printAnnotation.py

Prints the annotation strings for each element in a given model.

#!/usr/bin/env python
## 
## @file    printAnnotation.py
## @brief   Prints annotation strings for each element
## @author  Akiya Jouraku
## 
## <!--------------------------------------------------------------------------
## This sample program is distributed under a different license than the rest
## of libSBML.  This program uses the open-source MIT license, as follows:
##
## Copyright (c) 2013-2018 by the California Institute of Technology
## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
## and the University of Heidelberg (Germany), with support from the National
## Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
##
## Permission is hereby granted, free of charge, to any person obtaining a
## copy of this software and associated documentation files (the "Software"),
## to deal in the Software without restriction, including without limitation
## the rights to use, copy, modify, merge, publish, distribute, sublicense,
## and/or sell copies of the Software, and to permit persons to whom the
## Software is furnished to do so, subject to the following conditions:
##
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## all copies or substantial portions of the Software.
##
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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## DEALINGS IN THE SOFTWARE.
##
## Neither the name of the California Institute of Technology (Caltech), nor
## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
## of Heidelberg, nor the names of any contributors, may be used to endorse
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## 


import sys
import os.path
from libsbml import *

def printAnnotation(sb, id=""):
  if not sb.isSetAnnotation():
    return

  pid = ""

  if sb.isSetId():
      pid = sb.getId()
  print("----- " + sb.getElementName() + " (" + pid
                    + ") annotation -----" + "\n")
  print(sb.getAnnotationString() + "\n")
  print("\n")


def main (args):
  """Usage: printAnnotation filename
  """

  if len(args) != 2:
    print(main.__doc__)
    sys.exit(2)

  filename = args[1]
  document = readSBML(filename)

  errors = document.getNumErrors()

  print("filename: " + filename + "\n")

  if errors > 0:
      document.printErrors()
      return errors

  # Model

  m = document.getModel()
  printAnnotation(m)

  for i in range(0, m.getNumReactions()):
      re = m.getReaction(i)
      printAnnotation(re)

      # SpeciesReference (Reactant)

      for j in range(0, re.getNumReactants()):
          rt = re.getReactant(j)
          if rt.isSetAnnotation():
            print("     ")
          printAnnotation(rt, rt.getSpecies())

      # SpeciesReference (Product)

      for j in range(0, re.getNumProducts()):
          rt = re.getProduct(j)
          if rt.isSetAnnotation():
            print("     ")
          printAnnotation(rt, rt.getSpecies())

      # ModifierSpeciesReference (Modifiers)

      for j in range(0, re.getNumModifiers()):
          md = re.getModifier(j)
          if md.isSetAnnotation():
            print("     ")
          printAnnotation(md, md.getSpecies())

      # KineticLaw

      if re.isSetKineticLaw():
          kl = re.getKineticLaw()
          if kl.isSetAnnotation():
            print("   ")
          printAnnotation(kl)

          # Parameter
          for j in range(0, kl.getNumParameters()):
              pa = kl.getParameter(j)
              if pa.isSetAnnotation():
                print("      ")
              printAnnotation(pa)

  # Species
  for i in range(0, m.getNumSpecies()):
      sp = m.getSpecies(i)
      printAnnotation(sp)

  # Compartments
  for i in range(0, m.getNumCompartments()):
      sp = m.getCompartment(i)
      printAnnotation(sp)

  # FunctionDefinition
  for i in range (0, m.getNumFunctionDefinitions()):
      sp = m.getFunctionDefinition(i)
      printAnnotation(sp)

  # UnitDefinition
  for i in range (0, m.getNumUnitDefinitions()):
      sp = m.getUnitDefinition(i)
      printAnnotation(sp)

  # Parameter
  for i in range(0, m.getNumParameters()):
      sp = m.getParameter(i)
      printAnnotation(sp)

  # Rule
  for i in range(0, m.getNumRules()):
      sp = m.getRule(i)
      printAnnotation(sp)

  # InitialAssignment
  for i in range(0, m.getNumInitialAssignments()):
      sp = m.getInitialAssignment(i)
      printAnnotation(sp)

  # Event
  for i in range(0,m.getNumEvents()):
      sp = m.getEvent(i)
      printAnnotation(sp)

      # Trigger
      if sp.isSetTrigger():
          tg = sp.getTrigger()
          if tg.isSetAnnotation():
            print("   ")
          printAnnotation(tg)

      # Delay
      if sp.isSetDelay():
          dl = sp.getDelay()
          if dl.isSetAnnotation():
            print("   ")
          printAnnotation(dl)

      # EventAssignment
      for j in range(0,sp.getNumEventAssignments()):
          ea = sp.getEventAssignment(j)
          if ea.isSetAnnotation():
            print("   ")
          printAnnotation(ea)

  # SpeciesType
  for i in range(0,m.getNumSpeciesTypes()):
      sp = m.getSpeciesType(i)
      printAnnotation(sp)

  # Constraints
  for i in range(0,m.getNumConstraints()):
      sp = m.getConstraint(i)
      printAnnotation(sp)

  return errors


if __name__ == '__main__':
  main(sys.argv)