class Pagination(PartialSchema):
get_total = fields.Boolean(
required=False, description="Request the total number of elements"
)
page = fields.Int(
required=False,
description="Current page number",
validate=validate.Range(min=1),
)
size = fields.Int(
required=False,
description="Number of elements to retrieve",
validate=validate.Range(min=1, max=100),
)
sort_order = fields.Str(
validate=validate.OneOf(["asc", "desc"]), required=False, missing="asc"
)
sort_by = fields.Str(required=False, missing=None)
input_filter = fields.Str(required=False, missing=None)
@post_load
def verify_parameters(self, data, **kwargs):
if "get_total" in data:
data["page"] = None
data["size"] = None
else:
data.setdefault("get_total", False)
data.setdefault("page", 1)
data.setdefault("size", 20)
return data
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 TechmetaPutSchema(Schema):
name = fields.Str(required=False)
sequencing_date = fields.Date(format=DATE_FORMAT)
platform = fields.Str(allow_none=True, validate=validate.OneOf(PLATFORMS))
enrichment_kit = fields.Str()
@pre_load
def null_platform(self, data: Dict[str, Any], **kwargs: Any) -> Dict[str, Any]:
if "platform" in data and data["platform"] == "":
data["platform"] = None
return data
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 admin_user_input(request: FlaskRequest, is_post: bool) -> Type[Schema]:
is_admin = HTTPTokenAuth.is_session_user_admin(request, auth)
attributes: MarshmallowSchema = {}
if is_post:
# This is because Email is not typed on marshmallow
attributes["email"] = fields.Email( # type: ignore
required=is_post,
validate=validate.Length(max=100))
attributes["name"] = fields.Str(
required=is_post,
validate=validate.Length(min=1),
metadata={"label": "First Name"},
)
attributes["surname"] = fields.Str(
required=is_post,
validate=validate.Length(min=1),
metadata={"label": "Last Name"},
)
attributes["password"] = fields.Str(
required=is_post,
validate=validate.Length(min=auth.MIN_PASSWORD_LENGTH),
metadata={"password": True},
)
if Connector.check_availability("smtp"):
attributes["email_notification"] = fields.Bool(
metadata={"label": "Notify password by email"})
attributes["is_active"] = fields.Bool(
dump_default=True,
required=False,
metadata={"label": "Activate user"},
)
roles = {r.name: r.description for r in auth.get_roles()}
if not is_admin and RoleEnum.ADMIN.value in roles:
roles.pop(RoleEnum.ADMIN.value)
attributes["roles"] = fields.List(
fields.Str(validate=validate.OneOf(
choices=[r for r in roles.keys()],
labels=[r for r in roles.values()],
)),
dump_default=[auth.default_role],
required=False,
unique=True,
metadata={
"label": "Roles",
"description": "",
"extra_descriptions": auth.role_descriptions,
},
)
group_keys = []
group_labels = []
for g in auth.get_groups():
group_keys.append(g.uuid)
group_labels.append(f"{g.shortname} - {g.fullname}")
if len(group_keys) == 1:
default_group = group_keys[0]
else:
default_group = None
attributes["group"] = fields.Str(
required=is_post,
dump_default=default_group,
validate=validate.OneOf(choices=group_keys, labels=group_labels),
metadata={
"label": "Group",
"description": "The group to which the user belongs",
},
)
attributes["expiration"] = fields.DateTime(
required=False,
allow_none=True,
metadata={
"label": "Account expiration",
"description": "This user will be blocked after this date",
},
)
if custom_fields := mem.customizer.get_custom_input_fields(
request=request, scope=mem.customizer.ADMIN):
attributes.update(custom_fields)
class TechmetaInputSchema(Schema):
name = fields.Str(required=True)
sequencing_date = fields.Date(format=DATE_FORMAT)
platform = fields.Str(validate=validate.OneOf(PLATFORMS))
enrichment_kit = fields.Str()
def getInputSchema(request, is_post):
# as defined in Marshmallow.schema.from_dict
attributes: Dict[str, Union[fields.Field, type]] = {}
if is_post:
attributes["email"] = fields.Email(required=is_post)
attributes["name"] = fields.Str(required=is_post,
validate=validate.Length(min=1))
attributes["surname"] = fields.Str(required=is_post,
validate=validate.Length(min=1))
attributes["password"] = fields.Str(
required=is_post,
password=True,
validate=validate.Length(min=auth.MIN_PASSWORD_LENGTH),
)
if Connector.check_availability("smtp"):
attributes["email_notification"] = fields.Bool(
label="Notify password by email")
attributes["is_active"] = fields.Bool(label="Activate user",
default=True,
required=False)
roles = {r.name: r.description for r in auth.get_roles()}
attributes["roles"] = AdvancedList(
fields.Str(validate=validate.OneOf(
choices=[r for r in roles.keys()],
labels=[r for r in roles.values()],
)),
required=False,
label="Roles",
description="",
unique=True,
multiple=True,
)
group_keys = []
group_labels = []
for g in auth.get_groups():
group_keys.append(g.uuid)
group_labels.append(f"{g.shortname} - {g.fullname}")
if len(group_keys) == 1:
default_group = group_keys[0]
else:
default_group = None
attributes["group"] = fields.Str(
label="Group",
description="The group to which the user belongs",
required=is_post,
default=default_group,
validate=validate.OneOf(choices=group_keys, labels=group_labels),
)
attributes["expiration"] = fields.DateTime(
required=False,
allow_none=True,
label="Account expiration",
description="This user will be blocked after this date",
)
if custom_fields := mem.customizer.get_custom_input_fields(
request=request, scope=mem.customizer.ADMIN):
attributes.update(custom_fields)
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=is_post)
attributes["description"] = fields.Str(required=is_post)
if request:
if is_post:
study_uuid = request.view_args["uuid"]
study = graph.Study.nodes.get_or_none(uuid=study_uuid)
else:
dataset_uuid = request.view_args["uuid"]
dataset = graph.Dataset.nodes.get_or_none(uuid=dataset_uuid)
study = dataset.parent_study.single()
phenotype_keys = []
phenotype_labels = []
for p in study.phenotypes.all():
phenotype_keys.append(p.uuid)
phenotype_labels.append(p.name)
if len(phenotype_keys) == 1:
default_phenotype = phenotype_keys[0]
else:
default_phenotype = None
if not is_post:
# add option to remove the technical
phenotype_keys.append("-1")
phenotype_labels.append(" - ")
attributes["phenotype"] = fields.Str(
required=False,
allow_none=True,
dump_default=default_phenotype,
validate=validate.OneOf(choices=phenotype_keys,
labels=phenotype_labels),
)
techmeta_keys = []
techmeta_labels = []
for t in study.technicals.all():
techmeta_keys.append(t.uuid)
techmeta_labels.append(t.name)
if len(techmeta_keys) == 1:
default_techmeta = techmeta_keys[0]
else:
default_techmeta = None
if not is_post:
# add option to remove the technical
techmeta_keys.append("-1")
techmeta_labels.append(" - ")
attributes["technical"] = fields.Str(
required=False,
allow_none=True,
dump_default=default_techmeta,
validate=validate.OneOf(choices=techmeta_keys,
labels=techmeta_labels),
)
return Schema.from_dict(attributes, name="DatasetDefinition")
path="/dataset/<uuid>",
summary="Modify the status of a dataset",
responses={
200:
"Status successfully modified",
400:
"Status can't be modified",
404:
"This dataset cannot be found or you are not authorized to access",
},
)
@decorators.preload(callback=verify_dataset_status_update)
@decorators.use_kwargs({
"status":
fields.Str(required=True,
validate=validate.OneOf(["UPLOAD COMPLETED", "-1"]))
})
@decorators.database_transaction
def patch(
self,
uuid: str,
study: Any,
dataset: Any,
status: str,
user: User,
) -> Response:
# patch can only be done on dataset with status UPLOAD COMPLETED
if (dataset.status and dataset.status != "UPLOAD COMPLETED"
and not self.auth.is_admin(user)):
raise BadRequest(
class InputSchema(Schema):
# lowercase key without label defined. label will be key.title() in schema
mystr = fields.Str(required=True, validate=validate.Length(min=4))
# non-lowercase key without label defined. label will be == to key in schema
MYDATE = fields.Date(required=True)
MYDATETIME = fields.AwareDateTime(
required=True,
format=ISO8601UTC,
default_timezone=pytz.utc,
validate=validate.Range(
max=datetime.now(pytz.utc).replace(hour=23, minute=59, second=59),
min=datetime(1900, 1, 1, tzinfo=pytz.utc),
max_inclusive=True,
error="Invalid date",
),
)
myint_exclusive = fields.Int(
required=True,
# Explicit label definition... but missing description
validate=validate.Range(
min=1, max=10, min_inclusive=False, max_inclusive=False
),
metadata={
"label": "Int exclusive field",
},
)
myint_inclusive = fields.Int(
required=True,
# Both label and description explicit definition
validate=validate.Range(min=1, max=10),
metadata={
"label": "Int inclusive field",
"description": "This field accepts values in a defined range",
},
)
myselect = fields.Str(
required=True,
validate=validate.OneOf(choices=["a", "b"], labels=["A", "B"]),
)
myselect2 = fields.Str(
required=True,
# Wrong definition, number labels < number of choices
# Labels will be ignored and replaced by choices
validate=validate.OneOf(choices=["a", "b"], labels=["A"]),
)
mymaxstr = fields.Str(required=True, validate=validate.Length(max=7))
myequalstr = fields.Str(required=True, validate=validate.Length(equal=6))
# Note: requests (from pytest) has to json-dump the arrays and objects,
# but the normal Marshmallow fields does not json-load the inputs
# fields.Nested is a replacement of the default Nested field with the ability
# to receive json dumped data from requests or pytest
mynested = fields.Nested(Nested, required=True)
mynullablenested = fields.Nested(Nested, required=True, allow_none=True)
# fields.List is a replacement of the default List field with the ability
# to receive json dumped data from requests or pytest
# In json model the type of this field will be resolved as string[]
mylist = fields.List(fields.Str(), required=True)
# In json model the type of this field will be resolved as int[]
mylist2 = fields.List(CustomInt, required=True)
# In json model the type of this field will be resolved as mylist3[]
# The type is key[] ... should be something more explicative like FieldName[]
mylist3 = fields.List(CustomGenericField, required=True)
