def test_Date_copyConstructor(self):
date = libsbml.Date(2005, 12, 30, 12, 15, 45, 1, 2, 0)
self.assert_(date.getMonth() == 12)
self.assert_(date.getSecond() == 45)
date2 = libsbml.Date(date)
self.assert_(date2.getMonth() == 12)
self.assert_(date2.getSecond() == 45)
date2 = None
date = None
pass
def test_Date_assignmentOperator(self):
date = libsbml.Date(2005, 12, 30, 12, 15, 45, 1, 2, 0)
self.assert_(date.getMonth() == 12)
self.assert_(date.getSecond() == 45)
date2 = libsbml.Date()
date2 = date
self.assert_(date2.getMonth() == 12)
self.assert_(date2.getSecond() == 45)
date2 = None
date = None
pass
def test_Date_getDateAsString(self):
dd = "2005-02-02T14:56:11Z"
date = libsbml.Date(dd)
self.assert_(date != None)
self.assert_(date.getYear() == 2005)
self.assert_(date.getMonth() == 2)
self.assert_(date.getDay() == 2)
self.assert_(date.getHour() == 14)
self.assert_(date.getMinute() == 56)
self.assert_(date.getSecond() == 11)
self.assert_(date.getSignOffset() == 0)
self.assert_(date.getHoursOffset() == 0)
self.assert_(date.getMinutesOffset() == 0)
date.setYear(2012)
date.setMonth(3)
date.setDay(28)
date.setHour(23)
date.setMinute(4)
date.setSecond(32)
date.setSignOffset(1)
date.setHoursOffset(2)
date.setMinutesOffset(32)
self.assert_(("2012-03-28T23:04:32+02:32" == date.getDateAsString()))
_dummyList = [date]
_dummyList[:] = []
del _dummyList
pass
def test_Date_setDateAsString(self):
date = libsbml.Date(2007, 10, 23, 14, 15, 16, 1, 3, 0)
self.assert_(date != None)
i = date.setDateAsString("20081-12-30T12:15:45+02:00")
self.assert_(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE)
self.assert_(("2007-10-23T14:15:16+03:00" == date.getDateAsString()))
i = date.setDateAsString("200-12-30T12:15:45+02:00")
self.assert_(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE)
self.assert_(("2007-10-23T14:15:16+03:00" == date.getDateAsString()))
i = date.setDateAsString("")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(("2000-01-01T00:00:00Z" == date.getDateAsString()))
i = date.setDateAsString("2008-12-30T12:15:45+02:00")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(date.getYear() == 2008)
self.assert_(date.getMonth() == 12)
self.assert_(date.getDay() == 30)
self.assert_(date.getHour() == 12)
self.assert_(date.getMinute() == 15)
self.assert_(date.getSecond() == 45)
self.assert_(date.getSignOffset() == 1)
self.assert_(date.getHoursOffset() == 2)
self.assert_(date.getMinutesOffset() == 0)
_dummyList = [date]
_dummyList[:] = []
del _dummyList
pass
def test_Date_setters(self):
date = libsbml.Date(2005, 12, 30, 12, 15, 45, 1, 2, 0)
self.assert_(date != None)
date.setYear(2012)
date.setMonth(3)
date.setDay(28)
date.setHour(23)
date.setMinute(4)
date.setSecond(32)
date.setSignOffset(1)
date.setHoursOffset(2)
date.setMinutesOffset(32)
self.assert_(date.getYear() == 2012)
self.assert_(date.getMonth() == 3)
self.assert_(date.getDay() == 28)
self.assert_(date.getHour() == 23)
self.assert_(date.getMinute() == 4)
self.assert_(date.getSecond() == 32)
self.assert_(date.getSignOffset() == 1)
self.assert_(date.getHoursOffset() == 2)
self.assert_(date.getMinutesOffset() == 32)
self.assert_(("2012-03-28T23:04:32+02:32" == date.getDateAsString()))
_dummyList = [date]
_dummyList[:] = []
del _dummyList
pass
def test_L3_Species_ModelHistory(self):
(self.S).setMetaId("_3")
history = libsbml.ModelHistory()
i = (self.S).setModelHistory(history)
self.assert_(i == libsbml.LIBSBML_INVALID_OBJECT)
self.assertEqual(False, (self.S).isSetModelHistory())
mc = libsbml.ModelCreator()
date = libsbml.Date(2005, 12, 30, 12, 15, 45, 1, 2, 0)
mc.setFamilyName("Keating")
mc.setGivenName("Sarah")
mc.setEmail("*****@*****.**")
mc.setOrganisation("UH")
history.addCreator(mc)
history.setCreatedDate(date)
history.setModifiedDate(date)
i = (self.S).setModelHistory(history)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(True, (self.S).isSetModelHistory())
i = (self.S).unsetModelHistory()
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(False, (self.S).isSetModelHistory())
self.assert_((self.S).getModelHistory() == None)
_dummyList = [history]
_dummyList[:] = []
del _dummyList
pass
def test_RDFAnnotation2_modelWithHistoryWithCharacterReference(self):
h = libsbml.ModelHistory()
c = libsbml.ModelCreator()
c.setFamilyName("Dräger")
c.setGivenName("Andreas")
h.addCreator(c)
d = libsbml.Date(2005, 2, 2, 14, 56, 11)
h.setCreatedDate(d)
h.addModifiedDate(d)
self.m2.unsetModelHistory()
self.m2.setModelHistory(h)
ann = libsbml.RDFAnnotationParser.parseModelHistory(self.m2)
expected = wrapString(
"<annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
+ " <rdf:Description rdf:about=\"#_000001\">\n" +
" <dc:creator rdf:parseType=\"Resource\">\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:parseType=\"Resource\">\n" +
" <vCard:N rdf:parseType=\"Resource\">\n" +
" <vCard:Family>Dräger</vCard:Family>\n" +
" <vCard:Given>Andreas</vCard:Given>\n" +
" </vCard:N>\n" + " </rdf:li>\n" +
" </rdf:Bag>\n" + " </dc:creator>\n" +
" <dcterms:created rdf:parseType=\"Resource\">\n" +
" <dcterms:W3CDTF>2005-02-02T14:56:11Z</dcterms:W3CDTF>\n" +
" </dcterms:created>\n" +
" <dcterms:modified rdf:parseType=\"Resource\">\n" +
" <dcterms:W3CDTF>2005-02-02T14:56:11Z</dcterms:W3CDTF>\n" +
" </dcterms:modified>\n" + " </rdf:Description>\n" +
" </rdf:RDF>\n" + "</annotation>")
self.assertEqual(True, self.equals(expected, ann.toXMLString()))
pass
def test_Model_setgetModelHistory(self):
self.M.setMetaId("_001")
history = libsbml.ModelHistory()
mc = libsbml.ModelCreator()
date = libsbml.Date(2005, 12, 30, 12, 15, 45, 1, 2, 0)
mc.setFamilyName("Keating")
mc.setGivenName("Sarah")
mc.setEmail("*****@*****.**")
mc.setOrganisation("UH")
history.addCreator(mc)
history.setCreatedDate(date)
history.setModifiedDate(date)
self.assert_(self.M.isSetModelHistory() == False)
self.M.setModelHistory(history)
self.assert_(self.M.isSetModelHistory() == True)
newMC = history.getCreator(0)
self.assert_(newMC != None)
self.assert_(("Keating" == newMC.getFamilyName()))
self.assert_(("Sarah" == newMC.getGivenName()))
self.assert_(("*****@*****.**" == newMC.getEmail()))
self.assert_(("UH" == newMC.getOrganisation()))
self.M.unsetModelHistory()
self.assert_(self.M.isSetModelHistory() == False)
_dummyList = [history]
_dummyList[:] = []
del _dummyList
_dummyList = [mc]
_dummyList[:] = []
del _dummyList
pass
def date_now():
""" Get current time stamp for history.
:return: current libsbml Date
"""
time = datetime.datetime.now()
timestr = time.strftime('%Y-%m-%dT%H:%M:%S')
return libsbml.Date(timestr)
def test_Date_clone(self):
date = libsbml.Date(2005, 12, 30, 12, 15, 45, 1, 2, 0)
self.assert_(date.getMonth() == 12)
self.assert_(date.getSecond() == 45)
date2 = date.clone()
self.assert_(date2.getMonth() == 12)
self.assert_(date2.getSecond() == 45)
date2 = None
date = None
pass
def test_ModelHistory_addModifiedDate(self):
history = libsbml.ModelHistory()
self.assert_(history != None)
self.assert_(history.isSetModifiedDate() == False)
self.assert_(history.getNumModifiedDates() == 0)
date = libsbml.Date(2005, 12, 30, 12, 15, 45, 1, 2, 0)
history.addModifiedDate(date)
_dummyList = [date]
_dummyList[:] = []
del _dummyList
self.assert_(history.getNumModifiedDates() == 1)
self.assert_(history.isSetModifiedDate() == True)
newdate = history.getListModifiedDates().get(0)
self.assert_(newdate.getYear() == 2005)
self.assert_(newdate.getMonth() == 12)
self.assert_(newdate.getDay() == 30)
self.assert_(newdate.getHour() == 12)
self.assert_(newdate.getMinute() == 15)
self.assert_(newdate.getSecond() == 45)
self.assert_(newdate.getSignOffset() == 1)
self.assert_(newdate.getHoursOffset() == 2)
self.assert_(newdate.getMinutesOffset() == 0)
date1 = libsbml.Date(2008, 11, 2, 16, 42, 40, 1, 2, 0)
history.addModifiedDate(date1)
_dummyList = [date1]
_dummyList[:] = []
del _dummyList
self.assert_(history.getNumModifiedDates() == 2)
self.assert_(history.isSetModifiedDate() == True)
newdate1 = history.getModifiedDate(1)
self.assert_(newdate1.getYear() == 2008)
self.assert_(newdate1.getMonth() == 11)
self.assert_(newdate1.getDay() == 2)
self.assert_(newdate1.getHour() == 16)
self.assert_(newdate1.getMinute() == 42)
self.assert_(newdate1.getSecond() == 40)
self.assert_(newdate1.getSignOffset() == 1)
self.assert_(newdate1.getHoursOffset() == 2)
self.assert_(newdate1.getMinutesOffset() == 0)
_dummyList = [history]
_dummyList[:] = []
del _dummyList
pass
def test_ModelHistory_setModifiedDate2(self): mh = libsbml.ModelHistory() self.assert_( mh != None ) date = libsbml.Date(200,13,76,56,89,90,0,0,0) i = mh.setModifiedDate(date) self.assert_( i == libsbml.LIBSBML_INVALID_OBJECT ) self.assert_( mh.isSetModifiedDate() == False ) _dummyList = [ date ]; _dummyList[:] = []; del _dummyList _dummyList = [ mh ]; _dummyList[:] = []; del _dummyList pass
def test_ModelHistory_setCreatedDate2(self):
mh = libsbml.ModelHistory()
self.assert_( mh != None )
date = libsbml.Date("Jan 12")
i = mh.setCreatedDate(date)
self.assert_( i == libsbml.LIBSBML_INVALID_OBJECT )
self.assert_( mh.isSetCreatedDate() == False )
_dummyList = [ date ]; _dummyList[:] = []; del _dummyList
_dummyList = [ mh ]; _dummyList[:] = []; del _dummyList
pass
def change_modified_date(sbml):
"""
Change SBML modified date to now.
"""
history = sbml.getModel().getModelHistory()
if history:
history.setModifiedDate(libsbml.Date(w3c_time()))
# remove all but final modified date
while history.getListModifiedDates().getSize() > 1:
history.getListModifiedDates().remove(0)
def test_Date_setHoursOffset(self):
date = libsbml.Date(2005, 12, 30, 12, 15, 45, 1, 2, 0)
self.assert_(date != None)
i = date.setHoursOffset(434)
self.assert_(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE)
self.assert_(date.getHoursOffset() == 0)
i = date.setHoursOffset(11)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(date.getHoursOffset() == 11)
self.assert_(("2005-12-30T12:15:45+11:00" == date.getDateAsString()))
_dummyList = [date]
_dummyList[:] = []
del _dummyList
pass
def test_Validation_ModelHistory3(self):
mh = libsbml.ModelHistory()
self.assert_(mh != None)
self.assertEqual(False, (mh.hasRequiredAttributes()))
date = libsbml.Date(2007, 12, 30, 12, 15, 45, 1, 2, 0)
mh.setCreatedDate(date)
self.assertEqual(False, (mh.hasRequiredAttributes()))
mh.setModifiedDate(date)
self.assertEqual(False, (mh.hasRequiredAttributes()))
mc = libsbml.ModelCreator()
mc.setFamilyName("Keating")
mh.addCreator(mc)
self.assertEqual(False, (mh.hasRequiredAttributes()))
mh = None
pass
def test_ModelHistory_setModifiedDate1(self):
mh = libsbml.ModelHistory()
self.assert_( mh != None )
date = libsbml.Date("2005-12-30T12:15:32+02:00")
i = mh.setModifiedDate(date)
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
self.assert_( mh.isSetModifiedDate() == True )
self.assert_( date != mh.getModifiedDate() )
dateChar = mh.getModifiedDate().getDateAsString()
self.assert_(( "2005-12-30T12:15:32+02:00" == dateChar ))
i = mh.setModifiedDate(None)
self.assert_( i == libsbml.LIBSBML_OPERATION_FAILED )
self.assert_( mh.isSetModifiedDate() == True )
_dummyList = [ date ]; _dummyList[:] = []; del _dummyList
_dummyList = [ mh ]; _dummyList[:] = []; del _dummyList
pass
def test_Date_create(self):
date = libsbml.Date(2005, 12, 30, 12, 15, 45, 1, 2, 0)
self.assert_(date != None)
self.assert_(date.getYear() == 2005)
self.assert_(date.getMonth() == 12)
self.assert_(date.getDay() == 30)
self.assert_(date.getHour() == 12)
self.assert_(date.getMinute() == 15)
self.assert_(date.getSecond() == 45)
self.assert_(date.getSignOffset() == 1)
self.assert_(date.getHoursOffset() == 2)
self.assert_(date.getMinutesOffset() == 0)
_dummyList = [date]
_dummyList[:] = []
del _dummyList
pass
def test_Date_setDay(self):
date = libsbml.Date(2005, 2, 12, 12, 15, 45, 1, 2, 0)
self.assert_(date != None)
i = date.setDay(29)
self.assert_(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE)
self.assert_(date.getDay() == 1)
i = date.setDay(31)
self.assert_(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE)
self.assert_(date.getDay() == 1)
i = date.setDay(15)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(date.getDay() == 15)
self.assert_(("2005-02-15T12:15:45+02:00" == date.getDateAsString()))
_dummyList = [date]
_dummyList[:] = []
del _dummyList
pass
def test_Date_setMinute(self):
date = libsbml.Date(2005, 12, 30, 12, 15, 45, 1, 2, 0)
self.assert_(date != None)
i = date.setMinute(434)
self.assert_(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE)
self.assert_(date.getMinute() == 0)
i = date.setMinute(12121)
self.assert_(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE)
self.assert_(date.getMinute() == 0)
i = date.setMinute(32)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(date.getMinute() == 32)
self.assert_(("2005-12-30T12:32:45+02:00" == date.getDateAsString()))
_dummyList = [date]
_dummyList[:] = []
del _dummyList
pass
def test_Date_createFromString(self):
dd = "2012-12-02T14:56:11Z"
date = libsbml.Date(dd)
self.assert_(date != None)
self.assert_(("2012-12-02T14:56:11Z" == date.getDateAsString()))
self.assert_(date.getYear() == 2012)
self.assert_(date.getMonth() == 12)
self.assert_(date.getDay() == 2)
self.assert_(date.getHour() == 14)
self.assert_(date.getMinute() == 56)
self.assert_(date.getSecond() == 11)
self.assert_(date.getSignOffset() == 0)
self.assert_(date.getHoursOffset() == 0)
self.assert_(date.getMinutesOffset() == 0)
_dummyList = [date]
_dummyList[:] = []
del _dummyList
pass
def test_RDFAnnotation2_modelWithHistoryAndCVTerms(self):
h = libsbml.ModelHistory()
c = libsbml.ModelCreator()
c.setFamilyName("Keating")
c.setGivenName("Sarah")
h.addCreator(c)
d = libsbml.Date(2008, 11, 17, 18, 37, 0, 0, 0, 0)
h.setCreatedDate(d)
h.setModifiedDate(d)
self.m2.unsetModelHistory()
self.m2.setModelHistory(h)
cv = libsbml.CVTerm()
cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
cv.addResource("http://www.geneontology.org/#GO:0005892")
self.m2.addCVTerm(cv)
ann = libsbml.RDFAnnotationParser.parseModelHistory(self.m2)
expected = wrapString(
"<annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
+ " <rdf:Description rdf:about=\"#_000001\">\n" +
" <dc:creator rdf:parseType=\"Resource\">\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:parseType=\"Resource\">\n" +
" <vCard:N rdf:parseType=\"Resource\">\n" +
" <vCard:Family>Keating</vCard:Family>\n" +
" <vCard:Given>Sarah</vCard:Given>\n" +
" </vCard:N>\n" + " </rdf:li>\n" +
" </rdf:Bag>\n" + " </dc:creator>\n" +
" <dcterms:created rdf:parseType=\"Resource\">\n" +
" <dcterms:W3CDTF>2008-11-17T18:37:00Z</dcterms:W3CDTF>\n" +
" </dcterms:created>\n" +
" <dcterms:modified rdf:parseType=\"Resource\">\n" +
" <dcterms:W3CDTF>2008-11-17T18:37:00Z</dcterms:W3CDTF>\n" +
" </dcterms:modified>\n" + " <bqbiol:isVersionOf>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005892\"/>\n"
+ " </rdf:Bag>\n" + " </bqbiol:isVersionOf>\n" +
" </rdf:Description>\n" + " </rdf:RDF>\n" + "</annotation>")
if (ann != None):
self.assertEqual(True, self.equals(expected, ann.toXMLString()))
pass
pass
pass
def _create_history(creators: Union[List[Any], Dict[Any, Any]],
set_timestamps: bool = False) -> libsbml.ModelHistory:
"""Create the model history.
Sets the create and modified date to the current time.
Creators are a list or dictionary with values as
:param creators:
:param set_timestamps:
:return:
"""
h = libsbml.ModelHistory()
items: List[Any]
if isinstance(creators, dict):
items = list(creators.values())
else:
items = creators
# add all creators
for creator in items:
c = libsbml.ModelCreator()
if creator.familyName:
c.setFamilyName(creator.familyName)
if creator.givenName:
c.setGivenName(creator.givenName)
if creator.email:
c.setEmail(creator.email)
if creator.organization:
c.setOrganization(creator.organization)
check(h.addCreator(c), "add creator")
# create time is now
if set_timestamps:
datetime = date_now()
else:
datetime = libsbml.Date("1900-01-01T00:00:00")
check(h.setCreatedDate(datetime), "set creation date")
check(h.setModifiedDate(datetime), "set modified date")
return h
def test_ModelHistory_copyConstructor(self):
mh = libsbml.ModelHistory()
mc = libsbml.ModelCreator()
mc.setFamilyName("Keating")
mc.setGivenName("Sarah")
mc.setEmail("*****@*****.**")
mh.addCreator(mc)
mc = None
date = libsbml.Date(2005, 12, 30, 12, 15, 45, 1, 2, 0)
mh.setCreatedDate(date)
date = None
self.assert_(mh.getCreatedDate().getMonth() == 12)
self.assert_(mh.getCreatedDate().getSecond() == 45)
self.assert_(mh.getCreator(0).getFamilyName() == "Keating")
mh2 = libsbml.ModelHistory(mh)
self.assert_(mh2.getCreatedDate().getMonth() == 12)
self.assert_(mh2.getCreatedDate().getSecond() == 45)
self.assert_(mh2.getCreator(0).getFamilyName() == "Keating")
mh2 = None
mh = None
pass
def test_ModelHistory_setModifiedDate(self):
history = libsbml.ModelHistory()
self.assert_(history != None)
self.assert_(history.isSetModifiedDate() == False)
date = libsbml.Date(2005, 12, 30, 12, 15, 45, 1, 2, 0)
history.setModifiedDate(date)
_dummyList = [date]
_dummyList[:] = []
del _dummyList
self.assert_(history.isSetModifiedDate() == True)
newdate = history.getModifiedDate()
self.assert_(newdate.getYear() == 2005)
self.assert_(newdate.getMonth() == 12)
self.assert_(newdate.getDay() == 30)
self.assert_(newdate.getHour() == 12)
self.assert_(newdate.getMinute() == 15)
self.assert_(newdate.getSecond() == 45)
self.assert_(newdate.getSignOffset() == 1)
self.assert_(newdate.getHoursOffset() == 2)
self.assert_(newdate.getMinutesOffset() == 0)
_dummyList = [history]
_dummyList[:] = []
del _dummyList
pass
def test_Validation_Date4(self):
date = libsbml.Date(2007, 12, 30, 12, 15, 45, 1, 2, 0)
self.assert_(date != None)
self.assertEqual(True, date.representsValidDate())
date = None
pass
def test_Validation_Date3(self):
date = libsbml.Date("Jan 12")
self.assert_(date != None)
self.assertEqual(False, (date.representsValidDate()))
date = None
pass
def write_sbml_ec_model(
ec_model: Model,
filename: str,
f_replace=F_REPLACE,
units=True,
group_untyped_proteins: bool = True,
):
"""Write cobra model to filename.
Enzyme constraint changes: proteins are written as metabolites with
initialAmount.
The created model is SBML level 3 version 1 (L1V3) with
fbc package v2 (fbc-v2).
If the given filename ends with the suffix ".gz" (for example,
"myfile.xml.gz"), libSBML assumes the caller wants the file to be
written compressed in gzip format. Similarly, if the given filename
ends with ".zip" or ".bz2", libSBML assumes the caller wants the
file to be compressed in zip or bzip2 format (respectively). Files
whose names lack these suffixes will be written uncompressed. Special
considerations for the zip format: If the given filename ends with
".zip", the file placed in the zip archive will have the suffix
".xml" or ".sbml". For example, the file in the zip archive will
be named "test.xml" if the given filename is "test.xml.zip" or
"test.zip". Similarly, the filename in the archive will be
"test.sbml" if the given filename is "test.sbml.zip".
Warnings
--------
If :meth:`geckopy.Model.constrain_pool()` was called on the model, the
protein pool (exchange and metabolite) will be ignored and NOT written
to the SBML file. A `UserWarning` appears in this case.
Parameters
----------
cobra_model : geckopy.Model
Model instance which is written to SBML
filename : string
path to which the model is written
f_replace: dict of replacement functions for id replacement
group_untyped_proteins: bool
if True (default) the proteins whose id is not compliant with Uniprot
and which are not part of the :code:`Protein` group will be added to it.
This is an inplace operation!
"""
cobra_model = ec_model
protein_pool_metabolite = None
protein_pool_exchange = None
if hasattr(ec_model, "protein_pool_exchange"):
warnings.warn(
"Protein pool will not be serialized to the SBML document.")
protein_pool_metabolite = ec_model.common_protein_pool
protein_pool_exchange = ec_model.protein_pool_exchange
if f_replace is None:
f_replace = {}
if group_untyped_proteins:
prot_to_add = [
prot.id for prot in cobra_model.proteins
if not PROT_PATTERN.match(prot.id)
]
group_proteins(ec_model, prot_to_add)
sbml_ns = libsbml.SBMLNamespaces(3, 1) # SBML L3V1
sbml_ns.addPackageNamespace("fbc", 2) # fbc-v2
doc: libsbml.SBMLDocument = libsbml.SBMLDocument(sbml_ns)
doc.setPackageRequired("fbc", False)
doc.setSBOTerm(SBO_FBA_FRAMEWORK)
model: libsbml.Model = doc.createModel()
model_fbc: libsbml.FbcModelPlugin = model.getPlugin("fbc")
model_fbc.setStrict(True)
if cobra_model.id is not None:
model.setId(cobra_model.id)
model.setMetaId("meta_" + cobra_model.id)
else:
model.setMetaId("meta_model")
if cobra_model.name is not None:
model.setName(cobra_model.name)
# for parsing annotation corresponding to the model
_sbase_annotations(model, cobra_model.annotation)
# for parsing notes corresponding to the model
_sbase_notes_dict(model, cobra_model.notes)
# Meta information (ModelHistory) related to SBMLDocument
if hasattr(cobra_model, "_sbml"):
meta = cobra_model._sbml
if "annotation" in meta:
_sbase_annotations(doc, meta["annotation"])
if "notes" in meta:
_sbase_notes_dict(doc, meta["notes"])
history: libsbml.ModelHistory = libsbml.ModelHistory()
if "created" in meta and meta["created"]:
history.setCreatedDate(meta["created"])
else:
time = datetime.datetime.now()
timestr = time.strftime("%Y-%m-%dT%H:%M:%S")
date = libsbml.Date(timestr)
_check(history.setCreatedDate(date), "set creation date")
_check(history.setModifiedDate(date), "set modified date")
if "creators" in meta:
for cobra_creator in meta["creators"]: # noqa: E501
creator: libsbml.ModelCreator = libsbml.ModelCreator()
if cobra_creator.get("familyName", None):
creator.setFamilyName(cobra_creator["familyName"])
if cobra_creator.get("givenName", None):
creator.setGivenName(cobra_creator["givenName"])
if cobra_creator.get("organisation", None):
creator.setOrganisation(cobra_creator["organisation"])
if cobra_creator.get("email", None):
creator.setEmail(cobra_creator["email"])
_check(history.addCreator(creator),
"adding creator to ModelHistory.")
# TODO: Will be implemented as part of
# https://github.com/opencobra/cobrapy/issues/810
# _check(model.setModelHistory(history), 'set model history')
# Units
if units:
flux_udef = model.createUnitDefinition() # type:libsbml.UnitDefinition
flux_udef.setId(UNITS_FLUX[0])
for u in UNITS_FLUX[1]:
unit = flux_udef.createUnit() # type: libsbml.Unit
unit.setKind(u.kind)
unit.setExponent(u.exponent)
unit.setScale(u.scale)
unit.setMultiplier(u.multiplier)
# minimum and maximum value from model
if len(cobra_model.reactions) > 0:
min_value = min(cobra_model.reactions.list_attr("lower_bound"))
max_value = max(cobra_model.reactions.list_attr("upper_bound"))
else:
min_value = config.lower_bound
max_value = config.upper_bound
_create_parameter(model,
pid=LOWER_BOUND_ID,
value=min_value,
sbo=SBO_DEFAULT_FLUX_BOUND)
_create_parameter(model,
pid=UPPER_BOUND_ID,
value=max_value,
sbo=SBO_DEFAULT_FLUX_BOUND)
_create_parameter(model,
pid=ZERO_BOUND_ID,
value=0,
sbo=SBO_DEFAULT_FLUX_BOUND)
_create_parameter(model,
pid=BOUND_MINUS_INF,
value=-float("Inf"),
sbo=SBO_DEFAULT_FLUX_BOUND)
_create_parameter(model,
pid=BOUND_PLUS_INF,
value=float("Inf"),
sbo=SBO_DEFAULT_FLUX_BOUND)
# Compartments
for cid, name in cobra_model.compartments.items():
compartment: libsbml.Compartment = model.createCompartment()
compartment.setId(cid)
compartment.setName(name)
compartment.setConstant(True)
# Species
for metabolite in cobra_model.metabolites:
if metabolite == protein_pool_metabolite:
continue
specie: libsbml.Species = model.createSpecies()
specie.setId(f_replace[F_SPECIE_REV](metabolite.id) if f_replace
and F_SPECIE_REV in f_replace else metabolite.id)
specie.setConstant(False)
specie.setBoundaryCondition(False)
specie.setHasOnlySubstanceUnits(False)
specie.setName(metabolite.name)
specie.setCompartment(metabolite.compartment)
s_fbc: libsbml.FbcSpeciesPlugin = specie.getPlugin("fbc")
if metabolite.charge is not None:
s_fbc.setCharge(int(metabolite.charge))
if metabolite.formula is not None:
s_fbc.setChemicalFormula(metabolite.formula)
_sbase_annotations(specie, metabolite.annotation)
_sbase_notes_dict(specie, metabolite.notes)
for metabolite in ec_model.proteins:
specie: libsbml.Species = model.createSpecies()
specie.setId(f_replace[F_SPECIE_REV](metabolite.id) if f_replace
and F_SPECIE_REV in f_replace else metabolite.id)
specie.setConstant(False)
specie.setBoundaryCondition(False)
specie.setHasOnlySubstanceUnits(False)
specie.setName(metabolite.name)
specie.setCompartment(metabolite.compartment)
if isinstance(metabolite.concentration,
numbers.Number) and not isnan(metabolite.concentration):
specie.setInitialAmount(metabolite.concentration)
s_fbc: libsbml.FbcSpeciesPlugin = specie.getPlugin("fbc")
if metabolite.charge is not None:
s_fbc.setCharge(int(metabolite.charge))
if metabolite.formula is not None:
s_fbc.setChemicalFormula(metabolite.formula)
_sbase_annotations(specie, metabolite.annotation)
# Genes
for cobra_gene in cobra_model.genes:
gp: libsbml.GeneProduct = model_fbc.createGeneProduct()
gid = cobra_gene.id
if f_replace and F_GENE_REV in f_replace:
gid = f_replace[F_GENE_REV](gid)
gp.setId(gid)
gname = cobra_gene.name
if gname is None or len(gname) == 0:
gname = gid
gp.setName(gname)
gp.setLabel(gid)
_sbase_annotations(gp, cobra_gene.annotation)
_sbase_notes_dict(gp, cobra_gene.notes)
# Objective
objective: libsbml.Objective = model_fbc.createObjective()
objective.setId("obj")
objective.setType(SHORT_LONG_DIRECTION[cobra_model.objective.direction])
model_fbc.setActiveObjectiveId("obj")
# Reactions
reaction_coefficients = linear_reaction_coefficients(cobra_model)
for cobra_reaction in cobra_model.reactions:
if cobra_reaction == protein_pool_exchange:
continue
rid = cobra_reaction.id
if f_replace and F_REACTION_REV in f_replace:
rid = f_replace[F_REACTION_REV](rid)
reaction: libsbml.Reaction = model.createReaction()
reaction.setId(rid)
reaction.setName(cobra_reaction.name)
reaction.setFast(False)
reaction.setReversible((cobra_reaction.lower_bound < 0))
_sbase_annotations(reaction, cobra_reaction.annotation)
_sbase_notes_dict(reaction, cobra_reaction.notes)
# stoichiometry
for metabolite, stoichiometry in cobra_reaction._metabolites.items():
sid = metabolite.id
if f_replace and F_SPECIE_REV in f_replace:
sid = f_replace[F_SPECIE_REV](sid)
if stoichiometry < 0:
sref = (reaction.createReactant()
) # noqa: E501 type: libsbml.SpeciesReference
sref.setSpecies(sid)
sref.setStoichiometry(-stoichiometry)
sref.setConstant(True)
else:
sref = (reaction.createProduct()
) # noqa: E501 type: libsbml.SpeciesReference
sref.setSpecies(sid)
sref.setStoichiometry(stoichiometry)
sref.setConstant(True)
# bounds
r_fbc: libsbml.FbcReactionPlugin = reaction.getPlugin("fbc")
r_fbc.setLowerFluxBound(
_create_bound(
model,
cobra_reaction,
"lower_bound",
f_replace=f_replace,
units=units,
flux_udef=flux_udef,
))
r_fbc.setUpperFluxBound(
_create_bound(
model,
cobra_reaction,
"upper_bound",
f_replace=f_replace,
units=units,
flux_udef=flux_udef,
))
# GPR
gpr = cobra_reaction.gene_reaction_rule
if gpr is not None and len(gpr) > 0:
# replace ids in string
if f_replace and F_GENE_REV in f_replace:
gpr = gpr.replace("(", "( ")
gpr = gpr.replace(")", " )")
tokens = gpr.split()
for k in range(len(tokens)):
if tokens[k] not in ["and", "or", "(", ")"]:
tokens[k] = f_replace[F_GENE_REV](tokens[k])
gpr_new = " ".join(tokens)
else:
gpr_new = gpr
gpa: libsbml.GeneProductAssociation = (
r_fbc.createGeneProductAssociation()) # noqa: E501
# uses ids to identify GeneProducts (True),
# does not create GeneProducts (False)
_check(gpa.setAssociation(gpr_new, True, False),
"set gpr: " + gpr_new)
# objective coefficients
if reaction_coefficients.get(cobra_reaction, 0) != 0:
flux_obj: libsbml.FluxObjective = (objective.createFluxObjective()
) # noqa: E501
flux_obj.setReaction(rid)
flux_obj.setCoefficient(cobra_reaction.objective_coefficient)
# write groups
if len(cobra_model.groups) > 0:
doc.enablePackage(
"http://www.sbml.org/sbml/level3/version1/groups/version1",
"groups", True)
doc.setPackageRequired("groups", False)
model_group: libsbml.GroupsModelPlugin = model.getPlugin(
"groups") # noqa: E501
for cobra_group in cobra_model.groups:
group: libsbml.Group = model_group.createGroup()
if f_replace and F_GROUP_REV in f_replace:
gid = f_replace[F_GROUP_REV](cobra_group.id)
else:
gid = cobra_group.id
group.setId(gid)
group.setName(cobra_group.name)
group.setKind(cobra_group.kind)
_sbase_notes_dict(group, cobra_group.notes)
_sbase_annotations(group, cobra_group.annotation)
for cobra_member in cobra_group.members:
member: libsbml.Member = group.createMember()
mid = cobra_member.id
m_type = str(type(cobra_member))
# id replacements
if "Reaction" in m_type:
if f_replace and F_REACTION_REV in f_replace:
mid = f_replace[F_REACTION_REV](mid)
if "Metabolite" in m_type or "Protein" in m_type:
if f_replace and F_SPECIE_REV in f_replace:
mid = f_replace[F_SPECIE_REV](mid)
if "Gene" in m_type:
if f_replace and F_GENE_REV in f_replace:
mid = f_replace[F_GENE_REV](mid)
member.setIdRef(mid)
if cobra_member.name and len(cobra_member.name) > 0:
member.setName(cobra_member.name)
if isinstance(filename, str):
# write to path
libsbml.writeSBMLToFile(doc, filename)
elif hasattr(filename, "write"):
# write to file handle
sbml_str = libsbml.writeSBMLToString(doc)
filename.write(sbml_str)
