7fb3a6da4430d2c2d69c95c17b748525d49cca68
mmaddren
  Mon Jul 25 15:34:12 2011 -0700
temporary changes while switching branch
diff --git python/programs/mkGeoPkg/mkGeoPkg python/programs/mkGeoPkg/mkGeoPkg
index c7732ac..3a44ec5 100755
--- python/programs/mkGeoPkg/mkGeoPkg
+++ python/programs/mkGeoPkg/mkGeoPkg
@@ -511,31 +511,32 @@
 	if datatype.soft == HighThroughputSoftFile:
 		softfile, fileList = createHighThroughputSoftFile(database, composite, organism, compositeUrl, mdb, cv, track, md5sums, submission, expVars, geoMapping, series, datatype)
 	elif datatype.soft == MicroArraySoftFile:
 		softfile, fileList = createMicroArraySoftFile(database, composite, organism, compositeUrl, mdb, cv, track, md5sums, submission, expVars, geoMapping, series, datatype)
 	else:
 		raise KeyError('unsupported type')
 		
 	print 'Writing soft file'
 	outfileName = os.path.dirname(sys.argv[0]) + composite + '.soft'
 	outfile = open(outfileName, 'w')
 	outfile.write(str(softfile))
 	
 	fileString = outfileName
 	for file in fileList:
 		if not os.path.exists(file):
-			raise IOError(file)
+			#raise IOError(file)
+			print file + ' does not exist'
 		fileString = fileString + ' ' + downloadsDirectory + file
 		
 	fileString.strip()
 	callString = '/opt/aspera/connect/bin/ascp -i ~/encode_geo_key/encode_geo_key.ppk -QTr -l300m ' + fileString + ' asp-geo@upload.ncbi.nlm.nih.gov:ENCODE/' + composite
 	outscript = open(composite + minId + '-' + maxId + '.sh', 'w')
 	outscript.write('#!/bin/sh\n\n')
 	outscript.write('/opt/aspera/connect/bin/ascp -i ~/encode_geo_key/encode_geo_key.ppk -QTr -l300m \\\n')
 	
 	outscript.write(os.path.dirname(sys.argv[0]) + composite + '.soft' + ' \\\n')
 	
 	for file in fileList:
 		if not os.path.exists(downloadsDirectory + file):
 			raise FileError(downloadsDirectory + file + ' does not exist')
 		outscript.write(downloadsDirectory + file + ' \\\n')