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#!/usr/bin/env python3 |
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# -*- coding: utf-8 -*- |
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""" |
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Created on Tue Jul 24 15:49:23 2018 |
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@author: Paolo Cozzi <[email protected]> |
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""" |
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import logging |
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import ast |
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import re |
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from django.core.exceptions import ObjectDoesNotExist |
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from django.contrib import messages |
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from django.contrib.auth.mixins import LoginRequiredMixin |
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from django.db.models import Q |
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from django.http import HttpResponseRedirect |
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from django.views import View |
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from django.views.generic import ( |
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CreateView, DetailView, ListView, UpdateView, DeleteView) |
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from django.shortcuts import get_object_or_404, redirect |
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from django.urls import reverse_lazy, reverse |
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from common.constants import ( |
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WAITING, ERROR, SUBMITTED, NEED_REVISION, CRYOWEB_TYPE, CRB_ANIM_TYPE, |
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TIME_UNITS, VALIDATION_MESSAGES_ATTRIBUTES) |
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from common.helpers import get_deleted_objects, uid2biosample |
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from common.views import OwnerMixin |
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from crbanim.tasks import ImportCRBAnimTask |
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from cryoweb.tasks import import_from_cryoweb |
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from image_app.models import Submission, Name, Animal, Sample |
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from excel.tasks import ImportTemplateTask |
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from validation.helpers import construct_validation_message |
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from validation.models import ValidationSummary |
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from animals.tasks import BatchUpdateAnimals |
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from samples.tasks import BatchUpdateSamples |
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from .forms import SubmissionForm, ReloadForm |
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# Get an instance of a logger |
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logger = logging.getLogger(__name__) |
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class CreateSubmissionView(LoginRequiredMixin, CreateView): |
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form_class = SubmissionForm |
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model = Submission |
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# template name is derived from model position and views type. |
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# in this case, ir will be 'image_app/submission_form.html' so |
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# i need to clearly specify it |
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template_name = "submissions/submission_form.html" |
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def form_invalid(self, form): |
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messages.error( |
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self.request, |
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message="Please correct the errors below", |
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extra_tags="alert alert-dismissible alert-danger") |
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return super(CreateSubmissionView, self).form_invalid(form) |
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# add user to this object |
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def form_valid(self, form): |
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self.object = form.save(commit=False) |
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self.object.owner = self.request.user |
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# I will have a different loading function accordingly with data type |
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if self.object.datasource_type == CRYOWEB_TYPE: |
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# update object and force status |
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self.object.message = "waiting for data loading" |
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self.object.status = WAITING |
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self.object.save() |
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# a valid submission start a task |
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res = import_from_cryoweb.delay(self.object.pk) |
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logger.info( |
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"Start cryoweb importing process with task %s" % res.task_id) |
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# I will have a different loading function accordingly with data type |
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elif self.object.datasource_type == CRB_ANIM_TYPE: |
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# update object and force status |
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self.object.message = "waiting for data loading" |
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self.object.status = WAITING |
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self.object.save() |
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# create a task |
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my_task = ImportCRBAnimTask() |
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# a valid submission start a task |
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res = my_task.delay(self.object.pk) |
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logger.info( |
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"Start crbanim importing process with task %s" % res.task_id) |
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else: |
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# update object and force status |
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self.object.message = "waiting for data loading" |
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self.object.status = WAITING |
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self.object.save() |
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# create a task |
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my_task = ImportTemplateTask() |
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# a valid submission start a task |
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res = my_task.delay(self.object.pk) |
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logger.info( |
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"Start template importing process with task %s" % res.task_id) |
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# a redirect to self.object.get_absolute_url() |
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return HttpResponseRedirect(self.get_success_url()) |
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class MessagesSubmissionMixin(object): |
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"""Display messages in SubmissionViews""" |
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# https://stackoverflow.com/a/45696442 |
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def get_context_data(self, **kwargs): |
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data = super().get_context_data(**kwargs) |
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# get the submission message |
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message = self.submission.message |
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# check if data are loaded or not |
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if self.submission.status in [WAITING, SUBMITTED]: |
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messages.warning( |
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request=self.request, |
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message=message, |
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extra_tags="alert alert-dismissible alert-warning") |
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elif self.submission.status in [ERROR, NEED_REVISION]: |
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messages.error( |
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request=self.request, |
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message=message, |
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extra_tags="alert alert-dismissible alert-danger") |
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elif message is not None and message != '': |
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messages.info( |
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request=self.request, |
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message=message, |
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extra_tags="alert alert-dismissible alert-info") |
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return data |
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class DetailSubmissionView(MessagesSubmissionMixin, OwnerMixin, DetailView): |
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model = Submission |
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template_name = "submissions/submission_detail.html" |
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def get_context_data(self, **kwargs): |
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# pass self.object to a new submission attribute in order to call |
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# MessagesSubmissionMixin.get_context_data() |
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self.submission = self.object |
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# Call the base implementation first to get a context |
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context = super(DetailSubmissionView, self).get_context_data(**kwargs) |
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# add submission report to context |
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validation_summary = construct_validation_message(self.submission) |
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# HINT: is this computational intensive? |
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context["validation_summary"] = validation_summary |
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return context |
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class SubmissionValidationSummaryView(OwnerMixin, DetailView): |
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model = Submission |
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template_name = "submissions/submission_validation_summary.html" |
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def get_context_data(self, **kwargs): |
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context = super().get_context_data(**kwargs) |
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summary_type = self.kwargs['type'] |
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try: |
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validation_summary = self.object.validationsummary_set\ |
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.get(type=summary_type) |
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context['validation_summary'] = validation_summary |
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editable = list() |
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for message in validation_summary.messages: |
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message = ast.literal_eval(message) |
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if uid2biosample(message['offending_column']) in \ |
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[val for sublist in VALIDATION_MESSAGES_ATTRIBUTES for |
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val in sublist]: |
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editable.append(True) |
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else: |
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editable.append(False) |
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context['editable'] = editable |
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except ObjectDoesNotExist: |
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context['validation_summary'] = None |
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context['submission'] = Submission.objects.get(pk=self.kwargs['pk']) |
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return context |
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class SubmissionValidationSummaryFixErrorsView(OwnerMixin, ListView): |
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template_name = "submissions/submission_validation_summary_fix_errors.html" |
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def get_queryset(self): |
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self.summary_type = self.kwargs['type'] |
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self.submission = Submission.objects.get(pk=self.kwargs['pk']) |
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self.validation_summary = ValidationSummary.objects.get( |
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submission=self.submission, type=self.summary_type) |
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self.message = ast.literal_eval(self.validation_summary.messages[ |
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int(self.kwargs['message_counter']) |
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]) |
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self.offending_column = uid2biosample( |
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self.message['offending_column']) |
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# Special case fo 'unit' errors |
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if re.search(".* for field .* is not in the valid units list (.*)", |
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self.message['message']) or re.search( |
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"One of .* need to be present for the field .*", |
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self.message['message']): |
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self.offending_column += "_units" |
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self.show_units = True |
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else: |
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self.show_units = False |
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if self.summary_type == 'animal': |
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return Animal.objects.filter(id__in=self.message['ids']) |
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elif self.summary_type == 'sample': |
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return Sample.objects.filter(id__in=self.message['ids']) |
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def get_context_data(self, **kwargs): |
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# Call the base implementation first to get a context |
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context = super( |
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SubmissionValidationSummaryFixErrorsView, self |
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).get_context_data(**kwargs) |
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# add submission to context |
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context["message"] = self.message |
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context["type"] = self.summary_type |
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context['attribute_to_edit'] = self.offending_column |
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for attributes in VALIDATION_MESSAGES_ATTRIBUTES: |
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if self.offending_column in attributes: |
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context['attributes_to_show'] = [ |
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attr for attr in attributes if attr != self.offending_column |
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] |
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context['submission'] = self.submission |
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context['error_type'] = 'coordinate_check' |
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context['show_units'] = self.show_units |
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context['units'] = [unit.name for unit in TIME_UNITS] |
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return context |
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# a detail view since I need to operate on a submission object |
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# HINT: rename to a more informative name? |
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class EditSubmissionView(MessagesSubmissionMixin, OwnerMixin, ListView): |
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template_name = "submissions/submission_edit.html" |
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paginate_by = 10 |
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def get_queryset(self): |
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"""Subsetting names relying submission id""" |
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self.submission = get_object_or_404( |
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Submission, |
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pk=self.kwargs['pk'], |
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owner=self.request.user) |
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# unknown animals should be removed from a submission. They have no |
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# data in animal table nor sample |
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return Name.objects.select_related( |
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"validationresult", |
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"animal", |
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"sample").filter( |
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Q(submission=self.submission) & ( |
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Q(animal__isnull=False) | Q(sample__isnull=False)) |
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).order_by('id') |
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View Code Duplication |
def dispatch(self, request, *args, **kwargs): |
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handler = super(EditSubmissionView, self).dispatch( |
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request, *args, **kwargs) |
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# here I've done get_queryset. Check for submission status |
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if hasattr(self, "submission") and not self.submission.can_edit(): |
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message = "Cannot edit submission: current status is: %s" % ( |
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self.submission.get_status_display()) |
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logger.warning(message) |
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messages.warning( |
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request=self.request, |
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message=message, |
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extra_tags="alert alert-dismissible alert-warning") |
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return redirect(self.submission.get_absolute_url()) |
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return handler |
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def get_context_data(self, **kwargs): |
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# Call the base implementation first to get a context |
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context = super(EditSubmissionView, self).get_context_data(**kwargs) |
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# add submission to context |
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context["submission"] = self.submission |
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return context |
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class ListSubmissionsView(OwnerMixin, ListView): |
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model = Submission |
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template_name = "submissions/submission_list.html" |
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ordering = ['-created_at'] |
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paginate_by = 10 |
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class ReloadSubmissionView(OwnerMixin, UpdateView): |
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form_class = ReloadForm |
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model = Submission |
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template_name = 'submissions/submission_reload.html' |
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def form_invalid(self, form): |
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messages.error( |
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self.request, |
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message="Please correct the errors below", |
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extra_tags="alert alert-dismissible alert-danger") |
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return super(ReloadSubmissionView, self).form_invalid(form) |
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def form_valid(self, form): |
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self.object = form.save(commit=False) |
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# update object and force status |
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self.object.message = "waiting for data loading" |
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self.object.status = WAITING |
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self.object.save() |
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# HINT: can I change datasource type? |
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# call the proper method |
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if self.object.datasource_type == CRYOWEB_TYPE: |
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# a valid submission start a task |
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res = import_from_cryoweb.delay(self.object.pk) |
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logger.info( |
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"Start cryoweb reload process with task %s" % res.task_id) |
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elif self.object.datasource_type == CRB_ANIM_TYPE: |
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# a valid submission start a task |
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my_task = ImportCRBAnimTask() |
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# a valid submission start a task |
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res = my_task.delay(self.object.pk) |
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logger.info( |
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"Start crbanim reload process with task %s" % res.task_id) |
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else: |
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# a valid submission start a task |
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my_task = ImportTemplateTask() |
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# a valid submission start a task |
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res = my_task.delay(self.object.pk) |
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logger.info( |
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"Start template reload process with task %s" % res.task_id) |
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# a redirect to self.object.get_absolute_url() |
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return HttpResponseRedirect(self.get_success_url()) |
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class DeleteSubmissionView(OwnerMixin, DeleteView): |
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model = Submission |
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template_name = "submissions/submission_confirm_delete.html" |
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success_url = reverse_lazy('image_app:dashboard') |
358
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359
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|
View Code Duplication |
def dispatch(self, request, *args, **kwargs): |
|
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|
360
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handler = super(DeleteSubmissionView, self).dispatch( |
361
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request, *args, **kwargs) |
362
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|
363
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# here I've done get_queryset. Check for submission status |
364
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|
if hasattr(self, "object") and not self.object.can_edit(): |
365
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message = "Cannot delete %s: submission status is: %s" % ( |
366
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|
self.object, self.object.get_status_display()) |
367
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|
368
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logger.warning(message) |
369
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messages.warning( |
370
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request=self.request, |
371
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message=message, |
372
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extra_tags="alert alert-dismissible alert-warning") |
373
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374
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return redirect(self.object.get_absolute_url()) |
375
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376
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return handler |
377
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378
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|
# https://stackoverflow.com/a/39533619/4385116 |
379
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def get_context_data(self, **kwargs): |
380
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|
# determining related objects |
381
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# TODO: move this to a custom AJAX call |
382
|
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|
context = super().get_context_data(**kwargs) |
383
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|
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|
384
|
|
|
deletable_objects, model_count, protected = get_deleted_objects( |
385
|
|
|
[self.object]) |
386
|
|
|
|
387
|
|
|
# get only sample and animals from model_count |
388
|
|
|
info_deleted = {} |
389
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|
390
|
|
|
items = ['animals', 'samples'] |
391
|
|
|
|
392
|
|
|
for item in items: |
393
|
|
|
if item in model_count: |
394
|
|
|
info_deleted[item] = model_count[item] |
395
|
|
|
|
396
|
|
|
# add info to context |
397
|
|
|
context['info_deleted'] = dict(info_deleted).items() |
398
|
|
|
|
399
|
|
|
return context |
400
|
|
|
|
401
|
|
|
# https://ccbv.co.uk/projects/Django/1.11/django.views.generic.edit/DeleteView/#delete |
402
|
|
|
def delete(self, request, *args, **kwargs): |
403
|
|
|
""" |
404
|
|
|
Add a message after calling base delete method |
405
|
|
|
""" |
406
|
|
|
|
407
|
|
|
httpresponseredirect = super().delete(request, *args, **kwargs) |
408
|
|
|
|
409
|
|
|
message = "Submission %s was successfully deleted" % self.object.title |
410
|
|
|
logger.info(message) |
411
|
|
|
|
412
|
|
|
messages.info( |
413
|
|
|
request=self.request, |
414
|
|
|
message=message, |
415
|
|
|
extra_tags="alert alert-dismissible alert-info") |
416
|
|
|
|
417
|
|
|
return httpresponseredirect |
418
|
|
|
|
419
|
|
|
|
420
|
|
|
class FixValidation(View, OwnerMixin): |
421
|
|
|
def post(self, request, **kwargs): |
422
|
|
|
# Fetch all required ids from input names and use it as keys |
423
|
|
|
keys_to_fix = dict() |
424
|
|
|
for key_to_fix in request.POST: |
425
|
|
|
if 'to_edit' in key_to_fix: |
426
|
|
|
keys_to_fix[ |
427
|
|
|
int(re.search('to_edit(.*)', key_to_fix).groups()[0])] \ |
|
|
|
|
428
|
|
|
= request.POST[key_to_fix] |
429
|
|
|
|
430
|
|
|
pk = self.kwargs['pk'] |
431
|
|
|
record_type = self.kwargs['record_type'] |
432
|
|
|
attribute_to_edit = self.kwargs['attribute_to_edit'] |
433
|
|
|
|
434
|
|
|
submission = Submission.objects.get(pk=pk) |
435
|
|
|
submission.message = "waiting for data updating" |
436
|
|
|
submission.status = WAITING |
437
|
|
|
submission.save() |
438
|
|
|
|
439
|
|
|
# Update validation summary |
440
|
|
|
summary_obj, created = ValidationSummary.objects.get_or_create( |
441
|
|
|
submission=submission, type=record_type) |
442
|
|
|
summary_obj.submission = submission |
443
|
|
|
summary_obj.reset() |
444
|
|
|
|
445
|
|
|
# create a task |
446
|
|
|
if record_type == 'animal': |
447
|
|
|
my_task = BatchUpdateAnimals() |
448
|
|
|
elif record_type == 'sample': |
449
|
|
|
my_task = BatchUpdateSamples() |
450
|
|
|
else: |
451
|
|
|
return HttpResponseRedirect( |
452
|
|
|
reverse('submissions:detail', args=(pk,))) |
453
|
|
|
|
454
|
|
|
# a valid submission start a task |
455
|
|
|
res = my_task.delay(pk, keys_to_fix, attribute_to_edit) |
456
|
|
|
logger.info( |
457
|
|
|
"Start fix validation process with task %s" % res.task_id) |
458
|
|
|
return HttpResponseRedirect(reverse('submissions:detail', args=(pk,))) |
459
|
|
|
|