Class: Api::V2::SampleResource

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

Overview

TODO:

Figure out how to send a POST for a sample with sample metadata association. Currently, it is possible to create a sample and sample metadata seperately, but they are not associated with each other. How do you create the association, either in one request or after the individual requests?

Note:

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

Provides a JSON:API representation of Sample, which represents a biological or synthetic sample used in laboratory processes. This resource allows users to retrieve and filter samples based on various attributes such as UUID, name, or Sanger Sample ID.

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 for all samples

GET /api/v2/samples/

GET request for a specific sample by ID

GET /api/v2/samples/123/

POST request to create a new sample

POST /api/v2/samples/
{
  "data": {
    "type": "samples",
    "attributes": {
      "name": "Sample_A",
      "sanger_sample_id": "S12345",
      "control": false,
      "control_type": "positive"
    },
    "relationships": {
      "sample_metadata": {
        "data": {
          "type": "sample_metadata",
          "id": "1"
        }
      },
      "studies": {
        "data": [
          {
            "type": "studies",
            "id": "1"
          },
        ]
      },
      "component_samples": {
        "data": [
          {
            "type": "component_samples",
            "id": "1"
          },
        ]
      }
    }
  }
}

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

#component_samples ⇒ Array<ComponentSampleResource>

Note:

A sample may consist of multiple component samples.

Returns The component samples associated with this sample.

Returns:

  • (Array<ComponentSampleResource>) —

    The component samples associated with this sample.



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# File 'app/resources/api/v2/sample_resource.rb', line 120

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

#control ⇒ Boolean

Note:

Optional field.

Returns Indicates whether this sample is a control sample.

Returns:

  • (Boolean) —

    Indicates whether this sample is a control sample.



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# File 'app/resources/api/v2/sample_resource.rb', line 89

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

#control_type ⇒ String

Note:

Optional field.

Returns The type of control sample (e.g., positive control, negative control).

Returns:

  • (String) —

    The type of control sample (e.g., positive control, negative control).



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# File 'app/resources/api/v2/sample_resource.rb', line 94

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 field is optional.

Returns The name of the sample.

Returns:

  • (String) —

    The name of the sample.



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

#sample_manifest ⇒ SampleManifestResource

Note:

Optional relationship.

Returns The manifest to which this sample belongs, often linking it to a larger set of processed samples.

Returns:

  • (SampleManifestResource) —

    The manifest to which this sample belongs, often linking it to a larger set of processed samples.



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# File 'app/resources/api/v2/sample_resource.rb', line 110

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

#sample_metadata ⇒ SampleMetadataResource

Note:

Optional relationship.

Returns The metadata associated with this sample, containing additional details like collection method and donor information.

Returns:

  • (SampleMetadataResource) —

    The metadata associated with this sample, containing additional details like collection method and donor information.



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# File 'app/resources/api/v2/sample_resource.rb', line 104

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

#sanger_sample_id ⇒ String

Note:

This field is optional but commonly used for sample tracking.

Returns The unique identifier assigned to the sample within the Sanger Institute.

Returns:

  • (String) —

    The unique identifier assigned to the sample within the Sanger Institute.



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# File 'app/resources/api/v2/sample_resource.rb', line 79

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

#studies ⇒ Array<StudyResource>

Note:

A sample can be linked to multiple studies.

Returns The studies associated with this sample.

Returns:

  • (Array<StudyResource>) —

    The studies associated with this sample.



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# File 'app/resources/api/v2/sample_resource.rb', line 115

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 ⇒ String (readonly)

Note:

This value is automatically assigned upon creation and cannot be modified.

Returns The globally unique identifier (UUID) for this sample.

Returns:

  • (String) —

    The globally unique identifier (UUID) for this sample.



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# File 'app/resources/api/v2/sample_resource.rb', line 84

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

#filter_by_name ⇒ Object

Filters samples by their name.

Examples:

GET request filtering by name

GET /api/v2/samples?filter[name]=Sample_A


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# File 'app/resources/api/v2/sample_resource.rb', line 142

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

#filter_by_sanger_sample_id ⇒ Object

Filters samples by their Sanger Sample ID.

Examples:

GET request filtering by Sanger Sample ID

GET /api/v2/samples?filter[sanger_sample_id]=S12345


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

#filter_by_uuid ⇒ Object

Filters samples by their UUID.

Examples:

GET request filtering by UUID

GET /api/v2/samples?filter[uuid]=550e8400-e29b-41d4-a716-446655440000


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