Mercurial > repos > pablocarb > synbiodesign
annotate toolRPViz.py @ 22:638dcd2d93bc draft
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author | pablocarb |
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date | Fri, 14 Jun 2019 12:14:23 -0400 |
parents | cb029043c1d6 |
children | b30e3e5ee8f8 |
rev | line source |
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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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15 |
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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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25 |
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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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30 |
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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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39 |
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40 |
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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 ) |