class Epic(JsonObject):
""" Epic model """
id_ = IntegerProperty(name='id')
done = BooleanProperty()
key = IntegerProperty()
name = StringProperty()
color = ObjectProperty(EpicColor)
class AcceptedMessage(JsonObject):
message_id = IntegerProperty(required=True)
from_field = ObjectProperty(User, name='from', required=True)
date = IntegerProperty()
chat = ObjectProperty(Chat, required=True)
text = StringProperty(required=True)
class PrimerOutput(JsonObject):
sequence = StringProperty(required=True)
start = IntegerProperty(required=True)
length = IntegerProperty(required=True)
temperature = FloatProperty(required=True)
gc_content = FloatProperty(required=True)
degenerate_codons = ListProperty(str, required=True)
overlap_with_following = BooleanProperty(default=False, required=False)
class Version(JsonObject):
""" Version model """
id_ = IntegerProperty(name='id')
project_id = IntegerProperty(name='projectId')
name = StringProperty()
description = StringProperty()
archived = BooleanProperty()
released = BooleanProperty()
release_date = DateTimeProperty(name='releaseDate')
class Sprint(JsonObject):
""" Spring model """
id_ = IntegerProperty(name='id')
state = StringProperty(name='state')
name = StringProperty(name='name')
start_date = DateTimeProperty(name='startDate')
end_date = DateTimeProperty(name='endDate')
complete_date = DateTimeProperty(name='completeDate')
origin_board_id = IntegerProperty(name='originBoardId')
class MessageContainer(JsonObject):
# retry section
# Flow should be next
# try to send message -> received response with retry_after -> put to queue back
# and set retry_after and set create_time
retry_after = IntegerProperty(exclude_if_none=True)
create_time = IntegerProperty(exclude_if_none=True)
retry_count = IntegerProperty(exclude_if_none=True)
message_type = StringProperty(choices=['error', 'response'], required=True)
message = ObjectProperty(Message, required=True)
class Version(JsonObject):
""" Version model """
id_ = IntegerProperty(name='id')
projectId = IntegerProperty()
name = StringProperty()
description = StringProperty()
archived = BooleanProperty()
released = BooleanProperty()
releaseDate = CustomDateTimeProperty(
datetime_format="%Y-%m-%d %H:%M:%S.%z")
startDate = CustomDateTimeProperty(datetime_format="%Y-%m-%d %H:%M:%S.%z")
class PASResult(JsonObject):
fragment = StringProperty(required=True)
start = IntegerProperty(required=True)
end = IntegerProperty(required=True)
length = IntegerProperty(required=True)
overlap = StringProperty(required=False)
overlap_Tm = FloatProperty(required=False)
overlap_GC = FloatProperty(required=False)
overlap_length = IntegerProperty(required=False)
mutations = ListProperty(PASMutationFormatted, required=False)
oligos = ListProperty(PASOligoOutput, required=True)
class Command(JsonObject):
operation = StringProperty(
choices=['create', 'delete', 'select', 'list', 'current'],
required=True)
subject = StringProperty(choices=['file', 'sheet', 'topic'], required=True)
name = StringProperty()
virtual_id = IntegerProperty()
user_id = IntegerProperty()
chat_id = IntegerProperty()
def __eq__(self, other):
return self.operation == other.operation and self.subject == other.subject and self.name == other.name and self.virtual_id == other.virtual_id and self.user_id == other.user_id and self.chat_id == other.chat_id
class ListOrdersFilters(JsonObject):
"""
status_choices = ['WAITING', 'NOT_PAID', 'PAID', 'REVERTED']
paymentMethod = ['DEBIT_CARD', 'BOLETO', 'ONLINE_BANK_FINANCING',
'ONLINE_BANK_DEBIT', 'WALLET']
"""
createdAt = DateProperty(exclude_if_none=True)
paymentMethod = StringProperty(exclude_if_none=True)
value = StringProperty(exclude_if_none=True)
status = StringProperty(exclude_if_none=True)
limit = IntegerProperty(exclude_if_none=True)
offset = IntegerProperty(exclude_if_none=True)
class QCLMConfig(JsonObject):
min_primer_size = IntegerProperty(default=23)
opt_primer_size = IntegerProperty(default=23)
max_primer_size = IntegerProperty(default=60)
min_gc_content = FloatProperty(default=40)
opt_gc_content = FloatProperty(default=50)
max_gc_content = FloatProperty(default=60)
min_three_end_size = IntegerProperty(default=10)
opt_three_end_size = IntegerProperty(default=10)
max_three_end_size = IntegerProperty(default=40)
min_five_end_size = IntegerProperty(default=10)
opt_five_end_size = IntegerProperty(default=10)
max_five_end_size = IntegerProperty(default=40)
min_temperature = FloatProperty(default=75)
max_temperature = FloatProperty(default=90)
gc_clamp = IntegerProperty(default=1)
use_degeneracy_codon = BooleanProperty(default=True)
codon_usage_frequency_threshold = FloatProperty(default=0.1)
# Search only for solutions with non-overlapping primers?
non_overlapping_primers = BooleanProperty(default=False)
# Should we use the primer3 to check generated primers?
use_primer3 = BooleanProperty(default=True)
# The allowed range for primer melting temperatures, in deg C
temp_range_size = FloatProperty(default=5)
# Temperature calculator configuration
temperature_config = ObjectProperty(TemperatureConfig,
default=create_default_qclm_temperature_config())
# Weights used for non_optimality calculation.
temp_weight = FloatProperty(default=16) # for 1 deg C difference from the reaction temperature
primer_size_weight = FloatProperty(default=4) # for 1 base difference from the optimal primer size
three_end_size_weight = FloatProperty(default=8)
five_end_size_weight = FloatProperty(default=1)
gc_content_weight = FloatProperty(default=0)
mutation_coverage_weight = FloatProperty(default=160) # multiplies (1- <total mutation coverage>)
# For primers which break the hairpin/primer-dimer temperature constraints
hairpin_temperature_weight = FloatProperty(default=32) # for each deg C higher
primer_dimer_temperature_weight = FloatProperty(default=32) # formation temperature
# Step for iteration over possible melting temperature thresholds, in deg C
temp_threshold_step = FloatProperty(default=1)
organism=StringProperty(default="e-coli")
class SSMOutput(JsonObject):
input_data = ObjectProperty(SSMInput, required=True)
results = ListProperty(SSMMutationOutput, required=True)
full_sequence = StringProperty(required=True)
goi_offset = IntegerProperty(required=True)
new_sequence_start = IntegerProperty(required=True)
forward_flanking_primer_temperature = FloatProperty(required=True)
reverse_flanking_primer_temperature = FloatProperty(required=True)
min_three_end_temperature = FloatProperty()
max_three_end_temperature = FloatProperty()
min_overlap_temperature = FloatProperty()
max_overlap_temperature = FloatProperty()
class Plasmid(JsonObject):
gene_start_in_plasmid = IntegerProperty(default=None)
gene_end_in_plasmid = IntegerProperty(default=None)
plasmid_sequence = StringProperty(required=True)
def get_five_end(self, gene_of_interest, forward_primer):
self.check_sequence_occurrences(forward_primer, "Forward primer")
if self.gene_start_in_plasmid is None:
self.check_sequence_occurrences(gene_of_interest,
"Gene of interest")
gene_start = self.plasmid_sequence.find(gene_of_interest)
else:
gene_start = self.gene_start_in_plasmid
forward_position = self.plasmid_sequence.find(forward_primer)
if forward_position <= gene_start:
return self.plasmid_sequence[forward_position:gene_start]
else:
return self.plasmid_sequence[
forward_position:] + self.plasmid_sequence[:gene_start]
def get_three_end(self, gene_of_interest, reverse_primer):
reverse_complement = Seq.reverse_complement(reverse_primer)
self.check_sequence_occurrences(reverse_complement, "Reverse primer")
if self.gene_end_in_plasmid is None:
self.check_sequence_occurrences(gene_of_interest,
"Gene of interest")
gene_end = self.plasmid_sequence.find(gene_of_interest) + len(
gene_of_interest)
else:
gene_end = self.gene_end_in_plasmid
reverse_position = self.plasmid_sequence.find(reverse_complement)
reverse_primer_end = reverse_position + len(reverse_primer)
if reverse_primer_end > gene_end:
return self.plasmid_sequence[gene_end:reverse_primer_end]
else:
return self.plasmid_sequence[gene_end:] + \
self.plasmid_sequence[:reverse_primer_end]
def check_sequence_occurrences(self, sequence, name):
occurrences = self.plasmid_sequence.count(sequence)
if occurrences != 1:
if occurrences == 0:
raise ValueError("{} was not found in plasmid".format(name))
else:
raise ValueError("{} position is ambiguous".format(name))
class PASMutationSite(JsonObject):
""" List of mutations at a given amino acid position """
position = IntegerProperty(required=True)
# List of mutation. Each mutation is a amino acid IUPAC code, or a DNA codon.
mutations = ListProperty(PASMutation, required=True)
# frequency = FloatProperty(required=True)
def __gt__(self, other):
if type(other) == int:
return self.position > other
return self.position > other.position
def __lt__(self, other):
if type(other) == int:
return self.position < other
return self.position < other.position
def __eq__(self, other):
if type(other) == int:
return self.position == other
return self.position == other.position
# def __hash__(self):
# return hash(str(self.position))
def get_mutations_str_list(self):
return [mut.mutation for mut in self.mutations]
class Usage(JsonObject):
"""An Urjanet "Usage" object.
From Urjanet's documentation:
| The Usage table stores commodity-specific consumption data.
| Here, you will find information such as consumption amounts,
| read types, present and previous meter readings, and units
| of measure.
"""
# The primary key of the Usage object in the Urjanet database
PK = IntegerProperty(required=True)
# A string description of the usage measurement
UsageActualName = StringProperty()
# The measured amount of usage
UsageAmount = DecimalProperty()
# The rate component, e.g. "on peak", "off peak", etc.
RateComponent = StringProperty()
# The measurement type, "general_consumption", "demand", or "reactive_consumption"
MeasurementType = StringProperty()
# Unit of measure, typically kW or kWh
EnergyUnit = StringProperty()
# The start date for the usage measurement
IntervalStart = DateProperty()
# The end date for the usage measurement
IntervalEnd = DateProperty()
class PrimerOutput(JsonObject):
direction = StringProperty(required=True)
normal_order_sequence = StringProperty(required=True)
normal_order_start = IntegerProperty(required=True)
three_end_temperature = FloatProperty(required=True)
gc_content = FloatProperty(required=True)
parameters_in_range = BooleanProperty(required=True)
class Project(JsonObject):
key = StringProperty()
id_ = IntegerProperty(name='id')
name = StringProperty()
public = BooleanProperty()
type_ = StringProperty(name='type')
description = StringProperty(default="")
class Debug(JsonObject):
""" Represent a Debug menu """
log_level = IntegerProperty(default=0)
show_elapsed_time = BooleanProperty(default=False)
show_received_bytes = BooleanProperty(default=False)
show_arguments = BooleanProperty(default=False)
show_url = BooleanProperty(default=False)
class User(JsonObject):
name = StringProperty()
emailAddress = StringProperty()
id_ = IntegerProperty(name='id')
displayName = StringProperty()
active = BooleanProperty()
slug = StringProperty()
type_ = StringProperty(name="type")
class PullRequest(JsonObject):
id_ = IntegerProperty(name='id')
version = IntegerProperty()
title = StringProperty()
description = StringProperty()
state = StringProperty()
open_ = BooleanProperty(name="open")
closed = BooleanProperty()
createdDate = EpochProperty()
updatedDate = EpochProperty()
fromRef = ObjectProperty(Ref)
toRef = ObjectProperty(Ref)
locked = BooleanProperty()
author = ObjectProperty(PullRequestUser)
reviewers = ListProperty(PullRequestUser, default=[])
participants = ListProperty(PullRequestUser, default=[])
properties = ObjectProperty(PullRequestProperties)
class PASMutationFormatted(JsonObject):
position = IntegerProperty(required=True)
mutated_amino = StringProperty(required=True)
wild_type_amino = StringProperty(required=False)
wild_type_codon = StringProperty(required=False)
mutated_codon = StringProperty(required=True)
frequency = FloatProperty(required=True)
wild_type = BooleanProperty(required=True)
class Repo(JsonObject):
slug = StringProperty()
id_ = IntegerProperty(name='id')
name = StringProperty()
smcId = StringProperty()
state = StringProperty()
statusMessage = StringProperty()
forkable = BooleanProperty()
public = BooleanProperty()
class ShippingAddress(JsonObject):
street = StringProperty(required=True)
streetNumber = StringProperty(required=True)
complement = IntegerProperty(exclude_if_none=True)
district = StringProperty(required=True)
city = StringProperty(required=True)
state = StringProperty(required=True)
country = StringProperty(required=True)
zipCode = StringProperty(required=True)
class ReportsForm(JsonObject):
time = DateTimeProperty()
completion_time = DateTimeProperty()
start_time = DateTimeProperty()
duration = IntegerProperty()
submission_time = DateTimeProperty()
xmlns = StringProperty()
app_id = StringProperty()
user_id = StringProperty()
username = StringProperty()
class StatusCategory(JsonObject):
""" StatusCategory model for Status """
id_ = IntegerProperty(name='id')
key = StringProperty()
colorName = StringProperty()
name = StringProperty()
def color(self):
""" Convert to termcolor """
if self.colorName == 'blue-gray':
return 'blue'
return self.colorName
class Report(CaseReportMixin, JsonObject):
month = IntegerProperty(required=True)
year = IntegerProperty(required=True)
block = StringProperty(required=True)
def __init__(self, *args, **kwargs):
super(Report, self).__init__(*args, **kwargs)
self._extra_row_objects = []
_data_provider = None
@property
def data_provider(self):
return self._data_provider
@property
def datespan(self):
return DateSpan.from_month(self.month, self.year, inclusive=True)
def set_extra_row_objects(self, row_objects):
self._extra_row_objects = row_objects
class TaxJarLineItem(JsonObject):
# NB: SmartCalcs can return either string or integer
# `id` is a valid property, but isn't enforced here
# id = StringProperty()
product_identifier = StringProperty()
description = StringProperty()
quantity = IntegerProperty()
unit_price = TaxJarFloatProperty()
discount = TaxJarFloatProperty()
sales_tax = TaxJarFloatProperty()
class StagingMeterData(JsonObject):
usage_point = (
IntegerProperty()
) # DEPRECATED : OID of usage point objects in green button staging.
usage_point_id = StringProperty() # Use this instead.
duration = IntegerProperty()
address = ObjectProperty(StagingAddress)
account_number = StringProperty()
service_id = StringProperty()
utility = StringProperty()
tariff = StringProperty()
commodity = StringProperty()
def is_complete(self):
record = self.to_json()
record.pop("usage_point")
return all(x is not None for x in record.values())
def __eq__(self, other):
if not isinstance(other, StagingMeterData):
return False
return self.to_json() == other.to_json()
class Charge(JsonObject):
"""An Urjanet "Charge" object.
From the Urjanet documentation:
| The Charge table includes information related to the
| line-item charges on your utility bill. Here, you can
| find details such as charges names, rates, and currencies.
| If a charge is associated with more than one meter, Urjanet
| will prorate the charge based on the usage amount.
Note especially the description of proration, which can
manifest in some somewhat difficult to interpret data.
"""
# The primary key of the Charge object in the Urjanet database
PK = IntegerProperty(required=True)
# The line item name
ChargeActualName = StringProperty()
# The charge amount in dollars
ChargeAmount = DecimalProperty()
# The usage associated with this charge, if any
ChargeUnitsUsed = DecimalProperty()
# The units on the usage associated with this charge
UsageUnit = StringProperty()
# The rate associated with this charge (e.g. price per unit of usage)
ChargeRatePerUnit = DecimalProperty()
# The name of any third party provider (e.g. a CCA entity)
# This is useful for identifying CCA charges
ThirdPartyProvider = StringProperty()
# TODO: Explain this flag in more detail. It may be a somewhat
# misleading field. For now, avoid using it.
IsAdjustmentCharge = BooleanProperty()
# The start date for the period the charge applies to
IntervalStart = DateProperty()
# The end date for the period the charge applies to
IntervalEnd = DateProperty()
ChargeId = StringProperty()
class Meter(JsonObject):
"""An Urjanet "Meter" object
From Urjanet's documentation:
| The Meter table organizes usage information into specific
| "points" of service. Urjanet's definition of a meter is not
| limited to physical meters. The meter table captures data
| such as service types, tariffs, and usage periods.
"""
# The primary key of the Meter object in the Urjanet database
PK = IntegerProperty(required=True)
# The tariff assigned to the meter.
# Note: this is drawn from text in a PDF, and is not guaranteed
# to have a consistent format (that is, tariff's on separate meters
# cannot reliably be compared in a direct fashion)
Tariff = StringProperty()
# The service type of the meter (e.g. electric, natural_gas)
ServiceType = StringProperty()
# The "Point of Delivery" identifier for the meter. Interpretation
# of this field varies for different utilities. For Pacific Gas &
# Electric, this corresponds to a service ID.
PODid = StringProperty()
# The meter number for the meter. Interpretation of this field varies
# for different utilities.
MeterNumber = StringProperty()
# The start/end dates for the Meter object. These fields are a little
# difficult to interpret. Roughly speaking, they define, respectively, the
# earliest and latest date for which usage/charge information is available
# for the meter on a given statement. While this is usually set correctly,
# there are times where individual charge/usage date ranges do not fully
# interect with their parent meter.
IntervalStart = DateProperty()
IntervalEnd = DateProperty()
# The charges associated with this meter
charges = ListProperty(Charge)
# The usage values associated with this meter
usages = ListProperty(Usage)
