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refactor codebase for new euclid workflow usage with tests
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@Tooyosi
Tooyosi committed Oct 28, 2024
1 parent 6ae2f7e commit 06cc71c
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Showing 27 changed files with 528 additions and 120 deletions.
66 changes: 66 additions & 0 deletions app/modules/label_extractors/base_extractor.rb
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# frozen_string_literal: true

module LabelExtractors
class BaseExtractor

class UnknownTaskKey < StandardError; end
class UnknownLabelKey < StandardError; end
attr_reader :task_lookup_key, :task_prefix_label

def initialize(task_lookup_key)
@task_lookup_key = task_lookup_key
@task_prefix_label = task_prefix
end

# extract the keys from the reduction data payload hash
# and convert the keys to the workflow question tasks
#
# e.g. workflow type (GZ) are question type 'decision tree' tasks
# looking at the 'T0' task it correlates to 3 exclusive answers:
# 0 (smooth)
# 1 (features or disk)
# 2 (star or artifact)
#
# then combined with the label prefix used to identify the correlated task name for Zoobot
def extract(data_hash)
data_hash.transform_keys do |key|
# create the lable key used for column headers in the derived training catalogues
# note the hyphen and underscore formatting, see Zoobot label schema for more details
"#{task_prefix_label}-#{data_release_suffix}_#{data_payload_label(key)}"
end
end

def self.label_prefixes
self::TASK_KEY_LABEL_PREFIXES
end

def self.data_labels
self::TASK_KEY_DATA_LABELS
end

# Base version of question_answers_schema method to be customized by subclasses
def self.question_answers_schema
raise NotImplementedError, "Subclass must define `question_answers_schema`"
end

private

def task_prefix
prefix = self.class::TASK_KEY_LABEL_PREFIXES[task_lookup_key]
raise UnknownTaskKey, "key not found: #{task_lookup_key}" unless prefix

prefix
end

def data_payload_label(key)
label = self.class::TASK_KEY_DATA_LABELS.dig(task_lookup_key, key)
raise UnknownLabelKey, "key not found: #{key}" unless label

label
end

def data_release_suffix
self.class::data_release_suffix
end
end
end
6 changes: 3 additions & 3 deletions app/modules/label_extractors/finder.rb
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Expand Up @@ -7,13 +7,13 @@ class UnknownTaskKey < StandardError; end

# hard code Galaxy Zoo for now as these will fail due to missing constant lookup
# long term we can add these back in and make the lookup dynamic
EXTRACTOR_SCHEMA_CLASS_REGEX = /\Agalaxy_zoo_(decals|cosmic_dawn)_(.+)\z/.freeze
EXTRACTOR_SCHEMA_CLASS_REGEX = /\A(galaxy_zoo)_(decals|cosmic_dawn|euclid)_(.+)\z/.freeze

def self.extractor_instance(task_schema_lookup_key)
# simulate a regex lookup failure with the || [nil, task_schema_lookup_key] as it'll raise a NameError when trying to constantize
schema_name_and_task = EXTRACTOR_SCHEMA_CLASS_REGEX.match(task_schema_lookup_key) || [nil, task_schema_lookup_key]
schema_klass = "LabelExtractors::GalaxyZoo::#{schema_name_and_task[1].camelize}".constantize
task_key = schema_name_and_task[2].upcase
schema_klass = "LabelExtractors::#{schema_name_and_task[1].camelize}::#{schema_name_and_task[2].camelize}".constantize
task_key = schema_name_and_task[3].upcase
schema_klass.new(task_key)
rescue NameError => _e
raise UnknownExtractor, "no extractor class found for '#{schema_name_and_task[1]}'"
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59 changes: 3 additions & 56 deletions app/modules/label_extractors/galaxy_zoo/cosmic_dawn.rb
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Expand Up @@ -2,9 +2,7 @@

module LabelExtractors
module GalaxyZoo
class CosmicDawn

attr_reader :task_lookup_key, :task_prefix_label
class CosmicDawn < LabelExtractors::Shared::CosmicDawnAndEuclid

# GZ decision tree task schema and lable tables
#
Expand Down Expand Up @@ -111,60 +109,9 @@ class CosmicDawn

DATA_RELEASE_SUFFIX = 'cd'

def self.label_prefixes
TASK_KEY_LABEL_PREFIXES
end

def self.data_labels
TASK_KEY_DATA_LABELS
end

# provide a flat task question and answers list for the decals mission catalogues
def self.question_answers_schema
label_prefixes.map do |task_key, question_prefix|
data_labels[task_key].values.map do |answer_suffix|
"#{question_prefix}-#{DATA_RELEASE_SUFFIX}_#{answer_suffix}"
end
end.flatten
end

def initialize(task_lookup_key)
@task_lookup_key = task_lookup_key
@task_prefix_label = task_prefix
end

# extract the keys from the reduction data payload hash
# and convert the keys to the workflow question tasks
#
# e.g. workflow type (GZ) are question type 'decision tree' tasks
# looking at the 'T0' task it correlates to 3 exclusive answers:
# 0 (smooth)
# 1 (features or disk)
# 2 (problem)
#
# then combined with the label prefix used to identify the correlated task name for Zoobot
def extract(data_hash)
data_hash.transform_keys do |key|
# create the lable key used for column headers in the derived training catalogues
# note the hyphen and underscore formatting, see Zoobot label schema for more details
"#{task_prefix_label}-#{DATA_RELEASE_SUFFIX}_#{data_payload_label(key)}"
end
end

private

def task_prefix
prefix = TASK_KEY_LABEL_PREFIXES[task_lookup_key]
raise UnknownTaskKey, "key not found: #{task_lookup_key}" unless prefix

prefix
end

def data_payload_label(key)
label = TASK_KEY_DATA_LABELS.dig(task_lookup_key, key)
raise UnknownLabelKey, "key not found: #{key}" unless label

label
def self.data_release_suffix
DATA_RELEASE_SUFFIX
end
end
end
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43 changes: 4 additions & 39 deletions app/modules/label_extractors/galaxy_zoo/decals.rb
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@@ -1,8 +1,9 @@
# frozen_string_literal: true
require_relative '../base_extractor'

module LabelExtractors
module GalaxyZoo
class Decals
class Decals < BaseExtractor

attr_reader :task_lookup_key, :task_prefix_label, :data_release_suffix

Expand Down Expand Up @@ -95,13 +96,6 @@ class Decals
# longer term we may include gz2 , e.g. -dr12 (gz 1 & 2)
CATALOG_DATA_RELEASE_SUFFIXES = %w[dr5 dr8]

def self.label_prefixes
TASK_KEY_LABEL_PREFIXES
end

def self.data_labels
TASK_KEY_DATA_LABELS
end

# provide a flat task question and answers list for the decals mission catalogues
def self.question_answers_schema
Expand All @@ -120,38 +114,9 @@ def initialize(task_lookup_key, data_release_suffix = DEFAULT_DATA_RELEASE_SUFFI
@data_release_suffix = data_release_suffix
end

# extract the keys from the reduction data payload hash
# and convert the keys to the workflow question tasks
#
# e.g. workflow type (GZ) are question type 'decision tree' tasks
# looking at the 'T0' task it correlates to 3 exclusive answers:
# 0 (smooth)
# 1 (features or disk)
# 2 (star or artifact)
#
# then combined with the label prefix used to identify the correlated task name for Zoobot
def extract(data_hash)
data_hash.transform_keys do |key|
# create the lable key used for column headers in the derived training catalogues
# note the hyphen and underscore formatting, see Zoobot lable schema for more details
"#{task_prefix_label}-#{data_release_suffix}_#{data_payload_label(key)}"
end
end

private

def task_prefix
prefix = TASK_KEY_LABEL_PREFIXES[task_lookup_key]
raise UnknownTaskKey, "key not found: #{task_lookup_key}" unless prefix

prefix
end

def data_payload_label(key)
label = TASK_KEY_DATA_LABELS.dig(task_lookup_key, key)
raise UnknownLabelKey, "key not found: #{key}" unless label

label
def self.data_release_suffix
data_release_suffix
end
end
end
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114 changes: 114 additions & 0 deletions app/modules/label_extractors/galaxy_zoo/euclid.rb
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# frozen_string_literal: true

module LabelExtractors
module GalaxyZoo
class Euclid < LabelExtractors::Shared::CosmicDawnAndEuclid

attr_reader :task_lookup_key, :task_prefix_label

# Derived to conform to the existing catalogue schema for Zoobot euclid
# https://github.com/mwalmsley/galaxy-datasets/blob/eed30d3e37b5559d0427c339e8dc1d2a9dc2d004/galaxy_datasets/shared/label_metadata.py#L462
TASK_KEY_LABEL_PREFIXES = {
'T0' => 'smooth-or-featured',
'T1' => 'how-rounded',
'T2' => 'disk-edge-on',
'T3' => 'edge-on-bulge',
'T4' => 'bar',
'T5' => 'has-spiral-arms',
'T6' => 'spiral-winding',
'T7' => 'spiral-arm-count',
'T8' => 'bulge-size',
'T11' => 'merging', # T10 is not used for training and no T9 in prod :shrug:
'T12' => 'lensing',
'T13' => 'clumps',
'T14' => 'problem',
'T15' => 'artifact'
}.freeze
TASK_KEY_DATA_LABELS = {
'T0' => {
'0' => 'smooth',
'1' => 'featured-or-disk',
'2' => 'problem'
},
'T1' => {
'0' => 'round',
'1' => 'in-between',
'2' => 'cigar-shaped'
},
'T2' => {
'0' => 'yes',
'1' => 'no'
},
'T3' => {
'0' => 'rounded',
'1' => 'boxy',
'2' => 'none'
},
'T4' => {
'0' => 'no',
'1' => 'weak',
'2' => 'strong'
},
'T5' => {
'0' => 'yes',
'1' => 'no'
},
'T6' => {
'0' => 'tight',
'1' => 'medium',
'2' => 'loose'
},
'T7' => {
'0' => '1',
'1' => '2',
'2' => '3',
'3' => '4',
'4' => 'more-than-4',
'5' => 'cant-tell'
},
'T8' => {
'0' => 'none',
'1' => 'small',
'2' => 'moderate',
'3' => 'large',
'4' => 'dominant'
},
'T11' => {
'0' => 'merger',
'1' => 'major-disturbance',
'2' => 'minor-disturbance',
'3' => 'none'
},
'T12' => {
'0' => 'yes',
'1' => 'no'
},
'T13' => {
'0' => 'yes',
'1' => 'no'
},
'T14' => {
'0' => 'star',
'1' => 'artifact',
'2' => 'zoom'
},
'T15' => {
'0' => 'saturation',
'1' => 'diffraction',
'2' => 'satellite',
'3' => 'ray',
'4' => 'scattered',
'5' => 'other',
'6' => 'ghost'
}
}.freeze

DATA_RELEASE_SUFFIX = 'euclid'

private
def self.data_release_suffix
DATA_RELEASE_SUFFIX
end
end
end
end
23 changes: 23 additions & 0 deletions app/modules/label_extractors/shared/cosmic_dawn_and_euclid.rb
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@@ -0,0 +1,23 @@
# frozen_string_literal: true
require_relative '../base_extractor'

module LabelExtractors
module Shared
class CosmicDawnAndEuclid < BaseExtractor

def self.data_release_suffix
raise NotImplementedError, "Subclass must define `data_release_suffix`"
end

# provide a flat task question and answers list for the decals mission catalogues
def self.question_answers_schema
label_prefixes.map do |task_key, question_prefix|
data_labels[task_key].values.map do |answer_suffix|
"#{question_prefix}-#{data_release_suffix}_#{answer_suffix}"
end
end.flatten
end

end
end
end
5 changes: 3 additions & 2 deletions app/modules/zoobot.rb
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@@ -1,9 +1,10 @@
# frozen_string_literal: true

module Zoobot
def self.gz_label_column_headers
def self.label_column_headers(module_name='GalaxyZoo', extractor_name='CosmicDawn')
schema_klass = "LabelExtractors::#{module_name}::#{extractor_name}".constantize
# as data sets change, switch to different mission label extractors, e.g. Decals is older
%w[id_str file_loc] | LabelExtractors::GalaxyZoo::CosmicDawn.question_answers_schema
%w[id_str file_loc] | schema_klass.question_answers_schema
end

module Storage
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3 changes: 2 additions & 1 deletion app/services/batch/training/create_job.rb
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Expand Up @@ -14,7 +14,8 @@ def initialize(training_job, bajor_client = Bajor::Client.new)

def run
begin
bajor_job_url = bajor_client.create_training_job(training_job.manifest_path)
context = Context.find_by(workflow_id: training_job.workflow_id)
bajor_job_url = bajor_client.create_training_job(training_job.manifest_path, context.extractor_name)
training_job.update(state: :submitted, service_job_url: bajor_job_url, message: '')
rescue Bajor::Client::Error => e
# mark the jobs as failed and record the client error message
Expand Down
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