senaite /
senaite.core
| Total Complexity | 85 |
| Total Lines | 494 |
| Duplicated Lines | 6.07 % |
| Changes | 0 | ||
Duplicate code is one of the most pungent code smells. A rule that is often used is to re-structure code once it is duplicated in three or more places.
Common duplication problems, and corresponding solutions are:
Complex classes like bika.lims.exportimport.instruments.agilent.masshunter.quantitative 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.
| 1 | # -*- coding: utf-8 -*- |
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| 2 | # |
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| 3 | # This file is part of SENAITE.CORE |
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| 4 | # |
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| 5 | # Copyright 2018 by it's authors. |
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| 6 | # Some rights reserved. See LICENSE.rst, CONTRIBUTORS.rst. |
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| 7 | |||
| 8 | """ Agilent's 'Masshunter Quant' |
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| 9 | """ |
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| 10 | from DateTime import DateTime |
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| 11 | from Products.Archetypes.event import ObjectInitializedEvent |
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| 12 | from Products.CMFCore.utils import getToolByName |
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| 13 | from Products.Five.browser.pagetemplatefile import ViewPageTemplateFile |
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| 14 | from bika.lims import bikaMessageFactory as _ |
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| 15 | from bika.lims.utils import t |
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| 16 | from bika.lims import logger |
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| 17 | from bika.lims.browser import BrowserView |
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| 18 | from bika.lims.idserver import renameAfterCreation |
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| 19 | from bika.lims.utils import changeWorkflowState |
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| 20 | from bika.lims.utils import tmpID |
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| 21 | from cStringIO import StringIO |
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| 22 | from datetime import datetime |
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| 23 | from operator import itemgetter |
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| 24 | from plone.i18n.normalizer.interfaces import IIDNormalizer |
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| 25 | from zope.component import getUtility |
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| 26 | import csv |
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| 27 | import json |
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| 28 | import plone |
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| 29 | import zope |
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| 30 | import zope.event |
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| 31 | from bika.lims.exportimport.instruments.resultsimport import InstrumentCSVResultsFileParser,\ |
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| 32 | AnalysisResultsImporter |
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| 33 | import traceback |
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| 34 | |||
| 35 | title = "Agilent - Masshunter Quantitative" |
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| 36 | |||
| 37 | |||
| 38 | def Import(context, request): |
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| 39 | """ Read Agilent's Masshunter Quant analysis results |
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| 40 | """ |
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| 41 | infile = request.form['amhq_file'] |
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| 42 | fileformat = request.form['amhq_format'] |
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| 43 | artoapply = request.form['amhq_artoapply'] |
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| 44 | override = request.form['amhq_override'] |
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| 45 | instrument = request.form.get('instrument', None) |
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| 46 | errors = [] |
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| 47 | logs = [] |
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| 48 | |||
| 49 | # Load the most suitable parser according to file extension/options/etc... |
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| 50 | parser = None |
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| 51 | if not hasattr(infile, 'filename'): |
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| 52 | errors.append(_("No file selected")) |
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| 53 | elif fileformat == 'csv': |
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| 54 | parser = MasshunterQuantCSVParser(infile) |
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| 55 | else: |
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| 56 | errors.append(t(_("Unrecognized file format ${fileformat}", |
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| 57 | mapping={"fileformat": fileformat}))) |
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| 58 | |||
| 59 | if parser: |
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| 60 | # Load the importer |
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| 61 | status = ['sample_received', 'attachment_due', 'to_be_verified'] |
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| 62 | if artoapply == 'received': |
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| 63 | status = ['sample_received'] |
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| 64 | elif artoapply == 'received_tobeverified': |
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| 65 | status = ['sample_received', 'attachment_due', 'to_be_verified'] |
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| 66 | |||
| 67 | over = [False, False] |
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| 68 | if override == 'nooverride': |
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| 69 | over = [False, False] |
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| 70 | elif override == 'override': |
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| 71 | over = [True, False] |
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| 72 | elif override == 'overrideempty': |
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| 73 | over = [True, True] |
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| 74 | |||
| 75 | importer = MasshunterQuantImporter(parser=parser, |
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| 76 | context=context, |
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| 77 | allowed_ar_states=status, |
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| 78 | allowed_analysis_states=None, |
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| 79 | override=over, |
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| 80 | instrument_uid=instrument) |
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| 81 | tbex = '' |
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| 82 | try: |
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| 83 | importer.process() |
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| 84 | except: |
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| 85 | tbex = traceback.format_exc() |
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| 86 | errors = importer.errors |
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| 87 | logs = importer.logs |
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| 88 | warns = importer.warns |
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| 89 | if tbex: |
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| 90 | errors.append(tbex) |
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| 91 | |||
| 92 | results = {'errors': errors, 'log': logs, 'warns': warns} |
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|
introduced
by
|
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| 93 | |||
| 94 | return json.dumps(results) |
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| 95 | |||
| 96 | |||
| 97 | class MasshunterQuantCSVParser(InstrumentCSVResultsFileParser): |
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| 98 | |||
| 99 | HEADERKEY_BATCHINFO = 'Batch Info' |
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| 100 | HEADERKEY_BATCHDATAPATH = 'Batch Data Path' |
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| 101 | HEADERKEY_ANALYSISTIME = 'Analysis Time' |
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| 102 | HEADERKEY_ANALYSTNAME = 'Analyst Name' |
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| 103 | HEADERKEY_REPORTTIME = 'Report Time' |
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| 104 | HEADERKEY_REPORTERNAME = 'Reporter Name' |
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| 105 | HEADERKEY_LASTCALIBRATION = 'Last Calib Update' |
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| 106 | HEADERKEY_BATCHSTATE = 'Batch State' |
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| 107 | SEQUENCETABLE_KEY = 'Sequence Table' |
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| 108 | SEQUENCETABLE_HEADER_DATAFILE = 'Data File' |
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| 109 | SEQUENCETABLE_HEADER_SAMPLENAME = 'Sample Name' |
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| 110 | SEQUENCETABLE_PRERUN = 'prerunrespchk.d' |
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| 111 | SEQUENCETABLE_MIDRUN = 'mid_respchk.d' |
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| 112 | SEQUENCETABLE_POSTRUN = 'post_respchk.d' |
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| 113 | SEQUENCETABLE_NUMERICHEADERS = ('Inj Vol',) |
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| 114 | QUANTITATIONRESULTS_KEY = 'Quantification Results' |
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| 115 | QUANTITATIONRESULTS_TARGETCOMPOUND = 'Target Compound' |
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| 116 | QUANTITATIONRESULTS_HEADER_DATAFILE = 'Data File' |
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| 117 | QUANTITATIONRESULTS_PRERUN = 'prerunrespchk.d' |
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| 118 | QUANTITATIONRESULTS_MIDRUN = 'mid_respchk.d' |
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| 119 | QUANTITATIONRESULTS_POSTRUN = 'post_respchk.d' |
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| 120 | QUANTITATIONRESULTS_NUMERICHEADERS = ('Resp', 'ISTD Resp', 'Resp Ratio', |
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| 121 | 'Final Conc', 'Exp Conc', 'Accuracy') |
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| 122 | QUANTITATIONRESULTS_COMPOUNDCOLUMN = 'Compound' |
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| 123 | COMMAS = ',' |
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| 124 | |||
| 125 | def __init__(self, csv): |
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| 126 | InstrumentCSVResultsFileParser.__init__(self, csv) |
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| 127 | self._end_header = False |
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| 128 | self._end_sequencetable = False |
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| 129 | self._sequences = [] |
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| 130 | self._sequencesheader = [] |
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| 131 | self._quantitationresultsheader = [] |
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| 132 | self._numline = 0 |
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| 133 | |||
| 134 | def getAttachmentFileType(self): |
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| 135 | return "Agilent's Masshunter Quant CSV" |
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| 136 | |||
| 137 | def _parseline(self, line): |
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| 138 | if self._end_header == False: |
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| 139 | return self.parse_headerline(line) |
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| 140 | elif self._end_sequencetable == False: |
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| 141 | return self.parse_sequencetableline(line) |
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| 142 | else: |
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| 143 | return self.parse_quantitationesultsline(line) |
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| 144 | |||
| 145 | def parse_headerline(self, line): |
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| 146 | """ Parses header lines |
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| 147 | |||
| 148 | Header example: |
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| 149 | Batch Info,2013-03-20T07:11:09.9053262-07:00,2013-03-20T07:12:55.5280967-07:00,2013-03-20T07:11:07.1047817-07:00,,,,,,,,,,,,,, |
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| 150 | Batch Data Path,D:\MassHunter\Data\130129\QuantResults\130129LS.batch.bin,,,,,,,,,,,,,,,, |
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| 151 | Analysis Time,3/20/2013 7:11 AM,Analyst Name,Administrator,,,,,,,,,,,,,, |
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| 152 | Report Time,3/20/2013 7:12 AM,Reporter Name,Administrator,,,,,,,,,,,,,, |
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| 153 | Last Calib Update,3/20/2013 7:11 AM,Batch State,Processed,,,,,,,,,,,,,, |
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| 154 | ,,,,,,,,,,,,,,,,, |
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| 155 | """ |
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| 156 | if self._end_header == True: |
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| 157 | # Header already processed |
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| 158 | return 0 |
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| 159 | |||
| 160 | if line.startswith(self.SEQUENCETABLE_KEY): |
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| 161 | self._end_header = True |
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| 162 | if len(self._header) == 0: |
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| 163 | self.err("No header found", numline=self._numline) |
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| 164 | return -1 |
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| 165 | return 0 |
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| 166 | |||
| 167 | splitted = [token.strip() for token in line.split(',')] |
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| 168 | |||
| 169 | # Batch Info,2013-03-20T07:11:09.9053262-07:00,2013-03-20T07:12:55.5280967-07:00,2013-03-20T07:11:07.1047817-07:00,,,,,,,,,,,,,, |
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| 170 | if splitted[0] == self.HEADERKEY_BATCHINFO: |
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| 171 | if self.HEADERKEY_BATCHINFO in self._header: |
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| 172 | self.warn("Header Batch Info already found. Discarding", |
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| 173 | numline=self._numline, line=line) |
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| 174 | return 0 |
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| 175 | |||
| 176 | self._header[self.HEADERKEY_BATCHINFO] = [] |
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| 177 | for i in range(len(splitted) - 1): |
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| 178 | if splitted[i + 1]: |
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| 179 | self._header[self.HEADERKEY_BATCHINFO].append(splitted[i + 1]) |
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| 180 | |||
| 181 | # Batch Data Path,D:\MassHunter\Data\130129\QuantResults\130129LS.batch.bin,,,,,,,,,,,,,,,, |
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| 182 | elif splitted[0] == self.HEADERKEY_BATCHDATAPATH: |
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| 183 | if self.HEADERKEY_BATCHDATAPATH in self._header: |
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| 184 | self.warn("Header Batch Data Path already found. Discarding", |
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| 185 | numline=self._numline, line=line) |
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| 186 | return 0; |
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| 187 | |||
| 188 | if splitted[1]: |
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| 189 | self._header[self.HEADERKEY_BATCHDATAPATH] = splitted[1] |
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| 190 | else: |
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| 191 | self.warn("Batch Data Path not found or empty", |
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| 192 | numline=self._numline, line=line) |
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| 193 | |||
| 194 | # Analysis Time,3/20/2013 7:11 AM,Analyst Name,Administrator,,,,,,,,,,,,,, |
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| 195 | elif splitted[0] == self.HEADERKEY_ANALYSISTIME: |
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| 196 | View Code Duplication | if splitted[1]: |
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| 197 | try: |
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| 198 | d = datetime.strptime(splitted[1], "%m/%d/%Y %I:%M %p") |
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| 199 | self._header[self.HEADERKEY_ANALYSISTIME] = d |
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| 200 | except ValueError: |
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| 201 | self.err("Invalid Analysis Time format", |
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| 202 | numline=self._numline, line=line) |
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| 203 | else: |
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| 204 | self.warn("Analysis Time not found or empty", |
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| 205 | numline=self._numline, line=line) |
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| 206 | |||
| 207 | if splitted[2] and splitted[2] == self.HEADERKEY_ANALYSTNAME: |
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| 208 | if splitted[3]: |
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| 209 | self._header[self.HEADERKEY_ANALYSTNAME] = splitted[3] |
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| 210 | else: |
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| 211 | self.warn("Analyst Name not found or empty", |
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| 212 | numline=self._numline, line=line) |
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| 213 | else: |
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| 214 | self.err("Analyst Name not found", |
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| 215 | numline=self._numline, line=line) |
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| 216 | |||
| 217 | # Report Time,3/20/2013 7:12 AM,Reporter Name,Administrator,,,,,,,,,,,,,, |
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| 218 | elif splitted[0] == self.HEADERKEY_REPORTTIME: |
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| 219 | if splitted[1]: |
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| 220 | try: |
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| 221 | d = datetime.strptime(splitted[1], "%m/%d/%Y %I:%M %p") |
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| 222 | self._header[self.HEADERKEY_REPORTTIME] = d |
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| 223 | except ValueError: |
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| 224 | self.err("Invalid Report Time format", |
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| 225 | numline=self._numline, line=line) |
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| 226 | else: |
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| 227 | self.warn("Report time not found or empty", |
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| 228 | numline=self._numline, line=line) |
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| 229 | |||
| 230 | |||
| 231 | if splitted[2] and splitted[2] == self.HEADERKEY_REPORTERNAME: |
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| 232 | if splitted[3]: |
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| 233 | self._header[self.HEADERKEY_REPORTERNAME] = splitted[3] |
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| 234 | else: |
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| 235 | self.warn("Reporter Name not found or empty", |
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| 236 | numline=self._numline, line=line) |
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| 237 | |||
| 238 | else: |
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| 239 | self.err("Reporter Name not found", |
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| 240 | numline=self._numline, line=line) |
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| 241 | |||
| 242 | |||
| 243 | # Last Calib Update,3/20/2013 7:11 AM,Batch State,Processed,,,,,,,,,,,,,, |
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| 244 | elif splitted[0] == self.HEADERKEY_LASTCALIBRATION: |
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| 245 | if splitted[1]: |
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| 246 | try: |
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| 247 | d = datetime.strptime(splitted[1], "%m/%d/%Y %I:%M %p") |
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| 248 | self._header[self.HEADERKEY_LASTCALIBRATION] = d |
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| 249 | except ValueError: |
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| 250 | self.err("Invalid Last Calibration time format", |
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| 251 | numline=self._numline, line=line) |
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| 252 | |||
| 253 | else: |
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| 254 | self.warn("Last Calibration time not found or empty", |
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| 255 | numline=self._numline, line=line) |
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| 256 | |||
| 257 | |||
| 258 | if splitted[2] and splitted[2] == self.HEADERKEY_BATCHSTATE: |
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| 259 | if splitted[3]: |
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| 260 | self._header[self.HEADERKEY_BATCHSTATE] = splitted[3] |
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| 261 | else: |
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| 262 | self.warn("Batch state not found or empty", |
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| 263 | numline=self._numline, line=line) |
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| 264 | |||
| 265 | else: |
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| 266 | self.err("Batch state not found", |
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| 267 | numline=self._numline, line=line) |
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| 268 | |||
| 269 | |||
| 270 | return 0 |
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| 271 | |||
| 272 | def parse_sequencetableline(self, line): |
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| 273 | """ Parses sequence table lines |
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| 274 | |||
| 275 | Sequence Table example: |
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| 276 | Sequence Table,,,,,,,,,,,,,,,,, |
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| 277 | Data File,Sample Name,Position,Inj Vol,Level,Sample Type,Acq Method File,,,,,,,,,,, |
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| 278 | prerunrespchk.d,prerunrespchk,Vial 3,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 279 | DSS_Nist_L1.d,DSS_Nist_L1,P1-A2,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 280 | DSS_Nist_L2.d,DSS_Nist_L2,P1-B2,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 281 | DSS_Nist_L3.d,DSS_Nist_L3,P1-C2,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 282 | UTAK_DS_L1.d,UTAK_DS_L1,P1-D2,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 283 | UTAK_DS_L2.d,UTAK_DS_L2,P1-E2,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 284 | mid_respchk.d,mid_respchk,Vial 3,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 285 | UTAK_DS_low.d,UTAK_DS_Low,P1-F2,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 286 | FDBS_31.d,FDBS_31,P1-G2,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 287 | FDBS_32.d,FDBS_32,P1-H2,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 288 | LS_60-r001.d,LS_60,P1-G12,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 289 | LS_60-r002.d,LS_60,P1-G12,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 290 | LS_61-r001.d,LS_61,P1-H12,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 291 | LS_61-r002.d,LS_61,P1-H12,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 292 | post_respchk.d,post_respchk,Vial 3,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 293 | ,,,,,,,,,,,,,,,,, |
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| 294 | """ |
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| 295 | |||
| 296 | # Sequence Table,,,,,,,,,,,,,,,,, |
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| 297 | # prerunrespchk.d,prerunrespchk,Vial 3,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 298 | # mid_respchk.d,mid_respchk,Vial 3,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 299 | # ,,,,,,,,,,,,,,,,, |
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| 300 | if line.startswith(self.SEQUENCETABLE_KEY) \ |
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| 301 | or line.startswith(self.SEQUENCETABLE_PRERUN) \ |
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| 302 | or line.startswith(self.SEQUENCETABLE_MIDRUN) \ |
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| 303 | or self._end_sequencetable == True: |
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| 304 | |||
| 305 | # Nothing to do, continue |
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| 306 | return 0 |
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| 307 | |||
| 308 | # Data File,Sample Name,Position,Inj Vol,Level,Sample Type,Acq Method File,,,,,,,,,,, |
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| 309 | if line.startswith(self.SEQUENCETABLE_HEADER_DATAFILE): |
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| 310 | self._sequencesheader = [token.strip() for token in line.split(',') if token.strip()] |
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| 311 | return 0 |
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| 312 | |||
| 313 | # post_respchk.d,post_respchk,Vial 3,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 314 | # Quantitation Results,,,,,,,,,,,,,,,,, |
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| 315 | if line.startswith(self.SEQUENCETABLE_POSTRUN) \ |
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| 316 | or line.startswith(self.QUANTITATIONRESULTS_KEY) \ |
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| 317 | or line.startswith(self.COMMAS): |
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| 318 | self._end_sequencetable = True |
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| 319 | if len(self._sequences) == 0: |
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| 320 | self.err("No Sequence Table found", linenum=self._numline) |
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| 321 | return -1 |
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| 322 | |||
| 323 | # Jumps 2 lines: |
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| 324 | # Data File,Sample Name,Position,Inj Vol,Level,Sample Type,Acq Method File,,,,,,,,,,, |
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| 325 | # prerunrespchk.d,prerunrespchk,Vial 3,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 326 | return 2 |
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| 327 | |||
| 328 | # DSS_Nist_L1.d,DSS_Nist_L1,P1-A2,-1.00,,Sample,120824_VitD_MAPTAD_1D_MRM_practice.m,,,,,,,,,,, |
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| 329 | splitted = [token.strip() for token in line.split(',')] |
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| 330 | sequence = {} |
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| 331 | for colname in self._sequencesheader: |
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| 332 | sequence[colname] = '' |
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| 333 | |||
| 334 | for i in range(len(splitted)): |
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| 335 | token = splitted[i] |
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| 336 | if i < len(self._sequencesheader): |
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| 337 | colname = self._sequencesheader[i] |
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| 338 | if token and colname in self.SEQUENCETABLE_NUMERICHEADERS: |
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| 339 | try: |
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| 340 | sequence[colname] = float(token) |
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| 341 | except ValueError: |
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| 342 | self.warn( |
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| 343 | "No valid number ${token} in column ${index} (${column_name})", |
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| 344 | mapping={"token": token, |
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| 345 | "index": str(i + 1), |
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| 346 | "column_name": colname}, |
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| 347 | numline=self._numline, line=line) |
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| 348 | sequence[colname] = token |
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| 349 | else: |
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| 350 | sequence[colname] = token |
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| 351 | elif token: |
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| 352 | self.err("Orphan value in column ${index} (${token})", |
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| 353 | mapping={"index": str(i+1), |
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| 354 | "token": token}, |
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| 355 | numline=self._numline, line=line) |
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| 356 | self._sequences.append(sequence) |
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| 357 | |||
| 358 | def parse_quantitationesultsline(self, line): |
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| 359 | """ Parses quantitation result lines |
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| 360 | |||
| 361 | Quantitation results example: |
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| 362 | Quantitation Results,,,,,,,,,,,,,,,,, |
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| 363 | Target Compound,25-OH D3+PTAD+MA,,,,,,,,,,,,,,,, |
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| 364 | Data File,Compound,ISTD,Resp,ISTD Resp,Resp Ratio, Final Conc,Exp Conc,Accuracy,,,,,,,,, |
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| 365 | prerunrespchk.d,25-OH D3+PTAD+MA,25-OH D3d3+PTAD+MA,5816,274638,0.0212,0.9145,,,,,,,,,,, |
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| 366 | DSS_Nist_L1.d,25-OH D3+PTAD+MA,25-OH D3d3+PTAD+MA,6103,139562,0.0437,1.6912,,,,,,,,,,, |
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| 367 | DSS_Nist_L2.d,25-OH D3+PTAD+MA,25-OH D3d3+PTAD+MA,11339,135726,0.0835,3.0510,,,,,,,,,,, |
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| 368 | DSS_Nist_L3.d,25-OH D3+PTAD+MA,25-OH D3d3+PTAD+MA,15871,141710,0.1120,4.0144,,,,,,,,,,, |
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| 369 | mid_respchk.d,25-OH D3+PTAD+MA,25-OH D3d3+PTAD+MA,4699,242798,0.0194,0.8514,,,,,,,,,,, |
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| 370 | DSS_Nist_L3-r002.d,25-OH D3+PTAD+MA,25-OH D3d3+PTAD+MA,15659,129490,0.1209,4.3157,,,,,,,,,,, |
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| 371 | UTAK_DS_L1-r001.d,25-OH D3+PTAD+MA,25-OH D3d3+PTAD+MA,29846,132264,0.2257,7.7965,,,,,,,,,,, |
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| 372 | UTAK_DS_L1-r002.d,25-OH D3+PTAD+MA,25-OH D3d3+PTAD+MA,28696,141614,0.2026,7.0387,,,,,,,,,,, |
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| 373 | post_respchk.d,25-OH D3+PTAD+MA,25-OH D3d3+PTAD+MA,5022,231748,0.0217,0.9315,,,,,,,,,,, |
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| 374 | ,,,,,,,,,,,,,,,,, |
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| 375 | Target Compound,25-OH D2+PTAD+MA,,,,,,,,,,,,,,,, |
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| 376 | Data File,Compound,ISTD,Resp,ISTD Resp,Resp Ratio, Final Conc,Exp Conc,Accuracy,,,,,,,,, |
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| 377 | prerunrespchk.d,25-OH D2+PTAD+MA,25-OH D3d3+PTAD+MA,6222,274638,0.0227,0.8835,,,,,,,,,,, |
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| 378 | DSS_Nist_L1.d,25-OH D2+PTAD+MA,25-OH D3d3+PTAD+MA,1252,139562,0.0090,0.7909,,,,,,,,,,, |
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| 379 | DSS_Nist_L2.d,25-OH D2+PTAD+MA,25-OH D3d3+PTAD+MA,3937,135726,0.0290,0.9265,,,,,,,,,,, |
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| 380 | DSS_Nist_L3.d,25-OH D2+PTAD+MA,25-OH D3d3+PTAD+MA,826,141710,0.0058,0.7697,,,,,,,,,,, |
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| 381 | mid_respchk.d,25-OH D2+PTAD+MA,25-OH D3d3+PTAD+MA,7864,242798,0.0324,0.9493,,,,,,,,,,, |
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| 382 | DSS_Nist_L3-r002.d,25-OH D2+PTAD+MA,25-OH D3d3+PTAD+MA,853,129490,0.0066,0.7748,,,,,,,,,,, |
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| 383 | UTAK_DS_L1-r001.d,25-OH D2+PTAD+MA,25-OH D3d3+PTAD+MA,127496,132264,0.9639,7.1558,,,,,,,,,,, |
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| 384 | UTAK_DS_L1-r002.d,25-OH D2+PTAD+MA,25-OH D3d3+PTAD+MA,135738,141614,0.9585,7.1201,,,,,,,,,,, |
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| 385 | post_respchk.d,25-OH D2+PTAD+MA,25-OH D3d3+PTAD+MA,6567,231748,0.0283,0.9219,,,,,,,,,,, |
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| 386 | ,,,,,,,,,,,,,,,,, |
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| 387 | """ |
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| 388 | |||
| 389 | # Quantitation Results,,,,,,,,,,,,,,,,, |
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| 390 | # prerunrespchk.d,25-OH D3+PTAD+MA,25-OH D3d3+PTAD+MA,5816,274638,0.0212,0.9145,,,,,,,,,,, |
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| 391 | # mid_respchk.d,25-OH D3+PTAD+MA,25-OH D3d3+PTAD+MA,4699,242798,0.0194,0.8514,,,,,,,,,,, |
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| 392 | # post_respchk.d,25-OH D2+PTAD+MA,25-OH D3d3+PTAD+MA,6567,231748,0.0283,0.9219,,,,,,,,,,, |
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| 393 | # ,,,,,,,,,,,,,,,,, |
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| 394 | if line.startswith(self.QUANTITATIONRESULTS_KEY) \ |
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| 395 | or line.startswith(self.QUANTITATIONRESULTS_PRERUN) \ |
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| 396 | or line.startswith(self.QUANTITATIONRESULTS_MIDRUN) \ |
||
| 397 | or line.startswith(self.QUANTITATIONRESULTS_POSTRUN) \ |
||
| 398 | or line.startswith(self.COMMAS): |
||
| 399 | |||
| 400 | # Nothing to do, continue |
||
| 401 | return 0 |
||
| 402 | |||
| 403 | # Data File,Compound,ISTD,Resp,ISTD Resp,Resp Ratio, Final Conc,Exp Conc,Accuracy,,,,,,,,, |
||
| 404 | if line.startswith(self.QUANTITATIONRESULTS_HEADER_DATAFILE): |
||
| 405 | self._quantitationresultsheader = [token.strip() for token in line.split(',') if token.strip()] |
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| 406 | return 0 |
||
| 407 | |||
| 408 | # Target Compound,25-OH D3+PTAD+MA,,,,,,,,,,,,,,,, |
||
| 409 | if line.startswith(self.QUANTITATIONRESULTS_TARGETCOMPOUND): |
||
| 410 | # New set of Quantitation Results |
||
| 411 | splitted = [token.strip() for token in line.split(',')] |
||
| 412 | if not splitted[1]: |
||
| 413 | self.warn("No Target Compound found", |
||
| 414 | numline=self._numline, line=line) |
||
| 415 | return 0 |
||
| 416 | |||
| 417 | # DSS_Nist_L1.d,25-OH D2+PTAD+MA,25-OH D3d3+PTAD+MA,1252,139562,0.0090,0.7909,,,,,,,,,,, |
||
| 418 | splitted = [token.strip() for token in line.split(',')] |
||
| 419 | quantitation = {} |
||
| 420 | for colname in self._quantitationresultsheader: |
||
| 421 | quantitation[colname] = '' |
||
| 422 | |||
| 423 | for i in range(len(splitted)): |
||
| 424 | token = splitted[i] |
||
| 425 | View Code Duplication | if i < len(self._quantitationresultsheader): |
|
| 426 | colname = self._quantitationresultsheader[i] |
||
| 427 | if token and colname in self.QUANTITATIONRESULTS_NUMERICHEADERS: |
||
| 428 | try: |
||
| 429 | quantitation[colname] = float(token) |
||
| 430 | except ValueError: |
||
| 431 | self.warn( |
||
| 432 | "No valid number ${token} in column ${index} (${column_name})", |
||
| 433 | mapping={"token": token, |
||
| 434 | "index": str(i + 1), |
||
| 435 | "column_name": colname}, |
||
| 436 | numline=self._numline, line=line) |
||
| 437 | quantitation[colname] = token |
||
| 438 | else: |
||
| 439 | quantitation[colname] = token |
||
| 440 | elif token: |
||
| 441 | self.err("Orphan value in column ${index} (${token})", |
||
| 442 | mapping={"index": str(i+1), |
||
| 443 | "token": token}, |
||
| 444 | numline=self._numline, line=line) |
||
| 445 | |||
| 446 | if self.QUANTITATIONRESULTS_COMPOUNDCOLUMN in quantitation: |
||
| 447 | compound = quantitation[self.QUANTITATIONRESULTS_COMPOUNDCOLUMN] |
||
| 448 | |||
| 449 | # Look for sequence matches and populate rawdata |
||
| 450 | datafile = quantitation.get(self.QUANTITATIONRESULTS_HEADER_DATAFILE, '') |
||
| 451 | if not datafile: |
||
| 452 | self.err("No Data File found for quantitation result", |
||
| 453 | numline=self._numline, line=line) |
||
| 454 | |||
| 455 | else: |
||
| 456 | seqs = [sequence for sequence in self._sequences \ |
||
| 457 | if sequence.get('Data File', '') == datafile] |
||
| 458 | if len(seqs) == 0: |
||
| 459 | self.err("No sample found for quantitative result ${data_file}", |
||
| 460 | mapping={"data_file": datafile}, |
||
| 461 | numline=self._numline, line=line) |
||
| 462 | elif len(seqs) > 1: |
||
| 463 | self.err("More than one sequence found for quantitative result: ${data_file}", |
||
| 464 | mapping={"data_file": datafile}, |
||
| 465 | numline=self._numline, line=line) |
||
| 466 | else: |
||
| 467 | objid = seqs[0].get(self.SEQUENCETABLE_HEADER_SAMPLENAME, '') |
||
| 468 | if objid: |
||
| 469 | quantitation['DefaultResult'] = 'Final Conc' |
||
| 470 | quantitation['Remarks'] = _("Autoimport") |
||
| 471 | rows = self.getRawResults().get(objid, []) |
||
| 472 | raw = rows[0] if len(rows) > 0 else {} |
||
| 473 | raw[compound] = quantitation |
||
| 474 | self._addRawResult(objid, raw, True) |
||
| 475 | else: |
||
| 476 | self.err("No valid sequence for ${data_file}", |
||
| 477 | mapping={"data_file": datafile}, |
||
| 478 | numline=self._numline, line=line) |
||
| 479 | else: |
||
| 480 | self.err("Value for column '${column}' not found", |
||
| 481 | mapping={"column": self.QUANTITATIONRESULTS_COMPOUNDCOLUMN}, |
||
| 482 | numline=self._numline, line=line) |
||
| 483 | |||
| 484 | |||
| 485 | class MasshunterQuantImporter(AnalysisResultsImporter): |
||
| 486 | |||
| 487 | def __init__(self, parser, context, override, |
||
| 488 | allowed_ar_states=None, allowed_analysis_states=None, |
||
| 489 | instrument_uid=''): |
||
| 490 | AnalysisResultsImporter.__init__(self, parser, context, |
||
| 491 | override, allowed_ar_states, |
||
| 492 | allowed_analysis_states, |
||
| 493 | instrument_uid) |
||
| 494 |
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