build.bika.lims.exportimport.instruments.agilent.masshunter.masshunter.AgilentMasshunterParser.parse_headerline() - Code Metrics - Inspection of "fixing cobas integra instrument import interface (..." - senaite/senaite.core - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — master ( d8e2ec...90ae0b )

by Jordi

created 2019-03-11 15:48 UTC

AgilentMasshunterParser.parse_headerline() F

↳ Parent: build.bika.lims.exportimport.instruments.agilent.masshunter.masshunter

Complexity

Conditions

Size

Total Lines	191
Code Lines	122

Duplication

Lines	11
Ratio	5.76 %

Importance

Changes

Metric	Value
eloc	122
dl	11
loc	191
rs	0
c	0
b	0
f	0
cc	40
nop	2

How to fix Long Method Complexity

Long Method

Small methods make your code easier to understand, in particular if combined with a good name. Besides, if your method is small, finding a good name is usually much easier.

For example, if you find yourself adding comments to a method's body, this is usually a good sign to extract the commented part to a new method, and use the comment as a starting point when coming up with a good name for this new method.

Commonly applied refactorings include:

If many parameters/temporary variables are present:
- Replace temporary variables with Query
- Introduce parameter object; often combined with preserve whole object
- If the above two are insufficient: Replace method with method object
If you have long conditionals: Decompose Conditional
Otherwise: Extract method

Complexity

Complex classes like build.bika.lims.exportimport.instruments.agilent.masshunter.masshunter.AgilentMasshunterParser.parse_headerline() often do a lot of different things. To break such a class down, we need to identify a cohesive component within that class. A common approach to find such a component is to look for fields/methods that share the same prefixes, or suffixes.

Once you have determined the fields that belong together, you can apply the Extract Class refactoring. If the component makes sense as a sub-class, Extract Subclass is also a candidate, and is often faster.

# -*- coding: utf-8 -*-
#
# This file is part of SENAITE.CORE
#
# Copyright 2018 by it's authors.
# Some rights reserved. See LICENSE.rst, CONTRIBUTORS.rst.

""" Agilent's 'Masshunter'
"""
from bika.lims import bikaMessageFactory as _
from datetime import datetime
import json
import re
from bika.lims.exportimport.instruments.resultsimport import \
    InstrumentCSVResultsFileParser, AnalysisResultsImporter
import traceback

title = "Agilent - Masshunter"


def Import(context, request):

    """ Read Agilent Masshunter analysis results
    """
    form = request.form
    # TODO form['file'] sometimes returns a list
    infile = form['instrument_results_file'][0] if isinstance(
            form['instrument_results_file'], list) else \
        form['instrument_results_file']
    artoapply = form['artoapply']
    override = form['results_override']

    instrument = form.get('instrument', None)
    errors = []
    logs = []

    # Load the most suitable parser according to file extension/options/etc...
    parser = None
    if not hasattr(infile, 'filename'):
        errors.append(_("No file selected"))
    parser = AgilentMasshunterParser(infile)

    if parser:
        # Load the importer
        status = ['sample_received', 'attachment_due', 'to_be_verified']
        if artoapply == 'received':
            status = ['sample_received']
        elif artoapply == 'received_tobeverified':
            status = ['sample_received', 'attachment_due', 'to_be_verified']

        over = [False, False]
        if override == 'nooverride':
            over = [False, False]
        elif override == 'override':
            over = [True, False]
        elif override == 'overrideempty':
            over = [True, True]

        importer = AgilentMasshunterImporter(parser=parser,
                                             context=context,
                                             allowed_ar_states=status,
                                             allowed_analysis_states=None,
                                             override=over,
                                             instrument_uid=instrument)
        tbex = ''
        try:
            importer.process()
        except:
            tbex = traceback.format_exc()
        errors = importer.errors
        logs = importer.logs
        warns = importer.warns
        if tbex:
            errors.append(tbex)

    results = {'errors': errors, 'log': logs, 'warns': warns}


    return json.dumps(results)


class AgilentMasshunterParser(InstrumentCSVResultsFileParser):

    HEADERKEY_ANALYSISTIME = 'Analysis Time'
    HEADERKEY_ANALYSTNAME = 'Analyst Name'
    HEADERKEY_BATCHDATAPATH = 'Batch Data Path'
    HEADERKEY_BATCHNAME = 'Batch Name'
    HEADERKEY_BATCHSTATE = 'Batch State'
    HEADERKEY_LASTCALIBRATION = 'Calibration Last Updated Time'
    HEADERKEY_REPORTGENERATIONTIME = 'Report Generation Time'
    HEADERKEY_REPORTGENERATORNAME = 'Report Generator Name'
    HEADERKEY_REPORTRESULTSDATAPATH = 'Report Results Data Path'
    HEADERKEY_SCHEMAVERSION = 'SchemaVersion'
    HEADERKEY_QUANTBATCHVERSION = 'Quant Batch Version'
    HEADERKEY_QUANTREPORTVERSION = 'Quant Report Version'

    QUANTITATIONRESULTS_NUMERICHEADERS = ('CalculatedConcentration',
                                          'FinalConcentration',
                                          'FinalConcentration')
    COMMAS = ','

    def __init__(self, csv):
        InstrumentCSVResultsFileParser.__init__(self, csv)
        self._end_header = False
        self._quantitationresultsheader = []
        self._numline = 0

    def _parseline(self, line):
        if self._end_header is False:
            return self.parse_headerline(line)
        else:
            return self.parse_quantitationesultsline(line)

    def parse_headerline(self, line):
        """ Parses header lines

            Analysis Time	7/13/2017 9:55
            Analyst Name	MassHunter01\Agilent
            Batch Data Path	D:\MassHunter\GCMS\Terpenes\2017\July\20170711\
                    QuantResults\20170711 Sample Workup
            Batch Name	20170711 Sample Workup
            Batch State	Processed
            Calibration Last Updated Time	6/29/2017 15:57
            Report Generation Time	1/1/0001 12:00:00 AM
            Report Generator Name	None
            Report Results Data Path	None
            SchemaVersion	65586
            Quant Batch Version	B.08.00
            Quant Report Version	B.08.00
        """
        if self._end_header is True:
            # Header already processed
            return 0

        splitted = [token.strip() for token in line.split(self.COMMAS)]

        # Analysis Time	7/13/2017 9:55
        if splitted[0] == self.HEADERKEY_ANALYSISTIME:
            if splitted[1]:

                try:
                    d = datetime.strptime(splitted[1], "%m/%d/%Y %H:%M")
                    self._header[self.HEADERKEY_ANALYSISTIME] = d
                except ValueError:
                    self.err("Invalid Output Time format",
                             numline=self._numline, line=line)
            else:
                self.warn("Output Time not found or empty",
                          numline=self._numline, line=line)
                d = datetime.strptime(splitted[1], "%I:%M %p")

        # Analyst Name	MassHunter01\Agilent
        elif splitted[0] == self.HEADERKEY_ANALYSTNAME:
            if self.HEADERKEY_ANALYSTNAME in self._header:
                self.warn("Header File Data Name already found. Discarding",
                          numline=self._numline, line=line)
                return 0

            if splitted[1]:
                self._header[self.HEADERKEY_ANALYSTNAME] = splitted[1]
            else:
                self.warn("File Data Name not found or empty",
                          numline=self._numline, line=line)

        # Batch Data Path
        # D:\MassHunter\GCMS\Terpenes\2017\July\20170711\QuantResults\20170711
        elif splitted[0] == self.HEADERKEY_BATCHDATAPATH:
            if self.HEADERKEY_BATCHDATAPATH in self._header:
                self.warn("Header File Data Name already found. Discarding",
                          numline=self._numline, line=line)
                return 0

            if splitted[1]:
                self._header[self.HEADERKEY_BATCHDATAPATH] = splitted[1]
            else:
                self.warn("File Data Name not found or empty",
                          numline=self._numline, line=line)

        # Batch Name	20170711 Sample Workup
        elif splitted[0] == self.HEADERKEY_BATCHNAME:
            if self.HEADERKEY_BATCHNAME in self._header:
                self.warn("Header File Data Name already found. Discarding",
                          numline=self._numline, line=line)
                return 0

            if splitted[1]:
                self._header[self.HEADERKEY_BATCHNAME] = splitted[1]
            else:
                self.warn("File Data Name not found or empty",
                          numline=self._numline, line=line)

        # Batch State	Processed
        elif splitted[0] == self.HEADERKEY_BATCHSTATE:
            if self.HEADERKEY_BATCHSTATE in self._header:
                self.warn("Header File Data Name already found. Discarding",
                          numline=self._numline, line=line)
                return 0

            if splitted[1]:
                self._header[self.HEADERKEY_BATCHNAME] = splitted[1]
            else:
                self.warn("File Data Name not found or empty",
                          numline=self._numline, line=line)

        # Calibration Last Updated Time	6/29/2017 15:57
        elif splitted[0] == self.HEADERKEY_LASTCALIBRATION:
            if self.HEADERKEY_LASTCALIBRATION in self._header:
                self.warn("Header File Data Name already found. Discarding",
                          numline=self._numline, line=line)
                return 0

            if splitted[1]:
                self._header[self.HEADERKEY_LASTCALIBRATION] = splitted[1]
            else:
                self.warn("File Data Name not found or empty",
                          numline=self._numline, line=line)

        # Report Generation Time	1/1/0001 12:00:00 AM
        elif splitted[0] == self.HEADERKEY_REPORTGENERATIONTIME:
            if self.HEADERKEY_REPORTGENERATIONTIME in self._header:
                self.warn("Header File Data Name already found. Discarding",
                          numline=self._numline, line=line)
                return 0

            if splitted[1]:
                self._header[self.HEADERKEY_REPORTGENERATIONTIME] = splitted[1]
            else:
                self.warn("File Data Name not found or empty",
                          numline=self._numline, line=line)

        # Report Generator Name	None
        elif splitted[0] == self.HEADERKEY_REPORTGENERATORNAME:
            if self.HEADERKEY_REPORTGENERATORNAME in self._header:
                self.warn("Header File Data Name already found. Discarding",
                          numline=self._numline, line=line)
                return 0

            if splitted[1]:
                self._header[self.HEADERKEY_REPORTGENERATORNAME] = splitted[1]
            else:
                self.warn("File Data Name not found or empty",
                          numline=self._numline, line=line)

        # Report Results Data Path	None
        elif splitted[0] == self.HEADERKEY_REPORTRESULTSDATAPATH:
            if self.HEADERKEY_REPORTRESULTSDATAPATH in self._header:
                self.warn("Header File Data Name already found. Discarding",
                          numline=self._numline, line=line)
                return 0

            if splitted[1]:
                self._header[self.HEADERKEY_REPORTRESULTSDATAPATH] = \
                    splitted[1]
            else:
                self.warn("File Data Name not found or empty",
                          numline=self._numline, line=line)

        # SchemaVersion	65586
        elif splitted[0] == self.HEADERKEY_SCHEMAVERSION:
            if self.HEADERKEY_SCHEMAVERSION in self._header:
                self.warn("Header File Data Name already found. Discarding",
                          numline=self._numline, line=line)
                return 0

            if splitted[1]:
                self._header[self.HEADERKEY_SCHEMAVERSION] = splitted[1]
            else:
                self.warn("File Data Name not found or empty",
                          numline=self._numline, line=line)

        # Quant Batch Version	B.08.00
        elif splitted[0] == self.HEADERKEY_QUANTBATCHVERSION:
            if self.HEADERKEY_QUANTBATCHVERSION in self._header:
                self.warn("Header File Data Name already found. Discarding",
                          numline=self._numline, line=line)
                return 0

            if splitted[1]:
                self._header[self.HEADERKEY_QUANTBATCHVERSION] = splitted[1]
            else:
                self.warn("File Data Name not found or empty",
                          numline=self._numline, line=line)

        # Quant Report Version	B.08.00
        elif splitted[0] == self.HEADERKEY_QUANTREPORTVERSION:
            if self.HEADERKEY_QUANTREPORTVERSION in self._header:
                self.warn("Header File Data Name already found. Discarding",
                          numline=self._numline, line=line)
                return 0

            if splitted[1]:
                self._header[self.HEADERKEY_QUANTREPORTVERSION] = splitted[1]
            else:
                self.warn("File Data Name not found or empty",
                          numline=self._numline, line=line)

        # Blank lines
        if splitted[0] == '':
            self._end_header = True
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1
            return 0

        return 0

    def parse_quantitationesultsline(self, line):
        """ Parses quantitation result lines
            Please see samples/GC-MS output.txt
            [MS Quantitative Results] section
        """

        if line == ',,,,,,,,,,,,,,,,,,':
            return 0

        if line.startswith('SampleID'):
            self._end_header = True
            self._quantitationresultsheader = [token.strip() for token
                                               in line.split(self.COMMAS)
                                               if token.strip()]
            return 0

        splitted = [token.strip() for token in line.split(self.COMMAS)]
        quantitation = {'DefaultResult': 'FinalConcentration'}
        for colname in self._quantitationresultsheader:
            quantitation[colname] = ''

        for i in range(len(splitted)):
            token = splitted[i]
            if i < len(self._quantitationresultsheader):

                colname = self._quantitationresultsheader[i]
                if colname in self.QUANTITATIONRESULTS_NUMERICHEADERS:
                    try:
                        quantitation[colname] = float(token)
                    except ValueError:
                        self.warn(
                            "No valid number ${token} in column "
                            "${index} (${column_name})",
                            mapping={"token": token,
                                     "index": str(i + 1),
                                     "column_name": colname},
                            numline=self._numline, line=line)
                        quantitation[colname] = token
                else:
                    quantitation[colname] = token

            elif token:
                self.err("Orphan value in column ${index} (${token})",
                         mapping={"index": str(i+1),
                                  "token": token},
                         numline=self._numline, line=line)

        result = quantitation[quantitation['DefaultResult']]
        column_name = quantitation['DefaultResult']
        result = self.zeroValueDefaultInstrumentResults(column_name,
                                                        result, line)
        quantitation[quantitation['DefaultResult']] = result

        d = datetime.strptime(quantitation['AcqDateTime'], "%m/%d/%Y %H:%M")
        quantitation['AcqDateTime'] = d
        val = re.sub(r"\W", "", quantitation['Compound'])
        self._addRawResult(quantitation['DataFileName'],
                           values={val: quantitation},
                           override=False)

    def zeroValueDefaultInstrumentResults(self, column_name, result, line):
        result = str(result)
        if result.startswith('--') or result == '' or result == 'ND':
            return 0.0

        try:
            result = float(result)
            if result < 0.0:
                result = 0.0
        except ValueError:
            self.err(
                "No valid number ${result} in column (${column_name})",
                mapping={"result": result,
                         "column_name": column_name},
                numline=self._numline, line=line)
            return
        return result


class AgilentMasshunterImporter(AnalysisResultsImporter):

    def __init__(self, parser, context, override,
                 allowed_ar_states=None, allowed_analysis_states=None,
                 instrument_uid=''):
        AnalysisResultsImporter.__init__(self, parser, context,
                                         override, allowed_ar_states,
                                         allowed_analysis_states,
                                         instrument_uid)


1		# -- coding: utf-8 --
2		#
3		# This file is part of SENAITE.CORE
4		#
5		# Copyright 2018 by it's authors.
6		# Some rights reserved. See LICENSE.rst, CONTRIBUTORS.rst.
7
8		""" Agilent's 'Masshunter'
9		"""
10		from bika.lims import bikaMessageFactory as _
11		from datetime import datetime
12		import json
13		import re
14		from bika.lims.exportimport.instruments.resultsimport import \
15		InstrumentCSVResultsFileParser, AnalysisResultsImporter
16		import traceback
17
18		title = "Agilent - Masshunter"
19
20
21	View Code Duplication	def Import(context, request):
		0 ignored issues – show Duplication introduced 2018-07-25 08:58 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
22		""" Read Agilent Masshunter analysis results
23		"""
24		form = request.form
25		# TODO form['file'] sometimes returns a list
26		infile = form['instrument_results_file'][0] if isinstance(
27		form['instrument_results_file'], list) else \
28		form['instrument_results_file']
29		artoapply = form['artoapply']
30		override = form['results_override']
31
32		instrument = form.get('instrument', None)
33		errors = []
34		logs = []
35
36		# Load the most suitable parser according to file extension/options/etc...
37		parser = None
38		if not hasattr(infile, 'filename'):
39		errors.append(_("No file selected"))
40		parser = AgilentMasshunterParser(infile)
41
42		if parser:
43		# Load the importer
44		status = ['sample_received', 'attachment_due', 'to_be_verified']
45		if artoapply == 'received':
46		status = ['sample_received']
47		elif artoapply == 'received_tobeverified':
48		status = ['sample_received', 'attachment_due', 'to_be_verified']
49
50		over = [False, False]
51		if override == 'nooverride':
52		over = [False, False]
53		elif override == 'override':
54		over = [True, False]
55		elif override == 'overrideempty':
56		over = [True, True]
57
58		importer = AgilentMasshunterImporter(parser=parser,
59		context=context,
60		allowed_ar_states=status,
61		allowed_analysis_states=None,
62		override=over,
63		instrument_uid=instrument)
64		tbex = ''
65		try:
66		importer.process()
67		except:
68		tbex = traceback.format_exc()
69		errors = importer.errors
70		logs = importer.logs
71		warns = importer.warns
72		if tbex:
73		errors.append(tbex)
74
75		results = {'errors': errors, 'log': logs, 'warns': warns}
		0 ignored issues – show introduced 2018-07-25 08:58 UTC by Report Bug Copy Issue Report The variable `warns` does not seem to be defined in case `parser` on line `42` is `False`. Are you sure this can never be the case? Loading history...
76
77		return json.dumps(results)
78
79
80		class AgilentMasshunterParser(InstrumentCSVResultsFileParser):
81
82		HEADERKEY_ANALYSISTIME = 'Analysis Time'
83		HEADERKEY_ANALYSTNAME = 'Analyst Name'
84		HEADERKEY_BATCHDATAPATH = 'Batch Data Path'
85		HEADERKEY_BATCHNAME = 'Batch Name'
86		HEADERKEY_BATCHSTATE = 'Batch State'
87		HEADERKEY_LASTCALIBRATION = 'Calibration Last Updated Time'
88		HEADERKEY_REPORTGENERATIONTIME = 'Report Generation Time'
89		HEADERKEY_REPORTGENERATORNAME = 'Report Generator Name'
90		HEADERKEY_REPORTRESULTSDATAPATH = 'Report Results Data Path'
91		HEADERKEY_SCHEMAVERSION = 'SchemaVersion'
92		HEADERKEY_QUANTBATCHVERSION = 'Quant Batch Version'
93		HEADERKEY_QUANTREPORTVERSION = 'Quant Report Version'
94
95		QUANTITATIONRESULTS_NUMERICHEADERS = ('CalculatedConcentration',
96		'FinalConcentration',
97		'FinalConcentration')
98		COMMAS = ','
99
100		def __init__(self, csv):
101		InstrumentCSVResultsFileParser.__init__(self, csv)
102		self._end_header = False
103		self._quantitationresultsheader = []
104		self._numline = 0
105
106		def _parseline(self, line):
107		if self._end_header is False:
108		return self.parse_headerline(line)
109		else:
110		return self.parse_quantitationesultsline(line)
111
112		def parse_headerline(self, line):
113		""" Parses header lines
114
115		Analysis Time 7/13/2017 9:55
116		Analyst Name MassHunter01\Agilent
117		Batch Data Path D:\MassHunter\GCMS\Terpenes\2017\July\20170711\
118		QuantResults\20170711 Sample Workup
119		Batch Name 20170711 Sample Workup
120		Batch State Processed
121		Calibration Last Updated Time 6/29/2017 15:57
122		Report Generation Time 1/1/0001 12:00:00 AM
123		Report Generator Name None
124		Report Results Data Path None
125		SchemaVersion 65586
126		Quant Batch Version B.08.00
127		Quant Report Version B.08.00
128		"""
129		if self._end_header is True:
130		# Header already processed
131		return 0
132
133		splitted = [token.strip() for token in line.split(self.COMMAS)]
134
135		# Analysis Time 7/13/2017 9:55
136		if splitted[0] == self.HEADERKEY_ANALYSISTIME:
137	View Code Duplication	if splitted[1]:
		0 ignored issues – show Duplication introduced 2018-01-03 21:05 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
138		try:
139		d = datetime.strptime(splitted[1], "%m/%d/%Y %H:%M")
140		self._header[self.HEADERKEY_ANALYSISTIME] = d
141		except ValueError:
142		self.err("Invalid Output Time format",
143		numline=self._numline, line=line)
144		else:
145		self.warn("Output Time not found or empty",
146		numline=self._numline, line=line)
147		d = datetime.strptime(splitted[1], "%I:%M %p")
148
149		# Analyst Name MassHunter01\Agilent
150		elif splitted[0] == self.HEADERKEY_ANALYSTNAME:
151		if self.HEADERKEY_ANALYSTNAME in self._header:
152		self.warn("Header File Data Name already found. Discarding",
153		numline=self._numline, line=line)
154		return 0
155
156		if splitted[1]:
157		self._header[self.HEADERKEY_ANALYSTNAME] = splitted[1]
158		else:
159		self.warn("File Data Name not found or empty",
160		numline=self._numline, line=line)
161
162		# Batch Data Path
163		# D:\MassHunter\GCMS\Terpenes\2017\July\20170711\QuantResults\20170711
164		elif splitted[0] == self.HEADERKEY_BATCHDATAPATH:
165		if self.HEADERKEY_BATCHDATAPATH in self._header:
166		self.warn("Header File Data Name already found. Discarding",
167		numline=self._numline, line=line)
168		return 0
169
170		if splitted[1]:
171		self._header[self.HEADERKEY_BATCHDATAPATH] = splitted[1]
172		else:
173		self.warn("File Data Name not found or empty",
174		numline=self._numline, line=line)
175
176		# Batch Name 20170711 Sample Workup
177		elif splitted[0] == self.HEADERKEY_BATCHNAME:
178		if self.HEADERKEY_BATCHNAME in self._header:
179		self.warn("Header File Data Name already found. Discarding",
180		numline=self._numline, line=line)
181		return 0
182
183		if splitted[1]:
184		self._header[self.HEADERKEY_BATCHNAME] = splitted[1]
185		else:
186		self.warn("File Data Name not found or empty",
187		numline=self._numline, line=line)
188
189		# Batch State Processed
190		elif splitted[0] == self.HEADERKEY_BATCHSTATE:
191		if self.HEADERKEY_BATCHSTATE in self._header:
192		self.warn("Header File Data Name already found. Discarding",
193		numline=self._numline, line=line)
194		return 0
195
196		if splitted[1]:
197		self._header[self.HEADERKEY_BATCHNAME] = splitted[1]
198		else:
199		self.warn("File Data Name not found or empty",
200		numline=self._numline, line=line)
201
202		# Calibration Last Updated Time 6/29/2017 15:57
203		elif splitted[0] == self.HEADERKEY_LASTCALIBRATION:
204		if self.HEADERKEY_LASTCALIBRATION in self._header:
205		self.warn("Header File Data Name already found. Discarding",
206		numline=self._numline, line=line)
207		return 0
208
209		if splitted[1]:
210		self._header[self.HEADERKEY_LASTCALIBRATION] = splitted[1]
211		else:
212		self.warn("File Data Name not found or empty",
213		numline=self._numline, line=line)
214
215		# Report Generation Time 1/1/0001 12:00:00 AM
216		elif splitted[0] == self.HEADERKEY_REPORTGENERATIONTIME:
217		if self.HEADERKEY_REPORTGENERATIONTIME in self._header:
218		self.warn("Header File Data Name already found. Discarding",
219		numline=self._numline, line=line)
220		return 0
221
222		if splitted[1]:
223		self._header[self.HEADERKEY_REPORTGENERATIONTIME] = splitted[1]
224		else:
225		self.warn("File Data Name not found or empty",
226		numline=self._numline, line=line)
227
228		# Report Generator Name None
229		elif splitted[0] == self.HEADERKEY_REPORTGENERATORNAME:
230		if self.HEADERKEY_REPORTGENERATORNAME in self._header:
231		self.warn("Header File Data Name already found. Discarding",
232		numline=self._numline, line=line)
233		return 0
234
235		if splitted[1]:
236		self._header[self.HEADERKEY_REPORTGENERATORNAME] = splitted[1]
237		else:
238		self.warn("File Data Name not found or empty",
239		numline=self._numline, line=line)
240
241		# Report Results Data Path None
242		elif splitted[0] == self.HEADERKEY_REPORTRESULTSDATAPATH:
243		if self.HEADERKEY_REPORTRESULTSDATAPATH in self._header:
244		self.warn("Header File Data Name already found. Discarding",
245		numline=self._numline, line=line)
246		return 0
247
248		if splitted[1]:
249		self._header[self.HEADERKEY_REPORTRESULTSDATAPATH] = \
250		splitted[1]
251		else:
252		self.warn("File Data Name not found or empty",
253		numline=self._numline, line=line)
254
255		# SchemaVersion 65586
256		elif splitted[0] == self.HEADERKEY_SCHEMAVERSION:
257		if self.HEADERKEY_SCHEMAVERSION in self._header:
258		self.warn("Header File Data Name already found. Discarding",
259		numline=self._numline, line=line)
260		return 0
261
262		if splitted[1]:
263		self._header[self.HEADERKEY_SCHEMAVERSION] = splitted[1]
264		else:
265		self.warn("File Data Name not found or empty",
266		numline=self._numline, line=line)
267
268		# Quant Batch Version B.08.00
269		elif splitted[0] == self.HEADERKEY_QUANTBATCHVERSION:
270		if self.HEADERKEY_QUANTBATCHVERSION in self._header:
271		self.warn("Header File Data Name already found. Discarding",
272		numline=self._numline, line=line)
273		return 0
274
275		if splitted[1]:
276		self._header[self.HEADERKEY_QUANTBATCHVERSION] = splitted[1]
277		else:
278		self.warn("File Data Name not found or empty",
279		numline=self._numline, line=line)
280
281		# Quant Report Version B.08.00
282		elif splitted[0] == self.HEADERKEY_QUANTREPORTVERSION:
283		if self.HEADERKEY_QUANTREPORTVERSION in self._header:
284		self.warn("Header File Data Name already found. Discarding",
285		numline=self._numline, line=line)
286		return 0
287
288		if splitted[1]:
289		self._header[self.HEADERKEY_QUANTREPORTVERSION] = splitted[1]
290		else:
291		self.warn("File Data Name not found or empty",
292		numline=self._numline, line=line)
293
294		# Blank lines
295		if splitted[0] == '':
296		self._end_header = True
297		if len(self._header) == 0:
298		self.err("No header found", numline=self._numline)
299		return -1
300		return 0
301
302		return 0
303
304		def parse_quantitationesultsline(self, line):
305		""" Parses quantitation result lines
306		Please see samples/GC-MS output.txt
307		[MS Quantitative Results] section
308		"""
309
310		if line == ',,,,,,,,,,,,,,,,,,':
311		return 0
312
313		if line.startswith('SampleID'):
314		self._end_header = True
315		self._quantitationresultsheader = [token.strip() for token
316		in line.split(self.COMMAS)
317		if token.strip()]
318		return 0
319
320		splitted = [token.strip() for token in line.split(self.COMMAS)]
321		quantitation = {'DefaultResult': 'FinalConcentration'}
322		for colname in self._quantitationresultsheader:
323		quantitation[colname] = ''
324
325		for i in range(len(splitted)):
326		token = splitted[i]
327	View Code Duplication	if i < len(self._quantitationresultsheader):
		0 ignored issues – show Duplication introduced 2017-12-01 14:39 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
328		colname = self._quantitationresultsheader[i]
329		if colname in self.QUANTITATIONRESULTS_NUMERICHEADERS:
330		try:
331		quantitation[colname] = float(token)
332		except ValueError:
333		self.warn(
334		"No valid number ${token} in column "
335		"${index} (${column_name})",
336		mapping={"token": token,
337		"index": str(i + 1),
338		"column_name": colname},
339		numline=self._numline, line=line)
340		quantitation[colname] = token
341		else:
342		quantitation[colname] = token
343
344		elif token:
345		self.err("Orphan value in column ${index} (${token})",
346		mapping={"index": str(i+1),
347		"token": token},
348		numline=self._numline, line=line)
349
350		result = quantitation[quantitation['DefaultResult']]
351		column_name = quantitation['DefaultResult']
352		result = self.zeroValueDefaultInstrumentResults(column_name,
353		result, line)
354		quantitation[quantitation['DefaultResult']] = result
355
356		d = datetime.strptime(quantitation['AcqDateTime'], "%m/%d/%Y %H:%M")
357		quantitation['AcqDateTime'] = d
358		val = re.sub(r"\W", "", quantitation['Compound'])
359		self._addRawResult(quantitation['DataFileName'],
360		values={val: quantitation},
361		override=False)
362
363		def zeroValueDefaultInstrumentResults(self, column_name, result, line):
364		result = str(result)
365		if result.startswith('--') or result == '' or result == 'ND':
366		return 0.0
367
368		try:
369		result = float(result)
370		if result < 0.0:
371		result = 0.0
372		except ValueError:
373		self.err(
374		"No valid number ${result} in column (${column_name})",
375		mapping={"result": result,
376		"column_name": column_name},
377		numline=self._numline, line=line)
378		return
379		return result
380
381
382		class AgilentMasshunterImporter(AnalysisResultsImporter):
383
384		def __init__(self, parser, context, override,
385		allowed_ar_states=None, allowed_analysis_states=None,
386		instrument_uid=''):
387		AnalysisResultsImporter.__init__(self, parser, context,
388		override, allowed_ar_states,
389		allowed_analysis_states,
390		instrument_uid)
391

senaite / senaite.core

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AgilentMasshunterParser.parse_headerline() F

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