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def __init__(self, some_value):
pass
name = fields.StringField(required=True)
surname = fields.StringField(required=True)
age = fields.IntField()
toys = fields.ListField(Toy)
class Person(models.Base):
def __init__(self, some_value):
pass
name = fields.StringField(required=True)
surname = fields.StringField(required=True)
age = fields.IntField()
kids = fields.ListField(Kid)
car = fields.EmbeddedField(Car)
schema = Person.to_json_schema()
pattern = get_fixture('schema2.json')
self.assertTrue(compare_schemas(pattern, schema))
ac_asj = fields.IntField(help_text="Allele Count Ashkenazi Jewish", required=False, nullable=True)
ac_eas = fields.IntField(help_text="Allele Count East Asian", required=False, nullable=True)
ac_fin = fields.IntField(help_text="Allele Count European (Finnish)", required=False, nullable=True)
ac_nfe = fields.IntField(help_text="Allele Count European (Non-Finnish)", required=False, nullable=True)
ac_oth = fields.IntField(help_text="Allele Count Other", required=False, nullable=True)
ac_male = fields.IntField(help_text="Allele Count Male", required=False, nullable=True)
ac_female = fields.IntField(help_text="Allele Count Female", required=False, nullable=True)
hom = fields.IntField(help_text="Number of Homozygotes", required=False, nullable=True)
hemi = fields.IntField(help_text="Number of Hemizygotes", required=False, nullable=True)
ac_hom = fields.FloatField(help_text="Number of Homozygotes", required=False, nullable=True)
ac_hemi = fields.FloatField(help_text="Number of Hemizygotes", required=False, nullable=True)
an_afr = fields.IntField(help_text="Allele Number African", required=False, nullable=True)
an_amr = fields.IntField(help_text="Allele Number American", required=False, nullable=True)
an_asj = fields.IntField(help_text="Allele Number Ashkenazi Jewish", required=False, nullable=True)
an_eas = fields.IntField(help_text="Allele Number East Asian", required=False, nullable=True)
an_fin = fields.IntField(help_text="Allele Number European (Finnish)", required=False, nullable=True)
an_nfe = fields.IntField(help_text="Allele Number European (Non-Finnish)", required=False, nullable=True)
an_oth = fields.IntField(help_text="Allele Number Other", required=False, nullable=True)
an_male = fields.IntField(help_text="Allele Number Male", required=False, nullable=True)
an_female = fields.IntField(help_text="Allele Number Female", required=False, nullable=True)
hom_afr = fields.IntField(help_text="Number of Homozygotes African", required=False, nullable=True)
hom_amr = fields.IntField(help_text="Number of Homozygotes American", required=False, nullable=True)
hom_asj = fields.IntField(help_text="Number of Homozygotes Ashkenazi Jewish", required=False, nullable=True)
hom_eas = fields.IntField(help_text="Number of Homozygotes East Asian", required=False, nullable=True)
hom_fin = fields.IntField(help_text="Number of Homozygotes European (Finnish)", required=False, nullable=True)
hom_nfe = fields.IntField(help_text="Number of Homozygotes European (Non-Finnish)", required=False, nullable=True)
hom_oth = fields.IntField(help_text="Number of Homozygotes Other", required=False, nullable=True)
hom_male = fields.IntField(help_text="Number of Homozygotes Male", required=False, nullable=True)
hom_female = fields.IntField(help_text="Number of Homozygotes Female", required=False, nullable=True)
af_afr = fields.FloatField(help_text="Allele Frequency African", required=False, nullable=True)
af_amr = fields.FloatField(help_text="Allele Frequency American", required=False, nullable=True)
af_asj = fields.FloatField(help_text="Allele Frequency Ashkenazi Jewish", required=False, nullable=True)
nullable=True)
fathmm_mkl_non_coding_groups = fields.StringField(help_text="FATHMM_MKL non coding groups", required=False,
nullable=True)
whole_exome_freq = fields.ListField(items_types=(str, int, float,), help_text="Whole exome frequency", required=False,
nullable=True)
whole_genome_reseq_freq = fields.ListField(items_types=(str, int, float,), help_text="Whole genome reseq frequency",
required=False, nullable=True)
resistance_mutation = fields.ListField(items_types=(str,), help_text="Resistance mutation", required=False,
nullable=True)
drug_entries = fields.ListField(items_types=(CosmicLicensedDrugEntry,), help_text="Drug entries", required=False,
nullable=True)
class ComsicPublicDetails(models.Base):
num_samples = fields.IntField(help_text='Number of samples')
id = fields.StringField(help_text='Cosmic ID')
is_consistent = fields.BoolField(help_text='Cosmic ID is consistent across databases')
class CosmicPublic(models.Base):
version = fields.StringField(help_text="Version")
items = fields.ListField(items_types=(ComsicPublicDetails, ), help_text="Details", required=False, nullable=True)
class CosmicLicensed(models.Base):
version = fields.StringField(help_text="Version")
items = fields.ListField(items_types=(CosmicLicensedDetails,), help_text="Details")
'''
types = (netaddr.IPNetwork,)
def parse_value(self, value):
if value is not None:
return netaddr.IPNetwork(value)
def to_struct(self, obj):
if obj is not None:
return str(obj)
TimestampField = fields.FloatField
class MacAddressField(fields.BaseField):
'''A field representing a MAC address, specifically a netaddr.EUI.
In serialized form it is stored in UNIX MAC format:
"mac": "12:34:56:78:90:ab"
'''
types = (netaddr.EUI,)
def parse_value(self, value):
if value is not None:
return netaddr.EUI(value, dialect=netaddr.mac_unix_expanded)
def to_struct(self, obj):
if obj is not None:
obj.dialect = netaddr.mac_unix_expanded
return str(obj)
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from jsonmodels import models, fields
__author__ = "ckopanos"
class ExAC(models.Base):
version = fields.StringField(help_text="Version")
ac = fields.IntField(help_text="Allele Count", required=False, nullable=True)
an = fields.IntField(help_text="Allele Number", required=False, nullable=True)
ac_adj = fields.FloatField(help_text="Allele Count", required=False, nullable=True)
an_adj = fields.FloatField(help_text="Allele Number", required=False, nullable=True)
af = fields.FloatField(help_text="Allele Frequency", required=False, nullable=True)
ac_afr = fields.IntField(help_text="Allele Count African", required=False, nullable=True)
ac_amr = fields.IntField(help_text="Allele Count American", required=False, nullable=True)
ac_asj = fields.IntField(help_text="Allele Count Ashkenazi Jewish", required=False, nullable=True)
ac_eas = fields.IntField(help_text="Allele Count East Asian", required=False, nullable=True)
ac_fin = fields.IntField(help_text="Allele Count European (Finnish)", required=False, nullable=True)
ac_nfe = fields.IntField(help_text="Allele Count European (Non-Finnish)", required=False, nullable=True)
ac_oth = fields.IntField(help_text="Allele Count Other", required=False, nullable=True)
ac_sas = fields.IntField(help_text="Allele Count South Asian", required=False, nullable=True)
ac_male = fields.IntField(help_text="Allele Count Male", required=False, nullable=True)
ac_female = fields.IntField(help_text="Allele Count Female", required=False, nullable=True)
hom = fields.IntField(help_text="Number of Homozygotes", required=False, nullable=True)
from jsonmodels import models, fields
__author__ = "ckopanos"
class UniprotVariantsDetails(models.Base):
annotation_id = fields.StringField(help_text="Annotation ID", required=False, nullable=True)
protein_id = fields.StringField(help_text="Protein ID", required=False, nullable=True)
bed_comments = fields.ListField(help_text="Comments", items_types=(str, ), required=False, nullable=True)
gene = fields.StringField(help_text="Gene", required=False, nullable=True)
variant_type = fields.StringField(help_text="Variant type", required=False, nullable=True)
transcripts = fields.ListField(help_text="Transcripts", items_types=(str,), required=False, nullable=True)
pub_med_references = fields.ListField(help_text="PubMed References", items_types=(int,), required=False, nullable=True)
disease = fields.StringField(help_text="Disease", required=False, nullable=True)
disease_symbol = fields.StringField(help_text="Disease symbol", required=False, nullable=True)
disease_alt_symbol = fields.StringField(help_text="Disease alt symbol", required=False, nullable=True)
class UniprotVariants(models.Base):
version = fields.StringField(help_text="Version")
items = fields.ListField(help_text='Details', items_types=(UniprotVariantsDetails,))
__author__ = "ckopanos"
class ThousandGenomes(models.Base):
version = fields.StringField(help_text="Version")
ac = fields.ListField(items_types=(int,), help_text="Allele Count", required=False, nullable=True)
af = fields.ListField(items_types=(float,), help_text="Allele Frequency", required=False, nullable=True)
an = fields.ListField(items_types=(int,), help_text="Allele Number", required=False, nullable=True)
ns = fields.ListField(items_types=(int,), help_text="Number of Samples", required=False, nullable=True)
afr_af = fields.ListField(items_types=(float,), help_text="Allele Frequency African", required=False, nullable=True)
amr_af = fields.ListField(items_types=(float,), help_text="Allele Frequency American", required=False,
nullable=True)
eas_af = fields.ListField(items_types=(float,), help_text="Allele Frequency East Asian", required=False,
nullable=True)
eur_af = fields.ListField(items_types=(float,), help_text="Allele Frequency European", required=False,
nullable=True)
sas_af = fields.ListField(items_types=(float,), help_text="Allele Frequency South Asian", required=False,
nullable=True)
main_data = fields.StringField(help_text="Main data point", required=False, nullable=True)
network = df_fields.IpNetworkField()
@mf.register_model
@mf.construct_nb_db_model
class LogicalRouter(mf.ModelBase, mixins.Name, mixins.Version, mixins.Topic,
mixins.UniqueKey, mixins.BasicEvents):
"""Define the dragonflow db model for logical router.
Note that only the fields that dragonflow has used are defined here.
Fields like 'distributed' and 'external_gateway' are missed on purpose.
"""
table_name = "lrouter"
ports = fields.ListField(LogicalRouterPort)
routes = fields.ListField(host_route.HostRoute)
def add_router_port(self, router_port):
self.ports.append(router_port)
def remove_router_port(self, router_port_id):
for idx, router_port in enumerate(self.ports):
if router_port.id == router_port_id:
self.ports.pop(idx)
@mf.register_model
@mf.construct_nb_db_model(
indexes={
'lport': 'lport.id',
'floating_lport': 'floating_lport.id',
},
@mf.construct_nb_db_model
class Chassis(mf.ModelBase, mixins.BasicEvents):
table_name = 'chassis'
ip = df_fields.IpAddressField(required=True)
external_host_ip = df_fields.IpAddressField()
tunnel_types = df_fields.EnumListField(conf.CONF.df.tunnel_types,
required=True)
@mf.register_model
@mf.construct_nb_db_model
class Publisher(mf.ModelBase, mixins.Name):
table_name = 'publisher'
uri = fields.StringField()
last_activity_timestamp = fields.FloatField()
def is_stale(self):
timeout = conf.CONF.df.publisher_timeout
return (time.time() - self.last_activity_timestamp) > timeout
@classmethod
def on_get_all_post(self, instances):
return [o for o in instances if not o.is_stale()]
@mf.register_model
@mf.construct_nb_db_model
class Listener(mf.ModelBase):
table_name = "listener"
timestamp = df_fields.TimestampField()