def parse_resultsline(self, line):
""" Parses result lines
"""
splitted = [token.strip() for token in line.split(self._delimiter)]
if len(filter(lambda x: len(x), splitted)) == 0:
return 0
# AR id
if splitted[0] == 'Laboratory number':
self._ar_id = splitted[2]
return 0
if splitted[0] == 'Molecule':
self._kw = format_keyword(splitted[2])
return 0
if splitted[0] == 'Retention time in the molecule':
if self._retentiontime:
self._retentiontimeref = splitted[1]
else:
self._retentiontime = splitted[1]
return 0
if splitted[0].startswith('ion'):
ion_number = splitted[0].split(' ')[1]
mz_values = splitted[1].split('---')
self._ions.append({
'Ion{}mzmax'.format(ion_number): mz_values[0],
'Ion{}mzmin'.format(ion_number): mz_values[1],
'Ion{}Area'.format(ion_number): splitted[2],
'Ion{}AreaRef'.format(ion_number): splitted[3],
'Ion{}SigNseRat'.format(ion_number): splitted[4],
})
if splitted[0] == 'PARAMETERS TO BE CONSIDERED FOR THE CALCULATION':
# No result field
record = {
'DefaultResult': None,
'Remarks': '',
'DateTime': str(DateTime())[:16]
}
# Interim values
column_name = 'RetentionTime'
record[column_name] = self.get_result(column_name,
self._retentiontime, 0)
column_name = 'RetentionTimeRef'
record[column_name] = self.get_result(column_name,
self._retentiontimeref, 0)
for ion in self._ions:
for interim_key in ion.keys():
record[interim_key] = self.get_result(
interim_key, ion[interim_key], 0)
# Append record
self._addRawResult(self._ar_id, {self._kw: record})
return 0
def parse(self):
""" parse the data
"""
tree = ET.parse(self.getInputFile())
root = tree.getroot()
# Building Assay dictionary to query names by id from test results line
for as_ref in root.find("Assays").findall("AssayRef"):
self._assays[as_ref.get("KEY_AssayRef")] = as_ref.get("ID")
# Building Instruments dictionary to get Serial number by id
for ins in root.find("Instruments").findall("Instrument"):
self._instruments[ins.get("KEY_InstrumentData")] = \
ins.get("SerialNumber")
for t_req in root.iter("TestRequest"):
t_res = t_req.find("TestResult")
if len(t_res) == 0 or not t_res.get("Valid", "false") == "true":
continue
res_id = t_req.get("SampleID")
test_name = self._assays.get(t_req.get("KEY_AssayRef"))
test_name = format_keyword(test_name)
result = t_res.get("Value")
if not result:
continue
result = result.split(" cps/ml")[0]
detected = t_res.get("Detected")
# SOME ADDITIONAL DATA
# Getting instrument serial number from 'Run' element which is
# parent of 'TestRequest' elements
ins_serial = t_req.getParent().get("KEY_InstrumentData")
# Matrix is important for calculation.
matrix = t_req.get("Matrix")
# For now, using EasyQDirector as keyword, but this is not the
# right way. test_name must be used.
values = {
'EasyQDirector': {
"DefaultResult": "Result",
"Result": result,
"Detected": detected,
"Matrix": matrix,
"Instrument": ins_serial
}
}
self._addRawResult(res_id, values)
def parse_headerline(self, line):
""" Parses header lines
Keywords example:
Keyword1, Keyword2, Keyword3, ..., end
"""
if self._end_header:
# Header already processed
return 0
splitted = [token.strip() for token in line.split(self._delimiter)]
if splitted[0].startswith('Sample'):
self._kw = splitted[7].split(' ')[0]
self._kw = format_keyword(self._kw)
self._end_header = True
return 0
def parse_resultsline(self, line):
""" Parses result lines
"""
splitted = [token.strip() for token in line.split(self._delimiter)]
if len(filter(lambda x: len(x), splitted)) == 0:
return 0
# Header
if splitted[0] == 'Comp #':
self._header = splitted
return 0
# No default
record = {
'DefaultResult': None,
'Remarks': ''
}
# 4 Interim fields
value_column = 'Amount'
result = splitted[4]
result = self.get_result(value_column, result, 0)
record[value_column] = result
value_column = 'ReturnTime'
result = splitted[2]
result = self.get_result(value_column, result, 0)
record[value_column] = result
value_column = 'Area'
result = splitted[3]
result = self.get_result(value_column, result, 0)
record[value_column] = result
value_column = 'QVal'
result = splitted[6]
result = self.get_result(value_column, result, 0)
record[value_column] = result
# assign record to kw dict
kw = splitted[1]
kw = format_keyword(kw)
self._addRawResult(self._ar_id, {kw: record})
return 0
def parse_resultsline(self, line):
""" Parses result lines
"""
splitted = [token.strip() for token in line.split(self._delimiter)]
if len(filter(lambda x: len(x), splitted)) == 0:
return 0
# Header
if splitted[0].startswith('Score'):
self._header = splitted
return 0
ar_id = splitted[104]
kw = format_keyword(splitted[18])
analysis_date = str(DateTime())[:16]
# Result field
record = {
'DefaultResult': None,
'Remarks': '',
'DateTime': analysis_date
}
# Interim values can get added to record here
interims = [
('Label', 22),
('Area', 48),
('File', 54),
('End', 55),
('mz', 67),
('mzProd', 68),
('ReturnTime', 69),
('Start', 71),
('Width', 72),
('AcqMethod', 110),
]
for column_name, column_number in interims:
result = splitted[column_number]
record[column_name] = self.get_result(column_name, result, 0)
# Append record
self._addRawResult(ar_id, {kw: record})
return 0