Class: V1::Pacbio::PoolResource

Inherits:

JSONAPI::Resource

• Object
• JSONAPI::Resource
• V1::Pacbio::PoolResource

Includes:

Shared::RunSuitability

Defined in:

app/resources/v1/pacbio/pool_resource.rb

Overview

TODO:

Add POST and PATCH examples

Note:

Access this resource via the /v1/pacbio/pools/ endpoint.

Provides a JSON:API representation of Pacbio::Pool.

For more information about JSON:API see the JSON:API Specifications or look at the JSONAPI::Resources package for the service implementation of the JSON:API standard. This resource represents a Pacbio Pool and can return all pools, a single pool or multiple pools along with their relationships.

Filters:

• sample_name

• barcode

Primary relationships:

• tube TubeResource

• used_aliquots AliquotResource

• primary_aliquot AliquotResource

• requests RequestResource

• libraries LibraryResource

Relationship trees:

• used_aliquots.tag.tag_set

• requests.tube,tube

• libraries.tube

• libraries.request

• requests.plate.wells.requests

Examples:

curl -X GET http://localhost:3000/v1/pacbio/pools/1
curl -X GET http://localhost:3000/v1/pacbio/pools/
curl -X GET http://localhost:3000/v1/pacbio/pools/1?include=tube,used_aliquots,primary_aliquot,requests,libraries

https://locahost:3000/v1/pacbio/pools?filter[sample_name]=sample_name

https://locahost:3000/v1/pacbio/pools?filter[barcode]=TRAC-2-12068

https://locahost:3000/v1/pacbio/pools?filter[barcode]=TRAC-2-12068,TRAC-2-12066,TRAC-2-12067

https://localhost:3000/v1/pacbio/pools?filter[barcode]=TRAC-2-12068,TRAC-2-12066,TRAC-2-12067&include=used_aliquots.tag.tag_set,requests.tube,tube,libraries.tube,libraries.request,requests.plate.wells.requests

Direct Known Subclasses

Runs::PoolResource

Constant Summary

ALIQUOT_ATTRIBUTES =

%w[id volume concentration template_prep_kit_box_barcode insert_size
tag_id source_id source_type].freeze

Instance Attribute Summary

• #available_volume ⇒ Float

  The available volume of the pool.

• #barcode ⇒ String readonly

  The barcode of the pool (via tube).

• #concentration ⇒ Float

  The concentration of the pool.

• #created_at ⇒ String

  The creation time of the pool.

• #insert_size ⇒ Integer

  The insert size of the pool.

• #library_attributes ⇒ Hash

  The attributes of the library.

• #primary_aliquot_attributes ⇒ Hash

  The attributes of the primary aliquot.

• #source_identifier ⇒ String readonly

  The source identifier of the pool.

• #template_prep_kit_box_barcode ⇒ String

  The barcode of the template prep kit box.

• #updated_at ⇒ String

  The last update time of the pool.

• #used_aliquots_attributes ⇒ Array<Hash>

  The attributes of the used aliquots.

• #used_volume ⇒ Float

  The used volume of the pool.

• #volume ⇒ Float

  The volume of the pool.

Class Method Summary

• .default_sort ⇒ Object
• .records_for_populate(*_args) ⇒ Object

Instance Method Summary

• #fetchable_fields ⇒ Object
• #publish_messages_on_creation ⇒ Object
• #publish_messages_on_update ⇒ Object

Methods included from Shared::RunSuitability

#run_suitability

Instance Attribute Details

#available_volume ⇒ Float

Returns the available volume of the pool.

Returns:

• (Float) —

  the available volume of the pool

# File 'app/resources/v1/pacbio/pool_resource.rb', line 90

attributes :volume, :concentration, :template_prep_kit_box_barcode,
:insert_size, :created_at, :updated_at,
:library_attributes, :used_aliquots_attributes, :primary_aliquot_attributes,
:used_volume, :available_volume

#barcode ⇒ String (readonly)

Returns the barcode of the pool (via tube).

Returns:

• (String) —

  the barcode of the pool (via tube)

# File 'app/resources/v1/pacbio/pool_resource.rb', line 101

attribute :barcode, readonly: true

#concentration ⇒ Float

Returns the concentration of the pool.

Returns:

• (Float) —

  the concentration of the pool

# File 'app/resources/v1/pacbio/pool_resource.rb', line 90

attributes :volume, :concentration, :template_prep_kit_box_barcode,
:insert_size, :created_at, :updated_at,
:library_attributes, :used_aliquots_attributes, :primary_aliquot_attributes,
:used_volume, :available_volume

#created_at ⇒ String

Returns the creation time of the pool.

Returns:

• (String) —

  the creation time of the pool

# File 'app/resources/v1/pacbio/pool_resource.rb', line 90

attributes :volume, :concentration, :template_prep_kit_box_barcode,
:insert_size, :created_at, :updated_at,
:library_attributes, :used_aliquots_attributes, :primary_aliquot_attributes,
:used_volume, :available_volume

#insert_size ⇒ Integer

Returns the insert size of the pool.

Returns:

• (Integer) —

  the insert size of the pool

# File 'app/resources/v1/pacbio/pool_resource.rb', line 90

attributes :volume, :concentration, :template_prep_kit_box_barcode,
:insert_size, :created_at, :updated_at,
:library_attributes, :used_aliquots_attributes, :primary_aliquot_attributes,
:used_volume, :available_volume

#library_attributes ⇒ Hash

Returns the attributes of the library.

Returns:

• (Hash) —

  the attributes of the library

# File 'app/resources/v1/pacbio/pool_resource.rb', line 90

attributes :volume, :concentration, :template_prep_kit_box_barcode,
:insert_size, :created_at, :updated_at,
:library_attributes, :used_aliquots_attributes, :primary_aliquot_attributes,
:used_volume, :available_volume

#primary_aliquot_attributes ⇒ Hash

Returns the attributes of the primary aliquot.

Returns:

• (Hash) —

  the attributes of the primary aliquot

# File 'app/resources/v1/pacbio/pool_resource.rb', line 90

attributes :volume, :concentration, :template_prep_kit_box_barcode,
:insert_size, :created_at, :updated_at,
:library_attributes, :used_aliquots_attributes, :primary_aliquot_attributes,
:used_volume, :available_volume

#source_identifier ⇒ String (readonly)

Returns the source identifier of the pool.

Returns:

• (String) —

  the source identifier of the pool

# File 'app/resources/v1/pacbio/pool_resource.rb', line 97

attribute :source_identifier, readonly: true

#template_prep_kit_box_barcode ⇒ String

Returns the barcode of the template prep kit box.

Returns:

• (String) —

  the barcode of the template prep kit box

# File 'app/resources/v1/pacbio/pool_resource.rb', line 90

attributes :volume, :concentration, :template_prep_kit_box_barcode,
:insert_size, :created_at, :updated_at,
:library_attributes, :used_aliquots_attributes, :primary_aliquot_attributes,
:used_volume, :available_volume

#updated_at ⇒ String

Returns the last update time of the pool.

Returns:

• (String) —

  the last update time of the pool

# File 'app/resources/v1/pacbio/pool_resource.rb', line 90

attributes :volume, :concentration, :template_prep_kit_box_barcode,
:insert_size, :created_at, :updated_at,
:library_attributes, :used_aliquots_attributes, :primary_aliquot_attributes,
:used_volume, :available_volume

#used_aliquots_attributes ⇒ Array<Hash>

Returns the attributes of the used aliquots.

Returns:

• (Array<Hash>) —

  the attributes of the used aliquots

# File 'app/resources/v1/pacbio/pool_resource.rb', line 90

attributes :volume, :concentration, :template_prep_kit_box_barcode,
:insert_size, :created_at, :updated_at,
:library_attributes, :used_aliquots_attributes, :primary_aliquot_attributes,
:used_volume, :available_volume

#used_volume ⇒ Float

Returns the used volume of the pool.

Returns:

• (Float) —

  the used volume of the pool

# File 'app/resources/v1/pacbio/pool_resource.rb', line 90

attributes :volume, :concentration, :template_prep_kit_box_barcode,
:insert_size, :created_at, :updated_at,
:library_attributes, :used_aliquots_attributes, :primary_aliquot_attributes,
:used_volume, :available_volume

#volume ⇒ Float

Returns the volume of the pool.

Returns:

• (Float) —

  the volume of the pool

# File 'app/resources/v1/pacbio/pool_resource.rb', line 90

attributes :volume, :concentration, :template_prep_kit_box_barcode,
:insert_size, :created_at, :updated_at,
:library_attributes, :used_aliquots_attributes, :primary_aliquot_attributes,
:used_volume, :available_volume

Class Method Details

.default_sort ⇒ Object

# File 'app/resources/v1/pacbio/pool_resource.rb', line 108

def self.default_sort
  [{ field: 'created_at', direction: :desc }]
end

.records_for_populate(*_args) ⇒ Object

# File 'app/resources/v1/pacbio/pool_resource.rb', line 142

def self.records_for_populate(*_args)
  super.preload(source_wells: :plate)
end

Instance Method Details

#fetchable_fields ⇒ Object

# File 'app/resources/v1/pacbio/pool_resource.rb', line 138

def fetchable_fields
  super - %i[library_attributes used_aliquots_attributes primary_aliquot_attributes]
end

#publish_messages_on_creation ⇒ Object

# File 'app/resources/v1/pacbio/pool_resource.rb', line 154

def publish_messages_on_creation
  Emq::Publisher.publish(@model.primary_aliquot, Pipelines.pacbio, 'volume_tracking')
end

#publish_messages_on_update ⇒ Object

# File 'app/resources/v1/pacbio/pool_resource.rb', line 158

def publish_messages_on_update
  Messages.publish(@model.sequencing_runs, Pipelines.pacbio.message)
  Emq::Publisher.publish(@model.primary_aliquot, Pipelines.pacbio, 'volume_tracking')
end