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 Fields(JsonObject):
""" Fields model for issue"""
status = ObjectProperty(Status)
components = ListProperty(Component, default=None)
labels = ListProperty(StringProperty, default=None)
summary = StringProperty(default='')
assignee = ObjectProperty(User)
closed_sprints = ListProperty(Sprint, default=None, name='closedSprints')
reporter = ObjectProperty(User)
issue_type = ObjectProperty(IssueType)
parent_ = DefaultProperty(default=None, name='parent')
subtasks_ = DefaultProperty(default=None, name='subtasks')
@property
def parent(self):
""" Getter for parent issue """
if self.parent_:
return Issue(self.parent_)
return None
@property
def subtasks(self):
""" Getter for subtasks """
if self.subtasks_:
return list(map(Issue, self.subtasks_))
return None
class Customer(JsonObject):
ownId = StringProperty(required=True)
fullname = StringProperty(required=True)
email = StringProperty(required=True)
birthDate = StringProperty(required=True)
taxDocument = ObjectProperty(TaxDocument, required=True)
phone = ObjectProperty(Phone, required=True)
shippingAddress = ObjectProperty(ShippingAddress, required=True)
class ProtectedSaleOrder(JsonObject):
ownId = StringProperty(required=True)
amount = ObjectProperty(Amount, exclude_if_none=True)
items = ListProperty(Item, required=True)
customer = ObjectProperty(Customer, required=True)
checkoutPreferences = ObjectProperty(CheckoutPreferences,
exclude_if_none=True,
default=None)
class SSMMutationOutput(JsonObject):
mutation = StringProperty(required=True)
non_optimality = FloatProperty(required=True)
parameters_in_range = BooleanProperty(required=True)
# This is no longer used by the backend because we have second best.
# The frontend however still requires it, which is why we're keeping it.
result_found = BooleanProperty(required=True)
forward_primer = ObjectProperty(PrimerOutput)
reverse_primer = ObjectProperty(PrimerOutput)
overlap = ObjectProperty(OverlapOutput)
class SSMInput(JsonObject):
sequences = ObjectProperty(SSMSequences, required=True)
config = ObjectProperty(SSMConfig, required=True)
mutations = ListProperty(str, required=True)
degenerate_codon = StringProperty(required=True, default="NNS")
def parse_mutations(self, goi_offset):
return [
parse_codon_mutation(mutation, goi_offset)
for mutation in self.mutations
]
class QCLMInput(JsonObject):
sequences = ObjectProperty(QCLMSequences, required=True)
config = ObjectProperty(QCLMConfig, required=True)
mutations = ListProperty(str, required=True)
def parse_mutations(self, goi_offset: int) -> List[MutationSite]:
"""
Parses the user input in the format "E32W E32L E49K" and produces multi-amino
mutations in the format of "E32WL E49K"
"""
codon_muts = [parse_codon_mutation(mutation, goi_offset) for mutation in self.mutations]
return create_multi_amino_mutations(codon_muts)
class PASInput(JsonObject):
# Sequences for the synthesized gene.
# Expressed as ATGC or amino acid sequence.
sequences = ObjectProperty(PASSequences, required=True)
# Is the gene sequence a DNA (ATGC) sequence?
is_dna_sequence = BooleanProperty(required=True)
# Input parameters
config = ObjectProperty(PASConfig, required=True)
# List of mutations by position in the gene
mutations = ListProperty(PASMutationFormattedInput, required=False)
# Are mutations given as codons?
is_mutations_as_codons = BooleanProperty(required=True)
class _QuestionDiff(JsonObject):
question = ObjectProperty(_Change)
label = ObjectProperty(_Change)
type = ObjectProperty(_Change)
value = ObjectProperty(_Change)
calculate = ObjectProperty(_Change)
relevant = ObjectProperty(_Change)
required = ObjectProperty(_Change)
comment = ObjectProperty(_Change)
setvalue = ObjectProperty(_Change)
constraint = ObjectProperty(_Change)
options = DictProperty() # {option: _Change}
load_properties = DictProperty() # {case_type: {property: _Change}}
save_properties = DictProperty() # {case_type: {property: _Change}}
class TaxJarTax(JsonObject):
order_total_amount = TaxJarFloatProperty()
shipping = TaxJarFloatProperty()
taxable_amount = TaxJarFloatProperty()
amount_to_collect = TaxJarFloatProperty()
rate = TaxJarFloatProperty()
has_nexus = BooleanProperty()
freight_taxable = BooleanProperty()
tax_source = StringProperty()
jurisdictions = ObjectProperty(TaxJarJurisdictions)
breakdown = ObjectProperty(TaxJarBreakdown)
class Status(JsonObject):
""" Status model for issue fields """
description = StringProperty()
iconUrl = StringProperty()
name = StringProperty()
id_ = StringProperty(name='id')
statusCategory = ObjectProperty(StatusCategory)
class ByTypeWithTotal(JsonObject):
by_type = ListProperty(TypedIndicator)
totals = ObjectProperty(BasicIndicator)
all_types = BooleanProperty(default=False)
@property
def enabled(self):
return self.totals.enabled or self.all_types or len(self.enabled_types) > 0
@property
def enabled_types(self):
return [type_ for type_ in self.by_type if type_.enabled]
def types_by_date_range(self):
types_list = sorted([
TypeRange(type_.type, date_range) for type_ in self.enabled_types
for date_range in type_.date_ranges
], key=lambda x: x.range_slug)
return {
range_slug: {type_.type for type_ in group}
for range_slug, group in itertools.groupby(types_list, lambda x: x.range_slug)
}
def get_or_add_for_type(self, type_):
try:
return [by_type for by_type in self.by_type if by_type.type == type_][0]
except IndexError:
indicator = TypedIndicator(enabled=True, type=type_)
self.by_type.append(
indicator
)
return indicator
class Epic(JsonObject):
""" Epic model """
id_ = IntegerProperty(name='id')
done = BooleanProperty()
key = IntegerProperty()
name = StringProperty()
color = ObjectProperty(EpicColor)
class TaxJarBreakdown(JsonObject):
taxable_amount = TaxJarFloatProperty()
tax_collectable = TaxJarFloatProperty()
combined_tax_rate = TaxJarFloatProperty()
state_taxable_amount = TaxJarFloatProperty()
state_tax_rate = TaxJarFloatProperty()
state_tax_collectable = TaxJarFloatProperty()
county_taxable_amount = TaxJarFloatProperty()
county_tax_rate = TaxJarFloatProperty()
county_tax_collectable = TaxJarFloatProperty()
city_taxable_amount = TaxJarFloatProperty()
city_tax_rate = TaxJarFloatProperty()
city_tax_collectable = TaxJarFloatProperty()
special_district_taxable_amount = TaxJarFloatProperty()
special_tax_rate = TaxJarFloatProperty()
special_district_tax_collectable = TaxJarFloatProperty()
country_taxable_amount = TaxJarFloatProperty()
country_tax_rate = TaxJarFloatProperty()
country_tax_collectable = TaxJarFloatProperty()
gst_taxable_amount = TaxJarFloatProperty()
gst_tax_rate = TaxJarFloatProperty()
gst = TaxJarFloatProperty()
pst_taxable_amount = TaxJarFloatProperty()
pst_tax_rate = TaxJarFloatProperty()
pst = TaxJarFloatProperty()
qst_taxable_amount = TaxJarFloatProperty()
qst_tax_rate = TaxJarFloatProperty()
qst = TaxJarFloatProperty()
shipping = ObjectProperty(TaxJarShipping)
line_items = ListProperty(TaxJarBreakdownLineItem)
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 _FormMetadata(JsonObject):
unique_id = StringProperty()
name = DictProperty()
short_comment = StringProperty()
action_type = StringProperty()
form_filter = StringProperty()
questions = ListProperty(_FormMetadataQuestion)
error = DictProperty()
changes = ObjectProperty(_FormDiff)
class _ModuleMetadata(JsonObject):
unique_id = StringProperty()
name = DictProperty()
short_comment = StringProperty()
module_type = StringProperty()
is_surveys = BooleanProperty()
module_filter = StringProperty()
forms = ListProperty(_FormMetadata)
changes = ObjectProperty(_ModuleDiff)
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 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 PASConfig(JsonObject):
min_oligo_size = IntegerProperty(default=40)
max_oligo_size = IntegerProperty(default=90)
opt_oligo_size = IntegerProperty(default=56)
min_overlap_tm = FloatProperty(default=50)
max_overlap_tm = FloatProperty(default=65)
opt_overlap_tm = IntegerProperty(default=56) # this optimal temperature is for NEB like temperature calculator
min_overlap_length = IntegerProperty(default=15)
max_overlap_length = IntegerProperty(default=25)
opt_overlap_length = IntegerProperty(default=21)
min_gc_content = FloatProperty(default=40)
max_gc_content = FloatProperty(default=60)
use_degeneracy_codon = BooleanProperty(default=False)
organism = StringProperty(default="e-coli")
avoided_motifs = ListProperty(str)
codon_usage_frequency_threshold = FloatProperty(default=0.1)
# The allowed range for melting temperatures of fragment overlaps, in deg C
temp_range_size = FloatProperty(default=5)
# Temperature calculator configuration
temperature_config = ObjectProperty(TemperatureConfig,
default=create_default_pas_temperature_config())
# Weights used for non_optimality calculation.
temp_weight = FloatProperty(default=1)
gc_content_weight = FloatProperty(default=1)
length_weight = FloatProperty(default=1)
hairpin_homodimer_weight = FloatProperty(default=2)
# "Safe" temperature difference between a hairpin or homodimer formation and the reaction temperature
safe_temp_difference = FloatProperty(default=10)
# Step for iteration over possible melting temperature thresholds, in deg C
temp_threshold_step = FloatProperty(default=1)
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 SSMSequences(JsonObject):
forward_primer = StringProperty(required=True)
reverse_primer = StringProperty(required=True)
gene_of_interest = StringProperty(required=True)
five_end_flanking_sequence = StringProperty(default=None)
three_end_flanking_sequence = StringProperty(default=None)
plasmid = ObjectProperty(Plasmid, default=None)
def get_full_sequence_with_offset(self) -> Tuple[str, Tuple[int, int]]:
if self.plasmid is None:
# TODO finish implementation of this option and write tests
if self.five_end_flanking_sequence is None or self.three_end_flanking_sequence is None:
raise ValueError("""If plasmid is not specified - \
five end flanking sequence and three end flanking sequence must be specified"""
)
five_end = self.get_five_end(self.five_end_flanking_sequence,
self.forward_primer)
three_end = self.get_three_end(self.three_end_flanking_sequence,
self.reverse_primer)
else:
if self.five_end_flanking_sequence is not None or \
self.three_end_flanking_sequence is not None:
raise ValueError(
"If plasmid is specified - flanking sequences must be empty"
)
five_end = self.plasmid.get_five_end(self.gene_of_interest,
self.forward_primer)
three_end = self.plasmid.get_three_end(self.gene_of_interest,
self.reverse_primer)
full_sequence = five_end + self.gene_of_interest + three_end
offset = len(five_end)
return full_sequence, (offset, offset + len(self.gene_of_interest))
class CallCenterIndicatorConfig(JsonObject):
forms_submitted = ObjectProperty(BasicIndicator)
cases_total = ObjectProperty(ByTypeWithTotal)
cases_active = ObjectProperty(ByTypeWithTotal)
cases_opened = ObjectProperty(ByTypeWithTotal)
cases_closed = ObjectProperty(ByTypeWithTotal)
legacy_forms_submitted = BooleanProperty(False)
legacy_cases_total = BooleanProperty(False)
legacy_cases_active = BooleanProperty(False)
custom_form = ListProperty(TypedIndicator)
def includes_legacy(self):
return (self.legacy_forms_submitted or self.legacy_cases_total
or self.legacy_cases_active)
@classmethod
def default_config(cls, domain_name=None, include_legacy=True):
def default_basic():
return BasicIndicator(enabled=True,
date_ranges=set(const.DATE_RANGES))
def default_typed():
return ByTypeWithTotal(totals=default_basic(), all_types=True)
config = cls(
forms_submitted=default_basic(),
cases_total=default_typed(),
cases_active=default_typed(),
cases_opened=default_typed(),
cases_closed=default_typed(),
)
config.legacy_forms_submitted = include_legacy
config.legacy_cases_total = include_legacy
config.legacy_cases_active = include_legacy
for slug in const.PER_DOMAIN_FORM_INDICATORS.get(domain_name, {}):
for range in const.DATE_RANGES:
config.custom_form.append(
TypedIndicator(type=slug, date_range=range))
return config
def set_indicator(self, parsed_indicator):
if parsed_indicator.is_legacy:
indicator = getattr(self, parsed_indicator.category)
setattr(self, 'legacy_{}'.format(parsed_indicator.category), True)
if parsed_indicator.date_range:
date_range = parsed_indicator.date_range
if isinstance(indicator, ByTypeWithTotal):
indicator.totals.date_ranges.add(date_range)
else:
indicator.date_ranges.add(date_range)
elif parsed_indicator.category == const.CUSTOM_FORM:
self.custom_form.append(
TypedIndicator(enabled=True,
date_range=parsed_indicator.date_range,
type=parsed_indicator.type))
elif parsed_indicator.category == const.FORMS_SUBMITTED:
self.forms_submitted.enabled = True
if parsed_indicator.date_range:
self.forms_submitted.date_ranges.add(
parsed_indicator.date_range)
else:
indicator = getattr(self, parsed_indicator.category)
if parsed_indicator.type:
indicator = indicator.get_or_add_for_type(
parsed_indicator.type)
else:
indicator = indicator.totals
indicator.enabled = True
if parsed_indicator.date_range:
indicator.date_ranges.add(parsed_indicator.date_range)
class Foo(JsonObject):
# default string conversions
bar = ObjectProperty(Bar)
class Foo(JsonObject):
bar = ObjectProperty(Bar)
class Meta(object):
string_conversions = ()
class PASOutput(JsonObject):
input_data = ObjectProperty(PASInput, required=True)
results = ListProperty(PASResult, required=False)
message = StringProperty()
class _FormMetadataQuestion(FormQuestionResponse):
form_id = StringProperty()
load_properties = ListProperty(LoadSaveProperty)
save_properties = ListProperty(LoadSaveProperty)
changes = ObjectProperty(_QuestionDiff)
class InvalidCredentialsResponse(JsonObject):
success = BooleanProperty(required=True)
errors = ObjectProperty(_InvalidCredentialsErrors)
def __eq__(self, other):
return self.success == other.success and self.errors == other.errors
class TelegramResponse(JsonObject):
success = BooleanProperty(name='ok')
result = ObjectProperty(SentMessage)
description = StringProperty()
parameters = ObjectProperty(ResponseParameters)
