def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._columns = [] # The different columns names
self._linedata = {} # The line with the data
self._resid = ''
self._method = ''
self._date = ''
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._columns = [] # The different columns names
self._linedata = {} # The line with the data
self._resid = ''
self._method = ''
self._date = ''
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._columns = []
self._period = [
False, ''
] # Variable to control results from period beginning and end.
def __init__(self, rsf):
InstrumentCSVResultsFileParser.__init__(self, rsf)
self._columns = [] # The different columns names
self._values = {} # The analysis services from the same resid
self._resid = '' # A stored resid
self._rownum = None
self._end_header = False
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._columns = [] # The different columns names
self._end_header = False
# This list contains all the rows without interesting data
self.extrainfolist = ['Number', 'Average', 'Maximum', 'Minimum', 'Range', 'Std dev.',
'RSD(%)']
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._columns = [] # The different columns names
self._end_header = False
# This list contains all the rows without interesting data
self.extrainfolist = ['Number', 'Average', 'Maximum', 'Minimum', 'Range', 'Std dev.',
'RSD(%)']
def __init__(self, csv, analysiskey):
InstrumentCSVResultsFileParser.__init__(self, csv)
self.data_header = None
self.file_header = {}
# Set this flag when we find the header-line beginning with "Date,".
# Once this flag is set, all following lines are real data.
self.main_data_found = False
self.analysiskey = analysiskey
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._end_sequencetable = False
self._sequences = []
self._sequencesheader = []
self._quantitationresultsheader = []
self._numline = 0
def __init__(self, infile):
InstrumentCSVResultsFileParser.__init__(self, infile,
encoding='utf-8-sig')
self._separator = '\t' # values are separated by tabs
self._is_header = False
self._current_section = '' # current section of the file
self._columns = None # Column names of Analyte Result table
self._ar_keyword = None # Keyword of Analysis Service
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._end_sequencetable = False
self._sequences = []
self._sequencesheader = []
self._quantitationresultsheader = []
self._numline = 0
def __init__(self, infile):
InstrumentCSVResultsFileParser.__init__(self,
infile,
encoding='utf-8-sig')
self._separator = '\t' # values are separated by tabs
self._is_header = False
self._current_section = '' # current section of the file
self._columns = None # Column names of Analyte Result table
self._ar_keyword = None # Keyword of Analysis Service
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._columns = [] # The different columns names
self._values = {} # The analysis services from the same resid
self._rownum = None
self._end_header = False
# self._includedcolumns =['Ca', 'Cu',
# 'Fe', 'Mg']
self._includedcolumns = ['CD4_PERC', 'CD4', 'CD8_PERC', 'CD8']
def __init__(self, rsf, fileformat=None):
InstrumentCSVResultsFileParser.__init__(self, rsf)
self._columns = [] # The different columns names
self._values = {} # The analysis services from the same resid
self._resid = '' # A stored resid
self._rownum = None
self._end_header = False
self._fileformat = fileformat
self._separator = ',' if self._fileformat == 'csv' else '\t'
def __init__(self, infile):
InstrumentCSVResultsFileParser.__init__(self, infile,
encoding='utf-16-le')
self._cur_section = '' # Current section of CSV
self._cur_sub_section = '' # Current subsection of CSV
self._cur_res_id = '' # Sample or Patient ID of the current record
self._cur_values = {} # Values of the last record
self._is_header_line = False # To get headers of Analyte Result table
self._columns = [] # Column names of Analyte Result table
self._keyword = '' # Keyword of Analysis Service
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._end_sampleinformationtable = False
self._sampleinformationresults = []
self._sampleinformation = []
self._quantitationresultsheader = []
self._sampleinformationheader = []
self._numline = 0
def __init__(self, infile):
InstrumentCSVResultsFileParser.__init__(self, infile,
encoding='utf-16-le')
self._cur_section = '' # Current section of CSV
self._cur_sub_section = '' # Current subsection of CSV
self._cur_res_id = '' # Sample or Patient ID of the current record
self._cur_values = {} # Values of the last record
self._is_header_line = False # To get headers of Analyte Result table
self._columns = [] # Column names of Analyte Result table
self._keyword = '' # Keyword of Analysis Service
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._end_sampleinformationtable = False
self._sampleinformationresults = []
self._sampleinformation = []
self._quantitationresultsheader = []
self._sampleinformationheader = []
self._numline = 0
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._resid = '' # The Analysis Request ID
self._sampleIDs = {} # A dict with the samples ID for ech row
# self._sampleIDs example:
# {'A': ['CP', '', '', '', '', '', '', '', '', '', '', ''],
# 'B': ['CP', '', '', '', '', '', '', '', '', '', '', ''],
# 'C': ['CN', '', '', '', '', '', '', '', '', '', '', '']}
self._samplesID_section = False # Indicates if we are parsing the samples ID section
self._simple_results_section = False # indicates if we are parsing the no computed results section
self._simple_results = {} # This dictionary has the structure
# self._simple_results example:
# {'CN': {'leiatura1': '0.9638', 'leiatura2': '0.9785'},
# 'CP': {'leiatura1': '0.3407', 'leiatura2': '0.3456'}}
self._is_data_header = False # Indicates if we are parsing the final results header
self._data_header = [] # This list contains the values of the final/computed data header
self._data_section = False # Indicates if we are parsing the computed results section
def __init__(self, csv, analysiskey=None, defaultresult=None):
# analysiskey contains the value of the selected AS or None
# defaultresult contains the data column key which will be tagged as DefaultResult in the AS results dictionary.
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._columns = []
# When AS isn't selected we need to know which columns don't contain data. Since we don't know in
# which order this columns could be, we need to write an ugly list with the possible columns names to exclude.
self._excludedcolumns = ['Instrument ID', 'Analysis Date', 'Analysis Time', 'Rack No.', 'Tube Pos.',
'Sample ID No', 'Sample ID Info', 'Analysis Mode', 'Patient ID', 'Analysis Info.',
'Sample Judgment Info.', 'Positive(Diff)', 'Positive(Morph)', 'Positive(Count)',
'Error(Func)', 'Error(Result)', 'Order Info.', 'WBC Abnormal', 'WBC Suspect',
'RBC Abnormal', 'RBC Suspect', 'PLT Abnormal', 'PLT Suspect', 'Unit Info.',
'Validate', 'Action Message(Diff)', 'Action Message(Delta)', 'Sample Comment',
'Patient Name', 'Date of Birth', 'Sex', 'Patient comment', 'Ward', 'Doctor',
'Transmitted Parameters', 'Sequence No.']
self.analysiskey = analysiskey
self.defaultresult = defaultresult
def __init__(self, csv, analysiskey=None, defaultresult=None):
# analysiskey contains the value of the selected AS or None
# defaultresult contains the data column key which will be tagged as DefaultResult in the AS results dictionary.
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._columns = []
# When AS isn't selected we need to know which columns don't contain data. Since we don't know in
# which order this columns could be, we need to write an ugly list with the possible columns names to exclude.
self._excludedcolumns = [
'Instrument ID', 'Analysis Date', 'Analysis Time', 'Rack No.',
'Tube Pos.', 'Sample ID No', 'Sample ID Info', 'Analysis Mode',
'Patient ID', 'Analysis Info.', 'Sample Judgment Info.',
'Positive(Diff)', 'Positive(Morph)', 'Positive(Count)',
'Error(Func)', 'Error(Result)', 'Order Info.', 'WBC Abnormal',
'WBC Suspect', 'RBC Abnormal', 'RBC Suspect', 'PLT Abnormal',
'PLT Suspect', 'Unit Info.', 'Validate', 'Action Message(Diff)',
'Action Message(Delta)', 'Sample Comment', 'Patient Name',
'Date of Birth', 'Sex', 'Patient comment', 'Ward', 'Doctor',
'Transmitted Parameters', 'Sequence No.'
]
self.analysiskey = analysiskey
self.defaultresult = defaultresult
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._keywords = []
self._quantitationresultsheader = []
self._numline = 0
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._column_header = []
self._end_header = False
self._column_header_stripped = None
self.allowed_quan_types = ['ExtCal.Average', 'IntCal.Average']
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self.currentheader = None
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self.currentheader = None
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._columns = []
def __init__(self, tsv, analysis1, analysis2):
InstrumentCSVResultsFileParser.__init__(self, tsv)
self._analysis1 = analysis1
self._analysis2 = analysis2
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._columns = []
self.columns_name = False #To know if the next line contains
def __init__(self, csv, analysiskey):
InstrumentCSVResultsFileParser.__init__(self, csv)
self.analysiskey = analysiskey
self.header = None
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._currentresultsheader = []
self._currentanalysiskw = ''
self._numline = 0
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
def __init__(self , csv): InstrumentCSVResultsFileParser.__init__(self,csv) self.columns = [] self.resid='' #to be passes in addRawResult() self.is_head = True
def __init__(self, tsv, analysis1, analysis2):
InstrumentCSVResultsFileParser.__init__(self, tsv)
self._analysis1 = analysis1
self._analysis2 = analysis2
def __init__(self, csv, analysiskey):
InstrumentCSVResultsFileParser.__init__(self, csv)
self.analysiskey = analysiskey
self.header = None
def __init__(self, slk):
InstrumentCSVResultsFileParser.__init__(self, slk)
self._columns = {} #The diferents data columns names
self._linedata = {}#The line with the data
self._rownum = None
self._isFirst = True #Used to know if is the first linedata
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._resultsheader = []
self._numline = 0
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._column_header = []
self._end_header = False
self._column_header_stripped = None
self.allowed_quan_types = ['ExtCal.Average', 'IntCal.Average']
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
def __init__(self, csv, analysiskey):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._labels = False # If true, we are in a line where are the sample names
self._data = False # If true, we are in a line where are the analysis results
self._labels_values = {} # The labels' values
self.analysiskey = analysiskey # The analysis key whose results will be related
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._columns = []
self._period = [False,''] # Variable to control results from period beginning and end.
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._currentresultsheader = []
self._currentanalysiskw = ''
self._numline = 0
def __init__(self, csv, analysiskey):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._labels = False # If true, we are in a line where are the sample names
self._data = False # If true, we are in a line where are the analysis results
self._labels_values = {} # The labels' values
self.analysiskey = analysiskey # The analysis key whose results will be related
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._columns = []
self.columns_name = False #To know if the next line contains
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._columns = [] # The different columns names
self._linedata = {} # The line with the data
self._rownum = None
self._end_header = False
def __init__(self, tsv):
InstrumentCSVResultsFileParser.__init__(self, tsv)
self._end_header = False
self._columns = []
def __init__(self, infile, encoding=None):
InstrumentCSVResultsFileParser.__init__(self, infile)
self._end_header = False
self._delimiter = ','
def __init__(self, slk):
InstrumentCSVResultsFileParser.__init__(self, slk)
self._columns = {} #The diferents data columns names
self._linedata = {} #The line with the data
self._rownum = None
self._isFirst = True #Used to know if is the first linedata
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._end_header = False
self._keywords = []
self._quantitationresultsheader = []
self._numline = 0
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._columns = [] # The different columns names
self._linedata = {} # The line with the data
self._end_header = False
def __init__(self, csv):
InstrumentCSVResultsFileParser.__init__(self, csv)
self._columns = []
