def test_count_tabs(self):
'''
test if the amount of SBtabs in one file can be determined
'''
for sbtab in self.sbtabs:
amount = misc.count_tabs(sbtab.to_str())
self.assertEqual(amount, 1)
for doc in self.docs:
amount = misc.count_tabs(doc.to_str())
self.assertGreaterEqual(amount, 1)
def test_count_tabs(self):
'''
test if the amount of SBtabs in one file can be determined
'''
for sbtab in self.sbtabs:
amount = misc.count_tabs(sbtab.to_str())
self.assertEqual(amount, 1)
for doc in self.docs:
amount = misc.count_tabs(doc.to_str())
self.assertGreaterEqual(amount, 1)
def add_sbtab_string(self, sbtab_string, filename):
'''
add one or multiple SBtab files as string
'''
# set filename if not given
if not filename: filename = 'unnamed_sbtab'
# see if there are more than one SBtabs in the string
try: sbtab_amount = misc.count_tabs(sbtab_string)
except:
self.warnings.append('The SBtab file could not be read properly.')
# if there are more than one SBtabs, cut them in single SBtabs
if sbtab_amount > 1:
try:
sbtab_strings = misc.split_sbtabs(sbtab_string)
for i, sbtab_s in enumerate(sbtab_strings):
name_single = filename + '_' + str(i)
sbtab_single = SBtab.SBtabTable(sbtab_s, name_single)
self.add_sbtab(sbtab_single)
except:
self.warnings.append('The SBtab Table object could not be cre'\
'ated properly.')
else:
try:
sbtab = SBtab.SBtabTable(sbtab_string, filename)
self.add_sbtab(sbtab)
except:
self.warnings.append('The SBtab Table object could not be cre'\
'ated properly.')
def add_sbtab_string(self, sbtab_string, filename):
'''
Adds one or multiple SBtab files as a string.
Parameters
----------
sbtab_string: str
One string holding one or more SBtab tables.
filename: str
Name of the given SBtab.
'''
# set filename if not given
sbtab_count = len(self.sbtabs)
filename = 'unnamed_sbtab_%s.tsv'%(str(sbtab_count))
if not self.filename: self.filename = filename
if not self.name: self.name = filename
# see if there are more than one SBtabs in the string
try: sbtab_amount = misc.count_tabs(sbtab_string)
except:
raise SBtabError('The SBtab file could not be read properly.')
# here, we find a possible doc row
for row in sbtab_string.split('\n'):
if row.startswith('!!!'):
self.doc_row = self._dequote(row)
break
elif row.startswith('"!!!'):
rm1 = row.replace('""', '#')
rm2 = rm1.replace('"','')
self.doc_row = self._dequote(rm2.replace('#', '"'))
break
else:
self.doc_row = None
self.document_format = None
# determine if this is an SBtab or ObjTables Document
if self.doc_row:
if '!!!ObjTables' in self.doc_row:
self.document_format = 'ObjTables'
elif '!!!SBtab' in self.doc_row:
self.document_format = 'SBtab'
# if there are more than one SBtabs, cut them in single SBtabs
try:
if sbtab_amount > 1:
sbtab_strings = misc.split_sbtabs(sbtab_string)
for i, sbtab_s in enumerate(sbtab_strings):
name_single = str(i) + '_' + self.filename
sbtab_single = SBtabTable(sbtab_s, name_single)
logging.debug('name = %s, type = %s' % (sbtab_single.table_name, sbtab_single.table_type))
self.add_sbtab(sbtab_single)
else:
sbtab = SBtabTable(sbtab_string, filename)
self.add_sbtab(sbtab)
except Exception as e:
raise SBtabError('The SBtab Table object could not be cre'\
'ated properly: ' + str(e))
return True
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 test_split_sbtabs(self):
'''
test if multiple sbtabs in one input file can be splitted correctly
'''
for doc in self.docs:
amount = misc.count_tabs(doc.to_str())
sbtabs = misc.split_sbtabs(doc.to_str())
self.assertEqual(amount, len(sbtabs))
for sbtab in sbtabs:
self.assertEqual(sbtab[0:7], '!!SBtab')
def test_split_sbtabs(self):
'''
test if multiple sbtabs in one input file can be splitted correctly
'''
for doc in self.docs:
amount = misc.count_tabs(doc.to_str())
sbtabs = misc.split_sbtabs(doc.to_str())
self.assertEqual(amount, len(sbtabs))
for sbtab in sbtabs:
self.assertEqual(sbtab[0:7],'!!SBtab')
def add_sbtab_string(self, sbtab_string, filename):
'''
Adds one or multiple SBtab files as a string.
Parameters
----------
sbtab_string: str
One string holding one or more SBtab tables.
filename: str
Name of the given SBtab.
'''
# set filename if not given
if not filename:
sbtab_count = len(self.sbtabs)
filename = 'unnamed_sbtab_%s.tsv'%(str(sbtab_count))
if not self.filename:
self.filename = filename
# see if there are more than one SBtabs in the string
try: sbtab_amount = misc.count_tabs(sbtab_string)
except:
raise SBtabError('The SBtab file could not be read properly.')
# here, we find a possible doc row
for row in sbtab_string.split('\n'):
if row.startswith('!!!'):
self.doc_row = self._dequote(row)
break
elif row.startswith('"!!!'):
rm1 = row.replace('""', '#')
rm2 = rm1.replace('"','')
self.doc_row = self._dequote(rm2.replace('#', '"'))
break
# if there are more than one SBtabs, cut them in single SBtabs
try:
if sbtab_amount > 1:
sbtab_strings = misc.split_sbtabs(sbtab_string)
for i, sbtab_s in enumerate(sbtab_strings):
name_single = str(i) + '_' + self.filename
sbtab_single = SBtabTable(sbtab_s, name_single)
logging.debug('name = %s, type = %s' % (sbtab_single.table_name, sbtab_single.table_type))
self.add_sbtab(sbtab_single)
else:
sbtab = SBtabTable(sbtab_string, filename)
self.add_sbtab(sbtab)
except Exception as e:
raise SBtabError('The SBtab Table object could not be cre'\
'ated properly: ' + str(e))
return True
def sbtab2html_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)
# count given tabs and prepare file name w/o path
tab_amount = misc.count_tabs(f)
if '/' in args.sbtab:
name_pre = args.sbtab.split('/')[-1:]
else: name_pre = args.sbtab
if args.multiple:
try:
sbtab_doc = SBtab.SBtabDocument('sbtab_doc_prelim', f, args.sbtab)
for tab in sbtab_doc.sbtabs:
name = name_pre[0][:4] + '_' + tab.table_id + '.html'
try:
write_html(tab, name)
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, args.sbtab)
name = name_pre[0][:4] + '_' + sbtab.name + '.html'
else:
sbtab = SBtab.SBtabTable(f, args.sbtab)
name = name_pre[0][:4] + '_' + sbtab.table_id + '.html'
write_html(sbtab, name)
except:
raise SBtabError('The HTML file could not be created.')
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)