Class: Api::V2::TagGroupResource

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

Overview

TODO:

The below POST example is provided for reference, however it currently throws an error.

Note:

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

Provides a JSON:API representation of TagGroup A TagGroup represents a set of tags used in sequencing.

A Tag is a short, know sequence of DNA which gets applied to a sample. The tag remains attached through subsequent processing, and means that it is possible to identify the origin of a sample if multiple samples are subsequently pooled together.

This is because the example format of the tags attribute are not permitted.

For more information about JSON:API, see the JSON:API Specifications or refer to JSONAPI::Resources for Sequencescape's implementation.

Examples:

GET request for all tag groups

GET /api/v2/tag_groups/

GET request for a specific tag group by ID

GET /api/v2/tag_groups/123/

POST request to create a new tag group

POST /api/v2/tag_groups/
{
  "data": {
    "type": "tag_groups",
    "attributes": {
      "name": "My Tag Group",
      "tags": [
        { "map_id": 1,"oligo": "AAACGGCG"},
        { "map_id": 2,"oligo": "CAACGGCG"}
      ]
    },
    "relationships": {
      "tag_group_adapter_type": {
        "data": { "type": "tag_group_adapter_types", "id": 5 }
      }
    }
  }
}

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

#name ⇒ String

The name of the tag group. This attribute is required when creating a new tag group.

Returns:

  • (String) —

    The name of the tag group.



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# File 'app/resources/api/v2/tag_group_resource.rb', line 63

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

#tag_group_adapter_type ⇒ TagGroupAdapterTypeResource

Note:

This relationship is required

The adapter type associated with this tag group. This defines how the tags are used within a sequencing workflow.

Returns:



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

#tags ⇒ Array<Hash>

Returns the list of tags sorted by their index.

Returns:

  • (Array<Hash>) —

    The list of tags, each with an index and an oligo sequence.



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# File 'app/resources/api/v2/tag_group_resource.rb', line 68

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 identifier is automatically assigned upon creation and cannot be modified.

Returns The UUID of the tag group.

Returns:

  • (String) —

    The UUID of the tag group.



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# File 'app/resources/api/v2/tag_group_resource.rb', line 57

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 ⇒ String

Returns Filters tag groups by their name.

Examples:

Retrieve tag groups with a specific name

GET /api/v2/tag_groups?filter[name]=MyTagGroup

Returns:

  • (String) —

    Filters tag groups by their name.



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# File 'app/resources/api/v2/tag_group_resource.rb', line 98

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_tag_group_adapter_type_name ⇒ String

Returns Filters tag groups by their adapter type name.

Examples:

Retrieve tag groups associated with a specific adapter type

GET /api/v2/tag_groups?filter[tag_group_adapter_type_name]=Illumina

Returns:

  • (String) —

    Filters tag groups by their adapter type name.



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

#filter_by_visible ⇒ Boolean

Returns Filters tag groups based on visibility.

Examples:

Retrieve only visible tag groups

GET /api/v2/tag_groups?filter[visible]=true

Returns:

  • (Boolean) —

    Filters tag groups based on visibility.



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# File 'app/resources/api/v2/tag_group_resource.rb', line 92

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