annotate toolRPViz.py @ 22:638dcd2d93bc draft

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author pablocarb
date Fri, 14 Jun 2019 12:14:23 -0400
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children b30e3e5ee8f8
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1 #!/usr/bin/env python3
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2 # -*- coding: utf-8 -*-
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3 """
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4 Created on Mar 19
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5
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6 @author: Pablo Carbonell
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7 @description: Query RPViz: pathway visualizer.
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8
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9 """
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10 import requests
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11 import argparse
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12 import csv
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13 import os
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14 import json
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16 def arguments():
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17 parser = argparse.ArgumentParser(description='toolRPViz: Pathway visualizer. Pablo Carbonell, SYNBIOCHEM, 2019')
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18 parser.add_argument('infile',
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19 help='Pathways in SBML format.')
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20 parser.add_argument('outfile',
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21 help='HTML visualizer file.')
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22 parser.add_argument('-server', default='http://rpviz.synbiochem.co.uk/REST',
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23 help='RPViz server.')
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24 return parser
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26 def testApp(url):
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27 r = requests.get( url )
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28 res = json.loads( r.content.decode('utf-8') )
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29 print( res )
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31 def pathwayUpload(infile, outfile, url):
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32 files = { 'file': open(infile, 'rb' ) }
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33 r = requests.post( os.path.join(url, 'Query' ), files=files )
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34 res = json.loads( r.content.decode('utf-8') )
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35 html = res['data']['html']
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36 with open(outfile, 'w') as h:
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37 h.write(html)
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38 print( 'Success!')
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41 if __name__ == "__main__":
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42 parser = arguments()
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43 arg = parser.parse_args()
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44 assert os.path.exists(arg.infile)
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45 pathwayUpload( arg.infile, arg.outfile, arg.server )