Class: Api::V2::TubeRackResource

Inherits:
BaseResource
  • Object
show all
Defined in:
app/resources/api/v2/tube_rack_resource.rb

Overview

Note:

Access this resource via the /api/v2/tube_racks/ endpoint.

Provides a JSON:API representation of TubeRack.

This resource represents a tube rack, which can contain a collection of tubes, with locations specified for each tube in the rack. Tubes are linked via the RackedTubes association

For more information about JSON:API see the JSON:API Specifications or look at the JSONAPI::Resources package for Sequencescape's implementation of the JSON:API standard.

Examples:

GET request to fetch a Tube Rack by its ID:

GET /api/v2/tube_racks/{id}/

POST request to create a new Tube Rack with a name and barcode:

POST /api/v2/tube_racks/
{
  "data": {
    "type": "tube_racks",
    "attributes": {
        "size": 48,
        "name": "Rack A1",
        "tube_locations": {
            "A1": { "uuid": "558b931c-fb5f-11ef-86cc-000000000000" },
            "B1": { "uuid": "2abc4186-3718-11ec-9c4c-acde48001122" },
            "C1": { "uuid": "2ace27fc-3718-11ec-9c4c-acde48001122" }
        }
    }
  }
}

PATCH request to update the Tube Rack's size:

PATCH /api/v2/tube_racks/123
{
  "data": {
    "id": 123,
    "type": "tube_racks",
    "attributes": {
        "size": 96
    }
  }
}

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from BaseResource

apply_includes, creatable_fields, default_includes, #fetchable_fields, inclusions, resolve_relationship_names_to_relations, updatable_fields

Instance Attribute Details

#comments ⇒ CommentResource (readonly)

Note:

Comments are readonly and provide additional context or notes regarding the tube rack.

Returns A collection of comments related to the tube rack.

Returns:



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 114

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#created_at ⇒ String (readonly)

Returns The timestamp when the tube rack was created. Readonly.

Returns:

  • (String) —

    The timestamp when the tube rack was created. Readonly.



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 56

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#labware_barcode ⇒ Hash

Note:

The labware barcode can be returned in different formats, such as EAN13 or machine-readable formats.

Returns A hash containing the different types of barcodes associated with the tube rack.

Returns:

  • (Hash) —

    A hash containing the different types of barcodes associated with the tube rack.



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 62

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#name ⇒ String

Note:

This is a write-once attribute, meaning it cannot be modified once it has been set.

Returns The name of the tube rack.

Returns:

  • (String) —

    The name of the tube rack.



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 67

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#number_of_columns ⇒ Integer

Note:

A POST request errors when this attribute is provided. I believe these are automatically calculated based on the size of the tube rack.

Note:

This is a write-once attribute, meaning it cannot be modified once it has been set.

Returns The number of columns in the tube rack.

Returns:

  • (Integer) —

    The number of columns in the tube rack.



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 74

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#number_of_rows ⇒ Integer

Note:

A POST request errors when this attribute is provided. I believe these are automatically calculated based on the size of the tube rack.

Note:

This is a write-once attribute, meaning it cannot be modified once it has been set.

Returns The number of rows in the tube rack.

Returns:

  • (Integer) —

    The number of rows in the tube rack.



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 81

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#racked_tubes ⇒ RackedTubeResource

Note:

This relationship represents the tubes placed in the rack at specified coordinates.

Returns The tubes that have been placed in the tube rack.

Returns:



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 119

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#size ⇒ String

Note:

This attribute is required.

Returns The size of the tube rack (e.g., 48, 96).

Returns:

  • (String) —

    The size of the tube rack (e.g., 48, 96).



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 86

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#tube_locations ⇒ Void

Note:

This is a write-only attribute used to map tubes to specific coordinates in the rack.

Returns:

  • (Void)

Raises:

  • (RuntimeError) —

    If any of the provided UUIDs do not correspond to a valid tube.

See Also:



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 93

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#updated_at ⇒ String (readonly)

Returns The timestamp when the tube rack was last updated. Readonly.

Returns:

  • (String) —

    The timestamp when the tube rack was last updated. Readonly.



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 97

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#uuid(: uuid) ⇒ ActiveRecord::Relation (readonly)

Returns Filtered tube racks that match the provided UUID.

Examples:

GET /api/v2/tube_racks?filter=some-uuid-value

Returns:

  • (ActiveRecord::Relation) —

    Filtered tube racks that match the provided UUID.



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 101

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

Instance Method Details

#barcode(: barcode) ⇒ ActiveRecord::Relation

Returns Filtered tube racks that match the provided barcode.

Examples:

GET /api/v2/tube_racks?filter=1234567890123

Returns:

  • (ActiveRecord::Relation) —

    Filtered tube racks that match the provided barcode.



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 136

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#purpose_id(: purpose_id) ⇒ ActiveRecord::Relation

Returns Filtered tube racks that have the specified purpose ID.

Examples:

GET /api/v2/tube_racks?filter=12345

Returns:

  • (ActiveRecord::Relation) —

    Filtered tube racks that have the specified purpose ID.



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 158

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#purpose_name(: purpose_name) ⇒ ActiveRecord::Relation

Returns Filtered tube racks that have the specified purpose name.

Examples:

GET /api/v2/tube_racks?filter=Storage

Returns:

  • (ActiveRecord::Relation) —

    Filtered tube racks that have the specified purpose name.



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# File 'app/resources/api/v2/tube_rack_resource.rb', line 146

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end