Class: Api::V2::PlateResource

Inherits:
BaseResource
  • Object
show all
Includes:
SharedBehaviour::Labware
Defined in:
app/resources/api/v2/plate_resource.rb

Overview

Note:

This resource cannot be modified after creation: its endpoint will not accept PATCH requests.

Note:

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

Provides a JSON:API representation of Plate which is plastic labware containing Wells. The plate has a purpose like all labware and this denotes which pipeline it is being used in and what type of samples it holds / how it will be processed. Plates are not typically created directly using this resource, although they can be. Rather they are created via resources such as PlateCreationResource.

}

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:

POST request

POST /api/v2/plates/
{
  "data": {
      "type": "plates",
      "attributes": {
          "size": 96
      },
      "relationships": {
          "purpose": {
              "data": { "type": "purposes", "id": 1 }
          },
          "wells": {
              "data": [{ "type": "wells", "id": 4481 }]
          },
          "poly_metadata": {
           "data": [{ "type": "poly_metadata", "id": 10 }]
         }
    }
  }

GET request for all Plate resources

GET /api/v2/plates/

GET request for a Plate with ID 123

GET /api/v2/plates/123/

PATCH request to update metadata for a plate

PATCH /api/v2/plates/123/
{
  "data": {
    "type": "plates",
    "id": "123",
    "relationships": {
      "poly_metadata": {
        "data": [{ "type": "poly_metadata", "id": "456" }]
      }
    }
  }
}

Instance Attribute Summary collapse

Method Summary

Methods included from SharedBehaviour::Labware

#labware_barcode

Methods inherited from BaseResource

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

Instance Attribute Details

#number_of_columns ⇒ Int (readonly)

Returns The number of columns on the plate. This is determined by the AssetShape assigned to the plate by its purpose.

Returns:

  • (Int) —

    The number of columns on the plate. This is determined by the AssetShape assigned to the plate by its purpose.



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# File 'app/resources/api/v2/plate_resource.rb', line 87

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 ⇒ Int (readonly)

Returns The number of rows on the plate. This is determined by the AssetShape assigned to the plate by its purpose.

Returns:

  • (Int) —

    The number of rows on the plate. This is determined by the AssetShape assigned to the plate by its purpose.



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# File 'app/resources/api/v2/plate_resource.rb', line 82

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

#poly_metadata ⇒ PolyMetadatumResource (readonly)

Note:

This is a one-to-many relationship, where a Labware can have multiple pieces of metadata.

Note:

The poly_metadata must already exist in the database before it can be associated with a Labware.

Returns The associated metadata for the Labware.

Returns:

See Also:



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# File 'app/resources/api/v2/plate_resource.rb', line 73

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

#pooling_metadata ⇒ Hash (readonly)

Returns A hash containing submission UUIDs and corresponding pooling metadata.

Examples:

Hash representation

{
  "12345678-1234-1234-1234-1234567890ab": {
    "wells": ["A1", "A2", "A3"],
    "pool_complete": true,
    "insert_size": { "from": 1, "to": 1 },
    "library_type": { "name": "Bioscan" },
    "pcr_cycles": 0,
    "request_type": "limber_bioscan_library_prep",
    "for_multiplexing": false
  },
  "87654321-4321-4321-4321-ba0987654321": {
    "wells": ["B1", "B2", "B3"],
    "pool_complete": true,
    "insert_size": { "from": 1, "to": 1 },
    "library_type": { "name": "Bioscan" },
    "pcr_cycles": 0,
    "request_type": "limber_bioscan_library_prep",
    "for_multiplexing": false
  }
}

Returns:

  • (Hash) —

    A hash containing submission UUIDs and corresponding pooling metadata.



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# File 'app/resources/api/v2/plate_resource.rb', line 118

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 ⇒ Int

Note:

This can only be set once during creation. If it is not set, it will default to 96.

Returns The total number of wells on the plate.

Returns:

  • (Int) —

    The total number of wells on the plate.



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# File 'app/resources/api/v2/plate_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

#submission_pools ⇒ Array<SubmissionPoolResource> (readonly)

Returns An array of submission pools for this plate.

Returns:



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# File 'app/resources/api/v2/plate_resource.rb', line 130

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

#transfers_as_destination ⇒ Array<TransferResource> (readonly)

Returns An array of transfers with this plate as the destination.

Returns:

  • (Array<TransferResource>) —

    An array of transfers with this plate as the destination.



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# File 'app/resources/api/v2/plate_resource.rb', line 134

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

#wells ⇒ Array<WellResource>

Note:

This can only be set once during creation.

Returns An array of wells on this plate.

Returns:

  • (Array<WellResource>) —

    An array of wells on this plate.



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# File 'app/resources/api/v2/plate_resource.rb', line 139

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