class Profile(object):
name = related.StringField(default="__root__")
host = related.StringField(required=False)
schemas = related.ChildField(Namespace, required=False)
globals = related.ChildField(Namespace, required=False)
headers = related.ChildField(Namespace, required=False)
prefixes = related.SequenceField(str, default=None)
extensions = related.SequenceField(str, default=["rigor"])
includes = related.SequenceField(str, default=None)
excludes = related.SequenceField(str, default=None)
concurrency = related.IntegerField(default=5)
retries = related.IntegerField(default=0)
sleep = related.IntegerField(default=60)
retry_failed = related.BooleanField(default=False, required=False)
def __attrs_post_init__(self):
# circumvent frozen error due to immutable
extensions = [
ext[1:] if ext.startswith(".") else ext
for ext in self.extensions or []
]
object.__setattr__(self, "extensions", extensions)
def as_dict(self):
kwargs = related.to_dict(self)
kwargs.pop("profiles", None)
kwargs.pop("file_path", None)
return kwargs
class StatusResult(object):
status = related.StringField()
duration = related.IntegerField()
line = related.IntegerField(default=4)
@classmethod
def create(cls, success, duration):
status = {True: "passed", False: "failed"}.get(success, "skipped")
return cls(status=status, duration=duration)
class ExamQuestionAnswerMeta:
"""
Represents metadata of a question answer's object
"""
text = related.StringField('')
is_correct = related.BooleanField(False, required=False)
likelihood = related.IntegerField(1, required=False)
id = related.IntegerField(0)
def __str__(self):
return f"{self.id}: [{'+' if self.is_correct else '-'}] {self.text}"
class DetectorMapping:
detector = related.ChildField(DetectorUUID)
expression = related.ChildField(DetectorMappingExpression)
user = related.ChildField(DetectorMappingUser)
fields = related.SequenceField(str, required=False)
id = related.StringField(required=False)
last_modified_time_in_millis = related.IntegerField(
required=False, key="lastModifiedTimeInMillis")
created_time_in_millis = related.IntegerField(required=False,
key="createdTimeInMillis")
enabled = related.BooleanField(required=False)
class Counts(object):
key = related.StringField()
passed = related.IntegerField(default=0)
failed = related.IntegerField(default=0)
total = related.IntegerField(default=0)
def add(self, passed):
if passed:
self.passed += 1
else:
self.failed += 1
self.total += 1
class StepResult(object):
step = related.ChildField(Step)
success = related.BooleanField(default=True)
fetch = related.ChildField(Fetch, required=False)
response = related.ChildField(object, required=False)
transform = related.ChildField(object, required=False)
extract = related.ChildField(Namespace, required=False)
status = related.IntegerField(required=False)
validations = related.SequenceField(ValidationResult, required=False)
duration = related.IntegerField(required=False)
@property
def failed_validations(self):
return [v for v in self.validations if not v.success]
class UtilConfig(object):
lang1 = related.ChildField(LanguageInfo)
lang2 = related.ChildField(LanguageInfo)
redo = related.BooleanField(default=False)
path = related.StringField(default=".")
num = related.IntegerField(default=10)
record = related.BooleanField(default=True)
class BarGraphSettings:
result_limit = related.IntegerField(50, key='resultLimit')
sort_order = related.ChildField(SortOrder,
SortOrder.DESCENDING,
key='sortOrder')
sort_on = related.StringField('', key='sortOn')
stack_bars = related.BooleanField(False, key='stackBars')
class CommandConfig(object):
target_device_list = related.SequenceField(TargetDevice)
database = related.ChildField(Database, required=False)
influxdb = related.ChildField(Influxdb, required=False)
set_measurement_interval = related.IntegerField(required=False)
dry_run = related.BooleanField(default=False, required=False)
no_scan = related.BooleanField(default=False, required=False)
class Feature(object):
uri = related.StringField()
keyword = related.StringField()
id = related.StringField()
name = related.StringField()
line = related.IntegerField()
elements = related.SequenceField(Element, default=[])
description = related.StringField(required=False, default=None)
tags = related.SequenceField(Tag, required=False, default=None)
@classmethod
def create(cls, case_result):
case = case_result.case
uuid = "%s;%s" % (urllib.parse.quote_plus(case.name), case.uuid)
return cls(
uri=case.file_path,
keyword="Feature",
id=uuid,
name=case.name,
line=1,
elements=[
Element.create(scenario_result) for scenario_result in chain(
case_result.passed, case_result.failed)
],
tags=[Tag(name=tag) for tag in case.tags],
)
class BubbleChartSettings:
linear_fit = related.BooleanField(False, key='linearFit')
result_limit = related.IntegerField(100, key='resultLimit')
show_legend = related.BooleanField(False, key='showLegend')
x_axis = related.StringField('', key='xAxis')
y_axis = related.StringField('', key='yAxis')
z_axis = related.StringField('', key='zAxis')
class ExamQuestion:
id = related.StringField(None)
text = related.StringField('')
is_multiple_choice = related.BooleanField(False)
answers = related.SequenceField(ExamQuestionAnswer, None)
points = related.IntegerField(0)
@staticmethod
def from_meta(id: str, meta: ExamQuestionMeta):
meta.validate()
multiple_choice = meta.is_multiple_choice
answers_meta = meta.prepare_answers()
answers = [ExamQuestionAnswer.from_meta(ans) for ans in answers_meta]
return ExamQuestion(id=id,
text=meta.text,
is_multiple_choice=multiple_choice,
answers=answers,
points=meta.points)
def grade(self, meta: ExamQuestionMeta) -> int:
"""
Returns the score for this ExamQuestion instance
"""
grader = get_grader(meta.grader)
if grader:
return grader(meta, self)
return 0
class Element(object):
keyword = related.StringField()
id = related.StringField()
name = related.StringField()
line = related.IntegerField()
description = related.StringField()
type = related.StringField()
steps = related.SequenceField(Step, default=[])
@classmethod
def create(cls, scenario_result):
uuid = "%s;%s" % (urllib.parse.quote_plus(
scenario_result.case.name), scenario_result.uuid)
# scenario step + steps
steps = [Step.create(None, scenario_result)] + \
[Step.create(step_result, scenario_result)
for step_result in scenario_result.step_results]
return cls(
keyword="Scenario",
name=scenario_result.scenario.__name__,
id=uuid,
line=2,
description="",
type="scenario",
steps=steps,
)
class StoreData(object):
name = related.StringField()
id = related.IntegerField()
created_on = related.DateTimeField("%m/%d/%Y %H:%M:%S")
data_from = related.DateTimeField()
data_to = related.DateTimeField()
days = related.SequenceField(DayData)
class Step(object):
keyword = related.StringField()
line = related.IntegerField()
match = related.ChildField(Match)
name = related.StringField()
doc_string = related.ChildField(DocString, required=False, default=None)
result = related.ChildField(StatusResult, required=False, default=None)
@classmethod
def create(cls, step_result, scenario_result):
if step_result is None:
output = related.to_dict(scenario_result.scenario)
output['__file__'] = scenario_result.case.file_path
return cls(keyword="",
line=3,
name="Scenario Setup",
doc_string=DocString.section("SCENARIO", output),
match=Match(),
result=StatusResult.create(True, 0))
else:
return cls(
keyword="",
line=3,
name=step_result.step.description,
doc_string=DocString.create(step_result),
match=Match.create(step_result.step),
result=StatusResult.create(step_result.success,
step_result.duration),
)
class DocString(object):
value = related.StringField()
content_type = related.StringField(required=False)
line = related.IntegerField(default=6)
@classmethod
def section(cls, title, obj, **kwargs):
size = max(20, len(title))
bar = "=" * size
# if isinstance(obj, dict) and "html" in obj:
# content = str(obj["html"])
# else:
# content = related.to_yaml(obj, **kwargs) if obj else "None"
content = related.to_yaml(obj, **kwargs) if obj else "None"
return "\n".join([bar, str.center(title, size), bar, "", content, ""])
@classmethod
def create(cls, step_result):
return cls(value="\n".join([
cls.section("REQUEST", step_result.fetch),
cls.section("RESPONSE [%s]" %
step_result.status, step_result.response),
cls.section("TRANSFORM", step_result.transform),
cls.section("EXTRACT", step_result.extract),
cls.section("FAILURES",
step_result.failed_validations,
suppress_empty_values=False)
]))
class DashboardOptions:
title = related.StringField('New Dashboard')
column_count = related.IntegerField(DEFAULT_COLUMN_COUNT,
key='columnCount')
filter_panel_settings = related.ChildField(FilterPanelSettings,
FilterPanelSettings(),
key='filterPanelSettings')
class TrainHParams(RelatedConfigMixin):
"""Training hyper-parameters
"""
# patience in keras.callbacks.EarlyStopping
early_stop_patience = related.IntegerField(5, required=False)
# maximual number of epochs to train the model for
epochs = related.IntegerField(200, required=False)
batch_size = related.IntegerField(256, required=False)
balance_peak_classes = related.BooleanField(False, required=False)
# how frequently to evaluate (in fraction of the epoch)
train_epoch_frac = related.FloatField(1.0, required=False)
valid_epoch_frac = related.FloatField(1.0, required=False)
class SearchResults:
beatmaps: List[Beatmap] = related.SequenceField(Beatmap)
result_count: int = related.IntegerField()
@classmethod
def from_json(cls, stream: any):
return related.from_json(stream, cls)
class ExamQuestionAnswer:
id = related.IntegerField(0)
text = related.StringField('')
is_selected = related.BooleanField(False, required=False)
@staticmethod
def from_meta(meta: ExamQuestionAnswerMeta):
return ExamQuestionAnswer(id=meta.id, text=meta.text)
class Port(object):
""" https://docs.docker.com/compose/compose-file/#ports """
_short_form = related.StringField(required=False, repr=False, cmp=False)
target = related.IntegerField(required=False)
published = related.IntegerField(required=False)
protocol = related.ChildField(Protocol, default=Protocol.TCP)
mode = related.ChildField(Mode, default=Mode.HOST)
def __attrs_post_init__(self):
if self._short_form:
# todo: handle protocol and mode parsing
published, target = map(int, self._short_form.split(":"))
# set methods won't work because the class is immutable.
# workaround: https://github.com/python-attrs/attrs/issues/120
object.__setattr__(self, "published", published)
object.__setattr__(self, "target", target)
class DayData(object):
date = related.DateField()
logged_on = related.TimeField("%H:%M")
open_at = related.TimeField()
closed_on = related.TimeField()
customers = related.IntegerField()
day_type = related.ChildField(DayType)
sales = related.FloatField(required=False)
class LayoutItem:
id = related.StringField()
query_id = related.StringField(key='queryId')
item_type = related.ChildField(VisualizationType, key='type')
upper_x = related.IntegerField(key='upperX')
upper_y = related.IntegerField(key='upperY')
size_id = related.StringField(key='sizeId')
custom_fields = related.SequenceField(CustomField, [], key='customFields')
# TODO(stephen, anyone): Add full model for filter modal selections and
# frontend selections filter.
filter_modal_selections = related.ChildField(dict, {}, key='filterModalSelections')
front_end_selections_filter = related.ChildField(
dict, {}, key='frontendSelectionsFilter'
)
name = related.StringField(required=False)
is_advanced_query_item = related.BooleanField(False, key='isAdvancedQueryItem')
is_locked = related.BooleanField(False, key='isLocked')
setting_id = related.StringField(required=False, key='settingId')
class HeatTileSettings:
divergent_coloration = related.BooleanField(True, key='divergentColoration')
first_y_axis_selections = related.SequenceField(str, [], key='firstYaxisSelections')
invert_coloration = related.BooleanField(False, key='invertColoration')
log_scaling = related.BooleanField(True, key='logScaling')
result_limit = related.IntegerField(100, key='resultLimit')
selected_field = related.StringField('', key='selectedField')
show_time_on_y_axis = related.BooleanField(True, key='showTimeOnYAxis')
sort_order = related.ChildField(SortOrder, SortOrder.DESCENDING, key='sortOrder')
sort_on = related.StringField('', key='sortOn')
use_ethiopian_dates = related.BooleanField(False, key='useEthiopianDates')
class BumpChartSettings:
result_limit = related.IntegerField(25, key='resultLimit')
selected_field = related.StringField('', key='selectedField')
# NOTE(stephen): This is a mapping from field ID to True. That is difficult
# to represent with `related` and we'd prefer having a set on both the
# frontend and the backend. Fix this.
selected_keys = related.ChildField(dict, {}, key='selectedKeys')
sort_order = related.ChildField(SortOrder, SortOrder.DESCENDING, key='sortOrder')
theme = related.ChildField(BumpChartTheme, BumpChartTheme.DARK)
use_ethiopian_dates = related.BooleanField(False, key='useEthiopianDates')
class TimeSeriesSettings:
bucket_mean = related.BooleanField(False, key='bucketMean')
bucket_type = related.ChildField(
TimeSeriesBucket, TimeSeriesBucket.MONTH, key='bucketType'
)
log_scaling = related.BooleanField(False, key='logScaling')
result_limit = related.IntegerField(5, key='resultLimit')
sort_order = related.ChildField(SortOrder, SortOrder.DESCENDING, key='sortOrder')
sort_on = related.StringField('', key='sortOn')
use_ethiopian_dates = related.BooleanField(False, key='useEthiopianDates')
show_data_labels = related.BooleanField(False, key='showDataLabels')
rotate_labels = related.BooleanField(True, key='rotateLabels')
class ModelTest(RelatedLoadSaveMixin):
# predictions = related.
expect = AnyField(default=None, required=False)
precision_decimal = related.IntegerField(default=7, required=False)
# Arrays should be almost equal to `precision_decimal` places
# https://docs.scipy.org/doc/numpy-1.15.1/reference/generated/numpy.testing.assert_almost_equal.html
# abs(desired-actual) < 1.5 * 10**(-precision_decimal)
def __attrs_post_init__(self):
if self.expect is not None:
if not isinstance(self.expect, str):
# it has to be the url
if not (isinstance(self.expect, dict) and "url" in self.expect):
raise ValueError("expect is not a file path, expecting a url field with entries: url and md5")
self.expect = RemoteFile.from_config(self.expect)
class BarChartSettings:
# NOTE(stephen): This is a mapping from field ID to True. That is difficult
# to represent with `related` and we'd prefer having a set on both the
# frontend and the backend. Fix this.
disabled_fields = related.ChildField(dict, {}, key='disabledFields')
result_limit = related.IntegerField(50, key='resultLimit')
sort_order = related.ChildField(SortOrder, SortOrder.DESCENDING, key='sortOrder')
sort_on = related.StringField('', key='sortOn')
stack_bars = related.BooleanField(False, key='stackBars')
y2_line_graph = related.BooleanField(False, key='y2LineGraph')
x_tick_format = related.StringField('YYYY-MM-DD', key='xTickFormat')
remove_bar_spacing = related.BooleanField(False, key='removeBarSpacing')
rotate_x_axis_labels = related.BooleanField(True, key='rotateXAxisLabels')
rotate_data_value_labels = related.BooleanField(True, key='rotateDataValueLabels')
hide_grid_lines = related.BooleanField(False, key='hideGridLines')
hide_data_value_zeros = related.BooleanField(False, key='hideDataValueZeros')
class LayoutSize:
id = related.StringField()
rows = related.IntegerField()
columns = related.IntegerField()
class ModiscoHParams(RelatedLoadSaveMixin):
"""Modisco hyper-parameters
"""
# Modisco kwargs
sliding_window_size = related.IntegerField(21, required=False)
flank_size = related.IntegerField(10, required=False) # old=5
target_seqlet_fdr = related.FloatField(0.01, required=False)
min_seqlets_per_task = related.IntegerField(
1000, required=False) # NOTE - this is not used as of modisco 0.5
# Deprecated in modisco 0.5
min_passing_windows_frac = related.FloatField(0.03, required=False)
max_passing_windows_frac = related.FloatField(0.2, required=False)
# metaclustering
min_metacluster_size = related.IntegerField(2000, required=False)
min_metacluster_size_frac = related.FloatField(0.02, required=False)
# seqlets_to_patterns.TfModiscoSeqletsToPatternsFactory
trim_to_window_size = related.IntegerField(
30, required=False) # default: 30, old=15
initial_flank_to_add = related.IntegerField(
10, required=False) # default 10, old=5
kmer_len = related.IntegerField(8, required=False) # default 8, old=5
num_gaps = related.IntegerField(3, required=False) # default 3, old=1
num_mismatches = related.IntegerField(2,
required=False) # default 2, old=0
final_min_cluster_size = related.IntegerField(60, required=False)
max_seqlets_per_metacluster = related.IntegerField(20000, required=False)
# Other modisc-related kwargs
# What's the maximum cosine distance between strands to
# still consider the examples as representative?
# TODO - update back
# max_strand_distance = related.FloatField(0.2, required=False)
# TODO - specify for which ones to run?
# Original path to the file
path = related.StringField(required=False)
def get_modisco_kwargs(self):
d = self.get_config()
d.pop('counts', None)
return d
