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

Inherits:

JSONAPI::Resource

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

show all

Defined in:: app/resources/v1/pacbio/runs/well_resource.rb

Overview

Note:

This endpoint can’t be directly accessed via the /v1/pacbio/runs/wells/ endpoint

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

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)

as it is only accessible via the nested route under V1::Pacbio::Run using includes.

Instance Attribute Summary collapse

#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 collapse

.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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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)



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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



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# File 'app/resources/v1/pacbio/runs/well_resource.rb', line 66

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 80

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

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

Overview

Primary relationships:

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Attribute Details

#binding_kit_box_barcode ⇒ String

#ccs_analysis_output ⇒ String

#ccs_analysis_output_include_kinetics_information ⇒ Boolean

#ccs_analysis_output_include_low_quality_reads ⇒ Boolean

#column ⇒ String

#demultiplex_barcodes ⇒ String

#full_resolution_base_qual ⇒ Boolean

#generate_hifi ⇒ Boolean

#include_base_kinetics ⇒ Boolean

#include_fivemc_calls_in_cpg_motifs ⇒ Boolean

#library_concentration ⇒ Float

#library_type ⇒ String

#loading_target_p1_plus_p2 ⇒ Float

#movie_acquisition_time ⇒ Float

#movie_time ⇒ Float

#on_plate_loading_concentration ⇒ Float

#pacbio_plate_id ⇒ Integer

#polymerase_kit ⇒ String

#position ⇒ String

#pre_extension_time ⇒ Integer

#row ⇒ String

#use_adaptive_loading ⇒ Boolean

Class Method Details

.resource_klass_for(type) ⇒ Object

#binding_kit_box_barcode ⇒ `String`

#ccs_analysis_output ⇒ `String`

#ccs_analysis_output_include_kinetics_information ⇒ `Boolean`

#ccs_analysis_output_include_low_quality_reads ⇒ `Boolean`

#column ⇒ `String`

#demultiplex_barcodes ⇒ `String`

#full_resolution_base_qual ⇒ `Boolean`

#generate_hifi ⇒ `Boolean`

#include_base_kinetics ⇒ `Boolean`

#include_fivemc_calls_in_cpg_motifs ⇒ `Boolean`

#library_concentration ⇒ `Float`

#library_type ⇒ `String`

#loading_target_p1_plus_p2 ⇒ `Float`

#movie_acquisition_time ⇒ `Float`

#movie_time ⇒ `Float`

#on_plate_loading_concentration ⇒ `Float`

#pacbio_plate_id ⇒ `Integer`

#polymerase_kit ⇒ `String`

#position ⇒ `String`

#pre_extension_time ⇒ `Integer`

#row ⇒ `String`

#use_adaptive_loading ⇒ `Boolean`

.resource_klass_for(type) ⇒ `Object`