diff toolRPViz.py @ 19:dbc40b306014 draft

planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5-dirty

--- /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 )