senaite.core.exportimport.instruments.panalytical.omnia.AxiosXrfCSVParser.parse_headerline() - Code Metrics - senaite/senaite.core - Measure and Improve Code Quality continuously with Scrutinizer

AxiosXrfCSVParser.parse_headerline() F
last analyzed 2025-07-03 06:46 UTC

↳ Parent: senaite.core.exportimport.instruments.panalytical.omnia

Complexity

Conditions

Size

Total Lines	216
Code Lines	135

Duplication

Lines	23
Ratio	10.65 %

Importance

Changes

Metric	Value
cc	44
eloc	135
nop	2
dl	23
loc	216
rs	0
c	0
b	0
f	0

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 senaite.core.exportimport.instruments.panalytical.omnia.AxiosXrfCSVParser.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.
#
# SENAITE.CORE is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# this program; if not, write to the Free Software Foundation, Inc., 51
# Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# Copyright 2018-2025 by it's authors.
# Some rights reserved, see README and LICENSE.

from datetime import datetime

from bika.lims.utils import to_unicode
from senaite.core.exportimport.instruments.importer import \
    AnalysisResultsImporter
from senaite.core.exportimport.instruments.parser import \
    InstrumentCSVResultsFileParser


class AxiosXrfCSVMultiParser(InstrumentCSVResultsFileParser):

    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
                                  #analytic's columns name


    def _parseline(self, line):
        # Process the line differenly if it pertains at header or results block
        if self._end_header:
            return self.parse_resultline(line)
        else:
            sline = line.strip(',')
            return self.parse_headerline(sline)

    def splitLine(self, line):
        # If pertains at header it split the line by ':' and then remove ','
        # Else split by ',' and remove blank spaces
        if not self._end_header:
            sline = line.split(':')
            return [token.strip(',') for token in sline]

        return [token.strip() for token in line.split(',')]

    def csvDate2BikaDate(self,DateTime):
    #11/03/2014 14:46:46 --> %d/%m/%Y %H:%M %p
        dtobj = datetime.strptime(DateTime,"%d/%m/%Y %H:%M:%S")
        return dtobj.strftime("%Y%m%d %H:%M:%S")

    def parse_headerline(self, line):
        #Process incoming header line
        """11/03/2014 14:46:46
        PANalytical
        Results quantitative - Omnian 2013,

        Selected archive:,Omnian 2013
        Number of results selected:,4
        """
        
        # Save each header field (that we know) and its own value in the dict        
        if line.startswith('Results quantitative'):
            line = to_unicode(line)
            if len(self._header) == 0:
                self.err("Unexpected header format", numline=self._numline)
                return -1

            line = line.replace(',', "")
            splitted = line.split(' - ')
            self._header['Quantitative'] = splitted[1]
            return 1

        if line.startswith('Selected archive'):
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['Archive'] = splitted[1].replace('"', '').strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)
            return 0

        if line.startswith('Number of'):
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['NumResults'] = splitted[1].replace('"', '').strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)
            return 0

        if line.startswith('Seq.'):
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1
            #Grab column names
            self._columns = line.split(',')
            self._end_header = True
            return 1

        else:
            self._header['Date'] = line
            return 1



    def parse_resultline(self, line):
        # Process incoming results line
        if not line.strip():
            return 0
        if line.startswith(',,'):
            return 0

        rawdict = {}
        # Split by ","
        splitted = self.splitLine(line.strip(";"))

        # Adjunt separated values from split by ','
        for idx, result in enumerate(splitted):
            if result.startswith('"'):
                # It means that is the value's firts part
                # Consequently we take second part and append both
                result = (splitted[idx].strip('"') + "," + splitted[idx+1].strip('"'))
                splitted[idx] = result
                splitted.remove(splitted[idx+1])
                
        result_type = ''
        result_sum = ''
        for idx, result in enumerate(splitted):
            if self._columns[idx] == 'Result type':
                result_type = result
            elif self._columns[idx].startswith('Sample name'):
                    rid = result
            elif self._columns[idx].startswith('Seq.'):
                pass
            elif self._columns[idx] == 'Sum':
                    result_sum = result
            else:
                rawdict[self._columns[idx]] = {'DefaultResult':result_type,
                                               # Replace to obtain UK values from default
                                               'Concentration':result.replace(',','.'),
                                               'Sum':result_sum}
        try:
            rawdict['DateTime'] = {'DateTime':self.csvDate2BikaDate(self._header['Date']),
                                   'DefaultValue':'DateTime'}
        except Exception:
            pass
        if not rid:

            self.err("No Sample defined", numline=self._numline)
            return 0

        self._addRawResult(rid, rawdict, True)
        return 0


    def getAttachmentFileType(self):
        return "PANalytical - Omnia Axios XRF"

class AxiosXrfCSVParser(InstrumentCSVResultsFileParser):

    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
                                  #analytic's columns name

    def _parseline(self, line):
        # Process the line differenly if it pertains at header or results block
        if self._end_header:
            return self.parse_resultline(line)
        else:
            sline = line.strip(',')
            return self.parse_headerline(sline)

    def csvDate2BikaDate(self,DateTime):
    #11/03/2014 14:46:46 --> %d/%m/%Y %H:%M %p
        dtobj = datetime.strptime(DateTime,"%d/%m/%Y %H:%M:%S")
        return dtobj.strftime("%Y%m%d %H:%M:%S")

    def splitLine(self, line):
        # If pertains at header it split the line by ':' and then remove ','
        # Else split by ',' and remove blank spaces
        if not self._end_header:
            sline = line.split(':')
            return [token.strip(',') for token in sline]

        return [token.strip() for token in line.split(',')]

    def parse_headerline(self, line):
        #Process incoming header line
        r"""
        29/11/2013 10:15:44
        PANalytical
        "Quantification of sample ESFERA CINZA - 1g H3BO3 -  1:0,5 - NO PPC",

        R.M.S.:,"0,035"
        Result status:,
        Sum before normalization:,"119,5 %"
        Normalised to:,"100,0 %"
        Sample type:,Pressed powder
        Initial sample weight (g):,"2,000"
        Weight after pressing (g):,"3,000"
        Correction applied for medium:,No
        Correction applied for film:,No
        Used Compound list:,Oxides
        Results database:,omnian 2013
        Results database in:,c:\panalytical\superq\userdata
        """

        if line.startswith('"Quantification of sample') or line.startswith('Quantification of sample'):
            line = to_unicode(line)
            if len(self._header) == 0:
                self.warn('Unexpected header format', numline=self._numline)
                return -1
            # Remove non important string and double comas to obtein
            # the sample name free
            line = line.replace("Quantification of sample ", "")
            line = line.replace('"', "")
            splitted = line.split(' - ')

            if len(splitted) > 3:# Maybe we don't need this, i could be all the sample's identifier...
                self._header['Sample'] = splitted[0].strip(' ')
                self._header['Quantity'] = splitted[1]
                self._header['????'] = splitted[2]# At present we
                                                  # don't know what
                                                  # is that
                self._header['PPC'] = splitted[3]
            
            elif len(splitted) == 1:
                self._header['Sample'] = splitted[0].replace('Quantification of sample','').strip(' ')

            else:
                self.warn('Unexpected header format', numline=self._numline)
            return 1
        # Save each header field (that we know) and its own value in the dict
        if line.startswith('R.M.S.'):

            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['R.M.S.'] = splitted[1].replace('"', '').strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)
            return 0

        if line.startswith('Result status'):

            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['Result status'] = splitted[1].replace('"', '').strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)

            return 0

        if line.startswith('Sum before normalization'):
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['Sum'] = splitted[1].replace('"', '').strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)

            return 0

        if line.startswith('Normalised to'):
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['Normalized'] = splitted[1].replace('"', '').strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)

            return 0

        if line.startswith('Sample type'):

            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['Sample type'] = splitted[1].strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)

            return 0

        if line.startswith('Initial sample weight (g)'):
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['Initial sample weight'] = splitted[1].replace('"', '').strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)

            return 0

        if line.startswith('Weight after pressing (g)'):
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['Weight after pressing'] = splitted[1].replace('"', '').strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)

            return 0

        if line.startswith('Correction applied for medium'):
            if len(self._header) == 0:
                self.warn('Unexpected header format', numline=self._numline)
                return -1

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['Correction medium'] = splitted[1].replace('"', '').strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)

            return 0

        if line.startswith('Correction applied for film'):
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['Correction film'] = splitted[1].replace('"', '').strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)

            return 0

        if line.startswith('Used Compound list'):
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['Used compound'] = splitted[1].replace('"', '').strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)

            return 0
        if line.startswith('Results database:'):
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1

            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['Result database'] = splitted[1].replace('"', '').strip()
            else:
                self.warn('Unexpected header format', numline=self._numline)

            return 0

       
        if self.columns_name:
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1

            #Grab column names
            self._end_header = True
            self._columns = self.splitLine(line)
            return 1

        if line.startswith('Results database in'):
            if len(self._header) == 0:
                self.err("No header found", numline=self._numline)
                return -1
            
            splitted = self.splitLine(line)
            if len(splitted) > 1:
                self._header['Database path'] = splitted[1]+splitted[2]
                self.columns_name = True
            else:
                self.warn('Unexpected header format', numline=self._numline)
                
            return 1
            
        else:
            self._header['Date'] = line
            return 1

    def parse_resultline(self, line):
        # Process incoming results line
        if not line.strip():
            return 0

        rawdict = {}
        # Split by ","
        splitted = self.splitLine(line.strip(";"))
        # Look to know if the first value is an enumerate field
        try:
            int(splitted[0])
            rawdict["num"] = splitted[0]
            splitted = splitted[1:]
        except ValueError:
            pass

        # Enumerate the list to obtain: [(0,data0),(1,data1),...]
        e_splitted = list(enumerate(splitted))
        errors = ''

        com = False
        for idx, result in e_splitted:
            if result.startswith('"'):
                # It means that is the first value part
                # Consequently we take second part and append both
                result = (e_splitted[idx][1].strip('"') + "," + e_splitted[idx+1][1].strip('"'))
                e_splitted[idx] = (idx,result)
                e_splitted.remove(e_splitted[idx+1])
                com = True
                rawdict[self._columns[idx]] = result
                conc = self._columns[idx] # Main value's name
                                
               
            elif com:# We have rm the 2nd part value, consequently we
                    # need to decrement idx
                if len(self._columns) <= idx-1:
                    self.err("Orphan value in column ${index}",
                             mapping={"index":str(idx + 1)},
                             numline=self._numline)
                    break
                # We add and sync the result with its value's name
                rawdict[self._columns[idx-1]] = result

            else:
                if len(self._columns) <= idx:
                    self.err("Orphan value in column ${index}",
                             mapping={"index":str(idx + 1)},
                             numline=self._numline)
                    break
                rawdict[self._columns[idx]] = result

        aname = rawdict[self._columns[0]]# The fisrt column is analytic name  
        if not aname:
            self.err("No Analysis Name defined", numline=self._numline)
            return 0
        elif aname == "<H>":
            # <H> maybe is data error header? We need more examples...
            errors = rawdict.get('Compound')
            notes = rawdict.get('Calibration')
            rawdict['Notes'] = notes

        rid = self._header['Sample']
        if not rid:
            self.err("No Sample defined", numline=self._numline)
            return 0

        notes = rawdict.get('Notes', '')
        notes = "Notes: %s" % notes if notes else ''
        rawdict['DefaultResult'] = conc

        # Replace to obtain UK values from default
        rawdict[conc] = rawdict[conc].replace(',','.')
        rawdict['Remarks'] = ' '.join([errors, notes])
        rawres = self.getRawResults().get(rid, [])
        raw = rawres[0] if len(rawres) > 0 else {}
        raw[aname] = rawdict
        if 'DateTime' not in raw:
            try:
                raw['DateTime'] = {'DateTime':self.csvDate2BikaDate(self._header['Date']),
                                   'DefaultValue':'DateTime'}
            except Exception:
                pass
            
        self._addRawResult(rid, raw, True)
        return 0


    def getAttachmentFileType(self):
        return "PANalytical - Omnia Axios XRF"


class AxiosXrfImporter(AnalysisResultsImporter):

    def __init__(self, parser, context,  override,
                 allowed_ar_states=None, allowed_analysis_states=None,
                 instrument_uid=None):
        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		# SENAITE.CORE is free software: you can redistribute it and/or modify it under
6		# the terms of the GNU General Public License as published by the Free Software
7		# Foundation, version 2.
8		#
9		# This program is distributed in the hope that it will be useful, but WITHOUT
10		# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
11		# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
12		# details.
13		#
14		# You should have received a copy of the GNU General Public License along with
15		# this program; if not, write to the Free Software Foundation, Inc., 51
16		# Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
17		#
18		# Copyright 2018-2025 by it's authors.
19		# Some rights reserved, see README and LICENSE.
20
21		from datetime import datetime
22
23		from bika.lims.utils import to_unicode
24		from senaite.core.exportimport.instruments.importer import \
25		AnalysisResultsImporter
26		from senaite.core.exportimport.instruments.parser import \
27		InstrumentCSVResultsFileParser
28
29
30		class AxiosXrfCSVMultiParser(InstrumentCSVResultsFileParser):
31
32		def __init__(self, csv):
33		InstrumentCSVResultsFileParser.__init__(self, csv)
34		self._end_header = False
35		self._columns = []
36		self.columns_name = False #To know if the next line contains
37		#analytic's columns name
38
39
40		def _parseline(self, line):
41		# Process the line differenly if it pertains at header or results block
42		if self._end_header:
43		return self.parse_resultline(line)
44		else:
45		sline = line.strip(',')
46		return self.parse_headerline(sline)
47
48		def splitLine(self, line):
49		# If pertains at header it split the line by ':' and then remove ','
50		# Else split by ',' and remove blank spaces
51		if not self._end_header:
52		sline = line.split(':')
53		return [token.strip(',') for token in sline]
54
55		return [token.strip() for token in line.split(',')]
56
57		def csvDate2BikaDate(self,DateTime):
58		#11/03/2014 14:46:46 --> %d/%m/%Y %H:%M %p
59		dtobj = datetime.strptime(DateTime,"%d/%m/%Y %H:%M:%S")
60		return dtobj.strftime("%Y%m%d %H:%M:%S")
61
62		def parse_headerline(self, line):
63		#Process incoming header line
64		"""11/03/2014 14:46:46
65		PANalytical
66		Results quantitative - Omnian 2013,
67
68		Selected archive:,Omnian 2013
69		Number of results selected:,4
70		"""
71
72		# Save each header field (that we know) and its own value in the dict
73		if line.startswith('Results quantitative'):
74		line = to_unicode(line)
75		if len(self._header) == 0:
76		self.err("Unexpected header format", numline=self._numline)
77		return -1
78
79		line = line.replace(',', "")
80		splitted = line.split(' - ')
81		self._header['Quantitative'] = splitted[1]
82		return 1
83
84		if line.startswith('Selected archive'):
85		if len(self._header) == 0:
86		self.err("No header found", numline=self._numline)
87		return -1
88
89		splitted = self.splitLine(line)
90		if len(splitted) > 1:
91		self._header['Archive'] = splitted[1].replace('"', '').strip()
92		else:
93		self.warn('Unexpected header format', numline=self._numline)
94		return 0
95
96		if line.startswith('Number of'):
97		if len(self._header) == 0:
98		self.err("No header found", numline=self._numline)
99		return -1
100
101		splitted = self.splitLine(line)
102		if len(splitted) > 1:
103		self._header['NumResults'] = splitted[1].replace('"', '').strip()
104		else:
105		self.warn('Unexpected header format', numline=self._numline)
106		return 0
107
108		if line.startswith('Seq.'):
109		if len(self._header) == 0:
110		self.err("No header found", numline=self._numline)
111		return -1
112		#Grab column names
113		self._columns = line.split(',')
114		self._end_header = True
115		return 1
116
117		else:
118		self._header['Date'] = line
119		return 1
120
121
122
123		def parse_resultline(self, line):
124		# Process incoming results line
125		if not line.strip():
126		return 0
127		if line.startswith(',,'):
128		return 0
129
130		rawdict = {}
131		# Split by ","
132		splitted = self.splitLine(line.strip(";"))
133
134		# Adjunt separated values from split by ','
135		for idx, result in enumerate(splitted):
136		if result.startswith('"'):
137		# It means that is the value's firts part
138		# Consequently we take second part and append both
139		result = (splitted[idx].strip('"') + "," + splitted[idx+1].strip('"'))
140		splitted[idx] = result
141		splitted.remove(splitted[idx+1])
142
143		result_type = ''
144		result_sum = ''
145		for idx, result in enumerate(splitted):
146		if self._columns[idx] == 'Result type':
147		result_type = result
148		elif self._columns[idx].startswith('Sample name'):
149		rid = result
150		elif self._columns[idx].startswith('Seq.'):
151		pass
152		elif self._columns[idx] == 'Sum':
153		result_sum = result
154		else:
155		rawdict[self._columns[idx]] = {'DefaultResult':result_type,
156		# Replace to obtain UK values from default
157		'Concentration':result.replace(',','.'),
158		'Sum':result_sum}
159		try:
160		rawdict['DateTime'] = {'DateTime':self.csvDate2BikaDate(self._header['Date']),
161		'DefaultValue':'DateTime'}
162		except Exception:
163		pass
164		if not rid:
		0 ignored issues – show introduced 2018-07-25 08:58 UTC by Report Bug Copy Issue Report The variable `rid` does not seem to be defined in case the `for` loop on line `145` is not entered. Are you sure this can never be the case? Loading history...
165		self.err("No Sample defined", numline=self._numline)
166		return 0
167
168		self._addRawResult(rid, rawdict, True)
169		return 0
170
171
172		def getAttachmentFileType(self):
173		return "PANalytical - Omnia Axios XRF"
174
175		class AxiosXrfCSVParser(InstrumentCSVResultsFileParser):
176
177		def __init__(self, csv):
178		InstrumentCSVResultsFileParser.__init__(self, csv)
179		self._end_header = False
180		self._columns = []
181		self.columns_name = False #To know if the next line contains
182		#analytic's columns name
183
184		def _parseline(self, line):
185		# Process the line differenly if it pertains at header or results block
186		if self._end_header:
187		return self.parse_resultline(line)
188		else:
189		sline = line.strip(',')
190		return self.parse_headerline(sline)
191
192		def csvDate2BikaDate(self,DateTime):
193		#11/03/2014 14:46:46 --> %d/%m/%Y %H:%M %p
194		dtobj = datetime.strptime(DateTime,"%d/%m/%Y %H:%M:%S")
195		return dtobj.strftime("%Y%m%d %H:%M:%S")
196
197		def splitLine(self, line):
198		# If pertains at header it split the line by ':' and then remove ','
199		# Else split by ',' and remove blank spaces
200		if not self._end_header:
201		sline = line.split(':')
202		return [token.strip(',') for token in sline]
203
204		return [token.strip() for token in line.split(',')]
205
206		def parse_headerline(self, line):
207		#Process incoming header line
208		r"""
209		29/11/2013 10:15:44
210		PANalytical
211		"Quantification of sample ESFERA CINZA - 1g H3BO3 - 1:0,5 - NO PPC",
212
213		R.M.S.:,"0,035"
214		Result status:,
215		Sum before normalization:,"119,5 %"
216		Normalised to:,"100,0 %"
217		Sample type:,Pressed powder
218		Initial sample weight (g):,"2,000"
219		Weight after pressing (g):,"3,000"
220		Correction applied for medium:,No
221		Correction applied for film:,No
222		Used Compound list:,Oxides
223		Results database:,omnian 2013
224		Results database in:,c:\panalytical\superq\userdata
225		"""
226
227		if line.startswith('"Quantification of sample') or line.startswith('Quantification of sample'):
228		line = to_unicode(line)
229		if len(self._header) == 0:
230		self.warn('Unexpected header format', numline=self._numline)
231		return -1
232		# Remove non important string and double comas to obtein
233		# the sample name free
234		line = line.replace("Quantification of sample ", "")
235		line = line.replace('"', "")
236		splitted = line.split(' - ')
237
238		if len(splitted) > 3:# Maybe we don't need this, i could be all the sample's identifier...
239		self._header['Sample'] = splitted[0].strip(' ')
240		self._header['Quantity'] = splitted[1]
241		self._header['????'] = splitted[2]# At present we
242		# don't know what
243		# is that
244		self._header['PPC'] = splitted[3]
245
246		elif len(splitted) == 1:
247		self._header['Sample'] = splitted[0].replace('Quantification of sample','').strip(' ')
248
249		else:
250		self.warn('Unexpected header format', numline=self._numline)
251		return 1
252		# Save each header field (that we know) and its own value in the dict
253		if line.startswith('R.M.S.'):
254
255		if len(self._header) == 0:
256		self.err("No header found", numline=self._numline)
257		return -1
258
259		splitted = self.splitLine(line)
260		if len(splitted) > 1:
261		self._header['R.M.S.'] = splitted[1].replace('"', '').strip()
262		else:
263		self.warn('Unexpected header format', numline=self._numline)
264		return 0
265
266	View Code Duplication	if line.startswith('Result status'):
		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...
267		if len(self._header) == 0:
268		self.err("No header found", numline=self._numline)
269
270		splitted = self.splitLine(line)
271		if len(splitted) > 1:
272		self._header['Result status'] = splitted[1].replace('"', '').strip()
273		else:
274		self.warn('Unexpected header format', numline=self._numline)
275
276		return 0
277
278		if line.startswith('Sum before normalization'):
279		if len(self._header) == 0:
280		self.err("No header found", numline=self._numline)
281		return -1
282
283		splitted = self.splitLine(line)
284		if len(splitted) > 1:
285		self._header['Sum'] = splitted[1].replace('"', '').strip()
286		else:
287		self.warn('Unexpected header format', numline=self._numline)
288
289		return 0
290
291		if line.startswith('Normalised to'):
292		if len(self._header) == 0:
293		self.err("No header found", numline=self._numline)
294		return -1
295
296		splitted = self.splitLine(line)
297		if len(splitted) > 1:
298		self._header['Normalized'] = splitted[1].replace('"', '').strip()
299		else:
300		self.warn('Unexpected header format', numline=self._numline)
301
302		return 0
303
304	View Code Duplication	if line.startswith('Sample type'):
		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...
305		if len(self._header) == 0:
306		self.err("No header found", numline=self._numline)
307		return -1
308
309		splitted = self.splitLine(line)
310		if len(splitted) > 1:
311		self._header['Sample type'] = splitted[1].strip()
312		else:
313		self.warn('Unexpected header format', numline=self._numline)
314
315		return 0
316
317		if line.startswith('Initial sample weight (g)'):
318		if len(self._header) == 0:
319		self.err("No header found", numline=self._numline)
320		return -1
321
322		splitted = self.splitLine(line)
323		if len(splitted) > 1:
324		self._header['Initial sample weight'] = splitted[1].replace('"', '').strip()
325		else:
326		self.warn('Unexpected header format', numline=self._numline)
327
328		return 0
329
330		if line.startswith('Weight after pressing (g)'):
331		if len(self._header) == 0:
332		self.err("No header found", numline=self._numline)
333		return -1
334
335		splitted = self.splitLine(line)
336		if len(splitted) > 1:
337		self._header['Weight after pressing'] = splitted[1].replace('"', '').strip()
338		else:
339		self.warn('Unexpected header format', numline=self._numline)
340
341		return 0
342
343		if line.startswith('Correction applied for medium'):
344		if len(self._header) == 0:
345		self.warn('Unexpected header format', numline=self._numline)
346		return -1
347
348		splitted = self.splitLine(line)
349		if len(splitted) > 1:
350		self._header['Correction medium'] = splitted[1].replace('"', '').strip()
351		else:
352		self.warn('Unexpected header format', numline=self._numline)
353
354		return 0
355
356		if line.startswith('Correction applied for film'):
357		if len(self._header) == 0:
358		self.err("No header found", numline=self._numline)
359		return -1
360
361		splitted = self.splitLine(line)
362		if len(splitted) > 1:
363		self._header['Correction film'] = splitted[1].replace('"', '').strip()
364		else:
365		self.warn('Unexpected header format', numline=self._numline)
366
367		return 0
368
369		if line.startswith('Used Compound list'):
370		if len(self._header) == 0:
371		self.err("No header found", numline=self._numline)
372		return -1
373
374		splitted = self.splitLine(line)
375		if len(splitted) > 1:
376		self._header['Used compound'] = splitted[1].replace('"', '').strip()
377		else:
378		self.warn('Unexpected header format', numline=self._numline)
379
380		return 0
381		if line.startswith('Results database:'):
382		if len(self._header) == 0:
383		self.err("No header found", numline=self._numline)
384		return -1
385
386		splitted = self.splitLine(line)
387		if len(splitted) > 1:
388		self._header['Result database'] = splitted[1].replace('"', '').strip()
389		else:
390		self.warn('Unexpected header format', numline=self._numline)
391
392		return 0
393
394
395		if self.columns_name:
396		if len(self._header) == 0:
397		self.err("No header found", numline=self._numline)
398		return -1
399
400		#Grab column names
401		self._end_header = True
402		self._columns = self.splitLine(line)
403		return 1
404
405		if line.startswith('Results database in'):
406		if len(self._header) == 0:
407		self.err("No header found", numline=self._numline)
408		return -1
409
410		splitted = self.splitLine(line)
411		if len(splitted) > 1:
412		self._header['Database path'] = splitted[1]+splitted[2]
413		self.columns_name = True
414		else:
415		self.warn('Unexpected header format', numline=self._numline)
416
417		return 1
418
419		else:
420		self._header['Date'] = line
421		return 1
422
423		def parse_resultline(self, line):
424		# Process incoming results line
425		if not line.strip():
426		return 0
427
428		rawdict = {}
429		# Split by ","
430		splitted = self.splitLine(line.strip(";"))
431		# Look to know if the first value is an enumerate field
432		try:
433		int(splitted[0])
434		rawdict["num"] = splitted[0]
435		splitted = splitted[1:]
436		except ValueError:
437		pass
438
439		# Enumerate the list to obtain: [(0,data0),(1,data1),...]
440		e_splitted = list(enumerate(splitted))
441		errors = ''
442
443		com = False
444		for idx, result in e_splitted:
445		if result.startswith('"'):
446		# It means that is the first value part
447		# Consequently we take second part and append both
448		result = (e_splitted[idx][1].strip('"') + "," + e_splitted[idx+1][1].strip('"'))
449		e_splitted[idx] = (idx,result)
450		e_splitted.remove(e_splitted[idx+1])
451		com = True
452		rawdict[self._columns[idx]] = result
453		conc = self._columns[idx] # Main value's name
454
455
456		elif com:# We have rm the 2nd part value, consequently we
457		# need to decrement idx
458		if len(self._columns) <= idx-1:
459		self.err("Orphan value in column ${index}",
460		mapping={"index":str(idx + 1)},
461		numline=self._numline)
462		break
463		# We add and sync the result with its value's name
464		rawdict[self._columns[idx-1]] = result
465
466		else:
467		if len(self._columns) <= idx:
468		self.err("Orphan value in column ${index}",
469		mapping={"index":str(idx + 1)},
470		numline=self._numline)
471		break
472		rawdict[self._columns[idx]] = result
473
474		aname = rawdict[self._columns[0]]# The fisrt column is analytic name
475		if not aname:
476		self.err("No Analysis Name defined", numline=self._numline)
477		return 0
478		elif aname == "<H>":
479		# <H> maybe is data error header? We need more examples...
480		errors = rawdict.get('Compound')
481		notes = rawdict.get('Calibration')
482		rawdict['Notes'] = notes
483
484		rid = self._header['Sample']
485		if not rid:
486		self.err("No Sample defined", numline=self._numline)
487		return 0
488
489		notes = rawdict.get('Notes', '')
490		notes = "Notes: %s" % notes if notes else ''
491		rawdict['DefaultResult'] = conc
		0 ignored issues – show introduced 2018-07-25 08:58 UTC by Report Bug Copy Issue Report The variable `conc` does not seem to be defined in case the `for` loop on line `444` is not entered. Are you sure this can never be the case? Loading history...
492		# Replace to obtain UK values from default
493		rawdict[conc] = rawdict[conc].replace(',','.')
494		rawdict['Remarks'] = ' '.join([errors, notes])
495		rawres = self.getRawResults().get(rid, [])
496		raw = rawres[0] if len(rawres) > 0 else {}
497		raw[aname] = rawdict
498		if 'DateTime' not in raw:
499		try:
500		raw['DateTime'] = {'DateTime':self.csvDate2BikaDate(self._header['Date']),
501		'DefaultValue':'DateTime'}
502		except Exception:
503		pass
504
505		self._addRawResult(rid, raw, True)
506		return 0
507
508
509		def getAttachmentFileType(self):
510		return "PANalytical - Omnia Axios XRF"
511
512
513		class AxiosXrfImporter(AnalysisResultsImporter):
514
515		def __init__(self, parser, context, override,
516		allowed_ar_states=None, allowed_analysis_states=None,
517		instrument_uid=None):
518		AnalysisResultsImporter.__init__(self, parser, context,
519		override,
520		allowed_ar_states,
521		allowed_analysis_states,
522		instrument_uid)
523

senaite / senaite.core

AxiosXrfCSVParser.parse_headerline() F last analyzed 2025-07-03 06:46 UTC

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AxiosXrfCSVParser.parse_headerline() F
last analyzed 2025-07-03 06:46 UTC