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Y24-372 - Correct country of origin values for submissions #4433

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Y24-372 - Correct country of origin values for submissions #4433

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6 changes: 5 additions & 1 deletion app/models/accessionable/base.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,8 @@ class FieldSerializer
MISSING_DATA_AGGREEMENT_PRE2023 = 'missing: data agreement established pre-2023'
MISSING_ENDANGERED_SPECIES = 'missing: endangered species'
MISSING_HUMAN_IDENTIFIABLE = 'missing: human-identifiable'
MISSING_CONTROL_SAMPLE = 'missing: control sample'
MISSING_SAMPLE_GROUP = 'missing: sample group'

OTHER_DEFAULT_SETTINGS = [
NOT_COLLECTED,
Expand All @@ -107,7 +109,9 @@ class FieldSerializer
MISING_THIRD_PARTY_DATA,
MISSING_DATA_AGGREEMENT_PRE2023,
MISSING_ENDANGERED_SPECIES,
MISSING_HUMAN_IDENTIFIABLE
MISSING_HUMAN_IDENTIFIABLE,
MISSING_CONTROL_SAMPLE,
MISSING_SAMPLE_GROUP
].freeze

def value_for(value)
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18 changes: 18 additions & 0 deletions db/migrate/20241018131928_disable_invalid_insdc_countries.rb
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@@ -0,0 +1,18 @@
# frozen_string_literal: true

# This migration corrects the country list for missing samples/sample groups
# following EBI's checklist https://www.ebi.ac.uk/ena/browser/view/ERC000011
class DisableInvalidInsdcCountries < ActiveRecord::Migration[6.1]
def change
# Disable existing invalid countries
# We don't want to delete them yet in case they are used in existing records and existing manifests.
['not applicable: control sample', 'not applicable: sample group'].each do |name|
Insdc::Country.find_by(name:)&.invalid!
end

# Add missing countries
['missing: control sample', 'missing: sample group'].each do |name|
Insdc::Country.find_or_create_by(name: name, sort_priority: -2, validation_state: 0)
end
end
end
2 changes: 1 addition & 1 deletion db/schema.rb
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Expand Up @@ -10,7 +10,7 @@
#
# It's strongly recommended that you check this file into your version control system.

ActiveRecord::Schema.define(version: 2024_09_17_133813) do
ActiveRecord::Schema.define(version: 2024_10_18_131928) do

create_table "aliquot_indices", id: :integer, charset: "utf8mb4", collation: "utf8mb4_unicode_ci", options: "ENGINE=InnoDB ROW_FORMAT=DYNAMIC", force: :cascade do |t|
t.integer "aliquot_id", null: false
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6 changes: 5 additions & 1 deletion lib/accession/accession/tag.rb
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Expand Up @@ -72,6 +72,8 @@ module HelperTagValue
MISSING_DATA_AGGREEMENT_PRE2023 = 'missing: data agreement established pre-2023'
MISSING_ENDANGERED_SPECIES = 'missing: endangered species'
MISSING_HUMAN_IDENTIFIABLE = 'missing: human-identifiable'
MISSING_CONTROL_SAMPLE = 'missing: control sample'
MISSING_SAMPLE_GROUP = 'missing: sample group'

OTHER_DEFAULT_SETTINGS = [
NOT_COLLECTED,
Expand All @@ -84,7 +86,9 @@ module HelperTagValue
MISING_THIRD_PARTY_DATA,
MISSING_DATA_AGGREEMENT_PRE2023,
MISSING_ENDANGERED_SPECIES,
MISSING_HUMAN_IDENTIFIABLE
MISSING_HUMAN_IDENTIFIABLE,
MISSING_CONTROL_SAMPLE,
MISSING_SAMPLE_GROUP
].freeze

def incorrect_format_value
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