Added support for detecting endless synchronizations for DHIS2.

app/src/main/resources/logback-spring.xml

@@ -29,9 +29,9 @@
 
 <configuration debug="false">
   <property name="CONSOLE_LOG_PATTERN"
-    value="${CONSOLE_LOG_PATTERN:-%clr(%d{${LOG_DATEFORMAT_PATTERN:-yyyy-MM-dd HH:mm:ss.SSS}}){faint} %clr(${LOG_LEVEL_PATTERN:-%5p}) %clr(${PID:- }){magenta} %clr(---){faint} %clr([%15.15t]){faint} %clr(%-40.40logger{39}){cyan} %clr(:){faint} %X{fhirId} - %m%n${LOG_EXCEPTION_CONVERSION_WORD:-%wEx}}" />
+    value="${CONSOLE_LOG_PATTERN:-%clr(%d{${LOG_DATEFORMAT_PATTERN:-yyyy-MM-dd HH:mm:ss.SSS}}){faint} %clr(${LOG_LEVEL_PATTERN:-%5p}) %clr(${PID:- }){magenta} %clr(---){faint} %clr([%15.15t]){faint} %clr(%-40.40logger{39}){cyan} %clr(:){faint} %X{fhirId}%X{dhisId} - %m%n${LOG_EXCEPTION_CONVERSION_WORD:-%wEx}}" />
   <property name="FILE_LOG_PATTERN"
-    value="${FILE_LOG_PATTERN:-%d{${LOG_DATEFORMAT_PATTERN:-yyyy-MM-dd HH:mm:ss.SSS}} ${LOG_LEVEL_PATTERN:-%5p} ${PID:- } --- [%t] %-40.40logger{39} : %X{fhirId} - %m%n${LOG_EXCEPTION_CONVERSION_WORD:-%wEx}}" />
+    value="${FILE_LOG_PATTERN:-%d{${LOG_DATEFORMAT_PATTERN:-yyyy-MM-dd HH:mm:ss.SSS}} ${LOG_LEVEL_PATTERN:-%5p} ${PID:- } --- [%t] %-40.40logger{39} : %X{fhirId}%X{dhisId} - %m%n${LOG_EXCEPTION_CONVERSION_WORD:-%wEx}}" />
 
   <include resource="org/springframework/boot/logging/logback/defaults.xml" />
   <include resource="org/springframework/boot/logging/logback/console-appender.xml" />

app/src/test/java/org/dhis2/fhir/adapter/fhir/transform/impl/trackedentity/AbstractTrackedEntityInstanceTransformationAppTest.java → app/src/test/java/org/dhis2/fhir/adapter/fhir/transform/fhir/impl/trackedentity/AbstractTrackedEntityInstanceTransformationAppTest.java

@@ -1,4 +1,4 @@
-package org.dhis2.fhir.adapter.fhir.transform.impl.trackedentity;
+package org.dhis2.fhir.adapter.fhir.transform.fhir.impl.trackedentity;
 
 /*
  * Copyright (c) 2004-2018, University of Oslo

app/src/test/java/org/dhis2/fhir/adapter/fhir/transform/impl/trackedentity/PatientToTrackedEntityInstanceTransformationAppTest.java → app/src/test/java/org/dhis2/fhir/adapter/fhir/transform/fhir/impl/trackedentity/PatientToTrackedEntityInstanceTransformationAppTest.java

@@ -1,4 +1,4 @@
-package org.dhis2.fhir.adapter.fhir.transform.impl.trackedentity;
+package org.dhis2.fhir.adapter.fhir.transform.fhir.impl.trackedentity;
 
 /*
  * Copyright (c) 2004-2018, University of Oslo

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

@@ -31,6 +31,7 @@
 import org.dhis2.fhir.adapter.model.Identifiable;
 
 import javax.annotation.Nonnull;
+import java.time.ZonedDateTime;
 
 /**
  * Base interface of DHIS2 Resources.
@@ -39,6 +40,22 @@
  */
 public interface DhisResource extends Identifiable<String>
 {
+    /**
+     * @return the unique ID of the DHIS 2 organization unit to which this resource belongs,
+     * or <code>null</code> if this resource does not belong to any DHIS 2 organization unit.
+     */
+    String getOrgUnitId();
+
+    /**
+     * @return the unique ID of the resource (including the type of the resource).
+     */
+    DhisResourceId getResourceId();
+
+    /**
+     * @return the timestamp when the resource has been updated the last time.
+     */
+    ZonedDateTime getLastUpdated();
+
     /**
      * @return the concrete resource type of the resource.
      */

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/queue/DhisQueueConfig.java

@@ -28,9 +28,12 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
+import com.google.common.collect.ImmutableMap;
 import org.apache.activemq.artemis.jms.server.config.JMSQueueConfiguration;
 import org.apache.activemq.artemis.jms.server.config.impl.JMSQueueConfigurationImpl;
+import org.dhis2.fhir.adapter.dhis.sync.DhisResourceQueueItem;
 import org.dhis2.fhir.adapter.dhis.sync.impl.DhisSyncConfig;
+import org.dhis2.fhir.adapter.dhis.sync.impl.DhisSyncRequestQueueItem;
 import org.springframework.boot.autoconfigure.jms.artemis.ArtemisConfigurationCustomizer;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -40,6 +43,7 @@
 
 import javax.annotation.Nonnull;
 import javax.jms.ConnectionFactory;
+import java.util.Map;
 
 /**
  * Configuration of queues that are used by the adapter.
@@ -117,4 +121,21 @@ protected JmsTemplate dhisResourceQueueJmsTemplate( @Nonnull ConnectionFactory c
         jmsTemplate.setMessageConverter( jmsMessageConverter );
         return jmsTemplate;
     }
+
+    @Bean
+    @Nonnull
+    protected JmsJsonTypeIdMapping dhisJmsJsonTypeIdMapping()
+    {
+        return new JmsJsonTypeIdMapping()
+        {
+            @Nonnull
+            @Override
+            public Map<String, Class<?>> getTypeIdMappings()
+            {
+                return ImmutableMap.of(
+                    "dhisSyncRequest", DhisSyncRequestQueueItem.class,
+                    "dhisResource", DhisResourceQueueItem.class );
+            }
+        };
+    }
 }

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/queue/JmsJsonTypeIdMapping.java

@@ -0,0 +1,44 @@
+package org.dhis2.fhir.adapter.dhis.queue;
+
+/*
+ * 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.
+ */
+
+import javax.annotation.Nonnull;
+import java.util.Map;
+
+/**
+ * Returns mappings from a class to a type ID that will be stored in a JMS message
+ * instead of the full qualified class name.
+ *
+ * @author volsch
+ */
+public interface JmsJsonTypeIdMapping
+{
+    @Nonnull
+    Map<String, Class<?>> getTypeIdMappings();
+}

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/queue/QueueConfig.java

@@ -43,6 +43,9 @@
 
 import javax.annotation.Nonnull;
 import javax.jms.ConnectionFactory;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * General configuration of queues that are used by the adapter.
@@ -56,12 +59,16 @@ public class QueueConfig
     @Primary
     @Bean
     @Nonnull
-    protected MessageConverter jacksonJmsMessageConverter( @Nonnull ObjectMapper objectMapper )
+    protected MessageConverter jacksonJmsMessageConverter( @Nonnull ObjectMapper objectMapper, @Nonnull Collection<JmsJsonTypeIdMapping> typeIdMappings )
     {
+        final Map<String, Class<?>> resultingMappings = new HashMap<>();
+        typeIdMappings.forEach( tim -> resultingMappings.putAll( tim.getTypeIdMappings() ) );
+
         final MappingJackson2MessageConverter converter = new MappingJackson2MessageConverter();
         converter.setObjectMapper( objectMapper );
         converter.setTargetType( MessageType.TEXT );
         converter.setTypeIdPropertyName( "_type" );
+        converter.setTypeIdMappings( resultingMappings );
         return converter;
     }
 

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

@@ -29,14 +29,12 @@
  */
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
 import org.dhis2.fhir.adapter.data.model.ProcessedItemInfo;
 import org.dhis2.fhir.adapter.data.model.UuidDataGroupId;
 import org.dhis2.fhir.adapter.data.processor.DataItemQueueItem;
 
 import javax.annotation.Nonnull;
 import java.io.Serializable;
-import java.util.UUID;
 
 /**
  * Processing request for a DHIS2 resource synchronization that is enqueued and dequeued.
@@ -70,15 +68,4 @@ public void setDataGroupId( UuidDataGroupId dataGroupId )
     {
         super.setDataGroupId( dataGroupId );
     }
-
-    @JsonProperty
-    public UUID getRemoteSubscriptionResourceId()
-    {
-        return (getDataGroupId() == null) ? null : getDataGroupId().getId();
-    }
-
-    public void setRemoteSubscriptionResourceId( UUID remoteSubscriptionResourceId )
-    {
-        super.setDataGroupId( (remoteSubscriptionResourceId == null) ? null : new UuidDataGroupId( remoteSubscriptionResourceId ) );
-    }
 }

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

@@ -0,0 +1,52 @@
+package org.dhis2.fhir.adapter.dhis.sync;
+
+/*
+ * 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.
+ */
+
+import org.dhis2.fhir.adapter.dhis.model.DhisResource;
+import org.dhis2.fhir.adapter.dhis.model.DhisResourceId;
+
+import javax.annotation.Nonnull;
+import java.util.Optional;
+
+/**
+ * Utility methods to access DHIS resources.
+ *
+ * @author volsch
+ */
+public interface DhisResourceRepository
+{
+    @Nonnull
+    Optional<? extends DhisResource> findRefreshed( @Nonnull DhisResourceId dhisResourceId );
+
+    @Nonnull
+    Optional<? extends DhisResource> find( @Nonnull DhisResourceId dhisResourceId );
+
+    @Nonnull
+    DhisResource save( @Nonnull DhisResource resource );
+}