import sys
import pickle
from indra import reach
from indra.assemblers import GraphAssembler

if len(sys.argv) < 2:
    process_type = 'text'
else:
    process_type = sys.argv[1]

if process_type == 'text':
    txt = open('ras_pathway.txt', 'rt').read()
    rp = reach.process_text(txt, offline=True)
    st = rp.statements
elif process_type == 'json':
    rp = reach.process_json_file('reach_output.json')
    st = rp.statements
else:
    st = pickle.load(open('statements.pkl', 'rb'))
for s in st:
    print '%s\t%s' % (s, s.evidence[0].text)

graphpr = {'rankdir': 'TD'}
nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0}
ga = GraphAssembler(st, graph_properties=graphpr, node_properties=nodepr)
ga.make_model()
ga.save_dot('ras_pathway.dot')
ga.save_pdf('ras_pathway.pdf')

import sys
import pickle
from indra import trips
from indra import reach
from indra.assemblers import GraphAssembler


def process_reach(txt, reread):
    if reread:
        rp = reach.process_text(txt, offline=True)
        st = rp.statements
    else:
        rp = reach.process_json_file('reach_output.json')
        st = rp.statements
    for s in st:
        print('%s\t%s' % (s, s.evidence[0].text))
    return st

def process_trips(txt, reread):
    if reread:
        tp = trips.process_text(txt)
        st = tp.statements
    else:
        tp = trips.process_xml(open('trips_output.xml', 'r').read())
        st = tp.statements
    for s in st:
        print('%s\t%s' % (s, s.evidence[0].text))
    return st

def draw_graph(stmts):
    graphpr = {'rankdir': 'TD'}
    nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0}
    ga = GraphAssembler(st, graph_properties=graphpr, node_properties=nodepr)
    ga.make_model()
    ga.save_dot('ras_pathway.dot')
    ga.save_pdf('ras_pathway.pdf')

if __name__ == '__main__':
    reread = True
    txt = open('ras_pathway.txt', 'rt').read()
    print('-----')
    print(txt)
    print('-----')
    if len(sys.argv) < 2:
        print('Reader not specified')
        sys.exit()
    reader = sys.argv[1]
    if reader == 'reach':
        print('Using REACH')
        stmts = process_reach(txt, reread)
    elif reader == 'trips':
        print('Using TRIPS')
        stmts = process_trips(txt, reread)


Add TRIPS reading option to RAS pathway map
Add TRIPS reading option to RAS pathway map

  import sys
  import pickle
+ from indra import trips
  from indra import reach
  from indra.assemblers import GraphAssembler
  
- if len(sys.argv) < 2:
-     process_type = 'text'
- else:
-     process_type = sys.argv[1]
  
- if process_type == 'text':
+ def process_reach(txt, reread):
+     if reread:
+         rp = reach.process_text(txt, offline=True)
+         st = rp.statements
+     else:
+         rp = reach.process_json_file('reach_output.json')
+         st = rp.statements
+     for s in st:
+         print('%s\t%s' % (s, s.evidence[0].text))
+     return st
+ 
+ def process_trips(txt, reread):
+     if reread:
+         tp = trips.process_text(txt)
+         st = tp.statements
+     else:
+         tp = trips.process_xml(open('trips_output.xml', 'r').read())
+         st = tp.statements
+     for s in st:
+         print('%s\t%s' % (s, s.evidence[0].text))
+     return st
+ 
+ def draw_graph(stmts):
+     graphpr = {'rankdir': 'TD'}
+     nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0}
+     ga = GraphAssembler(st, graph_properties=graphpr, node_properties=nodepr)
+     ga.make_model()
+     ga.save_dot('ras_pathway.dot')
+     ga.save_pdf('ras_pathway.pdf')
+ 
+ if __name__ == '__main__':
+     reread = True
      txt = open('ras_pathway.txt', 'rt').read()
-     rp = reach.process_text(txt, offline=True)
-     st = rp.statements
- elif process_type == 'json':
-     rp = reach.process_json_file('reach_output.json')
-     st = rp.statements
- else:
-     st = pickle.load(open('statements.pkl', 'rb'))
- for s in st:
-     print '%s\t%s' % (s, s.evidence[0].text)
+     print('-----')
+     print(txt)
+     print('-----')
+     if len(sys.argv) < 2:
+         print('Reader not specified')
+         sys.exit()
+     reader = sys.argv[1]
+     if reader == 'reach':
+         print('Using REACH')
+         stmts = process_reach(txt, reread)
+     elif reader == 'trips':
+         print('Using TRIPS')
+         stmts = process_trips(txt, reread)
  
- graphpr = {'rankdir': 'TD'}
- nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0}
- ga = GraphAssembler(st, graph_properties=graphpr, node_properties=nodepr)
- ga.make_model()
- ga.save_dot('ras_pathway.dot')
- ga.save_pdf('ras_pathway.pdf')
  
Add TRIPS reading option to RAS pathway map
## Code Before:
import sys
import pickle
from indra import reach
from indra.assemblers import GraphAssembler

if len(sys.argv) < 2:
    process_type = 'text'
else:
    process_type = sys.argv[1]

if process_type == 'text':
    txt = open('ras_pathway.txt', 'rt').read()
    rp = reach.process_text(txt, offline=True)
    st = rp.statements
elif process_type == 'json':
    rp = reach.process_json_file('reach_output.json')
    st = rp.statements
else:
    st = pickle.load(open('statements.pkl', 'rb'))
for s in st:
    print '%s\t%s' % (s, s.evidence[0].text)

graphpr = {'rankdir': 'TD'}
nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0}
ga = GraphAssembler(st, graph_properties=graphpr, node_properties=nodepr)
ga.make_model()
ga.save_dot('ras_pathway.dot')
ga.save_pdf('ras_pathway.pdf')

## Instruction:
Add TRIPS reading option to RAS pathway map
## Code After:
import sys
import pickle
from indra import trips
from indra import reach
from indra.assemblers import GraphAssembler


def process_reach(txt, reread):
    if reread:
        rp = reach.process_text(txt, offline=True)
        st = rp.statements
    else:
        rp = reach.process_json_file('reach_output.json')
        st = rp.statements
    for s in st:
        print('%s\t%s' % (s, s.evidence[0].text))
    return st

def process_trips(txt, reread):
    if reread:
        tp = trips.process_text(txt)
        st = tp.statements
    else:
        tp = trips.process_xml(open('trips_output.xml', 'r').read())
        st = tp.statements
    for s in st:
        print('%s\t%s' % (s, s.evidence[0].text))
    return st

def draw_graph(stmts):
    graphpr = {'rankdir': 'TD'}
    nodepr = {'fontsize': 12, 'shape': 'plaintext', 'margin': '0,0', 'pad': 0}
    ga = GraphAssembler(st, graph_properties=graphpr, node_properties=nodepr)
    ga.make_model()
    ga.save_dot('ras_pathway.dot')
    ga.save_pdf('ras_pathway.pdf')

if __name__ == '__main__':
    reread = True
    txt = open('ras_pathway.txt', 'rt').read()
    print('-----')
    print(txt)
    print('-----')
    if len(sys.argv) < 2:
        print('Reader not specified')
        sys.exit()
    reader = sys.argv[1]
    if reader == 'reach':
        print('Using REACH')
        stmts = process_reach(txt, reread)
    elif reader == 'trips':
        print('Using TRIPS')
        stmts = process_trips(txt, reread)

