferenceDhisFhirIdOnly()
     {

diff --git a/...er/fhir/transform/fhir/impl/util/dstu3/Dstu3IdentifierFhirToDhisTransformerUtilsTest.java b/...er/fhir/transform/fhir/impl/util/dstu3/Dstu3IdentifierFhirToDhisTransformerUtilsTest.java
@@ -130,7 +130,7 @@ public void getReferenceIdentifierWithDefaultSystem()
         final Patient patient = new Patient();
         patient.addIdentifier().setSystem( "http://test.com" ).setValue( "ABC_123" );
 
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.PATIENT, "http://test.com", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.PATIENT, "http://test.com", null, null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );
@@ -152,7 +152,7 @@ public void getResourceIdentifierWithDefaultSystem()
         final Patient patient = new Patient();
         patient.addIdentifier().setSystem( "http://test.com" ).setValue( "ABC_123" );
 
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.PATIENT, "http://test.com", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.PATIENT, "http://test.com", null, null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );
@@ -189,7 +189,7 @@ public void getIncludedReferenceIdentifierWithDefaultSystem()
         final Patient patient = new Patient();
         patient.addIdentifier().setSystem( "http://test.com" ).setValue( "ABC_123" );
 
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.PATIENT, "http://test.com", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.PATIENT, "http://test.com", null, null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );

diff --git a/...pter/fhir/transform/fhir/impl/util/dstu3/Dstu3LocationFhirToDhisTransformerUtilsTest.java b/...pter/fhir/transform/fhir/impl/util/dstu3/Dstu3LocationFhirToDhisTransformerUtilsTest.java
@@ -111,7 +111,7 @@ public void findHierarchy()
         final UUID fhirClientResourceId = UUID.randomUUID();
         final FhirClientResource fhirClientResource = new FhirClientResource();
         fhirClientResource.setFhirClient( fhirClient );
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.LOCATION, "http://test.com", "OT_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.LOCATION, "http://test.com", "OT_", null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );

diff --git a/.../fhir/transform/fhir/impl/util/dstu3/Dstu3OrganizationFhirToDhisTransformerUtilsTest.java b/.../fhir/transform/fhir/impl/util/dstu3/Dstu3OrganizationFhirToDhisTransformerUtilsTest.java
@@ -126,7 +126,7 @@ public void existsNot()
     @Test
     public void existsWithPrefix()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );
@@ -142,7 +142,7 @@ public void existsWithPrefix()
     @Test
     public void existsNotWithPrefix()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );
@@ -164,7 +164,7 @@ public void findHierarchy()
         final UUID fhirClientResourceId = UUID.randomUUID();
         final FhirClientResource fhirClientResource = new FhirClientResource();
         fhirClientResource.setFhirClient( fhirClient );
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );

diff --git a/...2/fhir/adapter/fhir/transform/dhis/impl/util/r4/R4CodeDhisToFhirTransformerUtilsTest.java b/...2/fhir/adapter/fhir/transform/dhis/impl/util/r4/R4CodeDhisToFhirTransformerUtilsTest.java
@@ -191,7 +191,7 @@ public void getByMappedCodeNull()
     @Test
     public void getByMappedCode()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", null, null, null, false );
         final SystemCode systemCode = new SystemCode();
         systemCode.setSystemCode( "837232" );
 
@@ -215,7 +215,7 @@ public void getByMappedCode()
     @Test
     public void getByMappedCodeNotFound()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", null, null, null, false );
 
         final Map<String, Object> variables = new HashMap<>();
         variables.put( ScriptVariable.CONTEXT.getVariableName(), context );
@@ -237,7 +237,7 @@ public void getByMappedCodeNotFound()
     @Test
     public void getCodeWithoutPrefixPrefix()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", "SE_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", "SE_", null, null, false );
 
         final Map<String, Object> variables = new HashMap<>();
         variables.put( ScriptVariable.CONTEXT.getVariableName(), context );
@@ -253,7 +253,7 @@ public void getCodeWithoutPrefixPrefix()
     @Test
     public void getCodeWithoutPrefixNoPrefix()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", "SE_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", "SE_", null, null, false );
 
         final Map<String, Object> variables = new HashMap<>();
         variables.put( ScriptVariable.CONTEXT.getVariableName(), context );
@@ -269,7 +269,7 @@ public void getCodeWithoutPrefixNoPrefix()
     @Test
     public void getCodeWithoutPrefixNoPrefixSystem()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "TestSystem", null, null, null, false );
 
         final Map<String, Object> variables = new HashMap<>();
         variables.put( ScriptVariable.CONTEXT.getVariableName(), context );

diff --git a/...2/fhir/adapter/fhir/transform/fhir/impl/util/ReferenceFhirToDhisTransformerUtilsTest.java b/...2/fhir/adapter/fhir/transform/fhir/impl/util/ReferenceFhirToDhisTransformerUtilsTest.java
@@ -144,7 +144,7 @@ public void getResource()
         final FhirClientResource fhirClientResource = new FhirClientResource();
         fhirClientResource.setId( fhirClientResourceId );
         fhirClientResource.setFhirClient( fhirClient );
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );
@@ -187,7 +187,7 @@ public void getResourceRefreshed()
         final FhirClientResource fhirClientResource = new FhirClientResource();
         fhirClientResource.setId( fhirClientResourceId );
         fhirClientResource.setFhirClient( fhirClient );
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );
@@ -230,7 +230,7 @@ public void initReference()
         final FhirClientResource fhirClientResource = new FhirClientResource();
         fhirClientResource.setId( fhirClientResourceId );
         fhirClientResource.setFhirClient( fhirClient );
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com", "OT_", null, null, false );
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
         Mockito.doReturn( context ).when( variables ).get( Mockito.eq( "context" ) );

diff --git a/...2/fhir/adapter/fhir/transform/fhir/impl/util/r4/R4CodeFhirToDhisTransformerUtilsTest.java b/...2/fhir/adapter/fhir/transform/fhir/impl/util/r4/R4CodeFhirToDhisTransformerUtilsTest.java
@@ -335,7 +335,7 @@ public void getResourceCodes()
     @Test
     public void getMappedCodeNotFound()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com/2", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com/2", null, null, null, false );
 
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
@@ -349,7 +349,7 @@ public void getMappedCodeNotFound()
     @Test
     public void getMappedCodeFound()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com/2", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com/2", null, null, null, false );
 
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();
@@ -367,7 +367,7 @@ public void getMappedCodeFound()
     @Test
     public void getMappedCodeFoundMapped()
     {
-        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com/2", null, null, null );
+        final ResourceSystem resourceSystem = new ResourceSystem( FhirResourceType.ORGANIZATION, "http://test.com/2", null, null, null, false );
 
         Mockito.doReturn( scriptExecution ).when( scriptExecutionContext ).getScriptExecution();
         Mockito.doReturn( variables ).when( scriptExecution ).getVariables();