Mercurial > repos > pieterlukasse > prims_metabolomics2

changeset 24:2ab40f9266e4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
An update to the core of galaxy prevents the way the code is trying to write files. This patch fixes this.
author linda-bakker
date Tue, 20 Feb 2018 07:59:47 -0500
parents bee03dc123f2
children 9f03c8587d6b
files rankfilter_GCMS/nistpdf_to_tabular.py
diffstat 1 files changed, 5 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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)