submissions.views.SubmissionValidationSummaryView.get_context_data() - Code Metrics - Inspection of "Validation batch update" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — master (#41)

unknown

created 2019-07-23 15:00 UTC

SubmissionValidationSummaryView.get_context_data() A

↳ Parent: submissions.views

Complexity

Conditions

Size

Total Lines	21
Code Lines	20

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	20
dl	0
loc	21
rs	9.4
c	0
b	0
f	0
cc	4
nop	2

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jul 24 15:49:23 2018

@author: Paolo Cozzi <[email protected]>
"""

import logging
import ast
import re
from django.core.exceptions import ObjectDoesNotExist

from django.contrib import messages
from django.contrib.auth.mixins import LoginRequiredMixin
from django.db.models import Q
from django.http import HttpResponseRedirect
from django.views import View
from django.views.generic import (
    CreateView, DetailView, ListView, UpdateView, DeleteView)
from django.shortcuts import get_object_or_404, redirect
from django.urls import reverse_lazy, reverse

from common.constants import (
    WAITING, ERROR, SUBMITTED, NEED_REVISION, CRYOWEB_TYPE, CRB_ANIM_TYPE,
    TIME_UNITS, VALIDATION_MESSAGES_ATTRIBUTES, SAMPLE_STORAGE,
    SAMPLE_STORAGE_PROCESSING, ACCURACIES, ONTOLOGY_VALIDATION_MESSAGES,
    UNITS_VALIDATION_MESSAGES)
from common.helpers import get_deleted_objects, uid2biosample
from common.views import OwnerMixin
from crbanim.tasks import ImportCRBAnimTask
from cryoweb.tasks import import_from_cryoweb

from image_app.models import Submission, Name, Animal, Sample, DictUberon, \
    DictDevelStage, DictPhysioStage, DictSex, DictSpecie
from excel.tasks import ImportTemplateTask

from validation.helpers import construct_validation_message
from validation.models import ValidationSummary
from animals.tasks import BatchUpdateAnimals
from samples.tasks import BatchUpdateSamples

from .forms import SubmissionForm, ReloadForm
from .helpers import is_target_in_message

# Get an instance of a logger
logger = logging.getLogger(__name__)


class CreateSubmissionView(LoginRequiredMixin, CreateView):
    form_class = SubmissionForm
    model = Submission

    # template name is derived from model position and views type.
    # in this case, ir will be 'image_app/submission_form.html' so
    # i need to clearly specify it
    template_name = "submissions/submission_form.html"

    def form_invalid(self, form):
        messages.error(
            self.request,
            message="Please correct the errors below",
            extra_tags="alert alert-dismissible alert-danger")

        return super(CreateSubmissionView, self).form_invalid(form)

    # add user to this object
    def form_valid(self, form):
        self.object = form.save(commit=False)
        self.object.owner = self.request.user

        # I will have a different loading function accordingly with data type
        if self.object.datasource_type == CRYOWEB_TYPE:
            # update object and force status
            self.object.message = "waiting for data loading"
            self.object.status = WAITING
            self.object.save()

            # a valid submission start a task
            res = import_from_cryoweb.delay(self.object.pk)
            logger.info(
                "Start cryoweb importing process with task %s" % res.task_id)

        # I will have a different loading function accordingly with data type
        elif self.object.datasource_type == CRB_ANIM_TYPE:
            # update object and force status
            self.object.message = "waiting for data loading"
            self.object.status = WAITING
            self.object.save()

            # create a task
            my_task = ImportCRBAnimTask()

            # a valid submission start a task
            res = my_task.delay(self.object.pk)
            logger.info(
                "Start crbanim importing process with task %s" % res.task_id)

        else:
            # update object and force status
            self.object.message = "waiting for data loading"
            self.object.status = WAITING
            self.object.save()

            # create a task
            my_task = ImportTemplateTask()

            # a valid submission start a task
            res = my_task.delay(self.object.pk)
            logger.info(
                "Start template importing process with task %s" % res.task_id)

        # a redirect to self.object.get_absolute_url()
        return HttpResponseRedirect(self.get_success_url())


class MessagesSubmissionMixin(object):
    """Display messages in SubmissionViews"""

    # https://stackoverflow.com/a/45696442
    def get_context_data(self, **kwargs):
        data = super().get_context_data(**kwargs)

        # get the submission message
        message = self.submission.message

        # check if data are loaded or not
        if self.submission.status in [WAITING, SUBMITTED]:
            messages.warning(
                request=self.request,
                message=message,
                extra_tags="alert alert-dismissible alert-warning")

        elif self.submission.status in [ERROR, NEED_REVISION]:
            messages.error(
                request=self.request,
                message=message,
                extra_tags="alert alert-dismissible alert-danger")

        elif message is not None and message != '':
            messages.info(
                request=self.request,
                message=message,
                extra_tags="alert alert-dismissible alert-info")

        return data


class DetailSubmissionView(MessagesSubmissionMixin, OwnerMixin, DetailView):
    model = Submission
    template_name = "submissions/submission_detail.html"

    def get_context_data(self, **kwargs):
        # pass self.object to a new submission attribute in order to call
        # MessagesSubmissionMixin.get_context_data()
        self.submission = self.object

        # Call the base implementation first to get a context
        context = super(DetailSubmissionView, self).get_context_data(**kwargs)

        # add submission report to context
        validation_summary = construct_validation_message(self.submission)

        # HINT: is this computational intensive?
        context["validation_summary"] = validation_summary

        return context


class SubmissionValidationSummaryView(OwnerMixin, DetailView):
    model = Submission
    template_name = "submissions/submission_validation_summary.html"

    def get_context_data(self, **kwargs):
        context = super().get_context_data(**kwargs)
        summary_type = self.kwargs['type']
        try:
            validation_summary = self.object.validationsummary_set\
                .get(type=summary_type)
            context['validation_summary'] = validation_summary
            editable = list()
            for message in validation_summary.messages:
                message = ast.literal_eval(message)
                if uid2biosample(message['offending_column']) in \
                        [val for sublist in VALIDATION_MESSAGES_ATTRIBUTES for
                         val in sublist]:
                    editable.append(True)
                else:
                    editable.append(False)
            context['editable'] = editable
        except ObjectDoesNotExist:
            context['validation_summary'] = None
        context['submission'] = Submission.objects.get(pk=self.kwargs['pk'])
        return context


class SubmissionValidationSummaryFixErrorsView(OwnerMixin, ListView):
    template_name = "submissions/submission_validation_summary_fix_errors.html"

    def get_queryset(self):
        self.summary_type = self.kwargs['type']
        self.submission = Submission.objects.get(pk=self.kwargs['pk'])
        self.validation_summary = ValidationSummary.objects.get(
            submission=self.submission, type=self.summary_type)
        self.message = ast.literal_eval(self.validation_summary.messages[
                                            int(self.kwargs['message_counter'])
                                        ])
        self.offending_column = uid2biosample(
            self.message['offending_column'])
        if is_target_in_message(self.message['message'],
                                UNITS_VALIDATION_MESSAGES):
            self.show_units = True
            if self.offending_column == 'animal_age_at_collection':
                self.offending_column += "_units"
                self.units = [unit.name for unit in TIME_UNITS]
            elif self.offending_column == 'preparation_interval_units':
                self.units = [unit.name for unit in TIME_UNITS]
        elif re.search(".* of field .* is not in the valid values list .*",
                       self.message['message']):
            self.show_units = True
            if self.offending_column == 'storage':
                self.units = [unit.name for unit in SAMPLE_STORAGE]
            elif self.offending_column == 'storage_processing':
                self.units = [unit.name for unit in SAMPLE_STORAGE_PROCESSING]
            elif self.offending_column == 'collection_place_accuracy':
                self.units = [unit.name for unit in ACCURACIES]
            elif self.offending_column == 'birth_location_accuracy':
                self.units = [unit.name for unit in ACCURACIES]
        elif is_target_in_message(self.message['message'],
                                  ONTOLOGY_VALIDATION_MESSAGES):
            self.show_units = False
            self.units = None
            self.offending_column = 'term'
            if self.offending_column == 'organism_part':
                self.summary_type = 'dictuberon'
                return DictUberon.objects.filter(id__in=[Sample.objects.get(
                    pk=self.message['ids'][0]).organism_part_id])
            elif self.offending_column == 'developmental_stage':
                self.summary_type = 'dictdevelstage'
                return DictDevelStage.objects.filter(id__in=[Sample.objects.get(
                    pk=self.message['ids'][0]).developmental_stage_id])
            elif self.offending_column == 'physiological_stage':
                self.summary_type = 'dictphysiostage'
                return DictPhysioStage.objects.filter(id__in=[
                    Sample.objects.get(
                        pk=self.message['ids'][0]).physiological_stage_id])
            elif self.offending_column == 'sex':
                self.summary_type = 'dictsex'
                return DictSex.objects.filter(id__in=[Animal.objects.get(
                    pk=self.message['ids'][0]).sex_id])
            elif self.offending_column == 'species':
                self.summary_type = f'dictspecie_{self.summary_type}'
                if self.summary_type == 'dictspecie_animal':
                    return DictSpecie.objects.filter(id__in=[Animal.objects.get(
                        pk=self.message['ids'][0]).specie.id])
                elif self.summary_type == 'dictspecie_sample':
                    return DictSpecie.objects.filter(id__in=[Sample.objects.get(
                        pk=self.message['ids'][0]).specie.id])
        else:
            self.show_units = False
            self.units = None
        if self.summary_type == 'animal':
            return Animal.objects.filter(id__in=self.message['ids'])
        elif self.summary_type == 'sample':
            return Sample.objects.filter(id__in=self.message['ids'])

    def get_context_data(self, **kwargs):
        # Call the base implementation first to get a context
        context = super(
            SubmissionValidationSummaryFixErrorsView, self
        ).get_context_data(**kwargs)

        # add submission to context
        context["message"] = self.message
        context["type"] = self.summary_type
        context['attribute_to_edit'] = self.offending_column
        for attributes in VALIDATION_MESSAGES_ATTRIBUTES:
            if self.offending_column in attributes:
                context['attributes_to_show'] = [
                    attr for attr in attributes if attr != self.offending_column
                ]
        context['submission'] = self.submission
        context['error_type'] = 'coordinate_check'
        context['show_units'] = self.show_units
        if self.units:
            context['units'] = self.units
        return context


# a detail view since I need to operate on a submission object
# HINT: rename to a more informative name?
class EditSubmissionView(MessagesSubmissionMixin, OwnerMixin, ListView):
    template_name = "submissions/submission_edit.html"
    paginate_by = 10

    def get_queryset(self):
        """Subsetting names relying submission id"""
        self.submission = get_object_or_404(
            Submission,
            pk=self.kwargs['pk'],
            owner=self.request.user)

        # unknown animals should be removed from a submission. They have no
        # data in animal table nor sample
        return Name.objects.select_related(
                "validationresult",
                "animal",
                "sample").filter(
            Q(submission=self.submission) & (
                Q(animal__isnull=False) | Q(sample__isnull=False))
            ).order_by('id')

    def dispatch(self, request, *args, **kwargs):

        handler = super(EditSubmissionView, self).dispatch(
                request, *args, **kwargs)

        # here I've done get_queryset. Check for submission status
        if hasattr(self, "submission") and not self.submission.can_edit():
            message = "Cannot edit submission: current status is: %s" % (
                    self.submission.get_status_display())

            logger.warning(message)
            messages.warning(
                request=self.request,
                message=message,
                extra_tags="alert alert-dismissible alert-warning")

            return redirect(self.submission.get_absolute_url())

        return handler

    def get_context_data(self, **kwargs):
        # Call the base implementation first to get a context
        context = super(EditSubmissionView, self).get_context_data(**kwargs)

        # add submission to context
        context["submission"] = self.submission

        return context


class ListSubmissionsView(OwnerMixin, ListView):
    model = Submission
    template_name = "submissions/submission_list.html"
    ordering = ['-created_at']
    paginate_by = 10


class ReloadSubmissionView(OwnerMixin, UpdateView):
    form_class = ReloadForm
    model = Submission
    template_name = 'submissions/submission_reload.html'

    def form_invalid(self, form):
        messages.error(
            self.request,
            message="Please correct the errors below",
            extra_tags="alert alert-dismissible alert-danger")

        return super(ReloadSubmissionView, self).form_invalid(form)

    def form_valid(self, form):
        self.object = form.save(commit=False)

        # update object and force status
        self.object.message = "waiting for data loading"
        self.object.status = WAITING
        self.object.save()

        # HINT: can I change datasource type?

        # call the proper method
        if self.object.datasource_type == CRYOWEB_TYPE:
            # a valid submission start a task
            res = import_from_cryoweb.delay(self.object.pk)
            logger.info(
                "Start cryoweb reload process with task %s" % res.task_id)

        elif self.object.datasource_type == CRB_ANIM_TYPE:
            # a valid submission start a task
            my_task = ImportCRBAnimTask()

            # a valid submission start a task
            res = my_task.delay(self.object.pk)
            logger.info(
                "Start crbanim reload process with task %s" % res.task_id)

        else:
            # a valid submission start a task
            my_task = ImportTemplateTask()

            # a valid submission start a task
            res = my_task.delay(self.object.pk)
            logger.info(
                "Start template reload process with task %s" % res.task_id)

        # a redirect to self.object.get_absolute_url()
        return HttpResponseRedirect(self.get_success_url())


class DeleteSubmissionView(OwnerMixin, DeleteView):
    model = Submission
    template_name = "submissions/submission_confirm_delete.html"
    success_url = reverse_lazy('image_app:dashboard')

    def dispatch(self, request, *args, **kwargs):

        handler = super(DeleteSubmissionView, self).dispatch(
                request, *args, **kwargs)

        # here I've done get_queryset. Check for submission status
        if hasattr(self, "object") and not self.object.can_edit():
            message = "Cannot delete %s: submission status is: %s" % (
                    self.object, self.object.get_status_display())

            logger.warning(message)
            messages.warning(
                request=self.request,
                message=message,
                extra_tags="alert alert-dismissible alert-warning")

            return redirect(self.object.get_absolute_url())

        return handler

    # https://stackoverflow.com/a/39533619/4385116
    def get_context_data(self, **kwargs):
        # determining related objects
        # TODO: move this to a custom AJAX call
        context = super().get_context_data(**kwargs)

        deletable_objects, model_count, protected = get_deleted_objects(
            [self.object])

        # get only sample and animals from model_count
        info_deleted = {}

        items = ['animals', 'samples']

        for item in items:
            if item in model_count:
                info_deleted[item] = model_count[item]

        # add info to context
        context['info_deleted'] = dict(info_deleted).items()

        return context

    # https://ccbv.co.uk/projects/Django/1.11/django.views.generic.edit/DeleteView/#delete
    def delete(self, request, *args, **kwargs):
        """
        Add a message after calling base delete method
        """

        httpresponseredirect = super().delete(request, *args, **kwargs)

        message = "Submission %s was successfully deleted" % self.object.title
        logger.info(message)

        messages.info(
            request=self.request,
            message=message,
            extra_tags="alert alert-dismissible alert-info")

        return httpresponseredirect


class FixValidation(View, OwnerMixin):
    def post(self, request, **kwargs):
        # Fetch all required ids from input names and use it as keys
        keys_to_fix = dict()
        for key_to_fix in request.POST:
            if 'to_edit' in key_to_fix:
                keys_to_fix[
                    int(re.search('to_edit(.*)', key_to_fix).groups()[0])] \

                    = request.POST[key_to_fix]

        pk = self.kwargs['pk']
        record_type = self.kwargs['record_type']
        attribute_to_edit = self.kwargs['attribute_to_edit']

        submission = Submission.objects.get(pk=pk)
        submission.message = "waiting for data updating"
        submission.status = WAITING
        submission.save()

        # Update validation summary
        if record_type == 'dictuberon' or record_type == 'dictdevelstage' or \
                record_type == 'dictphysiostage':
            validation_summary_type = 'sample'
        elif record_type == 'dictsex':
            validation_summary_type = 'animal'
        else:
            validation_summary_type = record_type
        summary_obj, created = ValidationSummary.objects.get_or_create(
            submission=submission, type=validation_summary_type)
        summary_obj.submission = submission
        summary_obj.reset()

        # create a task
        if record_type == 'animal' or record_type == 'dictsex' or \
                record_type == 'dictspecie_animal':
            my_task = BatchUpdateAnimals()
        elif record_type == 'sample' or record_type == 'dictuberon' or \
                record_type == 'dictdevelstage' or \
                record_type == 'dictphysiostage' or \
                record_type == 'dictspecie_sample':
            my_task = BatchUpdateSamples()
        else:
            return HttpResponseRedirect(
                reverse('submissions:detail', args=(pk,)))

        # a valid submission start a task
        res = my_task.delay(pk, keys_to_fix, attribute_to_edit, record_type)
        logger.info(
            "Start fix validation process with task %s" % res.task_id)
        return HttpResponseRedirect(reverse('submissions:detail', args=(pk,)))


1		#!/usr/bin/env python3
2		# -- coding: utf-8 --
3		"""
4		Created on Tue Jul 24 15:49:23 2018
5
6		@author: Paolo Cozzi <[email protected]>
7		"""
8
9		import logging
10		import ast
11		import re
12		from django.core.exceptions import ObjectDoesNotExist
13
14		from django.contrib import messages
15		from django.contrib.auth.mixins import LoginRequiredMixin
16		from django.db.models import Q
17		from django.http import HttpResponseRedirect
18		from django.views import View
19		from django.views.generic import (
20		CreateView, DetailView, ListView, UpdateView, DeleteView)
21		from django.shortcuts import get_object_or_404, redirect
22		from django.urls import reverse_lazy, reverse
23
24		from common.constants import (
25		WAITING, ERROR, SUBMITTED, NEED_REVISION, CRYOWEB_TYPE, CRB_ANIM_TYPE,
26		TIME_UNITS, VALIDATION_MESSAGES_ATTRIBUTES, SAMPLE_STORAGE,
27		SAMPLE_STORAGE_PROCESSING, ACCURACIES, ONTOLOGY_VALIDATION_MESSAGES,
28		UNITS_VALIDATION_MESSAGES)
29		from common.helpers import get_deleted_objects, uid2biosample
30		from common.views import OwnerMixin
31		from crbanim.tasks import ImportCRBAnimTask
32		from cryoweb.tasks import import_from_cryoweb
33
34		from image_app.models import Submission, Name, Animal, Sample, DictUberon, \
35		DictDevelStage, DictPhysioStage, DictSex, DictSpecie
36		from excel.tasks import ImportTemplateTask
37
38		from validation.helpers import construct_validation_message
39		from validation.models import ValidationSummary
40		from animals.tasks import BatchUpdateAnimals
41		from samples.tasks import BatchUpdateSamples
42
43		from .forms import SubmissionForm, ReloadForm
44		from .helpers import is_target_in_message
45
46		# Get an instance of a logger
47		logger = logging.getLogger(__name__)
48
49
50		class CreateSubmissionView(LoginRequiredMixin, CreateView):
51		form_class = SubmissionForm
52		model = Submission
53
54		# template name is derived from model position and views type.
55		# in this case, ir will be 'image_app/submission_form.html' so
56		# i need to clearly specify it
57		template_name = "submissions/submission_form.html"
58
59		def form_invalid(self, form):
60		messages.error(
61		self.request,
62		message="Please correct the errors below",
63		extra_tags="alert alert-dismissible alert-danger")
64
65		return super(CreateSubmissionView, self).form_invalid(form)
66
67		# add user to this object
68		def form_valid(self, form):
69		self.object = form.save(commit=False)
70		self.object.owner = self.request.user
71
72		# I will have a different loading function accordingly with data type
73		if self.object.datasource_type == CRYOWEB_TYPE:
74		# update object and force status
75		self.object.message = "waiting for data loading"
76		self.object.status = WAITING
77		self.object.save()
78
79		# a valid submission start a task
80		res = import_from_cryoweb.delay(self.object.pk)
81		logger.info(
82		"Start cryoweb importing process with task %s" % res.task_id)
83
84		# I will have a different loading function accordingly with data type
85		elif self.object.datasource_type == CRB_ANIM_TYPE:
86		# update object and force status
87		self.object.message = "waiting for data loading"
88		self.object.status = WAITING
89		self.object.save()
90
91		# create a task
92		my_task = ImportCRBAnimTask()
93
94		# a valid submission start a task
95		res = my_task.delay(self.object.pk)
96		logger.info(
97		"Start crbanim importing process with task %s" % res.task_id)
98
99		else:
100		# update object and force status
101		self.object.message = "waiting for data loading"
102		self.object.status = WAITING
103		self.object.save()
104
105		# create a task
106		my_task = ImportTemplateTask()
107
108		# a valid submission start a task
109		res = my_task.delay(self.object.pk)
110		logger.info(
111		"Start template importing process with task %s" % res.task_id)
112
113		# a redirect to self.object.get_absolute_url()
114		return HttpResponseRedirect(self.get_success_url())
115
116
117		class MessagesSubmissionMixin(object):
118		"""Display messages in SubmissionViews"""
119
120		# https://stackoverflow.com/a/45696442
121		def get_context_data(self, **kwargs):
122		data = super().get_context_data(**kwargs)
123
124		# get the submission message
125		message = self.submission.message
126
127		# check if data are loaded or not
128		if self.submission.status in [WAITING, SUBMITTED]:
129		messages.warning(
130		request=self.request,
131		message=message,
132		extra_tags="alert alert-dismissible alert-warning")
133
134		elif self.submission.status in [ERROR, NEED_REVISION]:
135		messages.error(
136		request=self.request,
137		message=message,
138		extra_tags="alert alert-dismissible alert-danger")
139
140		elif message is not None and message != '':
141		messages.info(
142		request=self.request,
143		message=message,
144		extra_tags="alert alert-dismissible alert-info")
145
146		return data
147
148
149		class DetailSubmissionView(MessagesSubmissionMixin, OwnerMixin, DetailView):
150		model = Submission
151		template_name = "submissions/submission_detail.html"
152
153		def get_context_data(self, **kwargs):
154		# pass self.object to a new submission attribute in order to call
155		# MessagesSubmissionMixin.get_context_data()
156		self.submission = self.object
157
158		# Call the base implementation first to get a context
159		context = super(DetailSubmissionView, self).get_context_data(**kwargs)
160
161		# add submission report to context
162		validation_summary = construct_validation_message(self.submission)
163
164		# HINT: is this computational intensive?
165		context["validation_summary"] = validation_summary
166
167		return context
168
169
170		class SubmissionValidationSummaryView(OwnerMixin, DetailView):
171		model = Submission
172		template_name = "submissions/submission_validation_summary.html"
173
174		def get_context_data(self, **kwargs):
175		context = super().get_context_data(**kwargs)
176		summary_type = self.kwargs['type']
177		try:
178		validation_summary = self.object.validationsummary_set\
179		.get(type=summary_type)
180		context['validation_summary'] = validation_summary
181		editable = list()
182		for message in validation_summary.messages:
183		message = ast.literal_eval(message)
184		if uid2biosample(message['offending_column']) in \
185		[val for sublist in VALIDATION_MESSAGES_ATTRIBUTES for
186		val in sublist]:
187		editable.append(True)
188		else:
189		editable.append(False)
190		context['editable'] = editable
191		except ObjectDoesNotExist:
192		context['validation_summary'] = None
193		context['submission'] = Submission.objects.get(pk=self.kwargs['pk'])
194		return context
195
196
197		class SubmissionValidationSummaryFixErrorsView(OwnerMixin, ListView):
198		template_name = "submissions/submission_validation_summary_fix_errors.html"
199
200		def get_queryset(self):
201		self.summary_type = self.kwargs['type']
202		self.submission = Submission.objects.get(pk=self.kwargs['pk'])
203		self.validation_summary = ValidationSummary.objects.get(
204		submission=self.submission, type=self.summary_type)
205		self.message = ast.literal_eval(self.validation_summary.messages[
206		int(self.kwargs['message_counter'])
207		])
208		self.offending_column = uid2biosample(
209		self.message['offending_column'])
210		if is_target_in_message(self.message['message'],
211		UNITS_VALIDATION_MESSAGES):
212		self.show_units = True
213		if self.offending_column == 'animal_age_at_collection':
214		self.offending_column += "_units"
215		self.units = [unit.name for unit in TIME_UNITS]
216		elif self.offending_column == 'preparation_interval_units':
217		self.units = [unit.name for unit in TIME_UNITS]
218		elif re.search(".* of field .* is not in the valid values list .*",
219		self.message['message']):
220		self.show_units = True
221		if self.offending_column == 'storage':
222		self.units = [unit.name for unit in SAMPLE_STORAGE]
223		elif self.offending_column == 'storage_processing':
224		self.units = [unit.name for unit in SAMPLE_STORAGE_PROCESSING]
225		elif self.offending_column == 'collection_place_accuracy':
226		self.units = [unit.name for unit in ACCURACIES]
227		elif self.offending_column == 'birth_location_accuracy':
228		self.units = [unit.name for unit in ACCURACIES]
229		elif is_target_in_message(self.message['message'],
230		ONTOLOGY_VALIDATION_MESSAGES):
231		self.show_units = False
232		self.units = None
233		self.offending_column = 'term'
234		if self.offending_column == 'organism_part':
235		self.summary_type = 'dictuberon'
236		return DictUberon.objects.filter(id__in=[Sample.objects.get(
237		pk=self.message['ids'][0]).organism_part_id])
238		elif self.offending_column == 'developmental_stage':
239		self.summary_type = 'dictdevelstage'
240		return DictDevelStage.objects.filter(id__in=[Sample.objects.get(
241		pk=self.message['ids'][0]).developmental_stage_id])
242		elif self.offending_column == 'physiological_stage':
243		self.summary_type = 'dictphysiostage'
244		return DictPhysioStage.objects.filter(id__in=[
245		Sample.objects.get(
246		pk=self.message['ids'][0]).physiological_stage_id])
247		elif self.offending_column == 'sex':
248		self.summary_type = 'dictsex'
249		return DictSex.objects.filter(id__in=[Animal.objects.get(
250		pk=self.message['ids'][0]).sex_id])
251		elif self.offending_column == 'species':
252		self.summary_type = f'dictspecie_{self.summary_type}'
253		if self.summary_type == 'dictspecie_animal':
254		return DictSpecie.objects.filter(id__in=[Animal.objects.get(
255		pk=self.message['ids'][0]).specie.id])
256		elif self.summary_type == 'dictspecie_sample':
257		return DictSpecie.objects.filter(id__in=[Sample.objects.get(
258		pk=self.message['ids'][0]).specie.id])
259		else:
260		self.show_units = False
261		self.units = None
262		if self.summary_type == 'animal':
263		return Animal.objects.filter(id__in=self.message['ids'])
264		elif self.summary_type == 'sample':
265		return Sample.objects.filter(id__in=self.message['ids'])
266
267		def get_context_data(self, **kwargs):
268		# Call the base implementation first to get a context
269		context = super(
270		SubmissionValidationSummaryFixErrorsView, self
271		).get_context_data(**kwargs)
272
273		# add submission to context
274		context["message"] = self.message
275		context["type"] = self.summary_type
276		context['attribute_to_edit'] = self.offending_column
277		for attributes in VALIDATION_MESSAGES_ATTRIBUTES:
278		if self.offending_column in attributes:
279		context['attributes_to_show'] = [
280		attr for attr in attributes if attr != self.offending_column
281		]
282		context['submission'] = self.submission
283		context['error_type'] = 'coordinate_check'
284		context['show_units'] = self.show_units
285		if self.units:
286		context['units'] = self.units
287		return context
288
289
290		# a detail view since I need to operate on a submission object
291		# HINT: rename to a more informative name?
292		class EditSubmissionView(MessagesSubmissionMixin, OwnerMixin, ListView):
293		template_name = "submissions/submission_edit.html"
294		paginate_by = 10
295
296		def get_queryset(self):
297		"""Subsetting names relying submission id"""
298		self.submission = get_object_or_404(
299		Submission,
300		pk=self.kwargs['pk'],
301		owner=self.request.user)
302
303		# unknown animals should be removed from a submission. They have no
304		# data in animal table nor sample
305		return Name.objects.select_related(
306		"validationresult",
307		"animal",
308		"sample").filter(
309		Q(submission=self.submission) & (
310		Q(animal__isnull=False) \| Q(sample__isnull=False))
311		).order_by('id')
312
313	View Code Duplication	def dispatch(self, request, args, *kwargs):
		0 ignored issues – show Duplication introduced 2019-06-07 17:57 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
314		handler = super(EditSubmissionView, self).dispatch(
315		request, args, *kwargs)
316
317		# here I've done get_queryset. Check for submission status
318		if hasattr(self, "submission") and not self.submission.can_edit():
319		message = "Cannot edit submission: current status is: %s" % (
320		self.submission.get_status_display())
321
322		logger.warning(message)
323		messages.warning(
324		request=self.request,
325		message=message,
326		extra_tags="alert alert-dismissible alert-warning")
327
328		return redirect(self.submission.get_absolute_url())
329
330		return handler
331
332		def get_context_data(self, **kwargs):
333		# Call the base implementation first to get a context
334		context = super(EditSubmissionView, self).get_context_data(**kwargs)
335
336		# add submission to context
337		context["submission"] = self.submission
338
339		return context
340
341
342		class ListSubmissionsView(OwnerMixin, ListView):
343		model = Submission
344		template_name = "submissions/submission_list.html"
345		ordering = ['-created_at']
346		paginate_by = 10
347
348
349		class ReloadSubmissionView(OwnerMixin, UpdateView):
350		form_class = ReloadForm
351		model = Submission
352		template_name = 'submissions/submission_reload.html'
353
354		def form_invalid(self, form):
355		messages.error(
356		self.request,
357		message="Please correct the errors below",
358		extra_tags="alert alert-dismissible alert-danger")
359
360		return super(ReloadSubmissionView, self).form_invalid(form)
361
362		def form_valid(self, form):
363		self.object = form.save(commit=False)
364
365		# update object and force status
366		self.object.message = "waiting for data loading"
367		self.object.status = WAITING
368		self.object.save()
369
370		# HINT: can I change datasource type?
371
372		# call the proper method
373		if self.object.datasource_type == CRYOWEB_TYPE:
374		# a valid submission start a task
375		res = import_from_cryoweb.delay(self.object.pk)
376		logger.info(
377		"Start cryoweb reload process with task %s" % res.task_id)
378
379		elif self.object.datasource_type == CRB_ANIM_TYPE:
380		# a valid submission start a task
381		my_task = ImportCRBAnimTask()
382
383		# a valid submission start a task
384		res = my_task.delay(self.object.pk)
385		logger.info(
386		"Start crbanim reload process with task %s" % res.task_id)
387
388		else:
389		# a valid submission start a task
390		my_task = ImportTemplateTask()
391
392		# a valid submission start a task
393		res = my_task.delay(self.object.pk)
394		logger.info(
395		"Start template reload process with task %s" % res.task_id)
396
397		# a redirect to self.object.get_absolute_url()
398		return HttpResponseRedirect(self.get_success_url())
399
400
401		class DeleteSubmissionView(OwnerMixin, DeleteView):
402		model = Submission
403		template_name = "submissions/submission_confirm_delete.html"
404		success_url = reverse_lazy('image_app:dashboard')
405
406	View Code Duplication	def dispatch(self, request, args, *kwargs):
		0 ignored issues – show Duplication introduced 2019-06-07 17:57 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
407		handler = super(DeleteSubmissionView, self).dispatch(
408		request, args, *kwargs)
409
410		# here I've done get_queryset. Check for submission status
411		if hasattr(self, "object") and not self.object.can_edit():
412		message = "Cannot delete %s: submission status is: %s" % (
413		self.object, self.object.get_status_display())
414
415		logger.warning(message)
416		messages.warning(
417		request=self.request,
418		message=message,
419		extra_tags="alert alert-dismissible alert-warning")
420
421		return redirect(self.object.get_absolute_url())
422
423		return handler
424
425		# https://stackoverflow.com/a/39533619/4385116
426		def get_context_data(self, **kwargs):
427		# determining related objects
428		# TODO: move this to a custom AJAX call
429		context = super().get_context_data(**kwargs)
430
431		deletable_objects, model_count, protected = get_deleted_objects(
432		[self.object])
433
434		# get only sample and animals from model_count
435		info_deleted = {}
436
437		items = ['animals', 'samples']
438
439		for item in items:
440		if item in model_count:
441		info_deleted[item] = model_count[item]
442
443		# add info to context
444		context['info_deleted'] = dict(info_deleted).items()
445
446		return context
447
448		# https://ccbv.co.uk/projects/Django/1.11/django.views.generic.edit/DeleteView/#delete
449		def delete(self, request, args, *kwargs):
450		"""
451		Add a message after calling base delete method
452		"""
453
454		httpresponseredirect = super().delete(request, args, *kwargs)
455
456		message = "Submission %s was successfully deleted" % self.object.title
457		logger.info(message)
458
459		messages.info(
460		request=self.request,
461		message=message,
462		extra_tags="alert alert-dismissible alert-info")
463
464		return httpresponseredirect
465
466
467		class FixValidation(View, OwnerMixin):
468		def post(self, request, **kwargs):
469		# Fetch all required ids from input names and use it as keys
470		keys_to_fix = dict()
471		for key_to_fix in request.POST:
472		if 'to_edit' in key_to_fix:
473		keys_to_fix[
474		int(re.search('to_edit(.*)', key_to_fix).groups()[0])] \
		0 ignored issues – show Comprehensibility Best Practice introduced 2019-07-18 08:55 UTC by Report Bug Copy Issue Report The variable `int` does not seem to be defined. Loading history...
475		= request.POST[key_to_fix]
476
477		pk = self.kwargs['pk']
478		record_type = self.kwargs['record_type']
479		attribute_to_edit = self.kwargs['attribute_to_edit']
480
481		submission = Submission.objects.get(pk=pk)
482		submission.message = "waiting for data updating"
483		submission.status = WAITING
484		submission.save()
485
486		# Update validation summary
487		if record_type == 'dictuberon' or record_type == 'dictdevelstage' or \
488		record_type == 'dictphysiostage':
489		validation_summary_type = 'sample'
490		elif record_type == 'dictsex':
491		validation_summary_type = 'animal'
492		else:
493		validation_summary_type = record_type
494		summary_obj, created = ValidationSummary.objects.get_or_create(
495		submission=submission, type=validation_summary_type)
496		summary_obj.submission = submission
497		summary_obj.reset()
498
499		# create a task
500		if record_type == 'animal' or record_type == 'dictsex' or \
501		record_type == 'dictspecie_animal':
502		my_task = BatchUpdateAnimals()
503		elif record_type == 'sample' or record_type == 'dictuberon' or \
504		record_type == 'dictdevelstage' or \
505		record_type == 'dictphysiostage' or \
506		record_type == 'dictspecie_sample':
507		my_task = BatchUpdateSamples()
508		else:
509		return HttpResponseRedirect(
510		reverse('submissions:detail', args=(pk,)))
511
512		# a valid submission start a task
513		res = my_task.delay(pk, keys_to_fix, attribute_to_edit, record_type)
514		logger.info(
515		"Start fix validation process with task %s" % res.task_id)
516		return HttpResponseRedirect(reverse('submissions:detail', args=(pk,)))
517

cnr-ibba / IMAGE-InjectTool

Pull Request — master (#41)

SubmissionValidationSummaryView.get_context_data() A

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