Committing version 0.3.4 fixing a couple of bugs

Author: pditommaso

build.gradle

@@ -19,7 +19,7 @@
 
 apply plugin: 'groovy'
 apply plugin: 'codenarc'
-version = '0.3.3'
+version = '0.3.4'
 
 repositories {
     flatDir(dirs: file('lib'))

changelog.txt

@@ -2,8 +2,10 @@ NEXTFLOW CHANGE-LOG
 ===================
 
 0.3.4
-- Extending semnatics for method File.copyTo(source,target) so that when 'target' argument 
+- Extending semantic for method File.copyTo(source,target) so that when 'target' argument 
   is a directory, it copy the 'source' file to that folder, with the same name of the original file.
+- Bug: Fixed a ClassCastEx exception when the 'bin' folder is added to the PATH
+- Bug: Fixed an issue that raised an error "error=26 Text file busy" on some platforms (CentOS)  
 
 0.3.3 - 8 Aug 2013
 - Added optional parameters to 'chunkLines' and 'chunkFasta' methods

src/main/groovy/nextflow/Const.groovy

@@ -57,17 +57,17 @@ class Const {
     /**
      * The application version
      */
-    static final String APP_VER = "0.3.3"
+    static final String APP_VER = "0.3.4"
 
     /**
      * The app build time as linux/unix timestamp
      */
-    static final long APP_TIMESTAMP = 1376051851359
+    static final long APP_TIMESTAMP = 1377297870371
 
     /**
      * The app build number
      */
-    static final int APP_BUILDNUM = 752
+    static final int APP_BUILDNUM = 763
 
     /**
      * The date time formatter string

src/main/groovy/nextflow/executor/LocalExecutor.groovy

@@ -34,11 +34,11 @@ class LocalExecutor extends AbstractExecutor {
 
     private static final COMMAND_OUT_FILENAME = '.command.out'
 
-    private static final COMMAND_RUNNER_FILENAME = '.command.run'
+    private static final COMMAND_BASH_FILENAME = '.command.sh'
 
     private static final COMMAND_ENV_FILENAME = '.command.env'
 
-    private static final COMMAND_SCRIPT_FILENAME = '.command.sh'
+    private static final COMMAND_SCRIPT_FILENAME = '.command.run'
 
 
     /**
@@ -64,22 +64,23 @@ class LocalExecutor extends AbstractExecutor {
         /*
          * save the main script file
          */
+        def scriptStr = task.processor.normalizeScript(task.script.toString())
         def scriptFile = new File(scratch, COMMAND_SCRIPT_FILENAME)
-        scriptFile.text = task.processor.normalizeScript(task.script.toString())
+        scriptFile.text = scriptStr
+        def interpreter = task.processor.fetchInterpreter(scriptStr)
 
         /*
          * create the runner script which will launch the script
          */
         def runnerText = """
-                    source ${COMMAND_ENV_FILENAME}
-                    chmod +x ${COMMAND_SCRIPT_FILENAME}
-                    ./${COMMAND_SCRIPT_FILENAME}
+                    source $COMMAND_ENV_FILENAME
+                    $interpreter $COMMAND_SCRIPT_FILENAME
                     """
-        def runnerFile = new File(scratch, COMMAND_RUNNER_FILENAME)
+        def runnerFile = new File(scratch, COMMAND_BASH_FILENAME)
         runnerFile.text = task.processor.normalizeScript(runnerText)
 
         // the cmd list to launch it
-        List cmd = new ArrayList(taskConfig.shell ?: 'bash' as List ) << COMMAND_RUNNER_FILENAME
+        List cmd = new ArrayList(taskConfig.shell ?: 'bash' as List ) << COMMAND_BASH_FILENAME
         log.trace "Launch cmd line: ${cmd.join(' ')}"
 
         /*

src/main/groovy/nextflow/processor/MergeTaskProcessor.groovy

@@ -118,6 +118,7 @@ class MergeTaskProcessor extends TaskProcessor {
         scriptClosure.setResolveStrategy(Closure.DELEGATE_FIRST)
 
         def commandToRun = normalizeScript(scriptClosure.call()?.toString())
+        def interpreter = fetchInterpreter(commandToRun)
 
         /*
          * create a unique hash-code for this task run and save it into a list
@@ -137,7 +138,6 @@ class MergeTaskProcessor extends TaskProcessor {
         def scriptName = ".merge_command.sh.${index.toString().padLeft(4,'0')}"
         def scriptFile = new File(mergeTempFolder, scriptName)
         scriptFile.text = commandToRun
-        scriptFile.setExecutable(true)
 
         // the command to launch this command
         def scriptCommand = scriptFile.absolutePath
@@ -153,7 +153,7 @@ class MergeTaskProcessor extends TaskProcessor {
         }
 
         // create a unique script collecting all the commands
-        mergeScript << scriptCommand << '\n'
+        mergeScript << interpreter << ' ' << scriptCommand << '\n'
 
     }
 

src/main/groovy/nextflow/processor/TaskProcessor.groovy

@@ -224,6 +224,16 @@ abstract class TaskProcessor {
         return result.toString()
     }
 
+    def String fetchInterpreter( String script ) {
+        assert script != null
+
+        if( script[0] == '#' && script[1] == '!') {
+            return script.readLines()[0].substring(2)
+        }
+
+        return null
+    }
+
     /**
      * Wraps the target method by a closure declaring as many arguments as many are the user declared inputs
      * object.

src/test/groovy/nextflow/processor/TaskProcessorTest.groovy

@@ -40,7 +40,7 @@ class TaskProcessorTest extends Specification {
         when:
         def session = new Session([env: [X:"1", Y:"2"]])
         session.setBaseDir(home)
-        def processor = new DummyProcessor(new NopeExecutor(), session, new DummyScript(), new TaskConfig(), {})
+        def processor = new DummyProcessor(new NopeExecutor(), session, new TaskConfig())
         def builder = new ProcessBuilder()
         builder.environment().putAll( processor.getProcessEnvironment() )
 
@@ -53,7 +53,7 @@ class TaskProcessorTest extends Specification {
         when:
         session = new Session([env: [X:"1", Y:"2", PATH:'/some']])
         session.setBaseDir(home)
-        processor = new DummyProcessor(new NopeExecutor(), session, new DummyScript(), new TaskConfig(), {})
+        processor = new DummyProcessor(new NopeExecutor(), session, new TaskConfig())
         builder = new ProcessBuilder()
         builder.environment().putAll( processor.getProcessEnvironment() )
 
@@ -69,11 +69,32 @@ class TaskProcessorTest extends Specification {
 
     }
 
+    def testFetchInterpreter() {
+
+        when:
+        def processor = new DummyProcessor(new NopeExecutor(), new Session(), new TaskConfig())
+        def script =
+            '''
+            #!/bin/perl
+            do this
+            do that
+            '''
+        def i = processor.fetchInterpreter(script.stripIndent().trim())
+        then:
+        i == '/bin/perl'
+
+        when:
+        processor = new DummyProcessor(new NopeExecutor(), new Session(),  new TaskConfig())
+        i = processor.fetchInterpreter('do this')
+        then:
+        i == null
+    }
+
 
     static class DummyProcessor extends TaskProcessor {
 
-        DummyProcessor(AbstractExecutor executor, Session session, BaseScript script, TaskConfig taskConfig, Closure taskBlock) {
-            super(executor, session, script, taskConfig, taskBlock)
+        DummyProcessor(AbstractExecutor executor, Session session, TaskConfig taskConfig) {
+            super(executor, session, new DummyScript(), taskConfig, {})
         }
 
         @Override