There is now a configuration file for enabling and disabling the

preservation of the temporary files generated by CRLOGIC

ch.psi.fda/src/main/java/ch/psi/fda/aq/Acquisition.java

@@ -581,7 +581,10 @@ public class Acquisition {
 			}
 			else if(a instanceof ShellAction){
 				ShellAction sa = (ShellAction) a;
-				alist.add(new ch.psi.fda.core.actions.ShellAction(sa.getCommand()));
+				ch.psi.fda.core.actions.ShellAction action = new ch.psi.fda.core.actions.ShellAction(sa.getCommand());
+				action.setCheckExitValue(sa.isCheckExitValue());
+				action.setExitValue(sa.getExitValue());
+				alist.add(action);
 			}
 			else if(a instanceof ScriptAction){
 				
@@ -1025,6 +1028,7 @@ public class Acquisition {
 			boolean zigZag = dimension.isZigzag(); // default value is false
 			
 			CrlogicLoop actionLoop = new CrlogicLoop(configuration.getOtfCrlogicPrefix(), configuration.getOtfNfsServer(), configuration.getOtfNfsShare(), configuration.getOtfSmbShare(), zigZag);
+			actionLoop.setKeepTmpFiles(configuration.isOtfCrlogicKeepTmpFiles());
 			
 			actionLoop.getPreActions().addAll(mapActions(dimension.getPreAction()));
 			

ch.psi.fda/src/main/java/ch/psi/fda/aq/AcquisitionEngineConfiguration.java

@@ -38,13 +38,14 @@ public class AcquisitionEngineConfiguration {
 	
 	private static final AcquisitionEngineConfiguration instance = new AcquisitionEngineConfiguration();
 	
-	private String otfChannelPrefix = "";
-	private String otfNfsServer = "";
-	private String otfNfsShare = "";
-	private String otfSmbShare = "";
-	private String otfScalerPrefix = "";
-	private boolean otfUseCrlogic = false;
-	private String otfCrlogicPrefix = "";
+	private String otfChannelPrefix;
+	private String otfNfsServer;
+	private String otfNfsShare;
+	private String otfSmbShare;
+	private String otfScalerPrefix;
+	private boolean otfUseCrlogic;
+	private String otfCrlogicPrefix;
+	private boolean otfCrlogicKeepTmpFiles;
 	
 	/**
 	 * Base directory for data. The directory may contain date macros. The string may contain any @see java.text.SimpleDateFormat
@@ -102,7 +103,7 @@ public class AcquisitionEngineConfiguration {
 		}
 		
 		
-		
+		// The defaults are set here
 		otfChannelPrefix = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.channelPrefix", "");
 		otfScalerPrefix = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.scalerPrefix", "");
 		otfNfsServer = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.nfsServer", "");
@@ -110,6 +111,7 @@ public class AcquisitionEngineConfiguration {
 		otfSmbShare = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.smbShare", "");
 		otfUseCrlogic = new Boolean(properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.useCrlogic", "false"));
 		otfCrlogicPrefix = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.crlogicPrefix", "");
+		otfCrlogicKeepTmpFiles = new Boolean(properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.crlogicKeepTmpFiles", "false"));
 		
 		// Workaround
 //		dataBaseDirectory = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".data.baseDirectory", ".");
@@ -202,6 +204,13 @@ public class AcquisitionEngineConfiguration {
 		return otfCrlogicPrefix;
 	}
 
+	/**
+	 * @return the otfCrlogicKeepTmpFiles
+	 */
+	public boolean isOtfCrlogicKeepTmpFiles() {
+		return otfCrlogicKeepTmpFiles;
+	}
+
 	/**
 	 * @return the actorMoveTimeout
 	 */

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/CrlogicLoop.java

@@ -67,7 +67,7 @@ public class CrlogicLoop implements ActionLoop {
 	 */
 	private boolean dataGroup = false;
 	
-	boolean keepTmpFiles = true;
+	private boolean keepTmpFiles = false;
 	
 	private BlockingQueue<String> readQueue = new LinkedBlockingQueue<String>();
 	private volatile boolean stopReadoutThread = false;
@@ -876,5 +876,23 @@ public class CrlogicLoop implements ActionLoop {
 		}
 		return new DataQueue(dataQueue, m);
 	}
+
+
+	/**
+	 * @return the keepTmpFiles
+	 */
+	public boolean isKeepTmpFiles() {
+		return keepTmpFiles;
+	}
+
+
+	/**
+	 * @param keepTmpFiles the keepTmpFiles to set
+	 */
+	public void setKeepTmpFiles(boolean keepTmpFiles) {
+		this.keepTmpFiles = keepTmpFiles;
+	}
+	
+	
 	
 }

ch.psi.fda/src/main/resources/model-v1.xsd

@@ -194,7 +194,13 @@
     <xsd:complexType name="ShellAction">
     	<xsd:complexContent>
     		<xsd:extension base="Action">
-    			<xsd:attribute name="command" type="xsd:string" use="required"></xsd:attribute>
+    			<xsd:attribute name="command" type="xsd:string"
+    				use="required">
+    			</xsd:attribute>
+    			<xsd:attribute name="exitValue" type="xsd:int" default="0"></xsd:attribute>
+    			<xsd:attribute name="checkExitValue"
+    				type="xsd:boolean" default="true">
+    			</xsd:attribute>
     		</xsd:extension>
     	</xsd:complexContent>
     </xsd:complexType>

ch.psi.fda/src/test/resources/home/scans/templates/shellaction.xml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../src/model-v1.xsd">
+<!-- 
+1D Scan reading out scalar channels and the timestamp for each point
+ -->
+  <data format="txt"/>
+  <scan id="">
+  
+  	<preAction xsi:type="ShellAction" command="src/test/resources/testscripts/testscript1.sh one two" exitValue="1" checkExitValue="false"/>
+  </scan>
+  
+</configuration>

ch.psi.fda/src/test/resources/logging.properties

@@ -2,7 +2,7 @@
 handlers = java.util.logging.ConsoleHandler
 
 # Set the default logging level for the root logger
-.level=ALL
+.level=INFO
 
 # Set the default logging level for new ConsoleHandler instances
 java.util.logging.ConsoleHandler.level=ALL