From e37a638e0903c3644be8b6923b7be6dbb6afdd1c Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 26 Aug 2011 13:24:06 -0400
Subject: [PATCH] Fix for disallowed characters in GATKReportTable

-- Illegal characters are automatically replaced with _
---
 .../sting/gatk/report/GATKReportTable.java          |  4 +++-
 .../sting/queue/util/QJobReport.scala               | 13 +++++--------
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
index 152e1a57b..3e3aa29a7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
@@ -92,6 +92,8 @@ import java.util.regex.Pattern;
  * @author Khalid Shakir
  */
 public class GATKReportTable {
+    /** REGEX that matches any table with an invalid name */
+    public final static String INVALID_TABLE_NAME_REGEX = "[^a-zA-Z0-9_\\-\\.]";
     private static final GATKReportVersion LATEST_REPORT_VERSION = GATKReportVersion.V0_2;
     private String tableName;
     private String tableDescription;
@@ -111,7 +113,7 @@ public class GATKReportTable {
      * @return  true if the name is valid, false if otherwise
      */
     private boolean isValidName(String name) {
-        Pattern p = Pattern.compile("[^a-zA-Z0-9_\\-\\.]");
+        Pattern p = Pattern.compile(INVALID_TABLE_NAME_REGEX);
         Matcher m = p.matcher(name);
 
         return !m.find();
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala b/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala
index a1fa10cd8..04ae54c21 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala
@@ -51,7 +51,7 @@ trait QJobReport extends Logging {
     logger.info("info " + info)
     reportFeatures = Map(
       "iteration" -> 1,
-      "analysisName" -> self.analysisName,
+      "analysisName" -> getReportGroup,
       "jobName" -> QJobReport.workAroundSameJobNames(this),
       "intermediate" -> self.isIntermediate,
       "startTime" -> info.getStartTime.getTime,
@@ -59,15 +59,12 @@ trait QJobReport extends Logging {
       "formattedStartTime" -> info.getFormattedStartTime,
       "formattedDoneTime" -> info.getFormattedDoneTime,
       "runtime" -> info.getRuntimeInMs).mapValues((x:Any) => if (x != null) x.toString else "null") ++ reportFeatures
-
-//    // handle the special case of iterations
-//    reportFeatures.get("iteration") match {
-//      case None => reportFeatures("iteration") = 1
-//      case _ => ;
-//    }
+    // note -- by adding reportFeatures second we override iteration
+    // (or any other binding) with the user provided value
   }
 
-  def getReportGroup = analysisName
+  /** The report Group is the analysis name transform to only contain valid GATKReportTable characters */
+  def getReportGroup = self.analysisName.replaceAll(GATKReportTable.INVALID_TABLE_NAME_REGEX, "_")
   def getReportFeatures = reportFeatures
 
   def getReportFeatureNames: List[String] = getReportFeatures.keys.toList