def createElements():
elements = [
createSedDocument(),
createSedModel(),
createSedChange(),
createSedParameter(),
createSedVariable(),
createSedChangeAttribute(),
createSedChangeRemoveXML(),
createSedComputeChange(),
createSedSimulation(),
createSedUniformTimeCourse(),
createSedAlgorithm(),
createSedTask(),
createSedDataGenerator(),
createSedOutput(),
createSedCurve(),
createSedSurface(),
createSedDataSet(),
createSedReport(),
createSedPlot2D(),
createSedPlot3D()
]
for element in elements:
writeCode.createCode(element)
writeHeader.createHeader(element)
def createElements():
elements = [
createSedDocument(),
createSedDataDescription(),
createSedDataSource(),
createSedSlice(),
createSedModel(),
createSedChange(),
createSedParameter(),
createSedVariable(),
createSedChangeAttribute(),
createSedChangeAddXML(),
createSedChangeChangeXML(),
createSedChangeRemoveXML(),
createSedComputeChange(),
createSedSimulation(),
createSedUniformTimeCourse(),
createSedOneStep(),
createSedSteadyState(),
createSedAlgorithmParameter(),
createSedAlgorithm(),
#createSedAbstractTask(),
createSedTask(),
createSedRepeatedTask(),
createSedRange(),
createSedFunctionalRange(),
createSedUniformRange(),
createSedVectorRange(),
createSedSetValue(),
createSedSubTask(),
createSedDataGenerator(),
createSedOutput(),
createSedCurve(),
createSedSurface(),
createSedDataSet(),
createSedReport(),
createSedPlot2D(),
createSedPlot3D()
]
for element in elements:
writeCode.createCode(element)
writeHeader.createHeader(element)
def createElements():
elements = [
createSedDocument(),
createSedDataDescription(),
createSedDataSource(),
createSedSlice(),
createSedModel(),
createSedChange(),
createSedParameter(),
createSedVariable(),
createSedChangeAttribute(),
createSedChangeAddXML(),
createSedChangeChangeXML(),
createSedChangeRemoveXML(),
createSedComputeChange(),
createSedSimulation(),
createSedUniformTimeCourse(),
createSedOneStep(),
createSedSteadyState(),
createSedAlgorithmParameter(),
createSedAlgorithm(),
#createSedAbstractTask(),
createSedTask(),
createSedRepeatedTask(),
createSedRange(),
createSedFunctionalRange(),
createSedUniformRange(),
createSedVectorRange(),
createSedSetValue(),
createSedSubTask(),
createSedDataGenerator(),
createSedOutput(),
createSedCurve(),
createSedSurface(),
createSedDataSet(),
createSedReport(),
createSedPlot2D(),
createSedPlot3D()
]
for element in elements:
writeCode.createCode(element)
writeHeader.createHeader(element)
def generatePackageForDefinition(packageDefn):
name = packageDefn['name'].lower()
thisDir = os.getcwd()
extDir = './' + name + '/src/sbml/packages/' + name + '/extension'
sbmlDir = './' + name + '/src/sbml/packages/' + name + '/sbml'
cmnDir = './' + name + '/src/sbml/packages/' + name + '/common'
valDir = './' + name + '/src/sbml/packages/' + name + '/validator'
packDir = './' + name + '/src/sbml/packages'
bindDir = './' + name + '/src/bindings'
#check directories exist
if os.path.exists(extDir) == False:
createDirStruct.createDirectories(name)
#print 'directory structure for {0} not available - please run createDirStruct'.format(name)
#sys.exit(0)
os.chdir(extDir)
createExtensionFiles.main(packageDefn)
os.chdir(thisDir)
os.chdir(sbmlDir)
elements = packageDefn['sbmlElements']
for i in range(0, len(elements)):
element = elements[i]
writeCode.createCode(element)
writeHeader.createHeader(element)
os.chdir(thisDir)
os.chdir(cmnDir)
createCommonFiles.main(packageDefn)
os.chdir(thisDir)
os.chdir(valDir)
createValidatorFiles.main(packageDefn)
os.chdir(thisDir)
createCMakeFiles.main(packageDefn)
os.chdir(thisDir)
os.chdir(packDir)
createRegisterFiles.main(name)
os.chdir(thisDir)
os.chdir(bindDir)
createBindingsFiles.main(packageDefn)
os.chdir(thisDir)
createArchiveFile.main(name)
def generatePackageForDefinition(packageDefn):
name = packageDefn['name'].lower()
thisDir = os.getcwd()
extDir = './' + name + '/src/sbml/packages/' + name + '/extension'
sbmlDir = './' + name + '/src/sbml/packages/' + name + '/sbml'
cmnDir = './' + name + '/src/sbml/packages/' + name + '/common'
valDir = './' + name + '/src/sbml/packages/' + name + '/validator'
packDir = './' + name + '/src/sbml/packages'
bindDir = './' + name + '/src/bindings'
#check directories exist
if os.path.exists(extDir) == False:
createDirStruct.createDirectories(name)
#print 'directory structure for {0} not available - please run createDirStruct'.format(name)
#sys.exit(0)
os.chdir(extDir)
createExtensionFiles.main(packageDefn)
os.chdir(thisDir)
os.chdir(sbmlDir)
elements = packageDefn['sbmlElements']
for i in range (0, len(elements)):
element = elements[i]
writeCode.createCode(element)
writeHeader.createHeader(element)
os.chdir(thisDir)
os.chdir(cmnDir)
createCommonFiles.main(packageDefn)
os.chdir(thisDir)
os.chdir(valDir)
createValidatorFiles.main(packageDefn)
os.chdir(thisDir)
createCMakeFiles.main(packageDefn)
os.chdir(thisDir)
os.chdir(packDir)
createRegisterFiles.main(name)
os.chdir(thisDir)
os.chdir(bindDir)
createBindingsFiles.main(packageDefn)
os.chdir(thisDir)
createArchiveFile.main(name)
def createElements():
elements = [ createSedDocument(),
createSedModel(),
createSedChange(),
createSedParameter(),
createSedVariable(),
createSedChangeAttribute(),
createSedChangeRemoveXML(),
createSedComputeChange(),
createSedSimulation(),
createSedUniformTimeCourse(),
createSedAlgorithm(),
createSedTask(),
createSedDataGenerator(),
createSedOutput(),
createSedCurve(),
createSedSurface(),
createSedDataSet(),
createSedReport(),
createSedPlot2D(),
createSedPlot3D() ]
for element in elements:
writeCode.createCode(element)
writeHeader.createHeader(element)
# of Heidelberg, nor the names of any contributors, may be used to endorse
# or promote products derived from this software without specific prior
# written permission.
# ------------------------------------------------------------------------ -->
import sys
import createDirStruct
import writeCode
import writeHeader
if len(sys.argv) != 1:
print ('Usage: createSBMLFiles.py')
else:
element = createNewElementDictObj.createCompDeletion()
writeCode.createCode(element)
writeHeader.createHeader(element)
element = createNewElementDictObj.createCompSubModel()
writeCode.createCode(element)
writeHeader.createHeader(element)
element = createNewElementDictObj.createSBaseRef()
writeCode.createCode(element)
writeHeader.createHeader(element)
element = createNewElementDictObj.createCompPort()
writeCode.createCode(element)
writeHeader.createHeader(element)
element = createNewElementDictObj.createCompReplacedE()
writeCode.createCode(element)
writeHeader.createHeader(element)
element = createNewElementDictObj.createCompReplacedBy()
writeCode.createCode(element)
writeHeader.createHeader(element)
