merge develop

bootstrap.sh

@@ -96,10 +96,10 @@ if [ -n "$build" ] ; then
 	mkdir -p /tmp/home
 	docker run --rm -t -i -v "$PWD:/src" -u "`id -u`:`id -g`" -e HOME="/src/tmp/home" \
 		-e MAVEN_OPTS="-Dmaven.repo.local=/src/tmp/home/.m2/repository"	\
-		-w /src "$DEV_IMG" sh -c 'git config --global --add safe.directory /src && cd shanoir-ng-parent && mvn clean install -DskipTests'
+		-w /src "$DEV_IMG" sh -c 'cd shanoir-ng-parent && mvn clean install -DskipTests'
 
 	# 3. build the docker images
-	docker compose build
+	docker compose -f docker-compose-dev.yml build
 fi
 
 if [ -n "$deploy" ] ; then
@@ -136,14 +136,14 @@ if [ -n "$deploy" ] ; then
 	# 2. keycloak-database + keycloak
 	if [ -n "$keycloak" ] ; then
 		step "init: keycloak-database"
-		docker compose up -d keycloak-database
+		docker compose -f docker-compose-dev.yml up -d keycloak-database
 		wait_tcp_ready keycloak-database 3306
 
 		step "init: keycloak"
 		docker compose run --rm -e SHANOIR_MIGRATION=init keycloak
 
 		step "start: keycloak"
-		docker compose up -d keycloak
+		docker compose -f docker-compose-dev.yml up -d keycloak
 		docker-compose/common/oneshot --pgrp '\| *'				\
 				' INFO  \[io.quarkus\] .* Keycloak .* started in [0-9]*'	\
 				-- docker compose logs --no-color --follow keycloak >/dev/null
@@ -156,7 +156,7 @@ if [ -n "$deploy" ] ; then
 		for infra_ms_dcm4chee in ldap dcm4chee-database dcm4chee-arc
 		do
 			step "start: $infra_ms_dcm4chee infrastructure microservices dcm4chee"
-			docker compose up -d "$infra_ms_dcm4chee"
+			docker compose -f docker-compose-dev.yml up -d "$infra_ms_dcm4chee"
 		done
 	fi
 
@@ -165,7 +165,7 @@ if [ -n "$deploy" ] ; then
 	for infra_ms in rabbitmq solr
 	do
 		step "start: $infra_ms infrastructure microservice"
-		docker compose up -d "$infra_ms"
+		docker compose -f docker-compose-dev.yml up -d "$infra_ms"
 	done
 
 	# 5. Shanoir-NG microservices
@@ -175,10 +175,10 @@ if [ -n "$deploy" ] ; then
 		step "init: $ms microservice"
 		docker compose run --rm -e SHANOIR_MIGRATION=init "$ms"
 		step "start: $ms microservice"
-		docker compose up -d "$ms"
+		docker compose -f docker-compose-dev.yml up -d "$ms"
 	done
 
 	# 6. nginx
 	step "start: nginx"
-	docker compose up -d nginx
+	docker compose -f docker-compose-dev.yml up -d nginx
 fi

docker-compose.yml

@@ -17,7 +17,7 @@ services:
   #
   keycloak-database:
     container_name: "${SHANOIR_PREFIX}keycloak-database"
-    image: "ghcr.io/fli-iam/shanoir-ng/keycloak-database:ng_v2.3.1"
+    image: "ghcr.io/fli-iam/shanoir-ng/keycloak-database:NG_v2.5.0"
     environment:
       - MYSQL_DATABASE=keycloak
     ulimits:
@@ -43,7 +43,7 @@ services:
       - SHANOIR_KEYCLOAK_USER
       - SHANOIR_KEYCLOAK_PASSWORD
       - SHANOIR_ALLOWED_ADMIN_IPS
-    image: "ghcr.io/fli-iam/shanoir-ng/keycloak:ng_v2.3.1"
+    image: "ghcr.io/fli-iam/shanoir-ng/keycloak:NG_v2.5.0"
     volumes:
       - "keycloak-logs:/opt/keycloak/data/log"
     networks:
@@ -70,7 +70,7 @@ services:
   #
   database:
     container_name: "${SHANOIR_PREFIX}database"
-    image: "ghcr.io/fli-iam/shanoir-ng/database:ng_v2.4.1"
+    image: "ghcr.io/fli-iam/shanoir-ng/database:NG_v2.5.0"
     command: --max_allowed_packet 20000000
     env_file:
       - ./docker-compose/database/variables.env
@@ -91,7 +91,7 @@ services:
   #
   users:
     container_name: "${SHANOIR_PREFIX}users"
-    image: "ghcr.io/fli-iam/shanoir-ng/users:ng_v2.4.1"
+    image: "ghcr.io/fli-iam/shanoir-ng/users:NG_v2.5.0"
     environment:
       - SHANOIR_PREFIX
       - SHANOIR_URL_SCHEME
@@ -121,7 +121,7 @@ services:
   #
   studies:
     container_name: "${SHANOIR_PREFIX}studies"
-    image: "ghcr.io/fli-iam/shanoir-ng/studies:ng_v2.4.1"
+    image: "ghcr.io/fli-iam/shanoir-ng/studies:NG_v2.5.0"
     environment:
       - SHANOIR_PREFIX
       - SHANOIR_URL_SCHEME
@@ -146,7 +146,7 @@ services:
   #
   import:
     container_name: "${SHANOIR_PREFIX}import"
-    image: "ghcr.io/fli-iam/shanoir-ng/import:ng_v2.4.1"
+    image: "ghcr.io/fli-iam/shanoir-ng/import:NG_v2.5.0"
     environment:
       - SHANOIR_PREFIX
       - SHANOIR_URL_SCHEME
@@ -174,7 +174,7 @@ services:
   #
   datasets:
     container_name: "${SHANOIR_PREFIX}datasets"
-    image: "ghcr.io/fli-iam/shanoir-ng/datasets:ng_v2.4.1"
+    image: "ghcr.io/fli-iam/shanoir-ng/datasets:NG_v2.5.0"
     environment:
       - SHANOIR_PREFIX
       - SHANOIR_URL_SCHEME
@@ -202,7 +202,7 @@ services:
 
   preclinical:
     container_name: "${SHANOIR_PREFIX}preclinical"
-    image: "ghcr.io/fli-iam/shanoir-ng/preclinical:ng_v2.4.1"
+    image: "ghcr.io/fli-iam/shanoir-ng/preclinical:NG_v2.5.0"
     environment:
       - SHANOIR_PREFIX
       - SHANOIR_URL_SCHEME
@@ -227,7 +227,7 @@ services:
   #
   nifti-conversion:
     container_name: "${SHANOIR_PREFIX}nifti-conversion"
-    image: "ghcr.io/fli-iam/shanoir-ng/nifti-conversion:ng_v2.4.1"
+    image: "ghcr.io/fli-iam/shanoir-ng/nifti-conversion:NG_v2.5.0"
     environment:
       - SHANOIR_PREFIX
       - SHANOIR_URL_SCHEME
@@ -248,7 +248,7 @@ services:
   #
   solr:
     container_name: "${SHANOIR_PREFIX}solr"
-    image: "ghcr.io/fli-iam/shanoir-ng/solr:ng_v2.4.1"
+    image: "ghcr.io/fli-iam/shanoir-ng/solr:NG_v2.5.0"
     environment:
       - SOLR_LOG_LEVEL=SEVERE
     volumes:
@@ -321,7 +321,7 @@ services:
   #
   nginx:
     container_name: shanoir-ng-nginx
-    image: "ghcr.io/fli-iam/shanoir-ng/nginx:ng_v2.4.1"
+    image: "ghcr.io/fli-iam/shanoir-ng/nginx:NG_v2.5.0"
     environment:
       - SHANOIR_PREFIX
       - SHANOIR_URL_SCHEME

docker-compose/database/db-changes/datasets/0055_add_sortingindex_solr.sql

@@ -0,0 +1 @@
+ALTER TABLE shanoir_metadata ADD COLUMN sorting_index int(11);

docker-compose/solr/core/schema.xml

@@ -461,6 +461,7 @@
   <field name="studyName" type="lowercase"/>
   <field name="subjectName" type="lowercase"/>
   <field name="subjectId" type="plong"/>
+  <field name="sortingIndex" type="pint"/>
   <field name="subjectType" type="lowercase"/>
   <field name="tags" type="strings"/>
   <field name="processed" type="boolean" indexed="true" stored="true" required="true" />

shanoir-ng-anonymization/src/main/java/org/shanoir/anonymization/anonymization/AnonymizationServiceImpl.java

@@ -66,14 +66,15 @@ public void anonymize(ArrayList<File> dicomFiles, String profile) throws Excepti
 		tagsToDeleteForManufacturer = AnonymizationRulesSingleton.getInstance().getTagsToDeleteForManufacturer();
 		// init here for multi-threading reasons
 		Map<String, String> seriesInstanceUIDs = new HashMap<>();
+		Map<String, String> frameOfReferenceUIDs = new HashMap<>();
 		Map<String, String> studyInstanceUIDs = new HashMap<>();
 		Map<String, String> studyIds = new HashMap<>();
 		LOG.debug("anonymize : totalAmount={}", totalAmount);
 		int current = 0;
 		for (int i = 0; i < dicomFiles.size(); ++i) {
 			final File file = dicomFiles.get(i);
 			// Perform the anonymization
-			performAnonymization(file, anonymizationMap, false, "", "", seriesInstanceUIDs, studyInstanceUIDs, studyIds);
+			performAnonymization(file, anonymizationMap, false, "", "", seriesInstanceUIDs, frameOfReferenceUIDs, studyInstanceUIDs, studyIds);
 			current++;
 			final int currentPercent = current * 100 / totalAmount;
 			LOG.debug("anonymize : anonymization current percent= {} %", currentPercent);
@@ -99,14 +100,15 @@ public void anonymizeForShanoir(ArrayList<File> dicomFiles, String profile, Stri
 
 		// init here for multi-threading reasons
 		Map<String, String> seriesInstanceUIDs = new HashMap<>();
+		Map<String, String> frameOfReferenceUIDs = new HashMap<>();
 		Map<String, String> studyInstanceUIDs = new HashMap<>();
 		Map<String, String> studyIds = new HashMap<>();
 		LOG.debug("anonymize : totalAmount={}", totalAmount);
 		int current = 0;
 		for (int i = 0; i < dicomFiles.size(); ++i) {
 			final File file = dicomFiles.get(i);
 			// Perform the anonymization
-			performAnonymization(file, anonymizationMap, true, patientName, patientID, seriesInstanceUIDs, studyInstanceUIDs, studyIds);
+			performAnonymization(file, anonymizationMap, true, patientName, patientID, seriesInstanceUIDs, frameOfReferenceUIDs, studyInstanceUIDs, studyIds);
 			current++;
 			final int currentPercent = current * 100 / totalAmount;
 			LOG.debug("anonymize : anonymization current percent= {} %", currentPercent);
@@ -156,7 +158,7 @@ private void anonymizePatientMetaData(Attributes attributes, String patientName,
 	 * @throws Exception
 	 */
 	public void performAnonymization(final File dicomFile, Map<String, String> anonymizationMap, boolean isShanoirAnonymization,
-			String patientName, String patientID, Map<String, String> seriesInstanceUIDs,
+			String patientName, String patientID, Map<String, String> seriesInstanceUIDs, Map<String, String> frameOfReferenceUIDs,
 			Map<String, String> studyInstanceUIDs, Map<String, String> studyIds) throws Exception {
 		DicomInputStream din = null;
 		DicomOutputStream dos = null;
@@ -213,18 +215,17 @@ public void performAnonymization(final File dicomFile, Map<String, String> anony
 					anonymizeTag(tagInt, action, datasetAttributes);
 				// even: public tags
 				} else if (anonymizationMap.containsKey(tagString)) {
-					if (tagInt == Tag.SOPInstanceUID) {
-						anonymizeSOPInstanceUID(tagInt, datasetAttributes, mediaStorageSOPInstanceUIDGenerated);
-					} else if (tagInt == Tag.SeriesInstanceUID) {
-						anonymizeSeriesInstanceUID(tagInt, datasetAttributes, seriesInstanceUIDs);
-					} else if (tagInt == Tag.StudyInstanceUID) {
-						anonymizeStudyInstanceUID(tagInt, datasetAttributes, studyInstanceUIDs);
-					} else if (tagInt == Tag.StudyID) {
-						anonymizeStudyId(tagInt, datasetAttributes, studyIds);
-					} else {
-						final String action = anonymizationMap.get(tagString);
-						anonymizeTag(tagInt, action, datasetAttributes);
-					}
+                                    switch (tagInt) {
+                                        case Tag.SOPInstanceUID -> anonymizeSOPInstanceUID(tagInt, datasetAttributes, mediaStorageSOPInstanceUIDGenerated);
+                                        case Tag.SeriesInstanceUID -> anonymizeUID(tagInt, datasetAttributes, seriesInstanceUIDs);
+                                        case Tag.FrameOfReferenceUID -> anonymizeUID(tagInt, datasetAttributes, frameOfReferenceUIDs);
+                                        case Tag.StudyInstanceUID -> anonymizeUID(tagInt, datasetAttributes, studyInstanceUIDs);
+                                        case Tag.StudyID -> anonymizeStudyId(tagInt, datasetAttributes, studyIds);
+                                        default -> {
+                                            final String action = anonymizationMap.get(tagString);
+                                            anonymizeTag(tagInt, action, datasetAttributes);
+                                        }
+                                    }
 				} else {
 					if (0x50000000 <= tagInt && tagInt <= 0x50FFFFFF) {
 						final String action = anonymizationMap.get(CURVE_DATA_TAGS);
@@ -350,46 +351,6 @@ private void anonymizeSOPInstanceUID(int tagInt, Attributes attributes, String m
 		anonymizeTagAccordingToVR(attributes, tagInt, mediaStorageSOPInstanceUID);
 	}
 
-	private void anonymizeSeriesInstanceUID(int tagInt, Attributes attributes, Map<String, String> seriesInstanceUIDs) {
-		String value;
-		if (seriesInstanceUIDs != null && seriesInstanceUIDs.size() != 0
-				&& seriesInstanceUIDs.get(attributes.getString(tagInt)) != null) {
-			value = seriesInstanceUIDs.get(attributes.getString(tagInt));
-		} else {
-			UIDGeneration generator = new UIDGeneration();
-			String newUID = null;
-			try {
-				newUID = generator.getNewUID();
-			} catch (Exception e) {
-				LOG.error(e.getMessage());
-			}
-			value = newUID;
-			seriesInstanceUIDs.put(attributes.getString(tagInt), value);
-		}
-		anonymizeTagAccordingToVR(attributes, tagInt, value);
-	}
-
-	private void anonymizeStudyInstanceUID(int tagInt, Attributes attributes, Map<String, String> studyInstanceUIDs) {
-		String value;
-		if (studyInstanceUIDs != null && studyInstanceUIDs.size() != 0
-				&& studyInstanceUIDs.get(attributes.getString(tagInt)) != null) {
-			value = studyInstanceUIDs.get(attributes.getString(tagInt));
-			LOG.debug("Existing StudyInstanceUID reused: {}", value);
-		} else {
-			UIDGeneration generator = new UIDGeneration();
-			String newUID = null;
-			try {
-				newUID = generator.getNewUID();
-			} catch (Exception e) {
-				LOG.error(e.getMessage());
-			}
-			value = newUID;
-			LOG.info("New StudyInstanceUID generated for DICOM study/exam: {}", newUID);
-			studyInstanceUIDs.put(attributes.getString(tagInt), value);
-		}
-		anonymizeTagAccordingToVR(attributes, tagInt, value);
-	}
-
 	private void anonymizeStudyId(int tagInt, Attributes attributes, Map<String, String> studyIds) {
 		String value;
 		if (studyIds != null && studyIds.size() != 0 && studyIds.get(attributes.getString(tagInt)) != null) {
@@ -523,4 +484,30 @@ else if (vr.equals(VR.AE) || vr.equals(VR.AS) || vr.equals(VR.CS) || vr.equals(V
 		// VR.OD = Other Double String
 	}
 
+	private void anonymizeUID(int tagInt, Attributes attributes, Map<String, String> UIDs) {
+		String value;
+		if (UIDs != null && UIDs.size() != 0
+				&& UIDs.get(attributes.getString(tagInt)) != null) {
+			value = UIDs.get(attributes.getString(tagInt));
+			// We log only concerning the studyInstanceUID
+			if(Tag.StudyInstanceUID == tagInt) {
+				LOG.debug("Existing StudyInstanceUID reused: {}", value);
+			}
+		} else {
+			UIDGeneration generator = new UIDGeneration();
+			String newUID = null;
+			try {
+				newUID = generator.getNewUID();
+			} catch (Exception e) {
+				LOG.error(e.getMessage());
+			}
+			value = newUID;
+			if(Tag.StudyInstanceUID == tagInt) {
+				LOG.info("New StudyInstanceUID generated for DICOM study/exam: {}", newUID);
+			}
+			UIDs.put(attributes.getString(tagInt), value);
+		}
+		anonymizeTagAccordingToVR(attributes, tagInt, value);
+	}
+
 }

shanoir-ng-datasets/pom.xml

@@ -149,6 +149,7 @@
 					<profiles>
 						<profile>${spring.active.profile}</profile>
 					</profiles>
+					<classifier>exec</classifier>
 				</configuration>
 				<executions>
 					<execution>
@@ -168,7 +169,7 @@
 						<phase>package</phase>
 						<configuration>
 							<target>
-								<copy file="target/${project.build.finalName}.jar"
+								<copy file="target/${project.build.finalName}-exec.jar"
 									tofile="${basedir}/../docker-compose/datasets/${project.artifactId}.jar" />
 							</target>
 						</configuration>

shanoir-ng-datasets/src/main/java/org/shanoir/ng/configuration/amqp/RabbitMQDatasetsService.java

@@ -312,21 +312,15 @@ public void createDatasetAcquisition(final String studyStr) {
 
 
 	/**
-         * Receives a shanoirEvent as a json object, concerning a subject deletion
-         * @param eventAsString the task as a json string.
-         */
-	@RabbitListener(bindings = @QueueBinding(
-			key = ShanoirEventType.DELETE_SUBJECT_EVENT,
-			value = @Queue(value = RabbitMQConfiguration.DELETE_SUBJECT_QUEUE, durable = "true"),
-			exchange = @Exchange(value = RabbitMQConfiguration.EVENTS_EXCHANGE, ignoreDeclarationExceptions = "true",
-			autoDelete = "false", durable = "true", type=ExchangeTypes.TOPIC)), containerFactory = "singleConsumerFactory"
-			)
+	 * Receives a shanoirEvent as a json object, concerning a subject deletion
+	 * @param subjectIdAsString a string of the subject's id
+	 */
+	@RabbitListener(queues = RabbitMQConfiguration.DELETE_SUBJECT_QUEUE, containerFactory = "singleConsumerFactory")
 	@Transactional
-	public void deleteSubject(String eventAsString) throws AmqpRejectAndDontRequeueException {
+	public void deleteSubject(String subjectIdAsString) throws AmqpRejectAndDontRequeueException {
 		SecurityContextUtil.initAuthenticationContext("ROLE_ADMIN");
 		try {
-			ShanoirEvent event = objectMapper.readValue(eventAsString, ShanoirEvent.class);
-			Long subjectId = Long.valueOf(event.getObjectId());
+			Long subjectId = Long.valueOf(subjectIdAsString);
 			Set<Long> studyIds = new HashSet<>();
 
 			// Inverse order to remove copied examination before its source (if copied)
@@ -477,7 +471,7 @@ public void copyDatasetsToStudy(final String data) {
 				Long dsCount = datasetRepository.countDatasetsBySourceIdAndStudyId(datasetParentId, studyId);
 				Dataset datasetParent = datasetService.findById(datasetParentId);
 
-				if (datasetParent.getSourceId() != null) {
+				if (datasetParent.getSource() != null) {
 					LOG.info("[CopyDatasets] Selected dataset is a copy, please pick the original dataset.");
 					countCopy++;
 				} else if (dsCount != 0) {
@@ -502,7 +496,8 @@ public void copyDatasetsToStudy(final String data) {
 			event.setStatus(ShanoirEvent.SUCCESS);
 			event.setProgress(1.0f);
 			eventService.publishEvent(event);
-			solrService.indexDatasets(newDatasets);
+			if (newDatasets.size() > 0)
+				solrService.indexDatasets(newDatasets);
 
 		} catch (Exception e) {
 			if (event != null) {