old_contents: import sys
  
  from processor import BiopaxProcessor
  
  from indra.java_vm import autoclass, JavaException
  from indra.biopax import pathway_commons_client as pcc
  
  def process_pc_neighborhood(gene_names, neighbor_limit=1):
      model = pcc.graph_query('neighborhood', gene_names,
                              neighbor_limit=neighbor_limit)
      if model is not None:
          return process_model(model)
  
  
  def process_pc_pathsbetween(gene_names, neighbor_limit=1):
      model = pcc.graph_query('pathsbetween', gene_names,
                               neighbor_limit=neighbor_limit)
      if model is not None:
          return process_model(model)
  
  
  def process_pc_pathsfromto(source_genes, target_genes, neighbor_limit=1):
      model = pcc.run_pc_query('pathsfromto', source_genes, 
                               target_genes, neighbor_limit)
      if model is not None:
          return process_model(model)
  
  
  def process_owl(owl_filename):
      model = pcc.owl_to_model(owl_filename)
      return process_model(model)
  
  
  def process_model(model):
      bproc = BiopaxProcessor(model)
      # bproc.get_complexes()
      # bproc.get_phosphorylation()
      # bproc.print_statements()
      return bproc
  
  if __name__ == '__main__':
      pass
  
new_contents: import sys
  
  from processor import BiopaxProcessor
  
  from indra.java_vm import autoclass, JavaException
  from indra.biopax import pathway_commons_client as pcc
  
  def process_pc_neighborhood(gene_names, neighbor_limit=1):
      model = pcc.graph_query('neighborhood', gene_names,
                              neighbor_limit=neighbor_limit)
      if model is not None:
          return process_model(model)
  
  
  def process_pc_pathsbetween(gene_names, neighbor_limit=1):
      model = pcc.graph_query('pathsbetween', gene_names,
                               neighbor_limit=neighbor_limit)
      if model is not None:
          return process_model(model)
  
  
  def process_pc_pathsfromto(source_genes, target_genes, neighbor_limit=1):
      model = pcc.graph_query('pathsfromto', source_genes, 
                               target_genes, neighbor_limit)
      if model is not None:
          return process_model(model)
  
  
  def process_owl(owl_filename):
      model = pcc.owl_to_model(owl_filename)
      return process_model(model)
  
  
  def process_model(model):
      bproc = BiopaxProcessor(model)
      # bproc.get_complexes()
      # bproc.get_phosphorylation()
      # bproc.print_statements()
      return bproc
  
  if __name__ == '__main__':
      pass
  
subject: Fix calling pathway commons client in biopax api