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Seed minimal isa #1644

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merged 6 commits into from
Dec 8, 2023
Merged

Seed minimal isa #1644

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4dcf5bf
Adding minimal ISA starter template for source level sample types as …
Oct 19, 2023
2db9015
Add minimal template for the study sample level
Oct 19, 2023
34460f1
Add other templates
Oct 20, 2023
d80fde5
Latest update on the minimal isa starter
Oct 26, 2023
058fffd
Implement find_or_initialize for templates + fixing update statement
Oct 26, 2023
38357f1
Change Registered sample type name
kdp-cloud Nov 27, 2023
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202 changes: 202 additions & 0 deletions db/seeds/017_minimal_starter_isa_templates.seeds.rb
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Original file line number Diff line number Diff line change
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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')

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'))

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'))

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)

source_template.save
end

# 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')

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)

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'))

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'))

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'))

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'))

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)

sample_template.save
end

# 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')

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)

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'))

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'))

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'))

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'))

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)

material_template.save
end

# 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')

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)

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'))

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'))

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'))

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'))

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)

data_file_template.save
end

puts 'Seeded minimal templates for organizing ISA JSON compliant experiments.'
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