view danfix.patch @ 4:102bdfdda10b draft

Uploaded

diff -r ebadd2c92958 data_manager/rnastar_index_builder.py
--- a/data_manager/rnastar_index_builder.py Mon Sep 29 20:47:45 2014 -0400
+++ b/data_manager/rnastar_index_builder.py Fri Oct 03 13:35:35 2014 -0400
@@ -9,7 +9,7 @@
 import optparse
 import subprocess

-from galaxy.util.json import from_json_string, to_json_string
+from json import loads, dumps

 DEFAULT_DATA_TABLE_NAME = "rnastar_indexes"

@@ -44,20 +44,11 @@
    --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' %  pdict
     elif sjdbFileChrStartEnd:
         cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' % pdict
-    tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" )
     args = cl.split(' ')
-    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
+    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
     return_code = proc.wait()
     if return_code:
-        tmp_stderr.flush()
-        tmp_stderr.seek(0)
-        print >> sys.stderr, "Error building index: retcode=",retcode
-        while True:
-            chunk = tmp_stderr.read( CHUNK_SIZE )
-            if not chunk:
-                break
-            sys.stderr.write( chunk )
-    tmp_stderr.close()
+        sys.exit( return_code )
     data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
     _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )

@@ -86,7 +77,7 @@
     (options, args) = parser.parse_args()

     filename = options.out_file
-    params = from_json_string( open( filename ).read() )
+    params = loads( open( filename ).read() )
     target_directory = options.out_index_path
     os.mkdir( target_directory )
     data_manager_dict = {}
@@ -107,6 +98,7 @@


     #save info to json file
-    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+    open( filename, 'wb' ).write( dumps( data_manager_dict ) )

 if __name__ == "__main__": main()
+
diff -r ebadd2c92958 data_manager/rnastar_index_builder.xml
--- a/data_manager/rnastar_index_builder.xml    Mon Sep 29 20:47:45 2014 -0400
+++ b/data_manager/rnastar_index_builder.xml    Fri Oct 03 13:35:35 2014 -0400
@@ -22,7 +22,8 @@
 #end if
 </command>
     <stdio>
-        <regex match=".*" source="both" level="warning" description="stdout/err chatter:"/>
+        <exit_code range=":-1" err_level="fatal" />
+        <exit_code range="1:" err_level="fatal" />
     </stdio>

     <inputs>
@@ -124,3 +125,4 @@

     </help>
 </tool>