# HG changeset patch
# User dchristiany
# Date 1547564402 18000
# Node ID d2af5a5053fd02d7f14fca80b7ce363799198f03
# Parent  85532a48e4e400c6fbc4bfa71ea19598a27e83ce
planemo upload commit 8040003119a3d54866ec6ee9b9f659f2af554817-dirty

diff -r 85532a48e4e4 -r d2af5a5053fd data_manager/resource_building.py
--- a/data_manager/resource_building.py	Tue Jan 15 07:13:52 2019 -0500
+++ b/data_manager/resource_building.py	Tue Jan 15 10:00:02 2019 -0500
@@ -3,7 +3,7 @@
 The purpose of this script is to create source files from different databases to be used in other proteore tools
 """
 
-import os, sys, argparse, requests, time, csv, re, json, zipfile, shutil
+import os, sys, argparse, requests, time, csv, re, json, shutil
 from io import BytesIO
 from zipfile import ZipFile
 from galaxy.util.json import from_json_string, to_json_string
@@ -308,9 +308,9 @@
         shutil.rmtree("tmp_BioGRID", ignore_errors=True) 
 
         #download NCBI2Reactome.txt file and build dictionary
-        download = requests.get('https://www.reactome.org/download/current/NCBI2Reactome.txt')
-        decoded_content = download.content.decode('utf-8')
-        tab_file = csv.reader(decoded_content.splitlines(), delimiter='\t')
+        r = requests.get('https://www.reactome.org/download/current/NCBI2Reactome.txt')
+        r.encoding ="utf-8"
+        tab_file = csv.reader(r.content.splitlines(), delimiter='\t')
         dico_nodes = {}
         GeneID_index=0
         pathway_description_index=3
@@ -329,9 +329,9 @@
     ##Bioplex
     elif interactome=="bioplex":
 
-        download = requests.get("http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv")
-        decoded_content = download.content.decode('utf-8')
-        bioplex = csv.reader(decoded_content.splitlines(), delimiter='\t')
+        r = requests.get("http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv")
+        r.encoding ="utf-8"
+        bioplex = csv.reader(r.content.splitlines(), delimiter='\t')
         dico_network = {}
         dico_network["GeneID"]={}
         network_geneid_cols=[0,1,4,5,8]
@@ -344,9 +344,9 @@
             dico_network["UniProt-AC"][line[2]]=[line[i] for i in network_uniprot_cols]
             dico_GeneID_to_UniProt[line[0]]=line[2]
 
-        download = requests.get("https://reactome.org/download/current/UniProt2Reactome.txt")
-        decoded_content = download.content.decode('utf-8')
-        tab_file = csv.reader(decoded_content.splitlines(), delimiter='\t')
+        r = requests.get("https://reactome.org/download/current/UniProt2Reactome.txt")
+        r.encoding ="utf-8"
+        tab_file = csv.reader(r.content.splitlines(), delimiter='\t')
         dico_nodes = {}
         uniProt_index=0
         pathway_description_index=3
diff -r 85532a48e4e4 -r d2af5a5053fd data_manager/resource_building.xml
--- a/data_manager/resource_building.xml	Tue Jan 15 07:13:52 2019 -0500
+++ b/data_manager/resource_building.xml	Tue Jan 15 10:00:02 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.01.15.4" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.01.15.5" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>