def converter_sbml2sbtab_wrapper(args):
'''
commandline wrapper for the SBML to SBtab converter
'''
# open and create SBML
try:
f = open(args.sbml, 'r').read()
except:
raise SBtabError('SBML file %s could not be found.' % args.sbml)
try:
reader = libsbml.SBMLReader()
sbml = reader.readSBMLFromString(f)
except:
raise SBtabError('SBtab Document %s could not be created.' % args.sbml)
# create converter class
try:
converter = sbml2sbtab.SBMLDocument(sbml.getModel(), args.sbml)
(sbtab_doc, warnings) = converter.convert_to_sbtab()
print(warnings)
p = open('sbtab.tsv', 'w')
for sbtab in sbtab_doc.sbtabs:
p.write(sbtab.to_str() + '\n\n')
p.close()
except:
raise SBtabError('SBML Document %s could not be converted to SBtab.' %
args.sbml)
def test_object_creation(self):
'''
test if the SBML models can be used for object creation
'''
for i, sbml_doc in enumerate(self.sbml_docs):
conversion_object = sbml2sbtab.SBMLDocument(sbml_doc.getModel(), self.sbml_names[i])
self.assertIsNotNone(conversion_object)
def converter_sbml2sbtab_wrapper(args):
'''
commandline wrapper for the SBML to SBtab converter
'''
# open and create SBML
try:
f = open(args.sbml, 'r').read()
except:
raise SBtabError('SBML file %s could not be found.' % args.sbml)
if len(args.outfile) == 0:
args.outfile = "outfile.tsv"
try:
reader = libsbml.SBMLReader()
sbml = reader.readSBMLFromString(f)
except:
raise SBtabError('SBtab Document %s could not be created.' % args.sbml)
# create converter class
try:
converter = sbml2sbtab.SBMLDocument(sbml.getModel(), args.sbml)
(sbtab_doc, objtables_doc, warnings) = converter.convert_to_sbtab()
if len(warnings) > 0:
print(warnings)
outfile = args.outfile
if args.objtables:
if len(args.outfile) == 0:
outfile = 'objtables.tsv'
p = open(outfile, 'w')
p.write(objtables_doc.doc_row + '\n')
for objtable in objtables_doc.sbtabs:
p.write(objtable.to_str() + '\n\n')
p.close()
else:
if len(args.outfile) == 0:
outfile = 'sbtab.tsv'
p = open(args.outfile, 'w')
p.write(sbtab_doc.doc_row + '\n')
for sbtab in sbtab_doc.sbtabs:
p.write(sbtab.to_str() + '\n\n')
p.close()
except:
raise SBtabError('SBML Document %s could not be converted.' %
args.sbml)
def test_conversion(self):
'''
test if the conversion can be processed
'''
for i, sbml_doc in enumerate(self.sbml_docs):
# get previous SBML to compare to
previous_sbml = self.sbml_docs[i].getModel()
sbml_level = previous_sbml.getLevel()
# get SBtab document
conversion_object = sbml2sbtab.SBMLDocument(
sbml_doc.getModel(), self.sbml_names[i])
(sbtab_doc, warnings) = conversion_object.convert_to_sbtab()
# check general attributes of sbtab_doc
self.assertIsNotNone(sbtab_doc)
self.assertNotEqual(len(sbtab_doc.sbtabs), 0)
self.assertNotEqual(len(sbtab_doc.name_to_sbtab), 0)
self.assertNotEqual(len(sbtab_doc.type_to_sbtab), 0)
self.assertNotEqual(len(sbtab_doc.sbtab_filenames), 0)
self.assertEqual(len(sbtab_doc.sbtabs),
len(sbtab_doc.name_to_sbtab))
self.assertEqual(len(sbtab_doc.name_to_sbtab),
len(sbtab_doc.type_to_sbtab))
self.assertEqual(len(sbtab_doc.type_to_sbtab),
len(sbtab_doc.sbtab_filenames))
self.assertIsNotNone(sbtab_doc.doc_row)
self.assertEqual(sbtab_doc.doc_row[:8], '!!!SBtab')
# check single SBtab files
if previous_sbml.getNumCompartments() > 0:
self.assertIn('Compartment', sbtab_doc.type_to_sbtab)
compartment_sbtabs = sbtab_doc.type_to_sbtab['Compartment']
for c_sbtab in compartment_sbtabs:
# header row
self.assertEqual(c_sbtab.header_row[:7], '!!SBtab')
self.assertIn('TableType', c_sbtab.header_row)
# columns
self.assertEqual(len(c_sbtab.value_rows),
previous_sbml.getNumCompartments())
self.assertIn('!ID', c_sbtab.columns)
self.assertIn('!ID', c_sbtab.columns_dict)
self.assertIn('!Size', c_sbtab.columns)
self.assertIn('!Size', c_sbtab.columns_dict)
#if sbml_level == 3:
# self.assertIn('!Constant', c_sbtab.columns)
# self.assertIn('!Constant', c_sbtab.columns_dict)
# rows
for compartment in c_sbtab.value_rows:
self.assertEqual(len(compartment),
len(c_sbtab.columns))
self.assertNotEqual(
compartment[c_sbtab.columns_dict['!ID']], '')
self.assertNotEqual(
compartment[c_sbtab.columns_dict['!Name']], '')
self.assertNotEqual(
compartment[c_sbtab.columns_dict['!Size']], '')
#if sbml_level == 3:
# self.assertNotEqual(compartment[c_sbtab.columns_dict['!Constant']], '')
if previous_sbml.getNumSpecies() > 0:
self.assertIn('Compound', sbtab_doc.type_to_sbtab)
compound_sbtabs = sbtab_doc.type_to_sbtab['Compound']
for c_sbtab in compound_sbtabs:
# header row
self.assertEqual(c_sbtab.header_row[:7], '!!SBtab')
self.assertIn('TableType', c_sbtab.header_row)
# columns
self.assertEqual(len(c_sbtab.value_rows),
previous_sbml.getNumSpecies())
self.assertIn('!ID', c_sbtab.columns)
self.assertIn('!ID', c_sbtab.columns_dict)
self.assertIn('!Location', c_sbtab.columns)
self.assertIn('!Location', c_sbtab.columns_dict)
#if sbml_level == 3:
# self.assertIn('!Constant', c_sbtab.columns)
# self.assertIn('!Constant', c_sbtab.columns_dict)
# self.assertIn('!hasOnlySubstanceUnit', c_sbtab.columns)
# self.assertIn('!hasOnlySubstanceUnit', c_sbtab.columns_dict)
# self.assertIn('!boundaryCondition', c_sbtab.columns)
# self.assertIn('!boundaryCondition', c_sbtab.columns_dict)
# self.assertIn('!InitialValue', c_sbtab.columns)
# self.assertIn('!InitialValue', c_sbtab.columns_dict)
# rows
for compound in c_sbtab.value_rows:
self.assertEqual(len(compound), len(c_sbtab.columns))
self.assertNotEqual(
compound[c_sbtab.columns_dict['!ID']], '')
self.assertNotEqual(
compound[c_sbtab.columns_dict['!Location']], '')
#if sbml_level == 3:
# self.assertNotEqual(compound[c_sbtab.columns_dict['!Constant']], '')
# self.assertNotEqual(compound[c_sbtab.columns_dict['!hasOnlySubstanceUnit']], '')
# self.assertNotEqual(compound[c_sbtab.columns_dict['!boundaryCondition']], '')
# self.assertNotEqual(compound[c_sbtab.columns_dict['!InitialValue']], '')
if previous_sbml.getNumReactions() > 0:
self.assertIn('Reaction', sbtab_doc.type_to_sbtab)
reaction_sbtabs = sbtab_doc.type_to_sbtab['Reaction']
for r_sbtab in reaction_sbtabs:
# header row
self.assertEqual(r_sbtab.header_row[:7], '!!SBtab')
self.assertIn('TableType', r_sbtab.header_row)
# columns
self.assertEqual(len(r_sbtab.value_rows),
previous_sbml.getNumReactions())
self.assertIn('!ID', r_sbtab.columns)
self.assertIn('!ID', r_sbtab.columns_dict)
self.assertIn('!ReactionFormula', r_sbtab.columns)
self.assertIn('!ReactionFormula', r_sbtab.columns_dict)
#if sbml_level == 3:
# self.assertIn('!IsReversible', r_sbtab.columns)
# self.assertIn('!IsReversible', r_sbtab.columns_dict)
# self.assertIn('!Constant', r_sbtab.columns)
# self.assertIn('!Constant', r_sbtab.columns_dict)
# rows
for reaction in r_sbtab.value_rows:
self.assertEqual(len(reaction), len(r_sbtab.columns))
self.assertNotEqual(
reaction[r_sbtab.columns_dict['!ID']], '')
self.assertNotEqual(
reaction[r_sbtab.columns_dict['!ReactionFormula']],
'')
#if sbml_level == 3:
# self.assertNotEqual(reaction[r_sbtab.columns_dict['!Constant']], '')
# self.assertNotEqual(reaction[r_sbtab.columns_dict['!IsReversible']], '')
if previous_sbml.getNumParameters() > 0:
self.assertIn('Quantity', sbtab_doc.type_to_sbtab)
quantity_sbtabs = sbtab_doc.type_to_sbtab['Quantity']
for q_sbtab in quantity_sbtabs:
# header row
self.assertEqual(q_sbtab.header_row[:7], '!!SBtab')
self.assertIn('TableType', q_sbtab.header_row)
# columns
# we have a bug here for the export of local parameters;
# uncomment when fixed
#print(q_sbtab.value_rows)
#self.assertEqual(len(q_sbtab.value_rows), previous_sbml.getNumParameters())
self.assertIn('!ID', q_sbtab.columns)
self.assertIn('!ID', q_sbtab.columns_dict)
self.assertIn('!Value', q_sbtab.columns)
self.assertIn('!Value', q_sbtab.columns_dict)
self.assertIn('!Unit', q_sbtab.columns)
self.assertIn('!Unit', q_sbtab.columns_dict)
#if sbml_level == 3:
# self.assertIn('!Constant', q_sbtab.columns)
# self.assertIn('!Constant', q_sbtab.columns_dict)
# rows
for quantity in q_sbtab.value_rows:
self.assertEqual(len(quantity), len(q_sbtab.columns))
self.assertNotEqual(
quantity[q_sbtab.columns_dict['!ID']], '')
self.assertNotEqual(
quantity[q_sbtab.columns_dict['!Value']], '')
def converter():
response.title = T('SBtab - Standardised data tables for Systems Biology')
response.subtitle = T('SBML / SBtab Conversion')
session.sbmlid2label = {'24': '_SBML_L2V4', '31': '_SBML_L3V1'}
# initialise required variables and files
if not 'warnings_con' in session:
session.warnings_con = []
if not session.definition_file:
try:
sbtab_def = misc.open_definitions_file(
os.path.dirname(os.path.abspath(__file__)) +
'/../static/files/default_files/definitions.tsv')
session.definition_file = sbtab_def
session.definition_file_name = sbtab_def.filename
except:
session.warnings_con.append(
'There was an error reading the definition file.')
redirect(URL(''))
if 'sbtabs' not in session:
session.sbtabs = []
session.sbtab_filenames = []
session.sbtab_docnames = []
session.name2doc = {}
session.types = []
# #########################################################################
# form for SBtab files
lform = SQLFORM.factory(
Field('File',
'upload',
uploadfolder="/tmp",
label='Upload SBtab file to convert (.csv, .tsv, .xlsx)',
requires=IS_LENGTH(10485760,
1,
error_message='Max upload size: 10MB')))
if lform.process(formname='form_one').accepted:
session.warnings_con = []
response.flash = 'form accepted'
# validate file encoding and name
try:
sbtab_file = request.vars.File.value.decode('utf-8', 'ignore')
except:
session.warnings_con.append(
'The file does not adhere to spreadsheet standards.')
redirect(URL(''))
filename = request.vars.File.filename
if not filename.endswith('.tsv') and not filename.endswith(
'.csv') and not filename.endswith('.xlsx'):
session.warnings_con.append(
'The file does not have a correct file format. Please use csv/tsv/xlsx only.'
)
redirect(URL(''))
# convert from xlsx to csv if required
if filename.endswith('.xlsx'):
sbtab_file = request.vars.File.value
try:
sbtab_file = misc.xlsx_to_tsv(sbtab_file)
except:
session.warnings_con.append(
'The xlsx file could not be converted to SBtab. Please ensure file format validity.'
)
redirect(URL(''))
# check if there are more than one SBtab files in the file and create SBtabTable or SBtabDocument
try:
sbtab_amount = misc.count_tabs(sbtab_file)
except:
session.warnings_con.append(
'The SBtab %s could not be read properly.' % sbtab.filename)
redirect(URL(''))
if sbtab_amount > 1:
try:
sbtab_strings = misc.split_sbtabs(sbtab_file)
sbtab_doc = SBtab.SBtabDocument(filename)
session.sbtab_docnames.append(filename)
for i, sbtab_string in enumerate(sbtab_strings):
name_single = filename[:-4] + str(i) + filename[-4:]
sbtab = SBtab.SBtabTable(sbtab_string, name_single)
new_name = filename[:-4] + '_' + sbtab.table_id + filename[
-4:]
sbtab.set_filename(new_name)
if new_name not in session.sbtab_filenames:
sbtab_doc.add_sbtab(sbtab)
session.sbtabs.append(sbtab)
session.types.append(sbtab.table_type)
session.sbtab_filenames.append(new_name)
session.name2doc[new_name] = filename
else:
session.warnings_con.append(
'The SBtab %s is duplicate.' % sbtab.filename)
redirect(URL(''))
except:
session.warnings_con.append(
'The SBtab Document object could not be created properly.')
redirect(URL(''))
else:
try:
sbtab = SBtab.SBtabTable(sbtab_file, filename)
session.sbtabs.append(sbtab)
session.sbtab_filenames.append(sbtab.filename)
session.types.append(sbtab.table_type)
session.sbtab_docnames.append(sbtab.filename)
session.name2doc[sbtab.filename] = sbtab.filename
except:
session.warnings_con.append(
'The SBtab Table object could not be created properly.')
redirect(URL(''))
redirect(URL(''))
elif lform.errors:
response.flash = 'form has errors'
# #########################################################################
# form for SBML files
rform = SQLFORM.factory(
Field('File',
'upload',
uploadfolder="/tmp",
label='Upload SBML file to convert (.xml)',
requires=IS_LENGTH(52428800,
1,
error_message='Max upload size: 50MB')))
if rform.process(formname='form_two').accepted:
response.flash = 'form accepted'
session.warnings_con = []
filename = request.vars.File.filename
sbml_file = request.vars.File.value.decode('utf-8', 'ignore')
if filename[-3:] != 'xml' and filename[-4:] != 'sbml':
session.warnings_con.append(
'The uploaded file has a wrong extension for an SBML file.')
redirect(URL(''))
if 'sbmls' not in session:
session.sbmls = [sbml_file]
session.sbml_filenames = [filename]
else:
if filename not in session.sbml_filenames:
session.sbmls.append(sbml_file)
session.sbml_filenames.append(filename)
else:
session.warnings_con.append(
'An SBML file with the name %s is already stored.' %
filename)
redirect(URL(''))
redirect(URL(''))
elif rform.errors:
response.flash = 'form has errors'
# #########################################################################
# buttons
# convert (single) sbtab to sbml
if request.vars.c2sbml_button24 or request.vars.c2sbml_button31:
# determine requested SBML version
if request.vars.c2sbml_button24 != None:
sbml_version = '24'
c2sbml_button = request.vars.c2sbml_button24
else:
sbml_version = '31'
c2sbml_button = request.vars.c2sbml_button31
session.warnings_con = []
# get SBtab and add to SBtab document
try:
sbtab = session.sbtabs[int(c2sbml_button)]
sbtab_doc = SBtab.SBtabDocument(sbtab.filename, sbtab)
except:
session.warnings_con = [
'The SBtab %s could not be added to the document.' %
sbtab.filename
]
redirect(URL(''))
# convert SBtab document to SBML and add details to session
try:
ConvSBtabClass = sbtab2sbml.SBtabDocument(sbtab_doc)
(sbml, session.warnings_con
) = ConvSBtabClass.convert_to_sbml(sbml_version)
filename_new = sbtab.filename[:-4] + '.xml'
# if the sbml build up crashed:
if not sbml:
session.warnings_con.append('The SBtab file %s could not be c'\
'onverted to SBML. Please check file'\
'validity.' % sbtab.filename)
redirect(URL(''))
if 'sbmls' not in session:
session.sbmls = [sbml]
session.sbml_filenames = [filename_new]
else:
if not filename_new in session.sbml_filenames:
session.sbmls.append(sbml)
session.sbml_filenames.append(filename_new)
else:
session.warnings_con.append('A file with the name %s has alre'\
'ady been uploaded. Please rename'\
' your SBtab file/s before SBML c'\
'reation.' % filename_new)
except:
session.warnings_con.append('The conversion of SBtab %s to SBML was n'\
'ot successful.' % sbtab.filename)
redirect(URL(''))
# convert multiple sbtabs to sbml
if request.vars.convert_all_button24 or request.vars.convert_all_button31:
if request.vars.convert_all_button24 != None:
sbml_version = '24'
convert_all_button = request.vars.convert_all_button24
else:
sbml_version = '31'
convert_all_button = request.vars.convert_all_button31
session.warnings_con = []
# get SBtabs and add them to an SBtab document
convert_document = session.sbtab_docnames[int(convert_all_button)]
sbtabs = []
try:
for i, filename in enumerate(session.sbtab_filenames):
if session.name2doc[filename] == convert_document:
sbtabs.append(session.sbtabs[i])
sbtab_doc = SBtab.SBtabDocument(convert_document)
for sbtab in sbtabs:
sbtab_doc.add_sbtab(sbtab)
except:
session.warnings_con = ['The SBtabs could not be added to SBML.']
redirect(URL(''))
# convert SBtab document to SBML and add details to session
try:
ConvSBtabClass = sbtab2sbml.SBtabDocument(sbtab_doc)
(sbml, session.warnings_con
) = ConvSBtabClass.convert_to_sbml(sbml_version)
filename_new = sbtab_doc.name[:-4] + '.xml'
# if the sbml build up crashed:
if not sbml:
session.warnings_con.append('The SBtab file %s could not be c'\
'onverted to SBML. Please check file'\
'validity.' % sbtab_doc.name)
redirect(URL(''))
if 'sbmls' not in session:
session.sbmls = [sbml]
session.sbml_filenames = [filename_new]
else:
if not filename_new in session.sbml_filenames:
session.sbmls.append(sbml)
session.sbml_filenames.append(filename_new)
else:
session.warnings_con.append('A file with the name %s has alre'\
'ady been uploaded. Please rename'\
' your SBtab file/s before SBML c'\
'reation.' % filename_new)
redirect(URL(''))
except:
session.warnings_con.append('The conversion of SBtab %s to SBML was n'\
'ot successful.' % sbtab_doc.filename)
redirect(URL(''))
# download sbtab
if request.vars.dl_sbtab_button:
downloader_sbtab()
# download sbtab.xlsx
if request.vars.dl_xlsx_sbtab_button:
downloader_sbtab_xlsx()
# download all sbtabs
if request.vars.download_all_button:
download_document = session.sbtab_docnames[int(
request.vars.download_all_button)]
sbtab_list = []
for i, filename in enumerate(session.sbtab_filenames):
if session.name2doc[filename] == download_document:
sbtab_list.append(session.sbtabs[i])
downloader_sbtab_doc(sbtab_list, int(request.vars.download_all_button))
# remove all sbtabs
if request.vars.remove_all_button:
try:
remove_document = session.sbtab_docnames[int(
request.vars.remove_all_button)]
# gather indices of entries to remove
remove_sbtabs = []
remove_filenames = []
for i, s in enumerate(session.sbtabs):
if session.name2doc[s.filename] == remove_document:
remove_sbtabs.append(i)
# delete sbtabs, names, and types
remove = sorted(remove_sbtabs, reverse=True)
for i in remove:
remove_filenames.append(session.sbtab_filenames[i])
del session.sbtabs[i]
del session.sbtab_filenames[i]
del session.types[i]
# delete document name
del session.sbtab_docnames[int(request.vars.remove_all_button)]
# delete name2doc entries
for entry in remove_filenames:
del session.name2doc[entry]
session.warnings_con = []
redirect(URL(''))
except:
redirect(URL(''))
# erase single SBML
if request.vars.erase_sbml_button:
del session.sbmls[int(request.vars.erase_sbml_button)]
del session.sbml_filenames[int(request.vars.erase_sbml_button)]
session.warnings_con = []
redirect(URL(''))
# convert sbml to sbtab
if request.vars.c2sbtab_button:
session.warnings_con = []
try:
# initialise variables and parser
reader = libsbml.SBMLReader()
sbml_model = reader.readSBMLFromString(session.sbmls[int(
request.vars.c2sbtab_button)])
filename = session.sbml_filenames[int(request.vars.c2sbtab_button)]
# convert SBML to SBtab Document
ConvSBMLClass = sbml2sbtab.SBMLDocument(sbml_model.getModel(),
filename)
(sbtab_doc, objtables_doc,
session.warnings_con) = ConvSBMLClass.convert_to_sbtab()
if sbtab_doc.sbtabs == []:
session.warnings_con = [
'The SBML file seems to be invalid and could not be converted to SBtab.'
]
redirect(URL(''))
# append generated SBtabs to session variables
for sbtab in sbtab_doc.sbtabs:
if 'sbtabs' not in session:
session.sbtabs = [sbtab]
session.sbtab_filenames = [sbtab.filename]
if sbtab_doc.name not in session.sbtab_docnames:
session.sbtab_docnames.append(sbtab_doc.name)
session.types = [sbtab.table_type]
session.name2doc = {}
session.name2doc[sbtab.filename] = sbtab_doc.name
else:
if sbtab.filename not in session.sbtab_filenames:
session.sbtabs.append(sbtab)
session.sbtab_filenames.append(sbtab.filename)
session.name2doc[sbtab.filename] = sbtab_doc.name
if sbtab_doc.name not in session.sbtab_docnames:
session.sbtab_docnames.append(sbtab_doc.name)
session.types.append(sbtab.table_type)
except:
session.warnings_con = [
'The SBML file seems to be invalid and could not be converted to SBtab.'
]
redirect(URL(''))
# erase single SBtab
if request.vars.erase_sbtab_button:
del session.sbtabs[int(request.vars.erase_sbtab_button)]
# this IF is important: you must only delete the document from the list
# IF there are no more files attached to it
doc_name = session.name2doc[session.sbtab_filenames[int(
request.vars.erase_sbtab_button)]]
if list(session.name2doc.values()).count(doc_name) == 1:
session.sbtab_docnames.remove(doc_name)
del session.name2doc[session.sbtab_filenames[int(
request.vars.erase_sbtab_button)]]
del session.sbtab_filenames[int(request.vars.erase_sbtab_button)]
del session.types[int(request.vars.erase_sbtab_button)]
session.warnings_con = []
redirect(URL(''))
if request.vars.dl_sbml_button:
downloader_sbml()
return dict(UPL_FORML=lform,
UPL_FORMR=rform,
SBTAB_LIST=session.sbtabs,
SBML_LIST=session.sbmls,
NAME_LIST_SBTAB=session.sbtab_filenames,
NAME_LIST_SBML=session.sbml_filenames,
DOC_NAMES=session.sbtab_docnames,
NAME2DOC=session.name2doc,
WARNINGS_CON=session.warnings_con,
TYPES=session.types)