Ejemplo n.º 1
0
 def test_get_projects_new(self):
     newProjects = ','.join([' a ', 'b', '', ' ', ' a b '])
     data = {'projects': [], 'newProjects': newProjects}
     result = get_projects('ionadmin', data)
     self.assertEqual(len(result), 3,
                      'Incorrect number of projects created')
     Project.objects.get(name='a')
     Project.objects.get(name='b')
     Project.objects.get(name='a_b')
Ejemplo n.º 2
0
 def test_get_projects_new(self):
     newProjects = ','.join([' a ', 'b', '', ' ', ' a b '])
     data = {'projects':[],
             'newProjects': newProjects}
     result = get_projects('ionadmin', data)
     self.assertEqual(len(result), 3, 'Incorrect number of projects created')
     Project.objects.get(name='a')
     Project.objects.get(name='b')
     Project.objects.get(name='a_b')
Ejemplo n.º 3
0
 def test_get_projects_existing(self):
     projects = test_project.bulk_get_or_create_create_multi_projects(self)
     self.assertEqual(len(projects), 3, 'Incorrect number of projects created')
     Project.objects.get(name='a')
     Project.objects.get(name='b')
     Project.objects.get(name='a_b')
     projectNameAndIds = [str(p.id) + '|' + p.name for p in projects]
     
     data = {'projects':projectNameAndIds,
             'newProjects': []}
     result = get_projects('ionadmin', data)
     self.assertEqual(len(result), len(projects), 'Incorrect number of projects retrieved')
     Project.objects.get(name='a')
     Project.objects.get(name='b')
     Project.objects.get(name='a_b')
Ejemplo n.º 4
0
    def test_get_projects_existing(self):
        projects = test_project.bulk_get_or_create_create_multi_projects(self)
        self.assertEqual(len(projects), 3,
                         'Incorrect number of projects created')
        Project.objects.get(name='a')
        Project.objects.get(name='b')
        Project.objects.get(name='a_b')
        projectNameAndIds = [str(p.id) + '|' + p.name for p in projects]

        data = {'projects': projectNameAndIds, 'newProjects': []}
        result = get_projects('ionadmin', data)
        self.assertEqual(len(result), len(projects),
                         'Incorrect number of projects retrieved')
        Project.objects.get(name='a')
        Project.objects.get(name='b')
        Project.objects.get(name='a_b')
Ejemplo n.º 5
0
Archivo: views.py Proyecto: aidjek/TS
def save_plan_or_template(request, planOid):
    """
    Saving new or edited plan/template to db (source: plan template wizard)
    Editing a planned run from having 1 sample to 2 samples will result in one edited planned run and one new planned run
    """
    def isReusable(submitIntent):
        return not (submitIntent == 'savePlan' or submitIntent == 'updatePlan')

    if request.method != 'POST':
        logger.exception(format_exc())
        return HttpResponse(json.dumps({
            "error":
            "Error, unsupported HTTP Request method (%s) for plan update." %
            request.method
        }),
                            mimetype="application/json")

    # Process Inputs

    # pylint:disable=E1103
    json_data = simplejson.loads(request.raw_post_data)
    submitIntent = json_data.get('submitIntent', '')
    logger.debug(
        'views.save_plan_or_template POST.raw_post_data... simplejson Data: "%s"'
        % json_data)
    logger.debug("views.save_plan_or_template submitIntent=%s" % submitIntent)
    # saving Template or Planned Run
    isReusable = isReusable(submitIntent)
    runModeValue = json_data.get('runMode', 'single')
    isPlanGroupValue = runModeValue == 'pe' and not isReusable
    libraryKeyValue = json_data.get('libraryKey', '')
    forward3primeAdapterValue = json_data.get('forward3primeAdapter', '')

    msgvalue = 'Run Plan' if not isReusable else 'Template'
    if runModeValue == 'pe':
        return HttpResponse(json.dumps({
            "error":
            "Error, paired-end plan is no longer supported. %s will not be saved."
            % (msgvalue)
        }),
                            mimetype="application/html")

    planDisplayedNameValue = json_data.get('planDisplayedName', '').strip()
    noteValue = json_data.get('notes_workaround', '')

    # perform server-side validation to avoid things falling through the crack
    if not planDisplayedNameValue:
        return HttpResponse(json.dumps(
            {"error": "Error, please enter a %s Name." % (msgvalue)}),
                            mimetype="application/html")

    if not is_valid_chars(planDisplayedNameValue):
        return HttpResponse(json.dumps(
            {"error":
             "Error, %s Name" % (msgvalue) + ERROR_MSG_INVALID_CHARS}),
                            mimetype="application/html")

    if not is_valid_length(planDisplayedNameValue, MAX_LENGTH_PLAN_NAME):
        return HttpResponse(json.dumps({
            "error":
            "Error, %s Name" % (msgvalue) + ERROR_MSG_INVALID_LENGTH %
            (str(MAX_LENGTH_PLAN_NAME))
        }),
                            mimetype="application/html")

    if noteValue:
        if not is_valid_chars(noteValue):
            return HttpResponse(json.dumps({
                "error":
                "Error, %s note" % (msgvalue) + ERROR_MSG_INVALID_CHARS
            }),
                                mimetype="application/html")

        if not is_valid_length(noteValue, MAX_LENGTH_NOTES):
            return HttpResponse(json.dumps({
                "error":
                "Error, Note" + ERROR_MSG_INVALID_LENGTH %
                (str(MAX_LENGTH_NOTES))
            }),
                                mimetype="application/html")

    # Projects
    projectObjList = get_projects(request.user, json_data)

    # IonReporterUploader configuration and samples
    selectedPlugins = json_data.get('selectedPlugins', {})
    IRconfigList = json_data.get('irConfigList', [])

    IRU_selected = False
    for uploader in selectedPlugins.values():
        if 'ionreporteruploader' in uploader['name'].lower(
        ) and uploader['name'] != 'IonReporterUploader_V1_0':
            IRU_selected = True

    #if IRU is set to autoRun, user does not need to select the plugin explicitly. user could have set all IRU versions to autorun
    IRU_autorun_count = 0
    if not IRU_selected:
        IRU_autoruns = Plugin.objects.filter(
            name__icontains="IonReporter",
            selected=True,
            active=True,
            autorun=True).exclude(
                name__icontains="IonReporterUploader_V1_0").order_by('-name')
        IRU_autorun_count = IRU_autoruns.count()
        if IRU_autorun_count > 0:
            IRU_selected = True

    if IRU_selected:
        samples_IRconfig = json_data.get('sample_irConfig', '')

        if samples_IRconfig:
            samples_IRconfig = ','.join(samples_IRconfig)

        #generate UUID for unique setIds
        id_uuid = {}
        setids = [ir.get('setid', "") for ir in IRconfigList]

        if setids:
            for setid in set(setids):
                if setid:
                    id_uuid[setid] = str(uuid.uuid4())
            for ir_config in IRconfigList:
                setid = ir_config.get('setid', '')

                if setid:
                    ir_config['setid'] += '__' + id_uuid[setid]

        if IRU_autorun_count > 0 and not samples_IRconfig:
            #if more than one IRU version is set to autorun and user does not explicitly select one,
            #gui shows workflow config for IRU v1.0
            samples_IRconfig = json_data.get('samples_workaround', '')

    # Samples
    barcodeIdValue = json_data.get('barcodeId', '')
    barcodedSamples = ''
    sampleValidationErrorMsg = ''
    sampleValidationErrorMsg_leadingChars = ''
    sampleValidationErrorMsg_length = ''

    # one Plan will be created per entry in sampleList
    # samples for barcoded Plan have a separate field (barcodedSamples)

    if isReusable:
        # samples entered only when saving planned run (not template)
        sampleList = ['']
    elif barcodeIdValue:
        # a barcode Set is selected
        sampleList = ['']
        bcSamplesValues = json_data.get('bcSamples_workaround', '')
        bcDictionary = {}
        bcId = ""
        for token in bcSamplesValues.split(","):
            if ((token.find("bcKey|")) == 0):
                bcId, bcId_str = token.split("|")[1:]
            else:
                sample = token.strip()
                if bcId and sample:
                    if not is_valid_chars(sample):
                        sampleValidationErrorMsg += sample + ', '
                    elif is_invalid_leading_chars(sample):
                        sampleValidationErrorMsg_leadingChars += sample + ", "
                    elif not is_valid_length(sample, MAX_LENGTH_SAMPLE_NAME):
                        sampleValidationErrorMsg_length += sample + ", "

                    bcDictionary.setdefault(sample,
                                            {}).setdefault('barcodes',
                                                           []).append(bcId_str)
                bcId = ""

        barcodedSamples = simplejson.dumps(bcDictionary)
        logger.debug(
            "views.save_plan_or_template after simplejson.dumps... barcodedSamples=%s;"
            % (barcodedSamples))

        if not bcDictionary:
            transaction.rollback()
            return HttpResponse(json.dumps({
                "error":
                "Error, please enter at least one barcode sample name."
            }),
                                mimetype="application/html")

    else:
        # Non-barcoded samples
        sampleList = []
        if IRU_selected:
            samples = samples_IRconfig
        else:
            samples = json_data.get('samples_workaround', '')

        for sample in samples.split(','):
            if sample.strip():
                if not is_valid_chars(sample):
                    sampleValidationErrorMsg += sample + ', '
                elif is_invalid_leading_chars(sample):
                    sampleValidationErrorMsg_leadingChars += sample + ", "
                elif not is_valid_length(sample, MAX_LENGTH_SAMPLE_NAME):
                    sampleValidationErrorMsg_length += sample + ", "
                else:
                    sampleList.append(sample)

        logger.debug("views.save_plan_or_template sampleList=%s " %
                     (sampleList))

        if len(
                sampleList
        ) == 0 and not sampleValidationErrorMsg and not sampleValidationErrorMsg_leadingChars and not sampleValidationErrorMsg_length:
            transaction.rollback()
            return HttpResponse(json.dumps({
                "error":
                "Error, please enter a sample name for the run plan."
            }),
                                mimetype="application/html")

    # Samples validation
    if sampleValidationErrorMsg or sampleValidationErrorMsg_leadingChars or sampleValidationErrorMsg_length:
        message = ""
        if sampleValidationErrorMsg:
            message = "Error, sample name" + ERROR_MSG_INVALID_CHARS
            message = message + ' <br>Please fix: ' + sampleValidationErrorMsg + '<br>'
        if sampleValidationErrorMsg_leadingChars:
            message = message + "Error, sample name" + ERROR_MSG_INVALID_LEADING_CHARS
            message = message + ' <br>Please fix: ' + sampleValidationErrorMsg_leadingChars + '<br>'
        if sampleValidationErrorMsg_length:
            message = message + "Error, sample name" + ERROR_MSG_INVALID_LENGTH % (
                str(MAX_LENGTH_SAMPLE_NAME))
            message = message + ' <br>Please fix: ' + sampleValidationErrorMsg_length

        transaction.rollback()
        return HttpResponse(json.dumps({"error": message}),
                            mimetype="application/html")

    selectedPluginsValue = json_data.get('selectedPlugins', {})

    # end processing input data

    # Edit/Create Plan(s)

    if int(planOid) == 0:
        edit_existing_plan = False
    else:
        edit_existing_plan = True

    for i, sample in enumerate(sampleList):
        logger.debug(
            "...LOOP... views.save_plan_or_template SAMPLE=%s; isSystem=%s; isReusable=%s; isPlanGroup=%s "
            % (sample.strip(), json_data["isSystem"], isReusable,
               isPlanGroupValue))

        # add IonReporter config values for each sample
        if len(IRconfigList) > 0:
            for uploader in selectedPluginsValue.values():
                if 'ionreporteruploader' in uploader['name'].lower():
                    if len(IRconfigList) > 1 and not barcodeIdValue:
                        uploader['userInput'] = [IRconfigList[i]]
                    else:
                        uploader['userInput'] = IRconfigList

        if len(sampleList) > 1:
            inputPlanDisplayedName = planDisplayedNameValue + '_' + sample.strip(
            )
        else:
            inputPlanDisplayedName = planDisplayedNameValue

        selectedTemplatingKit = json_data.get('templatekitname', '')
        samplePrepInstrumentType = json_data.get('samplePrepInstrumentType',
                                                 '')
        if samplePrepInstrumentType == 'ionChef':
            selectedTemplatingKit = json_data.get('templatekitionchefname', '')

        #PDD-TODO: remove the x_ prefix. the x_ prefix is just a reminder what the obsolete attributes to remove during the next phase
        kwargs = {
            'planDisplayedName':
            inputPlanDisplayedName,
            "planName":
            inputPlanDisplayedName.replace(' ', '_'),
            'usePreBeadfind':
            toBoolean(json_data['usePreBeadfind'], False),
            'usePostBeadfind':
            toBoolean(json_data['usePostBeadfind'], False),
            'preAnalysis':
            True,
            'runType':
            json_data['runType'],
            'templatingKitName':
            selectedTemplatingKit,
            'controlSequencekitname':
            json_data.get('controlsequence', ''),
            'runMode':
            runModeValue,
            'isSystem':
            toBoolean(json_data['isSystem'], False),
            'isReusable':
            isReusable,
            'isPlanGroup':
            isPlanGroupValue,
            'username':
            request.user.username,
            'isFavorite':
            toBoolean(json_data.get('isFavorite', 'False'), False),
            'pairedEndLibraryAdapterName':
            json_data.get('pairedEndLibraryAdapterName', ''),
            'samplePrepKitName':
            json_data.get('samplePrepKitName', ''),
            'planStatus':
            "planned",
            'x_autoAnalyze':
            True,
            'x_barcodedSamples':
            barcodedSamples,
            'x_barcodeId':
            barcodeIdValue,
            'x_bedfile':
            json_data.get('bedfile', ''),
            'x_chipType':
            json_data.get('chipType', ''),
            'x_flows':
            json_data.get('flows', None),
            'x_forward3primeadapter':
            forward3primeAdapterValue,
            ###'_isReverseRun':  = self.isReverseRun
            'x_library':
            json_data.get('library', ''),
            'x_libraryKey':
            libraryKeyValue,
            'x_librarykitname':
            json_data.get('librarykitname', ''),
            'x_notes':
            noteValue,
            'x_regionfile':
            json_data.get('regionfile', ''),
            'x_sample':
            sample.strip().replace(' ', '_'),
            'x_sampleDisplayedName':
            sample.strip(),
            'x_selectedPlugins':
            selectedPluginsValue,
            'x_sequencekitname':
            json_data.get('sequencekitname', ''),
            'x_variantfrequency':
            json_data.get('variantfrequency', ''),
        }

        planTemplate = None

        #if we're changing a plan from having 1 sample to say 2 samples, we need to UPDATE 1 plan and CREATE 1 plan!!
        try:
            if not edit_existing_plan:
                planTemplate, extra_kwargs = PlannedExperiment.objects.save_plan(
                    -1, **kwargs)
            else:
                planTemplate, extra_kwargs = PlannedExperiment.objects.save_plan(
                    planOid, **kwargs)

                edit_existing_plan = False

            # Update QCtype thresholds
            qcTypes = QCType.objects.all()
            for qcType in qcTypes:
                qc_threshold = json_data.get(qcType.qcName, '')
                if qc_threshold:
                    # get existing PlannedExperimentQC if any
                    plannedExpQcs = PlannedExperimentQC.objects.filter(
                        plannedExperiment=planTemplate.id, qcType=qcType.id)
                    if len(plannedExpQcs) > 0:
                        for plannedExpQc in plannedExpQcs:
                            plannedExpQc.threshold = qc_threshold
                            plannedExpQc.save()
                    else:
                        kwargs = {
                            'plannedExperiment': planTemplate,
                            'qcType': qcType,
                            'threshold': qc_threshold
                        }
                        plannedExpQc = PlannedExperimentQC(**kwargs)
                        plannedExpQc.save()

            # add/remove projects
            if projectObjList:
                #TODO: refactor this logic to simplify using django orm
                projectNameList = [project.name for project in projectObjList]
                for currentProject in planTemplate.projects.all():
                    if currentProject.name not in projectNameList:
                        planTemplate.projects.remove(currentProject)
                for projectObj in projectObjList:
                    planTemplate.projects.add(projectObj)
            else:
                planTemplate.projects.clear()

        except ValidationError, err:
            transaction.rollback()
            logger.exception(format_exc())

            message = "Internal error while trying to save the plan. "
            for msg in err.messages:
                message += str(msg)
                message += " "

            return HttpResponse(json.dumps({"error": message}),
                                mimetype="application/json")

        except Exception as excp:
            transaction.rollback()
            logger.exception(format_exc())

            message = "Internal error while trying to save the plan. %s" % (
                excp.message)
            return HttpResponse(json.dumps({"error": message}),
                                mimetype="application/json")
Ejemplo n.º 6
0
Archivo: views.py Proyecto: aidjek/TS
def save_uploaded_plans_for_template(request):
    """add plans, with CSV validation"""
    logger.info(request)

    if request.method != 'POST':
        logger.exception(format_exc())
        transaction.rollback()
        return HttpResponse(json.dumps({
            "error":
            "Error, unsupported HTTP Request method (%s) for saving plan upload."
            % request.method
        }),
                            mimetype="application/json")

    postedfile = request.FILES['postedfile']
    destination = tempfile.NamedTemporaryFile(delete=False)

    for chunk in postedfile.chunks():
        destination.write(chunk)
    postedfile.close()
    destination.close()

    #check to ensure it is not empty
    headerCheck = open(destination.name, "rU")
    firstCSV = []
    for firstRow in csv.reader(headerCheck):
        firstCSV.append(firstRow)
        #logger.info("views.save_uploaded_plans_for_template() firstRow=%s;" %(firstRow))

    headerCheck.close()
    if not firstRow:
        os.unlink(destination.name)
        transaction.rollback()
        return HttpResponse(json.dumps(
            {"status": "Error: batch planning file is empty"}),
                            mimetype="text/html")

    index = 0
    plans = []
    rawPlanDataList = []
    failed = {}
    file = open(destination.name, "rU")
    reader = csv.DictReader(file)
    for index, row in enumerate(reader, start=1):
        errorMsg, aPlanDict, rawPlanDict, isToSkipRow = validate_csv_plan(row)

        logger.info(
            "views.save_uploaded_plans_for_template() index=%d; errorMsg=%s; planDict=%s"
            % (index, errorMsg, rawPlanDict))
        if errorMsg:
            logger.info(
                "views.save_uploaded_plans_for_template() ERROR MESSAGE index=%d; errorMsg=%s; planDict=%s"
                % (index, errorMsg, rawPlanDict))

            failed[index] = errorMsg
            continue
        elif isToSkipRow:
            logger.info(
                "views.save_uploaded_plans_for_template() SKIPPED ROW index=%d; row=%s"
                % (index, row))
            continue
        else:
            plans.append(aPlanDict)
            rawPlanDataList.append(rawPlanDict)

    destination.close()  # now close and remove the temp file
    os.unlink(destination.name)
    if index == 0:
        transaction.rollback()
        return HttpResponse(json.dumps({
            "status":
            "Error: There must be at least one plan! Please reload the page and try again with more plans."
        }),
                            mimetype="text/html")

    if failed:
        r = {
            "status": "Plan validation failed. The plans have not been saved.",
            "failed": failed
        }
        logger.info("views.save_uploaded_plans_for_template() failed=%s" % (r))

        transaction.rollback()
        return HttpResponse(json.dumps(r), mimetype="text/html")

    #saving to db needs to be the last thing to happen
    try:
        index = 0
        for planFamily in plans:
            plan = planFamily['plan']
            plan.save()

            expObj = planFamily['exp']
            expObj.plan = plan
            expObj.expName = plan.planGUID
            expObj.unique = plan.planGUID
            expObj.displayname = plan.planGUID
            expObj.save()

            easObj = planFamily['eas']
            easObj.experiment = expObj
            easObj.isEditable = True
            easObj.save()

            #saving/associating samples
            sampleDisplayedNames = planFamily['samples']
            sampleNames = [
                name.replace(' ', '_') for name in sampleDisplayedNames
            ]
            externalId = None
            for name, displayedName in zip(sampleNames, sampleDisplayedNames):
                sample_kwargs = {
                    'name': name,
                    'displayedName': displayedName,
                    'date': plan.date,
                    'status': plan.planStatus,
                    'externalId': externalId
                }

                sample = Sample.objects.get_or_create(
                    name=name, externalId=externalId,
                    defaults=sample_kwargs)[0]
                sample.experiments.add(expObj)
                sample.save()

            planDict = rawPlanDataList[index]

            # add QCtype thresholds
            qcTypes = QCType.objects.all()
            for qcType in qcTypes:
                qc_threshold = planDict.get(qcType.qcName, '')
                if qc_threshold:
                    # get existing PlannedExperimentQC if any
                    plannedExpQcs = PlannedExperimentQC.objects.filter(
                        plannedExperiment=plan.id, qcType=qcType.id)
                    if len(plannedExpQcs) > 0:
                        for plannedExpQc in plannedExpQcs:
                            plannedExpQc.threshold = qc_threshold
                            plannedExpQc.save()
                    else:
                        kwargs = {
                            'plannedExperiment': plan,
                            'qcType': qcType,
                            'threshold': qc_threshold
                        }
                        plannedExpQc = PlannedExperimentQC(**kwargs)
                        plannedExpQc.save()

            # add projects
            projectObjList = get_projects(request.user, planDict)
            for project in projectObjList:
                if project:
                    plan.projects.add(project)

            index += 1
    except:
        logger.exception(format_exc())
        transaction.rollback()
        return HttpResponse(json.dumps(
            {"status": "Error saving plans to database!"}),
                            mimetype="text/html")
        ##return HttpResponse(json.dumps({"error": "Internal error while trying to save the plan."}), mimetype="application/json")
    else:
        transaction.commit()
        r = {
            "status":
            "Plans Uploaded! The plans will be listed on the planned run page.",
            "failed": failed
        }
        return HttpResponse(json.dumps(r), mimetype="text/html")
Ejemplo n.º 7
0
 def test_get_projects(self):
     data = {'projects': [], 'newProjects': []}
     #        data = simplejson.loads(data)
     result = get_projects('ionadmin', data)
     self.assertFalse(result, 'list should be empty')
Ejemplo n.º 8
0
def save_plan_or_template(request, planOid):
    """
    Saving new or edited plan/template to db (source: plan template wizard)
    Editing a planned run from having 1 sample to 2 samples will result in one edited planned run and one new planned run
    """
    def isReusable(submitIntent):
        return not (submitIntent == 'savePlan' or submitIntent == 'updatePlan')


    if request.method != 'POST':
        logger.exception(format_exc())
        return HttpResponse(json.dumps({"error": "Error, unsupported HTTP Request method (%s) for plan update." % request.method}), mimetype="application/json")

    # Process Inputs

    # pylint:disable=E1103
    json_data = simplejson.loads(request.raw_post_data)
    submitIntent = json_data.get('submitIntent', '')
    logger.debug('views.save_plan_or_template POST.raw_post_data... simplejson Data: "%s"' % json_data)
    logger.debug("views.save_plan_or_template submitIntent=%s" % submitIntent)
    # saving Template or Planned Run
    isReusable = isReusable(submitIntent)
    runModeValue = json_data.get('runMode', 'single')
    isPlanGroupValue = runModeValue == 'pe' and not isReusable
    libraryKeyValue = json_data.get('libraryKey', '')
    forward3primeAdapterValue = json_data.get('forward3primeAdapter', '')

    msgvalue = 'Run Plan' if not isReusable else 'Template'
    if runModeValue == 'pe':
        return HttpResponse(json.dumps({"error": "Error, paired-end plan is no longer supported. %s will not be saved." % (msgvalue)}), mimetype="application/html")
    
    planDisplayedNameValue = json_data.get('planDisplayedName', '').strip()
    noteValue = json_data.get('notes_workaround', '')

    # perform server-side validation to avoid things falling through the crack    
    if not planDisplayedNameValue:
        return HttpResponse(json.dumps({"error": "Error, please enter a %s Name."  %(msgvalue)}), mimetype="application/html")

    if not is_valid_chars(planDisplayedNameValue):
        return HttpResponse(json.dumps({"error": "Error, %s Name" %(msgvalue) + ERROR_MSG_INVALID_CHARS}), mimetype="application/html")        
        
    if not is_valid_length(planDisplayedNameValue, MAX_LENGTH_PLAN_NAME):
        return HttpResponse(json.dumps({"error": "Error, %s Name"  %(msgvalue) + ERROR_MSG_INVALID_LENGTH  %(str(MAX_LENGTH_PLAN_NAME))}), mimetype="application/html")

    if noteValue:
        if not is_valid_chars(noteValue):
            return HttpResponse(json.dumps({"error": "Error, %s note" %(msgvalue) + ERROR_MSG_INVALID_CHARS}), mimetype="application/html")
        
        if not is_valid_length(noteValue, MAX_LENGTH_NOTES):
            return HttpResponse(json.dumps({"error": "Error, Note" + ERROR_MSG_INVALID_LENGTH  %(str(MAX_LENGTH_NOTES))}), mimetype="application/html")

    # Projects
    projectObjList = get_projects(request.user, json_data)

    # IonReporterUploader configuration and samples
    selectedPlugins = json_data.get('selectedPlugins', {})
    IRconfigList = json_data.get('irConfigList', [])

    IRU_selected = False
    for uploader in selectedPlugins.values():
        if 'ionreporteruploader' in uploader['name'].lower() and uploader['name'] != 'IonReporterUploader_V1_0':
            IRU_selected = True

    #if IRU is set to autoRun, user does not need to select the plugin explicitly. user could have set all IRU versions to autorun
    IRU_autorun_count = 0
    if not IRU_selected:
        IRU_autoruns = Plugin.objects.filter(name__icontains="IonReporter", selected=True, active=True, autorun=True).exclude(name__icontains="IonReporterUploader_V1_0").order_by('-name')
        IRU_autorun_count = IRU_autoruns.count()
        if IRU_autorun_count > 0:
            IRU_selected = True
    
    if IRU_selected:
        samples_IRconfig = json_data.get('sample_irConfig', '')

        if samples_IRconfig:
            samples_IRconfig = ','.join(samples_IRconfig)

        #generate UUID for unique setIds
        id_uuid = {}
        setids = [ir.get('setid', "") for ir in IRconfigList]

        if setids:
            for setid in set(setids):
                if setid:                    
                    id_uuid[setid] = str(uuid.uuid4())
            for ir_config in IRconfigList:
                setid = ir_config.get('setid', '')
                                
                if setid:
                    ir_config['setid'] += '__' + id_uuid[setid]

        if IRU_autorun_count > 0 and not samples_IRconfig:
            #if more than one IRU version is set to autorun and user does not explicitly select one, 
            #gui shows workflow config for IRU v1.0
            samples_IRconfig = json_data.get('samples_workaround', '')
        
    # Samples
    barcodeIdValue = json_data.get('barcodeId', '')
    barcodedSamples = ''
    sampleValidationErrorMsg = ''
    sampleValidationErrorMsg_leadingChars = ''
    sampleValidationErrorMsg_length = ''
        
    # one Plan will be created per entry in sampleList
    # samples for barcoded Plan have a separate field (barcodedSamples)

    if isReusable:
        # samples entered only when saving planned run (not template)
        sampleList = ['']
    elif barcodeIdValue:
        # a barcode Set is selected
        sampleList = ['']
        bcSamplesValues = json_data.get('bcSamples_workaround', '')
        bcDictionary = {}
        bcId = ""
        for token in bcSamplesValues.split(","):
            if ((token.find("bcKey|")) == 0):
                bcId, bcId_str = token.split("|")[1:]
            else:
                sample = token.strip()
                if bcId and sample:
                    if not is_valid_chars(sample):
                        sampleValidationErrorMsg += sample + ', '
                    elif is_invalid_leading_chars(sample):
                        sampleValidationErrorMsg_leadingChars += sample + ", "
                    elif not is_valid_length(sample, MAX_LENGTH_SAMPLE_NAME):
                        sampleValidationErrorMsg_length += sample + ", "
                        
                    bcDictionary.setdefault(sample, {}).setdefault('barcodes',[]).append(bcId_str)
                bcId = ""

        barcodedSamples = simplejson.dumps(bcDictionary)
        logger.debug("views.save_plan_or_template after simplejson.dumps... barcodedSamples=%s;" % (barcodedSamples))

        if not bcDictionary:
            transaction.rollback()
            return HttpResponse(json.dumps({"error": "Error, please enter at least one barcode sample name."}), mimetype="application/html")

    else:
        # Non-barcoded samples
        sampleList = []
        if IRU_selected:
            samples = samples_IRconfig
        else:
            samples = json_data.get('samples_workaround', '')

        for sample in samples.split(','):
            if sample.strip():
                if not is_valid_chars(sample):
                    sampleValidationErrorMsg += sample + ', '
                elif is_invalid_leading_chars(sample):
                    sampleValidationErrorMsg_leadingChars += sample + ", "
                elif not is_valid_length(sample, MAX_LENGTH_SAMPLE_NAME):
                    sampleValidationErrorMsg_length += sample + ", "
                else:
                    sampleList.append(sample)

        logger.debug("views.save_plan_or_template sampleList=%s " % (sampleList))

        if  len(sampleList) == 0 and not sampleValidationErrorMsg and not sampleValidationErrorMsg_leadingChars and not sampleValidationErrorMsg_length:
            transaction.rollback()
            return HttpResponse(json.dumps({"error": "Error, please enter a sample name for the run plan."}), mimetype="application/html")
    
    # Samples validation
    if sampleValidationErrorMsg or sampleValidationErrorMsg_leadingChars or sampleValidationErrorMsg_length:
        message = ""
        if sampleValidationErrorMsg:
            message = "Error, sample name" + ERROR_MSG_INVALID_CHARS
            message = message + ' <br>Please fix: ' + sampleValidationErrorMsg + '<br>'
        if sampleValidationErrorMsg_leadingChars:
            message = message + "Error, sample name" + ERROR_MSG_INVALID_LEADING_CHARS
            message = message + ' <br>Please fix: ' + sampleValidationErrorMsg_leadingChars + '<br>'
        if sampleValidationErrorMsg_length:
            message = message + "Error, sample name" + ERROR_MSG_INVALID_LENGTH  %(str(MAX_LENGTH_SAMPLE_NAME))
            message = message + ' <br>Please fix: ' + sampleValidationErrorMsg_length
          
        transaction.rollback()
        return HttpResponse(json.dumps({"error": message}), mimetype="application/html")

    selectedPluginsValue = json_data.get('selectedPlugins', {})

    # end processing input data

    # Edit/Create Plan(s)

    if int(planOid) == 0:
        edit_existing_plan = False
    else:
        edit_existing_plan = True

    for i, sample in enumerate(sampleList):
        logger.debug("...LOOP... views.save_plan_or_template SAMPLE=%s; isSystem=%s; isReusable=%s; isPlanGroup=%s "
                     % (sample.strip(), json_data["isSystem"], isReusable, isPlanGroupValue))

        # add IonReporter config values for each sample
        if len(IRconfigList) > 0:
            for uploader in selectedPluginsValue.values():
                if 'ionreporteruploader' in uploader['name'].lower():
                    if len(IRconfigList) > 1 and not barcodeIdValue:
                        uploader['userInput'] = [IRconfigList[i]]
                    else:
                        uploader['userInput'] = IRconfigList

        if len(sampleList) > 1:
            inputPlanDisplayedName = planDisplayedNameValue + '_' + sample.strip()
        else:
            inputPlanDisplayedName = planDisplayedNameValue
            
        selectedTemplatingKit = json_data.get('templatekitname', '')
        samplePrepInstrumentType = json_data.get('samplePrepInstrumentType', '')
        if samplePrepInstrumentType == 'ionChef':
            selectedTemplatingKit = json_data.get('templatekitionchefname', '')
        
        #PDD-TODO: remove the x_ prefix. the x_ prefix is just a reminder what the obsolete attributes to remove during the next phase
        kwargs = {
            'planDisplayedName': inputPlanDisplayedName,
            "planName": inputPlanDisplayedName.replace(' ', '_'),
            'usePreBeadfind': toBoolean(json_data['usePreBeadfind'], False),
            'usePostBeadfind': toBoolean(json_data['usePostBeadfind'], False),
            'preAnalysis': True,
            'runType': json_data['runType'],
            'templatingKitName': selectedTemplatingKit,
            'controlSequencekitname': json_data.get('controlsequence', ''),
            'runMode': runModeValue,
            'isSystem': toBoolean(json_data['isSystem'], False),
            'isReusable': isReusable,
            'isPlanGroup': isPlanGroupValue,
            'username': request.user.username,
            'isFavorite': toBoolean(json_data.get('isFavorite', 'False'), False),
            'pairedEndLibraryAdapterName': json_data.get('pairedEndLibraryAdapterName', ''),
            'samplePrepKitName': json_data.get('samplePrepKitName', ''),
            'planStatus' : "planned",

            'x_autoAnalyze': True,
            'x_barcodedSamples': barcodedSamples,
            'x_barcodeId': barcodeIdValue,
            'x_bedfile': json_data.get('bedfile', ''),
            'x_chipType': json_data.get('chipType', ''),
            'x_flows': json_data.get('flows', None),
            'x_forward3primeadapter': forward3primeAdapterValue,
            ###'_isReverseRun':  = self.isReverseRun
            'x_library': json_data.get('library', ''),
            'x_libraryKey': libraryKeyValue,
            'x_librarykitname': json_data.get('librarykitname', ''),
            'x_notes': noteValue,
            'x_regionfile': json_data.get('regionfile', ''),
            'x_sample': sample.strip().replace(' ', '_'),
            'x_sampleDisplayedName': sample.strip(),
            'x_selectedPlugins': selectedPluginsValue,
            'x_sequencekitname': json_data.get('sequencekitname', ''),
            'x_variantfrequency': json_data.get('variantfrequency', ''),
        }

        planTemplate = None
        
        #if we're changing a plan from having 1 sample to say 2 samples, we need to UPDATE 1 plan and CREATE 1 plan!!
        try:
            if not edit_existing_plan:
                planTemplate, extra_kwargs = PlannedExperiment.objects.save_plan(-1, **kwargs)             
            else:
                planTemplate, extra_kwargs = PlannedExperiment.objects.save_plan(planOid, **kwargs)
                
                edit_existing_plan = False

            # Update QCtype thresholds
            qcTypes = QCType.objects.all()
            for qcType in qcTypes:
                qc_threshold = json_data.get(qcType.qcName, '')
                if qc_threshold:
                    # get existing PlannedExperimentQC if any
                    plannedExpQcs = PlannedExperimentQC.objects.filter(plannedExperiment=planTemplate.id, qcType=qcType.id)
                    if len(plannedExpQcs) > 0:
                        for plannedExpQc in plannedExpQcs:
                            plannedExpQc.threshold = qc_threshold
                            plannedExpQc.save()
                    else:
                        kwargs = {
                            'plannedExperiment': planTemplate,
                            'qcType': qcType,
                            'threshold': qc_threshold
                        }
                        plannedExpQc = PlannedExperimentQC(**kwargs)
                        plannedExpQc.save()

            # add/remove projects
            if projectObjList:
                #TODO: refactor this logic to simplify using django orm
                projectNameList = [project.name for project in projectObjList]
                for currentProject in planTemplate.projects.all():
                    if currentProject.name not in projectNameList:
                        planTemplate.projects.remove(currentProject)
                for projectObj in projectObjList:
                    planTemplate.projects.add(projectObj)
            else:
                planTemplate.projects.clear()
                
        except ValidationError, err:
            transaction.rollback()
            logger.exception(format_exc())
            
            message = "Internal error while trying to save the plan. "
            for msg in err.messages:                
                message += str(msg)
                message += " "

            return HttpResponse(json.dumps({"error": message}), mimetype="application/json")

        except Exception as excp:
            transaction.rollback()
            logger.exception(format_exc())

            message = "Internal error while trying to save the plan. %s" %(excp.message)
            return HttpResponse(json.dumps({"error": message}), mimetype="application/json")
Ejemplo n.º 9
0
def save_uploaded_plans_for_template(request):
    """add plans, with CSV validation"""
    logger.info(request)
                            
    if request.method != 'POST':
        logger.exception(format_exc())
        transaction.rollback()
        return HttpResponse(json.dumps({"error": "Error, unsupported HTTP Request method (%s) for saving plan upload." % request.method}), mimetype="application/json")
               
    postedfile = request.FILES['postedfile']
    destination = tempfile.NamedTemporaryFile(delete=False)

    for chunk in postedfile.chunks():
        destination.write(chunk)
    postedfile.close()
    destination.close()

    #check to ensure it is not empty
    headerCheck = open(destination.name, "rU")
    firstCSV = []
    for firstRow in csv.reader(headerCheck):
        firstCSV.append(firstRow)            
        #logger.info("views.save_uploaded_plans_for_template() firstRow=%s;" %(firstRow))
        
    headerCheck.close()
    if not firstRow:
        os.unlink(destination.name)
        transaction.rollback()
        return HttpResponse(json.dumps({"status": "Error: batch planning file is empty"}), mimetype="text/html")
        
    index = 0
    plans = []
    rawPlanDataList = []
    failed = {}
    file = open(destination.name, "rU")
    reader = csv.DictReader(file)
    for index, row in enumerate(reader, start=1):
        errorMsg, aPlanDict, rawPlanDict, isToSkipRow = validate_csv_plan(row)
        
        logger.info("views.save_uploaded_plans_for_template() index=%d; errorMsg=%s; planDict=%s" %(index, errorMsg, rawPlanDict))
        if errorMsg:
            logger.info("views.save_uploaded_plans_for_template() ERROR MESSAGE index=%d; errorMsg=%s; planDict=%s" %(index, errorMsg, rawPlanDict))

            failed[index] = errorMsg
            continue
        elif isToSkipRow:
            logger.info("views.save_uploaded_plans_for_template() SKIPPED ROW index=%d; row=%s" %(index, row))            
            continue
        else:
            plans.append(aPlanDict)
            rawPlanDataList.append(rawPlanDict)

    destination.close()  # now close and remove the temp file
    os.unlink(destination.name)
    if index == 0:
        transaction.rollback()
        return HttpResponse(json.dumps({"status": "Error: There must be at least one plan! Please reload the page and try again with more plans."}), mimetype="text/html")

    if failed:
        r = {"status": "Plan validation failed. The plans have not been saved.", "failed": failed}
        logger.info("views.save_uploaded_plans_for_template() failed=%s" %(r))
       
        transaction.rollback()
        return HttpResponse(json.dumps(r), mimetype="text/html")

    #saving to db needs to be the last thing to happen
    try:
        index = 0
        for planFamily in plans:
            plan = planFamily['plan']
            plan.save()
                    
            expObj = planFamily['exp']
            expObj.plan = plan
            expObj.expName = plan.planGUID
            expObj.unique = plan.planGUID
            expObj.displayname = plan.planGUID
            expObj.save()

            easObj = planFamily['eas']
            easObj.experiment = expObj
            easObj.isEditable = True
            easObj.save()
            
            #saving/associating samples    
            sampleDisplayedNames = planFamily['samples']
            sampleNames = [name.replace(' ', '_') for name in sampleDisplayedNames]
            externalId = None
            for name, displayedName in zip(sampleNames,  sampleDisplayedNames): 
                sample_kwargs = {
                                'name' : name,
                                'displayedName' : displayedName,
                                'date' : plan.date,
                                'status' : plan.planStatus,
                                'externalId': externalId
                                }
    
                sample = Sample.objects.get_or_create(name=name, externalId=externalId, defaults=sample_kwargs)[0]
                sample.experiments.add(expObj)
                sample.save()
                        
            planDict = rawPlanDataList[index]
            
            # add QCtype thresholds
            qcTypes = QCType.objects.all()
            for qcType in qcTypes:
                qc_threshold = planDict.get(qcType.qcName, '')
                if qc_threshold:
                    # get existing PlannedExperimentQC if any
                    plannedExpQcs = PlannedExperimentQC.objects.filter(plannedExperiment=plan.id, qcType=qcType.id)
                    if len(plannedExpQcs) > 0:
                        for plannedExpQc in plannedExpQcs:
                            plannedExpQc.threshold = qc_threshold
                            plannedExpQc.save()
                    else:
                        kwargs = {
                            'plannedExperiment': plan,
                            'qcType': qcType,
                            'threshold': qc_threshold
                        }
                        plannedExpQc = PlannedExperimentQC(**kwargs)
                        plannedExpQc.save()

            # add projects
            projectObjList = get_projects(request.user, planDict)
            for project in projectObjList:
                if project:
                    plan.projects.add(project)

             
            index += 1
    except:
        logger.exception(format_exc())
        transaction.rollback()
        return HttpResponse(json.dumps({"status": "Error saving plans to database!"}), mimetype="text/html")
        ##return HttpResponse(json.dumps({"error": "Internal error while trying to save the plan."}), mimetype="application/json")
    else:
        transaction.commit()            
        r = {"status": "Plans Uploaded! The plans will be listed on the planned run page.", "failed": failed}
        return HttpResponse(json.dumps(r), mimetype="text/html")
Ejemplo n.º 10
0
def save_plan_or_template(request, planOid):
    """
    Saving new or edited plan/template to db (source: plan template wizard)
    Editing a planned run from having 1 sample to 2 samples will result in one edited planned run and one new planned run
    """
    def isReusable(submitIntent):
        return not (submitIntent == 'savePlan' or submitIntent == 'updatePlan')

    def isValidChars(value, validChars=r'^[a-zA-Z0-9-_\.\s\,]+$'):
        ''' Determines if value is valid: letters, numbers, spaces, dashes, underscores only '''
        return bool(re.compile(validChars).match(value))

    if request.method != 'POST':
        logger.exception(format_exc())
        return HttpResponse(json.dumps({
            "error":
            "Error, unsupported HTTP Request method (%s) for plan update." %
            request.method
        }),
                            mimetype="application/json")

    # Process Inputs

    # pylint:disable=E1103
    json_data = simplejson.loads(request.raw_post_data)
    submitIntent = json_data.get('submitIntent', '')
    logger.debug(
        'views.editplannedexperiment POST.raw_post_data... simplejson Data: "%s"'
        % json_data)
    logger.debug("views.editplannedexperiment submitIntent=%s" % submitIntent)
    # saving Template or Planned Run
    isReusable = isReusable(submitIntent)
    runModeValue = json_data.get('runMode', 'single')
    isPlanGroupValue = runModeValue == 'pe' and not isReusable
    libraryKeyValue = json_data.get('libraryKey', '')
    forward3primeAdapterValue = json_data.get('forward3primeAdapter', '')

    msgvalue = 'Run Plan' if not isReusable else 'Template'
    if runModeValue == 'pe':
        return HttpResponse(json.dumps({
            "error":
            "Error, paired-end plan is no longer supported. %s will not be saved."
            % (msgvalue)
        }),
                            mimetype="application/html")

    planDisplayedNameValue = json_data.get('planDisplayedName', '').strip()
    noteValue = json_data.get('notes_workaround', '')

    # perform server-side validation to avoid things falling through the crack
    if not planDisplayedNameValue:
        return HttpResponse(json.dumps(
            {"error": "Error, please enter a %s Name." % (msgvalue)}),
                            mimetype="application/html")

    if not isValidChars(planDisplayedNameValue):
        return HttpResponse(json.dumps({
            "error":
            "Error, %s Name should contain only numbers, letters, spaces, and the following: . - _"
            % (msgvalue)
        }),
                            mimetype="application/html")

    if noteValue and not isValidChars(noteValue):
        return HttpResponse(json.dumps({
            "error":
            "Error, %s note should contain only numbers, letters, spaces, and the following: . - _"
            % (msgvalue)
        }),
                            mimetype="application/html")

    # Projects
    projectObjList = get_projects(request.user, json_data)

    # IonReporterUploader configuration and samples
    selectedPlugins = json_data.get('selectedPlugins', {})
    IRconfigList = json_data.get('irConfigList', [])
    IRU_1_2_selected = False
    for uploader in selectedPlugins.get('planuploaders', []):
        if 'ionreporteruploader' in uploader['name'].lower(
        ) and uploader['name'] != 'IonReporterUploader_V1_0':
            IRU_1_2_selected = True
            samples_IRconfig = json_data.get('sample_irConfig', '')
            samples_IRconfig = ','.join(samples_IRconfig)

            #generate UUID for unique setIds
            id_uuid = {}
            setids = [ir['setid'] for ir in IRconfigList]
            for setid in set(setids):
                id_uuid[setid] = str(uuid.uuid4())
            for ir_config in IRconfigList:
                ir_config['setid'] += '__' + id_uuid[ir_config['setid']]

    # Samples

    barcodeIdValue = json_data.get('barcodeId', '')
    barcodedSamples = ''
    sampleValidationErrorMsg = ''

    # one Plan will be created per entry in sampleList
    # samples for barcoded Plan have a separate field (barcodedSamples)

    if isReusable:
        # samples entered only when saving planned run (not template)
        sampleList = ['']
    elif barcodeIdValue:
        # a barcode Set is selected
        sampleList = ['']
        bcSamplesValues = json_data.get('bcSamples_workaround', '')
        bcDictionary = {}
        bcId = ""
        for token in bcSamplesValues.split(","):
            if ((token.find("bcKey|")) == 0):
                bcId, bcId_str = token.split("|")[1:]
            else:
                sample = token.strip()
                if bcId and sample:
                    if not isValidChars(sample):
                        sampleValidationErrorMsg += sample + ', '

                    bcDictionary.setdefault(sample,
                                            {}).setdefault('barcodes',
                                                           []).append(bcId_str)
                bcId = ""

        barcodedSamples = simplejson.dumps(bcDictionary)
        logger.debug(
            "views.editplannedexperiment after simplejson.dumps... barcodedSamples=%s;"
            % (barcodedSamples))

        if not bcDictionary:
            transaction.rollback()
            return HttpResponse(json.dumps({
                "error":
                "Error, please enter at least one barcode sample name."
            }),
                                mimetype="application/html")

    else:
        # Non-barcoded samples
        sampleList = []
        if IRU_1_2_selected:
            samples = samples_IRconfig
        else:
            samples = json_data.get('samples_workaround', '')

        for sample in samples.split(','):
            if sample.strip():
                if not isValidChars(sample):
                    sampleValidationErrorMsg += sample + ', '
                else:
                    sampleList.append(sample)

        logger.debug("views.editplannedexperiment sampleList=%s " %
                     (sampleList))

        if len(sampleList) == 0:
            transaction.rollback()
            return HttpResponse(json.dumps({
                "error":
                "Error, please enter a sample name for the run plan."
            }),
                                mimetype="application/html")

    # Samples validation
    if sampleValidationErrorMsg:
        message = "Error, sample name should contain only numbers, letters, spaces, and the following: . - _"
        message = message + ' <br>Please fix: ' + sampleValidationErrorMsg
        transaction.rollback()
        return HttpResponse(json.dumps({"error": message}),
                            mimetype="application/html")

    selectedPluginsValue = json_data.get('selectedPlugins', [])

    # end processing input data

    # Edit/Create Plan(s)

    if int(planOid) == 0:
        edit_existing_plan = False
    else:
        edit_existing_plan = True

    for i, sample in enumerate(sampleList):
        logger.debug(
            "...LOOP... views.editplannedexperiment SAMPLE=%s; isSystem=%s; isReusable=%s; isPlanGroup=%s "
            % (sample.strip(), json_data["isSystem"], isReusable,
               isPlanGroupValue))

        # add IonReporter config values for each sample
        if len(IRconfigList) > 0:
            for uploader in selectedPluginsValue['planuploaders']:
                if 'ionreporter' in uploader['name'].lower():
                    if len(IRconfigList) > 1 and not barcodeIdValue:
                        uploader['userInput'] = [IRconfigList[i]]
                    else:
                        uploader['userInput'] = IRconfigList

        if len(sampleList) > 1:
            inputPlanDisplayedName = planDisplayedNameValue + '_' + sample.strip(
            )
        else:
            inputPlanDisplayedName = planDisplayedNameValue

        kwargs = {
            'planDisplayedName':
            inputPlanDisplayedName,
            "planName":
            inputPlanDisplayedName.replace(' ', '_'),
            'chipType':
            json_data.get('chipType', ''),
            'usePreBeadfind':
            toBoolean(json_data['usePreBeadfind'], False),
            'usePostBeadfind':
            toBoolean(json_data['usePostBeadfind'], False),
            'flows':
            json_data.get('flows', None),
            'autoAnalyze':
            True,
            'preAnalysis':
            True,
            'runType':
            json_data['runType'],
            'library':
            json_data.get('library', ''),
            'notes':
            noteValue,
            'bedfile':
            json_data.get('bedfile', ''),
            'regionfile':
            json_data.get('regionfile', ''),
            'variantfrequency':
            json_data.get('variantfrequency', ''),
            'librarykitname':
            json_data.get('librarykitname', ''),
            'sequencekitname':
            json_data.get('sequencekitname', ''),
            'barcodeId':
            barcodeIdValue,
            'templatingKitName':
            json_data.get('templatekitname', ''),
            'controlSequencekitname':
            json_data.get('controlsequence', ''),
            'runMode':
            runModeValue,
            'isSystem':
            toBoolean(json_data['isSystem'], False),
            'isReusable':
            isReusable,
            'isPlanGroup':
            isPlanGroupValue,
            'sampleDisplayedName':
            sample.strip(),
            "sample":
            sample.strip().replace(' ', '_'),
            'username':
            request.user.username,
            'isFavorite':
            toBoolean(json_data.get('isFavorite', 'False'), False),
            'barcodedSamples':
            barcodedSamples,
            'libraryKey':
            libraryKeyValue,
            'forward3primeadapter':
            forward3primeAdapterValue,
            'reverselibrarykey':
            json_data.get('reverselibrarykey', ''),
            'reverse3primeadapter':
            json_data.get('reverse3primeAdapter', ''),
            'pairedEndLibraryAdapterName':
            json_data.get('pairedEndLibraryAdapterName', ''),
            'samplePrepKitName':
            json_data.get('samplePrepKitName', ''),
            'selectedPlugins':
            selectedPluginsValue
        }

        #if we're changing a plan from having 1 sample to say 2 samples, we need to UPDATE 1 plan and CREATE 1 plan!!
        try:
            if not edit_existing_plan:
                planTemplate = PlannedExperiment(**kwargs)
            else:
                planTemplate = PlannedExperiment.objects.get(pk=planOid)
                for key, value in kwargs.items():
                    setattr(planTemplate, key, value)
                edit_existing_plan = False

            planTemplate.save()

            # Update QCtype thresholds
            qcTypes = QCType.objects.all()
            for qcType in qcTypes:
                qc_threshold = json_data.get(qcType.qcName, '')
                if qc_threshold:
                    # get existing PlannedExperimentQC if any
                    plannedExpQcs = PlannedExperimentQC.objects.filter(
                        plannedExperiment=planTemplate.id, qcType=qcType.id)
                    if len(plannedExpQcs) > 0:
                        for plannedExpQc in plannedExpQcs:
                            plannedExpQc.threshold = qc_threshold
                            plannedExpQc.save()
                    else:
                        kwargs = {
                            'plannedExperiment': planTemplate,
                            'qcType': qcType,
                            'threshold': qc_threshold
                        }
                        plannedExpQc = PlannedExperimentQC(**kwargs)
                        plannedExpQc.save()

            # add/remove projects
            if projectObjList:
                #TODO: refactor this logic to simplify using django orm
                projectNameList = [project.name for project in projectObjList]
                for currentProject in planTemplate.projects.all():
                    if currentProject.name not in projectNameList:
                        planTemplate.projects.remove(currentProject)
                for projectObj in projectObjList:
                    planTemplate.projects.add(projectObj)
            else:
                planTemplate.projects.clear()

        except:
            transaction.rollback()
            logger.exception(format_exc())
            return HttpResponse(json.dumps(
                {"error": "Internal error while trying to save the plan."}),
                                mimetype="application/json")
        else:
            transaction.commit()

    return HttpResponse(json.dumps(
        {"status": "plan template updated successfully"}),
                        mimetype="application/json")
Ejemplo n.º 11
0
    def test_get_projects(self):
        data = {'projects':[],
                'newProjects': []}
#        data = simplejson.loads(data)
        result =  get_projects('ionadmin', data)
        self.assertFalse(result, 'list should be empty')