Convert to Maven for builds and releases

.github/workflows/cs-comparison.yml

@@ -1,15 +1,9 @@
-# Run the full CS ingration comparison
-#
-# This is just a proof of concept for now since the raw input is not available as it
-# is too large to include in repository.
-
 name: cs-comparison
 
 on: workflow_dispatch
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
 
     steps:
@@ -19,11 +13,21 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          distribution: 'adopt'
+          distribution: 'temurin'
           java-version: '21'
-          cache: 'gradle'
+          cache: 'maven'
+
+      - name: Cache Maven packages
+        uses: actions/cache@v4
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
 
-      - name: CS Comparison
+      # Run the comparison using the test classpath
+      - name: Build and run CS Comparison
         run: |
-          chmod +x gradlew
-          ./gradlew :staging-client-java-cs:csIntegrationTest
+          chmod +x ./mvnw
+          ./mvnw -B test-compile -DskipTests
+          ./mvnw -B exec:java -DskipTests -Dexec.mainClass=com.imsweb.staging.cs.CsIntegrationTest -Dexec.classpathScope=test

.github/workflows/integration.yml

@@ -18,21 +18,30 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          distribution: 'adopt'
+          distribution: 'temurin'
           java-version: '21'
-          cache: 'gradle'
+          cache: 'maven'
+
+      - name: Cache Maven packages
+        uses: actions/cache@v4
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
 
       - name: Cache SonarCloud packages
         uses: actions/cache@v4
         with:
           path: ~/.sonar/cache
           key: ${{ runner.os }}-sonar
-          restore-keys: ${{ runner.os }}-sonar
+          restore-keys: |
+            ${{ runner.os }}-sonar
 
       - name: Build and test
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         run: |
-          chmod +x gradlew
-          ./gradlew build sonar
+          chmod +x ./mvnw
+          ./mvnw -B verify sonar:sonar

.github/workflows/publish.yml

@@ -1,35 +1,76 @@
-# Publish to Maven Central
+# Publish to Maven Central (Maven)
+#
+# Non-SNAPSHOT releases are done automatically on Git tag. SNAPSHOT releases are not handled by CI; use
+# the following command to release a SNAPSHOT (ensure the version in pom.xml is a SNAPSHOT version):
+#
+# $ .\mvnw.cmd deploy -DskipTests
+#
+# Note that to release locally you will need to set up a settings.xml file in you user
+# home .m2 directory. The username and password is generated at:
+#
+#    https://central.sonatype.com/usertoken.
+#
+# Here is the settings.xml file:
+#
+#  <settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
+#            xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+#            xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
+#                                https://maven.apache.org/xsd/settings-1.0.0.xsd">
+#     <servers>
+#        <server>
+#        <!-- must match <id>ossrh</id> in distributionManagement -->
+#           <id>central</id>
+#           <username>USERNAME FROM GENERATED TOKEN</username>
+#           <password>PASSWORD FROM GENERATED TOKEN</password>
+#        </server>
+#     </servers>
+#  </settings>
 
 name: publish
 
 on:
   repository_dispatch:
     types: manual-publish
   release:
-    types: [ created ]
+    types: [ published ]
 
 jobs:
   publish:
-
     runs-on: ubuntu-latest
 
+    permissions:
+      contents: read
+
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Set up JDK
+      - name: Set up JDK 21 for Maven Central
         uses: actions/setup-java@v4
         with:
-          distribution: 'adopt'
+          distribution: 'temurin'
           java-version: '21'
-          cache: 'gradle'
+          cache: 'maven'
+
+          # Must match <id> in <distributionManagement>
+          server-id: central
+
+          # These are Maven properties in settings.xml; values come from env below
+          server-username: MAVEN_CENTRAL_USERNAME
+          server-password: MAVEN_CENTRAL_PASSWORD
 
-      - name: Publish to Maven Central (Portal)
-        run: |
-          chmod +x gradlew
-          ./gradlew publishAndReleaseToMavenCentral --no-configuration-cache
+          # GPG setup (uses your in-memory private key)
+          gpg-private-key: ${{ secrets.SIGNING_KEY }}
+
+          # Name of env var that holds the passphrase (see pom passphraseEnvName)
+          gpg-passphrase: MAVEN_GPG_PASSPHRASE
+
+      - name: Publish to Maven Central
+        run: mvn -B -ntp clean deploy -P release -DskipTests -Dspotbugs.skip=true -Djacoco.skip=true
         env:
-          ORG_GRADLE_PROJECT_mavenCentralUsername: ${{ secrets.MAVEN_CENTRAL_USERNAME }}
-          ORG_GRADLE_PROJECT_mavenCentralPassword: ${{ secrets.MAVEN_CENTRAL_PASSWORD }}
-          ORG_GRADLE_PROJECT_signingInMemoryKey: ${{ secrets.SIGNING_KEY }}
-          ORG_GRADLE_PROJECT_signingInMemoryKeyPassword: ${{ secrets.SIGNING_PASSWORD }}
+          # Sonatype / Central credentials
+          MAVEN_CENTRAL_USERNAME: ${{ secrets.MAVEN_CENTRAL_USERNAME }}
+          MAVEN_CENTRAL_PASSWORD: ${{ secrets.MAVEN_CENTRAL_PASSWORD }}
+
+          # GPG passphrase (referenced by MAVEN_GPG_PASSPHRASE name)
+          MAVEN_GPG_PASSPHRASE: ${{ secrets.SIGNING_PASSWORD }}

.github/workflows/upload-algorithms.yml

@@ -3,38 +3,22 @@
 name: upload-algorithms
 
 on:
-  repository_dispatch:
-    types: manual-publish
   release:
-    types: [ created ]
+    types: [published]
 
 jobs:
   publish:
-
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Set up JDK
-        uses: actions/setup-java@v4
-        with:
-          distribution: 'adopt'
-          java-version: '21'
-
-      - name: Create algorithm zips
-        if: ${{startsWith(github.ref, 'refs/tags/v') }}
-        run: |
-          chmod +x gradlew
-          ./gradlew zipAlgorithms
-
       - name: Add algorithms to release
         uses: softprops/action-gh-release@v1
-        if: ${{startsWith(github.ref, 'refs/tags/v') }}
         with:
           files: |
-            algorithm-cs/build/algorithms/*.zip
-            algorithm-eod/build/algorithms/*.zip
-            algorithm-tnm/build/algorithms/*.zip
-            algorithm-pediatric/build/algorithms/*.zip
+            src/test/resources/algorithms/cs-*.zip
+            src/test/resources/algorithms/eod_public-*.zip
+            src/test/resources/algorithms/pediatric-*.zip
+            src/test/resources/algorithms/tnm-*.zip

.gitignore

@@ -1,9 +1,33 @@
-target
-build
-classes
-dist
-out
-/.idea
+HELP.md
+target/
+!**/src/main/**/target/
+!**/src/test/**/target/
+
+### STS ###
+.apt_generated
+.classpath
+.factorypath
+.project
+.settings
+.springBeans
+.sts4-cache
+
+### IntelliJ IDEA ###
+.idea
+*.iws
 *.iml
-.dbshell
-.gradle
+*.ipr
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+

.mvn/wrapper/MavenWrapperDownloader.java

@@ -0,0 +1,117 @@
+/*
+ * Copyright 2007-present the original author or authors.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import java.net.*;
+import java.io.*;
+import java.nio.channels.*;
+import java.util.Properties;
+
+public class MavenWrapperDownloader {
+
+    private static final String WRAPPER_VERSION = "0.5.6";
+    /**
+     * Default URL to download the maven-wrapper.jar from, if no 'downloadUrl' is provided.
+     */
+    private static final String DEFAULT_DOWNLOAD_URL = "https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/"
+        + WRAPPER_VERSION + "/maven-wrapper-" + WRAPPER_VERSION + ".jar";
+
+    /**
+     * Path to the maven-wrapper.properties file, which might contain a downloadUrl property to
+     * use instead of the default one.
+     */
+    private static final String MAVEN_WRAPPER_PROPERTIES_PATH =
+            ".mvn/wrapper/maven-wrapper.properties";
+
+    /**
+     * Path where the maven-wrapper.jar will be saved to.
+     */
+    private static final String MAVEN_WRAPPER_JAR_PATH =
+            ".mvn/wrapper/maven-wrapper.jar";
+
+    /**
+     * Name of the property which should be used to override the default download url for the wrapper.
+     */
+    private static final String PROPERTY_NAME_WRAPPER_URL = "wrapperUrl";
+
+    public static void main(String args[]) {
+        System.out.println("- Downloader started");
+        File baseDirectory = new File(args[0]);
+        System.out.println("- Using base directory: " + baseDirectory.getAbsolutePath());
+
+        // If the maven-wrapper.properties exists, read it and check if it contains a custom
+        // wrapperUrl parameter.
+        File mavenWrapperPropertyFile = new File(baseDirectory, MAVEN_WRAPPER_PROPERTIES_PATH);
+        String url = DEFAULT_DOWNLOAD_URL;
+        if(mavenWrapperPropertyFile.exists()) {
+            FileInputStream mavenWrapperPropertyFileInputStream = null;
+            try {
+                mavenWrapperPropertyFileInputStream = new FileInputStream(mavenWrapperPropertyFile);
+                Properties mavenWrapperProperties = new Properties();
+                mavenWrapperProperties.load(mavenWrapperPropertyFileInputStream);
+                url = mavenWrapperProperties.getProperty(PROPERTY_NAME_WRAPPER_URL, url);
+            } catch (IOException e) {
+                System.out.println("- ERROR loading '" + MAVEN_WRAPPER_PROPERTIES_PATH + "'");
+            } finally {
+                try {
+                    if(mavenWrapperPropertyFileInputStream != null) {
+                        mavenWrapperPropertyFileInputStream.close();
+                    }
+                } catch (IOException e) {
+                    // Ignore ...
+                }
+            }
+        }
+        System.out.println("- Downloading from: " + url);
+
+        File outputFile = new File(baseDirectory.getAbsolutePath(), MAVEN_WRAPPER_JAR_PATH);
+        if(!outputFile.getParentFile().exists()) {
+            if(!outputFile.getParentFile().mkdirs()) {
+                System.out.println(
+                        "- ERROR creating output directory '" + outputFile.getParentFile().getAbsolutePath() + "'");
+            }
+        }
+        System.out.println("- Downloading to: " + outputFile.getAbsolutePath());
+        try {
+            downloadFileFromURL(url, outputFile);
+            System.out.println("Done");
+            System.exit(0);
+        } catch (Throwable e) {
+            System.out.println("- Error downloading");
+            e.printStackTrace();
+            System.exit(1);
+        }
+    }
+
+    private static void downloadFileFromURL(String urlString, File destination) throws Exception {
+        if (System.getenv("MVNW_USERNAME") != null && System.getenv("MVNW_PASSWORD") != null) {
+            String username = System.getenv("MVNW_USERNAME");
+            char[] password = System.getenv("MVNW_PASSWORD").toCharArray();
+            Authenticator.setDefault(new Authenticator() {
+                @Override
+                protected PasswordAuthentication getPasswordAuthentication() {
+                    return new PasswordAuthentication(username, password);
+                }
+            });
+        }
+        URL website = new URL(urlString);
+        ReadableByteChannel rbc;
+        rbc = Channels.newChannel(website.openStream());
+        FileOutputStream fos = new FileOutputStream(destination);
+        fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+        fos.close();
+        rbc.close();
+    }
+
+}

.mvn/wrapper/maven-wrapper.properties

@@ -0,0 +1,2 @@
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.11/apache-maven-3.9.11-bin.zip
+wrapperUrl=https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.5.6/maven-wrapper-0.5.6.jar