required=False,
choices=[2, 10, 20, 30, 40, 50],
default=10,
help='Results per page {error_msg}')
# transient data model
from flask_restplus import fields
variantset = api.model(
'variant set', {
'id':
fields.Integer(readOnly=True,
description='The unique identifier of a variant set'),
'title':
fields.String(required=True, description='Article title'),
'body':
fields.String(required=True, description='Article content'),
'pub_date':
fields.DateTime,
'category_id':
fields.Integer(attribute='category.id'),
'category':
fields.String(attribute='category.id'),
})
pagination = api.model(
'A page of results', {
'page':
fields.Integer(description='Number of this page of results'),
'pages':
fields.Integer(description='Total number of pages of results'),
'per_page':
from flask_restplus import fields
from biolink.api.restplus import api
abstract_property_value = api.model('AbstractPropertyValue', {
'val': fields.String(readOnly=True, description='value part'),
'pred': fields.String(readOnly=True, description='predicate (attribute) part'),
'xrefs': fields.List(fields.String, description='Xrefs provenance for property-value'),
})
synonym_property_value = api.inherit('SynonymPropertyValue', abstract_property_value, {
})
xref_property_value = api.inherit('SynonymPropertyValue', abstract_property_value, {
})
definition_property_value = api.inherit('DefinitionPropertyValue', abstract_property_value, {
})
basic_property_value = api.inherit('DefinitionPropertyValue', abstract_property_value, {
})
meta = api.model('Meta', {
'definition': fields.Nested(definition_property_value), description='definition plus source'),
'comments': fields.List(fields.String(readOnly=True), description='comments'),
'subsets': fields.List(fields.String(readOnly=True), description='subsets (slims)'),
'xrefs': fields.List(fields.Nested(xref_property_value)), description='xrefs plus source'),
'synonyms': fields.List(fields.Nested(synonym_property_value)), description='synonyms plus scope, type and source'),
'basic_property_values': fields.List(fields.Nested(basic_property_value)), description='synonyms plus scope, type and source'),
})
from flask_restplus import fields
from biolink.api.restplus import api
# todo: split this into modules
# Solr
search_result = api.model(
'SearchResult', {
'numFound': fields.Integer,
'start': fields.Integer,
'facet_counts': fields.Raw
})
## BBOP/OBO Graphs
node = api.model(
'Node', {
'id': fields.String(readOnly=True, description='ID'),
'lbl': fields.String(readOnly=True, description='RDFS Label')
})
edge = api.model(
'Edge', {
'sub': fields.String(readOnly=True, description='Subject Node ID'),
'pred': fields.String(readOnly=True,
description='Predicate (Relation) ID'),
'obj': fields.String(readOnly=True, description='Subject Node ID'),
})
bbop_graph = api.model(
from flask_restplus import fields
from biolink.api.restplus import api
from biolink.datamodel.serializers import named_object_core
# Schema for posting to /sim/score
features = api.model(
'Feature', {
'id':
fields.String(description='curie formatted id'),
'label':
fields.String(description='curie formatted id'),
'type':
fields.String(description='feature type (only phenotype supported)'),
'isPresent':
fields.Boolean(description='is the feature present')
})
sufficiency_input = api.model(
'SufficiencyPostInput', {
'id':
fields.String(description='curie formatted id'),
'features':
fields.List(fields.Nested(features), description='list of features')
})
# Schema for output document for annotation sufficiency
sufficiency_output = api.model(
'SufficiencyOutput', {
'simple_score': fields.Float(description='simple score'),
'scaled_score': fields.Float(description='scaled score'),
'categorical_score': fields.Float(description='categorical score'),
from flask_restplus import fields
from biolink.api.restplus import api
# todo: split this into modules
# TODO: convert to marshmallow
# Solr
search_result = api.model(
'SearchResult', {
'numFound':
fields.Integer(
description='total number of associations matching query'),
'docs':
fields.List(fields.Raw, description='solr docs'),
'facet_counts':
fields.Raw(
description='Mapping between field names and association counts'),
'highlighting':
fields.Raw(description='Mapping between id and solr highlight')
})
autocomplete_result = api.model(
'AutocompleteResult', {
'id':
fields.String(description='curie formatted id'),
'label':
fields.List(fields.String, description='primary label (rdfs:label)'),
'match':
fields.String(
description=
from flask_restplus import fields
from biolink.api.restplus import api
abstract_property_value = api.model(
'AbstractPropertyValue', {
'val':
fields.String(readOnly=True, description='value part'),
'pred':
fields.String(readOnly=True, description='predicate (attribute) part'),
'xrefs':
fields.List(fields.String,
description='Xrefs provenance for property-value'),
})
synonym_property_value = api.inherit('SynonymPropertyValue',
abstract_property_value, {})
xref_property_value = api.inherit('SynonymPropertyValue',
abstract_property_value, {})
definition_property_value = api.inherit('DefinitionPropertyValue',
abstract_property_value, {})
basic_property_value = api.inherit('DefinitionPropertyValue',
abstract_property_value, {})
meta = api.model(
'Meta', {
'definition':
fields.Nested(definition_property_value,
description='definition plus source'),
from flask_restplus import fields
from biolink.api.restplus import api
# todo: split this into modules
# TODO: convert to marshmallow
# Solr
search_result = api.model(
'SearchResult', {
'numFound':
fields.Integer(
description='total number of associations matching query'),
'start':
fields.Integer(description='Cursor position'),
'facet_counts':
fields.Raw(
description='Mapping between field names and association counts'),
'facet_pivot':
fields.Raw(description='Populated in facet_pivots is passed'),
})
## BBOP/OBO Graphs
abstract_property_value = api.model(
'AbstractPropertyValue', {
'val':
fields.String(readOnly=True, description='value part'),
'pred':
fields.String(readOnly=True, description='predicate (attribute) part'),
'xrefs':
from flask_restplus import fields
from biolink.api.restplus import api
abstract_property_value = api.model(
'AbstractPropertyValue', {
'val':
fields.String(readOnly=True, description='value part'),
'pred':
fields.String(readOnly=True, description='predicate (attribute) part'),
'xrefs':
fields.List(fields.String,
description='Xrefs provenance for property-value'),
})
annotatable = api.model('Annotatable', {})
model = api.model(
'Model', {
'id':
fields.String(description='unique ID/CURIE/URI'),
'title':
fields.String(description='textual description'),
'state':
fields.String(description='production or development'),
'contributors':
fields.List(fields.String(),
description='list of IRIs of contributors'),
})
type_reference = api.model(
'TypeReference', {
