Merge pull request #116 in TELIMA/karnak from feat/MEP_20220221 to ma…

…ster * commit '25993e58830d703a9ae980d7c098265277c05cab': (70 commits) feat: - modify vesrion weasis-dicom-tools in order to fix "Go Away" exceptions - add in predestroy reset transfer in progress for destinations - handle 409 http exception in order to not rethrow exception = means file is already in the destination - set HTTP2 to HTTP1_1 feat: implement project key history => clean secret entity, remove unused column + add unit tests feat: implement project key history feat: implement project key history feat: modify docker-compose.yml new docker registry feat: modify docker-compose.yml new docker registry feat: modify docker-compose.yml new docker registry feat: modify docker-compose.yml new docker registry feat: remove escape character + add sequence transfer_status + set to 150000 history monitoring feat: add catch clauses in order to get the IOExceptions during transfer/transferOther for the monitoring and rethrow them fix: unit test because of renaming fwdDescription feat: add export functionality for monitoring view feat: downgrade liquibase to 4.3.5 because of liquibase/liquibase#2448 feat: add property in test application.yml feat: temporary deactivate feat: add automatic cleaning of monitoring history depending on a size limit fix forward node button save and delete destination feat: refresh multiple instances gateway setup feat: temporary deactivate feat: refresh multiple instances gateway setup ...
OsiriX-Foundation · Feb 21, 2022 · 4a25b1d · 4a25b1d
2 parents 69ab59e + 25993e5
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,37 @@
 # Changelog
 
+## [v0.9.9](https://github.com/OsiriX-Foundation/karnak/tree/v0.9.9) (2021-12-20)
+
+[Full Changelog](https://github.com/OsiriX-Foundation/karnak/compare/v0.9.8...v0.9.9)
+
+**Implemented enhancements:**
+
+- Update weasis-dicom-tools to 5.24.2 \(native lib to 4.5.3\) [\#177](https://github.com/OsiriX-Foundation/karnak/issues/177)
+- DeIdentification front: refactoring + behaviour activate/deactivate deidentification [\#174](https://github.com/OsiriX-Foundation/karnak/issues/174)
+- Notification Front: default values [\#172](https://github.com/OsiriX-Foundation/karnak/issues/172)
+- Karnak email address [\#159](https://github.com/OsiriX-Foundation/karnak/issues/159)
+- Change configuration when sending [\#31](https://github.com/OsiriX-Foundation/karnak/issues/31)
+
+## [v0.9.8](https://github.com/OsiriX-Foundation/karnak/tree/v0.9.8) (2021-08-26)
+
+[Full Changelog](https://github.com/OsiriX-Foundation/karnak/compare/v0.9.7...v0.9.8)
+
+**Implemented enhancements:**
+
+- Adjust clickable zone checkbox [\#169](https://github.com/OsiriX-Foundation/karnak/issues/169)
+- Add profile version in projects views [\#167](https://github.com/OsiriX-Foundation/karnak/issues/167)
+- Springboot/junit/liquibase versions upgrade  [\#165](https://github.com/OsiriX-Foundation/karnak/issues/165)
+- Enable/disable destination buttons \(save/delete\) when transfer is in progress  [\#163](https://github.com/OsiriX-Foundation/karnak/issues/163)
+- Destinations: loading spinner transfer activity [\#161](https://github.com/OsiriX-Foundation/karnak/issues/161)
+- Image transcoding with a specific transfer syntax [\#139](https://github.com/OsiriX-Foundation/karnak/issues/139)
+- Inject an external id provider [\#88](https://github.com/OsiriX-Foundation/karnak/issues/88)
+- Check that the expression does not corrupt the DICOM [\#74](https://github.com/OsiriX-Foundation/karnak/issues/74)
+- Improve the notification module UI [\#42](https://github.com/OsiriX-Foundation/karnak/issues/42)
+
+**Fixed bugs:**
+
+- Switching in the KHEOPS album cannot be applied with the KEEP action on the study UID and / or the serial UID [\#156](https://github.com/OsiriX-Foundation/karnak/issues/156)
+
 ## [v0.9.7](https://github.com/OsiriX-Foundation/karnak/tree/v0.9.7) (2021-06-11)
 
 [Full Changelog](https://github.com/OsiriX-Foundation/karnak/compare/v0.9.6...v0.9.7)

diff --git a/README.md b/README.md
@@ -9,11 +9,13 @@ output.
 For more information, see the
 online [Karnak user guide](https://osirix-foundation.github.io/karnak-documentation/)
 
+:warning: **Security**: Karnak is using Logback and is not affected by CVE-2021-44228. [CVE-2021-42550 has been fixed](https://github.com/OsiriX-Foundation/karnak/issues/180) since v0.9.9
+
 # Application Features
 
 ## Gateway
 
-- Allows to build mapping between a source and one or more destinations
+- Allows building mapping between a source and one or more destinations
 - Each destination can be DICOM or DICOMWeb
 - Filter the images providers by AETitle and/or hostname (ot ensure the authenticity of the source)
 
@@ -51,7 +53,7 @@ see [karnak-docker](https://github.com/OsiriX-Foundation/karnak-docker).
 - Enable Spring and Spring Boot for the project
 - Create a Spring Boot launcher from main of StartApplication.java
     - Working Directory must be the mvc directory
-    - In VM Options, add `-Djava.library.path="/tmp/dicom-opencv"`
+    - In VM Options, add `-Djava.library.path="/tmp/dicom-opencv"`. Note: the tmp folder must be adapted according to your system and `dicom-opencv` is mandatory as the last folder.
     - In Environment variables, add the following values. The following values work with our default
       configuration define with docker used for the development (see: "Configure locally
       Mainzelliste and Postgres database with docker-compose") :
@@ -78,20 +80,7 @@ see [karnak-docker](https://github.com/OsiriX-Foundation/karnak-docker).
             - `OIDC_CLIENT_ID=undefined`
             - `OIDC_CLIENT_SECRET=undefined`
             - `OIDC_ISSUER_URI=undefined`
-
-    Note: the tmp folder must be adapted according to your system and the dicom-opencv must the last folder.
-
-<!--
-## Debug in Eclipse - obsolete
-
- - Configure locally mainzelliste and Postgres database (see below)
- - From Eclipse Marketplace: install the latest Spring Tools
- - Create a Spring Boot App launcher from main of SartApplication.java
-    - Copy the KARNAK environment variables in docker/.env and paste into the Environment tab of the launcher    
-    - In the Arguments tab of the launcher, add in VM arguments: `-Djava.library.path="/tmp/dicom-opencv"`    
-    Note: the tmp folder must be adapted according to your system and the dicom-opencv must the last folder.
--->
-
+
 ## Configure locally Mainzelliste and Postgres database with docker-compose
 
 Minimum docker-compose version: **1.22**
@@ -117,15 +106,15 @@ Go on the root folder and launch the following command:
 * Full independent build: `docker build -t local/karnak:latest -f Dockerfile .`
 * Build from compile package:
     * `mvn clean install -P production`
-    * `docker build -t local/karnak:latest -f mvc/src/main/docker/Dockerfile .`
+    * `docker build -t local/karnak:latest -f src/main/docker/Dockerfile .`
 
 ## Run image from Docker Hub
 
 See [karnak-docker](https://github.com/OsiriX-Foundation/karnak-docker)
 
 ## Docker environment variables
 
-See [environment variables](https://github.com/OsiriX-Foundation/karnak-docker#environment-variables)
+See [all the environment variables](https://github.com/OsiriX-Foundation/karnak-docker#environment-variables)
 
 # Architecture
 

diff --git a/frontend/styles/empty.css b/frontend/styles/empty.css
diff --git a/pom.xml b/pom.xml
@@ -23,30 +23,35 @@
 
   <!-- Properties -->
   <properties>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
     <enforcer.jdk-version>[${java.version},)</enforcer.jdk-version>
     <enforcer.maven-version>[3.2.0,)</enforcer.maven-version>
-    <java.version>14</java.version>
+    <java.version>15</java.version>
+    <springframework.version>2.6.1</springframework.version>
     <javax.el.version>3.0.0</javax.el.version>
     <javax.mail.version>1.6.2</javax.mail.version>
+    <vaadin.version>21.0.9</vaadin.version>
+    <weasis-dicom-tools.version>5.25.1.1-IMG-RELEASE</weasis-dicom-tools.version>
+    <weasis.opencv.native.version>4.5.5-dcm</weasis.opencv.native.version>
+    <springdoc.version>1.6.0</springdoc.version>
+    <mockito.version>4.2.0</mockito.version>
+    <h2.version>1.4.200</h2.version>
+    <hug.springcloud.version>2.3.11-HSR11-1.0</hug.springcloud.version>
+    <jacoco-maven-plugin.version>0.8.7</jacoco-maven-plugin.version>
+    <junit.jupiter.version>5.8.2</junit.jupiter.version>
     <maven-surefire-plugin.version>3.0.0-M5</maven-surefire-plugin.version>
-    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-    <springframework.version>2.4.9</springframework.version>
-    <vaadin.version>19.0.6</vaadin.version>
-    <weasis-dicom-tools.version>5.23.3-IMG-RELEASE</weasis-dicom-tools.version>
-    <weasis.opencv.native.version>4.5.1-dcm</weasis.opencv.native.version>
-    <jacoco-maven-plugin.version>0.8.6</jacoco-maven-plugin.version>
     <sonar-maven-plugin.version>3.8.0.2131</sonar-maven-plugin.version>
     <sonar.java.source>${java.version}</sonar.java.source>
     <sonar.java.target>${java.version}</sonar.java.target>
     <sonar.projectKey>karnak</sonar.projectKey>
     <sonar.coverage.jacoco.xmlReportPaths>${project.basedir}/target/site/jacoco/jacoco.xml</sonar.coverage.jacoco.xmlReportPaths>
     <sonar.core.codeCoveragePlugin>jacoco</sonar.core.codeCoveragePlugin>
-    <h2.version>1.4.200</h2.version>
-    <junit.jupiter.version>5.7.2</junit.jupiter.version>
-    <mockito.version>3.9.0</mockito.version>
-    <springdoc.version>1.5.6</springdoc.version>
-    <hug.springcloud.version>2.3.11-HSR11-1.0</hug.springcloud.version>
+    <org.json.version>20211205</org.json.version>
+    <logback.version>1.2.9</logback.version>
+    <hazelcast.version>5.0.2</hazelcast.version>
+    <liquibase.version>4.3.5</liquibase.version>
+    <opencsv.version>5.5.2</opencsv.version>
   </properties>
 
   <!-- Distribution management for releases/snapshots -->
@@ -116,16 +121,16 @@
           </execution>
         </executions>
         <groupId>org.apache.maven.plugins</groupId>
-        <version>3.0.0-M3</version>
+        <version>3.0.0</version>
       </plugin>
       <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-compiler-plugin</artifactId>
+        <version>3.8.1</version>
         <configuration>
           <source>${java.version}</source>
           <target>${java.version}</target>
         </configuration>
-        <groupId>org.apache.maven.plugins</groupId>
-        <version>3.8.1</version>
       </plugin>
       <plugin>
         <groupId>org.jacoco</groupId>
@@ -187,6 +192,46 @@
               <type>so</type>
               <version>${weasis.opencv.native.version}</version>
             </artifactItem>
+            <artifactItem>
+              <artifactId>libopencv_java</artifactId>
+              <classifier>linux-aarch64</classifier>
+              <destFileName>libopencv_java.so</destFileName>
+              <groupId>org.weasis.thirdparty.org.opencv</groupId>
+              <outputDirectory>${project.build.directory}/native-lib/lib/linux-aarch64
+              </outputDirectory>
+              <type>so</type>
+              <version>${weasis.opencv.native.version}</version>
+            </artifactItem>
+            <artifactItem>
+              <artifactId>libopencv_java</artifactId>
+              <classifier>linux-armv7a</classifier>
+              <destFileName>libopencv_java.so</destFileName>
+              <groupId>org.weasis.thirdparty.org.opencv</groupId>
+              <outputDirectory>${project.build.directory}/native-lib/lib/linux-armv7a
+              </outputDirectory>
+              <type>so</type>
+              <version>${weasis.opencv.native.version}</version>
+            </artifactItem>
+            <artifactItem>
+              <artifactId>libopencv_java</artifactId>
+              <classifier>macosx-x86-64</classifier>
+              <destFileName>libopencv_java.dylib</destFileName>
+              <groupId>org.weasis.thirdparty.org.opencv</groupId>
+              <outputDirectory>${project.build.directory}/native-lib/lib/macosx-x86-64
+              </outputDirectory>
+              <type>dylib</type>
+              <version>${weasis.opencv.native.version}</version>
+            </artifactItem>
+            <artifactItem>
+              <artifactId>opencv_java</artifactId>
+              <classifier>windows-x86-64</classifier>
+              <destFileName>opencv_java.dll</destFileName>
+              <groupId>org.weasis.thirdparty.org.opencv</groupId>
+              <outputDirectory>${project.build.directory}/native-lib/lib/windows-x86-64
+              </outputDirectory>
+              <type>dll</type>
+              <version>${weasis.opencv.native.version}</version>
+            </artifactItem>
           </artifactItems>
           <outputDirectory>${project.build.directory}</outputDirectory>
         </configuration>
@@ -200,7 +245,7 @@
           </execution>
         </executions>
         <groupId>org.apache.maven.plugins</groupId>
-        <version>3.1.1</version>
+        <version>3.2.0</version>
       </plugin>
       <plugin>
         <artifactId>spring-boot-maven-plugin</artifactId>
@@ -242,7 +287,7 @@
       <plugin>
         <groupId>com.diffplug.spotless</groupId>
         <artifactId>spotless-maven-plugin</artifactId>
-        <version>2.6.1</version>
+        <version>2.17.7</version>
         <configuration>
           <!-- define a language-specific format -->
           <java>
@@ -320,6 +365,14 @@
       <artifactId>spring-boot-starter-web</artifactId>
       <groupId>org.springframework.boot</groupId>
     </dependency>
+    <dependency>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot-starter-mail</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot-starter-thymeleaf</artifactId>
+    </dependency>
 
     <dependency>
       <artifactId>cache-api</artifactId>
@@ -328,21 +381,27 @@
     </dependency>
 
     <dependency>
-      <artifactId>hazelcast</artifactId>
+      <artifactId>hazelcast-spring</artifactId>
       <groupId>com.hazelcast</groupId>
-      <version>4.1</version>
+      <version>${hazelcast.version}</version>
     </dependency>
 
+    <!--    <dependency>-->
+    <!--      <artifactId>hazelcast</artifactId>-->
+    <!--      <groupId>com.hazelcast</groupId>-->
+    <!--      <version>4.1</version>-->
+    <!--    </dependency>-->
+
     <dependency>
       <artifactId>liquibase-maven-plugin</artifactId>
       <groupId>org.liquibase</groupId>
-      <version>4.3.3</version>
+      <version>${liquibase.version}</version>
     </dependency>
 
     <dependency>
       <artifactId>json</artifactId>
       <groupId>org.json</groupId>
-      <version>20180813</version>
+      <version>${org.json.version}</version>
     </dependency>
 
     <dependency>
@@ -351,6 +410,12 @@
       <version>2.8.6</version>
     </dependency>
 
+    <dependency>
+      <groupId>com.opencsv</groupId>
+      <artifactId>opencsv</artifactId>
+      <version>${opencsv.version}</version>
+    </dependency>
+
     <dependency>
       <artifactId>weasis-dicom-tools</artifactId>
       <exclusions>
@@ -369,7 +434,6 @@
       </exclusions>
       <groupId>org.weasis</groupId>
       <version>${weasis-dicom-tools.version}</version>
-
     </dependency>
     <dependency>
       <artifactId>javax.mail</artifactId>
@@ -383,7 +447,6 @@
       <groupId>org.springframework.boot</groupId>
     </dependency>
 
-
     <!-- Vaadin Spring -->
     <dependency>
       <artifactId>vaadin-spring-boot-starter</artifactId>
@@ -490,12 +553,12 @@
     <dependency>
       <artifactId>vaadin-checkbox-flow</artifactId>
       <groupId>com.vaadin</groupId>
-      <version>3.1.0</version>
+      <version>${vaadin.version}</version>
     </dependency>
     <dependency>
       <artifactId>togglebutton</artifactId>
       <groupId>com.vaadin.componentfactory</groupId>
-      <version>1.0.0</version>
+      <version>1.0.1</version>
     </dependency>
     <dependency>
       <groupId>org.vaadin.klaudeta</groupId>
@@ -507,6 +570,7 @@
       <artifactId>validation-api</artifactId>
       <groupId>javax.validation</groupId>
     </dependency>
+
     <dependency>
       <artifactId>jul-to-slf4j</artifactId>
       <groupId>org.slf4j</groupId>
@@ -515,6 +579,7 @@
     <dependency>
       <artifactId>logback-classic</artifactId>
       <groupId>ch.qos.logback</groupId>
+      <version>${logback.version}</version>
     </dependency>
 
     <dependency>
@@ -584,6 +649,12 @@
       <artifactId>springdoc-openapi-ui</artifactId>
       <version>${springdoc.version}</version>
     </dependency>
+
+    <dependency>
+      <groupId>org.vaadin.artur</groupId>
+      <artifactId>spring-data-provider</artifactId>
+      <version>2.1.0</version>
+    </dependency>
   </dependencies>
 
   <!-- Dependency Management -->

diff --git a/src/main/java/org/karnak/StartApplication.java b/src/main/java/org/karnak/StartApplication.java
@@ -23,13 +23,15 @@
 import org.springframework.boot.autoconfigure.web.servlet.error.ErrorMvcAutoConfiguration;
 import org.springframework.boot.builder.SpringApplicationBuilder;
 import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
+import org.springframework.scheduling.annotation.EnableAsync;
 import org.springframework.scheduling.annotation.EnableScheduling;
 
 @SpringBootApplication(exclude = ErrorMvcAutoConfiguration.class)
 @EntityScan("org.karnak.backend.data.entity")
 @EnableJpaRepositories("org.karnak.backend.data.repo")
 @EnableVaadin(value = "org.karnak")
 @EnableScheduling
+@EnableAsync
 public class StartApplication implements CommandLineRunner {
 
   private static final Logger log = LoggerFactory.getLogger(StartApplication.class);

diff --git a/src/main/java/org/karnak/backend/api/KheopsApi.java b/src/main/java/org/karnak/backend/api/KheopsApi.java
@@ -35,7 +35,7 @@ public class KheopsApi {
   public KheopsApi() {
     httpClient =
         HttpClient.newBuilder() // one instance, reuse
-            .version(HttpClient.Version.HTTP_2)
+            .version(HttpClient.Version.HTTP_1_1)
             .build();
   }
 

diff --git a/src/main/java/org/karnak/backend/api/PseudonymApi.java b/src/main/java/org/karnak/backend/api/PseudonymApi.java
@@ -49,7 +49,7 @@ public class PseudonymApi {
 
   private final HttpClient httpClient =
       HttpClient.newBuilder() // one instance, reuse
-          .version(HttpClient.Version.HTTP_2)
+          .version(HttpClient.Version.HTTP_1_1)
           .build();
 
   private String sessionId;