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add rake task to update morpheus models #2198

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add rake task to update morpheus models #2198

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19 changes: 19 additions & 0 deletions lib/tasks/seek_upgrades.rake
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Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,14 @@ namespace :seek do
task upgrade_version_tasks: %i[
environment
db:seed:007_sample_attribute_types
db:seed:003_model_formats
db:seed:004_model_recommended_environments
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Copilot AI May 14, 2025

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The seed tasks are ordered with 007_sample_attribute_types before 003 and 004, which may lead to missing lookup values if dependencies aren’t loaded in the correct order. Consider reordering these seeds numerically.

Suggested change
db:seed:007_sample_attribute_types
db:seed:003_model_formats
db:seed:004_model_recommended_environments
db:seed:003_model_formats
db:seed:004_model_recommended_environments
db:seed:007_sample_attribute_types

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update_rdf
update_observation_unit_policies
fix_xlsx_marked_as_zip
add_policies_to_existing_sample_types
fix_previous_sample_type_permissions
update_morpheus_model
]

# these are the tasks that are executes for each upgrade as standard, and rarely change
Expand Down Expand Up @@ -91,6 +94,22 @@ namespace :seek do
end
end

task(update_morpheus_model: [:environment]) do
puts "... updating morpheus model"
Model.all.each do |model|
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Using Model.all loads every record into memory at once. For large datasets, switch to Model.find_each or find_in_batches to mitigate memory bloat.

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Model.all.each do |model|
Model.find_each do |model|

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next unless model.is_morpheus_supported?
unless model.model_format
model.model_format = ModelFormat.find_by(title: 'Morpheus')
end
unless model.recommended_environment
model.recommended_environment = RecommendedModelEnvironment.find_by(title: 'Morpheus')
end
Comment on lines +101 to +106
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If no ModelFormat titled 'Morpheus' exists, find_by returns nil and the subsequent update_column will silently set a null foreign key. Consider using find_by! or adding a guard to log or abort on missing reference.

Suggested change
unless model.model_format
model.model_format = ModelFormat.find_by(title: 'Morpheus')
end
unless model.recommended_environment
model.recommended_environment = RecommendedModelEnvironment.find_by(title: 'Morpheus')
end
begin
unless model.model_format
model.model_format = ModelFormat.find_by!(title: 'Morpheus')
end
unless model.recommended_environment
model.recommended_environment = RecommendedModelEnvironment.find_by!(title: 'Morpheus')
end
rescue ActiveRecord::RecordNotFound => e
puts "Error: #{e.message}. Ensure that the required 'Morpheus' records exist in the database."
abort("Aborting task due to missing 'Morpheus' records.")
end

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model.save
model.update_column(:model_format_id, model.model_format_id)
model.update_column(:recommended_environment_id, model.recommended_environment_id)
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The code calls model.save and then individual update_column calls, resulting in multiple database writes. Consider updating both foreign keys together with update_columns or just relying on save after setting associations.

Suggested change
model.save
model.update_column(:model_format_id, model.model_format_id)
model.update_column(:recommended_environment_id, model.recommended_environment_id)
model.update_columns(model_format_id: model.model_format_id, recommended_environment_id: model.recommended_environment_id)

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end
end

task(add_policies_to_existing_sample_types: [:environment]) do
puts '... Adding policies to existing sample types'
counter = 0
Expand Down
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