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 QCLMMutationOutput(JsonObject):
# List of mutations in the format "E42L"
mutations = ListProperty(str, required=True)
result_found = BooleanProperty(required=True)
# List of primers for the given mutations, however
# this is *ALWAYS only a single primer*!!!
# We keep it as a list because frontend depends on it.
primers = ListProperty(PrimerOutput)
class _InvalidCredentialsErrors(JsonObject):
email = ListProperty(StringProperty, required=True)
password = ListProperty(StringProperty, required=True)
message = StringProperty(required=True)
def __eq__(self, other):
# email and password lists should be sorted before comparing
return sorted(self.email) == sorted(other.email) and sorted(self.password) == sorted(other.password) and \
self.message == other.message
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 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 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 PASOligoOutput(JsonObject):
sequence = StringProperty(required=True)
mix_ratio = FloatProperty(required=True)
mutations = ListProperty(required=False)
reds = ListProperty(required=False)
blues = ListProperty(required=False)
def make_reverse_complement(self):
# TODO test this
self.sequence = reverse_complement(self.sequence)
# -3 because when we do reverse complement we reverse the order of indexes
# -> what was start of codon will be end of codon in the reverse complement
# thus we are moving from the end to start of codon in reversed sequence by subtracting 3
def reindexer(ind): return abs(len(self.sequence) - ind - 3)
self.reds = sorted(list(map(reindexer, self.reds)))
self.blues = sorted(list(map(reindexer, self.blues)))
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 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 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 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 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)
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 _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 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 TaxJarCustomer(JsonObject):
customer_id = StringProperty()
exemption_type = StringProperty()
name = StringProperty()
country = StringProperty()
state = StringProperty()
zip = StringProperty()
city = StringProperty()
street = StringProperty()
exempt_regions = ListProperty(TaxJarExemptRegion)
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 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 GridiumBillingPeriod(JsonObject):
"""A gridium billing period synthesized from Urjanet data."""
# The start date of the billing period
start = DateProperty()
# The end date of the billing period
end = DateProperty()
# The statement date of the billing period
statement = DateProperty()
# The tariff associated with this period
tariff = StringProperty()
# A list of URLs pointing to the source documents for this billing period (e.g. PDF bills)
source_urls = ListProperty(StringProperty)
# The total charge for this period
total_charge = DecimalProperty()
# The peak demand for this period
peak_demand = DecimalProperty()
# The total usage for this period
total_usage = DecimalProperty()
# The list of charges for this period
line_items = ListProperty(Charge)
# The service id (SAID) associated with this billing period
service_id = StringProperty()
# The utility account id (account number) associated with this billing period
utility_account_id = StringProperty()
# The utility associated with this billing period, may also be a third party provider
utility = StringProperty()
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 TaxJarOrder(JsonObject):
user_id = IntegerProperty()
transaction_id = StringProperty()
transaction_date = StringProperty()
from_country = StringProperty()
from_zip = StringProperty()
from_state = StringProperty()
from_city = StringProperty()
from_street = StringProperty()
to_country = StringProperty()
to_zip = StringProperty()
to_state = StringProperty()
to_city = StringProperty()
to_street = StringProperty()
amount = TaxJarFloatProperty()
shipping = TaxJarFloatProperty()
sales_tax = TaxJarFloatProperty()
line_items = ListProperty(TaxJarLineItem)
class PASMutationFormattedInput(JsonObject):
mutants = ListProperty(required=True)
position = IntegerProperty(required=True)
# TODO this should be also list if we have list of mutants
frequency = FloatProperty(required=True)
class Installment(JsonObject):
quantity = ListProperty(int, required=True)
discount = IntegerProperty(exclude_if_none=True)
addition = IntegerProperty(exclude_if_none=True)
class _FormMetadataQuestion(FormQuestionResponse):
form_id = StringProperty()
load_properties = ListProperty(LoadSaveProperty)
save_properties = ListProperty(LoadSaveProperty)
changes = ObjectProperty(_QuestionDiff)
class CheckoutPreferences(JsonObject):
redirectUrls = ObjectProperty(RedirectUrls)
installments = ListProperty(Installment, exclude_if_none=True)
class PASOutput(JsonObject):
input_data = ObjectProperty(PASInput, required=True)
results = ListProperty(PASResult, required=False)
message = StringProperty()
class ByTypeHierarchyRecord(JsonObject):
val = StringProperty()
text = StringProperty()
next = ListProperty(lambda: ByTypeHierarchyRecord, exclude_if_none=True)
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 DomainConfiguration(JsonObject):
geography_hierarchy = DictProperty()
by_type_hierarchy = ListProperty(ByTypeHierarchyRecord)
