})
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':
fields.Integer(description='Number of items per page of results'),
'total':
fields.Integer(description='Total number of results'),
})
page_of_variantsets = api.inherit(
'Page of variant sets', pagination,
{'items': fields.List(fields.Nested(variantset))})
class VariantSetsCollection(Resource):
@api.expect(pagination_arguments)
@api.marshal_with(page_of_variantsets)
def get(self):
"""
Returns list of variant sets.
"""
args = pagination_arguments.parse_args(request)
page = args.get('page', 1)
per_page = args.get('per_page', 10)
posts_query = VariantSet.query
})
bbop_graph = api.model(
'Graph', {
'nodes': fields.List(fields.Nested(node)),
'edges': fields.List(fields.Nested(edge)),
})
named_object = api.model(
'NamedObject', {
'id': fields.String(readOnly=True, description='ID'),
'label': fields.String(readOnly=True, description='RDFS Label'),
'category': fields.String(readOnly=True, description='Type of object')
})
relation = api.inherit('Relation', named_object, {})
publication = api.inherit(
'Publication',
named_object,
{
# authors etc
})
# todo: inherits
taxon = api.model(
'Taxon', {
'id': fields.String(readOnly=True, description='ID'),
'label': fields.String(readOnly=True, description='RDFS Label')
})
compare_input = api.model(
'CompareInput', {
'reference_ids':
fields.List(fields.String(description='curie formatted id'),
description='list of ids'),
'query_ids':
fields.List(fields.List(
fields.String(description='curie formatted id'),
description='list of ids'),
description='list of query profiles')
})
# Schema for output document for sim search
ic_node = api.inherit('IcNode', named_object_core, {
'IC': fields.Float(description='Information content'),
})
typed_node = api.inherit(
'TypedNode', named_object_core, {
'type': fields.String(description='node type (eg phenotype, disease)'),
'taxon': fields.Nested(named_object_core, description='taxon')
})
pairwise_match = api.model(
'PairwiseMatch', {
'reference': fields.Nested(ic_node, description='reference id'),
'match': fields.Nested(ic_node, description='match id'),
'lcs': fields.Nested(ic_node, description='lowest common subsumer')
})
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'),
})
})
## 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':
fields.List(fields.String,
description='Xrefs provenance for property-value'),
})
synonym_property_value = api.inherit('SynonymPropertyValue',
abstract_property_value, {})
summary_property_value = api.inherit('SummaryPropertyValue',
abstract_property_value, {})
association_property_value = api.inherit('AssociationPropertyValue',
abstract_property_value, {})
node = api.model(
'Node', {
'id':
fields.String(readOnly=True, description='ID or CURIE'),
'lbl':
fields.String(readOnly=True,
description='human readable label, maps to rdfs:label')
})