def cleanOptions(options):
options['dialogs'] = 'dialogs' in options
options['p'] = F.absfile(options.get('p', ''))
if options['dialogs']:
if not 'i' in options:
options['i'] = D.askForFile(defaultextension='*.xls',
filetypes=(('Excel classic', '*.xls'),
('Excel', '*.xlsx'),
('All files', '*.*')),
initialdir=options['p'],
multiple=False,
title="Definition of Target Reactions")
if not 'src' in options:
options['src'] = D.askForFile(
defaultextension='*.xls',
filetypes=(('Excel classic', '*.xls'), ('Excel', '*.xlsx'),
('All files', '*.*')),
initialdir=options['p'],
multiple=True,
title="Source fragments and their locations")
if not 'o' in options:
options['o'] = D.askForFile(defaultextension='*.gwl',
filetypes=(('Evo Worklist', '*.gwl'),
('Text file', '*.txt'),
('All files', '*.*')),
initialdir=options['p'],
multiple=False,
newfile=True,
title="Save Worklist output file as")
options['i'] = F.absfile(options['i'])
options['src'] = [F.absfile(f) for f in U.tolist(options['src'])]
options['o'] = F.absfile(options['o'])
options['useLabel'] = 'useLabel' in options
## options['srcplate'] = [s.strip() for s in U.tolist(options.get('srcplate',[]))]
return options
def __init__(self, fname, reportErrors=True):
"""
Worklist constructor.
>>> wl = Worklist('outputfile.gwl')
Args:
fname (str): file name for output worklist (will be created)
reportErrors (bool): report exceptions via dialog box to user [True]
"""
self.fname = F.absfile(fname)
self._f = None ## file handle
self.reportErrors = reportErrors
def cleanOptions(options):
options['dialogs'] = 'dialogs' in options
cwd = options.get('p', None)
if options['dialogs']:
if not 'i' in options:
options['i'] = D.askForFile(defaultextension='*.xls',
filetypes=(('Excel classic', '*.xls'),
('Excel', '*.xlsx'),
('All files', '*.*')),
initialdir=cwd,
multiple=False,
title="Cherrypicking Table")
if not 'src' in options:
options['src'] = D.askForFile(
defaultextension='*.xls',
filetypes=(('Excel classic', '*.xls'), ('Excel', '*.xlsx'),
('All files', '*.*')),
initialdir=cwd,
multiple=True,
title="Source samples and their locations")
if not 'o' in options:
options['o'] = D.askForFile(defaultextension='*.gwl',
filetypes=(('Evo Worklist', '*.gwl'),
('Text file', '*.txt'),
('All files', '*.*')),
initialdir=cwd,
multiple=False,
newfile=True,
title="Save Worklist output file as")
options['i'] = F.existingFile(
options['i'],
cwd=cwd,
errmsg='Cannot find cherrypicking input (-i) file.')
options['src'] = U.tolist(options['src'])
msg = 'Cannot find source (-src) file '
options['src'] = [
F.existingFile(f, cwd=cwd, errmsg=msg) for f in options['src']
]
options['o'] = F.absfile(options['o'], cwd=cwd)
options['columns'] = U.tolist(options.get('columns', []))
options['useLabel'] = 'barcode' not in options
return options
def generictest(self, options):
import evoware.fileutil as F
import os.path as O
self.f_out = F.absfile(self.f_project + '/' + options['o'])
run(options)
self.assertTrue(O.exists(self.f_out))
with open(self.f_out,'r') as f1, \
open(F.testRoot('results/distribute.gwl'),'r') as f2:
self.assertEqual(f1.readlines(), f2.readlines())
def cleanOptions( options ):
options['dialogs'] = 'dialogs' in options
options['p'] = F.absfile( options.get('p', ''))
if options['dialogs']:
if not 'i' in options:
options['i'] = D.askForFile(defaultextension='*.xls',
filetypes=(('Excel classic','*.xls'),('Excel','*.xlsx'),('All files','*.*')),
initialdir=options['p'],
multiple=False,
title="Definition of Target Reactions")
if not 'src' in options:
options['src'] = D.askForFile(defaultextension='*.xls',
filetypes=(('Excel classic','*.xls'),('Excel','*.xlsx'),('All files','*.*')),
initialdir=options['p'],
multiple=True,
title="Source templates and primers and their locations")
if not 'o' in options:
options['o'] = D.askForFile(defaultextension='*.gwl',
filetypes=(('Evo Worklist','*.gwl'),('Text file','*.txt'),('All files','*.*')),
initialdir=options['p'],
multiple=False,
newfile=True,
title="Save Worklist output file as")
options['i'] = F.absfile(options['i'])
options['src'] = [ F.absfile(f) for f in U.tolist(options['src']) ]
options['o'] = F.absfile(options['o'])
options['useLabel'] = 'useLabel' in options
## options['srcplate'] = [s.strip() for s in U.tolist(options.get('srcplate',[]))]
return options
def read(self, fname):
"""
Append data from given Excel file to internal list of rows and
dictionary of parameters.
Args:
fname (str) excel file name including path
Raises:
IOError: if file cannot be found (presumably)
`ExcelFormatError`: if header row cannot be found or interpreted
"""
book = X.open_workbook(F.absfile(fname))
sheet = book.sheets()[0]
try:
row = 0
values = []
## iterate until there is a row starting with HEADER_FIRST_VALUE
## capture any "param, <key>, <value>" entries until then
while not self.detectHeader(values):
values = [v for v in sheet.row_values(row) if v]
self.parsePreHeader(values)
row += 1
## parse table "header"
keys = self.parseHeader(values)
i = 0
for row in range(row, sheet.nrows):
values = sheet.row_values(row)
## ignore rows with empty first column
if values[0]:
d = dict(zip(keys, values))
self.cleanEntry(d)
self.addEntry(d)
i += 1
return i
except ExcelFormatError as why:
raise ExcelFormatError(
'Invalid Excel file (could not find header).')