Adds support reading FHIR QuestionnaireResponse.

Tests are still missing.
opensrp · Aug 18, 2019 · 80712f4 · 80712f4
1 parent dfb4de6
commit 80712f4
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Showing 40 changed files with 1,015 additions and 85 deletions.
diff --git a/app/src/test/java/org/dhis2/fhir/adapter/AbstractAppTest.java b/app/src/test/java/org/dhis2/fhir/adapter/AbstractAppTest.java
@@ -41,8 +41,14 @@
 import org.apache.activemq.artemis.jms.client.ActiveMQSession;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.dhis2.fhir.adapter.dhis.model.DhisResourceId;
+import org.dhis2.fhir.adapter.fhir.data.repository.FhirDhisAssignmentRepository;
 import org.dhis2.fhir.adapter.fhir.metadata.model.FhirResourceType;
+import org.dhis2.fhir.adapter.fhir.metadata.repository.FhirClientRepository;
+import org.dhis2.fhir.adapter.fhir.metadata.repository.RuleRepository;
 import org.dhis2.fhir.adapter.fhir.model.FhirVersion;
+import org.dhis2.fhir.adapter.fhir.security.AdapterSystemAuthenticationToken;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.runner.RunWith;
@@ -59,6 +65,8 @@
 import org.springframework.http.MediaType;
 import org.springframework.jms.UncategorizedJmsException;
 import org.springframework.jms.core.JmsTemplate;
+import org.springframework.security.core.Authentication;
+import org.springframework.security.core.context.SecurityContextHolder;
 import org.springframework.security.test.context.TestSecurityContextHolder;
 import org.springframework.test.context.TestPropertySource;
 import org.springframework.test.web.client.MockRestServiceServer;
@@ -74,6 +82,7 @@
 import javax.persistence.EntityManager;
 import java.nio.charset.StandardCharsets;
 import java.util.Objects;
+import java.util.UUID;
 
 import static com.github.tomakehurst.wiremock.client.WireMock.*;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@@ -173,6 +182,15 @@ public abstract class AbstractAppTest
     @Autowired
     protected PlatformTransactionManager transactionManager;
 
+    @Autowired
+    protected FhirDhisAssignmentRepository assignmentRepository;
+
+    @Autowired
+    protected RuleRepository ruleRepository;
+
+    @Autowired
+    protected FhirClientRepository fhirClientRepository;
+
     private long resourceDlQueueCount;
 
     @Nonnull
@@ -250,9 +268,33 @@ protected HttpHeaders createDefaultHeaders()
     {
         final HttpHeaders headers = new HttpHeaders();
         headers.setDate( System.currentTimeMillis() );
+
         return headers;
     }
 
+    protected void createAssignment( @Nonnull UUID ruleId, @Nonnull UUID fhirClientId, @Nonnull DhisResourceId dhisResourceId, @Nonnull IIdType fhirResourceId )
+    {
+        final Authentication authentication = SecurityContextHolder.getContext().getAuthentication();
+        SecurityContextHolder.getContext().setAuthentication( new AdapterSystemAuthenticationToken() );
+        try
+        {
+            assignmentRepository.saveFhirResourceId(
+                ruleRepository.findById( ruleId ).orElseGet( () -> {
+                    Assert.fail( "Rule could not be found: " + ruleId );
+                    return null;
+                } ),
+                fhirClientRepository.findById( fhirClientId ).orElseGet( () -> {
+                    Assert.fail( "FHIR client could not be found: " + fhirClientId );
+                    return null;
+                } ),
+                dhisResourceId, fhirResourceId );
+        }
+        finally
+        {
+            SecurityContextHolder.getContext().setAuthentication( authentication );
+        }
+    }
+
     protected void notifyResource( @Nonnull FhirResourceType resourceType, @Nullable String resourceSearchResponse,
         @Nullable String resourceId, @Nullable String resourceResponse, boolean payload ) throws Exception
     {
@@ -261,6 +303,7 @@ protected void notifyResource( @Nonnull FhirResourceType resourceType, @Nullable
             fhirMockServer.removeStub( previousResourceSearchStubMapping );
             previousResourceSearchStubMapping = null;
         }
+
         if ( StringUtils.isNotBlank( resourceSearchResponse ) )
         {
             final UrlPattern urlPattern = urlMatching( getBaseFhirContext() +
@@ -271,6 +314,7 @@ protected void notifyResource( @Nonnull FhirResourceType resourceType, @Nullable
                 .withHeader( "Content-Type", "application/fhir+json" )
                 .withBody( resourceSearchResponse ) ) );
         }
+
         if ( StringUtils.isNotBlank( resourceId ) && StringUtils.isNotBlank( resourceResponse ) )
         {
             fhirMockServer.stubFor( WireMock.get( urlEqualTo( getBaseFhirContext() +
@@ -306,16 +350,19 @@ protected void waitForEmptyResourceQueue() throws Exception
         {
             messageCount = getQueueMessageCount( fhirRestHookRequestQueueJmsTemplate, null ) +
                 getQueueMessageCount( fhirResourceQueueJmsTemplate, null );
+
             if ( messageCount > 0 )
             {
                 if ( (System.currentTimeMillis() - begin) > MAX_COMPLETED_POLL_TIME )
                 {
                     Assert.fail( "Waited more than " + MAX_COMPLETED_POLL_TIME + " ms, but there are still " + messageCount + " messages in the queues." );
                 }
+
                 Thread.sleep( 100L );
             }
         }
         while ( messageCount > 0 );
+
         Assert.assertEquals( "Resource dead letter queue contains messages.",
             resourceDlQueueCount, getQueueMessageCount( fhirResourceQueueJmsTemplate, RESOURCE_DL_QUEUE_NAME ) );
     }

diff --git a/...pter/fhir/transform/fhir/impl/programstage/AbstractProgramStageTransformationAppTest.java b/...pter/fhir/transform/fhir/impl/programstage/AbstractProgramStageTransformationAppTest.java
@@ -51,13 +51,9 @@ protected void expectMetadataRequests() throws Exception
     {
         systemDhis2Server.expect( ExpectedCount.between( 0, 1 ), method( HttpMethod.GET ) ).andExpect( header( "Authorization", testConfiguration.getDhis2SystemAuthorization() ) )
             .andExpect( requestTo( dhis2BaseUrl + "/api/" + dhis2ApiVersion + "/programs.json?paging=false&fields=id,name,code,description,lastUpdated,selectIncidentDatesInFuture,selectEnrollmentDatesInFuture,displayIncidentDate,registration," +
-                "withoutRegistration," +
-                "captureCoordinates,trackedEntityType%5Bid%5D,programTrackedEntityAttributes%5Bid,name,valueType,mandatory,allowFutureDate,trackedEntityAttribute%5Bid,name,code,valueType,generated%5D%5D,programStages%5Bid,program%5Bid%5D,lastUpdated,name," +
-                "description," +
-                "repeatable," +
-                "captureCoordinates," +
-                "generatedByEnrollmentDate,minDaysFromStart,programStageDataElements%5Bid,compulsory,allowProvidedElsewhere,dataElement%5Bid,name,code,formName,valueType,optionSetValue,optionSet%5Bid,name,options%5Bcode," +
-                "name%5D%5D%5D%5D%5D&filter=name:eq:Child%20Programme" ) )
+                "withoutRegistration,captureCoordinates,trackedEntityType%5Bid%5D,programTrackedEntityAttributes%5Bid,name,valueType,mandatory,allowFutureDate,trackedEntityAttribute%5Bid,name,code,valueType,generated%5D%5D,programStages%5Bid," +
+                "program%5Bid%5D,lastUpdated,name,description,repeatable,captureCoordinates,generatedByEnrollmentDate,minDaysFromStart,programStageDataElements%5Bid,compulsory,allowProvidedElsewhere,dataElement%5Bid,name,code,formName,valueType," +
+                "optionSetValue,optionSet%5Bid,name,options%5Bcode,name%5D%5D%5D%5D%5D&filter=name:eq:Child%20Programme" ) )
             .andRespond( withSuccess( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/all-programs.json", StandardCharsets.UTF_8 ), MediaType.APPLICATION_JSON ) );
         systemDhis2Server.expect( ExpectedCount.between( 0, 1 ), method( HttpMethod.GET ) ).andExpect( header( "Authorization", testConfiguration.getDhis2SystemAuthorization() ) )
             .andExpect( requestTo( dhis2BaseUrl + "/api/" + dhis2ApiVersion + "/trackedEntityTypes/MCPQUTHX1Ze.json?fields=id,name,trackedEntityTypeAttributes%5Bid,name,valueType,mandatory,trackedEntityAttribute%5Bid,name,code,valueType,generated," +
@@ -73,10 +69,9 @@ protected void expectMetadataRequests() throws Exception
         systemDhis2Server.expect( ExpectedCount.between( 0, 1 ), method( HttpMethod.GET ) ).andExpect( header( "Authorization", testConfiguration.getDhis2SystemAuthorization() ) )
             .andExpect( requestTo( dhis2BaseUrl + "/api/" + dhis2ApiVersion + "/programs.json?paging=false&" +
                 "fields=id,name,code,description,lastUpdated,selectIncidentDatesInFuture,selectEnrollmentDatesInFuture,displayIncidentDate,registration,withoutRegistration,captureCoordinates,trackedEntityType%5Bid%5D,programTrackedEntityAttributes%5Bid," +
-                "name,valueType," +
-                "mandatory,allowFutureDate,trackedEntityAttribute%5Bid,name,code,valueType,generated%5D%5D,programStages%5Bid,program%5Bid%5D,lastUpdated,name,description,repeatable,captureCoordinates,generatedByEnrollmentDate,minDaysFromStart," +
-                "programStageDataElements%5Bid,compulsory," +
-                "allowProvidedElsewhere,dataElement%5Bid,name,code,description,formName,valueType,optionSetValue,optionSet%5Bid,name,options%5Bcode,name%5D%5D%5D%5D%5D&filter=name:eq:Child%20Programme" ) )
+                "name,valueType,mandatory,allowFutureDate,trackedEntityAttribute%5Bid,name,code,valueType,generated%5D%5D,programStages%5Bid,program%5Bid%5D,lastUpdated,name,description,repeatable,captureCoordinates,generatedByEnrollmentDate," +
+                "minDaysFromStart,programStageDataElements%5Bid,compulsory,allowProvidedElsewhere,dataElement%5Bid,name,code,description,formName,valueType,optionSetValue,optionSet%5Bid,name,options%5Bcode," +
+                "name%5D%5D%5D%5D%5D&filter=name:eq:Child%20Programme" ) )
             .andRespond( withSuccess( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/single-program.json", StandardCharsets.UTF_8 ), MediaType.APPLICATION_JSON ) );
     }
 }
diff --git a/...r/impl/programstage/AbstractQuestionnaireResponseToProgramStageTransformationAppTest.java b/...r/impl/programstage/AbstractQuestionnaireResponseToProgramStageTransformationAppTest.java
@@ -28,15 +28,20 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
+import ca.uhn.fhir.model.primitive.IdDt;
 import com.github.tomakehurst.wiremock.client.WireMock;
 import org.apache.commons.io.IOUtils;
+import org.dhis2.fhir.adapter.dhis.model.DhisResourceId;
+import org.dhis2.fhir.adapter.dhis.model.DhisResourceType;
 import org.dhis2.fhir.adapter.fhir.metadata.model.FhirResourceType;
+import org.dhis2.fhir.adapter.fhir.model.FhirVersion;
 import org.junit.Test;
 import org.springframework.http.HttpMethod;
 import org.springframework.http.MediaType;
 import org.springframework.test.web.client.ExpectedCount;
 
 import java.nio.charset.StandardCharsets;
+import java.util.UUID;
 
 import static com.github.tomakehurst.wiremock.client.WireMock.aResponse;
 import static com.github.tomakehurst.wiremock.client.WireMock.urlPathEqualTo;
@@ -52,8 +57,11 @@ public abstract class AbstractQuestionnaireResponseToProgramStageTransformationA
     extends AbstractProgramStageTransformationAppTest
 {
     @Test
-    public void createEnrollment() throws Exception
+    public void createQuestionnaireResponse() throws Exception
     {
+        createAssignment( UUID.fromString( "c4e17e7d-880e-45b5-9bc5-568da8c79742" ), testConfiguration.getFhirClientId( FhirVersion.R4 ),
+            new DhisResourceId( DhisResourceType.ENROLLMENT, "ieR4nl4muff" ), new IdDt( "CarePlan", "90" ) );
+
         expectMetadataRequests();
         fhirMockServer.stubFor( WireMock.get( urlPathEqualTo( getBaseFhirContext() + "/Patient/15" ) ).willReturn( aResponse()
             .withHeader( "Content-Type", "application/fhir+json" )
@@ -62,27 +70,30 @@ public void createEnrollment() throws Exception
             .withHeader( "Content-Type", "application/fhir+json" )
             .withBody( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/fhir/test/" + getResourceDir() + "/get-organization-20.json", StandardCharsets.UTF_8 ) ) ) );
 
+        systemDhis2Server.expect( ExpectedCount.once(), method( HttpMethod.GET ) ).andExpect( header( "Authorization", testConfiguration.getDhis2SystemAuthorization() ) )
+            .andExpect( requestTo( dhis2BaseUrl + "/api/" + dhis2ApiVersion + "/programStages/MsWxkiY6tMS.json?fields=id,program%5Bid%5D,lastUpdated,name,description,repeatable,captureCoordinates,generatedByEnrollmentDate,minDaysFromStart," +
+                "programStageDataElements%5Bid,compulsory,allowProvidedElsewhere,dataElement%5Bid,name,code,formName,valueType,optionSetValue,optionSet%5Bid,name,options%5Bcode,name%5D%5D%5D%5D" ) )
+            .andRespond( withSuccess( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/single-program-stage.json", StandardCharsets.UTF_8 ), MediaType.APPLICATION_JSON ) );
+        systemDhis2Server.expect( ExpectedCount.between( 0, 1 ), method( HttpMethod.GET ) ).andExpect( header( "Authorization", testConfiguration.getDhis2SystemAuthorization() ) )
+            .andExpect( requestTo( dhis2BaseUrl + "/api/" + dhis2ApiVersion + "/programs/EPDyQuoRnXk.json?fields=id,name,code,description,lastUpdated,selectIncidentDatesInFuture,selectEnrollmentDatesInFuture,displayIncidentDate,registration," +
+                "withoutRegistration,captureCoordinates,trackedEntityType%5Bid%5D,programTrackedEntityAttributes%5Bid,name,valueType,mandatory,allowFutureDate,trackedEntityAttribute%5Bid,name,code,valueType,generated%5D%5D,programStages%5Bid," +
+                "program%5Bid%5D,lastUpdated,name,description,repeatable,captureCoordinates,generatedByEnrollmentDate,minDaysFromStart,programStageDataElements%5Bid,compulsory,allowProvidedElsewhere,dataElement%5Bid,name,code,formName,valueType," +
+                "optionSetValue,optionSet%5Bid,name,options%5Bcode,name%5D%5D%5D%5D%5D" ) )
+            .andRespond( withSuccess( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/single-program.json", StandardCharsets.UTF_8 ), MediaType.APPLICATION_JSON ) );
         systemDhis2Server.expect( ExpectedCount.between( 0, 1 ), method( HttpMethod.GET ) ).andExpect( header( "Authorization", testConfiguration.getDhis2SystemAuthorization() ) )
-            .andExpect( requestTo( dhis2BaseUrl + "/api/" + dhis2ApiVersion + "/organisationUnits.json?paging=false&fields=lastUpdated,id,code,name,shortName,displayName,level,openingDate,closedDate,coordinates,leaf,parent%5Bid%5D&filter=code:eq:OU_1357" ) )
-            .andRespond( withSuccess( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/default-org-unit-OU_1357.json", StandardCharsets.UTF_8 ), MediaType.APPLICATION_JSON ) );
+            .andExpect( requestTo( dhis2BaseUrl + "/api/" + dhis2ApiVersion + "/organisationUnits/ldXIdLNUNEn.json?fields=lastUpdated,id,code,name,shortName,displayName,level,openingDate,closedDate,coordinates,leaf,parent%5Bid%5D" ) )
+            .andRespond( withSuccess( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/default-org-unit-OU_1234.json", StandardCharsets.UTF_8 ), MediaType.APPLICATION_JSON ) );
 
         userDhis2Server.expect( ExpectedCount.once(), requestTo( dhis2BaseUrl + "/api/" + dhis2ApiVersion + "/trackedEntityInstances.json?trackedEntityType=MCPQUTHX1Ze&ouMode=ACCESSIBLE&filter=jD1NGmSntCt:EQ:PT_88589&pageSize=2&fields=" +
             "deleted,trackedEntityInstance,trackedEntityType,orgUnit,coordinates,lastUpdated,attributes%5Battribute,value,lastUpdated,storedBy%5D" ) )
             .andExpect( method( HttpMethod.GET ) ).andExpect( header( "Authorization", testConfiguration.getDhis2UserAuthorization() ) )
             .andRespond( withSuccess( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/default-tei-15-get.json", StandardCharsets.UTF_8 ), MediaType.APPLICATION_JSON ) );
 
-        systemDhis2Server.expect( ExpectedCount.between( 0, 1 ), method( HttpMethod.GET ) ).andExpect( header( "Authorization", testConfiguration.getDhis2SystemAuthorization() ) )
-            .andExpect( requestTo( dhis2BaseUrl + "/api/" + dhis2ApiVersion + "/organisationUnits/ldXIdLNUNEn.json?fields=lastUpdated,id,code,name,shortName,displayName,level,openingDate,closedDate,coordinates,leaf,parent%5Bid%5D" ) )
-            .andRespond( withSuccess( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/default-org-unit-OU_1234.json", StandardCharsets.UTF_8 ), MediaType.APPLICATION_JSON ) );
-
-        userDhis2Server.expect( ExpectedCount.between( 2, 4 ), requestTo( dhis2BaseUrl + "/api/" + dhis2ApiVersion + "/enrollments.json?program=EPDyQuoRnXk&programStatus=ACTIVE&trackedEntityInstance=JeR2Ul4mZfx&ouMode=ACCESSIBLE&fields=:all&" +
-            "order=lastUpdated:desc&pageSize=1" ) ).andExpect( method( HttpMethod.GET ) ).andExpect( header( "Authorization", testConfiguration.getDhis2UserAuthorization() ) )
-            .andRespond( withSuccess( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/default-enrollment-empty.json", StandardCharsets.UTF_8 ), MediaType.APPLICATION_JSON ) );
-        userDhis2Server.expect( ExpectedCount.once(), requestTo( dhis2BaseUrl + "/api/" + dhis2ApiVersion + "/enrollments.json?strategy=CREATE" ) ).andExpect( method( HttpMethod.POST ) )
+        userDhis2Server.expect( ExpectedCount.once(), requestTo( dhis2BaseUrl + "/api/" + dhis2ApiVersion + "/events.json?strategy=CREATE" ) ).andExpect( method( HttpMethod.POST ) )
             .andExpect( header( "Authorization", testConfiguration.getDhis2UserAuthorization() ) )
             .andExpect( content().contentTypeCompatibleWith( MediaType.APPLICATION_JSON ) )
-            .andExpect( content().json( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/default-enrollment-91-create.json", StandardCharsets.UTF_8 ) ) )
-            .andRespond( withSuccess( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/default-enrollment-91-create-response.json", StandardCharsets.UTF_8 ), MediaType.APPLICATION_JSON )
+            .andExpect( content().json( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/default-event-91-create.json", StandardCharsets.UTF_8 ) ) )
+            .andRespond( withSuccess( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/dhis/test/default-event-91-create-response.json", StandardCharsets.UTF_8 ), MediaType.APPLICATION_JSON )
                 .headers( createDefaultHeaders() ) );
 
         notifyResource( FhirResourceType.QUESTIONNAIRE_RESPONSE, null,

diff --git a/app/src/test/resources/data.sql b/app/src/test/resources/data.sql
@@ -2682,11 +2682,6 @@ imp_enrollment_org_lookup_script_id, imp_enrollment_date_lookup_script_id)
 VALUES('417d0db376bc48bebc4223e7a7e663b0', 0, 'QUESTIONNAIRE_RESPONSE', 'PATIENT', '762b4137a98b4b10a0f5629d93e23461', '25a97bb47b394ed48677db4bcaa28ccf', '521b3a008ecc487ba7e3fe12b68e388a', '385e52d28674403db42586b5d4e9faf0',
 '25a97bb47b394ed48677db4bcaa28ccf', '521b3a008ecc487ba7e3fe12b68e388a');
 
-INSERT INTO fhir_rule (id, version, name, description, enabled, evaluation_order, fhir_resource_type, dhis_resource_type, transform_imp_script_id, exp_enabled, fhir_create_enabled, fhir_update_enabled, fhir_delete_enabled)
-VALUES ('e113ec6ec61048aa9df2cf7739f40985', 0, 'Child Programme Birth Stage Questionnaire Response', NULL, TRUE, 0, 'QUESTIONNAIRE_RESPONSE', 'PROGRAM_STAGE_EVENT', '2d5ec1318fbc44d395c52544f7ff284f', TRUE, TRUE, TRUE, TRUE);
-INSERT INTO fhir_program_stage_rule (id, program_stage_id, enrollment_creation_enabled,event_creation_enabled)
-VALUES ('e113ec6ec61048aa9df2cf7739f40985','4c074c85be494b9d89739e16b9615dad', TRUE, TRUE);
-
 -- Tracker Program Child Programme, Birth: OPV Dose
 INSERT INTO fhir_rule_dhis_data_ref(id, version, rule_id, data_ref, script_arg_name, required)
 SELECT 'e66efbcb7142445a8e1ad1ef524977c1', 0, id, 'CODE:DE_2006104', 'dataElement', true

diff --git a/...src/test/resources/org/dhis2/fhir/adapter/dhis/test/default-event-91-create-response.json b/...src/test/resources/org/dhis2/fhir/adapter/dhis/test/default-event-91-create-response.json
@@ -0,0 +1,11 @@
+{
+  "status": "OK",
+  "response": {
+    "importSummaries": [
+      {
+        "status": "SUCCESS",
+        "reference": "deR4kl4mnf7"
+      }
+    ]
+  }
+}
diff --git a/app/src/test/resources/org/dhis2/fhir/adapter/dhis/test/default-event-91-create.json b/app/src/test/resources/org/dhis2/fhir/adapter/dhis/test/default-event-91-create.json
@@ -0,0 +1,22 @@
+{
+  "status": "ACTIVE",
+  "eventDate": "2018-11-10T00:00:00+01:00",
+  "dueDate": "2018-11-12T00:00:00+01:00",
+  "coordinate": null,
+  "dataValues": [
+    {
+      "value": "3666",
+      "providedElsewhere": false,
+      "dataElement": "BnplxU2jGvX"
+    },
+    {
+      "value": "1",
+      "providedElsewhere": false,
+      "dataElement": "ft7iD5ZzPxJ"
+    }
+  ],
+  "orgUnit": "ldXIdLNUNEn",
+  "program": "EPDyQuoRnXk",
+  "trackedEntityInstance": "JeR2Ul4mZfx",
+  "programStage": "MsWxkiY6tMS"
+}