Upgrade to Gradle 7 and bump dependencies. (#173)

* Upgrade to Gradle 7 and bump dependencies.

* update cloudbuild.yaml

* integration test gradle

* Get deid-redactor package working and remove some unnecessary deps/tags

cloudbuild.yaml

@@ -7,4 +7,4 @@ steps:
   - build
 
 substitutions:
-  _GRADLE_IMAGE: 'gradle:5.6-jdk11'
+  _GRADLE_IMAGE: 'gradle:7-jdk11'

dicom_util/build.gradle

@@ -29,38 +29,37 @@ compileJava {
 repositories {
     mavenCentral()
     maven { url 'https://jitpack.io' }
-    maven { url 'http://www.dcm4che.org/maven2/' }
+    maven { url 'https://www.dcm4che.org/maven2/' }
 }
 
 dependencies {
-    compile platform('com.google.cloud:libraries-bom:5.1.0')
-    compile platform('com.google.cloud:google-cloud-shared-dependencies:0.1.0')
-    compile "com.google.api-client:google-api-client"
-    compile "com.google.inject:guice:4.1.0"
+    implementation platform('com.google.cloud:libraries-bom:26.43.0')
+    implementation "com.google.api-client:google-api-client"
+    implementation "com.google.inject:guice:4.1.0"
 
-    compile "org.json:json:20170516"
-    compile "junit:junit:4.12"
-    compile "org.junit.jupiter:junit-jupiter-engine:5.0.0"
-    compile "org.dcm4che:dcm4che-core:5.31.2"
-    compile "org.dcm4che:dcm4che-net:5.31.2"
+    implementation "org.json:json:20240303"
+    testImplementation "junit:junit:4.12"
+    testImplementation "org.junit.jupiter:junit-jupiter-engine:5.0.0"
+    implementation "org.dcm4che:dcm4che-core:5.31.2"
+    implementation "org.dcm4che:dcm4che-net:5.31.2"
 
-    compile 'com.google.auth:google-auth-library-oauth2-http:0.17.2'
-    compile group: 'org.eclipse.jetty.http2', name: 'http2-client', version: '9.4.20.v20190813'
-    compile group: 'org.eclipse.jetty', name: 'jetty-alpn-java-client', version: '9.4.20.v20190813'
+    implementation 'com.google.auth:google-auth-library-oauth2-http'
+    implementation 'org.eclipse.jetty.http2:http2-client:9.4.55.v20240627'
+    implementation 'org.eclipse.jetty:jetty-alpn-java-client:9.4.55.v20240627'
 
-    compile group: 'org.slf4j', name: 'slf4j-reload4j', version: '2.0.12'
-    compile group: 'org.apache.logging.log4j', name: 'log4j-api', version: '2.23.0'
-    compile group: 'org.apache.logging.log4j', name: 'log4j-core', version: '2.23.0'
+    implementation group: 'org.slf4j', name: 'slf4j-reload4j', version: '2.0.12'
+    implementation group: 'org.apache.logging.log4j', name: 'log4j-api', version: '2.23.0'
+    implementation group: 'org.apache.logging.log4j', name: 'log4j-core', version: '2.23.0'
 
-    testCompile "com.google.truth:truth:1.0"
+    testImplementation "com.google.truth:truth:1.0"
 }
 
 configurations {
     testArtifacts
 }
 
 task testJar (type: Jar) {
-    baseName = "${project.name}-test"
+    archiveBaseName = "${project.name}-test"
     from sourceSets.test.output
 }
 

export/build.gradle

@@ -26,7 +26,7 @@ buildscript {
 plugins {
     id 'java'
     id 'application'
-    id 'com.github.hierynomus.license' version '0.14.0'
+    id 'com.github.hierynomus.license' version '0.16.1'
 }
 
 mainClassName = "com.google.cloud.healthcare.imaging.dicomadapter.ExportAdapter"
@@ -48,27 +48,27 @@ compileJava {
 repositories {
     mavenCentral()
     maven { url 'https://jitpack.io' }
-    maven { url 'http://www.dcm4che.org/maven2/' }
+    maven { url 'https://www.dcm4che.org/maven2/' }
 }
 
 dependencies {
-    compile platform('com.google.cloud:libraries-bom:5.1.0')
-    compile platform('com.google.cloud:google-cloud-shared-dependencies:0.1.0')
-    compile 'com.google.cloud:google-cloud-pubsub'
-    compile 'com.google.guava:guava:28.1-jre'
-    compile 'com.google.auth:google-auth-library-oauth2-http'
-    compile "com.google.api-client:google-api-client"
-
-    compile "com.beust:jcommander:1.72"
-    compile "org.dcm4che:dcm4che-core:5.31.2"
-    compile "org.dcm4che:dcm4che-net:5.31.2"
-    compile project(":dicom_util")
-    compile project(":util")
-
-    testCompile "com.google.truth:truth:1.0"
-    testCompile "junit:junit:4.2"
-    testCompile project(path: ":util", configuration: 'testArtifacts')
-    testCompile project(path: ":dicom_util", configuration: 'testArtifacts')
+    implementation platform('com.google.cloud:libraries-bom:26.43.0')
+    implementation 'com.google.cloud:google-cloud-pubsub'
+    implementation 'com.google.guava:guava:33.1.0-jre'
+    implementation 'com.google.auth:google-auth-library-oauth2-http'
+    implementation "com.google.api-client:google-api-client"
+    implementation "org.json:json:20240303"
+
+    implementation "com.beust:jcommander:1.72"
+    implementation "org.dcm4che:dcm4che-core:5.31.2"
+    implementation "org.dcm4che:dcm4che-net:5.31.2"
+    implementation project(":dicom_util")
+    implementation project(":util")
+
+    testImplementation "com.google.truth:truth:1.0"
+    testImplementation "junit:junit:4.2"
+    testImplementation project(path: ":util", configuration: 'testArtifacts')
+    testImplementation project(path: ":dicom_util", configuration: 'testArtifacts')
 }
 
 apply plugin: 'com.bmuschko.docker-java-application'
@@ -84,7 +84,7 @@ docker {
 task downloadOpensSourceLicenses(type: nl.javadude.gradle.plugins.license.DownloadLicenses) {
   // These libraries have their license in a non-standard location.
   licenses = specialCaseLicenses
-  dependencyConfiguration = 'compile'
+  dependencyConfiguration = 'runtimeClasspath'
   doLast {
     downloadLicensesText(buildDir)
   }
@@ -93,7 +93,7 @@ task downloadOpensSourceLicenses(type: nl.javadude.gradle.plugins.license.Downlo
 // Download full source jar for all dependencies.
 // https://stackoverflow.com/questions/16154458/how-to-copy-all-source-jars-using-gradle
 task downloadSourceJars( type: Copy ) {
-  def sources = configurations.runtime.resolvedConfiguration.resolvedArtifacts.collect { artifact ->
+  def sources = configurations.runtimeClasspath.resolvedConfiguration.resolvedArtifacts.collect { artifact ->
     project.dependencies.create( [
       group: artifact.moduleVersion.id.group,
       name: artifact.moduleVersion.id.name,

import/build.gradle

@@ -26,7 +26,7 @@ buildscript {
 plugins {
     id 'java'
     id 'application'
-    id 'com.github.hierynomus.license' version '0.14.0'
+    id 'com.github.hierynomus.license' version '0.16.1'
 }
 
 def transcoderJvmArgs = ["-Dorg.dcm4che3.imageio.codec.ImageReaderFactory=com/google/cloud/healthcare/imaging/dicomadapter/transcoder/ImageReaderFactory.properties",
@@ -55,38 +55,40 @@ compileJava {
 
 repositories {
     mavenCentral()
-    maven { url 'http://www.dcm4che.org/maven2/' }
+    maven { url 'https://www.dcm4che.org/maven2/' }
     maven { url 'https://jitpack.io' }
 }
 
 dependencies {
-    compile platform('com.google.cloud:libraries-bom:5.1.0')
-    compile platform('com.google.cloud:google-cloud-shared-dependencies:0.1.0')
-    compile 'com.google.guava:guava:28.1-jre'
-    compile 'com.google.auth:google-auth-library-oauth2-http'
-    compile "com.google.api-client:google-api-client"
+    implementation platform('com.google.cloud:libraries-bom:26.43.0')
+    implementation 'com.google.guava:guava:33.1.0-jre'
+    implementation 'com.google.auth:google-auth-library-oauth2-http'
+    implementation "com.google.api-client:google-api-client"
+    implementation "org.json:json:20240303"
 
-    compile "com.beust:jcommander:1.72"
-    compile "org.dcm4che:dcm4che-core:5.31.2"
-    compile "org.dcm4che:dcm4che-net:5.31.2"
+    implementation "com.beust:jcommander:1.72"
+    implementation "org.dcm4che:dcm4che-core:5.31.2"
+    implementation "org.dcm4che:dcm4che-net:5.31.2"
 
-    compile "org.dcm4che:dcm4che-imageio:5.31.2"
-    runtime "org.dcm4che:dcm4che-imageio-rle:5.31.2"
-    compile project(":jai-imageio-jpeg2000")
+    implementation "org.dcm4che:dcm4che-imageio:5.31.2"
+    runtimeOnly "org.dcm4che:dcm4che-imageio-rle:5.31.2"
+    implementation project(":jai-imageio-jpeg2000")
 
-    compile project(":dicom_util")
-    compile project(":util")
+    implementation project(":dicom_util")
+    implementation project(":util")
 
-    compile project(":deid-redactor")
+    implementation project(":deid-redactor")
 
-    compile "com.google.cloud:google-cloud-storage:1.98.0"
-    compile 'com.google.cloud:google-cloud-nio:0.116.0-alpha'
+    implementation "com.google.cloud:google-cloud-storage"
+    implementation 'com.google.cloud:google-cloud-nio'
 
-    testCompile "com.google.truth:truth:1.0"
-    testCompile "org.mockito:mockito-core:3.+"
-    testCompile "junit:junit:4.2"
-    testCompile project(path: ":dicom_util", configuration: 'testArtifacts')
-    testCompile project(path: ":util", configuration: 'testArtifacts')
+    testImplementation "com.google.truth:truth:1.0"
+    testImplementation "org.mockito:mockito-core:3.+"
+    testImplementation "junit:junit:4.2"
+    testImplementation project(path: ":dicom_util", configuration: 'testArtifacts')
+    testImplementation project(path: ":util", configuration: 'testArtifacts')
+
+    testImplementation 'org.eclipse.jetty:jetty-http:9.4.55.v20240627'
 }
 
 apply plugin: 'com.bmuschko.docker-java-application'
@@ -103,7 +105,7 @@ docker {
 task downloadOpensSourceLicenses(type: nl.javadude.gradle.plugins.license.DownloadLicenses) {
   // These libraries have their license in a non-standard location.
   licenses = specialCaseLicenses
-  dependencyConfiguration = 'compile'
+  dependencyConfiguration = 'runtimeClasspath'
   doLast {
     downloadLicensesText(buildDir)
   }
@@ -112,7 +114,7 @@ task downloadOpensSourceLicenses(type: nl.javadude.gradle.plugins.license.Downlo
 // Download full source jar for all dependencies.
 // https://stackoverflow.com/questions/16154458/how-to-copy-all-source-jars-using-gradle
 task downloadSourceJars( type: Copy ) {
-  def sources = configurations.runtime.resolvedConfiguration.resolvedArtifacts.collect { artifact ->
+  def sources = configurations.runtimeClasspath.resolvedConfiguration.resolvedArtifacts.collect { artifact ->
     project.dependencies.create( [
       group: artifact.moduleVersion.id.group,
       name: artifact.moduleVersion.id.name,

integration_test/cloudbuild-integration-test.yaml

@@ -1,6 +1,6 @@
 steps:
 # basic funtionality test
-- name: 'gradle:6.9.4-jdk11-focal'
+- name: 'gradle:7-jdk11-focal'
   id: basic-test
   args:
     - python3
@@ -10,21 +10,21 @@ steps:
     - 'IMAGEPROJECT=${_IMAGEPROJECT}'
 
 # http2 test
-- name: 'gradle:6.9.4-jdk11-focal'
+- name: 'gradle:7-jdk11-focal'
   id: http2-test
   args:
     - python3
     - ./integration_test/step_2.py
 
 # local backup test
-- name: 'gradle:6.9.4-jdk11-focal'
+- name: 'gradle:7-jdk11-focal'
   id: local-backup-test
   args:
     - python3
     - ./integration_test/step_3.py
 
 # gcs backup test
-- name: 'gradle:6.9.4-jdk11-focal'
+- name: 'gradle:7-jdk11-focal'
   id: gcs-backup-test
   args:
     - python3
@@ -51,4 +51,4 @@ substitutions:
 availableSecrets:
   secretManager:
   - versionName: projects/$PROJECT_ID/secrets/GH_TOKEN/versions/latest
-    env: GH_TOKEN
+    env: GH_TOKEN

third_party/deid-redactor/examples/tag_remover/build.gradle

@@ -23,7 +23,7 @@ repositories {
     google()
     jcenter()
     mavenCentral()
-    maven { url 'http://www.dcm4che.org/maven2/' }
+    maven { url 'https://www.dcm4che.org/maven2/' }
   }
 
 buildDir = "/tmp/gradle_build/redactor/examples"
@@ -33,7 +33,7 @@ dependencies {
   implementation 'commons-cli:commons-cli:1.4'
 
   testImplementation 'junit:junit:4.12'
-  testImplementation 'com.google.truth:truth:0.39'
+  testImplementation 'com.google.truth:truth:1.4.4'
   testImplementation 'commons-io:commons-io:2.6'
 }
 

third_party/deid-redactor/lib/build.gradle

@@ -16,17 +16,17 @@
 
 plugins {
     id 'java-library'
-    id 'com.google.protobuf' version "0.8.13"
-    id 'maven'
+    id 'com.google.protobuf' version "0.9.4"
 }
 
 repositories {
     google()
     jcenter()
     mavenCentral()
-    maven { url 'http://www.dcm4che.org/maven2/' }
+    maven { url 'https://www.dcm4che.org/maven2/' }
 }
 
+
 group = "com.google.cloud.healthcare.deid"
 archivesBaseName = "redactor"
 version = "0.1.0"
@@ -37,18 +37,18 @@ dependencies {
     implementation "org.dcm4che:dcm4che-core:3.3.8"
     implementation "org.dcm4che:dcm4che-imageio:3.3.8"
 
-    protobuf 'com.google.protobuf:protobuf-java:3.7.1'
+    implementation 'com.google.protobuf:protobuf-java:3.25.4'
 
-    api "com.google.api.grpc:proto-google-common-protos:1.16.0"
+    api "com.google.api.grpc:proto-google-common-protos:2.42.0"
 
     testImplementation 'junit:junit:4.12'
-    testImplementation 'com.google.truth:truth:0.39'
+    testImplementation 'com.google.truth:truth:1.4.4'
     testImplementation 'commons-io:commons-io:2.6'
 }
 
 protobuf {
   generatedFilesBaseDir = "/tmp/gradle_build/redactor/gen"
   protoc {
-    artifact = "com.google.protobuf:protoc:3.7.1";
+    artifact = "com.google.protobuf:protoc:3.25.4";
   }
 }

third_party/jai-imageio-jpeg2000/build.gradle

@@ -5,24 +5,24 @@
 plugins {
     id 'java'
     id 'maven-publish'
-    id 'com.github.hierynomus.license' version '0.14.0'
+    id 'com.github.hierynomus.license' version '0.16.1'
 }
 
 repositories {
     mavenCentral()
     mavenLocal()
     maven {
-        url = 'http://dl.bintray.com/jai-imageio/maven/'
+        url = 'https://dl.bintray.com/jai-imageio/maven/'
     }
 
     maven {
-        url = 'http://repo.maven.apache.org/maven2'
+        url = 'https://repo.maven.apache.org/maven2'
     }
 }
 
 dependencies {
-    compile 'com.github.jai-imageio:jai-imageio-core:1.4.0'
-    testCompile 'junit:junit:4.12'
+    implementation 'com.github.jai-imageio:jai-imageio-core:1.4.0'
+    testImplementation 'junit:junit:4.12'
 }
 
 group = 'com.github.jai-imageio'