Updated dependencies and Gradle wrapper.

.github/workflows/integration.yml

@@ -0,0 +1,37 @@
+# Build the project and run unit tests
+
+name: integration
+
+on: [ push, pull_request ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Set up JDK
+        uses: actions/setup-java@v2
+        with:
+          distribution: 'adopt'
+          java-version: '17'
+      - name: Cache Gradle packages
+        uses: actions/cache@v2
+        with:
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          restore-keys: ${{ runner.os }}-gradle
+      - name: Build and analyze
+        env:
+          SEER_API_KEY: ${{ secrets.SEER_API_KEY }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        run: |
+          chmod +x gradlew
+          ./gradlew build

.github/workflows/publish.yml

@@ -0,0 +1,34 @@
+# Publish to Maven Central
+
+name: publish
+
+on:
+  release:
+    types: [ created ]
+  workflow_dispatch: {}
+
+jobs:
+  publish:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up JDK
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'adopt'
+          java-version: '17'
+          cache: 'gradle'
+
+      - name: Publish
+        run: |
+          chmod +x gradlew
+          ./gradlew publishToSonatype closeAndReleaseSonatypeStagingRepository
+        env:
+          ORG_GRADLE_PROJECT_nexusUsername: ${{ secrets.NEXUS_USERNAME }}
+          ORG_GRADLE_PROJECT_nexusPassword: ${{ secrets.NEXUS_PASSWORD }}
+          ORG_GRADLE_PROJECT_signingKey: ${{ secrets.SEER_GPG_SECRET_KEY }}
+          ORG_GRADLE_PROJECT_signingPassword: ${{ secrets.SEER_GPG_PASSWORD }}

CHANGELOG.md

@@ -2,8 +2,10 @@
 
 **Version 1.3**
 
-- Updated validation library from version 2.28 to version 3.0.
-- Updated naaccr-xml library from version 9.0 to version 9.1.
+- Updated validation library from version 2.28 to version 3.2.
+- Updated naaccr-xml library from version 9.0 to version 10.1.
+- Updated SQLite driver from version 3.39.2.0 to version 3.43.2.1.
+- Updated log4j-api from version 2.18.0 to version 2.21.1.
 
 **Version 1.2**
 

build.gradle

@@ -3,56 +3,56 @@ import java.time.Duration
 plugins {
     id 'java-library'
     id 'checkstyle'
-    id 'com.github.spotbugs' version '5.0.12'
+    id 'com.github.spotbugs' version '5.2.1'
     id 'maven-publish'
     id 'signing'
-    id 'io.github.gradle-nexus.publish-plugin' version '1.1.0' // publish to Maven Central
-    id 'com.github.ben-manes.versions' version '0.43.0' // check for out-of-date dependencies (run manually)
-    id 'org.sonatype.gradle.plugins.scan' version '2.5.5' // scan for vulnerabilities
+    id 'io.github.gradle-nexus.publish-plugin' version '1.3.0' // publish to Maven Central
+    id 'com.github.ben-manes.versions' version '0.49.0' // check for out-of-date dependencies (run 'dependencyUpdates' manually)
+    id 'org.sonatype.gradle.plugins.scan' version '2.6.1' // scan for vulnerabilities
 }
 
 group = 'com.imsweb'
 version = file('VERSION').text.trim()
 description = 'This library allows a Genedits Metafile to be translated into Groovy edits that can be executed in the SEER Validation framework.'
 
-sourceCompatibility = JavaVersion.VERSION_1_8
-targetCompatibility = JavaVersion.VERSION_1_8
-
 println "Starting build using JDK ${Runtime.version().feature()}"
 
 repositories {
     mavenCentral()
 }
 
 dependencies {
-    api 'com.imsweb:validation:3.0'
-    api 'com.imsweb:naaccr-xml:9.1'
+    api 'com.imsweb:validation:3.2'
+    api 'com.imsweb:naaccr-xml:10.1'
     api 'com.imsweb:seerutils:5.6'
     api 'com.imsweb:staging-algorithm-cs:02.05.50.10'
 
-    implementation 'org.apache.commons:commons-lang3:3.12.0'
+    implementation 'org.apache.commons:commons-lang3:3.13.0'
     implementation 'net.sf.squirrel-sql.thirdparty-non-maven:java-cup:0.11a'
-    implementation 'org.xerial:sqlite-jdbc:3.39.2.0'
-    implementation 'org.apache.logging.log4j:log4j-api:2.18.0'
+    implementation 'org.xerial:sqlite-jdbc:3.43.2.1'
+    implementation 'org.apache.logging.log4j:log4j-api:2.21.1'
 
     testImplementation 'junit:junit:4.13.2'
-    testImplementation 'com.imsweb:data-generator:1.28'
-    testImplementation 'org.apache.logging.log4j:log4j-core:2.19.0'
+    testImplementation 'com.imsweb:data-generator:1.31'
+    testImplementation 'org.apache.logging.log4j:log4j-core:2.21.1'
 }
 
 // enforce UTF-8, display the compilation warnings
-tasks.withType(JavaCompile) {
+tasks.withType(JavaCompile).configureEach {
     options.encoding = 'UTF-8'
     options.compilerArgs << '-Xlint:unchecked' << '-Xlint:deprecation'
 }
 
 // the Javadoc was made way too strict in Java 8 and it's not worth the time fixing everything!
-tasks.withType(Javadoc) {
+tasks.withType(Javadoc).configureEach {
     options.addStringOption('Xdoclint:none', '-quiet')
 }
 
 // generate javadoc and sources (required by Nexus)
 java {
+    sourceCompatibility = JavaVersion.VERSION_1_8
+    targetCompatibility = JavaVersion.VERSION_1_8
+
     withJavadocJar()
     withSourcesJar()
 }
@@ -81,12 +81,11 @@ checkstyle {
 
 // spotbugs plugin settings
 spotbugs {
-    ignoreFailures = false
-    excludeFilter = file('config/spotbugs/spotbugs-exclude.xml')
+    excludeFilter.set(file('config/spotbugs/spotbugs-exclude.xml'))
 }
 
 // use this task to generate the edits parser for Genedits syntax
-task generateEditsParser {
+tasks.register('generateEditsParser') {
     doLast {
         // create lexer
         javaexec {
@@ -114,7 +113,7 @@ task generateEditsParser {
 }
 
 // use this task to generate the regex parser
-task generateRegexParser {
+tasks.register('generateRegexParser') {
     doLast {
         // create lexer
         javaexec {
@@ -152,9 +151,20 @@ ossIndexAudit {
             'sonatype-2022-6438'
     ]
 }
+check.dependsOn 'ossIndexAudit'
 
-if (project.hasProperty('branch_name') && (project.ext.get('branch_name') == 'master' || project.ext.get('branch_name') == 'main'))
-    check.dependsOn 'ossIndexAudit'
+def isNonStable = { String version ->
+    def stableKeyword = ['RELEASE', 'FINAL', 'GA'].any { it -> version.toUpperCase().contains(it) }
+    def regex = /^[0-9,.v-]+(-r)?$/
+    return (!stableKeyword && !(version ==~ regex)) || version == '021-11'
+}
+
+// https://github.com/ben-manes/gradle-versions-plugin
+tasks.named("dependencyUpdates").configure {
+    rejectVersionIf {
+        isNonStable(it.candidate.version)
+    }
+}
 
 // needed to deploy to Maven Central
 publishing {
@@ -204,6 +214,8 @@ publishing {
 
 // setup JAR signing
 signing {
+    required { !project.version.endsWith('-SNAPSHOT') }
+
     def signingKey = project.findProperty('signing.armored.key') ?: ''
     def signingPassword = project.findProperty('signing.armored.password') ?: ''
 
@@ -231,15 +243,9 @@ nexusPublishing {
     }
 }
 
-// don't try to release a snapshot to a non-snapshot repository, that won't work anyway
-if (version.endsWith('-SNAPSHOT')) {
-    gradle.startParameter.excludedTaskNames += 'signMavenJavaPublication'
-    gradle.startParameter.excludedTaskNames += 'closeAndReleaseSonatypeStagingRepository'
-}
-
 // Gradle wrapper, this allows to build the project without having to install Gradle!
 wrapper {
-    gradleVersion = '7.5.1'
+    gradleVersion = '8.4'
     distributionType = Wrapper.DistributionType.ALL
 }
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-all.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -205,6 +205,12 @@ set -- \
         org.gradle.wrapper.GradleWrapperMain \
         "$@"
 
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
 # Use "xargs" to parse quoted args.
 #
 # With -n1 it outputs one arg per line, with the quotes and backslashes removed.

gradlew.bat

@@ -14,7 +14,7 @@
 @rem limitations under the License.
 @rem
 
-@if "%DEBUG%" == "" @echo off
+@if "%DEBUG%"=="" @echo off
 @rem ##########################################################################
 @rem
 @rem  Gradle startup script for Windows
@@ -25,7 +25,7 @@
 if "%OS%"=="Windows_NT" setlocal
 
 set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
+if "%DIRNAME%"=="" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
@@ -40,7 +40,7 @@ if defined JAVA_HOME goto findJavaFromJavaHome
 
 set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto execute
+if %ERRORLEVEL% equ 0 goto execute
 
 echo.
 echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -75,13 +75,15 @@ set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
 
 :end
 @rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
+if %ERRORLEVEL% equ 0 goto mainEnd
 
 :fail
 rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
 rem the _cmd.exe /c_ return code!
-if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
+set EXIT_CODE=%ERRORLEVEL%
+if %EXIT_CODE% equ 0 set EXIT_CODE=1
+if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
+exit /b %EXIT_CODE%
 
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal