updated some SJQ code, refactored a bit of job running code.

src/java/io/compgen/cgpipe/CGPipe.java

@@ -36,6 +36,8 @@ public class CGPipe {
 	public static final File CGPIPE_HOME = new File(System.getenv("CGPIPE_HOME") != null ? System.getenv("CGPIPE_HOME") : System.getProperty("user.home"));
 	public static final File RCFILE = new File(CGPIPE_HOME,".cgpiperc");
 
+//	public static final Map<String, VarValue> globalConfig = new HashMap<String, VarValue>(); 
+
 	public static void main(String[] args) {
 		String fname = null;
 		String logFilename = null;
@@ -201,6 +203,9 @@ public static void main(String[] args) {
 					System.exit(1);
 				}
 			}
+
+			// Set the global config values
+//			globalConfig.putAll(root.cloneValues());
 
 			// Parse the AST and run it
 			Parser.exec(fname, root);

src/java/io/compgen/cgpipe/parser/TemplateParser.java

@@ -29,16 +29,16 @@ public class TemplateParser {
 	private boolean processedPre = false;
 	private boolean inScript = false;
 
-	public TemplateParser(List<NumberedLine> pre, List<NumberedLine> post) {
+	private TemplateParser(List<NumberedLine> pre, List<NumberedLine> post) {
 		this.pre = pre;
 		this.post = post;
 	}
 
-	public void addScriptLine(NumberedLine line) throws ASTParseException {
+	private void addScriptLine(NumberedLine line) throws ASTParseException {
 		curNode = curNode.parseLine(line);
 	}
 
-	public void addBodyLine(String body, NumberedLine line) throws ASTParseException {
+	private void addBodyLine(String body, NumberedLine line) throws ASTParseException {
 		processPre();
 		curNode = curNode.parseBody(body, line);
 	}

src/java/io/compgen/cgpipe/parser/target/BuildTarget.java

@@ -68,7 +68,7 @@ public JobDef eval(List<NumberedLine> pre, List<NumberedLine> post) throws ASTPa
 
 		TemplateParser.parseTemplate(lines, pre, post, jobRoot);
 
-		return new JobDef(jobRoot.getBody(), jobRoot.cloneValues("job."), outputs, inputs);
+		return new JobDef(jobRoot.getBody(), jobRoot.cloneValues(), outputs, inputs);
 	}
 
 	public boolean isSkippable() {

src/java/io/compgen/cgpipe/runner/JobRunner.java

@@ -32,7 +32,15 @@ public abstract class JobRunner {
 	abstract public void innerDone() throws RunnerException;
 	abstract protected void setConfig(String k, String val);
 
-	protected String defaultShell = "/bin/sh";
+	public static String defaultShell = null;
+	static {
+		for (String path: new String[] {"/bin/bash", "/usr/bin/bash", "/usr/local/bin/bash", "/bin/sh"}) {
+			if (new File(path).exists()) {
+				defaultShell=path;
+				break;
+			}
+		}
+	}
 
 	static protected Log log = LogFactory.getLog(JobRunner.class);
 
@@ -54,6 +62,10 @@ public static JobRunner load(RootContext cxt, boolean dryrun) throws RunnerExcep
 		if (runner == null) {
 			runner = "shell";
 		}
+
+		if (cxt.contains("cgpipe.shell")) {
+			defaultShell = cxt.getString("cgpipe.shell");
+		}
 
 		JobRunner.log.info("job-runner: " +runner);
 		JobRunner obj = null;
@@ -71,10 +83,6 @@ public static JobRunner load(RootContext cxt, boolean dryrun) throws RunnerExcep
 		default:
 			throw new RunnerException("Can't load job runner: "+runner);
 		}
-
-		if (cxt.contains("cgpipe.shell")) {
-			obj.defaultShell = cxt.getString("cgpipe.shell");
-		}
 
 		String prefix = "cgpipe.runner."+runner;
 		Map<String, VarValue> cxtvals = cxt.cloneValues(prefix);

src/java/io/compgen/cgpipe/runner/SGERunner.java

@@ -20,7 +20,7 @@ public class SGERunner extends JobRunner {
 	private boolean hvmemIsTotal = true;
 	private String account=null;
 	private String parallelEnv = "shm";
-	private String shell = ShellScriptRunner.findDefaultShell();
+	private String shell = ShellScriptRunner.defaultShell;
 
 	private int dryRunJobCount = 0;
 
@@ -303,7 +303,7 @@ private String buildScript(JobDef jobdef) {
 		              is to specify it as the amount of memory per-processor
 		              (only used when procs > 1)
 		
-		shell       - a shell to use for the script (default(s): /bin/bash, /usr/bin/bash, /usr/local/bin/bash, /bin/sh)
+		shell       - a shell to use for the script (default(s): /defaultShell/bash, /usr/defaultShell/bash, /usr/local/defaultShell/bash, /defaultShell/sh)
 
 	 */
 	@Override

src/java/io/compgen/cgpipe/runner/SJQRunner.java

@@ -14,6 +14,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.net.UnknownHostException;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -28,6 +29,7 @@ public class SJQRunner extends JobRunner {
 
 	private File socketFile = new File(CGPipe.CGPIPE_HOME, ".sjqserv");
 	private File passwdFile = new File(CGPipe.CGPIPE_HOME, ".sjqpass");
+	private File jobLogFile = new File(CGPipe.CGPIPE_HOME, ".sjqjobs");
 	private int maxProcs = Runtime.getRuntime().availableProcessors();
 	private String maxMem = null;
 	private String tempDir = null;
@@ -62,16 +64,32 @@ public void connect() throws IOException, CommandArgumentException, SJQServerExc
 			server.setSilent(false);
 			server.setPort(port);
 			server.setTimeout(30);
+			server.setJobLogFile(jobLogFile.getAbsolutePath());
 			server.start();
 		} else {
 			passwd = StringUtils.strip(StringUtils.readFile(passwdFile)); 
 		}
 
-		String addr = StringUtils.strip(StringUtils.readFile(socketFile));
-		if (addr != null && !addr.equals("")) {
-			String ip = addr.split(":")[0];
-			int port = Integer.parseInt(addr.split(":")[1]);
-			client = new SJQClient(ip, port, passwd);
+		try {
+			String addr = StringUtils.strip(StringUtils.readFile(socketFile));
+			if (addr != null && !addr.equals("")) {
+				String ip = addr.split(":")[0];
+				int port = Integer.parseInt(addr.split(":")[1]);
+					client = new SJQClient(ip, port, passwd);
+			}
+		} catch (IOException e) {
+			log.debug("Error connecting to server - trying again. "+ e.getMessage());
+			try {
+				String addr = StringUtils.strip(StringUtils.readFile(socketFile));
+				if (addr != null && !addr.equals("")) {
+					String ip = addr.split(":")[0];
+					int port = Integer.parseInt(addr.split(":")[1]);
+							client = new SJQClient(ip, port, passwd);
+				}
+			} catch (IOException e1) {
+				log.debug("Error connecting to server - again - Failing... "+ e.getMessage());
+				throw e1;
+			}
 		}
 	}
 
@@ -87,10 +105,10 @@ public boolean submit(JobDef jobdef) throws RunnerException {
 		}
 
 		try {
-			String jobId = client.submitJob(jobdef.getName(), jobdef.getBody(), 
+			String jobId = client.submitJob(jobdef.getName(), "#!"+ShellScriptRunner.defaultShell+"\n"+jobdef.getBody(), 
 					((int)jobdef.getSettingInt("job.procs", 1)), jobdef.getSetting("job.mem"), 
 					jobdef.getSetting("job.stderr"), jobdef.getSetting("job.stdout"), 
-					jobdef.getSetting("job.wd"), null, 
+					jobdef.getSetting("job.wd", new File(".").getCanonicalPath()), null, 
 					IterUtils.map(jobdef.getDependencies(), new MapFunc<JobDependency, String>() {
 						@Override
 						public String map(JobDependency dep) {
@@ -103,7 +121,7 @@ public String map(JobDependency dep) {
 				log.debug(jobId + " " + line);
 			}
 			return jobId != null;
-		} catch (ClientException | AuthException e) {
+		} catch (ClientException | AuthException | IOException e) {
 			e.printStackTrace();
 			throw new RunnerException(e);
 		}
@@ -150,6 +168,8 @@ protected void setConfig(String k, String val) {
 			this.socketFile = new File(val);
 		} else if (k.equals("cgpipe.runner.sjq.passwdfile")) {
 			this.passwdFile = new File(val);
+		} else if (k.equals("cgpipe.runner.sjq.joblog")) {
+			this.jobLogFile = new File(val);
 		} else if (k.equals("cgpipe.runner.sjq.maxprocs")) {
 			this.maxProcs = Integer.parseInt(val);
 		} else if (k.equals("cgpipe.runner.sjq.port")) {

src/java/io/compgen/cgpipe/runner/ShellScriptRunner.java

@@ -2,29 +2,17 @@
 
 import io.compgen.cgpipe.exceptions.RunnerException;
 
-import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 public class ShellScriptRunner extends JobRunner {
-	private static String[] defaultShellPaths = new String[] {"/bin/bash", "/usr/bin/bash", "/usr/local/bin/bash", "/bin/sh"};
-
-	public static String findDefaultShell() {
-		for (String path: defaultShellPaths) {
-			if (new File(path).exists()) {
-				return path;
-			}
-		}
-		return null;
-	}
-
-	public String bin = findDefaultShell();
 	protected Log log = LogFactory.getLog(ShellScriptRunner.class);
 
 	private List<JobDef> jobs = new ArrayList<JobDef>();
+	private String shellPath = defaultShell;
 
 	@Override
 	public boolean submit(JobDef jobdef) {
@@ -46,7 +34,7 @@ public void innerDone() throws RunnerException {
 		for (JobDef job: jobs) {
 			if (!job.getBody().equals("")) {
 				if (!header) {
-					out += "#!"+bin+"\n";
+					out += "#!"+shellPath+"\n";
 					header = true;
 				}
 				out += job.getJobId()+"() {\n";
@@ -66,7 +54,7 @@ public void innerDone() throws RunnerException {
 	@Override
 	protected void setConfig(String k, String val) {
 		if (k.equals("cgpipe.runner.shell.bin")) {
-			bin = val;
+			shellPath = val;
 		}
 	}
 

src/test-scripts/misc.mvpt

@@ -58,11 +58,8 @@ output3: output2
     touch output3
 
 output1 "output2":
-    <% if foo == "bar" %>
-    touch output1.bar
-    <% else %>
-    touch output1.notbar
-    <% endif %>
+    <% if foo == "bar" %> touch output1.bar
+    <% else %> touch output1.notbar <% endif %>
 
     <%
         for i in 1..5