def __call__(self, context):
brains = find(IProvider.__identifer__)
values = [b.getObject() for b in brains]
names = [" ".join([str(v.site_ID), v.first_name, v.last_name])
for v in values]
items = [(n, normalize(n)) for n in names]
return SimpleVocabulary.fromItems(items)
def __call__(self, context):
wells = ["-A", "-B", "-C", "-D", "-E", "-F", "-H"]
values = find(portal_type='iChip')
ichips = [v.Title for v in values]
unique_ichip_wells = []
for o in ichips:
for w in wells:
well_location = o + w
unique_ichip_wells.append(well_location)
items = [(i, normalize(i)) for i in unique_ichip_wells]
return SimpleVocabulary.fromItems(items)
def __call__(self, context):
wells = ["-A", "-B", "-C", "-D", "-E", "-F", "-H"]
values = find(portal_type='iChip')
ichips = [v.Title for v in values]
unique_ichip_wells = []
for o in ichips:
for w in wells:
well_location = o + w
unique_ichip_wells.append(well_location)
items = [(i, normalize(i)) for i in unique_ichip_wells]
return SimpleVocabulary.fromItems(items)
def __call__(self, context):
values = get_registry_record('immunarray.category_primary')
items = [(i, normalize(i)) for i in values]
return SimpleVocabulary.fromItems(items)
def __call__(self):
wb = self.load_workbook()
ws = wb.get_sheet_by_name('Form')
# A6 - add run number to 'FILE NAME'
ws['A6'].value += ' (Veracis Test Run %s)' % self.context.run_number
# A7 - PURPOSE
ws['A7'].value += ' %s' % self.context.assay_name
# A8 - DATE
ws['A8'].value += ' %s' % self.context.run_date
# D8 - PLANNED BY
ws['D8'].value += ' %s' % self.context.run_planner
# H8 - PERFORMED BY
ws['H8'].value += ' %s' % self.context.run_operator
# PLATE HEADERS are at 10, 27, 44, 61, 78
for plate_nr, plate_cell in enumerate([10, 27, 44, 61, 78]):
plate_nr += 1
# verify plate header exists in spreadsheet
plate_title = 'plate %s' % plate_nr
plate_header_cell = ws['A%s' % plate_cell]
assert plate_header_cell.value.lower() == plate_title
# verify the plate exists in run.plates
if len(self.context.plates) < plate_nr:
break
plate = self.context.plates[plate_nr - 1]
# ALIQUOT WELL ROWS are PLATE HEADER+[2..9] in COLS B,D,F,H
for chip_nr, chip_col in enumerate('BDFH'):
for well_nr in range(8):
uid = plate['chip-%s_well-%s' % (chip_nr + 1, well_nr + 1)]
if uid:
brain = find(UID=uid)[0]
row = plate_cell + (well_nr + 2)
cell = ws['%s%s' % (chip_col, row)]
cell.value = brain.Title
# +1 for ICHIP in rows C,E,G,I - and "COMMENTS" in J
row = plate_cell + 10
for chip_nr, chip_col in enumerate('CEGI'):
uid = plate['chip-id-%s' % (chip_nr + 1)]
if not uid:
raise MissingIChipForSlide(
"plate %s, slide %s" % (plate_nr, chip_nr + 1))
brain = find(UID=uid)[0]
cell = ws['%s%s' % (chip_col, row)]
cell.value = brain.Title
# comments in J
cell = ws['J%s' % row]
cell.value = plate['comments-ichip-%s' % (chip_nr + 1)]
# +1 for ICHIP in rows C,E,G,I - and "COMMENTS" in J
row = plate_cell + 10
for chip_nr, chip_col in enumerate('CEGI'):
uid = plate['chip-id-%s' % (chip_nr + 1)]
if not uid:
raise MissingIChipForSlide(
"plate %s, slide %s" % (plate_nr, chip_nr + 1))
brain = find(UID=uid)[0]
cell = ws['%s%s' % (chip_col, row)]
cell.value = brain.Title
# comments in J
cell = ws['J%s' % row]
cell.value = plate['comments-ichip-%s' % (chip_nr + 1)]
# +1 for SCAN SLOT C,E,G,I
row = plate_cell + 11
for chip_nr, slot_col in enumerate('CEGI'):
cell = ws['%s%s' % (slot_col, row)]
cell.value = plate['scan-slot-%s' % (chip_nr + 1)]
# +2 for COMMENTS in B,D,F,H
row = plate_cell + 13
for chip_nr, comment_col in enumerate('CEGI'):
cell = ws['%s%s' % (comment_col, row)]
cell.value = plate['comments-ichip-%s' % (chip_nr + 1)]
fn = "{}-{}".format(self.context.assay_name, self.context.run_number)
fn = normalize(fn) + ".xlsx"
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'application/vnd.ms-excel')
setheader("Content-Disposition", 'attachment;filename="%s"' % fn)
fn = tempfile.mktemp()
wb.save(fn)
data = open(fn).read()
self.request.RESPONSE.write(data)
def __call__(self):
wb = self.load_workbook()
ws = wb.get_sheet_by_name('Form')
# A6 - add run number to 'FILE NAME'
ws['A6'].value += ' (Veracis Test Run %s)' % self.context.run_number
# A7 - PURPOSE
ws['A7'].value += ' %s' % self.context.assay_name
# A8 - DATE
ws['A8'].value += ' %s' % self.context.run_date
# D8 - PLANNED BY
ws['D8'].value += ' %s' % self.context.run_planner
# H8 - PERFORMED BY
ws['H8'].value += ' %s' % self.context.run_operator
# PLATE HEADERS are at 10, 27, 44, 61, 78
for plate_nr, plate_cell in enumerate([10, 27, 44, 61, 78]):
plate_nr += 1
# verify plate header exists in spreadsheet
plate_title = 'plate %s' % plate_nr
plate_header_cell = ws['A%s' % plate_cell]
assert plate_header_cell.value.lower() == plate_title
# verify the plate exists in run.plates
if len(self.context.plates) < plate_nr:
break
plate = self.context.plates[plate_nr - 1]
# ALIQUOT WELL ROWS are PLATE HEADER+[2..9] in COLS B,D,F,H
for chip_nr, chip_col in enumerate('BDFH'):
for well_nr in range(8):
uid = plate['chip-%s_well-%s' % (chip_nr + 1, well_nr + 1)]
if uid:
brain = find(UID=uid)[0]
row = plate_cell + (well_nr + 2)
cell = ws['%s%s' % (chip_col, row)]
cell.value = brain.Title
# +1 for ICHIP in rows C,E,G,I - and "COMMENTS" in J
row = plate_cell + 10
for chip_nr, chip_col in enumerate('CEGI'):
uid = plate['chip-id-%s' % (chip_nr + 1)]
if not uid:
raise MissingIChipForSlide("plate %s, slide %s" %
(plate_nr, chip_nr + 1))
brain = find(UID=uid)[0]
cell = ws['%s%s' % (chip_col, row)]
cell.value = brain.Title
# comments in J
cell = ws['J%s' % row]
cell.value = plate['comments-ichip-%s' % (chip_nr + 1)]
# +1 for ICHIP in rows C,E,G,I - and "COMMENTS" in J
row = plate_cell + 10
for chip_nr, chip_col in enumerate('CEGI'):
uid = plate['chip-id-%s' % (chip_nr + 1)]
if not uid:
raise MissingIChipForSlide("plate %s, slide %s" %
(plate_nr, chip_nr + 1))
brain = find(UID=uid)[0]
cell = ws['%s%s' % (chip_col, row)]
cell.value = brain.Title
# comments in J
cell = ws['J%s' % row]
cell.value = plate['comments-ichip-%s' % (chip_nr + 1)]
# +1 for SCAN SLOT C,E,G,I
row = plate_cell + 11
for chip_nr, slot_col in enumerate('CEGI'):
cell = ws['%s%s' % (slot_col, row)]
cell.value = plate['scan-slot-%s' % (chip_nr + 1)]
# +2 for COMMENTS in B,D,F,H
row = plate_cell + 13
for chip_nr, comment_col in enumerate('CEGI'):
cell = ws['%s%s' % (comment_col, row)]
cell.value = plate['comments-ichip-%s' % (chip_nr + 1)]
fn = "{}-{}".format(self.context.assay_name, self.context.run_number)
fn = normalize(fn) + ".xlsx"
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'application/vnd.ms-excel')
setheader("Content-Disposition", 'attachment;filename="%s"' % fn)
fn = tempfile.mktemp()
wb.save(fn)
data = open(fn).read()
self.request.RESPONSE.write(data)
def __call__(self, context):
catalog = getToolByName(context, 'portal_catalog')
values = catalog(portal_type='iChip')
names = [([v.id]) for v in values]
items = [(n, normalize(n)) for n in names]
return SimpleVocabulary.fromItems(items)
def __call__(self, context):
catalog = getToolByName(context, 'portal_catalog')
values = catalog(portal_type='iChip')
names = [([v.id]) for v in values]
items = [(n, normalize(n)) for n in names]
return SimpleVocabulary.fromItems(items)
def __call__(self):
fieldnames = [
'iChipLot', 'Slide_ID', 'Well_ID', 'Plate', 'TestSession',
'SampleID', 'Analyze', 'Run_Number', 'SampleClass',
'Aliqout_ID']
io = StringIO()
writer = csv.DictWriter(io, fieldnames=fieldnames)
writer.writerow(dict(zip(fieldnames, fieldnames)))
for plate_nr, plate in enumerate(self.context.plates):
plate_nr += 1
for chip_nr in range(1, 5):
# get chip for this slide
uid = plate['chip-id-%s' % chip_nr]
if not uid:
raise MissingIChipForSlide(
"plate %s, slide %s" % (plate_nr, chip_nr))
chip = find(UID=uid)[0].getObject()
for well_nr in range(1, 9):
uid = plate['chip-%s_well-%s' % (chip_nr, well_nr)]
if uid:
aliquot = find(UID=uid)[0].getObject()
sample = self.get_parent_sample_from_aliquot(aliquot)
if IClinicalAliquot.providedBy(aliquot):
SampleClass = '1'
Aliquot_ID = aliquot.title
SampleID = '-'.join(
aliquot.title.split('-')[:2])
Analyze = '1'
elif self.is_hqc(sample):
SampleClass = '3'
Aliquot_ID = aliquot.title
SampleID = sample.source_id_one
Analyze = '1'
elif self.is_lqc(sample):
SampleClass = '5'
Aliquot_ID = aliquot.title
SampleID = sample.source_id_one
Analyze = '1'
else:
raise InvalidSample("Aliquot %s" % aliquot.title)
else:
SampleClass = '1'
Aliquot_ID = 'Blank'
SampleID = 'Blank'
Analyze = '0'
# noinspection PyUnboundLocalVariable
writer.writerow({
'iChipLot': chip.title.split("_")[0],
'Slide_ID': chip.title.split("_")[1],
'Well_ID': str(well_nr),
'Plate': str(plate_nr),
'TestSession': '1',
'SampleID': SampleID,
'Analyze': Analyze,
'Run_Number': self.context.run_number,
'SampleClass': SampleClass,
'Aliqout_ID': Aliquot_ID,
})
fn = "{}-{}".format(self.context.assay_name, self.context.run_number)
fn = normalize(fn) + ".csv"
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader("Content-Disposition", 'attachment;filename="%s"' % fn)
self.request.RESPONSE.write(io.getvalue())
