Bug fixes to allow us to generate GATKRunReports for very early errors that leave the engine in a corrupt state. Vastly better error handling of common command line problems. Analysis output now notes whether an exception is a a UserException or a StingException

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4278 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java

@@ -338,8 +338,8 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                 // if their argument has no value (null), and there's a default, return that default for the enum value
                 if (defaultEnumeration != null && value == null)
                     result = defaultEnumeration;
-                // if their argument has no value and there's no default, throw a missing argument value exception.
+                    // if their argument has no value and there's no default, throw a missing argument value exception.
-                // TODO: Clean this up so that null values never make it to this point.  To fix this, we'll have to clean up the implementation of -U.
+                    // TODO: Clean this up so that null values never make it to this point.  To fix this, we'll have to clean up the implementation of -U.
                 else if (value == null)
                     throw new MissingArgumentValueException(Collections.singleton(createDefaultArgumentDefinition(source)));
                 else
@@ -348,12 +348,16 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                 Constructor ctor = type.getConstructor(String.class);
                 result = ctor.newInstance(value);
             }
+        } catch (UserException e) {
+            throw e;
         } catch (InvocationTargetException e) {
-            throw new ReviewedStingException("constructFromString:InvocationTargetException: Failed conversion - this is most likely caused by using an incorrect data type (e.g. a double when an int is required)");
+            throw new UserException.CommandLineException(String.format("Failed to parse value %s for argument %s.  This is most commonly caused by providing an incorrect data type (e.g. a double when an int is required)",
+                            value, source.field.getName()));
         } catch (Exception e) {
             throw new DynamicClassResolutionException(String.class, e);
         }
 
+        // TODO FIXME!
 
         // WARNING: Side effect!
         parsingEngine.addTags(result,tags);

java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java

@@ -32,6 +32,7 @@ import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.simpleframework.xml.Element;
 import org.simpleframework.xml.ElementList;
 import org.simpleframework.xml.Serializer;
@@ -93,23 +94,23 @@ public class GATKRunReport {
     @Element(required = false, name = "exception")
     private final ExceptionToXML mException;
 
-    @Element(required = true, name = "argument_collection")
+    @Element(required = false, name = "argument_collection")
     private final GATKArgumentCollection mCollection;
 
     @Element(required = true, name = "working_directory")
     private String currentPath;
 
     @Element(required = true, name = "start_time")
-    private String startTime;
+    private String startTime = "ND";
 
     @Element(required = true, name = "end_time")
     private String endTime;
 
     @Element(required = true, name = "run_time")
-    private long runTime;
+    private long runTime = 0;
 
     @Element(required = true, name = "command_line")
-    private String cmdLine;
+    private String cmdLine = "COULD NOT BE DETERMINED";
 
     @Element(required = true, name = "walker_name")
     private String walkerName;
@@ -176,16 +177,21 @@ public class GATKRunReport {
 
         // what did we run?
         id = org.apache.commons.lang.RandomStringUtils.randomAlphanumeric(32);
-        cmdLine = CommandLineUtils.createApproximateCommandLineArgumentString(engine, walker);
+        try {
+            cmdLine = CommandLineUtils.createApproximateCommandLineArgumentString(engine, walker);
+        } catch (Exception ignore) { }
+
         this.mCollection = engine.getArguments();
         walkerName = engine.getWalkerName(walker.getClass());
         svnVersion = CommandLineGATK.getVersionNumber();
 
         // runtime performance metrics
-        startTime = dateFormat.format(engine.getStartTime());
         Date end = new java.util.Date();
         endTime = dateFormat.format(end);
-        runTime = (end.getTime() - engine.getStartTime().getTime()) / 1000L; // difference in seconds
+        if ( engine.getStartTime() != null ) { // made it this far during initialization
+            startTime = dateFormat.format(engine.getStartTime());
+            runTime = (end.getTime() - engine.getStartTime().getTime()) / 1000L; // difference in seconds
+        }
         tmpDir = System.getProperty("java.io.tmpdir");
 
         // deal with memory usage
@@ -310,8 +316,12 @@ public class GATKRunReport {
         @Element(required = false, name = "cause")
         ExceptionToXML cause = null;
 
+        @Element(required = false, name = "is-user-exception")
+        Boolean isUserException;
+
         public ExceptionToXML(Throwable e) {
             message = e.getMessage();
+            isUserException = e instanceof UserException;
             for (StackTraceElement element : e.getStackTrace()) {
                 stackTrace.add(element.toString());
             }