def main(lims, pid, epp_logger):
process = Process(lims,id = pid)
target_files = dict((r.samples[0].name, r) for r in process.result_files())
file_handler = ReadResultFiles(process)
QiT = QuantitConc(process, file_handler)
QiT.fit_model()
QiT.prepare_result_files_dict()
if QiT.model and 'Linearity of standards' in QiT.udfs.keys():
R2 = QiT.model[0]
if R2 >= QiT.udfs['Linearity of standards']:
QiT.abstract.insert(0,"R2 = {0}. Standards OK.".format(R2))
if QiT.result_files:
for sample, target_file in target_files.items():
rel_fluor_int = QiT.get_and_set_fluor_int(target_file)
QiT.calc_and_set_conc(target_file, rel_fluor_int)
QiT.abstract.append("Concentrations uploaded for {0} "
"samples.".format(QiT.no_samps))
else:
QiT.abstract.append("Upload input file(s) for samples.")
else:
QiT.abstract.insert(0, "R2 = {0}. Problem with standards! Redo "
"measurement!".format(R2))
else:
QiT.missing_udfs.append('Linearity of standards')
if QiT.missing_samps:
QiT.abstract.append("The following samples are missing in Quant-iT "
"result File 1 or 2: {0}.".format(', '.join(QiT.missing_samps)))
if QiT.missing_udfs:
QiT.abstract.append("Are all of the following udfs set? : {0}".format(
', '.join(QiT.missing_udfs)))
print >> sys.stderr, ' '.join(QiT.abstract)
def main(lims, pid, epp_logger):
process = Process(lims, id=pid)
target_files = dict((r.samples[0].name, r) for r in process.result_files())
file_handler = ReadResultFiles(process)
QiT = QuantitConc(process, file_handler)
QiT.fit_model()
QiT.prepare_result_files_dict()
if QiT.model and 'Linearity of standards' in QiT.udfs.keys():
R2 = QiT.model[0]
if R2 >= QiT.udfs['Linearity of standards']:
QiT.abstract.insert(0, "R2 = {0}. Standards OK.".format(R2))
if QiT.result_files:
for sample, target_file in target_files.items():
rel_fluor_int = QiT.get_and_set_fluor_int(target_file)
QiT.calc_and_set_conc(target_file, rel_fluor_int)
QiT.abstract.append("Concentrations uploaded for {0} "
"samples.".format(QiT.no_samps))
else:
QiT.abstract.append("Upload input file(s) for samples.")
else:
QiT.abstract.insert(
0, "R2 = {0}. Problem with standards! Redo "
"measurement!".format(R2))
else:
QiT.missing_udfs.append('Linearity of standards')
if QiT.missing_samps:
QiT.abstract.append("The following samples are missing in Quant-iT "
"result File 1 or 2: {0}.".format(', '.join(
QiT.missing_samps)))
if QiT.missing_udfs:
QiT.abstract.append("Are all of the following udfs set? : {0}".format(
', '.join(QiT.missing_udfs)))
print >> sys.stderr, ' '.join(QiT.abstract)
def main(lims, pid, epp_logger):
process = Process(lims,id = pid)
QiT = QuantitQC(process)
QiT.assign_QC_flag()
if QiT.flour_int_missing:
QiT.abstract.append("Fluorescence intensity is missing for {0} "
"samples.".format(QiT.flour_int_missing))
if QiT.missing_udfs:
QiT.abstract.append("Could not set QC flags. Some of the following "
"required udfs seems to be missing: {0}.".format(QiT.missing_udfs))
else:
QiT.abstract.append("{0} out of {1} samples failed "
"QC.".format(QiT.no_failed, len(process.result_files())))
if QiT.saturated:
QiT.abstract.append("{0} samples had saturated fluorescence "
"intensity.".format(QiT.saturated))
if QiT.hig_CV_fract:
QiT.abstract.append("{0} samples had high %CV.".format(QiT.hig_CV_fract))
if QiT.low_conc:
QiT.abstract.append("{0} samples had low concentration.".format(
QiT.low_conc))
if QiT.conc_missing:
QiT.abstract.append("Concentration is missing for {0} "
"sample(s).".format(QiT.conc_missing))
QiT.abstract = list(set(QiT.abstract))
print >> sys.stderr, ' '.join(QiT.abstract)
def main(lims, pid, epp_logger):
process = Process(lims, id=pid)
QiT = QuantitQC(process)
QiT.assign_QC_flag()
if QiT.flour_int_missing:
QiT.abstract.append("Fluorescence intensity is missing for {0} "
"samples.".format(QiT.flour_int_missing))
if QiT.missing_udfs:
QiT.abstract.append("Could not set QC flags. Some of the following "
"required udfs seems to be missing: {0}.".format(
QiT.missing_udfs))
else:
QiT.abstract.append("{0} out of {1} samples failed "
"QC.".format(QiT.no_failed,
len(process.result_files())))
if QiT.saturated:
QiT.abstract.append("{0} samples had saturated fluorescence "
"intensity.".format(QiT.saturated))
if QiT.hig_CV_fract:
QiT.abstract.append("{0} samples had high %CV.".format(
QiT.hig_CV_fract))
if QiT.low_conc:
QiT.abstract.append("{0} samples had low concentration.".format(
QiT.low_conc))
if QiT.conc_missing:
QiT.abstract.append("Concentration is missing for {0} "
"sample(s).".format(QiT.conc_missing))
QiT.abstract = list(set(QiT.abstract))
print >> sys.stderr, ' '.join(QiT.abstract)
def main(lims, pid, epp_logger):
process = Process(lims,id = pid)
sample_names = map(lambda a: a.name, process.analytes()[0])
target_files = process.result_files()
file_handler = ReadResultFiles(process)
files = file_handler.shared_files['Qubit Result File']
qubit_result_file = file_handler.format_file(files,
name = 'Qubit Result File',
first_header = 'Sample',
find_keys = sample_names)
missing_samples = 0
low_conc = 0
bad_formated = 0
abstract = []
udfs = dict(process.udf.items())
if udfs.has_key("Minimum required concentration (ng/ul)"):
min_conc = udfs["Minimum required concentration (ng/ul)"]
else:
min_conc = None
abstract.append("Set 'Minimum required concentration (ng/ul)' to get qc-flaggs based on this treshold!")
for target_file in target_files:
sample = target_file.samples[0].name
if qubit_result_file.has_key(sample):
sample_mesurements = qubit_result_file[sample]
if "Sample Concentration" in sample_mesurements.keys():
conc, unit = sample_mesurements["Sample Concentration"]
if conc == 'Out Of Range':
target_file.qc_flag = "FAILED"
elif conc.replace('.','').isdigit():
conc = float(conc)
if unit == 'ng/mL':
conc = np.true_divide(conc, 1000)
if min_conc:
if conc < min_conc:
target_file.qc_flag = "FAILED"
low_conc +=1
else:
target_file.qc_flag = "PASSED"
target_file.udf['Concentration'] = conc
target_file.udf['Conc. Units'] = 'ng/ul'
else:
bad_formated += 1
set_field(target_file)
else:
missing_samples += 1
if low_conc:
abstract.append('{0}/{1} samples have low concentration.'.format(low_conc, len(target_files)))
if missing_samples:
abstract.append('{0}/{1} samples are missing in Qubit Result File.'.format(missing_samples, len(target_files)))
if bad_formated:
abstract.append('There are {0} badly formated samples in Qubit Result File. Please fix these to get proper results.'.format(bad_formated))
print >> sys.stderr, ' '.join(abstract)
def old_main(lims, pid, epp_logger):
process = Process(lims,id = pid)
sample_names = map(lambda a: a.name, process.analytes()[0])
target_files = process.result_files()
file_handler = ReadResultFiles(process)
files = file_handler.shared_files['Qubit Result File']
qubit_result_file = file_handler.format_file(files,
name = 'Qubit Result File',
first_header = ['Test','Sample'],
find_keys = sample_names)
missing_samples = 0
low_conc = 0
bad_formated = 0
abstract = []
udfs = dict(process.udf.items())
if udfs.has_key("Minimum required concentration (ng/ul)"):
min_conc = udfs["Minimum required concentration (ng/ul)"]
else:
min_conc = None
abstract.append("Set 'Minimum required concentration (ng/ul)' to get qc-flaggs based on this treshold!")
for target_file in target_files:
sample = target_file.samples[0].name
if qubit_result_file.has_key(sample):
sample_mesurements = qubit_result_file[sample]
if "Sample Concentration" in sample_mesurements.keys():
conc, unit = sample_mesurements["Sample Concentration"]
if conc == 'Out Of Range':
target_file.qc_flag = "FAILED"
elif conc.replace('.','').isdigit():
conc = float(conc)
if unit == 'ng/mL':
conc = np.true_divide(conc, 1000)
if min_conc:
if conc < min_conc:
target_file.qc_flag = "FAILED"
low_conc +=1
else:
target_file.qc_flag = "PASSED"
target_file.udf['Concentration'] = conc
target_file.udf['Conc. Units'] = 'ng/ul'
else:
bad_formated += 1
set_field(target_file)
else:
missing_samples += 1
if low_conc:
abstract.append('{0}/{1} samples have low concentration.'.format(low_conc, len(target_files)))
if missing_samples:
abstract.append('{0}/{1} samples are missing in Qubit Result File.'.format(missing_samples, len(target_files)))
if bad_formated:
abstract.append('There are {0} badly formated samples in Qubit Result File. Please fix these to get proper results.'.format(bad_formated))
print >> sys.stderr, ' '.join(abstract)
def set_qc_flag(lims, process_id, cutoff=10):
"""Set qubit qc flags based on Dx Concentratie fluorescentie (ng/ul) values."""
process = Process(lims, id=process_id)
artifacts = process.result_files()
concentration_range = map(
float, re.findall('[\d\.]+',
process.udf['Concentratiebereik (ng/ul)']))
samples_measurements = {}
for artifact in artifacts:
sample = artifact.name.rstrip('Qubit').rstrip()
measurement = artifact.udf['Dx Conc. goedgekeurde meting (ng/ul)']
if sample in samples_measurements:
samples_measurements[sample].append(measurement)
else:
samples_measurements[sample] = [measurement]
for artifact in artifacts:
sample = artifact.name.rstrip('Qubit').rstrip()
sample_measurements = samples_measurements[sample]
sample_measurements_average = sum(sample_measurements) / float(
len(sample_measurements))
artifact.udf[
'Dx Concentratie fluorescentie (ng/ul)'] = sample_measurements_average
if concentration_range[
0] <= sample_measurements_average <= concentration_range[1]:
if len(sample_measurements) == 1:
artifact.qc_flag = 'PASSED'
elif len(sample_measurements) == 2:
sample_measurements_difference = abs(sample_measurements[0] -
sample_measurements[1])
sample_measurements_deviation = sample_measurements_difference / sample_measurements_average
if sample_measurements_deviation <= 0.1:
artifact.qc_flag = 'PASSED'
else:
artifact.qc_flag = 'FAILED'
else:
artifact.qc_flag = 'FAILED'
artifact.put()
def results(lims, process_id):
"""Upload magnis export to process."""
process = Process(lims, id=process_id)
lot_error = False
for output_file in process.result_files():
if output_file.name == 'Magnis export file':
magnis_xml_file = output_file.files[0]
magnis_data = xmltodict.parse(lims.get_file_contents(magnis_xml_file.id))
# Save lot nunmbers and check sample input strip barcode
for labware in magnis_data['RunInfo']['LabwareInfos']['Labware']:
if labware['@Name'] == 'Probe Input Strip':
process.udf['lot # SureSelect v7'] = labware['@LotNumber']
elif labware['@Name'] == 'Reagent Plate':
process.udf['lot # Magnis Sureselect XT HS reagent plate'] = labware['@LotNumber']
elif labware['@Name'] == 'Beads/Buffers Plate':
process.udf['lot # Magnis SureSelect XT Beads/Buffers Plate'] = labware['@LotNumber']
elif labware['@Name'] == 'Index Strip':
process.udf['lot # Dual BC strip'] = labware['@LotNumber']
index_strip_number = int(labware['@IndexStrip'])
elif labware['@Name'] == 'Reagent Strip':
process.udf['lot # BR Oligo strip (blockers)'] = labware['@LotNumber']
elif (
labware['@Name'] == 'Sample Input Strip' and
process.udf['Barcode sample input strip'] != labware['@BarCode']
):
lot_error = True
# Check sample reagents and fill Lotnr check flag
for output in process.analytes()[0]:
label_index_number = int(output.reagent_labels[0][3:5])
if lot_error or label_index_number != index_strip_number:
output.udf['Lotnr check'] = False
else:
output.udf['Lotnr check'] = True
output.put()
process.put()
