old_contents: import os
  from indra.util import _require_python3
  import indra.tools.assemble_corpus as ac
  from indra.tools.reading.submit_reading_pipeline_aws import \
      submit_run_reach, wait_for_complete
  from assemble_pysb import *
  import process_data
  
  def run_reading(pmid_fname):
      # Submit reading
      job_list = submit_run_reach('fallahi_eval', pmid_fname)
      # Wait for reading to complete
      reading_res = wait_for_complete(job_list)
  
  
  if __name__ == '__main__':
      data = process_data.read_rppa_data()
      gene_names = process_data.get_gene_names(data)
  
      reassemble = False
  
      raw_stmts_file = '%s/data/fallahi_reach.pkl' % os.environ['HOME']
      pre_stmts_file = '%s/data/fallahi_reach_preassembled.pkl' % \
                          os.environ['HOME']
  
      if reassemble:
          stmts = ac.load_statements(raw_stmts_file)
          stmts = ac.map_grounding(stmts)
          stmts = ac.filter_grounded_only(stmts)
          stmts = ac.filter_human_only(stmts)
          stmts = ac.expand_families(stmts)
          stmts = ac.filter_gene_list(stmts, gene_names, 'all')
          stmts = ac.map_sequence(stmts)
          stmts = ac.run_preassembly(stmts, return_toplevel=False)
          ac.dump_stmts(stmts, pre_stmts_file)
  
      stmts = ac.load_statements(pre_stmts_file)
      model = assemble_pysb(stmts, gene_names)
  
new_contents: import os
  from indra.util import _require_python3
  import indra.tools.assemble_corpus as ac
  from indra.tools.reading.submit_reading_pipeline_aws import \
      submit_run_reach, wait_for_complete
  from assemble_pysb import *
  import process_data
  
  def run_reading(pmid_fname):
      # Submit reading
      job_list = submit_run_reach('fallahi_eval', pmid_fname)
      # Wait for reading to complete
      reading_res = wait_for_complete(job_list)
  
  
  if __name__ == '__main__':
      data = process_data.read_rppa_data()
      gene_names = process_data.get_gene_names(data)
  
      reassemble = False
  
      raw_stmts_file = '%s/data/fallahi_reach.pkl' % os.environ['HOME']
      pre_stmts_file = '%s/data/fallahi_reach_preassembled.pkl' % \
                          os.environ['HOME']
  
      if reassemble:
          stmts = ac.load_statements(raw_stmts_file)
          stmts = ac.map_grounding(stmts)
          stmts = ac.filter_grounded_only(stmts)
          stmts = ac.filter_human_only(stmts)
          stmts = ac.expand_families(stmts)
          stmts = ac.filter_gene_list(stmts, gene_names, 'all')
          stmts = ac.map_sequence(stmts)
          stmts = ac.run_preassembly(stmts, return_toplevel=False)
          ac.dump_statements(stmts, pre_stmts_file)
  
      stmts = ac.load_statements(pre_stmts_file)
      model = assemble_pysb(stmts, gene_names)
  
subject: Fix dump_statements