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…_isa Seed minimal isa
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| # Source - ISA minimal starter template | ||
| source_template = Template.find_or_initialize_by(title: 'Source - ISA minimal starter template', level: 'study source', | ||
| group: 'ISA minimal starter') | ||
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| source_temp_attributes = [] | ||
| source_temp_attributes << TemplateAttribute.new(title: 'Source Name', | ||
| description: 'Sources are considered as the starting biological material used in a study.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: true, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'source')) | ||
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| source_temp_attributes << TemplateAttribute.new(title: 'Source Characteristic 1', | ||
| description: 'A characteristic of the source.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: false, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'source_characteristic')) | ||
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| disable_authorization_checks do | ||
| source_template.update(group_order: 1, | ||
| temporary_name: '1_Source - ISA minimal starter template', | ||
| version: '1.0.0', | ||
| isa_config: 'isaconfig-default_v2015-07-02/studySample.xml', | ||
| repo_schema_id: 'none', | ||
| organism: 'any', | ||
| projects: [Project.find_or_create_by(title: 'Default Project')], | ||
| policy: Policy.public_policy, | ||
| template_attributes: source_temp_attributes) | ||
|
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| source_template.save | ||
| end | ||
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| # Sample - ISA minimal starter template | ||
| sample_template = Template.find_or_initialize_by(title: 'Sample - ISA minimal starter template', level: 'study sample', | ||
| group: 'ISA minimal starter') | ||
|
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| sample_temp_attributes = [] | ||
| sample_temp_attributes << TemplateAttribute.new(title: 'Input', | ||
| description: 'Registered Samples in the platform used as input for this protocol.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'Registered Sample List'), | ||
| is_title: false, | ||
| required: true) | ||
|
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| sample_temp_attributes << TemplateAttribute.new(title: 'Name of a protocol with samples as outputs', | ||
| description: 'Type of experimental step that generates samples as outputs from the study sources.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: false, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'protocol')) | ||
|
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| sample_temp_attributes << TemplateAttribute.new(title: 'Name of protocol parameter 1', | ||
| description: 'A parameter for the protocol.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: false, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'parameter_value')) | ||
|
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| sample_temp_attributes << TemplateAttribute.new(title: 'Sample Name', | ||
| description: 'Samples are considered as biological material sampled from sources and used in the study.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: true, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'sample')) | ||
|
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||
| sample_temp_attributes << TemplateAttribute.new(title: 'Sample Characteristic 1', | ||
| description: 'A characteristic of the sample.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: false, | ||
| required: true, | ||
| sample_controlled_vocab: nil, | ||
| isa_tag: IsaTag.find_by(title: 'sample_characteristic')) | ||
|
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||
| disable_authorization_checks do | ||
| sample_template.update(group_order: 2, | ||
| temporary_name: '2_Sample - ISA minimal starter template', | ||
| version: '1.0.0', | ||
| isa_config: 'isaconfig-default_v2015-07-02/studySample.xml', | ||
| isa_measurement_type: 'sample', | ||
| isa_protocol_type: 'protocol with samples as outputs collection', | ||
| repo_schema_id: 'none', | ||
| organism: 'any', | ||
| projects: [Project.find_or_create_by(title: 'Default Project')], | ||
| policy: Policy.public_policy, | ||
| template_attributes: sample_temp_attributes) | ||
|
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| sample_template.save | ||
| end | ||
|
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| # Material output assay - ISA minimal starter template | ||
| material_template = Template.find_or_initialize_by(title: 'Material output assay - ISA minimal starter template', | ||
| level: 'assay - material', group: 'ISA minimal starter') | ||
|
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| material_temp_attributes = [] | ||
| material_temp_attributes << TemplateAttribute.new(title: 'Input', | ||
| description: 'Registered Samples in the platform used as input for this protocol.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'Registered Sample List'), | ||
| is_title: false, | ||
| required: true) | ||
|
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||
| material_temp_attributes << TemplateAttribute.new(title: 'Name of a protocol with material output', | ||
| description: 'Type of assay or experimental step performed that generates a material output.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: false, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'protocol')) | ||
|
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||
| material_temp_attributes << TemplateAttribute.new(title: 'Name of protocol parameter 1', | ||
| description: 'A parameter for the protocol.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: false, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'parameter_value')) | ||
|
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| material_temp_attributes << TemplateAttribute.new(title: 'Output material Name', | ||
| description: 'Name of the major material output resulting from the application of the protocol.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: true, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'other_material')) | ||
|
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| material_temp_attributes << TemplateAttribute.new(title: 'Output material characteristic 1', | ||
| description: 'Characteristic 1 of the output material.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: false, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'other_material_characteristic')) | ||
|
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| disable_authorization_checks do | ||
| material_template.update(group_order: 3, | ||
| temporary_name: '3_Material output assay - ISA minimal starter template', | ||
| version: '1.0.0', | ||
| isa_config: 'none', | ||
| isa_measurement_type: 'any', | ||
| isa_technology_type: 'any', | ||
| isa_protocol_type: 'protocol with material output', | ||
| repo_schema_id: 'none', | ||
| organism: 'any', | ||
| projects: [Project.find_or_create_by(title: 'Default Project')], | ||
| policy: Policy.public_policy, | ||
| template_attributes: material_temp_attributes) | ||
|
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| material_template.save | ||
| end | ||
|
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| # Data file output assay - ISA minimal starter template | ||
| data_file_template = Template.find_or_initialize_by(title: 'Data file output assay - ISA minimal starter template', | ||
| level: 'assay - data file', group: 'ISA minimal starter') | ||
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| data_file_temp_attributes = [] | ||
| data_file_temp_attributes << TemplateAttribute.new(title: 'Input', | ||
| description: 'Registered Samples in the platform used as input for this protocol.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'Registered Sample List'), | ||
| is_title: false, | ||
| required: true) | ||
|
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| data_file_temp_attributes << TemplateAttribute.new(title: 'Name of a protocol with data file output', | ||
| description: 'Type of assay or experimental step performed that generates a data file output.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: false, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'protocol')) | ||
|
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| data_file_temp_attributes << TemplateAttribute.new(title: 'Name of protocol parameter 1', | ||
| description: 'A parameter for the protocol.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: false, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'data_file_comment')) | ||
|
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| data_file_temp_attributes << TemplateAttribute.new(title: 'Data file Name', | ||
| description: 'Name of the major data file output resulting from the application of the protocol.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: true, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'data_file')) | ||
|
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| data_file_temp_attributes << TemplateAttribute.new(title: 'Data file characteristic 1', | ||
| description: 'Characteristic 1 of the data file output.', | ||
| sample_attribute_type: SampleAttributeType.find_by(title: 'String'), | ||
| is_title: false, | ||
| required: true, | ||
| isa_tag: IsaTag.find_by(title: 'data_file_comment')) | ||
|
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| disable_authorization_checks do | ||
| data_file_template.update(group_order: 4, | ||
| temporary_name: '4_Data file output assay - ISA minimal starter template', | ||
| version: '1.0.0', | ||
| isa_config: 'none', | ||
| isa_measurement_type: 'any', | ||
| isa_technology_type: 'any', | ||
| isa_protocol_type: 'protocol with data file output', | ||
| repo_schema_id: 'none', | ||
| organism: 'any', | ||
| projects: [Project.find_or_create_by(title: 'Default Project')], | ||
| policy: Policy.public_policy, | ||
| template_attributes: data_file_temp_attributes) | ||
|
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| data_file_template.save | ||
| end | ||
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| puts 'Seeded minimal templates for organizing ISA JSON compliant experiments.' |