Changeset 2460

Timestamp:

May 26, 2014, 9:32:59 AM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #593: Start masking and alignment

Improved error handling in script. Check that data folder exists before starting.

File:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/MaskAlignServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/MaskAlignServlet.java

@@ -300 +300 @@
         for (int mgNo = 0; mgNo < jsonMerged.size(); mgNo++)
         {
+          dc = sc.newDbControl();
           JSONObject jsonMg = (JSONObject)jsonMerged.get(mgNo);
           Number mergedId = (Number)jsonMg.get("id");
@@ -345 +346 @@
           
           ScriptBuilder script = new ScriptBuilder(jobFolder);
+          script.comment("Exit script immediately if an error occurs");
+          script.cmd("set -e");
+          script.newLine();
           script.comment("Setting up scripting environment and copying script to tmp folder");
           script.cmd("export ScriptDir=" + cluster.getScriptFolder());
@@ -364 +368 @@
           script.comment("Copy FASTQ files to tmp folder");
           script.progress(10, "Copying FASTQ files");
+          script.cmd("if [ ! -d \""+projectRoot + "/" + fastQFolder+"\" ]; then");
+          script.cmd("echo \"Can't find data folder "+fastQFolder+" in " + projectRoot + "\" 1>&2");
+          script.cmd("exit 1");
+          script.cmd("fi");
           script.cmd("mkdir fastq");
           script.cmd("cp " + projectRoot + "/" + fastQFolder + "/*.fastq.gz fastq");