Issue #79 Added tests and comments

src/main/groovy/nextflow/scm/AssetManager.groovy

@@ -240,7 +240,7 @@ class AssetManager {
 
         def result = new ScriptFile(getMainScriptFile())
         result.revisionInfo = getCurrentRevisionAndName()
-        result.repository = getGitRepositoryUrl()
+        result.repository = getGitConfigRemoteUrl()
         result.localPath = localPath.toPath()
 
         return result
@@ -703,13 +703,25 @@ class AssetManager {
         return result ? result.name : null
     }
 
+    /**
+     * Models revision information of a project repository.
+     */
     @Canonical
     static class RevisionInfo {
 
+        /**
+         * Git commit ID
+         */
         String commitId
 
+        /**
+         * Git tab or branch name
+         */
         String revision
 
+        /**
+         * @return A formatted string containing the commitId and revision properties
+         */
         String toString() {
 
             if( !commitId ) {

src/main/groovy/nextflow/script/ScriptFile.groovy

@@ -35,20 +35,44 @@ import nextflow.scm.AssetManager
 @ToString(includeNames = true)
 class ScriptFile {
 
+    /**
+     * Pipeline main script file
+     */
     Path main
 
+    /**
+     * (remote) project repository URL
+     */
     String repository
 
+    /**
+     * The
+     */
     AssetManager.RevisionInfo revisionInfo
 
+    /**
+     * (local) project repository path
+     */
     Path localPath
 
+    /**
+     * @return Directory where the main script file is stored
+     */
     Path getParent() { main?.parent }
 
+    /**
+     * @return Main script file content as a text string
+     */
     String getText() { main?.text }
 
+    /**
+     * @return Repository commitId
+     */
     String getCommitId() { revisionInfo?.commitId }
 
+    /**
+     * @return Repository tag or branch
+     */
     String getRevision() { revisionInfo?.revision }
 
     ScriptFile( File file ) {

src/main/groovy/nextflow/script/WorkflowMetadata.groovy

@@ -19,7 +19,6 @@
  */
 
 package nextflow.script
-
 import java.nio.file.Path
 
 import groovy.transform.CompileStatic
@@ -28,8 +27,8 @@ import groovy.transform.ToString
 import groovy.util.logging.Slf4j
 import nextflow.Const
 import nextflow.util.Duration
-
 /**
+ * Models workflow metadata properties and notification handler
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
@@ -69,18 +68,48 @@ class WorkflowMetadata {
         owner.session.onShutdown { invokeOnComplete() }
     }
 
-    void onComplete( Closure closure ) {
-        events << closure
+    /**
+     * Implements the following idiom in the pipeline script:
+     * <pre>
+     *     window.onComplete {
+     *         // do something
+     *     }
+     * </pre>
+     *
+     * @param action The action handler
+     */
+    void onComplete( Closure action ) {
+        events << action
     }
 
-    @PackageScope
-    void registerConfigAction( Map config ) {
+    /**
+     * Implements the following idiom in the pipeline script:
+     * <pre>
+     *     window.onComplete = {
+     *         // do something
+     *     }
+     * </pre>
+     *
+     * @param action The action handler
+     */
+    void setOnComplete( Closure action ) {
+        events << action
+    }
+
+    private void registerConfigAction( Map config ) {
         if( !config ) return
         if( config.onComplete instanceof Closure ) {
             events.add( (Closure)config.onComplete )
         }
     }
 
+    /**
+     * This method is required in order to allow the {@code onComplete} closure
+     * defined in the {@code nextflow.config} file to access the {@code workflow}
+     * object.
+     *
+     * @return The workflow object itself.
+     */
     def getWorkflow() { return this }
 
     @PackageScope
@@ -99,6 +128,9 @@ class WorkflowMetadata {
         }
     }
 
+    /**
+     * @return Render the workflow properties
+     */
     String toString() {
         def result = new StringBuilder()
         result << 'repository: ' << repository

src/test/groovy/nextflow/scm/AssetManagerTest.groovy

@@ -20,6 +20,7 @@
 
 package nextflow.scm
 import nextflow.exception.AbortOperationException
+import org.eclipse.jgit.api.Git
 import org.junit.Rule
 import spock.lang.Requires
 import spock.lang.Specification
@@ -317,5 +318,41 @@ class AssetManagerTest extends Specification {
 
     }
 
+    def 'should create a script file object' () {
+
+        given:
+        def dir = tempDir.root
+        // create the repo dir
+        dir.resolve('main.nf').text = "println 'Hello world'"
+        dir.resolve('nextflow.config').text = 'manifest {  }'
+
+        def init = Git.init()
+        def repo = init.setDirectory( dir.toFile() ).call()
+        repo.add().addFilepattern('.').call()
+        def commit = repo.commit().setAll(true).setMessage('First commit').call()
+        repo.close()
+
+        // append fake remote data
+        dir.resolve('.git/config') << '''
+            [remote "origin"]
+                url = https://github.com/nextflow-io/nextflow.git
+                fetch = +refs/heads/*:refs/remotes/origin/*
+            [branch "master"]
+                remote = origin
+                merge = refs/heads/master
+            '''
+            .stripIndent()
+
+        when:
+        def manager = new AssetManager().setLocalPath(dir.toFile())
+        def script = manager.getScriptFile()
+        then:
+        script.localPath == dir
+        script.commitId == commit.name().substring(0,10)
+        script.revision == 'master'
+        script.parent == dir
+        script.text == "println 'Hello world'"
+        script.repository == 'https://github.com/nextflow-io/nextflow.git'
+    }
 
 }

src/test/groovy/nextflow/script/WorkflowMetadataTest.groovy

@@ -0,0 +1,115 @@
+/*
+ * Copyright (c) 2013-2015, Centre for Genomic Regulation (CRG).
+ * Copyright (c) 2013-2015, Paolo Di Tommaso and the respective authors.
+ *
+ *   This file is part of 'Nextflow'.
+ *
+ *   Nextflow is free software: you can redistribute it and/or modify
+ *   it under the terms of the GNU General Public License as published by
+ *   the Free Software Foundation, either version 3 of the License, or
+ *   (at your option) any later version.
+ *
+ *   Nextflow is distributed in the hope that it will be useful,
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *   GNU General Public License for more details.
+ *
+ *   You should have received a copy of the GNU General Public License
+ *   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package nextflow.script
+
+import java.nio.file.Files
+
+import nextflow.Const
+import nextflow.Session
+import nextflow.scm.AssetManager
+import nextflow.util.Duration
+import org.eclipse.jgit.api.Git
+import spock.lang.Specification
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class WorkflowMetadataTest extends Specification {
+
+    def 'should populate workflow object' () {
+
+        given:
+        final begin = new Date()
+        def dir = Files.createTempDirectory('test')
+        /*
+         * create the github repository
+         */
+        dir.resolve('main.nf').text = "println 'Hello world'"
+        dir.resolve('nextflow.config').text = 'manifest {  }'
+
+        def init = Git.init()
+        def repo = init.setDirectory( dir.toFile() ).call()
+        repo.add().addFilepattern('.').call()
+        def commit = repo.commit().setAll(true).setMessage('First commit').call()
+        repo.close()
+
+        // append fake remote data
+        dir.resolve('.git/config') << '''
+            [remote "origin"]
+                url = https://github.com/nextflow-io/nextflow.git
+                fetch = +refs/heads/*:refs/remotes/origin/*
+            [branch "master"]
+                remote = origin
+                merge = refs/heads/master
+            '''
+                .stripIndent()
+
+        /*
+         * create ScriptFile object
+         */
+        def manager = new AssetManager().setLocalPath(dir.toFile())
+        def script = manager.getScriptFile()
+
+        /*
+         * config file onComplete handler
+         */
+        def handlerInvoked = false
+        def session = new Session([workflow: [onComplete: { -> handlerInvoked=true } ]  ])
+
+        /*
+         * script runner
+         */
+        def runner = Mock(ScriptRunner)
+        runner.getScriptFile() >> script
+        runner.fetchContainers() >> 'busybox/latest'
+        runner.commandLine >> 'nextflow run -this -that'
+        runner.session >> session
+
+        when:
+        def workflow = new WorkflowMetadata(runner)
+        then:
+        workflow.repository == 'https://github.com/nextflow-io/nextflow.git'
+        workflow.commitId == commit.name().substring(0,10)
+        workflow.revision == 'master'
+        workflow.container == 'busybox/latest'
+        workflow.localPath == dir
+        workflow.startTime >= begin
+        workflow.startTime <= new Date()
+        workflow.endTime == null
+        workflow.commandLine == 'nextflow run -this -that'
+        workflow.nextflow.version == Const.APP_VER
+        workflow.nextflow.build == Const.APP_BUILDNUM
+        workflow.nextflow.timestamp == Const.APP_TIMESTAMP_UTC
+
+        when:
+        workflow.invokeOnComplete()
+        then:
+        workflow.endTime > workflow.startTime
+        workflow.endTime <= new Date()
+        workflow.duration == new Duration( workflow.endTime.time - workflow.startTime.time )
+        handlerInvoked
+
+        cleanup:
+        dir?.deleteDir()
+    }
+
+}