class RelatedIdentifierSchemaV1(BaseSchema):
"""Related identifier schema."""
RELATIONS = [
"IsCitedBy", "Cites", "IsSupplementTo", "IsSupplementedBy",
"IsContinuedBy", "Continues", "IsDescribedBy", "Describes",
"HasMetadata", "IsMetadataFor", "HasVersion", "IsVersionOf",
"IsNewVersionOf", "IsPreviousVersionOf", "IsPartOf", "HasPart",
"IsReferencedBy", "References", "IsDocumentedBy", "Documents",
"IsCompiledBy", "Compiles", "IsVariantFormOf", "IsOriginalFormOf",
"IsIdenticalTo", "IsReviewedBy", "Reviews", "IsDerivedFrom",
"IsSourceOf", "IsRequiredBy", "Requires", "IsObsoletedBy", "Obsoletes"
]
SCHEMES = [
"ARK", "arXiv", "bibcode", "DOI", "EAN13", "EISSN", "Handle", "IGSN",
"ISBN", "ISSN", "ISTC", "LISSN", "LSID", "PMID", "PURL", "UPC", "URL",
"URN", "w3id"
]
identifier = SanitizedUnicode(required=True)
scheme = SanitizedUnicode(
required=True,
validate=validate.OneOf(choices=SCHEMES,
error=_('Invalid related identifier scheme. ' +
'{input} not one of {choices}.')))
relation_type = SanitizedUnicode(
required=True,
validate=validate.OneOf(
choices=RELATIONS,
error=_('Invalid relation type. {input} not one of {choices}.')))
resource_type = Nested(ResourceTypeSchemaV1)
class LicenseSchemaV1(BaseSchema):
"""License schema."""
license = SanitizedUnicode(required=True)
uri = SanitizedUnicode()
identifier = SanitizedUnicode()
scheme = SanitizedUnicode()
class MetadataSchemaV1(InvenioRecordMetadataSchemaV1Mixin,
DCObjectSchemaV1Mixin, StrictKeysMixin):
"""Schema for the record metadata."""
ALLOWED_SCHEMAS = ACL_ALLOWED_SCHEMAS
PREFERRED_SCHEMA = ACL_PREFERRED_SCHEMA
owners = fields.List(fields.Int(), dump_only=True)
abstract = MultilingualStringSchemaV1(required=True)
description = MultilingualStringSchemaV1(required=True)
contributors = SanitizedUnicode(required=False)
event = fields.Nested(EventSchemaV1(), required=False)
difficulty = SanitizedUnicode(required=True)
license = SanitizedUnicode(required=True)
formats = fields.Nested(FormatSchemaV1(many=True),
many=True,
required=False)
source = fields.URL()
@pre_load
def set_owners(self, in_data, **kwargs):
if current_user.is_authenticated:
in_data['owners'] = [current_user.get_id()]
return in_data
class Meta:
unknown = INCLUDE
class CommunitiesRequestV1(BaseSchema):
"""Community Request Schema."""
id = SanitizedUnicode(required=True)
comid = SanitizedUnicode(required=True)
title = SanitizedUnicode(required=True)
request_id = SanitizedUnicode()
created_by = fields.Integer()
links = fields.Method('get_links')
def get_links(self, obj):
"""Get links."""
res = {
'self':
api_link_for('community_inclusion_request',
id=obj['comid'],
request_id=obj['request_id']),
'community':
api_link_for('community', id=obj['comid']),
}
for action in ('accept', 'reject', 'comment'):
res[action] = api_link_for('community_inclusion_request_action',
id=obj['comid'],
request_id=obj['request_id'],
action=action)
return res
class OrganisationMetadataSchemaV1(StrictKeysMixin):
"""Schema for the organisation metadata."""
pid = PersistentIdentifier()
code = SanitizedUnicode(required=True)
name = SanitizedUnicode(required=True)
isShared = fields.Boolean()
isDedicated = fields.Boolean()
# When loading, if $schema is not provided, it's retrieved by
# Record.schema property.
schema = GenFunction(load_only=True,
attribute="$schema",
data_key="$schema",
deserialize=schema_from_organisation)
permissions = fields.Dict(dump_only=True)
@pre_dump
def add_permissions(self, item):
"""Add permissions to record.
:param item: Dict representing the record.
:returns: Modified dict.
"""
item['permissions'] = {
'read': OrganisationPermission.read(current_user, item),
'update': OrganisationPermission.update(current_user, item),
'delete': OrganisationPermission.delete(current_user, item)
}
return item
class TaxonomySchemaV1(StrictKeysMixin):
"""Taxonomy schema."""
id = Integer(required=False)
slug = SanitizedUnicode(required=False)
path = SanitizedUnicode(required=False)
title = Nested(TaxonomyTitleSchemaV1(), many=True, required=False)
level = Integer(required=False)
links = Nested(TaxonomyLinksSchemaV1(), required=False)
ref = SanitizedUnicode(required=False, dump_to='$ref', load_from='$ref', attribute="$ref")
descendants_count = Integer(required=False, dump_only=True)
@pre_load
def convert_ref(self, in_data, **kwargs):
ref = None
if '$ref' in in_data:
ref = in_data['$ref']
elif 'links' in in_data:
ref = (in_data['links'] or {}).get('self', None)
if not ref:
raise ValidationError('Either links or $ref must be provided for a Taxonomy record') # noqa
path = url_to_path(ref)
try:
tax, term = Taxonomy.find_taxonomy_and_term(path)
except NoResultFound:
raise ValidationError('Taxonomy $ref link is invalid: {}'.format(ref)) # noqa
if not tax:
raise ValidationError('Taxonomy $ref link is invalid: {}'.format(ref)) # noqa
return {'$ref': ref}
def app_config(app_config):
"""Override conftest.py's app_config
"""
# Added custom configuration
app_config['RDM_RECORDS_METADATA_NAMESPACES'] = {
'dwc': {
'@context': 'https://example.com/dwc/terms'
},
'nubiomed': {
'@context': 'https://example.com/nubiomed/terms'
}
}
app_config['RDM_RECORDS_METADATA_EXTENSIONS'] = {
'dwc': {
'family': {
'elasticsearch': 'keyword',
'marshmallow': SanitizedUnicode(required=True)
},
'behavior': {
'elasticsearch': 'text',
'marshmallow': SanitizedUnicode()
}
},
'nubiomed': {
'right_or_wrong': {
'elasticsearch': 'boolean',
'marshmallow': Bool()
}
}
}
return app_config
class InstitutionsMixin:
relatedID = Nested(RelatedIDSchema)
aliases = List(SanitizedUnicode())
ico = SanitizedUnicode()
url = Url()
provider = Boolean(missing=False)
formerNames = List(SanitizedUnicode())
class OutputSchemaV1(StrictKeysMixin):
"""Output & Product Schema"""
output_doi = SanitizedUnicode()
output_type = SanitizedUnicode()
output_title = SanitizedUnicode()
output_abstract = SanitizedUnicode()
output_link = SanitizedUnicode()
class ToolSchemaV1(StrictKeysMixin):
"""Tool Schema"""
tool_doi = SanitizedUnicode()
tool_type = SanitizedUnicode()
tool_title = SanitizedUnicode()
tool_abstract = SanitizedUnicode()
tool_link = SanitizedUnicode()
class DocsetSchemaV1(StrictKeysMixin):
"""DocumentSet Schema"""
docset_doi = SanitizedUnicode()
docset_title = SanitizedUnicode()
docset_abstract = SanitizedUnicode()
docset_keywords = fields.List(SanitizedUnicode(), many=True)
docset_notes = SanitizedUnicode()
class CommunitiesRequest(Schema):
"""Community Request Schema."""
id = SanitizedUnicode(required=True)
comid = SanitizedUnicode(required=True)
title = SanitizedUnicode(required=True)
request_id = SanitizedUnicode()
created_by = fields.Integer()
class MetadataSchemaV1(StrictKeysMixin):
"""Schema for the record metadata."""
{{ cookiecutter.datamodel_pid_name }} = PersistentIdentifier()
title = SanitizedUnicode(required=True, validate=validate.Length(min=3))
keywords = fields.List(SanitizedUnicode(), many=True)
publication_date = DateString()
contributors = Nested(ContributorSchemaV1, many=True, required=True)
class MetadataSchemaV1(SchemaEnforcingMixin, StrictKeysMixin):
"""Schema for the record metadata."""
control_number = PersistentIdentifier()
title = SanitizedUnicode(required=True, validate=validate.Length(min=3))
keywords = fields.List(SanitizedUnicode(), many=True)
publication_date = DateString()
contributors = Nested(ContributorSchemaV1, many=True, required=True)
class ContributorSchemaV1(StrictKeysMixin):
"""Contributor schema."""
ids = fields.Nested(PersonIdsSchemaV1, many=True)
name = SanitizedUnicode(required=True)
role = SanitizedUnicode()
affiliations = fields.List(SanitizedUnicode())
email = fields.Email()
class AuthorMetadataSchemaV1(StrictKeysMixin):
"""Schema for the author metadata."""
_oai = Nested(OaiSchemaV1)
id = PersistentIdentifier()
name = SanitizedUnicode(required=True)
organization = SanitizedUnicode(required=False)
class Meta:
unknown = INCLUDE
class ReferenceSchemaV1(BaseSchema):
"""Reference schema."""
SCHEMES = ["ISNI", "GRID", "Crossref Funder ID", "Other"]
reference_string = SanitizedUnicode(required=True)
identifier = SanitizedUnicode()
scheme = SanitizedUnicode(validate=validate.OneOf(
choices=SCHEMES,
error=_('Invalid reference scheme. {input} not one of {choices}.')))
def test_taxonomy_field():
extra = {
"title": SanitizedUnicode(required=False),
"language": List(SanitizedUnicode(required=False))
}
schema = TaxonomyField(extra=extra, name="taxonomy")
assert type(schema) == TaxonomyNested
assert "title" in schema.nested.fields.keys()
assert "language" in schema.nested.fields.keys()
class NResultsMetadataSchemaV1(CommonMetadataSchemaV2):
N_certifyingAuthority = TaxonomyField(
mixins=[TitledMixin, NcertifyingAuthorityMixin])
N_dateCertified = DateString()
N_economicalParameters = SanitizedUnicode(validate=Length(max=1024))
N_internalID = SanitizedUnicode()
N_referenceNumber = SanitizedUnicode()
N_resultUsage = TaxonomyField(mixins=[TitledMixin])
N_technicalParameters = SanitizedUnicode(validate=Length(max=3000))
N_type = TaxonomyField(mixins=[TitledMixin], required=True)
class FileSchema(Schema):
"""File schema."""
type = fields.String()
checksum = fields.String()
size = fields.Integer()
key = SanitizedUnicode()
version_id = SanitizedUnicode()
bucket_id = SanitizedUnicode()
mimetype = SanitizedUnicode()
storage_class = SanitizedUnicode()
class TitleSchemaV1(BaseSchema):
"""Schema for the additional title."""
title = SanitizedUnicode(required=True, validate=validate.Length(min=3))
type = SanitizedUnicode(missing='MainTitle')
lang = SanitizedUnicode(validate=validate_iso639_3)
@validates_schema
def validate_data(self, data, **kwargs):
"""Validate type."""
validate_entry('titles.type', data)
class FundingReferenceSchema(StrictKeysMixin):
projectID = SanitizedUnicode()
projectName = SanitizedUnicode()
fundingProgram = SanitizedUnicode()
funder = TaxonomyField(mixins=[FunderMixin, TitledMixin])
@validates_schema
def required_fields(self, data, **kwargs):
if data.get("projectID"):
if not data.get("funder"):
raise ValidationError("Funder is required")
class DCObjectSchemaV2Mixin(Schema):
title = MultilingualStringV2(required=True)
alternative = MultilingualStringV2(required=False)
abstract = MultilingualStringV2(required=False)
creator = SanitizedUnicode(required=True)
contributor = SanitizedUnicode(required=False)
dateSubmitted = DateString(required=False)
available = DateString(required=False)
created = DateString(required=True)
modified = DateString(required=True)
description = MultilingualStringV2(required=False)
identifier = SanitizedUnicode(required=True)
class MetadataSchemaV1(DraftValidationSchemaV1Mixin, DraftEnabledSchema,
StrictKeysMixin):
"""Schema for the record metadata."""
id = PersistentIdentifier()
title = SanitizedUnicode(required=True,
validate=validate.Length(min=1, max=10))
keywords = fields.List(SanitizedUnicode(), many=True)
publication_date = DateString()
schema = SanitizedUnicode(required=True,
attribute='$schema',
**load_dump('$schema'))
class MetadataSchemaV1(StrictKeysMixin):
"""Schema for the record metadata."""
def get_id(self, obj):
"""Get record id."""
pid = self.context.get('pid')
return pid.pid_value if pid else missing
id = fields.Function(serialize=get_id, deserialize=get_id)
title = SanitizedUnicode()
authors = SanitizedUnicode()
description = SanitizedUnicode()
items = SanitizedUnicode()
class MetadataSchemaV1(StrictKeysMixin):
"""Schema for the record metadata."""
id = PersistentIdentifier()
title = SanitizedUnicode()
resource_type = SanitizedUnicode()
docset = fields.Nested(DocsetSchemaV1, many=False)
publications = fields.Nested(PublicationchemaV1, many=True)
datasets = fields.Nested(DatasetSchemaV1, many=True)
tools = Nested(ToolSchemaV1, many=True)
outputs = Nested(OutputSchemaV1, many=True)
virtenvs = Nested(VirtenvSchemaV1, many=True)
contributors = Nested(ContributorSchemaV1, many=True)
class ContributorSchemaV1(StrictKeysMixin):
"""Contributor schema."""
ids = fields.Nested(PersonIdsSchemaV1, many=True)
name = SanitizedUnicode(required=True)
affiliations = fields.List(SanitizedUnicode())
email = fields.Email()
roles = fields.List(SanitizedUnicode())
@post_dump(pass_many=False)
def no_email(self, contributor, **kwargs):
contributor['email'] = ''
return contributor
class MetadataSchemaV1(StrictKeysMixin):
"""Schema for the record metadata."""
id = PersistentIdentifier()
title = SanitizedUnicode(required=True, validate=validate.Length(min=3))
keywords = fields.List(SanitizedUnicode(), many=True)
publication_date = DateString()
contributors = Nested(ContributorSchemaV1, many=True, required=True)
_schema = GenFunction(
attribute="$schema",
data_key="$schema",
deserialize=schema_from_context, # to be added only when loading
)
class DepositMetadataSchemaV1(StrictKeysMixin):
"""Schema for the deposit metadata."""
pid = PersistentIdentifier()
contributors = fields.List(fields.Dict())
diffusion = fields.Dict()
document = fields.Dict()
logs = fields.List(fields.Dict())
metadata = fields.Dict()
status = SanitizedUnicode()
step = SanitizedUnicode()
user = fields.Dict()
projects = fields.List(fields.Dict())
_files = fields.List(fields.Dict())
_bucket = SanitizedUnicode()
# When loading, if $schema is not provided, it's retrieved by
# Record.schema property.
schema = GenFunction(load_only=True,
attribute="$schema",
data_key="$schema",
deserialize=schema_from_deposit)
permissions = fields.Dict(dump_only=True)
@pre_dump
def add_permissions(self, item, **kwargs):
"""Add permissions to record.
:param item: Dict representing the record
:returns: Dict of modified record.
"""
item['permissions'] = {
'read': DepositPermission.read(current_user_record, item),
'update': DepositPermission.update(current_user_record, item),
'delete': DepositPermission.delete(current_user_record, item)
}
return item
@pre_load
def remove_fields(self, data, **kwargs):
"""Removes computed fields.
:param data: Dict of record data.
:returns: Modified data.
"""
data.pop('permissions', None)
return data
class DescriptionSchemaV1(BaseSchema):
"""Schema for the additional descriptions."""
DESCRIPTION_TYPES = [
"Abstract", "Methods", "SeriesInformation", "TableOfContents",
"TechnicalInfo", "Other"
]
description = SanitizedUnicode(required=True,
validate=validate.Length(min=3))
type = SanitizedUnicode(
required=True,
validate=validate.OneOf(
choices=DESCRIPTION_TYPES,
error=_(
'Invalid description type. {input} not one of {choices}.')))
lang = SanitizedUnicode(validate=validate_iso639_3)
