class MapSettings:
base_layer = related.ChildField(BaseMapLayer, BaseMapLayer.STREETS, key='baseLayer')
current_display = related.StringField('dots', key='currentDisplay')
map_center = related.ChildField(Coordinates, [0.0, 0.0], key='mapCenter')
overlay_layers = related.SequenceField(
str, DEFAULT_OVERLAY_LAYERS, key='overlayLayers'
)
selected_field = related.StringField('', key='selectedField')
selected_geo_tiles = related.StringField('', key='selectedGeoTiles')
zoom_level = related.FloatField(1.0, key='zoomLevel')
show_administrative_boundaries = related.BooleanField(
True, key='showAdminBoundaries'
)
show_labels = related.BooleanField(False, key='showLabels')
fill_opacity = related.FloatField(0.8, key='fillOpacity')
tooltip_font_color = related.StringField(FONT_COLOR_DEFAULT, key='tooltipFontColor')
tooltip_font_family = related.StringField(
FONT_FAMILY_DEFAULT, key='tooltipFontFamily'
)
tooltip_font_size = related.StringField(FONT_12, key='tooltipFontSize')
tooltip_bold = related.BooleanField(False, key='tooltipBold')
# HACK(stephen, moriah): This setting is really poorly designed. It encodes
# a color value + alpha as a dict instead of rgba or hex + alpha which can
# be represented as a string. FIX THIS OR REMOVE IT.
tooltip_background_color = related.ChildField(
dict, DEFAULT_MAP_TOOLTIP_BACKGROUND, key='tooltipBackgroundColor'
)
class ConstantThresholdThresholds:
weak_upper_threshold = related.FloatField(key="upperWeak", required=False)
strong_upper_threshold = related.FloatField(key="upperStrong",
required=False)
weak_lower_threshold = related.FloatField(key="lowerWeak", required=False)
strong_lower_threshold = related.FloatField(key="lowerStrong",
required=False)
class EvalHParams(RelatedConfigMixin):
"""Training hyper-parameters
"""
# Hyper-parameters to compute the auPR
pos_min_threshold = related.FloatField(0.05, required=False)
neg_max_threshold = related.FloatField(0.01, required=False)
# each position in the positive class should be
# supported by at least `required_min_pos_counts` of reads
required_min_pos_counts = related.FloatField(2.5, required=False)
# For which pools to compute the evaluation metrics
binsizes = related.SequenceField(int, [1, 10], required=False)
class Alarm:
ou_id = related.IntegerField(key="ouId", required=False)
ou_name = related.StringField(key="ouName", required=False)
bsis_name = related.StringField(key="bsisName", required=False)
dispatched_bsis_name = related.StringField(key="dispatchedBsisName",
required=False)
kind = related.ChildField(AlarmKind, required=False)
sub_kind = related.StringField(key="subKind", required=False)
description = related.StringField(required=False)
acquired = related.DateTimeField(key="aquired", required=False)
expiration = related.DateTimeField(required=False)
latitude = related.FloatField(required=False)
longitude = related.FloatField(required=False)
location_accuracy = related.ChildField(LocationAccuracy,
key="locAccuracy",
required=False)
distance_to_fire_station = related.FloatField(key="distanceToFireStation",
required=False)
adm_territory = related.StringField(key="admTeryt", required=False)
locality = related.StringField(required=False)
street = related.StringField(required=False)
address_point = related.StringField(key="addrPoint", required=False)
apartment = related.StringField(required=False)
notified = related.IntegerField(required=False)
confirmed = related.IntegerField(required=False)
declined = related.IntegerField(required=False)
commanders = related.IntegerField(required=False)
drivers = related.IntegerField(required=False)
drivers_cat_c = related.IntegerField(key="driversCatC", required=False)
firstAid = related.IntegerField(required=False)
status = related.ChildField(AlarmNotificationStatus, required=False)
modified = related.DateTimeField(required=False)
rec_ver_no = related.IntegerField(key="recVerNo", required=False)
deleted = related.BooleanField(required=False)
swd_id = related.IntegerField(key="swdId", required=False)
id = related.IntegerField(required=False)
@property
def address(self):
result = ""
if self.locality:
result += self.locality.strip()
if self.street:
result += ", {}".format(self.street.strip())
if self.address_point:
result += " {}".format(self.address_point.strip())
if self.apartment:
result += "/{}".format(self.apartment.strip())
return result
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
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 TableSettings:
inverted_fields = related.SequenceField(str, [], key='invertedFields')
table_format = related.ChildField(TableFormat, TableFormat.TABLE, key='tableFormat')
enable_pagination = related.BooleanField(True, key='enablePagination')
row_height = related.FloatField(30, key='rowHeight')
add_total_row = related.BooleanField(False, key='addTotalRow')
header_font_family = related.StringField(
FONT_FAMILY_DEFAULT, key='headerFontFamily'
)
header_color = related.StringField(FONT_COLOR_DEFAULT, key='headerColor')
header_font_size = related.StringField(FONT_12, key='headerFontSize')
header_background = related.StringField('#fff', key='headerBackground')
header_border_color = related.StringField('#d9d9d9', key='headerBorderColor')
row_font_family = related.StringField(FONT_FAMILY_DEFAULT, key='rowFontFamily')
row_color = related.StringField(FONT_COLOR_DEFAULT, key='rowColor')
row_font_size = related.StringField(FONT_12, key='rowFontSize')
row_background = related.StringField('#fff', key='rowBackground')
row_alternate_background = related.StringField(
'#f0f0f0', key='rowAlternateBackground'
)
row_border_color = related.StringField('#d9d9d9', key='rowBorderColor')
footer_font_family = related.StringField(
FONT_FAMILY_DEFAULT, key='footerFontFamily'
)
footer_color = related.StringField(FONT_COLOR_DEFAULT, key='footerColor')
footer_font_size = related.StringField(FONT_12, key='footerFontSize')
footer_background = related.StringField('#fff', key='footerBackground')
footer_border_color = related.StringField('#fff', key='footerBorderColor')
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 Step(object):
description = related.StringField()
request = related.ChildField(Requestor)
extract = related.ChildField(Namespace, default=Namespace())
iterate = related.ChildField(Iterator, default=Iterator())
validate = related.SequenceField(Validator, required=False)
condition = related.BooleanField(required=False, default=None)
transform = related.StringField(required=False, default=None)
name = related.StringField(required=False, default=None)
sleep = related.FloatField(required=False, default=0.01)
class AnimatedMapSettings:
base_layer = related.ChildField(BaseMapLayer, BaseMapLayer.STREETS, key='baseLayer')
current_display = related.StringField('dots', key='currentDisplay')
map_center = related.ChildField(Coordinates, [0.0, 0.0], key='mapCenter')
overlay_layers = related.SequenceField(
str, DEFAULT_OVERLAY_LAYERS, key='overlayLayers'
)
selected_field = related.StringField('', key='selectedField')
selected_geo_tiles = related.StringField('', key='selectedGeoTiles')
zoom_level = related.FloatField(1.0, key='zoomLevel')
class Company(object):
name = related.StringField()
uuid = related.UUIDField()
email = related.RegexField("[^@]+@[^@]+", required=False)
is_active = related.BooleanField(required=False)
url = related.URLField(required=False)
meta = related.ChildField(dict, required=False)
nicknames = related.SequenceField(str, required=False)
temperature = related.FloatField(required=False)
guess = related.SetField(int, required=False)
established = related.DateField('%m/%d/%Y', required=False)
closed = related.DateField(required=False) # default formatter (%Y-%m-%d)
class ConstantThresholdHyperparameters:
strategy = related.ChildField(ConstantThresholdStrategy)
lower_weak_multiplier = related.FloatField(default=4.0, required=False)
lower_strong_multiplier = related.FloatField(default=5.0, required=False)
upper_weak_multiplier = related.FloatField(default=4.0, required=False)
upper_strong_multiplier = related.FloatField(default=5.0, required=False)
hampel_window_size = related.FloatField(default=10, required=False)
hampel_n_signma = related.FloatField(default=3, required=False)
class EnvDbEntry(RelatedConfigMixin):
"""
Compatible Models explicitly and the possible (intermediate) groups (derive from kipoi/models/shared/envs/models.yaml (can be model group too) or models in the group if it was a group: sub_models = list_subcomponents(parsed_model, parsed_source, "model") - TODO - check kipoi.cli.env.merge_deps)
Store all the parsed args
Store the conda version
Store the kipoi version
Timestamp
successful
cli_path
"""
conda_version = related.StringField(required=True)
kipoi_version = related.StringField(required=True)
timestamp = related.FloatField(required=True)
compatible_models = related.SequenceField(str, required=True)
create_args = related.ChildField(EnvCreateArgs, required=True)
successful = related.BooleanField(default=False, required=False)
cli_path = related.StringField(default=None, required=False)
class Step(object):
description = related.StringField()
request = related.ChildField(Requestor)
extract = related.ChildField(Namespace, default=Namespace())
iterate = related.ChildField(Iterator, default=Iterator())
validate = related.SequenceField(Validator, required=False)
condition = related.BooleanField(required=False, default=None)
transform = related.StringField(required=False, default=None)
name = related.StringField(required=False, default=None)
sleep = related.FloatField(required=False, default=0.01)
retryable = related.BooleanField(required=False, default=False)
def is_retryable(self):
return self.is_get() or self.retryable
def is_get(self):
return self.request and self.request.method == Method.GET
class YAxisSettings(XAxisSettings):
range_from = related.FloatField(required=False, key='rangeFrom')
range_to = related.FloatField(required=False, key='rangeTo')
class MyChild(object):
my_int = related.IntegerField(key="int")
my_float = related.FloatField(key="float")
my_uuid = related.UUIDField(key="uuid")
