build.bika.lims.exportimport.instruments.resultsimport.InstrumentResultsFileParser.getInputFile() - 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
InstrumentResultsFileParser.getInputFile() A

↳ Parent: build.bika.lims.exportimport.instruments.resultsimport
Complexity

Conditions
Size

Total Lines	4
Code Lines	2
Duplication

Lines	0
Ratio	0 %
Importance

Changes
Metric	Value
eloc	2
dl	0
loc	4
rs	10
c	0
b	0
f	0
cc	1
nop	1
# -*- coding: utf-8 -*-
#
# This file is part of SENAITE.CORE
#
# Copyright 2018 by it's authors.
# Some rights reserved. See LICENSE.rst, CONTRIBUTORS.rst.

import codecs
from datetime import datetime
from DateTime import DateTime
from Products.CMFCore.utils import getToolByName
from Products.CMFPlone.utils import _createObjectByType
from bika.lims import api
from bika.lims import bikaMessageFactory as _, logger
from bika.lims.catalog import CATALOG_ANALYSIS_REQUEST_LISTING
from bika.lims.exportimport.instruments.logger import Logger
from bika.lims.idserver import renameAfterCreation
from bika.lims.utils import t
from bika.lims.utils import tmpID
from bika.lims.workflow import doActionFor


class InstrumentResultsFileParser(Logger):

    def __init__(self, infile, mimetype):
        Logger.__init__(self)
        self._infile = infile
        self._header = {}
        self._rawresults = {}
        self._mimetype = mimetype
        self._numline = 0

    def getInputFile(self):
        """ Returns the results input file
        """
        return self._infile

    def parse(self):
        """ Parses the input results file and populates the rawresults dict.
            See getRawResults() method for more info about rawresults format
            Returns True if the file has been parsed successfully.
            Is highly recommended to use _addRawResult method when adding
            raw results.
            IMPORTANT: To be implemented by child classes
        """
        raise NotImplementedError

    def getAttachmentFileType(self):
        """ Returns the file type name that will be used when creating the
            AttachmentType used by the importer for saving the results file as
            an attachment in each Analysis matched.
            By default returns self.getFileMimeType()
        """
        return self.getFileMimeType()

    def getFileMimeType(self):
        """ Returns the results file type
        """
        return self._mimetype

    def getHeader(self):
        """ Returns a dictionary with custom key, values
        """
        return self._header

    def _addRawResult(self, resid, values={}, override=False):
        """ Adds a set of raw results for an object with id=resid
            resid is usually an Analysis Request ID or Worksheet's Reference
            Analysis ID. The values are a dictionary in which the keys are
            analysis service keywords and the values, another dictionary with
            the key,value results.
            The column 'DefaultResult' must be provided, because is used to map
            to the column from which the default result must be retrieved.

            Example:
            resid  = 'DU13162-001-R1'
            values = {
                'D2': {'DefaultResult': 'Final Conc',
                       'Remarks':       '',
                       'Resp':          '5816',
                       'ISTD Resp':     '274638',
                       'Resp Ratio':    '0.0212',
                       'Final Conc':    '0.9145',
                       'Exp Conc':      '1.9531',
                       'Accuracy':      '98.19' },

                'D3': {'DefaultResult': 'Final Conc',
                       'Remarks':       '',
                       'Resp':          '5816',
                       'ISTD Resp':     '274638',
                       'Resp Ratio':    '0.0212',
                       'Final Conc':    '0.9145',
                       'Exp Conc':      '1.9531',
                       'Accuracy':      '98.19' }
                }
        """
        if override or resid not in self._rawresults.keys():
            self._rawresults[resid] = [values]
        else:
            self._rawresults[resid].append(values)

    def _emptyRawResults(self):
        """ Remove all grabbed raw results
        """
        self._rawresults = {}

    def getObjectsTotalCount(self):
        """ The total number of objects (ARs, ReferenceSamples, etc.) parsed
        """
        return len(self.getRawResults())

    def getResultsTotalCount(self):
        """ The total number of analysis results parsed
        """
        count = 0
        for val in self.getRawResults().values():
            count += len(val)
        return count

    def getAnalysesTotalCount(self):
        """ The total number of different analyses parsed
        """
        return len(self.getAnalysisKeywords())

    def getAnalysisKeywords(self):
        """ The analysis service keywords found
        """
        analyses = []
        for rows in self.getRawResults().values():
            for row in rows:
                analyses = list(set(analyses + row.keys()))
        return analyses

    def getRawResults(self):
        """ Returns a dictionary containing the parsed results data
            Each dict key is the results row ID (usually AR ID or Worksheet's
            Reference Sample ID). Each item is another dictionary, in which the
            key is a the AS Keyword.
            Inside the AS dict, the column 'DefaultResult' must be
            provided, that maps to the column from which the default
            result must be retrieved.
            If 'Remarks' column is found, it value will be set in Analysis
            Remarks field when using the deault Importer.

            Example:
            raw_results['DU13162-001-R1'] = [{

                'D2': {'DefaultResult': 'Final Conc',
                       'Remarks':       '',
                       'Resp':          '5816',
                       'ISTD Resp':     '274638',
                       'Resp Ratio':    '0.0212',
                       'Final Conc':    '0.9145',
                       'Exp Conc':      '1.9531',
                       'Accuracy':      '98.19' },

                'D3': {'DefaultResult': 'Final Conc',
                       'Remarks':       '',
                       'Resp':          '5816',
                       'ISTD Resp':     '274638',
                       'Resp Ratio':    '0.0212',
                       'Final Conc':    '0.9145',
                       'Exp Conc':      '1.9531',
                       'Accuracy':      '98.19' }]

            in which:
            - 'DU13162-001-R1' is the Analysis Request ID,
            - 'D2' column is an analysis service keyword,
            - 'DefaultResult' column maps to the column with default result
            - 'Remarks' column with Remarks results for that Analysis
            - The rest of the dict columns are results (or additional info)
              that can be set to the analysis if needed (the default importer
              will look for them if the analysis has Interim fields).

            In the case of reference samples:
            Control/Blank:
            raw_results['QC13-0001-0002'] = {...}

            Duplicate of sample DU13162-009 (from AR DU13162-009-R1)
            raw_results['QC-DU13162-009-002'] = {...}

        """
        return self._rawresults

    def resume(self):
        """ Resumes the parse process
            Called by the Results Importer after parse() call
        """
        if len(self.getRawResults()) == 0:
            self.warn("No results found")
            return False
        return True


class InstrumentCSVResultsFileParser(InstrumentResultsFileParser):

    def __init__(self, infile, encoding=None):
        InstrumentResultsFileParser.__init__(self, infile, 'CSV')
        # Some Instruments can generate files with different encodings, so we
        # may need this parameter
        self._encoding = encoding

    def parse(self):
        infile = self.getInputFile()
        self.log("Parsing file ${file_name}",
                 mapping={"file_name": infile.filename})
        jump = 0
        # We test in import functions if the file was uploaded
        try:
            if self._encoding:
                f = codecs.open(infile.name, 'r', encoding=self._encoding)
            else:
                f = open(infile.name, 'rU')
        except AttributeError:
            f = infile
        for line in f.readlines():
            self._numline += 1
            if jump == -1:
                # Something went wrong. Finish
                self.err("File processing finished due to critical errors")
                return False
            if jump > 0:
                # Jump some lines
                jump -= 1
                continue

            if not line or not line.strip():
                continue

            line = line.strip()
            jump = 0
            if line:
                jump = self._parseline(line)

        self.log(
            "End of file reached successfully: ${total_objects} objects, "
            "${total_analyses} analyses, ${total_results} results",
            mapping={"total_objects": self.getObjectsTotalCount(),
                     "total_analyses": self.getAnalysesTotalCount(),
                     "total_results": self.getResultsTotalCount()}
        )
        return True

    def splitLine(self, line):
        sline = line.split(',')
        return [token.strip() for token in sline]

    def _parseline(self, line):
        """ Parses a line from the input CSV file and populates rawresults
            (look at getRawResults comment)
            returns -1 if critical error found and parser must end
            returns the number of lines to be jumped in next read. If 0, the
            parser reads the next line as usual
        """
        raise NotImplementedError


class InstrumentTXTResultsFileParser(InstrumentResultsFileParser):

    def __init__(self, infile, separator, encoding=None,):
        InstrumentResultsFileParser.__init__(self, infile, 'TXT')
        # Some Instruments can generate files with different encodings, so we
        # may need this parameter
        self._separator = separator
        self._encoding = encoding

    def parse(self):
        infile = self.getInputFile()
        self.log("Parsing file ${file_name}", mapping={"file_name": infile.filename})
        jump = 0
        lines = self.read_file(infile)
        for line in lines:
            self._numline += 1
            if jump == -1:
                # Something went wrong. Finish
                self.err("File processing finished due to critical errors")
                return False
            if jump > 0:
                # Jump some lines
                jump -= 1
                continue

            if not line:
                continue

            jump = 0
            if line:
                jump = self._parseline(line)

        self.log(
            "End of file reached successfully: ${total_objects} objects, "
            "${total_analyses} analyses, ${total_results} results",
            mapping={"total_objects": self.getObjectsTotalCount(),
                     "total_analyses": self.getAnalysesTotalCount(),
                     "total_results": self.getResultsTotalCount()}
        )
        return True

    def read_file(self, infile):
        """Given an input file read its contents, strip whitespace from the
         beginning and end of each line and return a list of the preprocessed
         lines read.

        :param infile: file that contains the data to be read
        :return: list of the read lines with stripped whitespace
        """
        try:
            encoding = self._encoding if self._encoding else None
            mode = 'r' if self._encoding else 'rU'
            with codecs.open(infile.name, mode, encoding=encoding) as f:
                lines = f.readlines()
        except AttributeError:
            lines = infile.readlines()
        lines = [line.strip() for line in lines]
        return lines

    def split_line(self, line):
        sline = line.split(self._separator)
        return [token.strip() for token in sline]

    def _parseline(self, line):
        """ Parses a line from the input CSV file and populates rawresults
            (look at getRawResults comment)
            returns -1 if critical error found and parser must end
            returns the number of lines to be jumped in next read. If 0, the
            parser reads the next line as usual
        """
        raise NotImplementedError


class AnalysisResultsImporter(Logger):

    def __init__(self, parser, context,
                 override=[False, False],
                 allowed_ar_states=None,
                 allowed_analysis_states=None,
                 instrument_uid=None):
        Logger.__init__(self)
        self._parser = parser
        self.context = context
        self._allowed_ar_states = allowed_ar_states
        self._allowed_analysis_states = allowed_analysis_states
        self._override = override
        self._idsearch = ['getId', 'getClientSampleID']
        self._priorizedsearchcriteria = ''
        self.bsc = getToolByName(self.context, 'bika_setup_catalog')
        self.bac = getToolByName(self.context, 'bika_analysis_catalog')
        self.ar_catalog = getToolByName(
            self.context, CATALOG_ANALYSIS_REQUEST_LISTING)
        self.pc = getToolByName(self.context, 'portal_catalog')
        self.bc = getToolByName(self.context, 'bika_catalog')
        self.wf = getToolByName(self.context, 'portal_workflow')
        if not self._allowed_ar_states:
            self._allowed_ar_states = ['sample_received',
                                       'attachment_due',
                                       'to_be_verified']
        if not self._allowed_analysis_states:
            self._allowed_analysis_states = [
                'unassigned', 'assigned', 'to_be_verified'
            ]
        if not self._idsearch:
            self._idsearch = ['getId']
        self.instrument_uid = instrument_uid

    def getParser(self):
        """ Returns the parser that will be used for the importer
        """
        return self._parser

    def getAllowedARStates(self):
        """ The allowed Analysis Request states
            The results import will only take into account the analyses
            contained inside an Analysis Request which current state is one
            from these.
        """
        return self._allowed_ar_states

    def getAllowedAnalysisStates(self):
        """ The allowed Analysis states
            The results import will only take into account the analyses
            if its current state is in the allowed analysis states.
        """
        return self._allowed_analysis_states

    def getOverride(self):
        """ If the importer must override previously entered results.
            [False, False]: The results will not be overriden
            [True, False]: The results will be overriden only if there's no
                           result entered yet,
            [True, True]: The results will be always overriden, also if the
                          parsed result is empty.
        """
        return self._override

    def getKeywordsToBeExcluded(self):
        """ Returns an array with the analysis codes/keywords to be excluded
            by the importer. By default, an empty array
        """
        return []

    def process(self):
        self._parser.parse()
        parsed = self._parser.resume()
        self._errors = self._parser.errors
        self._warns = self._parser.warns
        self._logs = self._parser.logs
        self._priorizedsearchcriteria = ''

        if parsed is False:
            return False

        # Allowed analysis states
        allowed_ar_states_msg = [t(_(s)) for s in self.getAllowedARStates()]
        allowed_an_states_msg = [
                t(_(s)) for s in self.getAllowedAnalysisStates()]
        self.log("Allowed Sample states: ${allowed_states}",
                 mapping={'allowed_states': ', '.join(allowed_ar_states_msg)})
        self.log("Allowed analysis states: ${allowed_states}",
                 mapping={'allowed_states': ', '.join(allowed_an_states_msg)})

        # Exclude non existing ACODEs
        acodes = []
        ancount = 0
        instprocessed = []
        importedars = {}
        importedinsts = {}
        rawacodes = self._parser.getAnalysisKeywords()
        exclude = self.getKeywordsToBeExcluded()
        for acode in rawacodes:
            if acode in exclude or not acode:
                continue
            service = self.bsc(getKeyword=acode)
            if not service:
                self.warn('Service keyword ${analysis_keyword} not found',
                          mapping={"analysis_keyword": acode})
            else:
                acodes.append(acode)
        if len(acodes) == 0:
            self.warn("Service keywords: no matches found")

        # Attachments will be created in any worksheet that contains
        # analyses that are updated by this import
        attachments = {}
        infile = self._parser.getInputFile()

        for objid, results in self._parser.getRawResults().iteritems():
            # Allowed more than one result for the same sample and analysis.
            # Needed for calibration tests
            for result in results:
                analyses = self._getZODBAnalyses(objid)
                inst = None
                if len(analyses) == 0 and self.instrument_uid:
                    # No registered analyses found, but maybe we need to
                    # create them first if an instruemnt id has been set in
                    insts = self.bsc(portal_type='Instrument',
                                     UID=self.instrument_uid)
                    if len(insts) == 0:
                        # No instrument found
                        self.warn("No Sample with "
                                  "'${allowed_ar_states}' "
                                  "states found, And no QC"
                                  "analyses found for ${object_id}",
                                  mapping={"allowed_ar_states": ', '.join(
                                      allowed_ar_states_msg),
                                          "object_id": objid})
                        self.warn("Instrument not found")
                        continue

                    inst = insts[0].getObject()

                    # Create a new ReferenceAnalysis and link it to
                    # the Instrument
                    # Here we have an objid (i.e. R01200012) and
                    # a dict with results (the key is the AS keyword).
                    # How can we create a ReferenceAnalysis if we don't know
                    # which ReferenceSample we might use?
                    # Ok. The objid HAS to be the ReferenceSample code.
                    refsample = self.bc(portal_type='ReferenceSample', id=objid)
                    if refsample and len(refsample) == 1:
                        refsample = refsample[0].getObject()

                    elif refsample and len(refsample) > 1:
                        # More than one reference sample found!
                        self.warn(
                            "More than one reference sample found for"
                            "'${object_id}'",
                            mapping={"object_id": objid})
                        continue

                    else:
                        # No reference sample found!
                        self.warn("No Reference Sample found for ${object_id}",
                                  mapping={"object_id": objid})
                        continue

                    # For each acode, create a ReferenceAnalysis and attach it
                    # to the Reference Sample
                    services = self.bsc(portal_type='AnalysisService')
                    service_uids = [service.UID for service in services
                                    if service.getObject().getKeyword()
                                    in result.keys()]
                    analyses = inst.addReferences(refsample, service_uids)

                elif len(analyses) == 0:
                    # No analyses found
                    self.warn("No Sample with "
                              "'${allowed_ar_states}' "
                              "states neither QC analyses found "
                              "for ${object_id}",
                              mapping={
                                 "allowed_ar_states": ', '.join(
                                     allowed_ar_states_msg),
                                 "object_id": objid})
                    continue

                # Look for timestamp
                capturedate = result.get('DateTime', {}).get('DateTime', None)
                if capturedate:
                    del result['DateTime']
                for acode, values in result.iteritems():
                    if acode not in acodes:
                        # Analysis keyword doesn't exist
                        continue

                    ans = [analysis for analysis in analyses
                           if analysis.getKeyword() == acode]

                    if len(ans) > 1:
                        self.warn("More than one analysis found for "
                                  "${object_id} and ${analysis_keyword}",
                                  mapping={"object_id": objid,
                                           "analysis_keyword": acode})
                        continue

                    elif len(ans) == 0:
                        self.warn("No analyses found for ${object_id} "
                                  "and ${analysis_keyword}",
                                  mapping={"object_id": objid,
                                           "analysis_keyword": acode})
                        continue

                    analysis = ans[0]

                    # Create attachment in worksheet linked to this analysis.
                    # Only if this import has not already created the
                    # attachment
                    # And only if the filename of the attachment is unique in
                    # this worksheet.  Otherwise we will attempt to use
                    # existing attachment.
                    ws = analysis.getWorksheet()
                    if ws:
                        if ws.getId() not in attachments:
                            fn = infile.filename
                            fn_attachments = self.get_attachment_filenames(ws)
                            if fn in fn_attachments.keys():
                                attachments[ws.getId()] = fn_attachments[fn]
                            else:
                                attachments[ws.getId()] = \
                                    self.create_attachment(ws, infile)

                    if capturedate:
                        values['DateTime'] = capturedate
                    processed = self._process_analysis(objid, analysis, values)
                    if processed:
                        ancount += 1
                        if inst:
                            # Calibration Test (import to Instrument)
                            instprocessed.append(inst.UID())
                            importedinst = inst.title in importedinsts.keys() \
                                and importedinsts[inst.title] or []
                            if acode not in importedinst:
                                importedinst.append(acode)
                            importedinsts[inst.title] = importedinst
                        else:
                            ar = analysis.portal_type == 'Analysis' \
                                and analysis.aq_parent or None
                            if ar and ar.UID:
                                importedar = ar.getId() in importedars.keys() \
                                            and importedars[ar.getId()] or []
                                if acode not in importedar:
                                    importedar.append(acode)
                                importedars[ar.getId()] = importedar

                        if ws:
                            self.attach_attachment(
                                analysis, attachments[ws.getId()])
                        else:
                            self.warn(
                                "Attachment cannot be linked to analysis as "
                                "it is not assigned to a worksheet (%s)" %
                                analysis)

        for arid, acodes in importedars.iteritems():
            acodesmsg = ["Analysis %s" % acod for acod in acodes]
            self.log(
                    "${request_id}: ${analysis_keywords} imported sucessfully",
                    mapping={"request_id": arid,
                             "analysis_keywords": acodesmsg})

        for instid, acodes in importedinsts.iteritems():
            acodesmsg = ["Analysis %s" % acod for acod in acodes]
            msg = "%s: %s %s" % (instid,
                                 ", ".join(acodesmsg),
                                 "imported sucessfully")
            self.log(msg)

        if self.instrument_uid:
            self.log(
                "Import finished successfully: ${nr_updated_ars} Samples, "
                "${nr_updated_instruments} Instruments and "
                "${nr_updated_results} "
                "results updated",
                mapping={"nr_updated_ars": str(len(importedars)),
                         "nr_updated_instruments": str(len(importedinsts)),
                         "nr_updated_results": str(ancount)})
        else:
            self.log(
                "Import finished successfully: ${nr_updated_ars} Samples and "
                "${nr_updated_results} results updated",
                mapping={"nr_updated_ars": str(len(importedars)),
                         "nr_updated_results": str(ancount)})

    def create_mime_attachmenttype(self):
        # Create the AttachmentType for mime type if not exists
        attachmentType = self.bsc(portal_type="AttachmentType",
                                  title=self._parser.getAttachmentFileType())
        if not attachmentType:
            folder = self.context.bika_setup.bika_attachmenttypes
            obj = _createObjectByType("AttachmentType", folder, tmpID())
            obj.edit(title=self._parser.getAttachmentFileType(),
                     description="Autogenerated file type")
            obj.unmarkCreationFlag()
            renameAfterCreation(obj)
            attuid = obj.UID()
        else:
            attuid = attachmentType[0].UID
        return attuid

    def create_attachment(self, ws, infile):
        attuid = self.create_mime_attachmenttype()
        attachment = None
        if attuid and infile:
            attachment = _createObjectByType("Attachment", ws, tmpID())
            logger.info("Creating %s in %s" % (attachment, ws))
            attachment.edit(
                AttachmentFile=infile,
                AttachmentType=attuid,
                AttachmentKeys='Results, Automatic import')
            attachment.reindexObject()
        return attachment

    def attach_attachment(self, analysis, attachment):
        """
        Attach a file or a given set of files to an analysis

        :param analysis: analysis where the files are to be attached
        :param attachment: files to be attached. This can be either a
        single file or a list of files
        :return: None
        """
        if not attachment:
            return
        if isinstance(attachment, list):
            for attach in attachment:
                self.attach_attachment(analysis, attach)
            return
        # current attachments
        an_atts = analysis.getAttachment()
        atts_filenames = [att.getAttachmentFile().filename for att in an_atts]
        if attachment.getAttachmentFile().filename not in atts_filenames:
            an_atts.append(attachment)
            logger.info(
                "Attaching %s to %s" % (attachment.UID(), analysis))
            analysis.setAttachment([att.UID() for att in an_atts])
            analysis.reindexObject()
        else:
            self.warn("Attachment %s was not linked to analysis %s" %
                      (attachment.UID(), analysis))

    def get_attachment_filenames(self, ws):
        fn_attachments = {}
        for att in ws.objectValues('Attachment'):
            fn = att.getAttachmentFile().filename
            if fn not in fn_attachments:
                fn_attachments[fn] = []
            fn_attachments[fn].append(att)
        return fn_attachments

    def _getObjects(self, objid, criteria, states):
        # self.log("Criteria: %s %s") % (criteria, obji))
        obj = []
        if criteria in ['arid']:
            obj = self.ar_catalog(
                           getId=objid,
                           review_state=states)
        elif criteria == 'csid':
            obj = self.ar_catalog(
                           getClientSampleID=objid,
                           review_state=states)
        elif criteria == 'aruid':
            obj = self.ar_catalog(
                           UID=objid,
                           review_state=states)
        elif criteria == 'rgid':
            obj = self.bac(portal_type=['ReferenceAnalysis',
                                        'DuplicateAnalysis'],
                           getReferenceAnalysesGroupID=objid)
        elif criteria == 'rid':
            obj = self.bac(portal_type=['ReferenceAnalysis',
                                        'DuplicateAnalysis'], id=objid)
        elif criteria == 'ruid':
            obj = self.bac(portal_type=['ReferenceAnalysis',
                                        'DuplicateAnalysis'], UID=objid)
        if obj and len(obj) > 0:
            self._priorizedsearchcriteria = criteria
        return obj

    def _getZODBAnalyses(self, objid):
        """ Searches for analyses from ZODB to be filled with results.
            objid can be either AR ID or Worksheet's Reference Sample IDs.
            Only analyses that matches with getAnallowedAnalysisStates() will
            be returned. If not a ReferenceAnalysis, getAllowedARStates() is
            also checked.
            Returns empty array if no analyses found
        """
        # ars = []
        analyses = []
        searchcriteria = ['getId', 'getClientSampleID']
        allowed_ar_states = self.getAllowedARStates()
        allowed_an_states = self.getAllowedAnalysisStates()
        # allowed_ar_states_msg = [_(s) for s in allowed_ar_states]
        allowed_an_states_msg = [_(s) for s in allowed_an_states]

        # Acceleration of searches using priorization
        if self._priorizedsearchcriteria in ['rgid', 'rid', 'ruid']:
            # Look from reference analyses
            analyses = self._getZODBAnalysesFromReferenceAnalyses(
                    objid, self._priorizedsearchcriteria)
        if len(analyses) == 0:
            # Look from ar and derived
            analyses = self._getZODBAnalysesFromAR(objid,
                                                   '',
                                                   searchcriteria,
                                                   allowed_ar_states)

        # Discard analyses that don't match with allowed_an_states
        analyses = [analysis for analysis in analyses
                    if analysis.portal_type != 'Analysis' or
                    self.wf.getInfoFor(analysis, 'review_state')
                    in allowed_an_states]

        if len(analyses) == 0:
            self.warn(
                "No analyses '${allowed_analysis_states}' "
                "states found for ${object_id}",
                mapping={"allowed_analysis_states": ', '.join(
                    allowed_an_states_msg),
                         "object_id": objid})

        return analyses

    def _getZODBAnalysesFromAR(self, objid, criteria,
                               allowedsearches, arstates):
        ars = []
        analyses = []
        if criteria:
            ars = self._getObjects(objid, criteria, arstates)
            if not ars or len(ars) == 0:
                return self._getZODBAnalysesFromAR(objid, None,
                                                   allowedsearches, arstates)
        else:
            sortorder = ['arid', 'csid', 'aruid']
            for crit in sortorder:
                if (crit == 'arid' and 'getId' in allowedsearches) \
                    or (crit == 'csid' and 'getClientSampleID'
                                in allowedsearches) \
                        or (crit == 'aruid' and 'getId' in allowedsearches):
                    ars = self._getObjects(objid, crit, arstates)
                    if ars and len(ars) > 0:
                        break

        if not ars or len(ars) == 0:
            return self._getZODBAnalysesFromReferenceAnalyses(objid, None)

        elif len(ars) > 1:
            self.err("More than one Sample found for ${object_id}",
                     mapping={"object_id": objid})
            return []

        ar = ars[0].getObject()
        analyses = [analysis.getObject() for analysis in ar.getAnalyses()]

        return analyses

    def _getZODBAnalysesFromReferenceAnalyses(self, objid, criteria):
        analyses = []
        if criteria:
            refans = self._getObjects(objid, criteria, [])
            if len(refans) == 0:
                return []

            elif criteria == 'rgid':
                return [an.getObject() for an in refans]

            elif len(refans) == 1:
                # The search has been made using the internal identifier
                # from a Reference Analysis (id or uid). That is not usual.
                an = refans[0].getObject()
                worksheet = an.getWorksheet()
                if worksheet:
                    # A regular QC test (assigned to a Worksheet)
                    return [an, ]
                elif an.getInstrument():
                    # An Internal Calibration Test
                    return [an, ]
                else:
                    # Oops. This should never happen!
                    # A ReferenceAnalysis must be always assigned to
                    # a Worksheet (Regular QC) or to an Instrument
                    # (Internal Calibration Test)
                    self.err("The Reference Analysis ${object_id} has neither "
                             "instrument nor worksheet assigned",
                             mapping={"object_id": objid})
                    return []
            else:
                # This should never happen!
                # Fetching ReferenceAnalysis for its id or uid should
                # *always* return a unique result
                self.err(
                    "More than one Reference Analysis found for ${obect_id}",
                    mapping={"object_id": objid})
                return []

        else:
            sortorder = ['rgid', 'rid', 'ruid']
            for crit in sortorder:
                analyses = self._getZODBAnalysesFromReferenceAnalyses(objid,
                                                                      crit)
                if len(analyses) > 0:
                    return analyses

        return analyses

    def calculateTotalResults(self, objid, analysis):
        """ If an AR(objid) has an analysis that has a calculation
        then check if param analysis is used on the calculations formula.
        Here we are dealing with two types of analysis.
        1. Calculated Analysis - Results are calculated.
        2. Analysis - Results are captured and not calculated
        :param objid: AR ID or Worksheet's Reference Sample IDs
        :param analysis: Analysis Object
        """
        analyses = self._getZODBAnalyses(objid)
        # Filter Analyses With Calculation
        analyses_with_calculation = filter(
                                        lambda an: an.getCalculation(),
                                        analyses)
        for analysis_with_calc in analyses_with_calculation:
            # Get the calculation to get the formula so that we can check
            # if param analysis keyword is used on the calculation formula
            calcultion = analysis_with_calc.getCalculation()
            formula = calcultion.getMinifiedFormula()
            # The analysis that we are currenly on
            analysis_keyword = analysis.getKeyword()
            if analysis_keyword not in formula:
                continue

            # If the analysis_keyword is in the formula, it means that this
            # analysis is a dependent on that calculated analysis
            calc_passed = analysis_with_calc.calculateResult(override=self._override[1])
            if calc_passed:
                api.do_transition_for(analysis_with_calc, "submit")
                self.log(
                    "${request_id}: calculated result for "
                    "'${analysis_keyword}': '${analysis_result}'",
                    mapping={"request_id": objid,
                             "analysis_keyword": analysis_with_calc.getKeyword(),
                             "analysis_result": str(analysis_with_calc.getResult())}
                )


    def _process_analysis(self, objid, analysis, values):
        resultsaved = False
        acode = analysis.getKeyword()
        defresultkey = values.get("DefaultResult", "")
        capturedate = None
        # Look for timestamp
        if "DateTime" in values.keys():
            try:
                dt = values.get('DateTime')
                capturedate = DateTime(datetime.strptime(dt,
                                                         '%Y%m%d %H:%M:%S'))
            except:
                capturedate = None
                pass
            del values['DateTime']

        fields_to_reindex = []
        # get interims
        interimsout = []
        interims = hasattr(analysis, 'getInterimFields') \
                   and analysis.getInterimFields() or []
        for interim in interims:
            keyword = interim['keyword']
            title = interim['title']
            if values.get(keyword, '') or values.get(keyword, '') == 0:
                res = values.get(keyword)
                self.log("${request_id} result for "
                         "'${analysis_keyword}:${interim_keyword}': "
                         "'${result}'",
                         mapping={"request_id": objid,
                                  "analysis_keyword": acode,
                                  "interim_keyword": keyword,
                                  "result": str(res)}
                         )
                ninterim = interim.copy()
                ninterim['value'] = res
                interimsout.append(ninterim)
                resultsaved = True
            elif values.get(title, '') or values.get(title, '') == 0:
                res = values.get(title)
                self.log("%s/'%s:%s': '%s'" % (objid, acode, title, str(res)))
                ninterim = interim.copy()
                ninterim['value'] = res
                interimsout.append(ninterim)
                resultsaved = True
            else:
                interimsout.append(interim)
        # write interims
        if len(interimsout) > 0:
            analysis.setInterimFields(interimsout)
            analysis.calculateResult(override=self._override[1])

        # Set result if present.
        res = values.get(defresultkey, '')
        if res or res == 0 or self._override[1] == True:
            # self.log("${object_id} result for '${analysis_keyword}': '${result}'",
            #          mapping={"obect_id": obid,
            #                   "analysis_keyword": acode,
            #                   "result": str(res)})
            # TODO incorporar per veure detall d'importacio
            analysis.setResult(res)
            if capturedate:
                analysis.setResultCaptureDate(capturedate)
            resultsaved = True

        if resultsaved == False:
            self.log(
                "${request_id} result for '${analysis_keyword}': '${result}'",
                mapping={"request_id": objid,
                         "analysis_keyword": acode,
                         "result": ""})

        if resultsaved:
            doActionFor(analysis, 'submit')
            self.calculateTotalResults(objid, analysis)
            fields_to_reindex.append('Result')

        if (resultsaved) \
            and values.get('Remarks', '') \
            and analysis.portal_type == 'Analysis' \
            and (analysis.getRemarks() != '' or self._override[1] == True):
            analysis.setRemarks(values['Remarks'])
            fields_to_reindex.append('Remarks')

        if len(fields_to_reindex):
            analysis.reindexObject(idxs=fields_to_reindex)
        return resultsaved

senaite / senaite.core

Push — master ( d8e2ec...90ae0b )

InstrumentResultsFileParser.getInputFile() A

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

Filter issues like
