Merge branch 'master' into twobit

igvteam · Oct 2, 2023 · d4e1bfb · d4e1bfb
2 parents df59d5a + 227302e
commit d4e1bfb
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Showing 197 changed files with 7,728 additions and 3,955 deletions.
diff --git a/.github/workflows/gradle_test.yml b/.github/workflows/gradle_test.yml
@@ -7,13 +7,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up JDK 11
-        uses: actions/setup-java@v1
+      - uses: actions/checkout@v3
+      - name: Set up JDK 17
+        uses: actions/setup-java@v3
         with:
-          java-version: 11
+          java-version: 17
+          distribution: temurin 
       - name: Cache Gradle packages
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             ~/.gradle/caches
@@ -30,4 +31,4 @@ jobs:
         # Restoring these files from a GitHub Actions cache might cause problems for future builds.
         run: |
           rm -f ~/.gradle/caches/modules-2/modules-2.lock
-          rm -f ~/.gradle/caches/modules-2/gc.properties
+          rm -f ~/.gradle/caches/modules-2/gc.properties
diff --git a/.gitignore b/.gitignore
@@ -20,3 +20,6 @@ out/
 *.csi.gz
 *.sai
 /test/batch/snapshots/
+/src/main/java/org/broad/igv/sam/mods/BMScale.java
+/src/main/java/org/broad/igv/sam/mods/BMScale.form
+/ignore/
diff --git a/build.gradle b/build.gradle
@@ -1,6 +1,6 @@
 // The MIT License (MIT)
 //
-// Copyright (c) 2007-2019 Broad Institute
+// Copyright (c) 2007-2019 Broad Institut≈e
 //
 // Permission is hereby granted, free of charge, to any person obtaining a copy
 // of this software and associated documentation files (the "Software"), to deal
@@ -27,26 +27,25 @@ apply plugin: 'application'
 
 import org.apache.tools.ant.filters.ReplaceTokens
 
-//import proguard.gradle.ProGuardTask
-
 mainClassName = 'org.broad.igv.ui.Main'
 ext.moduleName = 'org.igv'
 
-// Build sourceset for ProGuard
 buildscript {
     repositories {
         mavenCentral()
     }
-    dependencies {
-        [group: 'net.sf.proguard', name: 'proguard-gradle', version: '6.1.1']
-        classpath 'net.sf.proguard:proguard-gradle:6.1.1'
-    }
 }
 
 repositories {
     mavenCentral()
 }
 
+java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(17)
+    }
+}
+
 sourceSets {
     main {
         resources {
@@ -111,7 +110,7 @@ dependencies {
             [group: 'org.xerial.snappy', name: 'snappy-java', version: '1.1.7.3'],
             [group: 'org.apache.commons', name: 'commons-jexl', version: '2.1.1'],
             [group: 'org.apache.commons', name: 'commons-lang3', version: '3.9'],
-            [group: 'com.github.samtools', name: 'htsjdk', version: '3.0.0'],
+            [group: 'com.github.samtools', name: 'htsjdk', version: '3.0.5'],
             [group: 'org.swinglabs', name: 'swing-layout', version: '1.0.3'],
             //[group: 'org.bidib.com.jidesoft', name: 'jide-common', version: '3.7.3'],  // no longer in Maven Central
             [group: 'com.google.guava', name: 'guava', version: '27.0.1-jre'],
@@ -123,14 +122,18 @@ dependencies {
             // Amazon deps
             [group: 'software.amazon.awssdk', name: 'cognitoidentity', version: '2.16.7'],
             [group: 'software.amazon.awssdk', name: 'sts', version: '2.16.7'],
-            [group: 'software.amazon.awssdk', name: 's3', version: '2.16.7']
+            [group: 'software.amazon.awssdk', name: 's3', version: '2.16.7'],
+            [group: 'software.amazon.awssdk', name: 'sso', version: '2.16.7']
     )
 
     testImplementation(
-            [group: 'junit', name: 'junit', version: '4.12'],
+            [group: 'junit', name: 'junit', version: '4.13'],
             [group: 'com.sparkjava', name: 'spark-core', version: '2.2'],
             [group: 'org.glassfish.jersey.core', name: 'jersey-common', version: '2.22.4']
     )
+    testRuntimeOnly(
+           [group: 'org.junit.vintage', name:'junit-vintage-engine', version:'5.8.2']
+    )
 }
 
 
@@ -178,35 +181,7 @@ tasks.withType(Test) {
     systemProperties['org.xerial.snappy.tempdir'] = 'build/tmp'
     maxHeapSize = '2g'
     maxParallelForks = Runtime.runtime.availableProcessors().intdiv(2) ?: 1
-}
-
-compileTestJava {
-    inputs.property("moduleName", moduleName)
-    doFirst {
-        options.compilerArgs = [
-                '--module-path', classpath.asPath,
-                '--add-modules', 'junit',
-                '--patch-module', "$moduleName=" + files(sourceSets.test.java.srcDirs).asPath,
-        ]
-        classpath = files()
-    }
-}
-
-test {
-    inputs.property("moduleName", moduleName)
-
-    doFirst {
-        jvmArgs = [
-                '-Dcom.sun.xml.bind.v2.bytecode.ClassTailor.noOptimize',
-                '--module-path', classpath.asPath,
-                '--add-modules', 'junit',
-                '--add-modules', 'ALL-MODULE-PATH',
-                '--add-reads', "$moduleName=junit",
-                '@scripts/test_suite.args',
-                '--patch-module', "$moduleName=" + files(sourceSets.test.java.outputDir, sourceSets.main.output.resourcesDir).asPath,
-        ]
-        classpath = files()
-    }
+    useJUnitPlatform()
 }
 
 task createDist(type: Copy, dependsOn: jar) {
@@ -228,10 +203,11 @@ task createDist(type: Copy, dependsOn: jar) {
     }
     // Copies all Maven-fetched dependency jars
     with copySpec {
-        from configurations.default {
+        from configurations.runtimeClasspath {
             exclude '**/*log4j*.jar' 
         }
         into "lib"
+        duplicatesStrategy DuplicatesStrategy.EXCLUDE
     }
     with copySpec { from("genomes/sizes") {} into "lib/genomes" }
 
@@ -243,32 +219,32 @@ tasks.distTar.enabled = false
 tasks.startScripts.enabled = false
 
 task createDistZip(type: Zip, dependsOn: createDist) {
-    archiveName = "IGV_${version}.zip"
+    archiveFileName = "IGV_${archiveVersion}.zip"
     from("${buildDir}/IGV-dist")
-    into "IGV_${version}"
+    into "IGV_${archiveVersion}"
 }
 
 task createLinuxDistZip(type: Zip, dependsOn: createDist) {
-    archiveName = "IGV_Linux_${version}.zip"
+    archiveFileName = "IGV_Linux_${archiveVersion}.zip"
     from("${buildDir}/IGV-dist") {
         exclude "*.bat"
         exclude "*.command"
         exclude 'igvtools*'
         exclude 'lib/genomes'
     }
-    into "IGV_Linux_${version}"
+    into "IGV_Linux_${archiveVersion}"
 }
 
 task createLinuxWithJavaDistZip(type: Zip, dependsOn: createDist) {
-    archiveName = "IGV_Linux_${version}_WithJava.zip"
-    with copySpec { from jdkBundleLinux into "jdk-11" }
+    archiveFileName = "IGV_Linux_${archiveVersion}_WithJava.zip"
+    with copySpec { from jdkBundleLinux into "jdk-17" }
     from("${buildDir}/IGV-dist") {
         exclude "*.bat"
         exclude "*.command"
         exclude 'igvtools*'
         exclude 'lib/genomes'
     }
-    into "IGV_Linux_${version}"
+    into "IGV_Linux_${archiveVersion}"
     doLast {
         if (jdkBundleLinux == "") {
             throw new GradleException("Required property not set: jdkBundleLinux");
@@ -277,26 +253,27 @@ task createLinuxWithJavaDistZip(type: Zip, dependsOn: createDist) {
 }
 
 task createMacDistZip(type: Zip, dependsOn: createDist) {
-    archiveName = "IGV_Mac_${version}.zip"
+    archiveFileName = "IGV_Mac_${archiveVersion}.zip"
     from("${buildDir}/IGV-dist") {
         exclude "*.bat"
         exclude "*_hidpi*"
         exclude "igvtools*"
         exclude 'lib/genomes'
     }
-    into "IGV_Mac_${version}"
+
+    into "IGV_Mac_${archiveVersion}"
 }
 
 task createMacWithJavaDistZip(type: Zip, dependsOn: createDist) {
-    archiveName = "IGV_Mac_${version}_WithJava.zip"
-    with copySpec { from jdkBundleMac into "jdk-11" }
+    archiveFileName = "IGV_Mac_${archiveVersion}_WithJava.zip"
+    with copySpec { from jdkBundleMac into "jdk-17" }
     from("${buildDir}/IGV-dist") {
         exclude "*.bat"
         exclude "*_hidpi*"
         exclude "igvtools*"
         exclude 'lib/genomes'
     }
-    into "IGV_Mac_${version}"
+    into "IGV_Mac_${archiveVersion}"
     doLast {
         if (jdkBundleMac == "") {
             throw new GradleException("Required property not set: jdkBundleMac");
@@ -338,7 +315,7 @@ task createMacAppDist(type: Copy, dependsOn: createDist) {
 }
 
 task createMacAppDistZip(type: Zip, dependsOn: createMacAppDist) {
-    archiveName = "IGV_MacApp_${version}.zip"
+    archiveFileName = "IGV_MacApp_${archiveVersion}.zip"
     from("${buildDir}/IGV-MacApp-dist")
 
     doLast {
@@ -347,8 +324,8 @@ task createMacAppDistZip(type: Zip, dependsOn: createMacAppDist) {
 }
 
 task createMacAppWithJavaDistZip(type: Zip, dependsOn: createMacAppDist) {
-    archiveName = "IGV_MacApp_${version}_WithJava.zip"
-    with copySpec { from jdkBundleMac into "IGV_${version}.app/Contents/jdk-11" }
+    archiveFileName = "IGV_MacApp_${archiveVersion}_WithJava.zip"
+    with copySpec { from jdkBundleMac into "IGV_${archiveVersion}.app/Contents/jdk-17" }
     from("${buildDir}/IGV-MacApp-dist")
 
     doLast {
@@ -382,7 +359,7 @@ task createWinDist(type: Copy, dependsOn: createDist) {
 }
 
 task createWinWithJavaDist(type: Copy, dependsOn: createWinDist) {
-    with copySpec { from jdkBundleWindows into "IGV_${version}/jdk-11" }
+    with copySpec { from jdkBundleWindows into "IGV_${version}/jdk-17" }
     with copySpec {
         from("${buildDir}/IGV-WinExe-dist/IGV_${version}") { exclude 'installer.nsi' }
         into "IGV_${version}"
@@ -464,7 +441,8 @@ task fullJar(type: Jar, dependsOn: jar) {
                 "Application-Name": "IGV",
                 "Built-By": System.getProperty('user.name'),
                 "Main-Class": mainClassName,
-                "Class-Path": configurations.default.collect { it.getName() }.join(' ')
+
+                "Class-Path": configurations.runtimeClasspath.collect { it.getName() }.join(' ')
         )
     }
 }
@@ -474,16 +452,3 @@ task fullJar(type: Jar, dependsOn: jar) {
 //if (!makensisCommand == "" && !signcodeCommand == "") {
 //    dependsOn signWinExeDist
 //}
-
-// XXX: META-INF versions support (Java11) seem to clash with proguard at this point in time:
-// https://sourceforge.net/p/proguard/bugs/665/
-// https://sourceforge.net/p/proguard/discussion/182456/thread/8c56b22dc2/?limit=25
-//task myproguard(type: ProGuardTask) {
-////    configuration 'proguard.txt'
-//
-//    injars "${buildDir}/IGV-dist/lib"
-//    outjars "${buildDir}/libs/igv-proguard.jar"
-//
-//    //libraryjars "${buildDir}/IGV-dist/lib", jarfilter:"lib/**.jar(!META-INF/**)"
-//    //libraryjars "${System.getProperty('java.home')}/lib/rt.jar"
-//}
diff --git a/examples/oauth/oauth-config-amazon.json b/examples/oauth/oauth-config-amazon.json
@@ -1,16 +1,15 @@
 {
-   "client_id": "3f4ujenfmr77tg12idlkebpkoh",
-   "client_secret": "en1q6638m4dogrr6erhrmitim67sjilc6htjnfmf6ljk2q3j9og",
+   "apiKey": "",
+   "project_id": "igv",
    "auth_provider": "Amazon",
    "auth_provider_x509_cert_url": "https://www.googleapis.com/oauth2/v1/certs",
-   "aws_region": "ap-southeast-2",
+   "aws_region": "us-east-1",
    "scope": "email%20openid%20profile",
-   "redirect_uris": [
-      "http://localhost:60151/oauthCallback"
-   ],
-   "authorization_endpoint": "https://igv-demo.auth.ap-southeast-2.amazoncognito.com/login",
-   "token_endpoint": "https://igv-demo.auth.ap-southeast-2.amazoncognito.com/token",
-   "aws_cognito_fed_pool_id": "ap-southeast-2:15b7bf93-18ca-40d5-99e9-38b4eb69363e",
-   "aws_cognito_pool_id": "ap-southeast-2_IYMvlZzmv",
-   "aws_cognito_role_arn": "arn:aws:iam::YOUR_AWS_ACCOUNT:role/YOUR_Cognito_igvAuth_Role"
-}
+   "client_id": "eu7vd09a3dsfasdfd7r4kjomqg",
+   "client_secret": "s2416djkq5liigbrjdhktdsdgerefktsv04f9p810a3nc9",
+   "authorization_endpoint": "https://igv-demo.auth.us-east-1.amazoncognito.com/login",
+   "token_endpoint": "https://igv-demo.auth.us-east-1.amazoncognito.com/token",
+   "aws_cognito_fed_pool_id": "us-east-1:2926325e-0938-4dfc-840a-fa8a3e4f63f7",
+   "aws_cognito_pool_id": "us-east-1_v98erojsdkfj",
+   "aws_cognito_role_arn": "arn:aws:iam::3940820579:role/Cognito_igvAuth_Role"
+}
diff --git a/examples/oauth/oauth-config-google.json b/examples/oauth/oauth-config-google.json
@@ -1,11 +1,7 @@
 {
-  "client_id": "661332306814-gb4r480jnb6rres3iv8a5f48dms5ququu.apps.googleusercontent.com",
-  "client_secret": "MFqdc7apizmtb8n08Ze810V6",
+  "client_id": "YOUR_CLIENT_ID",
+  "client_secret": "YOUR_CLIENT_SECRET",
   "auth_uri": "https://accounts.google.com/o/oauth2/auth",
   "token_uri": "https://accounts.google.com/o/oauth2/token",
-  "auth_provider_x509_cert_url": "https://www.googleapis.com/oauth2/v1/certs",
-  "redirect_uris": [
-    "http://localhost:60151/oauthCallback"
-  ],
-  "hosts": ["www.googleapis.com", "storage.cloud.google.com", "storage.googleapis.com"]
+  "auth_provider_x509_cert_url": "https://www.googleapis.com/oauth2/v1/certs"
 }
diff --git a/examples/oauth/oauth-config-microsoft.json b/examples/oauth/oauth-config-microsoft.json
@@ -1,11 +1,11 @@
 {
-  "client_id": "hbq82djj-qwer-7iub-j7zq-7i8nv72n48nq",
-  "client_secret": "cVAX64fXRikCLmtAow/cktrAtaHz/tmB3WHKhnbXN2Gq",
-  "authorization_endpoint": "https://login.microsoftonline.com/77nwe2q2-e53r-uq2p-7vdh-9z7px83zmtiv/oauth2/authorize",
-  "token_endpoint": "https://login.microsoftonline.com/77nwe2q2-e53r-wk32-7vdh-9z7px83zmtiv/oauth2/token",
+  "client_id": "YOUR_CLIENT_ID",
+  "client_secret": "YOUR_CLIENT_SECRET",
+  "authorization_endpoint": "https://login.microsoftonline.com/.../oauth2/authorize",
+  "token_endpoint": "https://login.microsoftonline.com/.../oauth2/token",
   "hosts": ["prod_host.mayo.edu", "dev_host.mayo.edu", "int_host.mayo.edu"],
-  "auth_provider": "Mayo Clinic",
-  "app_id_uri": "https://orgtools.onmicrosoft.com/6q9qk3mr-pu78-eu73-vx5a-nqw2aqidutm9",
+  "auth_provider": "YOUR PROVIDER",
+  "app_id_uri": "https://orgtools.onmicrosoft.com/...",
   "scope": "openid"
 }
 
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-5.5.1-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.0.2-bin.zip
+networkTimeout=10000
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists