Class: V1::Pacbio::Runs::WellResource

Inherits:

JSONAPI::Resource

• Object
• JSONAPI::Resource
• V1::Pacbio::Runs::WellResource

Defined in:

app/resources/v1/pacbio/runs/well_resource.rb

Overview

Note:

Access this resource via the /v1/pacbio/runs/wells endpoint.

Provides a JSON:API resource for the Pacbio::Well model.

== Description

WellResource exposes the attributes and relationships of a Pacbio Well, which represents a single well on a Pacbio plate. It allows clients to retrieve, create, and update wells, including their associated libraries, pools, used aliquots, and annotations.

Primary relationships:

• used_aliquots - Has many used aliquots (Aliquot)

• libraries - Has many libraries (Pacbio::Library)

• pools - Has many pools (Pacbio::Pool)

• annotations - Has many annotations (Annotation)

Instance Attribute Summary

• #binding_kit_box_barcode ⇒ String

  The barcode of the binding kit box.

• #ccs_analysis_output ⇒ String

  The CCS analysis output.

• #ccs_analysis_output_include_kinetics_information ⇒ Boolean

  Whether to include kinetics information in the CCS analysis output.

• #ccs_analysis_output_include_low_quality_reads ⇒ Boolean

  Whether to include low quality reads in the CCS analysis output.

• #column ⇒ String

  The column of the well.

• #demultiplex_barcodes ⇒ String

  The demultiplex barcodes.

• #full_resolution_base_qual ⇒ Boolean

  Whether to apply full resolution base qual.

• #generate_hifi ⇒ Boolean

  Whether to generate HiFi reads.

• #include_base_kinetics ⇒ Boolean

  Whether to include base kinetics.

• #include_fivemc_calls_in_cpg_motifs ⇒ Boolean

  Whether to include 5mC calls in CpG motifs.

• #library_concentration ⇒ Float

  The library concentration in pM.

• #library_type ⇒ String

  The library type.

• #loading_target_p1_plus_p2 ⇒ Float

  The loading target (P1 + P2).

• #movie_acquisition_time ⇒ Float

  The movie acquisition time in hours.

• #movie_time ⇒ Float

  The movie time in hours.

• #on_plate_loading_concentration ⇒ Float

  The on plate loading concentration.

• #pacbio_plate_id ⇒ Integer

  The ID of the Pacbio plate.

• #polymerase_kit ⇒ String

  The polymerase kit.

• #position ⇒ String

  The position of the well.

• #pre_extension_time ⇒ Integer

  The pre-extension time.

• #row ⇒ String

  The row of the well.

• #use_adaptive_loading ⇒ Boolean

  Whether to use adaptive loading.

Class Method Summary

• .resource_klass_for(type) ⇒ Object

  JSON API Resources builds up a representation of the relationships on a give resource.

Instance Attribute Details

#binding_kit_box_barcode ⇒ String

Returns the barcode of the binding kit box.

Returns:

• (String) —

  the barcode of the binding kit box

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#ccs_analysis_output ⇒ String

Returns the CCS analysis output.

Returns:

• (String) —

  the CCS analysis output

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#ccs_analysis_output_include_kinetics_information ⇒ Boolean

Returns whether to include kinetics information in the CCS analysis output.

Returns:

• (Boolean) —

  whether to include kinetics information in the CCS analysis output

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#ccs_analysis_output_include_low_quality_reads ⇒ Boolean

Returns whether to include low quality reads in the CCS analysis output.

Returns:

• (Boolean) —

  whether to include low quality reads in the CCS analysis output

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#column ⇒ String

Returns the column of the well.

Returns:

• (String) —

  the column of the well

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#demultiplex_barcodes ⇒ String

Returns the demultiplex barcodes.

Returns:

• (String) —

  the demultiplex barcodes

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#full_resolution_base_qual ⇒ Boolean

Returns whether to apply full resolution base qual.

Returns:

• (Boolean) —

  whether to apply full resolution base qual

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#generate_hifi ⇒ Boolean

Returns whether to generate HiFi reads.

Returns:

• (Boolean) —

  whether to generate HiFi reads

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#include_base_kinetics ⇒ Boolean

Returns whether to include base kinetics.

Returns:

• (Boolean) —

  whether to include base kinetics

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#include_fivemc_calls_in_cpg_motifs ⇒ Boolean

Returns whether to include 5mC calls in CpG motifs.

Returns:

• (Boolean) —

  whether to include 5mC calls in CpG motifs

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#library_concentration ⇒ Float

Returns the library concentration in pM.

Returns:

• (Float) —

  the library concentration in pM

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#library_type ⇒ String

Returns the library type.

Returns:

• (String) —

  the library type

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#loading_target_p1_plus_p2 ⇒ Float

Returns the loading target (P1 + P2).

Returns:

• (Float) —

  the loading target (P1 + P2)

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#movie_acquisition_time ⇒ Float

Returns the movie acquisition time in hours.

Returns:

• (Float) —

  the movie acquisition time in hours

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#movie_time ⇒ Float

Returns the movie time in hours.

Returns:

• (Float) —

  the movie time in hours

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#on_plate_loading_concentration ⇒ Float

Returns the on plate loading concentration.

Returns:

• (Float) —

  the on plate loading concentration

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#pacbio_plate_id ⇒ Integer

Returns the ID of the Pacbio plate.

Returns:

• (Integer) —

  the ID of the Pacbio plate

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#polymerase_kit ⇒ String

Returns the polymerase kit.

Returns:

• (String) —

  the polymerase kit

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#position ⇒ String

Returns the position of the well.

Returns:

• (String) —

  the position of the well

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#pre_extension_time ⇒ Integer

Returns the pre-extension time.

Returns:

• (Integer) —

  the pre-extension time

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#row ⇒ String

Returns the row of the well.

Returns:

• (String) —

  the row of the well

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

#use_adaptive_loading ⇒ Boolean

Returns whether to use adaptive loading.

Returns:

• (Boolean) —

  whether to use adaptive loading

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 103

attributes :row, :column, :pacbio_plate_id, :position,
:annotations_attributes,
*Rails.configuration.pacbio_smrt_link_versions.options.keys

Class Method Details

.resource_klass_for(type) ⇒ Object

JSON API Resources builds up a representation of the relationships on a give resource. Whilst doing to it asks the associated resource for its type, before using this method on the parent resource to attempt to look up the model. Unfortunately this is forced to use the same namespace by default.

# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 117

def self.resource_klass_for(type)
  case type.downcase.pluralize
  when 'libraries' then Pacbio::LibraryResource
  when 'pools' then Pacbio::PoolResource
  when 'annotations' then Pacbio::Runs::AnnotationResource
  else
    super
  end
end