1#
2# @file    TestReadFromFile7.py
3# @brief   Reads test-data/l2v3-all.xml into memory and tests it.
4#
5# @author  Akiya Jouraku (Python conversion)
6# @author  Sarah Keating
7#
8# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
9#
10# DO NOT EDIT THIS FILE.
11#
12# This file was generated automatically by converting the file located at
13# src/sbml/test/TestReadFromFile7.cpp
14# using the conversion program dev/utilities/translateTests/translateTests.pl.
15# Any changes made here will be lost the next time the file is regenerated.
16#
17# -----------------------------------------------------------------------------
18# This file is part of libSBML.  Please visit http://sbml.org for more
19# information about SBML, and the latest version of libSBML.
20#
21# Copyright 2005-2010 California Institute of Technology.
22# Copyright 2002-2005 California Institute of Technology and
23#                     Japan Science and Technology Corporation.
24#
25# This library is free software; you can redistribute it and/or modify it
26# under the terms of the GNU Lesser General Public License as published by
27# the Free Software Foundation.  A copy of the license agreement is provided
28# in the file named "LICENSE.txt" included with this software distribution
29# and also available online as http://sbml.org/software/libsbml/license.html
30# -----------------------------------------------------------------------------
31
32import sys
33import unittest
34import libsbml
35
36
37class TestReadFromFile7(unittest.TestCase):
38
39
40  def test_read_l2v3_all(self):
41    reader = libsbml.SBMLReader()
42    filename = "../../sbml/test/test-data/"
43    filename += "l2v3-all.xml"
44    d = reader.readSBML(filename)
45    if (d == None):
46      pass
47    self.assert_( d.getLevel() == 2 )
48    self.assert_( d.getVersion() == 3 )
49    m = d.getModel()
50    self.assert_( m != None )
51    self.assert_( m.getId() ==  "l2v3_all" )
52    self.assert_( m.getNumCompartments() == 1 )
53    c = m.getCompartment(0)
54    self.assert_( c != None )
55    self.assert_( c.getId() ==  "a" )
56    self.assert_( c.getCompartmentType() ==  "hh" )
57    self.assert_( c.getSBOTerm() == 236 )
58    self.assert_( c.getSBOTermID() ==  "SBO:0000236" )
59    self.assert_( c.getSize() == 2.3 )
60    self.assert_( m.getNumCompartmentTypes() == 1 )
61    ct = m.getCompartmentType(0)
62    self.assert_( ct != None )
63    self.assert_( ct.getId() ==  "hh" )
64    self.assert_( ct.getSBOTerm() == 236 )
65    self.assert_( ct.getSBOTermID() ==  "SBO:0000236" )
66    self.assert_( m.getNumSpeciesTypes() == 1 )
67    st = m.getSpeciesType(0)
68    self.assert_( st != None )
69    self.assert_( st.getId() ==  "gg" )
70    self.assert_( st.getName() ==  "dd" )
71    self.assert_( st.getSBOTerm() == 236 )
72    self.assert_( st.getSBOTermID() ==  "SBO:0000236" )
73    lost = m.getListOfSpeciesTypes()
74    st1 = lost.get(0)
75    self.assert_( st1 == st )
76    st1 = lost.get("gg")
77    self.assert_( st1 == st )
78    self.assert_( m.getNumConstraints() == 1 )
79    con = m.getConstraint(0)
80    self.assert_( con != None )
81    ast = con.getMath()
82    self.assert_((  "lt(x, 3)" == libsbml.formulaToString(ast) ))
83    self.assert_( m.getNumEvents() == 1 )
84    e = m.getEvent(0)
85    self.assert_( e != None )
86    self.assert_( e.getId() ==  "e1" )
87    self.assert_( e.getSBOTerm() == 231 )
88    self.assert_( e.getSBOTermID() ==  "SBO:0000231" )
89    self.assertEqual( True, e.isSetDelay() )
90    delay = e.getDelay()
91    self.assert_( delay != None )
92    self.assert_( delay.getSBOTerm() == 64 )
93    self.assert_( delay.getSBOTermID() ==  "SBO:0000064" )
94    ast = delay.getMath()
95    self.assert_((  "p + 3" == libsbml.formulaToString(ast) ))
96    self.assertEqual( True, e.isSetTrigger() )
97    trigger = e.getTrigger()
98    self.assert_( trigger != None )
99    self.assert_( trigger.getSBOTerm() == 64 )
100    self.assert_( trigger.getSBOTermID() ==  "SBO:0000064" )
101    ast = trigger.getMath()
102    self.assert_((  "lt(x, 3)" == libsbml.formulaToString(ast) ))
103    loe = m.getListOfEvents()
104    e1 = loe.get(0)
105    self.assert_( e1 == e )
106    e1 = loe.get("e1")
107    self.assert_( e1 == e )
108    self.assert_( e.getNumEventAssignments() == 1 )
109    ea = e.getEventAssignment(0)
110    self.assert_( ea != None )
111    self.assert_( ea.getVariable() ==  "a" )
112    self.assert_( ea.getSBOTerm() == 64 )
113    self.assert_( ea.getSBOTermID() ==  "SBO:0000064" )
114    ast = ea.getMath()
115    self.assert_((  "x * p3" == libsbml.formulaToString(ast) ))
116    loea = e.getListOfEventAssignments()
117    ea1 = loea.get(0)
118    self.assert_( ea1 == ea )
119    ea1 = loea.get("a")
120    self.assert_( ea1 == ea )
121    self.assert_( m.getNumFunctionDefinitions() == 1 )
122    fd = m.getFunctionDefinition(0)
123    self.assert_( fd != None )
124    self.assert_( fd.getId() ==  "fd" )
125    self.assert_( fd.getSBOTerm() == 64 )
126    self.assert_( fd.getSBOTermID() ==  "SBO:0000064" )
127    ast = fd.getMath()
128    self.assert_((  "lambda(x, pow(x, 3))" == libsbml.formulaToString(ast) ))
129    lofd = m.getListOfFunctionDefinitions()
130    fd1 = lofd.get(0)
131    self.assert_( fd1 == fd )
132    fd1 = lofd.get("fd")
133    self.assert_( fd1 == fd )
134    self.assert_( m.getNumInitialAssignments() == 1 )
135    ia = m.getInitialAssignment(0)
136    self.assert_( ia != None )
137    self.assert_( ia.getSymbol() ==  "p1" )
138    ast = ia.getMath()
139    self.assert_((  "x * p3" == libsbml.formulaToString(ast) ))
140    self.assert_( m.getNumRules() == 3 )
141    alg = m.getRule(0)
142    self.assert_( alg != None )
143    self.assert_( alg.getSBOTerm() == 64 )
144    self.assert_( alg.getSBOTermID() ==  "SBO:0000064" )
145    ast = alg.getMath()
146    self.assert_((  "pow(x, 3)" == libsbml.formulaToString(ast) ))
147    ar = m.getRule(1)
148    self.assert_( ar != None )
149    self.assert_( ar.getVariable() ==  "p2" )
150    self.assert_( ar.getSBOTerm() == 64 )
151    self.assert_( ar.getSBOTermID() ==  "SBO:0000064" )
152    ast = ar.getMath()
153    self.assert_((  "x * p3" == libsbml.formulaToString(ast) ))
154    rr = m.getRule(2)
155    self.assert_( rr != None )
156    self.assert_( rr.getVariable() ==  "p3" )
157    self.assert_( rr.getSBOTerm() == 64 )
158    self.assert_( rr.getSBOTermID() ==  "SBO:0000064" )
159    ast = rr.getMath()
160    self.assert_((  "p1 / p" == libsbml.formulaToString(ast) ))
161    self.assert_( m.getNumSpecies() == 1 )
162    s = m.getSpecies(0)
163    self.assert_( s != None )
164    self.assert_( s.getId() ==  "s" )
165    self.assert_( s.getSpeciesType() ==  "gg" )
166    self.assert_( s.getCompartment() ==  "a" )
167    self.assert_( s.getSBOTerm() == 236 )
168    self.assert_( s.getSBOTermID() ==  "SBO:0000236" )
169    self.assertEqual( True, s.isSetInitialAmount() )
170    self.assertEqual( False, s.isSetInitialConcentration() )
171    self.assert_( s.getInitialAmount() == 0 )
172    self.assert_( m.getNumReactions() == 1 )
173    r = m.getReaction(0)
174    self.assert_( r != None )
175    self.assert_( r.getId() ==  "r" )
176    self.assertEqual( False, r.getReversible() )
177    self.assertEqual( True, r.getFast() )
178    self.assertEqual( True, r.isSetKineticLaw() )
179    kl = r.getKineticLaw()
180    self.assert_( kl != None )
181    self.assertEqual( True, kl.isSetMath() )
182    ast = kl.getMath()
183    self.assert_((  "s * k / p" == libsbml.formulaToString(ast) ))
184    self.assert_( kl.getNumParameters() == 2 )
185    p = kl.getParameter(0)
186    self.assert_( p != None )
187    self.assert_( p.getId() ==  "k" )
188    self.assert_( p.getUnits() ==  "litre" )
189    self.assert_( p.getValue() == 9 )
190    ud = p.getDerivedUnitDefinition()
191    self.assert_( ud.getNumUnits() == 1 )
192    self.assert_( ud.getUnit(0).getKind() == libsbml.UNIT_KIND_LITRE )
193    self.assert_( ud.getUnit(0).getExponent() == 1 )
194    lop = kl.getListOfParameters()
195    p1 = lop.get(0)
196    self.assert_( p1 == p )
197    p1 = lop.get("k")
198    self.assert_( p1 == p )
199    p = kl.getParameter(1)
200    self.assert_( p != None )
201    self.assert_( p.getId() ==  "k1" )
202    self.assert_( p.getUnits() ==  "ud1" )
203    self.assert_( p.getValue() == 9 )
204    ud = p.getDerivedUnitDefinition()
205    self.assert_( ud.getNumUnits() == 1 )
206    self.assert_( ud.getUnit(0).getKind() == libsbml.UNIT_KIND_MOLE )
207    self.assert_( ud.getUnit(0).getExponent() == 1 )
208    self.assert_( r.getNumReactants() == 1 )
209    self.assert_( r.getNumProducts() == 0 )
210    self.assert_( r.getNumModifiers() == 0 )
211    sr = r.getReactant(0)
212    self.assert_( sr != None )
213    self.assert_( sr.getSpecies() ==  "s" )
214    self.assert_( sr.getSBOTerm() == 11 )
215    self.assert_( sr.getSBOTermID() ==  "SBO:0000011" )
216    stoich = sr.getStoichiometryMath()
217    self.assert_( stoich != None )
218    self.assert_( stoich.getSBOTerm() == 64 )
219    self.assert_( stoich.getSBOTermID() ==  "SBO:0000064" )
220    ast = stoich.getMath()
221    self.assert_((  "s * p" == libsbml.formulaToString(ast) ))
222    self.assert_( m.getNumUnitDefinitions() == 1 )
223    ud = m.getUnitDefinition(0)
224    self.assert_( ud != None )
225    self.assert_( ud.getId() ==  "ud1" )
226    loud = m.getListOfUnitDefinitions()
227    ud1 = loud.get(0)
228    self.assert_( ud1 == ud )
229    ud1 = loud.get("ud1")
230    self.assert_( ud1 == ud )
231    self.assert_( ud.getNumUnits() == 1 )
232    u = ud.getUnit(0)
233    self.assert_( u != None )
234    self.assert_( u.getKind() == libsbml.UNIT_KIND_MOLE )
235    lou = ud.getListOfUnits()
236    u1 = lou.get(0)
237    self.assert_( u1 == u )
238    d = None
239    pass
240
241def suite():
242  suite = unittest.TestSuite()
243  suite.addTest(unittest.makeSuite(TestReadFromFile7))
244
245  return suite
246
247if __name__ == "__main__":
248  if unittest.TextTestRunner(verbosity=1).run(suite()).wasSuccessful() :
249    sys.exit(0)
250  else:
251    sys.exit(1)
252