Merge pull request #15 from nextflow-io/improve-gradle

Improve Gradle build

build.gradle

@@ -0,0 +1,16 @@
+import nextflow.gradle.plugins.NextflowPlugin
+
+apply plugin: NextflowPlugin
+
+ext{
+    github_organization = 'nextflow-io'
+    github_username = project.findProperty('github_username') ?: 'abhi18av'
+    github_access_token = project.findProperty('github_access_token') ?: System.getenv('GITHUB_TOKEN')
+    github_commit_email = project.findProperty('github_commit_email') ?: '[email protected]'
+}
+
+nextflowPlugin{
+    githubOrganization = github_organization
+    extensionPoints = [
+    ]
+}

buildSrc/build.gradle

@@ -0,0 +1,12 @@
+plugins {
+    id 'groovy-gradle-plugin'
+    id "io.nextflow.nf-build-plugin" version "1.0.1"
+}
+
+repositories {
+    mavenCentral()
+}
+
+dependencies {
+    implementation 'commons-codec:commons-codec:1.15'
+}

buildSrc/src/main/groovy/nextflow/gradle/plugins/GenerateIdxTask.groovy

@@ -0,0 +1,41 @@
+package nextflow.gradle.plugins
+
+import org.gradle.api.DefaultTask
+import org.gradle.api.file.RegularFileProperty
+import org.gradle.api.provider.ListProperty
+import org.gradle.api.tasks.Internal
+import org.gradle.api.tasks.OutputFile
+import org.gradle.api.tasks.TaskAction
+
+
+abstract class GenerateIdxTask extends DefaultTask{
+
+    @Internal
+    abstract ListProperty<String> extensionPoints
+
+    @OutputFile
+    final abstract RegularFileProperty outputFile =
+            project.objects.fileProperty().convention(project.layout.buildDirectory.file(
+                    "resources/main/META-INF/extensions.idx"))
+
+    GenerateIdxTask() {
+        setGroup('nextflow')
+    }
+
+    @TaskAction
+    def runTask() {
+        def output = outputFile.get().asFile
+
+        if( extensionPoints.getOrElse([]).size() ){
+            output.text = extensionPoints.getOrElse([]).join('\n')
+            return
+        }
+
+        def matcher = new SourcesMatcher(project)
+        def extensionsClassName = matcher.pluginExtensions
+        def traceClassName = matcher.traceObservers
+        def all = extensionsClassName+traceClassName
+        output.text = all.join('\n')
+    }
+
+}

buildSrc/src/main/groovy/nextflow/gradle/plugins/JsonPluginTask.groovy

@@ -0,0 +1,67 @@
+package nextflow.gradle.plugins
+
+import groovy.json.JsonOutput
+import org.apache.commons.codec.digest.DigestUtils
+import org.gradle.api.DefaultTask
+import org.gradle.api.GradleException
+import org.gradle.api.file.RegularFileProperty
+import org.gradle.api.provider.Property
+import org.gradle.api.tasks.Internal
+import org.gradle.api.tasks.OutputFile
+import org.gradle.api.tasks.TaskAction
+import org.gradle.api.tasks.bundling.Jar
+
+import java.time.OffsetDateTime
+import java.time.format.DateTimeFormatter
+
+abstract class JsonPluginTask extends DefaultTask{
+
+    @Internal
+    abstract Property<String> getDownloadUrl()
+
+    @Internal
+    final abstract RegularFileProperty zipFile =
+            project.objects.fileProperty().convention(project.layout.buildDirectory.file(
+                    "plugin/${project.name}-${project.version}.zip"))
+
+    @OutputFile
+    final abstract RegularFileProperty outputFile =
+            project.objects.fileProperty().convention(project.layout.buildDirectory.file(
+                    "plugin/${project.name}-${project.version}-meta.json"))
+
+
+    JsonPluginTask(){
+        setGroup('nextflow')
+        dependsOn 'zipPlugin'
+    }
+
+
+    protected String resolveURL(){
+        "${downloadUrl.get()}/${project.version}/${project.name}-${project.version}.zip"
+    }
+
+    protected static String now() {
+        OffsetDateTime.now().format(DateTimeFormatter.ISO_DATE_TIME)
+    }
+
+    protected static String computeSha512(File file) {
+        if( !file.exists() )
+            throw new GradleException("Missing file: $file -- cannot compute SHA-512")
+        return DigestUtils.sha512Hex(file.bytes)
+    }
+
+    @TaskAction
+    def runTask() {
+        def jarTask = project.tasks.findByName('jar') as Jar
+        def manifest = jarTask.manifest
+        def json = [
+                version: "$project.version",
+                date: now(),
+                url: resolveURL(),
+                requires: manifest.attributes['Plugin-Requires'],
+                sha512sum: computeSha512(zipFile.get().asFile)
+        ]
+        outputFile.get().asFile.text = JsonOutput.prettyPrint(JsonOutput.toJson(json))
+    }
+
+}

buildSrc/src/main/groovy/nextflow/gradle/plugins/NextflowPlugin.groovy

@@ -0,0 +1,29 @@
+package nextflow.gradle.plugins
+
+import org.gradle.api.Plugin
+import org.gradle.api.Project
+
+class NextflowPlugin implements Plugin<Project>{
+
+    @Override
+    void apply(Project target) {
+
+        NextflowPluginExtension nextflowPluginExtension = target.extensions.create('nextflowPlugin',NextflowPluginExtension)
+
+        target.subprojects.find{it.name=="plugins"}.subprojects.each{ project ->
+            project.tasks.register('zipPlugin', ZipPluginTask,{
+
+            })
+            project.tasks.register('unzipPlugin', UnzipPluginTask,{
+
+            })
+            project.tasks.register('jsonPlugin', JsonPluginTask, {
+                downloadUrl = nextflowPluginExtension.downloadUrl
+            })
+            project.tasks.register('generateIdx', GenerateIdxTask, {
+                extensionPoints = nextflowPluginExtension.extensionPoints
+            })
+            project.tasks.findByName("processResources")?.dependsOn(project.tasks.findByName("generateIdx"))
+        }
+    }
+}

buildSrc/src/main/groovy/nextflow/gradle/plugins/NextflowPluginExtension.groovy

@@ -0,0 +1,68 @@
+package nextflow.gradle.plugins
+
+import org.gradle.api.Project
+import org.gradle.api.provider.ListProperty
+import org.gradle.api.provider.Property
+
+class NextflowPluginExtension {
+
+    final Property<String> downloadUrl
+
+    final Property<String> nextflowVersion
+
+    final Property<String> githubOrganization
+
+    final Property<String> pluginClassName
+
+    final ListProperty<String> extensionPoints
+
+    final private Project project
+
+    NextflowPluginExtension(Project project){
+        this.project = project
+        nextflowVersion = project.objects.property(String)
+        downloadUrl = project.objects.property(String)
+        githubOrganization = project.objects.property(String)
+        pluginClassName = project.objects.property(String)
+        extensionPoints = project.objects.listProperty(String)
+    }
+
+    void setNextflowVersion(String nextflowVersion){
+        this.nextflowVersion.set(nextflowVersion)
+    }
+
+    String getNextflowVersion(){
+        this.nextflowVersion.getOrElse("23.04.0")
+    }
+
+    void setDownloadUrl(String downloadUrl){
+        this.downloadUrl.set(downloadUrl)
+    }
+
+    String getDownloadUrl() {
+        return downloadUrl.getOrElse("https://github.com/${getGithubOrganization()}/${project.name}/releases/download")
+    }
+
+    String getGithubOrganization() {
+        return githubOrganization.get()
+    }
+
+    void setGithubOrganization(String githubOrganization){
+        this.githubOrganization.set(githubOrganization)
+    }
+
+    String getPluginClassName() {
+        SourcesMatcher matcher = new SourcesMatcher(project)
+        String resolved = matcher.pluginClassName
+        return pluginClassName.getOrElse(resolved)
+    }
+
+    void setPluginClassName(String pluginClassName){
+        this.pluginClassName.set(pluginClassName)
+    }
+
+    void setExtensionPoints(List<String> extensions){
+        this.extensionPoints.set(extensions)
+    }
+
+}

buildSrc/src/main/groovy/nextflow/gradle/plugins/SourcesMatcher.groovy

@@ -0,0 +1,48 @@
+package nextflow.gradle.plugins
+
+import org.gradle.api.Project
+import org.gradle.api.tasks.SourceSet
+import org.gradle.api.tasks.SourceSetContainer
+
+class SourcesMatcher {
+
+    Project project
+    SourcesMatcher(Project project){
+        this.project = project
+    }
+
+
+    String getPluginClassName(){
+        return findSources(/class (\w+) extends BasePlugin/).first()
+    }
+
+    List<String> getPluginExtensions(){
+        return findSources(/class (\w+) extends PluginExtensionPoint/) +
+                findSources(/class (\w+) extends Executor implements ExtensionPoint/)
+    }
+
+    List<String> getTraceObservers(){
+        return findSources(/class (\w+) implements TraceObserverFactory/)
+    }
+
+    List<String> findSources( def regexp ){
+        def sourceSets = project.extensions.getByType(SourceSetContainer)
+        def mainSourceSet = sourceSets.findByName(SourceSet.MAIN_SOURCE_SET_NAME)
+        def sources = mainSourceSet.allSource
+        def root = project.projectDir
+
+        def matcher = sources.findAll{
+            def source = it.text
+            def matcher = source =~ regexp
+            if( matcher.size() != 1 ){
+                return null
+            }
+            it
+        }
+        matcher.collect { file ->
+            def source = file.toString() - "$root.absolutePath/src/main/"
+            return source.split('\\.').dropRight(1).join().split(File.separator).drop(1).join('.')
+        }
+    }
+
+}

buildSrc/src/main/groovy/nextflow/gradle/plugins/UnzipPluginTask.groovy

@@ -0,0 +1,15 @@
+package nextflow.gradle.plugins
+import org.gradle.api.tasks.Copy
+
+
+class UnzipPluginTask extends Copy{
+
+    UnzipPluginTask(){
+        setGroup('nextflow')
+        dependsOn project.tasks.zipPlugin
+        outputs.upToDateWhen {false}
+        from project.zipTree(project.tasks.zipPlugin.outputs.files.first())
+        into "${System.getProperty("user.home")}/.nextflow/plugins/${project.name}-${project.version}"
+    }
+
+}

buildSrc/src/main/groovy/nextflow/gradle/plugins/ZipPluginTask.groovy

@@ -0,0 +1,44 @@
+package nextflow.gradle.plugins
+
+
+import org.gradle.api.file.RegularFileProperty
+import org.gradle.api.tasks.OutputFile
+import org.gradle.api.tasks.bundling.Jar
+
+
+class ZipPluginTask extends Jar{
+
+    @OutputFile
+    final abstract RegularFileProperty outputFile =
+            project.objects.fileProperty().convention(project.layout.buildDirectory.file(
+                    "plugin/${project.name}-${project.version}.zip"))
+
+    ZipPluginTask() {
+        setGroup('nextflow')
+
+        dependsOn(project.tasks.findByName('build'))
+        dependsOn(project.tasks.generateIdx)
+
+        into( 'classes',{
+            with project.tasks.findByName('jar')
+        })
+
+        into('lib',{
+            from(project.configurations.find {it.name=='runtimeClasspath'})
+        })
+
+        manifest {
+            Jar jar = project.tasks.findByName('jar') as Jar
+            from(jar.manifest)
+        }
+
+        archiveExtension.set('zip')
+        setPreserveFileTimestamps(false)
+        setReproducibleFileOrder(true)
+
+        def directory = project.objects.fileProperty().convention(
+                project.layout.buildDirectory.file("plugin"))
+        getDestinationDirectory().set(directory.get().asFile)
+    }
+
+}

gradle.properties

@@ -0,0 +1 @@
+version=0.0.2-rc1