# HG changeset patch
# User pablocarb
# Date 1560430611 14400
# Node ID dbc40b3060148999cd67ef7c0c9e5c761e7f3b18
# Parent 612a2f94522f0f621ee8527dcb4c8a9e5335231b
planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5-dirty
diff -r 612a2f94522f -r dbc40b306014 outfile.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/outfile.html Thu Jun 13 08:56:51 2019 -0400
@@ -0,0 +1,139 @@
+
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+ Viewer
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diff -r 612a2f94522f -r dbc40b306014 rpVisualizer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpVisualizer.xml Thu Jun 13 08:56:51 2019 -0400
@@ -0,0 +1,25 @@
+
+ Pathway visualizer
+
+ python-libsbml
+ networkx
+ beautifulsoup4
+ rdkit
+
+ $__tool_directory__/info.log;
+ PYTHONPATH="$__tool_directory__" python $__tool_directory__/toolVisualizer.py $input1 $output1
+ ]]>
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diff -r 612a2f94522f -r dbc40b306014 rpviz.xml
--- a/rpviz.xml Tue Jun 11 12:09:38 2019 -0400
+++ b/rpviz.xml Thu Jun 13 08:56:51 2019 -0400
@@ -1,25 +1,19 @@
-
+
Pathway visualizer
- python-libsbml
- networkx
- beautifulsoup4
- rdkit
+ requests
$__tool_directory__/info.log;
- PYTHONPATH="$__tool_directory__" python $__tool_directory__/toolVisualizer.py $input1 $output1
+ python $__tool_directory__/toolRPViz.py $input1 $output1 -server $server
]]>
+
diff -r 612a2f94522f -r dbc40b306014 toolRPViz.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/toolRPViz.py Thu Jun 13 08:56:51 2019 -0400
@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mar 19
+
+@author: Pablo Carbonell
+@description: Query RPViz: pathway visualizer.
+
+"""
+import requests
+import argparse
+import csv
+import os
+import json
+
+def arguments():
+ parser = argparse.ArgumentParser(description='toolRPViz: Pathway visualizer. Pablo Carbonell, SYNBIOCHEM, 2019')
+ parser.add_argument('infile',
+ help='Pathways in SBML format.')
+ parser.add_argument('outfile',
+ help='HTML visualizer file.')
+ parser.add_argument('-server', default='http://rpviz.synbiochem.co.uk/REST',
+ help='RPViz server.')
+ return parser
+
+def testApp(url):
+ r = requests.get( url )
+ res = json.loads( r.content.decode('utf-8') )
+ print( res )
+
+def pathwayUpload(infile, outfile, url):
+ files = { 'file': open(infile, 'rb' ) }
+ r = requests.post( os.path.join(url, 'Query' ), files=files )
+ res = json.loads( r.content.decode('utf-8') )
+ html = res['data']['html']
+ with open(outfile, 'w') as h:
+ h.write(html)
+ print( 'Success!')
+
+def testHTML(f='outfile.html', outfile):
+ content = open(f).read()
+ with open(outfile, 'w') as h:
+ outfile.write(content)
+
+
+if __name__ == "__main__":
+ parser = arguments()
+ arg = parser.parse_args()
+ assert os.path.exists(arg.infile)
+ testHTML( 'outfile.html', arg.outfile )
+# pathwayUpload( arg.infile, arg.outfile, arg.server )