Mercurial > repos > pablocarb > synbiodesign

comparison toolRPViz.py @ 29:d854b21ada0c draft

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planemo upload commit c56eddc745b70354680c2a2b605840ed72bb98ef
author pablocarb
date Wed, 07 Aug 2019 05:13:27 -0400
parents b30e3e5ee8f8
children
comparison
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28:501f39987c9b 29:d854b21ada0c
11 import argparse 11 import argparse
12 import csv 12 import csv
13 import os 13 import os
14 import json 14 import json
15 import tarfile 15 import tarfile
16 import shutil
16 17
17 def arguments(): 18 def arguments():
18 parser = argparse.ArgumentParser(description='toolRPViz: Pathway visualizer. Pablo Carbonell, SYNBIOCHEM, 2019') 19 parser = argparse.ArgumentParser(description='toolRPViz: Pathway visualizer. Pablo Carbonell, SYNBIOCHEM, 2019')
19 parser.add_argument('infile', 20 parser.add_argument('infile',
20 help='Pathways in SBML format.') 21 help='Pathways in SBML format.')
37 r = requests.get( url ) 38 r = requests.get( url )
38 res = json.loads( r.content.decode('utf-8') ) 39 res = json.loads( r.content.decode('utf-8') )
39 print( res ) 40 print( res )
40 41
41 def pathwayUpload( arg ): 42 def pathwayUpload( arg ):
42 files = { 'file': open(arg.infile, 'rb' ) } 43 # Post request
43 data = {'selenzyme_table': arg.selenzyme_table, 'input_format': arg.input_format} 44 data = {'selenzyme_table': arg.selenzyme_table, 'input_format': arg.input_format}
45 files = { 'file': open(arg.infile, 'rb' ), 'data': ('data.json', json.dumps(data)) }
44 print('Sending query to '+arg.server) 46 print('Sending query to '+arg.server)
45 r=requests.post( arg.server+'/Query',files=files,data=data ) 47 r=requests.post(arg.server+'/Query',files=files)
46 if arg.outfolder is None: 48 # Read response
47 arg.outfolder = os.path.dirname( arg.outfile ) 49 if not os.path.exists(arg.outfolder):
48 if not os.path.exists(outfolder):
49 os.mkdir(arg.outfolder) 50 os.mkdir(arg.outfolder)
50 outtar = os.path.join( arg.outfolder, 'out.tar' ) 51 outtar = os.path.join( arg.outfolder, 'out.tar' )
51 open(outtar,'wb').write( r.content ) 52 open(outtar,'wb').write( r.content )
52 print( 'Response successfully received' ) 53 print( 'Response successfully received' )
53 tar = tarfile.open(outtar) 54 tar = tarfile.open(outtar)
54 tar.extractall(path=arg.outfolder) 55 tar.extractall(path=arg.outfolder)
55 html = os.path.join( arg.outfolder, 'index.html' ) 56 html = os.path.join( arg.outfolder, 'index.html' )
56 shutil.cp( html, arg.outfile ) 57 shutil.copy( html, arg.outfile )
57 print( 'Files extracted' ) 58 print( 'Files extracted' )
58 59
59 60
60 if __name__ == "__main__": 61 if __name__ == "__main__":
61 parser = arguments() 62 parser = arguments()