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Merge pull request #122 from jgi-kbase/dev-gradle
Add Gradle and update dockerfile / docker-compose
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| # | ||
| # https://help.github.com/articles/dealing-with-line-endings/ | ||
| # | ||
| # Linux start script should use lf | ||
| /gradlew text eol=lf | ||
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| # These are Windows script files and should use crlf | ||
| *.bat text eol=crlf | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,200 @@ | ||
| /* | ||
| * This file was generated by the Gradle 'init' task. | ||
| */ | ||
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| plugins { | ||
| id 'java' | ||
| id 'war' | ||
| id 'jacoco' | ||
| id 'org.ajoberstar.grgit' version '4.1.1' | ||
| } | ||
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| // TODO NOW switch to std gradle layout | ||
| // TODO NOW use jitpacked workspace client and shadow jar when available and remove jars | ||
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| repositories { | ||
| mavenCentral() | ||
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| maven { | ||
| name = "Clojars" | ||
| url = "https://repo.clojars.org/" | ||
| } | ||
| maven { | ||
| name = "JitPack" | ||
| url = 'https://jitpack.io' | ||
| } | ||
| } | ||
| task buildGitCommitFile { | ||
| doLast { | ||
| def commitId = grgit.head().id | ||
| // is there a variable for builddir/classes/java/main? | ||
| file("$buildDir/classes/java/main/us/kbase/assemblyhomology/gitcommit").text = commitId | ||
| } | ||
| } | ||
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| compileJava { | ||
| // TODO BUILD remove when we no longer support java 8, use `options.release = 11` if needed | ||
| java.sourceCompatibility = JavaVersion.VERSION_1_8 | ||
| java.targetCompatibility = JavaVersion.VERSION_1_8 | ||
| finalizedBy buildGitCommitFile | ||
| } | ||
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| test { | ||
| /* | ||
| * TODO TEST Figure out why tests fail without this and remove. Might have something to do | ||
| * with the stfuLoggers() call in many of the tests, might kill logging for tests that | ||
| * require it | ||
| * Although it seems to make Mongo start up correctly as well which is odd | ||
| */ | ||
| forkEvery = 1 | ||
| /* | ||
| * TODO TEST split tests into mongo wrapper tests & all other tests (incl. integration). | ||
| * Set up GHA to run the non-mongo tests with a single version of mongo and run the | ||
| * mongo tests with matrixed mongo versions. Combine coverage at the end somehow | ||
| */ | ||
| systemProperty "ASSEMHOMOL_TEST_CONFIG", "./test.cfg" | ||
| testLogging { | ||
| exceptionFormat = 'full' | ||
| showStandardStreams = true | ||
| } | ||
| finalizedBy jacocoTestReport | ||
| } | ||
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| // TODO TEST add a test that starts the server in a docker container and checks some simple cmds | ||
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| jacocoTestReport { | ||
| reports { | ||
| xml.required = true | ||
| csv.required = true | ||
| } | ||
| } | ||
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| javadoc { | ||
| options { | ||
| // I don't know why this isn't working, but it's not worth spending time on right now | ||
| links "https://docs.oracle.com/javase/8/docs/api/" | ||
| } | ||
| } | ||
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| war { | ||
| webXml = file('war/web.xml') | ||
| } | ||
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| configurations { | ||
| // can't directly access testImplementation, so extend and access | ||
| testimpl.extendsFrom testImplementation | ||
| } | ||
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| task generateCLIScript { | ||
| dependsOn compileJava | ||
| doLast { | ||
| def dependencies = configurations.runtimeClasspath.collect { File file -> | ||
| file.absolutePath | ||
| } | ||
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| def classpath = dependencies.join(':') | ||
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| def scriptContent = """#!/bin/sh | ||
| CLASSPATH=$classpath | ||
| java -cp build/classes/java/main:\$CLASSPATH us.kbase.assemblyhomology.cli.AssemblyHomologyCLI \$@ | ||
| """ | ||
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| file("$buildDir/assembly_homology").text = scriptContent | ||
| file("$buildDir/assembly_homology").setExecutable(true) | ||
| } | ||
| } | ||
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| task buildAll { | ||
| dependsOn generateCLIScript | ||
| dependsOn war | ||
| dependsOn javadoc | ||
| } | ||
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| sourceSets { | ||
| main { | ||
| java { | ||
| srcDirs = ["src"] | ||
| exclude '**/test/**' | ||
| } | ||
| } | ||
| test { | ||
| java { | ||
| srcDirs = ["src"] | ||
| include '**/test/**' | ||
| } | ||
| resources { | ||
| srcDirs = ["src"] | ||
| include "**/*.msh" | ||
| include "**/*.txt" | ||
| include "**/wsjars" | ||
| } | ||
| } | ||
| } | ||
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| def fromURL = { url, name -> | ||
| File file = new File("$buildDir/download/${name}.jar") | ||
| file.parentFile.mkdirs() | ||
| if (!file.exists()) { | ||
| new URL(url).withInputStream { downloadStream -> | ||
| file.withOutputStream { fileOut -> | ||
| fileOut << downloadStream | ||
| } | ||
| } | ||
| } | ||
| files(file.absolutePath) | ||
| } | ||
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| dependencies { | ||
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| implementation fromURL( | ||
| 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/workspace/WorkspaceService-0.8.0.jar', | ||
| 'WorkspaceService-0.8.0' | ||
| ) | ||
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| implementation 'org.ini4j:ini4j:0.5.2' | ||
| implementation 'commons-io:commons-io:2.4' | ||
| implementation 'com.beust:jcommander:1.72' | ||
| implementation 'org.mongodb:mongo-java-driver:3.10.1' | ||
| implementation 'com.google.guava:guava:18.0' | ||
| implementation "com.github.kbase:auth2_client_java:0.5.0" | ||
| implementation('com.github.kbase:java_common:0.3.0') { | ||
| exclude group: 'net.java.dev.jna' // breaks mac builds, not needed | ||
| exclude group: 'org.eclipse.jetty.aggregate' // ugh, java common pollutes everything | ||
| exclude group: 'com.fasterxml.jackson.core' // breaks everything if we upgrade | ||
| exclude group: 'javax.servlet', module: 'servlet-api' // 2.5 vs 3.1 below | ||
| } | ||
| implementation 'com.github.zafarkhaja:java-semver:0.9.0' | ||
| implementation 'org.yaml:snakeyaml:1.18' | ||
| implementation 'ch.qos.logback:logback-classic:1.1.2' | ||
| implementation 'org.slf4j:slf4j-api:1.7.25' | ||
| // TODO DEPS Need to rework the java common logger to not use syslog4j at all since it's | ||
| // abandonware and has a ton of CVEs, even in the newer versions. | ||
| implementation "org.syslog4j:syslog4j:0.9.46" | ||
| implementation 'com.fasterxml.jackson.core:jackson-annotations:2.5.4' | ||
| implementation 'com.fasterxml.jackson.core:jackson-databind:2.5.4' | ||
| implementation 'com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.5.4' | ||
| implementation 'org.glassfish.jersey.containers:jersey-container-servlet:2.23.2' | ||
| implementation 'org.glassfish.jersey.media:jersey-media-json-jackson:2.23.2' | ||
| implementation 'javax.servlet:javax.servlet-api:3.0.1' | ||
| implementation 'javax.xml.bind:jaxb-api:2.4.0-b180830.0359' | ||
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| testImplementation "com.github.kbase:auth2:0.7.1" | ||
| testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.1.10' | ||
| testImplementation 'junit:junit:4.12' | ||
| testImplementation('org.eclipse.jetty:jetty-servlet:9.3.11.v20160721') { | ||
| exclude group: "javax.servlet", module: "javax.servlet-api" // upgrading breaks tests | ||
| } | ||
| testImplementation 'org.mockito:mockito-core:3.0.0' | ||
| testImplementation 'org.apache.commons:commons-lang3:3.5' | ||
| testImplementation('com.github.kbase:java_test_utilities:0.1.0') { | ||
| exclude group: 'com.fasterxml.jackson.core' // upgrading breaks stuff | ||
| } | ||
| } | ||
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| task showTestClassPath { | ||
| doLast { | ||
| configurations.testimpl.each { println it } | ||
| } | ||
| } |
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