feat(244) dynamic uris

.github/workflows/mega-linter.yml

@@ -6,14 +6,16 @@ on:
   # Trigger mega-linter at every push. Action will also be visible from Pull Requests to main
   push: # Comment this line to trigger action only on pull-requests (not recommended if you don't pay for GH Actions)
 
-permissions: read-all
+permissions:
+  issues: write
+  pull-requests: write
 
 env: # Comment env block if you do not want to apply fixes
   # Apply linter fixes configuration
   APPLY_FIXES: all # When active, APPLY_FIXES must also be defined as environment variable (in github/workflows/mega-linter.yml or other CI tool)
   #APPLY_FIXES_EVENT: pull_request # Decide which event triggers application of fixes in a commit or a PR (pull_request, push, all)
   #APPLY_FIXES_MODE: pull_request # If APPLY_FIXES is used, defines if the fixes are directly committed (commit) or posted in a PR (pull_request)
-  DISABLE_LINTERS: SPELL_CSPELL,COPYPASTE_JSCPD,REPOSITORY_GITLEAKS
+  DISABLE_LINTERS: SPELL_CSPELL,COPYPASTE_JSCPD,REPOSITORY_GITLEAKS,GROOVY_NPM_GROOVY_LINT
   FILTER_REGEX_EXCLUDE: .*/.*gradle
 
 concurrency:

.groovylintrc.json

@@ -28,6 +28,9 @@
         "JUnitPublicNonTestMethod": {
             "enabled": false
         },
+        "JUnitTestMethodWithoutAssert": {
+            "enabled": false
+        },
         "JavaIoPackageAccess": {
             "enabled": false
         },

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [0.8.7] 2024-10-23
+
+- Use package cache instead of `params` to find output URIs
+  (in order to support dynamic URIs set by, e.g. `main.nf`)
+- Allow setting metadata from inside the workflow
+
 ## [0.8.6] 2024-09-11
 
 - Fix addOverlay bug on subfolders

Makefile

@@ -16,11 +16,11 @@ REPORT ?= ./plugins/$(PROJECT)/build/reports/tests/test/index.html
 
 verify: #compile
 	echo $(WRITE_BUCKET)
-	./gradlew check || open $(REPORT)
+	./gradlew test ${ONE} || open $(REPORT)
 
 fast:
-	./gradlew ${mm}test --fail-fast || open ./plugins/nf-quilt/build/reports/tests/test/index.html
-
+	./gradlew test ${ONE} --fail-fast || open $(REPORT)
+# example: make fast ONE="--tests QuiltProductTest"
 check-env:
 	echo $(VERSION)
 	echo $(WRITE_BUCKET)
@@ -38,7 +38,7 @@ compile:
 	./gradlew compileGroovy exportClasspath
 	@echo "DONE `date`"
 
-nextflow-git:
+nextflow:
 	if [ ! -d "$(NF_DIR)" ]; then git clone https://github.com/nextflow-io/nextflow.git  "$(NF_DIR)"; fi
 	cd "$(NF_DIR)"; git checkout && make compile && git restore .; cd ..
 

README.md

@@ -93,8 +93,8 @@ From the command-line, do, e.g.:
 ```bash
 # export NXF_VER=23.04.3
 export LOG4J_DEBUG=true  # for verbose logging
-export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.8.6/nf-quilt-0.8.6-meta.json
-nextflow run main.nf -plugins [email protected].6
+export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.8.7/nf-quilt-0.8.7-meta.json
+nextflow run main.nf -plugins [email protected].7
 ```
 
 For Tower, you can use the "Pre-run script" to set the environment variables.

build.gradle

@@ -194,9 +194,8 @@ def getRuntimeConfigs() {
 task exportClasspath {
     dependsOn allprojects.jar
     doLast {
-        def home = System.getProperty('user.home')
         def all = getRuntimeConfigs()
-        def libs = all.collect { File file ->  /*println file.canonicalPath.replace(home, '$HOME');*/ file.canonicalPath;  }
+        def libs = all.collect { File file -> file.canonicalPath;  }
         ['nextflow', 'nf-commons', 'nf-httfs'].each { libs << file("modules/$it/build/libs/${it}-${version}.jar").canonicalPath }
         file('.launch.classpath').text = libs.unique().join(':')
     }

gradle-groovysh-init.gradle

@@ -1,49 +1,49 @@
-gradle.projectsLoaded {
-    rootProject {
-        afterEvaluate { project ->
-            if (!project.repositories.any{it.name == 'MavenRepo'}) {
-                project.repositories {
-                    // To be able to load org.codehaus.groovy:groovy-groovysh
-                    mavenCentral()
-                }
-            }
-
-            project.configurations {
-                groovyshdependencies
-            }
-
-            project.dependencies {
-                groovyshdependencies("org.codehaus.groovy:groovy-groovysh:${GroovySystem.version}") {
-                    exclude group: 'org.codehaus.groovy'
-                }
-            }
-
-            project.tasks.register('groovysh') {
-                group 'debug'
-                description 'Runs an interactive shell in the context of the project.'
-                doLast {
-                    URLClassLoader groovyObjectClassLoader = GroovyObject.class.classLoader
-                    def groovyshClass
-                    def groovyShell
-
-                    // Add dependency jars to classloader
-                    configurations.groovyshdependencies.each {File file ->
-                        groovyObjectClassLoader.addURL(file.toURL())
-                    }
-                    Class.forName('jline.console.history.FileHistory', true, groovyObjectClassLoader)
-                    groovyshClass = Class.forName('org.codehaus.groovy.tools.shell.Groovysh', true, groovyObjectClassLoader)
-
-                    if (groovyshClass) {
-                        groovyShell = groovyshClass.newInstance()
-                    }
-                    if (groovyShell) {
-                        groovyShell.interp.context.variables.put("gradle", gradle)
-                        groovyShell.interp.context.variables.put("settings", gradle.settings)
-                        groovyShell.interp.context.variables.put("project", project)
-                        groovyShell.run('')
-                    }
-                }
-            }
-        }
-    }
-}
+gradle.projectsLoaded {
+    rootProject {
+        afterEvaluate { project ->
+            if (!project.repositories.any { it.name == 'MavenRepo' }) {
+                project.repositories {
+                    // To be able to load org.codehaus.groovy:groovy-groovysh
+                    mavenCentral()
+                }
+        }
+
+            project.configurations {
+                groovyshdependencies
+            }
+
+            project.dependencies {
+                groovyshdependencies("org.codehaus.groovy:groovy-groovysh:${GroovySystem.version}") {
+                    exclude group: 'org.codehaus.groovy'
+                }
+            }
+
+            project.tasks.register('groovysh') {
+                group 'debug'
+                description 'Runs an interactive shell in the context of the project.'
+                doLast {
+                    URLClassLoader groovyObjectClassLoader = GroovyObject.classLoader
+                    def groovyshClass
+                    def groovyShell
+
+                    // Add dependency jars to classloader
+                    configurations.groovyshdependencies.each { File file ->
+                        groovyObjectClassLoader.addURL(file.toURL())
+                    }
+                    Class.forName('jline.console.history.FileHistory', true, groovyObjectClassLoader)
+                    groovyshClass = Class.forName('org.codehaus.groovy.tools.shell.Groovysh', true, groovyObjectClassLoader)
+
+                    if (groovyshClass) {
+                        groovyShell = groovyshClass.newInstance()
+                    }
+                    if (groovyShell) {
+                        groovyShell.interp.context.variables.put('gradle', gradle)
+                        groovyShell.interp.context.variables.put('settings', gradle.settings)
+                        groovyShell.interp.context.variables.put('project', project)
+                        groovyShell.run('')
+                    }
+                }
+            }
+    }
+}
+}

groovysh-task.gradle

@@ -1,54 +1,52 @@
-gradle.projectsLoaded {
-    rootProject {
-        afterEvaluate { project ->
-            if (!project.repositories.any{it.name == 'MavenRepo'}) {
-                project.repositories {
-                    // To be able to load org.apache.groovy:groovy-groovysh and dependencies
-                    mavenCentral {
-                        content {
-                            includeGroup 'org.apache.groovy'
-                            includeGroup 'jline'
-                            includeGroup 'com.github.javaparser'
-                            includeGroup 'org.ow2.asm'
-                            includeGroup 'org.abego.treelayout'
-                            includeGroup 'org.apache.ivy'
-                        }
-                    }
-                }
-            }
-            project.configurations {
-                groovyshdependencies
-            }
-
-            project.dependencies {
-                groovyshdependencies "org.apache.groovy:groovy-groovysh:4.0.23"
-            }
-
-            project.tasks.register('groovysh') {
-                group 'debug'
-                description 'Runs an interactive shell in the context of the project. Use :inspect command to inspect project, gradle, settings or other objects.'
-                doLast {
-                    URLClassLoader groovyshClassLoader = new URLClassLoader();
-                    configurations.groovyshdependencies.each {File file ->
-                        groovyshClassLoader.addURL(file.toURI().toURL())
-                    }
-
-                    def fileHistoryClass
-                    def groovyshClass
-                    def groovyShell
-                    fileHistoryClass = Class.forName('jline.console.history.FileHistory', true, groovyshClassLoader)
-                    groovyshClass = Class.forName('org.apache.groovy.groovysh.Groovysh', true, groovyshClassLoader)
-                    if (groovyshClass) {
-                        groovyShell = groovyshClass.newInstance()
-                        if (groovyShell) {
-                            groovyShell.interp.context.variables.put("gradle", gradle)
-                            groovyShell.interp.context.variables.put("settings", gradle.settings)
-                            groovyShell.interp.context.variables.put("project", project)
-                            groovyShell.run('# Available objects: gradle, settings, project\n# Try :inspect project')
-                        }
-                    }
-                }
-            }
-        }
-    }
-}
+gradle.projectsLoaded {
+    rootProject {
+        afterEvaluate { project ->
+            if (!project.repositories.any { it.name == 'MavenRepo' }) {
+                project.repositories {
+                    // To be able to load org.apache.groovy:groovy-groovysh and dependencies
+                    mavenCentral {
+                        content {
+                            includeGroup 'org.apache.groovy'
+                            includeGroup 'jline'
+                            includeGroup 'com.github.javaparser'
+                            includeGroup 'org.ow2.asm'
+                            includeGroup 'org.abego.treelayout'
+                            includeGroup 'org.apache.ivy'
+                        }
+                    }
+                }
+        }
+            project.configurations {
+                groovyshdependencies
+            }
+
+            project.dependencies {
+                groovyshdependencies 'org.apache.groovy:groovy-groovysh:4.0.23'
+            }
+
+            project.tasks.register('groovysh') {
+                group 'debug'
+                description 'Runs an interactive shell in the context of the project. Use :inspect command to inspect project, gradle, settings or other objects.'
+                doLast {
+                    URLClassLoader groovyshClassLoader = new URLClassLoader()
+                    configurations.groovyshdependencies.each { File file ->
+                        groovyshClassLoader.addURL(file.toURI().toURL())
+                    }
+
+                    def groovyshClass
+                    def groovyShell
+                    groovyshClass = Class.forName('org.apache.groovy.groovysh.Groovysh', true, groovyshClassLoader)
+                    if (groovyshClass) {
+                        groovyShell = groovyshClass.newInstance()
+                        if (groovyShell) {
+                            groovyShell.interp.context.variables.put('gradle', gradle)
+                            groovyShell.interp.context.variables.put('settings', gradle.settings)
+                            groovyShell.interp.context.variables.put('project', project)
+                            groovyShell.run('# Available objects: gradle, settings, project\n# Try :inspect project')
+                        }
+                    }
+                }
+            }
+    }
+}
+}

plugins/build.gradle

@@ -15,9 +15,9 @@
  */
 
 plugins {
-    id "java"
-    id "groovy"
-    id "io.nextflow.nf-build-plugin" version "1.0.1"
+    id 'java'
+    id 'groovy'
+    id 'io.nextflow.nf-build-plugin' version '1.0.1'
 }
 
 ext.github_organization = project.findProperty('github_organization') ?: 'nextflow-io'
@@ -29,8 +29,9 @@ ext.github_index_url = "https://github.com/${github_organization}/plugins/main/p
 jar.enabled = false
 
 String computeSha512(File file) {
-    if( !file.exists() )
+    if (!file.exists()) {
         throw new GradleException("Missing file: $file -- cannot compute SHA-512")
+    }
     return org.apache.commons.codec.digest.DigestUtils.sha512Hex(file.bytes)
 }
 
@@ -40,15 +41,15 @@ String now() {
 
 List<String> allPlugins() {
     def plugins = []
-    new File(rootProject.rootDir, 'plugins') .eachDir { if(it.name.startsWith('nf-')) plugins.add(it.name) }
+    new File(rootProject.rootDir, 'plugins') .eachDir { if (it.name.startsWith('nf-')) plugins.add(it.name) }
     return plugins
 }
 
 String metaFromManifest(String meta, File file) {
     def str = file.text
     def regex = ~/(?m)^$meta:\s*([\w-\.<>=]+)$/
     def m = regex.matcher(str)
-    if( m.find() ) {
+    if (m.find()) {
         def ver = m.group(1)
         println "Set plugin '${file.parentFile.parentFile.parentFile.parentFile.name}' version=${ver}"
         return ver
@@ -68,7 +69,7 @@ subprojects {
         mavenCentral()
     }
 
-    version = metaFromManifest('Plugin-Version',file('src/resources/META-INF/MANIFEST.MF'))
+    version = metaFromManifest('Plugin-Version', file('src/resources/META-INF/MANIFEST.MF'))
 
     tasks.withType(Jar) {
         duplicatesStrategy = DuplicatesStrategy.INCLUDE
@@ -94,7 +95,7 @@ subprojects {
 "version": "${project.version}",
 "date": "${timestamp}",
 "url": "https://github.com/${github_organization}/${project.name}/releases/download/${project.version}/${project.name}-${project.version}.zip",
-"requires": "${metaFromManifest('Plugin-Requires',file('src/resources/META-INF/MANIFEST.MF'))}",
+"requires": "${metaFromManifest('Plugin-Requires', file('src/resources/META-INF/MANIFEST.MF'))}",
 "sha512sum": "${computeSha512(zip)}"
 }
 """
@@ -129,10 +130,10 @@ subprojects {
     /*
     * "install" the plugin the project root build/plugins directory
     */
-    project.parent.tasks.getByName("assemble").dependsOn << copyPluginZip
+    project.parent.tasks.getByName('assemble').dependsOn << copyPluginZip
 
     task uploadPlugin(type: io.nextflow.gradle.tasks.GithubUploader, dependsOn: makeZip) {
-        assets = providers.provider {["$buildDir/libs/${project.name}-${project.version}.zip",
+        assets = providers.provider { ["$buildDir/libs/${project.name }-${project.version }.zip",
                                       "$buildDir/libs/${project.name}-${project.version}-meta.json" ]}
         release = providers.provider { project.version }
         repo = providers.provider { project.name }
@@ -141,7 +142,6 @@ subprojects {
         authToken = github_access_token
         skipExisting = true
     }
-
 }
 
 task upload(dependsOn: [subprojects.uploadPlugin]) { }
@@ -151,11 +151,11 @@ classes.dependsOn subprojects.copyPluginLibs
 /*
  * Merge and publish the plugins index file
  */
-task publishIndex( type: io.nextflow.gradle.tasks.GithubRepositoryPublisher ) {
+task publishIndex(type: io.nextflow.gradle.tasks.GithubRepositoryPublisher) {
     indexUrl = github_index_url
     repos = allPlugins()
     owner = github_organization
     githubUser = github_username
     githubEmail = github_commit_email
     githubToken = github_access_token
-}
+}