def converter_sbtab2sbml_wrapper(args):
'''
commandline wrapper for the SBtab to SBML converter
'''
# open and create SBtab
try:
f = open(args.sbtab, 'r').read()
except:
raise SBtabError('SBtab file %s could not be found.' % args.sbtab)
try:
sbtab_doc = SBtab.SBtabDocument('conversion_document', f, args.sbtab)
except:
raise SBtabError('SBtab Document %s could not be created.' % args.sbtab)
if len(args.outfile)>0:
outfile = args.outfile
else:
outfile = 'sbml.xml'
# create converter class
if args.version:
if args.version != '31' and args.version != '24':
raise SBtabError('SBtab to SBML conversion does currently only support SBML Level and Version 2.4 and 3.1.')
try:
converter = sbtab2sbml.SBtabDocument(sbtab_doc)
(sbml, warnings) = converter.convert_to_sbml(args.version)
if len(warnings)>0:
print('Warnings:')
print(warnings)
p = open(outfile,'w')
p.write(sbml)
p.close()
except:
raise SBtabError('SBtab Document %s could not be converted to SBML.' % args.sbtab)
else:
try:
converter = sbtab2sbml.SBtabDocument(sbtab_doc)
(sbml, warnings) = converter.convert_to_sbml('31')
if len(warnings)>0:
print('Warnings:')
print(warnings)
p = open(outfile,'w')
p.write(sbml)
p.close()
except:
raise SBtabError('SBtab Document %s could not be converted to SBML.' % args.sbtab)
def setUp(self):
'''
setup SBtabTable class with files from test directory
'''
self.table_names = [
f for f in os.listdir('python/tests/tables/')
if os.path.isfile(os.path.join('python/tests/tables/', f))
]
self.doc_names = [
f for f in os.listdir('python/tests/docs/')
if os.path.isfile(os.path.join('python/tests/docs/', f))
]
self.sbtab_docs = []
self.convert_document_objects = []
for i, t in enumerate(self.table_names):
if t.startswith('_'): continue
p = open('python/tests/tables/' + t, 'r')
p_content = p.read()
sbtab_doc = SBtab.SBtabDocument('test_' + str(i),
sbtab_init=p_content,
filename=t)
if 'Reaction' in sbtab_doc.type_to_sbtab.keys(
) or 'Compound' in sbtab_doc.type_to_sbtab.keys():
conv = sbtab2sbml.SBtabDocument(sbtab_doc)
self.convert_document_objects.append(conv)
self.sbtab_docs.append(sbtab_doc)
p.close()
for i, d in enumerate(self.doc_names):
if not d.startswith('_'):
p = open('python/tests/docs/' + d, 'r')
p_content = p.read()
sbtab_doc = SBtab.SBtabDocument('test_' + str(i),
sbtab_init=p_content,
filename=d)
if 'Reaction' in sbtab_doc.type_to_sbtab.keys(
) or 'Compound' in sbtab_doc.type_to_sbtab.keys():
conv = sbtab2sbml.SBtabDocument(sbtab_doc)
self.convert_document_objects.append(conv)
self.sbtab_docs.append(sbtab_doc)
p.close()
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)