def setUp(self):
'''
setup SBtabDocument class with files from test directory
'''
#self.table_names = [f for f in os.listdir('tables/') if os.path.isfile(os.path.join('tables/', f))]
self.table_names = [
'teusink_compartment.csv', 'teusink_compound.csv',
'teusink_data.tsv', 'teusink_reaction.tsv'
]
self.doc_names = [
f for f in os.listdir('python/tests/docs/')
if os.path.isfile(os.path.join('python/tests/docs/', f))
]
self.sbtabs = []
for t in self.table_names:
p = open('python/tests/tables/' + t, 'r')
p_content = p.read()
sbtab = SBtab.SBtabTable(p_content, t)
# initialise SBtabDocument with the SBtabTable, but only save the table for further testing
sbtab_doc = SBtab.SBtabDocument('test_doc', sbtab_init=sbtab)
self.sbtabs.append(sbtab)
p.close()
self.docs = []
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)
self.docs.append(sbtab_doc)
p.close()
def sbtab2html_wrapper(sbtab, multiple, output, template, links, pageheader, definitions_file,show_table_text=True):
'''
commandline wrapper for sbtab_to_html function
'''
print(pageheader)
# open and create SBtab
try:
f = open(sbtab, 'r').read()
except:
raise SBtabError('SBtab file %s could not be found.' % sbtab)
# count given tabs and prepare file name w/o path
tab_amount = misc.count_tabs(f)
if '/' in sbtab:
name_pre = sbtab.split('/')[-1:]
else:
name_pre = sbtab
# count given tabs and prepare file name w/o path
if output is not None:
outfile_dir, outfile_file = os.path.split(output)
if not os.path.exists(outfile_dir):
os.mkdir(outfile_dir)
outfile_file=os.path.splitext(outfile_file)[0]
name_pre[0] = outfile_file
else:
outfile_dir = '.'
file_basename = os.path.splitext(name_pre[0])[0]
if tab_amount > 1:
multiple = True
if multiple:
try:
sbtab_doc = SBtab.SBtabDocument('sbtab_doc_prelim', f, sbtab)
for tab in sbtab_doc.sbtabs:
if len(file_basename):
name = outfile_dir + '/' + file_basename + '_' + tab.table_id + '.html'
else:
name = outfile_dir + '/' + tab.table_id + '.html'
try:
write_html(tab, name, template, links, pageheader, definitions_file,show_table_text=show_table_text)
except:
raise SBtabError('The HTML file %s could not be created.' % name)
except:
raise SBtabError('The multiple HTML files could not be created.')
else:
try:
if tab_amount > 1:
sbtab = SBtab.SBtabDocument('sbtab_doc_prelim', f, sbtab)
name = outfile_dir + '/' + file_basename + '_' + sbtab.table_id + '.html'
else:
sbtab = SBtab.SBtabTable(f, sbtab)
name = outfile_dir + '/' + file_basename + '.html'
write_html(sbtab, name, template, links, pageheader, definitions_file,show_table_text=show_table_text)
except:
raise SBtabError('The HTML file could not be created.')
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.sbtabs = []
self.sbtab_docs = []
for i, t in enumerate(self.table_names):
if t.startswith('_'): continue
p = open('python/tests/tables/' + t, 'r')
p_content = p.read()
sbtab = SBtab.SBtabTable(p_content, t)
self.sbtabs.append(sbtab)
p.close()
for i, d in enumerate(self.doc_names):
if d.startswith('_'): continue
p = open('python/tests/docs/' + d, 'r')
p_content = p.read()
sbtab_doc = SBtab.SBtabDocument('test_'+str(i),sbtab_init=p_content, filename=d)
self.sbtab_docs.append(sbtab_doc)
p.close()
def test_build_empty_object(self):
'''
test if empty SBtabDocument can be built
'''
sbtab_doc = SBtab.SBtabDocument('empty_doc')
self.assertEqual(type(sbtab_doc), SBtab.SBtabDocument)
self.assertIsNone(sbtab_doc.filename)
self.assertEqual(sbtab_doc.sbtabs, [])
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 validator_wrapper(args):
'''
commandline wrapper for the SBtab validator
'''
# open and create SBtab
try:
f = open(args.sbtab, 'r').read()
except:
raise SBtabError('SBtab file %s could not be found.' % args.sbtab)
if args.document:
try:
sbtab_doc = SBtab.SBtabDocument('validation_document', f,
args.sbtab)
except:
raise SBtabError('SBtab Document %s could not be created.' %
args.document_name)
else:
try:
sbtab = SBtab.SBtabTable(f, args.sbtab)
except:
raise SBtabError('SBtab Table %s could not be created.' %
args.sbtab)
# if definitions file is given create SBtab object
if args.sbtab_definitions:
try:
d = open(args.sbtab_definitions, 'r').read()
sbtab_def = SBtab.SBtabTable(d, args.sbtab_definitions)
except:
raise SBtabError('The definitions file %s could not be found.' %
args.sbtab_definitions)
else:
sbtab_def = None
# create validator class and validate SBtab object
if args.document:
try:
validate_doc = validatorSBtab.ValidateDocument(
sbtab_doc, sbtab_def)
warnings = validate_doc.validate_document()
print(warnings)
except:
raise SBtabError('SBtab Document %s could not be validated.' %
args.document_name)
else:
try:
validate_table = validatorSBtab.ValidateTable(sbtab, sbtab_def)
warnings = validate_table.return_output()
print(warnings)
except:
raise SBtabError('SBtab Table %s could not be validated.' %
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.sbml_names = [
f for f in os.listdir('python/tests/sbml/')
if os.path.isfile(os.path.join('python/tests/sbml/', f))
]
self.sbtabs = []
for t in self.table_names:
if not t.startswith('_'):
p = open('python/tests/tables/' + t, 'r')
p_content = p.read()
sbtab = SBtab.SBtabTable(p_content, t)
self.sbtabs.append(sbtab)
p.close()
self.docs = []
for i, d in enumerate(self.doc_names):
if not d.startswith('_'):
p = open('python/tests/docs/' + d, 'r')
p_content = p.read()
sbtab = SBtab.SBtabDocument('test_' + str(i),
sbtab_init=p_content,
filename=d)
self.docs.append(sbtab)
p.close()
self.sbml_docs = []
self.sbml_strings = []
reader = libsbml.SBMLReader()
for i, s in enumerate(self.sbml_names):
if s.startswith('_'): continue
# save SBML objects
doc = reader.readSBML('python/tests/sbml/' + s)
self.sbml_docs.append(doc)
# also save the strings
sbml = open('python/tests/sbml/' + s, 'r')
self.sbml_strings.append(sbml.read())
sbml.close()
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 convert_to_sbtab(self):
'''
Generates the SBtab files.
'''
self.warnings = []
sbtab_doc = SBtab.SBtabDocument(self.filename)
for table_type in supported_table_types:
try:
function_name = 'self.'+table_type.lower()+'_sbtab()'
sbtab = eval(function_name)
if sbtab != False:
sbtab_doc.add_sbtab(sbtab)
except:
self.warnings.append('Could not generate SBtab %s.' % table_type)
return (sbtab_doc, self.warnings)
def converter_objtables2sbtab_wrapper(args):
'''
commandline wrapper for the ObjTables to SBtab converter
'''
# open ObjTables file
try:
f = open(args.objtables, 'r').read()
except:
raise SBtabError('SBtab file %s could not be found.' % args.objtables)
try:
objtables_doc = SBtab.SBtabDocument('conversion_document', f,
args.objtables)
except:
raise SBtabError('SBtab Document %s could not be created.' %
args.objtables)
# if definitions file is given create SBtab object
if args.definitions_file:
try:
d = open(args.definitions_file, 'r').read()
sbtab_def = SBtab.SBtabTable(d, args.definitions_file)
except:
raise SBtabError('The definitions file %s could not be found.' %
args.definitions_file)
else:
sbtab_def = None
# create converter class
try:
sbtab_doc = create_sbtab_from_obj_tables_doc(objtables_doc, sbtab_def)
if len(args.outfile) > 0:
outfile = args.outfile
else:
outfile = 'sbtab.tsv'
p = open(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('SBtab Document %s could not be converted.' %
args.sbtab)
def test_xlsx_to_tsv_and_tab_to_xlsx(self):
'''
test if xlsx files can be converted to tsv files
(ALSO test if SBtab files can be converted to xlsx)
'''
for sbtab in self.sbtabs:
# first convert SBtab objects to xlsx
sbtab_xlsx = misc.tab_to_xlsx(sbtab)
self.assertEqual(type(sbtab_xlsx), bytes)
# then convert to tsv string
sbtab_tsv = misc.xlsx_to_tsv(sbtab_xlsx)
self.assertEqual(type(sbtab_tsv), str)
self.assertEqual(sbtab_tsv[0:2], '!!')
# last: try to convert the string to an SBtab document,
# also test if the final sbtab equals the initial one
sbtab_doc = SBtab.SBtabDocument(sbtab.filename, sbtab_tsv,
sbtab.filename)
self.assertEqual(type(sbtab_doc), SBtab.SBtabDocument)
self.assertEqual(sbtab.filename, sbtab_doc.filename)
self.assertEqual(sbtab.columns, sbtab_doc.sbtabs[0].columns)
def test_write_sbtab_doc(self):
'''
function writes SBtabDocument to hard drive
'''
for doc in self.docs:
self.assertTrue(doc.write())
get_back = open(doc.filename, 'r')
get_back_content = get_back.read()
get_back_doc = SBtab.SBtabDocument(doc.name, get_back_content,
doc.filename)
get_back.close()
self.assertEqual(doc.doc_row.rstrip(),
get_back_doc.doc_row.rstrip())
old_sbtabs = doc.sbtabs
new_sbtabs = get_back_doc.sbtabs
for i, os in enumerate(old_sbtabs):
self.assertEqual(os.header_row, new_sbtabs[i].header_row)
self.assertEqual(os.columns, new_sbtabs[i].columns)
self.assertEqual(os.value_rows, new_sbtabs[i].value_rows)
self.assertEqual(os.table_type, new_sbtabs[i].table_type)
self.assertEqual(os.table_name, new_sbtabs[i].table_name)
def convert_to_sbtab(self):
'''
Generates the SBtab files from the SBML document.
Returns: (SBtab.SBtabDocument, list)
SBtab document with SBtab tables that contain the content of the SBML model.
A list of warnings that may be issued during the conversion process.
'''
self.warnings = []
sbtab_doc = SBtab.SBtabDocument(self.filename)
doc_row = "!!!SBtab Document='%s' Name='%s' SBtabVersion='1.0'" % (
self.model.getId(), self.model.getId())
sbtab_doc.set_doc_row(doc_row)
try:
fbc = self.model.getPlugin('fbc')
if fbc: self.fbc = True
except:
pass
# the layout test needs to be a bit deeper than fbc, since
# a form of the layout plugin also exists in ancient versions
# of SBML2.x
try:
layout = self.model.getPlugin('layout').getLayout(0)
layout_id = layout.getId()
if layout_id: self.layout = True
except:
pass
for table_type in supported_table_types:
try:
function_name = 'self.' + table_type.lower() + '_sbtab()'
sbtab = eval(function_name)
if sbtab != False:
sbtab_doc.add_sbtab(sbtab)
except:
self.warnings.append('Could not generate SBtab %s.' %
table_type)
if self.fbc:
try:
sbtab = self.fbc_objective()
if sbtab != False:
sbtab_doc.add_sbtab(sbtab)
except:
self.warnings.append(
'Could not generate SBtab FBC Objective Function.')
try:
sbtab = self.fbc_gene()
if sbtab != False:
sbtab_doc.add_sbtab(sbtab)
except:
self.warnings.append('Could not generate SBtab FBC Gene.')
if self.layout:
try:
sbtab = self.layout_sbtab()
if sbtab != False:
sbtab_doc.add_sbtab(sbtab)
except:
self.warnings.append('Could not generate SBtab Layout.')
return (sbtab_doc, self.warnings)
def validator():
"""
example action using the internationalization operator T and flash
rendered by views/default/index.html or views/generic.html
if you need a simple wiki simple replace the two lines below with:
return auth.wiki()
"""
response.title = T('SBtab - Standardised data tables for Systems Biology')
response.subtitle = T('Online Validator')
lform = SQLFORM.factory(
Field('File',
'upload',
uploadfolder="/tmp",
label='Upload SBtab file (.csv, .tsv, .xlsx)',
requires=IS_LENGTH(10485760,
1,
error_message='Max upload size: 10MB')))
filename = None
output = []
# load the definition file which is required for validation
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_val.append(
'There was an error reading the definition file.')
#update session lists
if lform.process().accepted:
response.flash = 'form accepted'
# initialise session variables
session.warnings_val = []
if 'sbtabs' not in session:
session.sbtabs = []
session.sbtab_filenames = []
session.sbtab_docnames = []
session.types = []
session.name2doc = {}
# validate file name
try:
sbtab_file = request.vars.File.value.decode('utf-8', 'ignore')
except:
session.warnings_val.append(
'The file has a faulty encryption. Please use UTF-8 instead.')
redirect(URL(''))
filename = request.vars.File.filename
if not filename.endswith('.tsv') and not filename.endswith(
'.csv') and not filename.endswith('.xlsx'):
session.warnings_val.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_val.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_val.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)
if sbtab_doc.document_format == 'ObjTables':
session.warnings_val.append(
'This SBtab validator cannot be used for ObjTables files.'
)
redirect(URL(''))
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_val.append(
'The SBtab %s is duplicate. The document cannot be validated. All TableIDs in a document need to be unique.'
% sbtab.filename)
redirect(URL(''))
except:
session.warnings_val.append(
'The SBtab Document object could not be created properly.')
redirect(URL(''))
else:
try:
sbtab = SBtab.SBtabTable(sbtab_file, filename)
if sbtab.table_format == 'ObjTables':
session.warnings_val.append(
'This SBtab validator cannot be used for ObjTables files.'
)
redirect(URL(''))
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_val.append(
'The SBtab Table object could not be created properly.')
redirect(URL(''))
elif lform.errors:
response.flash = 'form has errors'
# buttons
# validate
if request.vars.validate_button:
try:
filename = session.sbtab_filenames[int(
request.vars.validate_button)]
TableValidClass = validatorSBtab.ValidateTable(
session.sbtabs[int(request.vars.validate_button)],
session.definition_file)
output = TableValidClass.return_output()
except:
session.warnings_val.append(
'The file could not be validated. It seems to be broken.')
redirect(URL(''))
# erase
if request.vars.erase_button:
flname = session.sbtab_filenames[int(request.vars.erase_button)]
del session.sbtabs[int(request.vars.erase_button)]
del session.sbtab_filenames[int(request.vars.erase_button)]
del session.types[int(request.vars.erase_button)]
doc_name = session.name2doc[flname]
# this IF is important: you must only delete the document from the list
# IF there are no more files attached to it
if list(session.name2doc.values()).count(doc_name) == 1:
session.sbtab_docnames.remove(doc_name)
del session.name2doc[flname]
session.warnings_val = []
redirect(URL(''))
# erase all
if request.vars.remove_all_button_val:
try:
remove_document = session.sbtab_docnames[int(
request.vars.remove_all_button_val)]
# 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 rs in remove:
remove_filenames.append(session.sbtab_filenames[rs])
del session.sbtabs[rs]
del session.sbtab_filenames[rs]
del session.types[rs]
# delete document name
del session.sbtab_docnames[int(request.vars.remove_all_button_val)]
# delete name2doc entries
for entry in remove_filenames:
del session.name2doc[entry]
session.warnings_val = []
redirect(URL(''))
except:
redirect(URL(''))
return dict(UPL_FORM=lform,
DEF_FILE_NAME=session.definition_file_name,
SBTAB_LIST=session.sbtabs,
NAME_LIST=session.sbtab_filenames,
SBTAB_VAL=filename,
DOC_NAMES=session.sbtab_docnames,
NAME2DOC=session.name2doc,
OUTPUT=output,
WARNINGS=session.warnings_val)
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)
def validator():
"""
example action using the internationalization operator T and flash
rendered by views/default/index.html or views/generic.html
if you need a simple wiki simple replace the two lines below with:
return auth.wiki()
"""
response.title = T('SBtab - Standardised data tables for Systems Biology')
response.subtitle = T('Online Validator')
lform = SQLFORM.factory(
Field('File',
'upload',
uploadfolder="/tmp",
label='Upload SBtab file (.csv, .tsv, .xls)',
requires=IS_LENGTH(10485760,
1,
error_message='Max upload size: 10MB')))
sbtab_val = None
output = []
#update session lists
if lform.process().accepted:
response.flash = 'form accepted'
# initialise session variables
session.warnings_val = []
if 'sbtabs' not in session:
session.sbtabs = []
session.sbtab_filenames = []
session.sbtab_docnames = []
session.types = []
session.name2doc = {}
# load the definition file which is required for validation
if not session.definition_file:
try:
def_file_open = open(
'./applications/sbtab_web/static/files/default_files/definitions.tsv'
)
def_file = def_file_open.read()
definition_name = 'definitions.tsv'
sbtab_def = SBtab.SBtabTable(def_file, definition_name)
session.definition_file = sbtab_def
session.definition_file_name = sbtab_def.filename
except:
session.warnings_val.append(
'There was an error reading the definition file.')
# validate file name
try:
sbtab_file = request.vars.File.value.decode('utf-8', 'ignore')
except:
session.warnings_val.append(
'The file has a faulty encryption. Please use UTF-8 instead.')
redirect(URL(''))
filename = request.vars.File.filename
if not filename.endswith('.tsv') and not filename.endswith(
'.csv') and not filename.endswith('.xls'):
session.warnings_val.append(
'The file does not have a correct file format. Please use csv/tsv/xls only.'
)
redirect(URL(''))
# convert from xls to csv if required
if filename.endswith('.xls'):
try:
sbtab_file = misc.xls2csv(sbtab_file, filename)
except:
session.warnings_val.append(
'The xls 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_val.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:]
if name_single not in session.sbtab_filenames:
sbtab = SBtab.SBtabTable(sbtab_string, name_single)
sbtab_doc.add_sbtab(sbtab)
session.sbtabs.append(sbtab)
session.types.append(sbtab.table_type)
session.sbtab_filenames.append(name_single)
session.name2doc[name_single] = filename
else:
session.warnings_val.append(
'The SBtab %s is duplicate.' % sbtab.filename)
redirect(URL(''))
except:
session.warnings_val.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_val.append(
'The SBtab Table object could not be created properly.')
redirect(URL(''))
elif lform.errors:
response.flash = 'form has errors'
# buttons
# validate
if request.vars.validate_button:
sbtab_val = session.sbtab_filenames[int(request.vars.validate_button)]
TableValidClass = validatorSBtab.ValidateTable(
session.sbtabs[int(request.vars.validate_button)],
session.definition_file)
output = TableValidClass.return_output()
# erase
if request.vars.erase_button:
flname = session.sbtab_filenames[int(request.vars.erase_button)]
del session.sbtabs[int(request.vars.erase_button)]
del session.sbtab_filenames[int(request.vars.erase_button)]
del session.types[int(request.vars.erase_button)]
del session.sbtab_docnames[int(request.vars.erase_button)]
del session.name2doc[flname]
session.warnings_val = []
redirect(URL(''))
# erase all
if request.vars.remove_all_button_val:
try:
remove_document = session.sbtab_docnames[int(
request.vars.remove_all_button_val)]
remove_sbtabs = []
for i, docname in enumerate(session.sbtab_docnames):
if docname == remove_document:
remove_sbtabs.append(i)
remove = sorted(remove_sbtabs, reverse=True)
for i in remove:
del session.sbtabs[i]
del session.name2doc[session.sbtab_filenames[i]]
del session.sbtab_filenames[i]
del session.types[i]
del session.sbtab_docnames[i]
session.warnings_val = []
except:
session.warnings_val.append(
'The document could not be removed. Please reload session.')
redirect(URL(''))
return dict(UPL_FORM=lform,
DEF_FILE_NAME=session.definition_file_name,
SBTAB_LIST=session.sbtabs,
NAME_LIST=session.sbtab_filenames,
SBTAB_VAL=sbtab_val,
DOC_NAMES=session.sbtab_docnames,
NAME2DOC=session.name2doc,
OUTPUT=output,
WARNINGS=session.warnings_val)