seed examples for creating extended metadata type for SEEK resources

db/seeds/extended_metadata_drafts/extended_study_metadata_example.seeds.rb

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+puts 'Seeded My Study Metadata Example'
+
+
+string_type = SampleAttributeType.find_or_initialize_by(title: 'String')
+string_type.update(base_type: Seek::Samples::BaseType::STRING)
+
+text_type = SampleAttributeType.find_or_initialize_by(title: 'Text')
+text_type.update(base_type: Seek::Samples::BaseType::TEXT)
+
+date_type = SampleAttributeType.find_or_initialize_by(title: 'Date')
+date_type.update(base_type: Seek::Samples::BaseType::DATE)
+
+
+date_time_type = SampleAttributeType.find_or_initialize_by(title: 'Date time')
+date_time_type.update(base_type: Seek::Samples::BaseType::DATE_TIME)
+
+int_type = SampleAttributeType.find_or_initialize_by(title: 'Integer')
+int_type.update(base_type: Seek::Samples::BaseType::INTEGER, placeholder: '1')
+
+float_type = SampleAttributeType.find_or_initialize_by(title: 'Real number')
+float_type.update(base_type: Seek::Samples::BaseType::FLOAT, placeholder: '0.5')
+
+boolean_type = SampleAttributeType.find_or_initialize_by(title: 'Boolean')
+boolean_type.update(base_type: Seek::Samples::BaseType::BOOLEAN)
+
+cv_type = SampleAttributeType.find_or_initialize_by(title: 'Controlled Vocabulary')
+cv_type.update(base_type: Seek::Samples::BaseType::CV)
+
+cv_type_list = SampleAttributeType.find_or_initialize_by(title: 'Controlled Vocabulary List')
+cv_type_list.update(base_type: Seek::Samples::BaseType::CV_LIST)
+
+linked_extended_metadata_type = SampleAttributeType.find_or_initialize_by(title: 'Linked Extended Metadata')
+linked_extended_metadata_type.update(base_type: Seek::Samples::BaseType::LINKED_EXTENDED_METADATA)
+
+linked_extended_metadata_type_list = SampleAttributeType.find_or_initialize_by(title: 'Linked Extended Metadata (multiple)')
+linked_extended_metadata_type_list.update(base_type: Seek::Samples::BaseType::LINKED_EXTENDED_METADATA_MULTI)
+
+
+def create_sample_controlled_vocab_terms_attributes(array)
+  attributes = []
+  array.each do |type|
+    attributes << { label: type }
+  end
+  attributes
+end
+
+
+disable_authorization_checks do
+
+
+  resource_use_rights_label_cv = SampleControlledVocab.where(title: 'Study Use Rights Label').first_or_create!(
+    sample_controlled_vocab_terms_attributes: create_sample_controlled_vocab_terms_attributes(['CC0 1.0 (Creative Commons Zero v1.0 Universal)',
+                                                                                               'CC BY 4.0 (Creative Commons Attribution 4.0 International)',
+                                                                                               'CC BY-NC 4.0 (Creative Commons Attribution Non Commercial 4.0 International)',
+                                                                                               'CC BY-SA 4.0 (Creative Commons Attribution Share Alike 4.0 International)',
+                                                                                               'CC BY-NC-SA 4.0 (Creative Commons Attribution Non Commercial Share Alike 4.0 International)',
+                                                                                               'All rights reserved',
+                                                                                               'Other',
+                                                                                               'Not applicable']))
+
+  resource_use_rights_label = ExtendedMetadataAttribute.new(title: 'resource_use_rights_label', required: true, sample_attribute_type: cv_type, sample_controlled_vocab: resource_use_rights_label_cv)
+
+  resource_use_rights_description = ExtendedMetadataAttribute.new(title: 'resource_use_rights_description', required: false, sample_attribute_type: text_type)
+
+  resource_use_rights_authors_confirmation = ExtendedMetadataAttribute.new(title: 'resource_use_rights_authors_confirmation', required: true, sample_attribute_type: boolean_type)
+
+
+
+
+  # Define role
+  role_type_cv = SampleControlledVocab.where(title: 'Role Type').first_or_create!(
+    sample_controlled_vocab_terms_attributes: create_sample_controlled_vocab_terms_attributes(['Contact', 'Principal investigator', 'Creator/Author', 'Funder (public)', 'Funder (private)',
+                                                                                               'Sponsor (primary)', 'Sponsor (secondary)', 'Sponsor-Investigator', 'Data collector', 'Data curator',
+                                                                                               'Data manager', 'Distributor', 'Editor', 'Hosting institution', 'Producer', 'Project leader', 'Project manager',
+                                                                                               'Project member', 'Publisher', 'Registration agency', 'Registration authority', 'Related person', 'Researcher',
+                                                                                               'Research group', 'Rights holder', 'Supervisor', 'Work package leader', 'Other']))
+
+
+  role_name_personal_title_cv = SampleControlledVocab.where(title: 'Role Name Personal Title').first_or_create!(
+    sample_controlled_vocab_terms_attributes: create_sample_controlled_vocab_terms_attributes(['Mr.', 'Ms.', 'Dr.', 'Prof. Dr.', 'Other']))
+
+  role_name_identifier_scheme_cv = SampleControlledVocab.where(title: 'Role Name Identifier Scheme').first_or_create!(
+    sample_controlled_vocab_terms_attributes: create_sample_controlled_vocab_terms_attributes(%w[ORCID ROR GRID ISNI]))
+
+
+
+  unless ExtendedMetadataType.where(title:'role_name_identifiers', supported_type:'ExtendedMetadata').any?
+    emt = ExtendedMetadataType.new(title: 'role_name_identifiers', supported_type:'ExtendedMetadata')
+
+    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.save!
+  end
+
+  unless ExtendedMetadataType.where(title:'role_emt', supported_type:'ExtendedMetadata').any?
+    emt = ExtendedMetadataType.new(title: 'role_emt', supported_type:'ExtendedMetadata')
+    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: '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 )
+
+
+    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",
+                                                                                               "North Macedonia","Norway","Poland","Portugal","Romania","Serbia","Slovakia","Slovenia","Spain","Sweden","Switzerland","United Kingdom",]))
+
+
+
+  resource_type_general_cv = SampleControlledVocab.where(title: 'resource_type_general').first_or_create!(
+    sample_controlled_vocab_terms_attributes: create_sample_controlled_vocab_terms_attributes(['Audiovisual', 'Book', 'Book chapter', 'Collection', 'Computational notebook',
+                                                                                               'Conference paper', 'Conference proceeding', 'Data paper', 'Dataset',
+                                                                                               'Dissertation', 'Event', 'Image', 'Interactive resource', 'Journal', 'Journal article',
+                                                                                               'Model', 'Output management plan', 'Peer review', 'Physical object', 'Preprint',
+                                                                                               'Report', 'Service', 'Software', 'Sound', 'Standard', 'Text', 'Workflow', 'Other'])
+  )
+
+  study_primary_design_cv = SampleControlledVocab.where(title: 'study_primary_design').first_or_create!(
+    sample_controlled_vocab_terms_attributes: create_sample_controlled_vocab_terms_attributes(['Interventional','Non-Interventional'])
+  )
+
+
+
+  unless ExtendedMetadataType.where(title:'resource_use_rights_emt', supported_type:'ExtendedMetadata').any?
+    emt = ExtendedMetadataType.new(title: 'resource_use_rights_emt', supported_type:'ExtendedMetadata')
+    emt.extended_metadata_attributes << resource_use_rights_label
+    emt.extended_metadata_attributes << resource_use_rights_description
+    emt.extended_metadata_attributes << resource_use_rights_authors_confirmation
+
+    emt.save!
+  end
+
+
+  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.save!
+  end
+
+  unless ExtendedMetadataType.where(title:'study_design_emt', supported_type:'ExtendedMetadata').any?
+    emt = ExtendedMetadataType.new(title: 'study_design_emt', supported_type:'ExtendedMetadata')
+    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 )
+    emt.save!
+  end
+
+
+
+  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'.
+      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: '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: '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)
+    emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_start_time', required:true, sample_attribute_type: date_time_type)
+    emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_end_date', sample_attribute_type: date_type)
+    emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_end_time', sample_attribute_type: date_time_type)
+    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

db/seeds/extended_metadata_drafts/family_example.seeds.rb

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+cv_type = SampleAttributeType.find_or_initialize_by(title: 'Controlled Vocabulary')
+cv_type.update(base_type: Seek::Samples::BaseType::CV)
+
+cv_type_list = SampleAttributeType.find_or_initialize_by(title: 'Controlled Vocabulary List')
+cv_type_list.update(base_type: Seek::Samples::BaseType::CV_LIST)
+
+
+def create_sample_controlled_vocab_terms_attributes(array)
+  attributes = []
+  array.each do |type|
+    attributes << { label: type }
+  end
+  attributes
+end
+
+
+disable_authorization_checks do
+
+  # Define the inner extended metadata type 'person' with attributes 'first_name' and 'last_name'.
+  # The 'supported_type' is set to 'ExtendedMetadata' to denote it as the inner extended metadata type.
+  #
+  unless ExtendedMetadataType.where(title:'person', supported_type:'ExtendedMetadata').any?
+    emt = ExtendedMetadataType.new(title: 'person', supported_type:'ExtendedMetadata')
+    emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'first_name', sample_attribute_type: SampleAttributeType.where(title:'String').first)
+    emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'last_name', sample_attribute_type: SampleAttributeType.where(title:'String').first)
+    emt.save!
+  end
+
+  # Define the extended metadata type 'family', which contains the nested extended metadata attributes
+  unless ExtendedMetadataType.where(title:'family', supported_type:'Investigation').any?
+    emt = ExtendedMetadataType.new(title: 'family', supported_type:'Investigation')
+
+    emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'dad',
+                                                                  sample_attribute_type: SampleAttributeType.where(title:'Linked Extended Metadata').first, linked_extended_metadata_type: ExtendedMetadataType.where(title:'person', supported_type:'ExtendedMetadata').first )
+
+    emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'mom',
+                                                                  sample_attribute_type: SampleAttributeType.where(title:'Linked Extended Metadata').first, linked_extended_metadata_type: ExtendedMetadataType.where(title:'person', supported_type:'ExtendedMetadata').first )
+
+    emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'child',
+                                                                  sample_attribute_type: SampleAttributeType.where(title:'Linked Extended Metadata (multiple)').first, linked_extended_metadata_type: ExtendedMetadataType.where(title:'person', supported_type:'ExtendedMetadata').first )
+
+
+    emt.save!
+    puts 'Family metadata'
+  end
+
+end
+