def UpdateSourceMaterials(instance, event):
"""Update remaining material for anything that was used in the solution
"""
mu = instance.materials_used
if mu:
for x in mu: # {'material title (key)':'mass/volume'(value),}
brains = find(object_provides=IMaterial.__identifier__, Title=x)
if brains:
material = brains[0].getObject()
temp = Decimal(material.remaining_amount) - Decimal(mu[x])
material.remaining_amount = float(temp)
else:
logger.warn(
"%s: Update source materials: material not found: %s" %
(instance, x))
su = instance.solutions_used
if su:
for x in su: # {'solution title (key)':'mass/volume'(value),}
brains = find(object_provides=ISolution.__identifier__, Title=x)
if brains:
solution = brains[0].getObject()
temp = Decimal(solution.remaining_amount) - Decimal(su[x])
solution.remaining_amount = float(temp)
else:
logger.warn(
"%s: Update source materials: solution not found: %s" %
(instance, x))
def UpdateSourceMaterials(instance, event):
"""Update remaining material for anything that was used in the solution
"""
mu = instance.materials_used
if mu:
for x in mu: # {'material title (key)':'mass/volume'(value),}
brains = find(object_provides=IMaterial.__identifier__, Title=x)
if brains:
material = brains[0].getObject()
temp = Decimal(material.remaining_amount) - Decimal(mu[x])
material.remaining_amount = float(temp)
else:
logger.warn(
"%s: Update source materials: material not found: %s" %
(instance, x))
su = instance.solutions_used
if su:
for x in su: # {'solution title (key)':'mass/volume'(value),}
brains = find(object_provides=ISolution.__identifier__, Title=x)
if brains:
solution = brains[0].getObject()
temp = Decimal(solution.remaining_amount) - Decimal(su[x])
solution.remaining_amount = float(temp)
else:
logger.warn(
"%s: Update source materials: solution not found: %s" %
(instance, x))
def get_aliquot_from_fn(self, fn):
sample_id = fn.split('_')[0]
brains = find(object_provides=ISample.__identifier__, id=sample_id)
if not brains:
msg = "%s: Can't find sample '%s'" % (fn, sample_id)
raise RuntimeError(msg)
sample = brains[0].getObject()
# run through the plates, till we find one containing an aliquot
# which is a child of this sample:
aliquot = None
for plate in self.run.plates:
for key, value in plate.items():
try:
obj = find(UID=value)[0].getObject()
except IndexError:
continue
if obj.aq_parent.aq_parent == sample:
aliquot = obj
break
if aliquot:
break
else:
msg = "Aliquot not found for file: %s" % fn
raise RuntimeError(msg)
return aliquot
def get_assay_solutions(self):
"""Dynamically return a list of possible batches, for each type of
solution required by the assay
"""
vocabs = []
assay = self.get_assay()
if not assay:
return vocabs
if assay.needed_solutions:
for solution_type_name in assay.needed_solutions:
type_batches = find(Type=solution_type_name,
expires={
'query': datetime.today().date(),
'range': 'min'
},
sort_on='expires')
tmp = []
for batch in type_batches:
tmp.append([
batch.id, batch.Title,
batch.expires.strftime('%Y-%m-%d')
])
vocabs.append([solution_type_name, tmp])
return vocabs
def get_assay(self):
assay_name = self.assay_name
if assay_name:
brains = find(portal_type='iChipAssay', Title=assay_name)
if not brains:
raise InvalidAssaySelected(self.assay_name)
return brains[0].getObject()
def queryClinicalSamples(self, assay):
"""Get all the samples that are review_state='received', and which
contain an "AssayRequest" who's title matches the assay_name, and who
have a review_state of (re_run or to_be_tested).
"""
sample_data = []
for testable_state in ['re_run', 'to_be_tested']:
# this does get Clinical Samples keep reading jp
brains = find(portal_type="AssayRequest",
Title=assay.title,
review_state=testable_state)
tmp = []
for brain in brains:
assay_request = brain.getObject()
sample = assay_request.aq_parent
tmp.append({
'uid': sample.UID(),
'draw_date': sample.collection_date,
'test_status': get_state(assay_request),
'sample': sample
})
tmp = sorted(tmp, key=itemgetter('draw_date'))
sample_data.extend(tmp)
max_nr_samples = self.maxNumberOfSamplesToRun(assay)
return sample_data[:max_nr_samples]
def getiChipsForTesting(self, assay):
"""Get ALL iChips that can be used for the selected assay
[[<iChipLotID>,[<iChip>,<iChip>,<iChip>]]]
"""
ichips_for_assay = []
brains = find(portal_type='iChipLot',
review_state='released',
sort_on='expires')
if not brains:
raise NoIchipLotsFound
ichiplots = []
for brain in brains:
ichiplot = brain.getObject()
if assay.title in ichiplot.intended_assay \
and int(ichiplot.frames) == int(assay.framecount):
# commercial needs, correct assay
# want to order the ichiplots in this list by exp date
ichiplots.append(ichiplot)
for ichiplot in ichiplots:
ichips = ichiplot.objectValues()
filtered = [ic for ic in ichips if get_state(ic) == 'released']
ichips_for_assay.append([ichiplot, filtered])
return ichips_for_assay
def __call__(self, context):
"""Pull all Veracis IDs for R&D and QC samples and get the next one.
"""
brains = find(portal_type=context.REQUEST.URL.split('++')[-1])
if not brains:
return 1
return max([b.getObject().bottle_number for b in brains]) + 1
def __call__(self, context):
brains = find(object_provides=IQCSample.__identifier__,
review_state='in_use')
items = []
for b in brains:
items.append(SimpleVocabulary.createTerm(b.veracis_id))
return SimpleVocabulary(items)
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):
brains = find(
object_provides='immunarray.lims.interfaces.material.IMaterial',
remaining_amount={'query': 1, 'range': 'min'},
sort_on='sortable_title',
**self.kwargs)
return SimpleVocabulary.fromValues([brain.Title for brain in brains])
def process_raw_flipped(self, path):
"""Store flipped images in ichips
"""
flpath = join(path, 'Raw', 'Flipped')
log = []
for fn in os.listdir(flpath):
if 'jpg' not in fn:
continue
splits = fn.lower().split('_')
ichip_id = splits[1].replace('.', '-') + "_%03d" % int(splits[2])
brains = find(object_provides=IiChip.__identifier__, id=ichip_id)
if not brains:
msg = "%s/%s: Can't find ichip '%s'" % (flpath, fn, ichip_id)
raise RuntimeError(msg)
ichip = brains[0].getObject()
try:
img = create(container=ichip, type='Image', id=fn, title=fn)
except BadRequest as e:
msg = "Run import has already been performed! (%s)" % e.message
raise BadRequest(msg)
except Unauthorized:
msg = "Failed to create %s in ichip %s" % (fn, ichip.title)
raise Unauthorized(msg)
ts = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M")
log.append(u"%s: Added image to ichip %s: %s" % (ts, ichip.id, img))
return log
def get_assay(self):
assay_name = self.assay_name
if assay_name:
brains = find(portal_type='iChipAssay', Title=assay_name)
if not brains:
raise InvalidAssaySelected(self.assay_name)
return brains[0].getObject()
def getiChipsForTesting(self, assay):
"""Get ALL iChips that can be used for the selected assay
[[<iChipLotID>,[<iChip>,<iChip>,<iChip>]]]
"""
ichips_for_assay = []
brains = find(portal_type='iChipLot',
review_state='released',
sort_on='expires')
if not brains:
raise NoIchipLotsFound
ichiplots = []
for brain in brains:
ichiplot = brain.getObject()
if assay.title in ichiplot.intended_assay \
and int(ichiplot.frames) == int(assay.framecount):
# commercial needs, correct assay
# want to order the ichiplots in this list by exp date
ichiplots.append(ichiplot)
for ichiplot in ichiplots:
ichips = ichiplot.objectValues()
filtered = [ic for ic in ichips if get_state(ic) == 'released']
ichips_for_assay.append([ichiplot, filtered])
return ichips_for_assay
def get_sequence_start(veracis_id):
"""Discover the next available aliquot number for the sample with
the provided veracis_id.
"""
brains = find(object_provides=[IQCAliquot.__identifier__,
IRandDAliquot.__identifier__],
veracis_id=veracis_id)
return len(brains) + 1
def __call__(self, context):
values = find(object_provides=IQCSample.__identifier__)
qcsample_ids = [v.UID for v in values]
items = []
for uid in qcsample_ids:
a = get(UID=uid)
items.append(SimpleVocabulary.createTerm(a.veracis_id))
return SimpleVocabulary(items)
def get_aliquots(self, *interfaces):
items = set()
for plate in self.run.plates:
for key, val in plate.items():
brains = find(object_provides=interfaces, UID=val)
if brains:
items.add(brains[0].getObject())
return items
def _get_navigation_root(context):
"""Find the correct navigation root."""
documents = content.find(portal_type='Document', id='front-page')
if len(documents) == 0:
return portal.get()
front_page = documents[0].getObject()
return portal.get_navigation_root(front_page)
def save_run(self):
"""Create initial run
"""
values = get_serializeArray_form_values(self.request)
try:
assay = find(object_provides=IiChipAssay.__identifier__,
Title=values['assay_name'])[0].getObject()
except IndexError:
raise InvalidAssaySelected(values['assay_name'])
plates, ichips, aliquots = self.transmogrify_inputs(values['plates'])
plates = self.remove_empty_plates(plates)
plates = self.reorder_plates(plates)
solutions = [values[x] for x in values if x.startswith('solution-')]
self.transition_plate_contents(ichips, aliquots, 'queue')
lab_users = LabUsersUserVocabulary(self).by_value
planner = lab_users.get(values['run_planner'], '')
operator = lab_users.get(values['run_planner'], '')
brain = find(object_provides=ITestRuns.__identifier__)[0]
folder = brain.getObject()
try:
run_number = int(values['run_number'])
except (ValueError, TypeError):
raise TypeError("Run number must be a number.")
run = create(
folder,
'TestRun',
title=values['assay_name'],
assay_name=assay.title,
assay_uid=assay.UID(),
run_number=run_number,
run_date=values['run_date'],
run_planner=planner.title if planner else '',
run_operator=operator.title if operator else '',
plates=plates,
solutions=solutions
)
return run
def framecount(self):
"""Return the framecount from the assigned ichip-assay
"""
try:
ia = find(UID=self.assay_uid)[0].getObject()
except IndexError:
msg = "Shouldn't happen, Can't resolve ichip assay for testrun."
raise RuntimeError(msg)
return ia.framecount if ia.framecount else 5
def patient_from_aliquot(self, aliquot):
brains = find(object_provides=IPatient.__identifier__)
sample = self.get_sample_from_aliquot(aliquot)
for brain in brains:
patient = brain.getObject()
if sample.usn in patient.tested_unique_sample_ids:
return patient
aid = aliquot.id
raise RuntimeError("Cannot find patient linked with aliquot %s" % aid)
def getQCSampleObject(self, veracis_id):
"""input veracis_id, get qc sample object
"""
brains = find(portal_type='QCSample',
review_state='in_use',
veracis_id=veracis_id)
if not brains:
raise QCSampleNotFound("Veracis ID: %s" % veracis_id)
return brains[0].getObject()
def getQCSampleObject(self, veracis_id):
"""input veracis_id, get qc sample object
"""
brains = find(portal_type='QCSample',
review_state='in_use',
veracis_id=veracis_id)
if not brains:
raise QCSampleNotFound("Veracis ID: %s" % veracis_id)
return brains[0].getObject()
def save_run(self):
"""Create initial run
"""
values = get_serializeArray_form_values(self.request)
try:
assay = find(object_provides=IiChipAssay.__identifier__,
Title=values['assay_name'])[0].getObject()
except IndexError:
raise InvalidAssaySelected(values['assay_name'])
plates, ichips, aliquots = self.transmogrify_inputs(values['plates'])
plates = self.remove_empty_plates(plates)
plates = self.reorder_plates(plates)
solutions = [values[x] for x in values if x.startswith('solution-')]
self.transition_plate_contents(ichips, aliquots, 'queue')
lab_users = LabUsersUserVocabulary(self).by_value
planner = lab_users.get(values['run_planner'], '')
operator = lab_users.get(values['run_planner'], '')
brain = find(object_provides=ITestRuns.__identifier__)[0]
folder = brain.getObject()
try:
run_number = int(values['run_number'])
except (ValueError, TypeError):
raise TypeError("Run number must be a number.")
run = create(folder,
'TestRun',
title=values['assay_name'],
assay_name=assay.title,
assay_uid=assay.UID(),
run_number=run_number,
run_date=values['run_date'],
run_planner=planner.title if planner else '',
run_operator=operator.title if operator else '',
plates=plates,
solutions=solutions)
return run
def __call__(self, context):
"""Pull all Veracis IDs for R&D and QC samples and get the next one.
"""
brains = find(portal_type=['QCSample', 'RandDSample'],
sort_on='veracis_id',
sort_order='reverse', limit=1)
if brains:
_id = str(int(brains[0].veracis_id) + 1)
return unicode(_id)
logger.info("assignVeracisId: No QC or RandD samples: using ID '1000'")
return u"1000"
def provider_from_aliquot(self, aliquot):
sample = self.get_sample_from_aliquot(aliquot)
provider_name = sample.sample_ordering_healthcare_provider
brains = find(object_provides=IProvider.__identifier__, Title=provider_name)
if len(brains) > 1:
raise RuntimeError("Found more than one provider with title='%s'" % provider_name)
try:
provider = brains[0].getObject()
except IndexError:
raise RuntimeError("Provider not found matching title='%s'" % provider_name)
return provider
def update_kit_count(self, site_id):
"""Update site kits on hand count to be reduced by 1
"""
site_objects = find(portal_type='Site')
for i in site_objects:
if i.Title == site_id:
uid = i.UID
site = api.content.get(UID=uid)
site.kits_on_site -= 1
# Account for free kits, so that number counts down
if site.free_kits_left > 0:
site.free_kits_left -= 1
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 update_kit_count(self, site_id):
"""Update site kits on hand count to be reduced by 1
"""
site_objects = find(portal_type='Site')
for i in site_objects:
if i.Title == site_id:
uid = i.UID
site = api.content.get(UID=uid)
site.kits_on_site -= 1
# Account for free kits, so that number counts down
if site.free_kits_left > 0:
site.free_kits_left -= 1
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):
"""Pull all box numbers and get the next one.
"""
brains = find(portal_type=['CommercialBox', 'RandDBox', 'QCBox'],
sort_on='box_number',
sort_order='reverse',
limit=1)
if brains:
_id = str(int(brains[0].box_number) + 1)
return unicode(_id)
logger.info("assignBoxNumber: No Boxes Exist: using ID '1'")
return u"1"
def __call__(self, context):
"""Pull all Veracis IDs for R&D and QC samples and get the next one.
"""
brains = find(portal_type=['QCSample', 'RandDSample'],
sort_on='veracis_id',
sort_order='reverse',
limit=1)
if brains:
_id = str(int(brains[0].veracis_id) + 1)
return unicode(_id)
logger.info("assignVeracisId: No QC or RandD samples: using ID '1000'")
return u"1000"
def collectAliquots(self, sample_object, **kwargs):
"""Get in array of objects to see if they are the last in the chain
and return a list of objects back. Check if each is a working aliquot
that meets the needs of the assay
Type is the value of the index called 'Type'. It's set (for aliquots)
in the adapters/indexers.py.
"""
path = '/'.join(sample_object.getPhysicalPath())
brains = find(path={'query': path, 'depth': -1},
sort_on='id',
**kwargs)
items = [b.getObject() for b in brains]
return items
def transmogrify_inputs(self, plates):
"""Convert titles to UIDs for all ichips and aliquots
"""
ichips, aliquots = [], []
# A single plate run must be converted to a list of plates
if isinstance(plates, dict):
plates = [plates]
for plate in plates:
for chip_nr in range(1, 5):
for well_nr in range(1, 9):
key = "chip-{}_well-{}".format(chip_nr, well_nr)
if plate.get(key, False):
brains = find(object_provides=IAliquot.__identifier__,
Title=plate[key])
plate[key] = brains[0].UID
aliquots.append(brains[0].getObject())
key = "chip-id-{}".format(chip_nr)
if plate.get(key, False):
brains = find(object_provides=IiChip.__identifier__,
Title=plate[key])
plate[key] = brains[0].UID
ichips.append(brains[0].getObject())
return plates, ichips, aliquots
def transmogrify_inputs(self, plates):
"""Convert titles to UIDs for all ichips and aliquots
"""
ichips, aliquots = [], []
# A single plate run must be converted to a list of plates
if isinstance(plates, dict):
plates = [plates]
for plate in plates:
for chip_nr in range(1, 5):
for well_nr in range(1, 9):
key = "chip-{}_well-{}".format(chip_nr, well_nr)
if plate.get(key, False):
brains = find(object_provides=IAliquot.__identifier__,
Title=plate[key])
plate[key] = brains[0].UID
aliquots.append(brains[0].getObject())
key = "chip-id-{}".format(chip_nr)
if plate.get(key, False):
brains = find(object_provides=IiChip.__identifier__,
Title=plate[key])
plate[key] = brains[0].UID
ichips.append(brains[0].getObject())
return plates, ichips, aliquots
def collectAliquots(self, sample_object, **kwargs):
"""Get in array of objects to see if they are the last in the chain
and return a list of objects back. Check if each is a working aliquot
that meets the needs of the assay
Type is the value of the index called 'Type'. It's set (for aliquots)
in the adapters/indexers.py.
"""
path = '/'.join(sample_object.getPhysicalPath())
brains = find(path={
'query': path,
'depth': -1
},
sort_on='id',
**kwargs)
items = [b.getObject() for b in brains]
return items
def get_run(self, path):
run_nr = self.get_run_nr(path)
# get the run nr so we can loop the plates
brains = find(object_provides=IVeracisRunBase.__identifier__,
run_number=run_nr)
if not brains:
msg = "No test run found with run_number=%s." % run_nr
raise RuntimeError(msg)
run = brains[0].getObject()
# verify that run is in correct state for import.
state = get_state(run)
if state != 'scanning':
if state == 'resulted':
return None
msg = "Test run %s is in state '%s'. Expected state: 'scanning'" \
% (run.title, state)
raise RunInIncorrectState(msg)
return run
def get_assay_solutions(self):
"""Dynamically return a list of possible batches, for each type of
solution required by the assay
"""
vocabs = []
assay = self.get_assay()
if not assay:
return vocabs
for solution_type_name in assay.needed_solutions:
type_batches = find(Type=solution_type_name,
expires={'query': datetime.today().date(),
'range': 'min'},
sort_on='expires')
tmp = []
for batch in type_batches:
tmp.append([batch.id,
batch.Title,
batch.expires.strftime('%Y-%m-%d')])
vocabs.append([solution_type_name, tmp])
return vocabs
def store_aliquot(self, uid, usn, aliquot_type, target_box_type):
# get active box from workflow state, if one doesn't exist make it,
# check for aliquot space in box, if none make a new box
aliquot_type = aliquot_type # Bulk or Working
target_box_type = target_box_type # CommercialBox, RandDBox, QCBox
# find the active box of the type we need,
brains = find(portal_type=target_box_type, review_state='active')
if brains is not None:
for brain in brains:
cb = brain.getObject()
if cb.box_type == aliquot_type:
if cb.remaining_volume > 0:
box_to_use = cb.UID
entry_key = str(len(cb.aliquot.keys()) + 1)
entry_value = [usn, uid] # Aliquot ID, UID
# thing to add it to cb.aliquot_dic
else:
# change box workflow to full
try:
transition(cb, "filled")
except:
msg = "Could not transition %s, action='filled'" % \
cb.Title
raise ObjectInInvalidState(msg)
# see if rack has empty space, if not bail, and
# alert user make a new aliquot_type, and return
# this UID
rack = cb.aq_parent
new_box = api.content.create(
container=rack,
type=target_box_type,
title="",
box_type=aliquot_type,
max_samples=81,
remaining_volume=80,
aliquot_dic={u'1', [usn, uid]})
else:
print "No Active Box for Parameters sent"
def store_aliquot(self, uid, usn, aliquot_type, target_box_type):
# get active box from workflow state, if one doesn't exist make it,
# check for aliquot space in box, if none make a new box
aliquot_type = aliquot_type # Bulk or Working
target_box_type = target_box_type # CommercialBox, RandDBox, QCBox
# find the active box of the type we need,
brains = find(portal_type=target_box_type, review_state='active')
if brains is not None:
for brain in brains:
cb = brain.getObject()
if cb.box_type == aliquot_type:
if cb.remaining_volume > 0:
box_to_use = cb.UID
entry_key = str(len(cb.aliquot.keys()) + 1)
entry_value = [usn, uid] # Aliquot ID, UID
# thing to add it to cb.aliquot_dic
else:
# change box workflow to full
try:
transition(cb, "filled")
except:
msg = "Could not transition %s, action='filled'" % \
cb.Title
raise ObjectInInvalidState(msg)
# see if rack has empty space, if not bail, and
# alert user make a new aliquot_type, and return
# this UID
rack = cb.aq_parent
new_box = api.content.create(
container=rack,
type=target_box_type,
title="",
box_type=aliquot_type,
max_samples=81,
remaining_volume=80,
aliquot_dic={u'1', [usn, uid]})
else:
print "No Active Box for Parameters sent"
def run_objects(instance):
clinicalaliquots = []
qcaliquots = []
ichips = []
assayrequests = []
for plate in instance.plates:
for key, value in plate.items():
brains = find(UID=value)
if brains:
obj = brains[0].getObject()
_items = qcaliquots + clinicalaliquots + ichips + assayrequests
if not obj or obj in _items:
continue
if IiChip.providedBy(obj):
ichips.append(obj)
elif IQCAliquot.providedBy(obj):
qcaliquots.append(obj)
elif IClinicalAliquot.providedBy(obj):
clinicalaliquots.append(obj)
# get assayrequest
ar = get_assayrequest_from_aliquot(obj)
assayrequests.append(ar)
return assayrequests, clinicalaliquots, ichips, qcaliquots
def queryClinicalSamples(self, assay):
"""Get all the samples that are review_state='received', and which
contain an "AssayRequest" who's title matches the assay_name, and who
have a review_state of (re_run or to_be_tested).
"""
sample_data = []
for testable_state in ['re_run', 'to_be_tested']:
# this does get Clinical Samples keep reading jp
brains = find(portal_type="AssayRequest",
Title=assay.title,
review_state=testable_state)
tmp = []
for brain in brains:
assay_request = brain.getObject()
sample = assay_request.aq_parent
tmp.append({'uid': sample.UID(),
'draw_date': sample.collection_date,
'test_status': get_state(assay_request),
'sample': sample})
tmp = sorted(tmp, key=itemgetter('draw_date'))
sample_data.extend(tmp)
max_nr_samples = self.maxNumberOfSamplesToRun(assay)
return sample_data[:max_nr_samples]
def process_results_xlsx(self, path):
"""Take values from path/Out/Results/SLEkey_Results.xlsx, and write
them to the database
"""
run = self.get_run(path)
# Get the first sheet
filename = join(path, 'Out', 'Results', 'SLEkey_Results.xlsx')
wb = openpyxl.load_workbook(filename)
ws = wb.get_sheet_by_name('Sheet1')
# header rows for blocks containg QC and Clinical aliquot/sample info
qc_head_row = self.findnextSerial_Numberrow(ws, 1)
clin_head_row = self.findnextSerial_Numberrow(ws, qc_head_row + 1)
# get column letters of all qc headers that start with "ichip*"
qc_ichip_cols = []
passfail_col = None
for col in all_cols:
coord = "%s%s" % (col, qc_head_row)
val = "%s" % ws[coord].value
if val:
if val.lower().startswith("fina"):
passfail_col = coord
if val.lower().startswith("ichip"):
qc_ichip_cols.append(col)
ichip_passfail_combos = []
if passfail_col:
for row in range(qc_head_row + 1, clin_head_row):
passfail = "%s" % ws["%s%s" % (passfail_col, row)].value
ichip_titles = []
for col in qc_ichip_cols:
ichip_titles.append(ws["%s%s" % (col, row)].value)
ichip_passfail_combos.append([ichip_titles, passfail])
# for each plate
for plate in run.plates:
plate_ichips = []
plate_ichiplot_titles = []
# get all unique ichip lot numbers in a list
for key, uid in plate.items():
if key.startswith('ichip-id'):
ichip = find(UID=uid)[0].getObject()
plate_ichips.append(ichip)
ichiplot_title = ichip.title.upper().split('-')[0]
if ichiplot_title not in plate_ichiplot_titles:
plate_ichiplot_titles.append(ichiplot_title)
for combo in ichip_passfail_combos:
if sorted(plate_ichiplot_titles) == sorted(combo[0]):
for ichip in plate_ichips:
transition(ichip, 'qc_' + combo[1].lower())
# 'consume' qc aliquots.
for uid in plate.values():
brains = find(object_provides=IQCAliquot.__identifier__,
UID=uid, review_state='in_process')
if brains:
transition(brains[0].getObject(), 'done')
# find the column at which the following headers are located:
cols = {'Sample_ID': '',
'SLE_key_Score': '',
'SLE_key_Classification': '',
'Assay_QC_Status': ''}
if not all(cols):
msg = "One of the column headers can't be located:" % pformat(cols)
raise SpreadsheetParseError(msg)
for col in all_cols:
coord = "%s%s" % (col, clin_head_row)
value = ws[coord].value
if value in cols:
cols[value] = col
# get values from each row and colum into aliquot_results. results is:
# {sample_id: [SLE_key_Score,
# SLE_key_Classification,
# Assay_QC_Status],}
aliquot_results = {}
first_empty = self.get_first_empty_row(ws, clin_head_row)
for row in range(clin_head_row + 1, first_empty):
sample_id = ws["%s%s" % (cols['Sample_ID'], row)].value
score = ws["%s%s" % (cols['SLE_key_Score'], row)].value
classif = ws["%s%s" % (cols['SLE_key_Classification'], row)].value
status = ws["%s%s" % (cols['Assay_QC_Status'], row)].value
aliquot_results[sample_id] = {
'SLE_key_Score': score,
'SLE_key_Classification': "%s" % classif,
'Assay_QC_Status': "%s" % status
}
log = []
_used_uids = []
for plate in run.plates:
for uid in plate.values():
if uid in _used_uids:
continue
_used_uids.append(uid)
brains = find(UID=uid)
if not brains:
continue
aliquot = brains[0].getObject()
if not IAliquot.providedBy(aliquot):
continue
sample = self.get_sample_from_aliquot(aliquot)
if IClinicalSample.providedBy(sample):
if sample.title not in aliquot_results:
msg = "Sample '%s' not in spreadsheet results: %s" % \
(sample.title, pformat(aliquot_results))
raise RuntimeError(msg)
result = aliquot_results[sample.title]
ar = self.get_ar_from_sample(sample, run.assay_name)
state = result['Assay_QC_Status'].lower()
ar.aliquot_evaluated = aliquot.title
ar.date_resulted = self.get_date(ws)
# assayrequest is associated with multiple aliquots,
# so we only transition if the AR's state is expected.
if get_state(ar) == 'in_process':
transition(ar, 'qc_' + state)
aliquot.numeric_result = result['SLE_key_Score']
aliquot.text_result = result['SLE_key_Classification']
ts = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M")
log.append("%s: Sample: %s, Aliquot: %s, Results: %s, %s" % (
ts,
sample.title,
aliquot.title,
result['SLE_key_Score'],
result['SLE_key_Classification'],
))
return log
def is_lqc(self, sample):
assay = find(UID=self.context.assay_uid)[0].getObject()
lqc_id = assay.qc_low_choice
return sample.id.split('-')[0] == lqc_id
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 is_lqc(self, sample):
assay = find(UID=self.context.assay_uid)[0].getObject()
lqc_id = assay.qc_low_choice
return sample.id.split('-')[0] == lqc_id
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)
