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clean up seed file
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@whomingbird
whomingbird committed Feb 1, 2024
1 parent 755b553 commit 279695e
Showing 1 changed file with 13 additions and 25 deletions.
38 changes: 13 additions & 25 deletions db/seeds/extended_metadata_drafts/extended_study_metadata_example.seeds.rb
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
puts 'Seeded My Study Metadata Example'


string_type = SampleAttributeType.find_or_initialize_by(title: 'String')
string_type.update(base_type: Seek::Samples::BaseType::STRING)

Expand Down Expand Up @@ -90,7 +89,7 @@ def create_sample_controlled_vocab_terms_attributes(array)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'scheme', required:true,
sample_attribute_type: cv_type, sample_controlled_vocab: role_name_identifier_scheme_cv,
description: "scheme")
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'identifier', sample_attribute_type: SampleAttributeType.where(title:'String').first)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'identifier', sample_attribute_type: string_type )
emt.save!
end

Expand All @@ -99,22 +98,20 @@ def create_sample_controlled_vocab_terms_attributes(array)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'role_name_personal_title', required:true,
sample_attribute_type: cv_type, sample_controlled_vocab: role_name_personal_title_cv,
description: "role_name_personal_title", label: "personal title")
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'first_name', sample_attribute_type: SampleAttributeType.where(title:'String').first, label: "first name", description: "First name of the role")
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'last_name', sample_attribute_type: SampleAttributeType.where(title:'String').first, label: "last name", description: "Last name of the role")
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'first_name', sample_attribute_type: string_type, label: "first name", description: "First name of the role")
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'last_name', sample_attribute_type: string_type, label: "last name", description: "Last name of the role")
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'role_type', required:true,
sample_attribute_type: cv_type, sample_controlled_vocab: role_type_cv, description: "role type", label: "Role type")


emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'role_name_identifiers',
sample_attribute_type: SampleAttributeType.where(title:'Linked Extended Metadata (multiple)').first, linked_extended_metadata_type: ExtendedMetadataType.where(title:'role_name_identifiers', supported_type:'ExtendedMetadata').first )
sample_attribute_type: linked_extended_metadata_type_list, linked_extended_metadata_type: ExtendedMetadataType.where(title:'role_name_identifiers', supported_type:'ExtendedMetadata').first )


emt.save!
end


# ************************ role related end *********************************

study_country_cv = SampleControlledVocab.where(title: 'European Study Country').first_or_create!(
sample_controlled_vocab_terms_attributes: create_sample_controlled_vocab_terms_attributes(["Albania","Austria","Belgium","Bosnia and Herzegovina","Bulgaria","Croatia","Cyprus",
"Czech Republic","Denmark","Estonia","Finland","France","Germany","Greece","Hungary","Iceland","Ireland","Italy","Latvia","Lithuania","Luxembourg","Malta","Montenegro","Netherlands",
Expand Down Expand Up @@ -148,9 +145,9 @@ def create_sample_controlled_vocab_terms_attributes(array)

unless ExtendedMetadataType.where(title:'study_conditions_emt', supported_type:'ExtendedMetadata').any?
emt = ExtendedMetadataType.new(title: 'study_conditions_emt', supported_type:'ExtendedMetadata')
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_conditions', sample_attribute_type: SampleAttributeType.where(title:'String').first,description: "study_conditions", label: "study_conditions", required:true)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_conditions_classification',sample_attribute_type: SampleAttributeType.where(title:'String').first,description: "study_conditions_classification", label: "study_conditions_classification")
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_conditions_classification_code',sample_attribute_type: SampleAttributeType.where(title:'String').first,description: "study_conditions_classification_code", label: "study_conditions_classification_code")
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_conditions', sample_attribute_type: string_type, description: "study_conditions", label: "study_conditions", required:true)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_conditions_classification',sample_attribute_type: string_type, description: "study_conditions_classification", label: "study_conditions_classification")
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_conditions_classification_code',sample_attribute_type: string_type, description: "study_conditions_classification_code", label: "study_conditions_classification_code")
emt.save!
end

Expand All @@ -159,7 +156,7 @@ def create_sample_controlled_vocab_terms_attributes(array)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_primary_design', required:true,
sample_attribute_type: cv_type, sample_controlled_vocab: study_primary_design_cv)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_conditions',
sample_attribute_type: SampleAttributeType.where(title:'Linked Extended Metadata (multiple)').first, linked_extended_metadata_type: ExtendedMetadataType.where(title:'study_conditions_emt', supported_type:'ExtendedMetadata').first )
sample_attribute_type:linked_extended_metadata_type_list, linked_extended_metadata_type: ExtendedMetadataType.where(title:'study_conditions_emt', supported_type:'ExtendedMetadata').first )
emt.save!
end

Expand All @@ -168,21 +165,19 @@ def create_sample_controlled_vocab_terms_attributes(array)
unless ExtendedMetadataType.where(title:'My Study Metadata Example', supported_type:'Study').any?

emt = ExtendedMetadataType.new(title: 'My Study Metadata Example', supported_type:'Study')
###################################################################

emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(
title: 'title', # The attribute's identifier or name .
required: true, # Indicates whether this attribute is mandatory for the associated metadata.
sample_attribute_type: SampleAttributeType.where(title: 'String').first, # Specifies the attribute type, here set to 'String'.
sample_attribute_type: string_type, # Specifies the attribute type, here set to 'String'.
description: 'the title of your study', # A brief description providing additional details about the attribute. By default, it is set to the empty string.
label: 'study title' # The label to be displayed in the user interface, conveying the purpose of the attribute. By default, it is set to the value of the 'title' attribute."
)

emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'description', required:true, sample_attribute_type: SampleAttributeType.where(title:'Text').first)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'description', required:true, sample_attribute_type: text_type )

emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_age', required:true, sample_attribute_type: SampleAttributeType.where(title:'Integer').first)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'cholesterol_level', required:true, sample_attribute_type: SampleAttributeType.where(title:'Real number').first)

###################################################################
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_age', required:true, sample_attribute_type: int_type)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'cholesterol_level', required:true, sample_attribute_type: float_type)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'resource_type_general', required:true,
sample_attribute_type: cv_type, sample_controlled_vocab: resource_type_general_cv)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_start_date', required:true, sample_attribute_type: date_type)
Expand All @@ -192,19 +187,12 @@ def create_sample_controlled_vocab_terms_attributes(array)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_country', required:true, sample_attribute_type: cv_type_list, sample_controlled_vocab: study_country_cv)
emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'resource_use_rights',
sample_attribute_type: linked_extended_metadata_type, linked_extended_metadata_type: ExtendedMetadataType.where(title:'resource_use_rights_emt', supported_type:'ExtendedMetadata').first )

emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'resource_role',
sample_attribute_type: linked_extended_metadata_type_list, linked_extended_metadata_type: ExtendedMetadataType.where(title:'role_emt', supported_type:'ExtendedMetadata').first )

emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_design',
sample_attribute_type: linked_extended_metadata_type, linked_extended_metadata_type: ExtendedMetadataType.where(title:'study_design_emt', supported_type:'ExtendedMetadata').first )

emt.save!
puts 'My study metadata is created'
end





end

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