Merge branch 'develop' into angular-17-to-18-novite

fli-iam · Nov 22, 2024 · 1b837b5 · 1b837b5
2 parents fd7d5e0 + 33018fa
commit 1b837b5
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Showing 111 changed files with 1,438 additions and 660 deletions.
diff --git a/bootstrap.sh b/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
diff --git a/docker-compose.yml b/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

diff --git a/shanoir-ng-datasets/pom.xml b/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>

diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/BidsDataset.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/BidsDataset.java
@@ -1,15 +1,15 @@
 package org.shanoir.ng.dataset.modality;
 
 import jakarta.persistence.Entity;
+
 import org.shanoir.ng.dataset.model.Dataset;
+import org.shanoir.ng.dataset.model.DatasetType;
 
 @Entity
 public class BidsDataset extends Dataset {
 
 	private static final long serialVersionUID = 7476089535424633518L;
-
-	public static final String datasetType = "BIDS";
-
+
 	/** BIDS data type. */
 	private String bidsDataType;
 
@@ -23,8 +23,8 @@ public BidsDataset(Dataset other) {
 	}
 
 	@Override
-	public String getType() {
-		return datasetType;
+	public DatasetType getType() {
+		return DatasetType.BIDS;
 	}
 
 	public String getBidsDataType() {

diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/CalibrationDataset.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/CalibrationDataset.java
@@ -15,7 +15,9 @@
 package org.shanoir.ng.dataset.modality;
 
 import jakarta.persistence.Entity;
+
 import org.shanoir.ng.dataset.model.Dataset;
+import org.shanoir.ng.dataset.model.DatasetType;
 
 /**
  * Calibration dataset.
@@ -26,8 +28,6 @@
 @Entity
 public class CalibrationDataset extends Dataset {
 
-	public static final String datasetType = "Calibration";
-
 	/**
 	 * UID
 	 */
@@ -67,8 +67,8 @@ public void setCalibrationDatasetType(CalibrationDatasetType calibrationDatasetT
 	}
 
 	@Override
-	public String getType() {
-		return "Calibration";
+	public DatasetType getType() {
+		return DatasetType.Calibration;
 	}
 
 }
diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/CtDataset.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/CtDataset.java
@@ -15,7 +15,9 @@
 package org.shanoir.ng.dataset.modality;
 
 import jakarta.persistence.Entity;
+
 import org.shanoir.ng.dataset.model.Dataset;
+import org.shanoir.ng.dataset.model.DatasetType;
 
 /**
  * CT dataset.
@@ -26,8 +28,6 @@
 @Entity
 public class CtDataset extends Dataset {
 
-	public static final String datasetType = "Ct";
-
 //	private String pixelData;
 //	
 //	private String patientExamination;
@@ -49,8 +49,8 @@ public CtDataset(Dataset other) {
 	private static final long serialVersionUID = -1035190618348031062L;
 
 	@Override
-	public String getType() {
-		return "Ct";
+	public DatasetType getType() {
+		return DatasetType.Ct;
 	}
 
 }
diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/EegDataset.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/EegDataset.java
@@ -17,6 +17,7 @@
 import jakarta.persistence.CascadeType;
 import jakarta.persistence.Entity;
 import jakarta.persistence.OneToMany;
+
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 import org.shanoir.ng.dataset.model.Dataset;
@@ -27,6 +28,8 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import org.shanoir.ng.dataset.model.DatasetType;
+
 /**
  * EEG dataset.
  * 
@@ -35,17 +38,15 @@
  */
 @Entity
 public class EegDataset extends Dataset {
-
-	public static final String datasetType = "Eeg";
-
+
 	/**
 	 * UID
 	 */
 	private static final long serialVersionUID = -7618433089837302003L;
 
 	@Override
-	public String getType() {
-		return "Eeg";
+	public DatasetType getType() {
+		return DatasetType.Eeg;
 	}
 
 	private float samplingFrequency;

diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/GenericDataset.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/GenericDataset.java
@@ -1,15 +1,13 @@
 package org.shanoir.ng.dataset.modality;
 
-import jakarta.persistence.Entity;
-import net.bytebuddy.description.type.TypeList;
 import org.shanoir.ng.dataset.model.Dataset;
+import org.shanoir.ng.dataset.model.DatasetType;
+
+import jakarta.persistence.Entity;
 
 @Entity
 public class GenericDataset extends Dataset {
 
-	public static final String datasetType = "Generic";
-
-
 	/**
 	 * Serial version UUID
 	 */
@@ -24,8 +22,8 @@ public GenericDataset(Dataset other) {
 	}
 
 	@Override
-	public String getType() {
-		return datasetType;
+	public DatasetType getType() {
+		return DatasetType.Generic;
 	}
 
 }
diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/MeasurementDataset.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/MeasurementDataset.java
@@ -1,24 +1,24 @@
 package org.shanoir.ng.dataset.modality;
 
 import jakarta.persistence.Entity;
+
 import org.shanoir.ng.dataset.model.Dataset;
+import org.shanoir.ng.dataset.model.DatasetType;
 
 @Entity
 public class MeasurementDataset extends Dataset {
 
 	private static final long serialVersionUID = 7476089535424634218L;
 
-	public static final String datasetType = "Measurement";
-
 	public MeasurementDataset() {}
 
 	public MeasurementDataset(Dataset other) {
 		super(other);
 	}
 
 	@Override
-	public String getType() {
-		return datasetType;
+	public DatasetType getType() {
+		return DatasetType.Measurement;
 	}
 
 }
diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/MegDataset.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/MegDataset.java
@@ -14,8 +14,10 @@
 
 package org.shanoir.ng.dataset.modality;
 
-import jakarta.persistence.Entity;
 import org.shanoir.ng.dataset.model.Dataset;
+import org.shanoir.ng.dataset.model.DatasetType;
+
+import jakarta.persistence.Entity;
 
 /**
  * MEG dataset.
@@ -26,8 +28,6 @@
 @Entity
 public class MegDataset extends Dataset {
 
-	public static final String datasetType = "Meg";
-
 	/**
 	 * UID
 	 */
@@ -40,8 +40,8 @@ public MegDataset(Dataset other) {
 	}
 
 	@Override
-	public String getType() {
-		return "Meg";
+	public DatasetType getType() {
+		return DatasetType.Meg;
 	}
 
 }