class BaseRegistrationSerializer(NodeSerializer):
title = ser.CharField(read_only=True)
description = ser.CharField(read_only=True)
category_choices = NodeSerializer.category_choices
category_choices_string = NodeSerializer.category_choices_string
category = HideIfWithdrawal(
ser.ChoiceField(read_only=True,
choices=category_choices,
help_text='Choices: ' + category_choices_string))
date_modified = VersionedDateTimeField(source='last_logged',
read_only=True)
fork = HideIfWithdrawal(ser.BooleanField(read_only=True, source='is_fork'))
collection = HideIfWithdrawal(
ser.BooleanField(read_only=True, source='is_collection'))
access_requests_enabled = HideIfWithdrawal(
ser.BooleanField(read_only=True))
node_license = HideIfWithdrawal(NodeLicenseSerializer(read_only=True))
tags = HideIfWithdrawal(
JSONAPIListField(child=NodeTagField(), required=False))
public = HideIfWithdrawal(
ser.BooleanField(
source='is_public',
required=False,
help_text='Nodes that are made public will give read-only access '
'to everyone. Private nodes require explicit read '
'permission. Write and admin access are the same for '
'public and private nodes. Administrators on a parent '
'node have implicit read permissions for all child nodes'))
current_user_permissions = HideIfWithdrawal(
ser.SerializerMethodField(
help_text='List of strings representing the permissions '
'for the current user on this node.'))
pending_embargo_approval = HideIfWithdrawal(
ser.BooleanField(
read_only=True,
source='is_pending_embargo',
help_text=
'The associated Embargo is awaiting approval by project admins.'))
pending_registration_approval = HideIfWithdrawal(
ser.BooleanField(
source='is_pending_registration',
read_only=True,
help_text=
'The associated RegistrationApproval is awaiting approval by project admins.'
))
pending_withdrawal = HideIfWithdrawal(
ser.BooleanField(
source='is_pending_retraction',
read_only=True,
help_text=
'The registration is awaiting withdrawal approval by project admins.'
))
withdrawn = ser.BooleanField(
source='is_retracted',
read_only=True,
help_text='The registration has been withdrawn.')
date_registered = VersionedDateTimeField(
source='registered_date',
read_only=True,
help_text='Date time of registration.')
date_withdrawn = VersionedDateTimeField(
source='retraction.date_retracted',
read_only=True,
help_text='Date time of when this registration was retracted.')
embargo_end_date = HideIfWithdrawal(
ser.SerializerMethodField(
help_text='When the embargo on this registration will be lifted.'))
withdrawal_justification = ser.CharField(source='retraction.justification',
read_only=True)
template_from = HideIfWithdrawal(
ser.CharField(
read_only=True,
allow_blank=False,
allow_null=False,
help_text=
'Specify a node id for a node you would like to use as a template for the '
'new node. Templating is like forking, except that you do not copy the '
'files, only the project structure. Some information is changed on the top '
'level project by submitting the appropriate fields in the request body, '
'and some information will not change. By default, the description will '
'be cleared and the project will be made private.'))
registration_supplement = ser.SerializerMethodField()
registered_meta = HideIfWithdrawal(
ser.SerializerMethodField(
help_text=
'A dictionary with supplemental registration questions and responses.'
))
registered_by = HideIfWithdrawal(
RelationshipField(
related_view='users:user-detail',
related_view_kwargs={'user_id': '<registered_user._id>'}))
registered_from = HideIfWithdrawal(
RelationshipField(
related_view='nodes:node-detail',
related_view_kwargs={'node_id': '<registered_from._id>'}))
children = HideIfWithdrawal(
RelationshipField(
related_view='registrations:registration-children',
related_view_kwargs={'node_id': '<_id>'},
related_meta={'count': 'get_node_count'},
))
comments = HideIfWithdrawal(
RelationshipField(related_view='registrations:registration-comments',
related_view_kwargs={'node_id': '<_id>'},
related_meta={'unread': 'get_unread_comments_count'},
filter={'target': '<_id>'}))
contributors = RelationshipField(
related_view='registrations:registration-contributors',
related_view_kwargs={'node_id': '<_id>'},
related_meta={'count': 'get_contrib_count'})
implicit_contributors = RelationshipField(
related_view='registrations:registration-implicit-contributors',
related_view_kwargs={'node_id': '<_id>'},
help_text=
'This feature is experimental and being tested. It may be deprecated.')
files = HideIfWithdrawal(
RelationshipField(related_view='registrations:registration-providers',
related_view_kwargs={'node_id': '<_id>'}))
wikis = HideIfWithdrawal(
RelationshipField(
related_view='registrations:registration-wikis',
related_view_kwargs={'node_id': '<_id>'},
))
forked_from = HideIfWithdrawal(
RelationshipField(
related_view=lambda n: 'registrations:registration-detail'
if getattr(n, 'is_registration', False) else 'nodes:node-detail',
related_view_kwargs={'node_id': '<forked_from_id>'}))
template_node = HideIfWithdrawal(
RelationshipField(
related_view='nodes:node-detail',
related_view_kwargs={'node_id': '<template_node._id>'}))
license = HideIfWithdrawal(
RelationshipField(
related_view='licenses:license-detail',
related_view_kwargs={
'license_id': '<node_license.node_license._id>'
},
))
logs = HideIfWithdrawal(
RelationshipField(
related_view='registrations:registration-logs',
related_view_kwargs={'node_id': '<_id>'},
))
forks = HideIfWithdrawal(
RelationshipField(related_view='registrations:registration-forks',
related_view_kwargs={'node_id': '<_id>'}))
node_links = ShowIfVersion(HideIfWithdrawal(
RelationshipField(
related_view='registrations:registration-pointers',
related_view_kwargs={'node_id': '<_id>'},
related_meta={'count': 'get_pointers_count'},
help_text=
'This feature is deprecated as of version 2.1. Use linked_nodes instead.'
)),
min_version='2.0',
max_version='2.0')
parent = HideIfWithdrawal(
RelationshipField(related_view='registrations:registration-detail',
related_view_kwargs={'node_id': '<parent_node._id>'},
filter_key='parent_node'))
root = HideIfWithdrawal(
RelationshipField(related_view='registrations:registration-detail',
related_view_kwargs={'node_id': '<root._id>'}))
affiliated_institutions = HideIfWithdrawal(
RelationshipField(
related_view='registrations:registration-institutions',
related_view_kwargs={'node_id': '<_id>'}))
registration_schema = RelationshipField(
related_view='metaschemas:metaschema-detail',
related_view_kwargs={'metaschema_id': '<registered_schema_id>'})
registrations = HideIfRegistration(
RelationshipField(related_view='nodes:node-registrations',
related_view_kwargs={'node_id': '<_id>'}))
draft_registrations = HideIfRegistration(
RelationshipField(related_view='nodes:node-draft-registrations',
related_view_kwargs={'node_id': '<_id>'}))
preprints = HideIfWithdrawal(
HideIfRegistration(
RelationshipField(related_view='nodes:node-preprints',
related_view_kwargs={'node_id': '<_id>'})))
identifiers = HideIfWithdrawal(
RelationshipField(related_view='registrations:identifier-list',
related_view_kwargs={'node_id': '<_id>'}))
linked_nodes = HideIfWithdrawal(
RelationshipField(related_view='registrations:linked-nodes',
related_view_kwargs={'node_id': '<_id>'},
related_meta={'count': 'get_node_links_count'},
self_view='registrations:node-pointer-relationship',
self_view_kwargs={'node_id': '<_id>'}))
linked_registrations = HideIfWithdrawal(
RelationshipField(
related_view='registrations:linked-registrations',
related_view_kwargs={'node_id': '<_id>'},
related_meta={'count': 'get_registration_links_count'},
self_view='registrations:node-registration-pointer-relationship',
self_view_kwargs={'node_id': '<_id>'}))
view_only_links = HideIfWithdrawal(
RelationshipField(
related_view='registrations:registration-view-only-links',
related_view_kwargs={'node_id': '<_id>'},
related_meta={'count': 'get_view_only_links_count'},
))
citation = HideIfWithdrawal(
RelationshipField(related_view='registrations:registration-citation',
related_view_kwargs={'node_id': '<_id>'}))
links = LinksField({
'self': 'get_registration_url',
'html': 'get_absolute_html_url'
})
def get_registration_url(self, obj):
return absolute_reverse(
'registrations:registration-detail',
kwargs={
'node_id':
obj._id,
'version':
self.context['request'].parser_context['kwargs']['version']
})
def get_absolute_url(self, obj):
return self.get_registration_url(obj)
def create(self, validated_data):
auth = get_user_auth(self.context['request'])
draft = validated_data.pop('draft')
registration_choice = validated_data.pop('registration_choice',
'immediate')
embargo_lifted = validated_data.pop('lift_embargo', None)
reviewer = is_prereg_admin_not_project_admin(self.context['request'],
draft)
try:
draft.validate_metadata(metadata=draft.registration_metadata,
reviewer=reviewer,
required_fields=True)
except ValidationValueError as e:
raise exceptions.ValidationError(e.message)
registration = draft.register(auth, save=True)
if registration_choice == 'embargo':
if not embargo_lifted:
raise exceptions.ValidationError(
'lift_embargo must be specified.')
embargo_end_date = embargo_lifted.replace(tzinfo=pytz.utc)
try:
registration.embargo_registration(auth.user, embargo_end_date)
except ValidationError as err:
raise exceptions.ValidationError(err.message)
else:
try:
registration.require_approval(auth.user)
except NodeStateError as err:
raise exceptions.ValidationError(err)
registration.save()
return registration
def get_registered_meta(self, obj):
if obj.registered_meta:
meta_values = obj.registered_meta.values()[0]
try:
return json.loads(meta_values)
except TypeError:
return meta_values
except ValueError:
return meta_values
return None
def get_embargo_end_date(self, obj):
if obj.embargo_end_date:
return obj.embargo_end_date
return None
def get_registration_supplement(self, obj):
if obj.registered_schema:
schema = obj.registered_schema.first()
if schema is None:
return None
return schema.name
return None
def get_current_user_permissions(self, obj):
return NodeSerializer.get_current_user_permissions(self, obj)
def update(self, registration, validated_data):
auth = Auth(self.context['request'].user)
# Update tags
if 'tags' in validated_data:
new_tags = validated_data.pop('tags', [])
try:
registration.update_tags(new_tags, auth=auth)
except NodeStateError as err:
raise Conflict(err.message)
is_public = validated_data.get('is_public', None)
if is_public is not None:
if is_public:
try:
registration.update(validated_data, auth=auth)
except NodeUpdateError as err:
raise exceptions.ValidationError(err.reason)
except NodeStateError as err:
raise exceptions.ValidationError(err.message)
else:
raise exceptions.ValidationError(
'Registrations can only be turned from private to public.')
return registration
class Meta:
type_ = 'registrations'
class PreprintSerializer(JSONAPISerializer):
filterable_fields = frozenset([
'id',
'date_created',
'date_modified',
'date_published',
'original_publication_date',
'provider',
'is_published',
'subjects',
'reviews_state',
'node_is_public',
])
id = IDField(source='_id', read_only=True)
subjects = ser.SerializerMethodField()
date_created = DateByVersion(read_only=True)
date_modified = DateByVersion(read_only=True)
date_published = DateByVersion(read_only=True)
original_publication_date = DateByVersion(required=False)
doi = ser.CharField(source='article_doi', required=False, allow_null=True)
is_published = ser.BooleanField(required=False)
is_preprint_orphan = ser.BooleanField(read_only=True)
license_record = NodeLicenseSerializer(required=False, source='license')
title = ser.CharField(source='node.title', required=False)
description = ser.CharField(required=False,
allow_blank=True,
allow_null=True,
source='node.description')
tags = JSONAPIListField(child=NodeTagField(),
required=False,
source='node.tags')
node_is_public = ser.BooleanField(read_only=True, source='node__is_public')
contributors = RelationshipField(
related_view='nodes:node-contributors',
related_view_kwargs={'node_id': '<node._id>'},
)
reviews_state = ser.CharField(read_only=True, max_length=15)
date_last_transitioned = DateByVersion(read_only=True)
citation = RelationshipField(related_view='preprints:preprint-citation',
related_view_kwargs={'preprint_id': '<_id>'})
identifiers = RelationshipField(
related_view='preprints:identifier-list',
related_view_kwargs={'preprint_id': '<_id>'})
node = NodeRelationshipField(related_view='nodes:node-detail',
related_view_kwargs={'node_id': '<node._id>'},
read_only=False)
license = PreprintLicenseRelationshipField(
related_view='licenses:license-detail',
related_view_kwargs={'license_id': '<license.node_license._id>'},
read_only=False)
provider = PreprintProviderRelationshipField(
related_view='preprint_providers:preprint_provider-detail',
related_view_kwargs={'provider_id': '<provider._id>'},
read_only=False)
files = RelationshipField(related_view='nodes:node-providers',
related_view_kwargs={'node_id': '<_id>'})
primary_file = PrimaryFileRelationshipField(
related_view='files:file-detail',
related_view_kwargs={'file_id': '<primary_file._id>'},
lookup_url_kwarg='file_id',
read_only=False)
actions = RelationshipField(related_view='preprints:preprint-action-list',
related_view_kwargs={'preprint_id': '<_id>'})
links = LinksField({
'self': 'get_preprint_url',
'html': 'get_absolute_html_url',
'doi': 'get_article_doi_url',
'preprint_doi': 'get_preprint_doi_url'
})
class Meta:
type_ = 'preprints'
def get_subjects(self, obj):
return [[TaxonomyField().to_representation(subj) for subj in hier]
for hier in obj.subject_hierarchy]
def get_preprint_url(self, obj):
return absolute_reverse(
'preprints:preprint-detail',
kwargs={
'preprint_id':
obj._id,
'version':
self.context['request'].parser_context['kwargs']['version']
})
def get_absolute_url(self, obj):
return self.get_preprint_url(obj)
def get_article_doi_url(self, obj):
return 'https://dx.doi.org/{}'.format(
obj.article_doi) if obj.article_doi else None
def get_preprint_doi_url(self, obj):
doi_identifier = obj.get_identifier('doi')
return 'https://dx.doi.org/{}'.format(
doi_identifier.value) if doi_identifier else None
def run_validation(self, *args, **kwargs):
# Overrides construtor for validated_data to allow writes to a SerializerMethodField
# Validation for `subjects` happens in the model
_validated_data = super(PreprintSerializer,
self).run_validation(*args, **kwargs)
if 'subjects' in self.initial_data:
_validated_data['subjects'] = self.initial_data['subjects']
return _validated_data
def update(self, preprint, validated_data):
assert isinstance(
preprint,
PreprintService), 'You must specify a valid preprint to be updated'
assert isinstance(
preprint.node, Node
), 'You must specify a preprint with a valid node to be updated.'
auth = get_user_auth(self.context['request'])
if not preprint.node.has_permission(auth.user, 'admin'):
raise exceptions.PermissionDenied(
detail='User must be an admin to update a preprint.')
published = validated_data.pop('is_published', None)
if published and preprint.provider.is_reviewed:
raise Conflict(
'{} uses a moderation workflow, so preprints must be submitted for review instead of published directly. Submit a preprint by creating a `submit` Action at {}'
.format(
preprint.provider.name,
absolute_reverse(
'actions:create-action',
kwargs={
'version':
self.context['request'].parser_context['kwargs']
['version']
})))
save_node = False
save_preprint = False
recently_published = False
primary_file = validated_data.pop('primary_file', None)
if primary_file:
self.set_field(preprint.set_primary_file, primary_file, auth)
save_node = True
old_tags = set(preprint.node.tags.values_list('name', flat=True))
if validated_data.get('node') and 'tags' in validated_data['node']:
current_tags = set(validated_data['node'].pop('tags', []))
elif self.partial:
current_tags = set(old_tags)
else:
current_tags = set()
for new_tag in (current_tags - old_tags):
preprint.node.add_tag(new_tag, auth=auth)
for deleted_tag in (old_tags - current_tags):
preprint.node.remove_tag(deleted_tag, auth=auth)
if 'node' in validated_data:
preprint.node.update(fields=validated_data.pop('node'))
save_node = True
if 'subjects' in validated_data:
subjects = validated_data.pop('subjects', None)
self.set_field(preprint.set_subjects, subjects, auth)
save_preprint = True
if 'article_doi' in validated_data:
preprint.node.preprint_article_doi = validated_data['article_doi']
save_node = True
if 'license_type' in validated_data or 'license' in validated_data:
license_details = get_license_details(preprint, validated_data)
self.set_field(preprint.set_preprint_license, license_details,
auth)
save_preprint = True
if 'original_publication_date' in validated_data:
preprint.original_publication_date = validated_data[
'original_publication_date']
save_preprint = True
if published is not None:
if not preprint.primary_file:
raise exceptions.ValidationError(
detail=
'A valid primary_file must be set before publishing a preprint.'
)
self.set_field(preprint.set_published, published, auth)
save_preprint = True
recently_published = published
preprint.node.set_privacy('public')
save_node = True
if save_node:
try:
preprint.node.save()
except ValidationError as e:
# Raised from invalid DOI
raise exceptions.ValidationError(detail=e.messages[0])
if save_preprint:
preprint.save()
# Send preprint confirmation email signal to new authors on preprint! -- only when published
# TODO: Some more thought might be required on this; preprints made from existing
# nodes will send emails making it seem like a new node.
if recently_published:
for author in preprint.node.contributors:
if author != auth.user:
project_signals.contributor_added.send(
preprint.node,
contributor=author,
auth=auth,
email_template='preprint')
return preprint
def set_field(self, func, val, auth, save=False):
try:
func(val, auth)
except PermissionsError as e:
raise exceptions.PermissionDenied(detail=e.message)
except (ValueError, ValidationError, NodeStateError) as e:
raise exceptions.ValidationError(detail=e.message)
class RegistrationSerializer(NodeSerializer):
category_choices = NodeSerializer.category_choices
category_choices_string = NodeSerializer.category_choices_string
category = HideIfWithdrawal(
ser.ChoiceField(choices=category_choices,
help_text="Choices: " + category_choices_string))
date_modified = HideIfWithdrawal(ser.DateTimeField(read_only=True))
fork = HideIfWithdrawal(ser.BooleanField(read_only=True, source='is_fork'))
collection = HideIfWithdrawal(
ser.BooleanField(read_only=True, source='is_collection'))
node_license = HideIfWithdrawal(NodeLicenseSerializer())
tags = HideIfWithdrawal(
JSONAPIListField(child=NodeTagField(), required=False))
public = HideIfWithdrawal(
ser.BooleanField(
source='is_public',
required=False,
help_text='Nodes that are made public will give read-only access '
'to everyone. Private nodes require explicit read '
'permission. Write and admin access are the same for '
'public and private nodes. Administrators on a parent '
'node have implicit read permissions for all child nodes'))
current_user_permissions = HideIfWithdrawal(
ser.SerializerMethodField(
help_text='List of strings representing the permissions '
'for the current user on this node.'))
pending_embargo_approval = HideIfWithdrawal(
ser.BooleanField(
read_only=True,
source='is_pending_embargo',
help_text=
'The associated Embargo is awaiting approval by project admins.'))
pending_registration_approval = HideIfWithdrawal(
ser.BooleanField(
source='is_pending_registration',
read_only=True,
help_text=
'The associated RegistrationApproval is awaiting approval by project admins.'
))
pending_withdrawal = HideIfWithdrawal(
ser.BooleanField(
source='is_pending_retraction',
read_only=True,
help_text=
'The registration is awaiting withdrawal approval by project admins.'
))
withdrawn = ser.BooleanField(
source='is_retracted',
read_only=True,
help_text='The registration has been withdrawn.')
date_registered = ser.DateTimeField(source='registered_date',
read_only=True,
help_text='Date time of registration.')
embargo_end_date = HideIfWithdrawal(
ser.SerializerMethodField(
help_text='When the embargo on this registration will be lifted.'))
withdrawal_justification = ser.CharField(source='retraction.justification',
read_only=True)
template_from = HideIfWithdrawal(
ser.CharField(
required=False,
allow_blank=False,
allow_null=False,
help_text=
'Specify a node id for a node you would like to use as a template for the '
'new node. Templating is like forking, except that you do not copy the '
'files, only the project structure. Some information is changed on the top '
'level project by submitting the appropriate fields in the request body, '
'and some information will not change. By default, the description will '
'be cleared and the project will be made private.'))
registration_supplement = ser.SerializerMethodField()
registered_meta = HideIfWithdrawal(
ser.SerializerMethodField(
help_text=
'A dictionary with supplemental registration questions and responses.'
))
registered_by = HideIfWithdrawal(
RelationshipField(
related_view='users:user-detail',
related_view_kwargs={'user_id': '<registered_user_id>'}))
registered_from = HideIfWithdrawal(
RelationshipField(
related_view='nodes:node-detail',
related_view_kwargs={'node_id': '<registered_from_id>'}))
children = HideIfWithdrawal(
RelationshipField(
related_view='registrations:registration-children',
related_view_kwargs={'node_id': '<pk>'},
related_meta={'count': 'get_node_count'},
))
comments = HideIfWithdrawal(
RelationshipField(related_view='registrations:registration-comments',
related_view_kwargs={'node_id': '<pk>'},
related_meta={'unread':
'get_unread_comments_count'}))
contributors = RelationshipField(
related_view='registrations:registration-contributors',
related_view_kwargs={'node_id': '<pk>'},
related_meta={'count': 'get_contrib_count'})
files = HideIfWithdrawal(
RelationshipField(related_view='registrations:registration-providers',
related_view_kwargs={'node_id': '<pk>'}))
wikis = HideIfWithdrawal(
RelationshipField(
related_view='registrations:registration-wikis',
related_view_kwargs={'node_id': '<pk>'},
))
forked_from = HideIfWithdrawal(
RelationshipField(
related_view=lambda n: 'registrations:registration-detail'
if getattr(n, 'is_registration', False) else 'nodes:node-detail',
related_view_kwargs={'node_id': '<forked_from_id>'}))
license = HideIfWithdrawal(
RelationshipField(
related_view='licenses:license-detail',
related_view_kwargs={
'license_id': '<node_license.node_license._id>'
},
))
forks = HideIfWithdrawal(
RelationshipField(related_view='registrations:registration-forks',
related_view_kwargs={'node_id': '<pk>'}))
node_links = HideIfWithdrawal(
RelationshipField(related_view='registrations:registration-pointers',
related_view_kwargs={'node_id': '<pk>'},
related_meta={'count': 'get_pointers_count'}))
parent = HideIfWithdrawal(
RelationshipField(related_view='registrations:registration-detail',
related_view_kwargs={'node_id': '<parent_node._id>'},
filter_key='parent_node'))
logs = HideIfWithdrawal(
RelationshipField(
related_view='registrations:registration-logs',
related_view_kwargs={'node_id': '<pk>'},
))
root = HideIfWithdrawal(
RelationshipField(related_view='registrations:registration-detail',
related_view_kwargs={'node_id': '<root._id>'}))
affiliated_institutions = HideIfWithdrawal(
RelationshipField(
related_view='registrations:registration-institutions',
related_view_kwargs={'node_id': '<pk>'}))
registrations = HideIfRegistration(
RelationshipField(related_view='nodes:node-registrations',
related_view_kwargs={'node_id': '<pk>'}))
identifiers = HideIfWithdrawal(
RelationshipField(related_view='registrations:identifier-list',
related_view_kwargs={'node_id': '<pk>'}))
# TODO: Finish me
# TODO: Override create?
links = LinksField({
'self': 'get_registration_url',
'html': 'get_absolute_html_url'
})
def get_registration_url(self, obj):
return absolute_reverse('registrations:registration-detail',
kwargs={'node_id': obj._id})
def get_absolute_url(self, obj):
return self.get_registration_url(obj)
def get_registered_meta(self, obj):
if obj.registered_meta:
meta_values = obj.registered_meta.values()[0]
try:
return json.loads(meta_values)
except TypeError:
return meta_values
except ValueError:
return meta_values
return None
def get_embargo_end_date(self, obj):
if obj.embargo_end_date:
return obj.embargo_end_date
return None
def get_registration_supplement(self, obj):
if obj.registered_schema:
schema = obj.registered_schema[0]
if schema is None:
return None
return schema.name
return None
def get_current_user_permissions(self, obj):
return NodeSerializer.get_current_user_permissions(self, obj)
def update(self, *args, **kwargs):
raise exceptions.APIException('Registrations cannot be modified.')
class Meta:
type_ = 'registrations'
class PreprintSerializer(TaxonomizableSerializerMixin, MetricsSerializerMixin,
JSONAPISerializer):
filterable_fields = frozenset([
'id',
'date_created',
'date_modified',
'date_published',
'original_publication_date',
'provider',
'is_published',
'subjects',
'reviews_state',
'node_is_public',
])
available_metrics = frozenset([
'downloads',
'views',
])
id = IDField(source='_id', read_only=True)
type = TypeField()
date_created = VersionedDateTimeField(source='created', read_only=True)
date_modified = VersionedDateTimeField(source='modified', read_only=True)
date_published = VersionedDateTimeField(read_only=True)
original_publication_date = VersionedDateTimeField(required=False,
allow_null=True)
doi = ser.CharField(source='article_doi', required=False, allow_null=True)
title = ser.CharField(required=True, max_length=512)
description = ser.CharField(required=False,
allow_blank=True,
allow_null=True)
is_published = NoneIfWithdrawal(ser.BooleanField(required=False))
is_preprint_orphan = NoneIfWithdrawal(ser.BooleanField(read_only=True))
license_record = NodeLicenseSerializer(required=False, source='license')
tags = JSONAPIListField(child=NodeTagField(), required=False)
node_is_public = ser.BooleanField(
read_only=True,
source='node__is_public',
help_text='Is supplementary project public?')
preprint_doi_created = NoneIfWithdrawal(
VersionedDateTimeField(read_only=True))
date_withdrawn = VersionedDateTimeField(read_only=True, allow_null=True)
withdrawal_justification = HideIfNotWithdrawal(
ser.CharField(required=False, read_only=True, allow_blank=True))
current_user_permissions = ser.SerializerMethodField(
help_text='List of strings representing the permissions '
'for the current user on this preprint.', )
public = ser.BooleanField(source='is_public',
required=False,
read_only=True)
contributors = RelationshipField(
related_view='preprints:preprint-contributors',
related_view_kwargs={'preprint_id': '<_id>'},
)
reviews_state = ser.CharField(source='machine_state',
read_only=True,
max_length=15)
date_last_transitioned = NoneIfWithdrawal(
VersionedDateTimeField(read_only=True))
citation = NoneIfWithdrawal(
RelationshipField(
related_view='preprints:preprint-citation',
related_view_kwargs={'preprint_id': '<_id>'},
))
identifiers = NoneIfWithdrawal(
RelationshipField(
related_view='preprints:identifier-list',
related_view_kwargs={'preprint_id': '<_id>'},
))
node = NoneIfWithdrawal(
NodeRelationshipField(
related_view='nodes:node-detail',
related_view_kwargs={'node_id': '<node._id>'},
read_only=False,
many=False,
self_view='preprints:preprint-node-relationship',
self_view_kwargs={'preprint_id': '<_id>'},
))
license = PreprintLicenseRelationshipField(
related_view='licenses:license-detail',
related_view_kwargs={'license_id': '<license.node_license._id>'},
read_only=False,
)
provider = PreprintProviderRelationshipField(
related_view='providers:preprint-providers:preprint-provider-detail',
related_view_kwargs={'provider_id': '<provider._id>'},
read_only=False,
)
files = NoneIfWithdrawal(
RelationshipField(
related_view='preprints:preprint-storage-providers',
related_view_kwargs={'preprint_id': '<_id>'},
))
primary_file = NoneIfWithdrawal(
PrimaryFileRelationshipField(
related_view='files:file-detail',
related_view_kwargs={'file_id': '<primary_file._id>'},
read_only=False,
))
review_actions = RelationshipField(
related_view='preprints:preprint-review-action-list',
related_view_kwargs={'preprint_id': '<_id>'},
)
requests = NoneIfWithdrawal(
RelationshipField(
related_view='preprints:preprint-request-list',
related_view_kwargs={'preprint_id': '<_id>'},
))
links = LinksField(
{
'self': 'get_preprint_url',
'html': 'get_absolute_html_url',
'doi': 'get_article_doi_url',
'preprint_doi': 'get_preprint_doi_url',
}, )
class Meta:
type_ = 'preprints'
def get_preprint_url(self, obj):
return absolute_reverse(
'preprints:preprint-detail',
kwargs={
'preprint_id':
obj._id,
'version':
self.context['request'].parser_context['kwargs']['version']
})
def get_absolute_url(self, obj):
return self.get_preprint_url(obj)
def get_article_doi_url(self, obj):
return 'https://doi.org/{}'.format(
obj.article_doi) if obj.article_doi else None
def get_current_user_permissions(self, obj):
user = self.context['request'].user
all_perms = ['read', 'write', 'admin']
user_perms = []
for p in all_perms:
if obj.has_permission(user, p):
user_perms.append(p)
return user_perms
def get_preprint_doi_url(self, obj):
doi = None
doi_identifier = obj.get_identifier('doi')
if doi_identifier:
doi = doi_identifier.value
# if a preprint hasn't been published yet, don't show the DOI prematurely
elif obj.is_published:
client = obj.get_doi_client()
doi = client.build_doi(preprint=obj) if client else None
return 'https://doi.org/{}'.format(doi) if doi else None
def update(self, preprint, validated_data):
assert isinstance(
preprint,
Preprint), 'You must specify a valid preprint to be updated'
auth = get_user_auth(self.context['request'])
if not preprint.has_permission(auth.user, osf_permissions.WRITE):
raise exceptions.PermissionDenied(
detail=
'User must have admin or write permissions to update a preprint.'
)
published = validated_data.pop('is_published', None)
if published and preprint.provider.is_reviewed:
raise Conflict(
'{} uses a moderation workflow, so preprints must be submitted for review instead of published directly. Submit a preprint by creating a `submit` Action at {}'
.format(
preprint.provider.name,
absolute_reverse(
'preprints:preprint-review-action-list',
kwargs={
'version':
self.context['request'].parser_context['kwargs']
['version'],
'preprint_id':
preprint._id,
},
),
))
save_preprint = False
recently_published = False
primary_file = validated_data.pop('primary_file', None)
if primary_file:
self.set_field(preprint.set_primary_file, primary_file, auth)
save_preprint = True
old_tags = set(preprint.tags.values_list('name', flat=True))
if 'tags' in validated_data:
current_tags = set(validated_data.pop('tags', []))
elif self.partial:
current_tags = set(old_tags)
else:
current_tags = set()
for new_tag in (current_tags - old_tags):
preprint.add_tag(new_tag, auth=auth)
for deleted_tag in (old_tags - current_tags):
preprint.remove_tag(deleted_tag, auth=auth)
if 'node' in validated_data:
node = validated_data.pop('node', None)
self.set_field(preprint.set_supplemental_node, node, auth)
save_preprint = True
if 'subjects' in validated_data:
subjects = validated_data.pop('subjects', None)
self.set_field(preprint.set_subjects, subjects, auth)
save_preprint = True
if 'title' in validated_data:
title = validated_data['title']
self.set_field(preprint.set_title, title, auth)
save_preprint = True
if 'description' in validated_data:
description = validated_data['description']
self.set_field(preprint.set_description, description, auth)
save_preprint = True
if 'article_doi' in validated_data:
preprint.article_doi = validated_data['article_doi']
save_preprint = True
if 'license_type' in validated_data or 'license' in validated_data:
license_details = get_license_details(preprint, validated_data)
self.set_field(preprint.set_preprint_license, license_details,
auth)
save_preprint = True
if 'original_publication_date' in validated_data:
preprint.original_publication_date = validated_data[
'original_publication_date'] or None
save_preprint = True
if published is not None:
if not preprint.primary_file:
raise exceptions.ValidationError(
detail=
'A valid primary_file must be set before publishing a preprint.'
)
self.set_field(preprint.set_published, published, auth)
save_preprint = True
recently_published = published
preprint.set_privacy('public', log=False, save=True)
if save_preprint:
preprint.save()
if recently_published:
for author in preprint.contributors:
if author != auth.user:
project_signals.contributor_added.send(
preprint,
contributor=author,
auth=auth,
email_template='preprint')
return preprint
def set_field(self, func, val, auth, save=False):
try:
func(val, auth)
except PermissionsError as e:
raise exceptions.PermissionDenied(detail=str(e))
except (ValueError, ValidationError, NodeStateError) as e:
raise exceptions.ValidationError(detail=e.message)
class PreprintSerializer(JSONAPISerializer):
filterable_fields = frozenset([
'id', 'title', 'tags', 'date_created', 'date_modified', 'contributors',
'subjects', 'doi'
])
title = ser.CharField(required=False)
subjects = JSONAPIListField(child=TaxonomyField(),
required=False,
source='preprint_subjects')
provider = ser.CharField(source='preprint_provider', required=False)
date_created = ser.DateTimeField(read_only=True, source='preprint_created')
date_modified = ser.DateTimeField(read_only=True)
id = IDField(source='_id', required=False)
abstract = ser.CharField(source='description', required=False)
tags = JSONAPIListField(child=NodeTagField(), required=False)
doi = ser.CharField(source='preprint_doi', required=False)
primary_file = PrimaryFileRelationshipField(
related_view='files:file-detail',
related_view_kwargs={'file_id': '<preprint_file._id>'},
lookup_url_kwarg='file_id',
read_only=False)
files = RelationshipField(related_view='nodes:node-providers',
related_view_kwargs={'node_id': '<pk>'})
providers = RelationshipField(
related_view='preprints:preprint-preprint_providers',
related_view_kwargs={'node_id': '<pk>'},
self_view='preprints:preprint-relationships-preprint_providers',
self_view_kwargs={'node_id': '<pk>'})
links = LinksField({
'self': 'get_preprint_url',
'html': 'get_absolute_html_url',
'doi': 'get_doi_url'
})
contributors = RelationshipField(
related_view='nodes:node-contributors',
related_view_kwargs={'node_id': '<pk>'},
related_meta={'count': 'get_contrib_count'},
)
class Meta:
type_ = 'preprints'
def get_preprint_url(self, obj):
return absolute_reverse('preprints:preprint-detail',
kwargs={'node_id': obj._id})
def get_absolute_url(self, obj):
return self.get_preprint_url(obj)
def get_doi_url(self, obj):
return 'https://dx.doi.org/{}'.format(
obj.preprint_doi) if obj.preprint_doi else None
def create(self, validated_data):
node = Node.load(validated_data.pop('_id', None))
if not node:
raise exceptions.NotFound('Unable to find Node with specified id.')
auth = get_user_auth(self.context['request'])
if not node.has_permission(auth.user, permissions.ADMIN):
raise exceptions.PermissionDenied
if node.is_preprint:
raise Conflict(
'This node already stored as a preprint, use the update method instead.'
)
primary_file = validated_data.pop('primary_file', None)
if not primary_file:
raise exceptions.ValidationError(
detail='You must specify a primary_file to create a preprint.')
self.set_node_field(node.set_preprint_file, primary_file, auth)
subjects = validated_data.pop('preprint_subjects', None)
if not subjects:
raise exceptions.ValidationError(
detail=
'You must specify at least one subject to create a preprint.')
self.set_node_field(node.set_preprint_subjects, subjects, auth)
tags = validated_data.pop('tags', None)
if tags:
for tag in tags:
node.add_tag(tag, auth, save=False, log=False)
for key, value in validated_data.iteritems():
setattr(node, key, value)
try:
node.save()
except ValidationValueError as e:
raise exceptions.ValidationError(detail=e.message)
# Send preprint confirmation email signal to new authors on preprint!
for author in node.contributors:
if author != auth.user:
project_signals.contributor_added.send(
node,
contributor=author,
auth=auth,
email_template='preprint')
return node
def update(self, node, validated_data):
from website.models import Node
assert isinstance(node,
Node), 'You must specify a valid node to be updated.'
auth = get_user_auth(self.context['request'])
primary_file = validated_data.pop('primary_file', None)
if primary_file:
self.set_node_field(node.set_preprint_file, primary_file, auth)
subjects = validated_data.pop('preprint_subjects', None)
if subjects:
self.set_node_field(node.set_preprint_subjects, subjects, auth)
old_tags = set([tag._id for tag in node.tags])
if 'tags' in validated_data:
current_tags = set(validated_data.pop('tags', []))
elif self.partial:
current_tags = set(old_tags)
else:
current_tags = set()
for new_tag in (current_tags - old_tags):
node.add_tag(new_tag, auth=auth)
for deleted_tag in (old_tags - current_tags):
node.remove_tag(deleted_tag, auth=auth)
for key, value in validated_data.iteritems():
setattr(node, key, value)
try:
node.save()
except ValidationValueError as e:
raise exceptions.ValidationError(detail=e.message)
return node
def set_node_field(self, func, val, auth):
try:
func(val, auth, save=False)
except PermissionsError:
raise exceptions.PermissionDenied(
'Not authorized to update this node.')
except ValueError as e:
raise exceptions.ValidationError(detail=e.message)