Class: Bio::BaseSpace::File

Inherits:
Model
  • Object
show all
Defined in:
lib/basespace/model/file.rb

Overview

Represents a BaseSpace file object.

Instance Attribute Summary

Attributes inherited from Model

#attributes, #swagger_types

Instance Method Summary collapse

Methods inherited from Model

#get_attr, #method_missing, #set_attr

Constructor Details

#initialize ⇒ File

Create a new File instance.



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# File 'lib/basespace/model/file.rb', line 24

def initialize
  @swagger_types = {
    'Name'          => 'str',
    'HrefCoverage'  => 'str',
    'HrefParts'     => 'str',
    'DateCreated'   => 'datetime',
    'UploadStatus'  => 'str',
    'Id'            => 'str',
    'Href'          => 'str',
    'HrefContent'   => 'str',
    'HrefVariants'  => 'str',
    'ContentType'   => 'str',
    'Path'          => 'str',
    'Size'          => 'int',
  }
  @attributes = {
    'Name'          => nil, # str
    # If set, provides the relative Uri to fetch the mean coverage statistics for data stored in the file
    'HrefCoverage'  => nil, # str
    # If set, provides the relative Uri to fetch a list of completed file parts for multi-part file uploads in progress
    'HrefParts'     => nil, # str
    'DateCreated'   => nil, # datetime
    'UploadStatus'  => nil, # str
    'Id'            => nil, # str
    'Href'          => nil, # str
    'HrefContent'   => nil, # str
    # If set, provides the relative Uri to fetch the variants stored in the file
    'HrefVariants'  => nil, # str
    'ContentType'   => nil, # str
    'Path'          => nil, # str
    'Size'          => nil, # int
  }
end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method in the class Bio::BaseSpace::Model

Instance Method Details

#delete_file(api) ⇒ Object

Delete the file; not implemented yet.

api

A BaseSpaceAPI instance with delete permissions on the file object.



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# File 'lib/basespace/model/file.rb', line 116

def delete_file(api)
  raise 'Not yet implemented'
end

#download_file(api, local_dir, range = []) ⇒ Object

Download the file object to the specified local directory or a byte range of the file, by specifying the start and stop byte in the range.

api

A BaseSpaceAPI instance with read access to the file object.

local_dir

The local directory to place the file in.

:range+

Two-item array with start and stop byte of the file chunk that needs retrieved.



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# File 'lib/basespace/model/file.rb', line 98

def download_file(api, local_dir, range = [])
  if range.empty?
    return api.file_download(get_attr('Id'),local_dir, get_attr('Name'))
  else
    return api.file_download(get_attr('Id'),local_dir, get_attr('Name'), range)
  end
end

#filter_variant(api, chrom, start_pos, end_pos, qp = nil) ⇒ Object

Returns a list of Variant objects available in the specified region.

api

BaseSpaceAPI instance.

chrom

Chromosome as a string - for example ‘chr2’.

start_pos

The start position of region of interest as a string.

end_pos

The end position of region of interest as a string.

qp: TODO queryParameters object for custom filtering.



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# File 'lib/basespace/model/file.rb', line 140

def filter_variant(api, chrom, start_pos, end_pos, qp = nil)
  is_init
  is_valid_file_option('vcf')
  set_attr('Id', get_attr('HrefVariants').split('/').last)
  return api.filter_variant_set(get_attr('Id'), chrom, start_pos, end_pos, 'txt')
end

#get_coverage_meta(api, chrom) ⇒ Object

Return an object of CoverageMetadata for the selected region.

api

BaseSpaceAPI instance.

chrom

Chromosome as a string - for example ‘chr2’.



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# File 'lib/basespace/model/file.rb', line 151

def get_coverage_meta(api, chrom)
  is_init
  is_valid_file_option('bam')
  set_attr('Id', get_attr('HrefCoverage').split('/').last)
  return api.get_coverage_meta_info(get_attr('Id'), chrom)
end

#get_file_url(api) ⇒ Object

Return the S3 URL of the file.

api

A BaseSpaceAPI instance with read access to the file object.



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# File 'lib/basespace/model/file.rb', line 109

def get_file_url(api)
  return api.file_url(get_attr('Id'))
end

#get_interval_coverage(api, chrom, start_pos, end_pos) ⇒ Object

Return a coverage object for the specified region and chromosome.

api

BaseSpaceAPI instance.

chrom

Chromosome as a string - for example ‘chr2’.

start_pos

The start position of region of interest as a string.

end_pos

The end position of region of interest as a string.



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# File 'lib/basespace/model/file.rb', line 126

def get_interval_coverage(api, chrom, start_pos, end_pos)
  is_init
  is_valid_file_option('bam')
  set_attr('Id', get_attr('HrefCoverage').split('/').last)
  return api.get_interval_coverage(get_attr('Id'), chrom, start_pos, end_pos)
end

#get_variant_meta(api) ⇒ Object

Return the the meta info for a VCF file as a VariantInfo object.

api

BaseSpaceAPI instance.



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# File 'lib/basespace/model/file.rb', line 161

def get_variant_meta(api)
  is_init
  is_valid_file_option('vcf')
  set_attr('Id', get_attr('HrefVariants').split('/').last)
  return api.get_variant_metadata(get_attr('Id'), 'txt')
end

#is_init ⇒ Object

Tests if the File instance has been initialized.

Throws ModelNotInitializedError, if the instance has not been populated yet.

Raises:



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# File 'lib/basespace/model/file.rb', line 76

def is_init
  raise ModelNotInitializedError.new('The File model has not been initialized yet') unless get_attr('Id')
end

#is_valid_file_option(filetype) ⇒ Object

Tests if the File instance matches the filetype parameter.

filetype

The filetype for coverage or variant requests (bam|vcf).



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# File 'lib/basespace/model/file.rb', line 83

def is_valid_file_option(filetype)
  if filetype == 'bam'
    raise WrongFiletypeError.new(get_attr('Name')) unless get_attr('HrefCoverage')
  end
  if filetype == 'vcf'
    raise WrongFiletypeError.new(get_attr('Name')) unless get_attr('HrefVariants')
  end
end

#to_s ⇒ Object

Returns the name of the file, its ID, size and upload status.



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# File 'lib/basespace/model/file.rb', line 59

def to_s
  str = get_attr('Name')
  begin
    str += " - id: '#{get_attr('Id')}', size: '#{get_attr('Size')}'"
    str += ", status: '#{get_attr('UploadStatus')}'" if get_attr('UploadStatus')
  rescue => err
    # [TODO] What to do with this 'err'?
    $stderr.puts "    # ----- File#to_s ----- "
    $stderr.puts "    # Error: #{err}"
    $stderr.puts "    # "
  end
  return str
end