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(TaxonomizableSerializerMixin, 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)
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)
doi = ser.CharField(source='article_doi', required=False, allow_null=True)
title = ser.CharField(source='node.title', required=False)
description = ser.CharField(required=False,
allow_blank=True,
allow_null=True,
source='node.description')
date_withdrawn = VersionedDateTimeField(read_only=True, allow_null=True)
withdrawal_justification = HideIfNotWithdrawal(
ser.CharField(required=False, read_only=True, allow_blank=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,
source='node.tags')
node_is_public = NoneIfWithdrawal(
ser.BooleanField(read_only=True, source='node__is_public'))
preprint_doi_created = NoneIfWithdrawal(
VersionedDateTimeField(read_only=True))
contributors = RelationshipField(
related_view='nodes:node-contributors',
related_view_kwargs={'node_id': '<node._id>'},
)
reviews_state = NoneIfWithdrawal(
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))
license = PreprintLicenseRelationshipField(
related_view='licenses:license-detail',
related_view_kwargs={'license_id': '<license.node_license._id>'},
read_only=False)
provider = NoneIfWithdrawal(
PreprintProviderRelationshipField(
related_view=
'providers:preprint-providers:preprint-provider-detail',
related_view_kwargs={'provider_id': '<provider._id>'},
read_only=False))
files = NoneIfWithdrawal(
RelationshipField(related_view='nodes:node-providers',
related_view_kwargs={'node_id': '<_id>'}))
primary_file = NoneIfWithdrawal(
PrimaryFileRelationshipField(
related_view='files:file-detail',
related_view_kwargs={'file_id': '<primary_file._id>'},
read_only=False))
review_actions = NoneIfWithdrawal(
RelationshipField(related_view='preprints:preprint-review-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_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_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,
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(
'preprints:preprint-review-action-list',
kwargs={
'version':
self.context['request'].parser_context['kwargs']
['version'],
'preprint_id':
preprint._id
})))
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)