Submissions App

Submission statuses are described in Common statuses

submissions.forms

submissions.forms module contents

Created on Tue Jul 24 15:51:05 2018

@author: Paolo Cozzi <cozzi@ibba.cnr.it>

class submissions.forms.ReloadForm(*args, **kwargs)

Bases: submissions.forms.SubmissionFormMixin, common.forms.RequestFormMixin, django.forms.models.ModelForm

class Meta

Bases: object

fields = ('datasource_type', 'datasource_version', 'uploaded_file')

help_texts = {'datasource_type': 'example: CryoWeb. Need an empty template file? download it from <a href="/media/Image_sample_empty_template_20191002_v2.1.xlsx">here</a>', 'uploaded_file': 'Need to be in UTF-8 or ASCII format'}

model

alias of uid.models.Submission

base_fields = {'agree_reload': <django.forms.fields.BooleanField object>, 'datasource_type': <django.forms.fields.TypedChoiceField object>, 'datasource_version': <django.forms.fields.CharField object>, 'uploaded_file': <django.forms.fields.FileField object>}

declared_fields = {'agree_reload': <django.forms.fields.BooleanField object>}

is_reload = True

property media

Return all media required to render the widgets on this form.

class submissions.forms.SubmissionForm(*args, **kwargs)

Bases: submissions.forms.SubmissionFormMixin, common.forms.RequestFormMixin, django.forms.models.ModelForm

class Meta

Bases: object

fields = ('title', 'description', 'gene_bank_name', 'gene_bank_country', 'organization', 'datasource_type', 'datasource_version', 'uploaded_file')

help_texts = {'datasource_type': 'example: CryoWeb. Need an empty template file? download it from <a href="/media/Image_sample_empty_template_20191002_v2.1.xlsx">here</a>', 'organization': 'Who owns the data. Not listed? please <a href="mailto:bioinfo.ibba@gmail.com?subject=please add my organization">contact us</a>', 'uploaded_file': 'Need to be in UTF-8 or ASCII format'}

model

alias of uid.models.Submission

base_fields = {'datasource_type': <django.forms.fields.TypedChoiceField object>, 'datasource_version': <django.forms.fields.CharField object>, 'description': <django.forms.fields.CharField object>, 'gene_bank_country': <django.forms.models.ModelChoiceField object>, 'gene_bank_name': <django.forms.fields.CharField object>, 'organization': <django.forms.models.ModelChoiceField object>, 'title': <django.forms.fields.CharField object>, 'uploaded_file': <django.forms.fields.FileField object>}

declared_fields = {}

property media

Return all media required to render the widgets on this form.

class submissions.forms.SubmissionFormMixin

Bases: submissions.forms.UniqueSubmissionMixin

check_crbanim_columns()

Check if a CRBanim file has mandatory columns

check_file_encoding()

check_template_file()

Check if template file has columns and sheets

clean()

class submissions.forms.UniqueSubmissionMixin

Bases: object

check_submission_exists()

Test if I already have a submission with the same data

is_reload = False

class submissions.forms.UpdateSubmissionForm(*args, **kwargs)

Bases: submissions.forms.UniqueSubmissionMixin, common.forms.RequestFormMixin, django.forms.models.ModelForm

class Meta

Bases: object

fields = ('title', 'description', 'gene_bank_name', 'gene_bank_country', 'organization', 'datasource_type', 'datasource_version')

help_texts = {'organization': 'Who owns the data. Not listed? please <a href="mailto:bioinfo.ibba@gmail.com?subject=please add my organization">contact us</a>'}

model

alias of uid.models.Submission

base_fields = {'datasource_type': <django.forms.fields.TypedChoiceField object>, 'datasource_version': <django.forms.fields.CharField object>, 'description': <django.forms.fields.CharField object>, 'gene_bank_country': <django.forms.models.ModelChoiceField object>, 'gene_bank_name': <django.forms.fields.CharField object>, 'organization': <django.forms.models.ModelChoiceField object>, 'title': <django.forms.fields.CharField object>}

clean()

Hook for doing any extra form-wide cleaning after Field.clean() has been called on every field. Any ValidationError raised by this method will not be associated with a particular field; it will have a special-case association with the field named ‘__all__’.

declared_fields = {}

property media

Return all media required to render the widgets on this form.

submissions.helpers

submissions.helpers module contents

Created on Thu Jun 27 11:52:37 2019

@author: Paolo Cozzi <cozzi@ibba.cnr.it>

class submissions.helpers.AnimalResource

Bases: import_export.resources.ModelResource

class Meta

Bases: object

export_order = ('id', 'name', 'biosample_id', 'material', 'status', 'last_changed', 'last_submitted')

fields = ('id', 'name', 'biosample_id', 'material', 'status', 'last_changed', 'last_submitted')

model

alias of uid.models.Animal

dehydrate_status(animal)

Convert a numeric status field into the displayed column

fields = {'biosample_id': <import_export.fields.Field: biosample_id>, 'id': <import_export.fields.Field: id>, 'last_changed': <import_export.fields.Field: last_changed>, 'last_submitted': <import_export.fields.Field: last_submitted>, 'material': <import_export.fields.Field: material>, 'name': <import_export.fields.Field: name>, 'status': <import_export.fields.Field: status>}

class submissions.helpers.SampleResource

Bases: import_export.resources.ModelResource

class Meta

Bases: object

export_order = ('id', 'name', 'biosample_id', 'material', 'status', 'last_changed', 'last_submitted')

fields = ('id', 'name', 'biosample_id', 'material', 'status', 'last_changed', 'last_submitted')

model

alias of uid.models.Sample

dehydrate_status(sample)

Convert a numeric status field into the displayed column

fields = {'biosample_id': <import_export.fields.Field: biosample_id>, 'id': <import_export.fields.Field: id>, 'last_changed': <import_export.fields.Field: last_changed>, 'last_submitted': <import_export.fields.Field: last_submitted>, 'material': <import_export.fields.Field: material>, 'name': <import_export.fields.Field: name>, 'status': <import_export.fields.Field: status>}

submissions.helpers.is_target_in_message(target, messages)

This function will return true if target in message

Parameters

target (str) – target to search

submissions.helpers.send_message(submission_obj, validation_message=None)

Update submission.status and submission message using django channels

Parameters

• submission_obj (uid.models.Submission) – an UID submission object

• validation_message (dict) – set validation message

submissions.tasks

submissions.tasks module contents

Created on Tue Jul 9 16:10:06 2019

@author: Paolo Cozzi <cozzi@ibba.cnr.it>

class submissions.tasks.BatchUpdateMixin

Bases: submissions.tasks.SubmissionTaskMixin

Mixin to do batch update of fields to fix validation

batch_update(submission_id, ids, attribute)

item_cls = None

class submissions.tasks.ImportGenericTaskMixin

Bases: submissions.tasks.SubmissionTaskMixin, common.tasks.NotifyAdminTaskMixin

A mixing used to import datasource into UID

action = None

run(submission_id)

a function to upload data into UID

class submissions.tasks.SubmissionTaskMixin

Bases: object

A mixin to extend Task to support UID Submission objects

action = None

get_uid_submission(submission_id)

Get a UID Submission instance from an id

Parameters

submission_id (int) – the submission id

Returns

a UID submission instance

Return type

Submission

mail_to_owner(submission_obj, subject, body)

max_body_size = 5000

on_failure(exc, task_id, args, kwargs, einfo)

Override the default on_failure method

send_message(submission_obj, construct_message=False)

Update submission.status and submission message using django channels

Parameters

• submission_obj (uid.models.Submission) – an UID submission object

• construct_message (bool) – construct validation message or not

update_submission_status(submission_obj, status, message, construct_message=False)

Mark submission with status, then send message

Parameters

• submission_obj (uid.models.Submission) – an UID submission object

• status (int) – a common.constants.STATUSES value

• message (str) – the message to send

• construct_message (bool) – construct validation message or not

submissions.views

submissions.views module contents

Created on Tue Jul 24 15:49:23 2018

@author: Paolo Cozzi <cozzi@ibba.cnr.it>

class submissions.views.BatchDeleteMixin

Bases: submissions.views.DeleteSubmissionMixin, common.views.OwnerMixin

delete_type = None

get_context_data(**kwargs)

Add custom values to template context

model

alias of uid.models.Submission

post(request, *args, **kwargs)

class submissions.views.CreateSubmissionView(**kwargs)

Bases: django.contrib.auth.mixins.LoginRequiredMixin, common.views.FormInvalidMixin, django.views.generic.edit.CreateView

form_class

alias of submissions.forms.SubmissionForm

form_valid(form)

If the form is valid, save the associated model.

model

alias of uid.models.Submission

template_name = 'submissions/submission_form.html'

class submissions.views.DeleteAnimalsView(**kwargs)

Bases: submissions.views.BatchDeleteMixin, django.views.generic.detail.DetailView

delete_type = 'Animals'

model

alias of uid.models.Submission

template_name = 'submissions/submission_batch_delete.html'

class submissions.views.DeleteSamplesView(**kwargs)

Bases: submissions.views.BatchDeleteMixin, django.views.generic.detail.DetailView

delete_type = 'Samples'

model

alias of uid.models.Submission

template_name = 'submissions/submission_batch_delete.html'

class submissions.views.DeleteSubmissionMixin

Bases: object

Prevent a delete relying on statuses

dispatch(request, *args, **kwargs)

class submissions.views.DeleteSubmissionView(**kwargs)

Bases: submissions.views.DeleteSubmissionMixin, common.views.OwnerMixin, django.views.generic.edit.DeleteView

delete(request, *args, **kwargs)

Add a message after calling base delete method

get_context_data(**kwargs)

Insert the single object into the context dict.

model

alias of uid.models.Submission

success_url = '/uid/dashboard/'

template_name = 'submissions/submission_confirm_delete.html'

class submissions.views.DetailSubmissionView(**kwargs)

Bases: submissions.views.MessagesSubmissionMixin, common.views.OwnerMixin, django.views.generic.detail.DetailView

get_context_data(**kwargs)

Insert the single object into the context dict.

model

alias of uid.models.Submission

template_name = 'submissions/submission_detail.html'

class submissions.views.EditSubmissionMixin

Bases: object

A mixin to deal with Updates, expecially when searching ListViews

dispatch(request, *args, **kwargs)

class submissions.views.EditSubmissionView(**kwargs)

Bases: submissions.views.EditSubmissionMixin, submissions.views.MessagesSubmissionMixin, common.views.OwnerMixin, django.views.generic.list.ListView

get_context_data(**kwargs)

Get the context for this view.

get_queryset()

Subsetting names relying submission id

headers = ['id', 'name', 'material', 'biosample_id', 'status', 'last_changed', 'last_submitted']

paginate_by = 10

template_name = 'submissions/submission_edit.html'

class submissions.views.ExportSubmissionView(**kwargs)

Bases: common.views.OwnerMixin, django.views.generic.detail.BaseDetailView

get(request, *args, **kwargs)

A view that streams a large CSV file.

model

alias of uid.models.Submission

class submissions.views.FixValidation(**kwargs)

Bases: common.views.OwnerMixin, django.views.generic.edit.BaseUpdateView

model

alias of uid.models.Submission

post(request, **kwargs)

Handle POST requests: instantiate a form instance with the passed POST variables and then check if it’s valid.

class submissions.views.ListSubmissionsView(**kwargs)

Bases: common.views.OwnerMixin, django.views.generic.list.ListView

model

alias of uid.models.Submission

ordering = ['-created_at']

paginate_by = 10

template_name = 'submissions/submission_list.html'

class submissions.views.MessagesSubmissionMixin

Bases: object

Display messages in SubmissionViews

get_context_data(**kwargs)

class submissions.views.ReloadSubmissionView(**kwargs)

Bases: common.views.OwnerMixin, common.views.FormInvalidMixin, django.views.generic.edit.UpdateView

form_class

alias of submissions.forms.ReloadForm

form_valid(form)

If the form is valid, save the associated model.

model

alias of uid.models.Submission

template_name = 'submissions/submission_reload.html'

class submissions.views.SubmissionValidationSummaryFixErrorsView(**kwargs)

Bases: submissions.views.EditSubmissionMixin, common.views.OwnerMixin, django.views.generic.list.ListView

get_context_data(**kwargs)

Get the context for this view.

get_queryset()

Define columns that need to change

template_name = 'submissions/submission_validation_summary_fix_errors.html'

class submissions.views.SubmissionValidationSummaryView(**kwargs)

Bases: common.views.OwnerMixin, django.views.generic.detail.DetailView

get_context_data(**kwargs)

Insert the single object into the context dict.

model

alias of uid.models.Submission

template_name = 'submissions/submission_validation_summary.html'

class submissions.views.UpdateSubmissionView(**kwargs)

Bases: common.views.OwnerMixin, common.views.FormInvalidMixin, django.views.generic.edit.UpdateView

form_class

alias of submissions.forms.UpdateSubmissionForm

model

alias of uid.models.Submission

template_name = 'submissions/submission_update.html'