# HG changeset patch
# User melissacline
# Date 1421277669 28800
# Node ID 6eeb3ca663fbcd422420fc5f47dc8eba0d2ff095
# Parent  ca4510434edac3bb29df75e385e5ac1dbbc3cc5f
Fixed dataset delete bugs (the full pathname was needed) plus changed xena_import to give a checkbox for turning on column normalization

diff -r ca4510434eda -r 6eeb3ca663fb xena_delete.py
--- a/xena_delete.py	Wed Jan 14 12:47:23 2015 -0800
+++ b/xena_delete.py	Wed Jan 14 15:21:09 2015 -0800
@@ -29,9 +29,11 @@
     # is generated, output a traceback and exit with nonzero status.  If
     # no exception was generated, indicate a successful import and exit
     # with zero status.
-    xenaDeleteCmd = "java -jar %s --delete %s -p %s" % (xena.jarPath(),
-                                                        args.datasetName,
-                                                        xena.port())
+    xenaDeleteCmd = "java -jar %s --delete %s/%s -p %s" % (xena.jarPath(),
+                                                           xenaFileDir,
+                                                           args.datasetName,
+                                                           xena.port())
+    print "Issuing command", xenaDeleteCmd
     try:
         subprocess.call(xenaDeleteCmd, shell=True)
     except:
diff -r ca4510434eda -r 6eeb3ca663fb xena_import.py
--- a/xena_import.py	Wed Jan 14 12:47:23 2015 -0800
+++ b/xena_import.py	Wed Jan 14 15:21:09 2015 -0800
@@ -52,6 +52,7 @@
     parser.add_argument("--type", type=str)
     parser.add_argument("--dataSubType", type=str, default=None)
     parser.add_argument("--label", type=str, default=None)
+    parser.add_argument("--colNormalization", type=bool, default=False)
     args = parser.parse_args()
 
     fp2 = open(args.outfile, "w")
@@ -78,6 +79,10 @@
             metadata['dataSubType'] = args.dataSubType
         if args.label is not None:
             metadata['label'] = args.label
+        if args.colNormalization:
+            metadata['colNormalization'] = "true"
+        else:
+            updateColNormalization(metadata)
         jsonMetadata = json.dumps(metadata, indent=2) 
         fp = open(jsonMetadataTargetPathname, "w")
         fp.write("%s\n" % (jsonMetadata))
diff -r ca4510434eda -r 6eeb3ca663fb xena_import.xml
--- a/xena_import.xml	Wed Jan 14 12:47:23 2015 -0800
+++ b/xena_import.xml	Wed Jan 14 15:21:09 2015 -0800
@@ -24,6 +24,9 @@
             --label  "${xenaInputData.name}"
         #end if
     #end if
+    #if $colNormalization:
+        --colNormalization 1
+    #end if
   </command>
   <inputs>
     <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/>
@@ -112,6 +115,7 @@
         <param type="text" name="label" label="Display Name (Optional)" optional="true"/>
       </when>
     </conditional>
+    <param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/>
   </inputs>
   <outputs>
     <data format="txt" name="outfile"/>