# HG changeset patch
# User linda-bakker
# Date 1519131587 18000
# Node ID 2ab40f9266e41b64cba6f41090b86685ed480de7
# Parent  bee03dc123f2123eaa799c680e4d122e9da4da99
An update to the core of galaxy prevents the way the code is trying to write files. This patch fixes this.

diff -r bee03dc123f2 -r 2ab40f9266e4 rankfilter_GCMS/nistpdf_to_tabular.py
--- a/rankfilter_GCMS/nistpdf_to_tabular.py	Tue Feb 20 07:29:49 2018 -0500
+++ b/rankfilter_GCMS/nistpdf_to_tabular.py	Tue Feb 20 07:59:47 2018 -0500
@@ -15,8 +15,9 @@
 
 """
 
-import sys
+import sys,os
 import pdfread
+import tempfile
 from subprocess import call
 
 # NB: THIS TOOL SHOULD BE DEPRECATED ONCE NIST-Wrapper tool is stable and released. NIST-Wrapper tool already produces the necessary tabular file.
@@ -40,6 +41,8 @@
 
 
 if __name__ == '__main__':
-    pdf_as_text = sys.argv[1]+".txt"
+    #pdf_as_text = sys.argv[1]+".txt"
+    pdf_as_text = tempfile.mkstemp()[1]
     convert_pdftotext(sys.argv[1], pdf_as_text)
     pdfread.convert_pdftotext2tabular(pdf_as_text, sys.argv[2], sys.argv[3], False)
+    os.remove(pdf_as_text)