chore: docker image & build script upgrades

milaboratory · Jul 9, 2022 · 91451e3 · 91451e3
1 parent 62f41d0
commit 91451e3
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Showing 3 changed files with 86 additions and 22 deletions.
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -26,12 +26,12 @@ jobs:
     needs:
       - init
 
-    uses: milaboratory/github-ci/.github/workflows/java-gradle-app.yaml@v2
+    uses: milaboratory/github-ci/.github/workflows/java-gradle.yaml@v2
     with:
       # Environment
-      java-version: '8'
-      app-name: MiXCR
-      app-name-slug: 'mixcr'
+      java-version: '11'
+      product-name: MiXCR
+      product-name-slug: 'mixcr'
 
       # Tests
       test-unit: true
@@ -50,15 +50,17 @@ jobs:
       test-integration-cache-key: 'tests-sequences-v1'
 
       # Distribution
-      dist-docker: false
       dist-archive: ${{ github.event_name != 'schedule' }}
-      dist-archive-tasks: 'distributionZip'
-      dist-archive-paths: './distributions/*.zip'
+      dist-archive-tasks: distributionZip
+      dist-archive-paths: ./distributions/mixcr*.zip
+      dist-archive-s3: true
+      dist-archive-s3-add-sha: true
 
-      # Release to S3
-      release-to-s3: ${{ github.event_name != 'schedule' }}
-      release-s3-add-version: true
-      release-s3-add-sha: ${{ fromJSON(needs.init.outputs.is-release) && 'false' || '8' }}
+      dist-docker: true
+      dist-docker-tasks: |
+        buildDockerImage
+        buildIMGTDockerImage
+      dist-docker-image-name: mixcr
 
       # Send notifications
       notify-telegram: true
@@ -71,9 +73,6 @@ jobs:
         miRepoAccessKeyId=${{ secrets.AWS_CI_ACCESS_KEY_ID }}
         miRepoSecretAccessKey= ${{ secrets.AWS_CI_SECRET_ACCESS_KEY }}
 
-        miGitHubMavenUser=${{ github.actor }}
-        miGitHubMavenToken=${{ secrets.GITHUB_TOKEN }}
-
       AWS_KEY_ID: ${{ secrets.AWS_CI_ACCESS_KEY_ID }}
       AWS_KEY_SECRET: ${{ secrets.AWS_CI_SECRET_ACCESS_KEY }}
 

diff --git a/build.gradle.kts b/build.gradle.kts
@@ -1,5 +1,8 @@
+import com.bmuschko.gradle.docker.tasks.image.DockerBuildImage
+import com.bmuschko.gradle.docker.tasks.image.Dockerfile
 import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar
 import com.palantir.gradle.gitversion.VersionDetails
+import de.undercouch.gradle.tasks.download.Download
 import groovy.lang.Closure
 import org.gradle.api.tasks.testing.logging.TestExceptionFormat.FULL
 import java.net.InetAddress
@@ -25,6 +28,8 @@ plugins {
     id("org.jetbrains.kotlin.plugin.dataframe") version "0.8.0-rc-8"
     id("com.palantir.git-version") version "0.13.0" // don't upgrade, latest version that runs on Java 8
     id("com.github.johnrengelman.shadow") version "7.1.2"
+    id("com.bmuschko.docker-java-application") version "7.4.0"
+    id("de.undercouch.download") version "5.1.0"
 }
 // Make IDE aware of the generated code:
 kotlin.sourceSets.getByName("main").kotlin.srcDir("build/generated/ksp/main/kotlin/")
@@ -46,6 +51,9 @@ val isRelease = boolProperty("mi-release")
 
 val longTests: String? by project
 val miCiStage = properties["mi-ci-stage"] as String?
+
+group = "com.milaboratory"
+version = if (version != "unspecified") version else ""
 description = "MiXCR"
 
 java {
@@ -81,8 +89,8 @@ repositories {
 }
 
 val milibVersion = "2.0.0-3-master"
-val repseqioVersion = "1.4.0-5-master"
-val mitoolVersion = "1.1.0-2-main"
+val repseqioVersion = "1.4.1-1-master"
+val mitoolVersion = "1.1.0-9-main"
 val miplotsVersion = "1.0.0-12-master"
 val jacksonBomVersion = "2.13.3"
 
@@ -152,8 +160,67 @@ val distributionZip by tasks.registering(Zip::class) {
     from(shadowJar) {
         rename("-.*\\.jar", "\\.jar")
     }
-    from("${project.rootDir}/mixcr")
+    from("${project.rootDir}/${project.name}")
+    from("${project.rootDir}/LICENSE")
+}
+
+val prepareDockerContext by tasks.registering(Copy::class) {
+    group = "docker"
+    from(shadowJar) {
+        rename("-.*\\.jar", "\\.jar")
+    }
+    from("${project.rootDir}/${project.name}")
     from("${project.rootDir}/LICENSE")
+    into(layout.buildDirectory.dir("docker"))
+}
+
+val prepareIMGTDockerContext by tasks.registering(Download::class) {
+    group = "docker"
+    dependsOn(prepareDockerContext)
+    src("https://github.com/repseqio/library-imgt/releases/download/v8/imgt.202214-2.sv8.json.gz")
+    dest(layout.buildDirectory.dir("docker"))
+}
+
+val commonDockerContents: Dockerfile.() -> Unit = {
+    from("eclipse-temurin:17-jre")
+    label(mapOf("maintainer" to "MiLaboratories Inc <support@milaboratories.com>"))
+    workingDir("/data")
+    runCommand("mkdir /opt/${project.name}")
+    environmentVariable("PATH", "/opt/${project.name}:\${PATH}")
+    copyFile("LICENSE", "/opt/${project.name}/LICENSE")
+    copyFile(project.name, "/opt/${project.name}/${project.name}")
+    entryPoint(project.name)
+    copyFile("${project.name}.jar", "/opt/${project.name}/${project.name}.jar")
+}
+
+val createDockerfile by tasks.registering(Dockerfile::class) {
+    group = "docker"
+    dependsOn(prepareDockerContext)
+    commonDockerContents()
+}
+
+val imgtDockerfile = layout.buildDirectory.file("docker/Dockerfile.imgt")
+
+val createIMGTDockerfile by tasks.registering(Dockerfile::class) {
+    group = "docker"
+    dependsOn(createDockerfile)
+    dependsOn(prepareIMGTDockerContext)
+    destFile.set(imgtDockerfile)
+    commonDockerContents()
+    copyFile("imgt*", "/opt/${project.name}/")
+}
+
+val buildDockerImage by tasks.registering(DockerBuildImage::class) {
+    group = "docker"
+    dependsOn(createDockerfile)
+    images.set(setOf(project.name) + if (version == "") emptySet() else setOf("${project.name}:${version}"))
+}
+
+val buildIMGTDockerImage by tasks.registering(DockerBuildImage::class) {
+    group = "docker"
+    dependsOn(createIMGTDockerfile)
+    dockerFile.set(imgtDockerfile)
+    images.set(setOf(project.name + ":latest-imgt") + if (version == "") emptySet() else setOf("${project.name}:${version}-imgt"))
 }
 
 publishing {

diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java
@@ -36,10 +36,7 @@
 import gnu.trove.list.array.TIntArrayList;
 import picocli.CommandLine;
 
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Objects;
+import java.util.*;
 import java.util.function.IntFunction;
 import java.util.function.ToIntFunction;
 
@@ -153,7 +150,8 @@ public void run1() throws Exception {
                 OutputPort<NSequenceWithQuality[]> cInput = CUtils.wrap(mainReader, mapper);
 
                 // Running correction
-                correctionResult = corrector.correct(cInput, tagNames, mainReader);
+                // TODO Collections.EMPTY_MAP -> presets
+                correctionResult = corrector.correct(cInput, tagNames, Collections.EMPTY_MAP, mainReader);
                 report = corrector.getReport();
             } else {
                 correctionResult = null;