class Output(Schema):
val = fields.Integer()
created = fields.DateTime()
modified1 = fields.DateTime()
modified2 = fields.DateTime()
user = Neo4jSchema(
User,
fields=(
"uuid",
"email",
"name",
"surname",
"is_active",
"last_password_change",
),
)
group1 = Neo4jSchema(Group, fields="*")
group2 = Neo4jSchema(Group, fields=("*", ))
group3 = Neo4jSchema(Group, fields=["*"])
group4 = Neo4jSchema(Group, fields=[])
group5 = Neo4jSchema(Group, fields=["fullname", "shortname"])
group6 = Neo4jSchema(Group, fields="")
group7 = Neo4jSchema(Group, fields=None)
choices1 = Neo4jChoice(CHOICES_tuple)
choices2 = Neo4jChoice(CHOICES_dict)
def build_schema(self, model: Type[Any]) -> None:
# Get the full list of parent classes from model to object
classes = inspect.getmro(model)
starting_point = False
# Iterate in reversed order to start from object
for c in reversed(classes):
# Skip all parentes up to StructuredNode and StructuredRel (included)
if not starting_point:
# Found the starting point, next class will be descended up to model
if c == StructuredNode or c == StructuredRel:
starting_point = True
# skip all parent up to StructuredNode and StructuredRel INCLUDED
continue
# Iterate all class attributes to find neomodel properties
for attribute in c.__dict__:
prop = getattr(c, attribute)
if not isinstance(prop, properties.Property):
continue
# self.fields can be None when the special value * is given in input
if self.fields and attribute not in self.fields:
continue
# log.info("Including property {}.{}", model.__name__, attribute)
if isinstance(prop, properties.StringProperty):
if prop.choices is None:
self.declared_fields[attribute] = fields.Str()
else:
self.declared_fields[attribute] = fields.Neo4jChoice(
prop.choices)
elif isinstance(prop, properties.BooleanProperty):
self.declared_fields[attribute] = fields.Boolean()
elif isinstance(prop, properties.IntegerProperty):
self.declared_fields[attribute] = fields.Integer()
elif isinstance(prop, properties.FloatProperty):
self.declared_fields[attribute] = fields.Float()
elif isinstance(prop, properties.EmailProperty):
# This is because Nested is not typed on marshmallow
self.declared_fields[attribute] = fields.Email(
) # type: ignore
elif isinstance(prop, properties.DateTimeProperty):
self.declared_fields[attribute] = fields.AwareDateTime()
elif isinstance(prop, properties.DateProperty):
self.declared_fields[attribute] = fields.Date()
elif isinstance(prop, properties.UniqueIdProperty):
self.declared_fields[attribute] = fields.Str()
else: # pragma: no cover
log.error(
"Unsupport neomodel property: {}, fallback to StringProperty",
prop.__class__.__name__,
)
self.declared_fields[attribute] = fields.Str()
class PrivateStatsOutput(Schema):
num_users = fields.Integer(required=False)
num_studies = fields.Integer(required=False)
num_datasets = fields.Integer(required=False)
num_datasets_per_group = fields.Dict(required=False,
keys=fields.Str(),
values=fields.Integer())
num_datasets_with_vcf = fields.Integer(required=False)
num_datasets_with_vcf_per_group = fields.Dict(required=False,
keys=fields.Str(),
values=fields.Integer())
num_datasets_with_gvcf = fields.Integer(required=False)
num_datasets_with_gvcf_per_group = fields.Dict(required=False,
keys=fields.Str(),
values=fields.Integer())
num_files = fields.Integer(required=False)
class PhenotypeOutputSchema(Schema):
uuid = fields.Str(required=True)
name = fields.Str(required=True)
age = fields.Integer()
sex = fields.Str(required=True, validate=validate.OneOf(SEX))
hpo = fields.List(fields.Nested(Hpo), required=False)
birth_place = fields.Nested(GeoData, required=False)
relationships = fields.Nested(
Relationships,
metadata={"description": "family relationships between phenotypes"},
)
def getInputSchema(request: FlaskRequest, is_post: bool) -> Type[Schema]:
graph = neo4j.get_instance()
# as defined in Marshmallow.schema.from_dict
attributes: Dict[str, Union[fields.Field, type]] = {}
attributes["name"] = fields.Str(required=True)
attributes["age"] = fields.Integer(allow_none=True, validate=validate.Range(min=0))
attributes["sex"] = fields.Str(
required=True, validate=validate.OneOf(SEX), metadata={"description": ""}
)
attributes["hpo"] = fields.List(
fields.Str(),
metadata={
"label": "HPO",
"autocomplete_endpoint": "/api/hpo",
"autocomplete_show_id": True,
"autocomplete_id_bind": "hpo_id",
"autocomplete_label_bind": "label",
},
)
geodata_keys = []
geodata_labels = []
for g in graph.GeoData.nodes.all():
geodata_keys.append(g.uuid)
geodata_labels.append(g.province)
if len(geodata_keys) == 1:
default_geodata = geodata_keys[0]
else:
default_geodata = None
attributes["birth_place"] = fields.Str(
required=False,
allow_none=True,
metadata={
"label": "Birth Place",
"description": "",
},
dump_default=default_geodata,
validate=validate.OneOf(choices=geodata_keys, labels=geodata_labels),
)
return Schema.from_dict(attributes, name="PhenotypeDefinition")
class FileOutput(Schema):
uuid = fields.Str(required=True)
name = fields.Str(required=True)
type = fields.Str(required=False)
size = fields.Integer(required=False)
status = fields.Str(required=False)
def test_responses(self, faker: Faker) -> None:
class MySchema(Schema):
name = fields.Str()
f = "myfield"
assert (
ResponseMaker.get_schema_type(f, fields.Str(metadata={"password": True}))
== "password"
)
assert ResponseMaker.get_schema_type(f, fields.Bool()) == "boolean"
assert ResponseMaker.get_schema_type(f, fields.Boolean()) == "boolean"
assert ResponseMaker.get_schema_type(f, fields.Date()) == "date"
assert ResponseMaker.get_schema_type(f, fields.DateTime()) == "datetime"
assert ResponseMaker.get_schema_type(f, fields.AwareDateTime()) == "datetime"
assert ResponseMaker.get_schema_type(f, fields.NaiveDateTime()) == "datetime"
assert ResponseMaker.get_schema_type(f, fields.Decimal()) == "number"
# This is because Email is not typed on marshmallow
assert ResponseMaker.get_schema_type(f, fields.Email()) == "email" # type: ignore
assert ResponseMaker.get_schema_type(f, fields.Float()) == "number"
assert ResponseMaker.get_schema_type(f, fields.Int()) == "int"
assert ResponseMaker.get_schema_type(f, fields.Integer()) == "int"
assert ResponseMaker.get_schema_type(f, fields.Number()) == "number"
assert ResponseMaker.get_schema_type(f, fields.Str()) == "string"
assert ResponseMaker.get_schema_type(f, fields.String()) == "string"
assert ResponseMaker.get_schema_type(f, fields.Dict()) == "dictionary"
assert ResponseMaker.get_schema_type(f, fields.List(fields.Str())) == "string[]"
assert ResponseMaker.get_schema_type(f, fields.Nested(MySchema())) == "nested"
# Unsupported types, fallback to string
assert ResponseMaker.get_schema_type(f, fields.URL()) == "string"
assert ResponseMaker.get_schema_type(f, fields.Url()) == "string"
assert ResponseMaker.get_schema_type(f, fields.UUID()) == "string"
# assert ResponseMaker.get_schema_type(f, fields.Constant("x")) == "string"
assert ResponseMaker.get_schema_type(f, fields.Field()) == "string"
# assert ResponseMaker.get_schema_type(f, fields.Function()) == "string"
# assert ResponseMaker.get_schema_type(f, fields.Mapping()) == "string"
# assert ResponseMaker.get_schema_type(f, fields.Method()) == "string"
# assert ResponseMaker.get_schema_type(f, fields.Raw()) == "string"
# assert ResponseMaker.get_schema_type(f, fields.TimeDelta()) == "string"
assert not ResponseMaker.is_binary(None)
assert not ResponseMaker.is_binary("")
assert not ResponseMaker.is_binary("application/json")
assert ResponseMaker.is_binary("application/octet-stream")
assert ResponseMaker.is_binary("application/x-bzip")
assert ResponseMaker.is_binary("application/x-bzip2")
assert ResponseMaker.is_binary("application/pdf")
assert ResponseMaker.is_binary("application/msword")
assert ResponseMaker.is_binary("application/rtf")
assert ResponseMaker.is_binary("application/x-tar")
assert ResponseMaker.is_binary("application/gzip")
assert ResponseMaker.is_binary("application/zip")
assert ResponseMaker.is_binary("application/x-7z-compressed")
assert not ResponseMaker.is_binary("text/plain")
assert not ResponseMaker.is_binary("text/css")
assert not ResponseMaker.is_binary("text/csv")
assert not ResponseMaker.is_binary("text/html")
assert not ResponseMaker.is_binary("text/javascript")
assert not ResponseMaker.is_binary("text/xml")
assert ResponseMaker.is_binary("image/gif")
assert ResponseMaker.is_binary("image/jpeg")
assert ResponseMaker.is_binary("image/png")
assert ResponseMaker.is_binary("image/svg+xml")
assert ResponseMaker.is_binary("image/tiff")
assert ResponseMaker.is_binary("image/webp")
assert ResponseMaker.is_binary("image/bmp")
assert ResponseMaker.is_binary("image/aac")
assert ResponseMaker.is_binary("audio/midi")
assert ResponseMaker.is_binary("audio/mpeg")
assert ResponseMaker.is_binary("audio/wav")
assert ResponseMaker.is_binary("audio/anyother")
assert ResponseMaker.is_binary("video/mpeg")
assert ResponseMaker.is_binary("video/ogg")
assert ResponseMaker.is_binary("video/webm")
assert ResponseMaker.is_binary("video/anyother")
assert ResponseMaker.is_binary("video/anyother")
assert not ResponseMaker.is_binary(faker.pystr())
response = EndpointResource.response("", code=200)
assert response[1] == 200 # type: ignore
response = EndpointResource.response(None, code=200)
assert response[1] == 204 # type: ignore
response = EndpointResource.response(None, code=200, head_method=True)
assert response[1] == 200 # type: ignore
class PublicStatsOutput(Schema):
num_users = fields.Integer(required=False)
num_studies = fields.Integer(required=False)
num_datasets = fields.Integer(required=False)
num_datasets_with_vcf = fields.Integer(required=False)
num_files = fields.Integer(required=False)