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198 changes: 198 additions & 0 deletions
198
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 |
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| puts 'Seeded My Study Metadata Example' | ||
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| string_type = SampleAttributeType.find_or_initialize_by(title: 'String') | ||
| string_type.update(base_type: Seek::Samples::BaseType::STRING) | ||
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| text_type = SampleAttributeType.find_or_initialize_by(title: 'Text') | ||
| text_type.update(base_type: Seek::Samples::BaseType::TEXT) | ||
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| date_type = SampleAttributeType.find_or_initialize_by(title: 'Date') | ||
| date_type.update(base_type: Seek::Samples::BaseType::DATE) | ||
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| date_time_type = SampleAttributeType.find_or_initialize_by(title: 'Date time') | ||
| date_time_type.update(base_type: Seek::Samples::BaseType::DATE_TIME) | ||
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| int_type = SampleAttributeType.find_or_initialize_by(title: 'Integer') | ||
| int_type.update(base_type: Seek::Samples::BaseType::INTEGER, placeholder: '1') | ||
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| float_type = SampleAttributeType.find_or_initialize_by(title: 'Real number') | ||
| float_type.update(base_type: Seek::Samples::BaseType::FLOAT, placeholder: '0.5') | ||
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| boolean_type = SampleAttributeType.find_or_initialize_by(title: 'Boolean') | ||
| boolean_type.update(base_type: Seek::Samples::BaseType::BOOLEAN) | ||
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| cv_type = SampleAttributeType.find_or_initialize_by(title: 'Controlled Vocabulary') | ||
| cv_type.update(base_type: Seek::Samples::BaseType::CV) | ||
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| cv_type_list = SampleAttributeType.find_or_initialize_by(title: 'Controlled Vocabulary List') | ||
| cv_type_list.update(base_type: Seek::Samples::BaseType::CV_LIST) | ||
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| 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) | ||
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| 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) | ||
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| def create_sample_controlled_vocab_terms_attributes(array) | ||
| attributes = [] | ||
| array.each do |type| | ||
| attributes << { label: type } | ||
| end | ||
| attributes | ||
| end | ||
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| disable_authorization_checks do | ||
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| 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'])) | ||
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| 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) | ||
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| resource_use_rights_description = ExtendedMetadataAttribute.new(title: 'resource_use_rights_description', required: false, sample_attribute_type: text_type) | ||
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| resource_use_rights_authors_confirmation = ExtendedMetadataAttribute.new(title: 'resource_use_rights_authors_confirmation', required: true, sample_attribute_type: boolean_type) | ||
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| # 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'])) | ||
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| 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'])) | ||
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| 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])) | ||
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| unless ExtendedMetadataType.where(title:'role_name_identifiers', supported_type:'ExtendedMetadata').any? | ||
| emt = ExtendedMetadataType.new(title: 'role_name_identifiers', supported_type:'ExtendedMetadata') | ||
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| 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: string_type ) | ||
| emt.save! | ||
| end | ||
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| 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: 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") | ||
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| emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'role_name_identifiers', | ||
| sample_attribute_type: linked_extended_metadata_type_list, linked_extended_metadata_type: ExtendedMetadataType.where(title:'role_name_identifiers', supported_type:'ExtendedMetadata').first ) | ||
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| emt.save! | ||
| end | ||
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| 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",])) | ||
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| 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']) | ||
| ) | ||
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| 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']) | ||
| ) | ||
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| 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 | ||
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| emt.save! | ||
| end | ||
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| 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: 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 | ||
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| 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:linked_extended_metadata_type_list, linked_extended_metadata_type: ExtendedMetadataType.where(title:'study_conditions_emt', supported_type:'ExtendedMetadata').first ) | ||
| emt.save! | ||
| end | ||
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| unless ExtendedMetadataType.where(title:'My Study Metadata Example', supported_type:'Study').any? | ||
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| emt = ExtendedMetadataType.new(title: 'My Study Metadata Example', supported_type:'Study') | ||
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| 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: 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." | ||
| ) | ||
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| emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'description', required:true, sample_attribute_type: text_type ) | ||
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| 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) | ||
| 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 ) | ||
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| emt.save! | ||
| puts 'My study metadata is created' | ||
| end | ||
| end |
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