Class: Bio::BaseSpace::BaseSpaceAPI

Inherits:
BaseAPI
  • Object
show all
Defined in:
lib/basespace/api/basespace_api.rb

Overview

The main API class used for all communication with the BaseSpace REST server.

Constant Summary collapse

TOKEN_URL =

URIs for obtaining a access token, user verification code, and app trigger information.

'/oauthv2/token'
DEVICE_URL = 
"/oauthv2/deviceauthorization"
WEB_AUTHORIZE = 
'/oauth/authorize'

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from BaseAPI

#get_access_token, #get_server_uri, #hash2urlencode, #list_request, #make_curl_request, #set_access_token, #set_timeout, #single_request, #to_s, #to_str, #update_access_token

Constructor Details

#initialize(client_key, client_secret, api_server, version, app_session_id = nil, access_token = nil) ⇒ BaseSpaceAPI

Create a new object for communicating with the BaseSpace REST server; preferred method of calling is through the ‘start’ class method.

client_key

Client key to use for authentication (provided when registering an App).

client_secret

Client secret key to use for authentication (provided when registering an App).

api_server

URI of the BaseSpace API server.

version

API version to use.

app_session_id

App session ID that was generated by application triggering.

access_token

Access token provided by App triggering.



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# File 'lib/basespace/api/basespace_api.rb', line 56

def initialize(client_key, client_secret, api_server, version, app_session_id = nil, access_token = nil)
  end_with_slash = %r(/$)
  unless api_server[end_with_slash]
    api_server += '/'
  end
  
  @app_session_id  = app_session_id
  @key             = client_key
  @secret          = client_secret
  @api_server      = api_server + version
  @version         = version
  @weburl          = api_server.sub('api.', '')
  @timeout         = nil

  super(access_token)
end

Instance Attribute Details

#app_session_id ⇒ Object (readonly)

Returns the value of attribute app_session_id.



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# File 'lib/basespace/api/basespace_api.rb', line 36

def app_session_id
  @app_session_id
end

Class Method Details

.start ⇒ Object

Load credentials and start a new BaseSpace session.



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# File 'lib/basespace/api/basespace_api.rb', line 39

def self.start
  if opts = Bio::BaseSpace.load_credentials
    self.new(opts['client_id'], opts['client_secret'], opts['basespace_url'], opts['api_version'], opts['app_session_id'], opts['access_token'])
  else
    raise "Please specify your BaseSpace credentials in the credentials.json file or use Bio::BaseSpace::BaseSpaceAPI.new with arguments"
  end
end

Instance Method Details

#app_result_file_upload(id, local_path, file_name, directory, content_type, multipart = 0) ⇒ Object

Uploads a file associated with an AppResult to BaseSpace and returns the corresponding file object.

id

AppResult ID.

local_path

The local path to the file to be uploaded.

file_name

The desired filename in the AppResult folder on the BaseSpace server.

directory

The directory the file should be placed in.

content_type

The content-type of the file.



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# File 'lib/basespace/api/basespace_api.rb', line 612

def app_result_file_upload(id, local_path, file_name, directory, content_type, multipart = 0)
  my_model       = 'FileResponse'
  resource_path  = '/appresults/{Id}/files'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'POST'
  query_params   = {}
  header_params  = {}
  verbose        = false

  query_params['name']           = file_name
  query_params['directory']      = directory 
  header_params['Content-Type']  = content_type

  # three cases, two for multipart, starting 
  if multipart == 1
    query_params['multipart']  = 'true'
    post_data    = nil
    force_post   = true
    # Set force post as this need to use POST though no data is being streamed
    return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose, force_post)
  elsif multipart == 2
    query_params = {'uploadstatus' => 'complete'}
    post_data    = nil
    force_post   = true
    # Set force post as this need to use POST though no data is being streamed
    return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose, force_post)
  else
    post_data = ::File.open(local_path).read
    return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose)
  end
end

#create_app_result(id, name, desc, samples = [], app_session_id = nil) ⇒ Object

Create an AppResult object.

id

ID of the project in which the AppResult is to be added.

name

The name of the AppResult.

desc

A describtion of the AppResult.

samples

List of samples (if any).

app_session_id

If no app_session_id is given, the id used to initialize the BaseSpaceAPI instance will be used. If app_session_id is set equal to an empty string, a new appsession will be created.



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# File 'lib/basespace/api/basespace_api.rb', line 560

def create_app_result(id, name, desc, samples = [], app_session_id = nil)
  if (not @app_session_id) and (not app_session_id)
    raise "This BaseSpaceAPI instance has no app_session_id set and no alternative id was supplied for method create_app_result"
  end
  
  my_model       = 'AppResultResponse'
  resource_path  = '/projects/{ProjectId}/appresults'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{ProjectId}', id)
  method         = 'POST'
  query_params   = {}
  header_params  = {}
  post_data      = {}
  verbose        = false
  
  if app_session_id
    query_params['appsessionid']  = app_session_id
  else
    query_params['appsessionid']  = @app_session_id      # default case, we use the current appsession
  end
  
  # add the sample references
  if samples.length > 0
    ref = []
    samples.each do |s|
      d = { "Rel" => "using", "Type" => "Sample", "HrefContent" => @version + '/samples/' + s.id }
      ref << d
    end
    post_data['References']  = ref
  end

  # case, an appSession is provided, we need to check if the a
  if query_params.has_key?('appsessionid')
    sid = query_params['appsessionid']
    session = get_app_session(sid)
    unless session.can_work_on
      raise 'AppSession status must be "running," to create and AppResults. Current status is: ' + session.status
    end
  end
      
  post_data['Name']         = name
  post_data['Description']  = desc
  return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose)
end

#create_project(name) ⇒ Object

Creates a project with the specified name and returns a project object. If a project with this name already exists, the existing project is returned.

name

Name of the project.



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# File 'lib/basespace/api/basespace_api.rb', line 240

def create_project(name)
  #: v1pre3/projects, it requires 1 input parameter which is Name
  my_model       = 'ProjectResponse'
  resource_path  = '/projects/'
  resource_path  = resource_path.sub('{format}', 'json')
  method         = 'POST'
  query_params   = {}
  header_params  = {}
  post_data      = {}
  post_data['Name']  = name
  verbose        = false
  return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose)
end

#file_download(id, local_dir, name, range = []) ⇒ Object

Downloads a BaseSpace file to a local directory.

id

File ID.

local_dir

The local directory to place the file in.

name

The name of the local file.

range

The byte range of the file to retrieve (not yet implemented).



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# File 'lib/basespace/api/basespace_api.rb', line 651

def file_download(id, local_dir, name, range = [])  #@ReservedAssignment
  resource_path  = '/files/{Id}/content'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = {}
  header_params  = {}

  query_params['redirect'] = 'meta' # we need to add this parameter to get the Amazon link directly 
  
  response = @api_client.call_api(resource_path, method, query_params, nil, header_params)
  if response['ResponseStatus'].has_key?('ErrorCode')
    raise 'BaseSpace error: ' + response['ResponseStatus']['ErrorCode'].to_s + ": " + response['ResponseStatus']['Message']
  end
  
  # get the Amazon URL 
  file_url = response['Response']['HrefContent']

  header = nil
  unless range.empty?
    # puts "Case range request" 
    header = { 'Range' => format('bytes=%s-%s', range[0], range[1]) }
  end
  
  # Do the download
  ::File.open(::File.join(local_dir, name), "wb") do |fp|
    http_opts = {}
    uri = URI.parse(file_url)
    if uri.scheme == "https"
      http_opts[:use_ssl] = true
    end
    res = Net::HTTP.start(uri.host, uri.port, http_opts) { |http|
      # [TODO] Do we need user and pass here also?
      case RUBY_VERSION
      when /^1.9/
        if uri.query and not uri.query.empty?
          http.get(uri.path + '?' + uri.query, header)
        else
          http.get(uri.path, header)
        end
      else
        http.get(uri, header)
      end
    }
    fp.print res.body
  end

  return 1
end

#file_url(id) ⇒ Object

Returns URL of a file on S3.

id

File ID.



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# File 'lib/basespace/api/basespace_api.rb', line 704

def file_url(id)  # @ReservedAssignment
  resource_path  = '/files/{Id}/content'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = {}
  header_params  = {}

  query_params['redirect'] = 'meta' # we need to add this parameter to get the Amazon link directly 
  
  response = @api_client.call_api(resource_path, method, query_params, nil, header_params)
  if response['ResponseStatus'].has_key?('ErrorCode')
    raise 'BaseSpace error: ' + response['ResponseStatus']['ErrorCode'].to_s + ": " + response['ResponseStatus']['Message']
  end
  
  # return the Amazon URL 
  return response['Response']['HrefContent']
end

#filter_variant_set(id, chrom, start_pos, end_pos, format, qp = {'SortBy' => 'Position'}) ⇒ Object

List the variants in a set of variants. Maximum returned records is 1000.

id

ID of the variant file.

chrom

The chromosome of interest.

start_pos

The start position of the sequence of interest.

end_pos

The start position of the sequence of interest.

format

Set to ‘vcf’ to get the results as lines in VCF format.

qp

An (optional) object of type QueryParameters for custom sorting and filtering.



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# File 'lib/basespace/api/basespace_api.rb', line 495

def filter_variant_set(id, chrom, start_pos, end_pos, format, qp = {'SortBy' => 'Position'})
  query_pars     = qp.kind_of?(Hash) ? QueryParameters.new(qp) : qp
  query_pars.validate
  my_model       = 'Variant'
  resource_path  = '/variantset/{Id}/variants/chr{Chrom}'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Chrom}', chrom)
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = query_pars.get_parameter_dict
  header_params  = {}
  query_params['StartPos']  = start_pos
  query_params['EndPos']    = end_pos
  query_params['Format']    = format
  verbose        = false
  return list_request(my_model, resource_path, method, query_params, header_params, verbose)
end

#get_access(obj, access_type = 'write', web = nil, redirect_url = nil, state = nil) ⇒ Object

Request access to a data object.

obj

The data object we wish to get access to.

access_type

The type of access (read|write), default is write.

web

If the App is web-based, then set this parameter to ‘true’. The default value is false, which means that the request is for a device based App.

redirect_url

For the web-based case, a redirection URL.

state

(unclear from Python port)



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# File 'lib/basespace/api/basespace_api.rb', line 177

def get_access(obj, access_type = 'write', web = nil, redirect_url = nil, state = nil)
  scope_str = obj.get_access_str(access_type)
  if web
    return get_web_verification_code(scope_str, redirect_url, state)
  else
    return get_verification_code(scope_str)
  end
end

#get_accessible_runs_by_user(id, qp = {}) ⇒ Object

Returns a list of accessible runs for the User with the given ID.

id

User id.

qp

An object of type QueryParameters for custom sorting and filtering.



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# File 'lib/basespace/api/basespace_api.rb', line 335

def get_accessible_runs_by_user(id, qp = {})
  query_pars     = qp.kind_of?(Hash) ? QueryParameters.new(qp) : qp
  query_pars.validate
  my_model       = 'RunCompact'
  resource_path  = '/users/{Id}/runs'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = query_pars.get_parameter_dict
  header_params  = {}
  return list_request(my_model, resource_path, method, query_params, header_params)
end

#get_app_result_by_id(id) ⇒ Object

Returns an AppResult object corresponding to ID.

param id

The ID of the AppResult.



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# File 'lib/basespace/api/basespace_api.rb', line 271

def get_app_result_by_id(id)
  my_model       = 'AppResultResponse'
  resource_path  = '/appresults/{Id}'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = {}
  header_params  = {}
  return single_request(my_model, resource_path, method, query_params, header_params)
end

#get_app_result_files(id, qp = {}) ⇒ Object

Returns a list of File objects for the AppResult with the given ID.

id

The ID of the AppResult.

+qp: An object of type QueryParameters for custom sorting and filtering.



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# File 'lib/basespace/api/basespace_api.rb', line 286

def get_app_result_files(id, qp = {})
  query_pars     = qp.kind_of?(Hash) ? QueryParameters.new(qp) : qp
  query_pars.validate
  my_model       = 'File'
  resource_path  = '/appresults/{Id}/files'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = query_pars.get_parameter_dict
  header_params  = {}
  verbose        = false
  return list_request(my_model, resource_path, method, query_params, header_params, verbose)
end

#get_app_results_by_project(id, qp = {}, statuses = []) ⇒ Object

Returns a list of AppResult object associated with the project with ID.

id

The project ID.

qp

An object of type QueryParameters for custom sorting and filtering.

statuses

A list of AppResult statuses to filter by.



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# File 'lib/basespace/api/basespace_api.rb', line 353

def get_app_results_by_project(id, qp = {}, statuses = [])
  query_pars     = qp.kind_of?(Hash) ? QueryParameters.new(qp) : qp
  query_pars.validate
  my_model       = 'AppResult'
  resource_path  = '/projects/{Id}/appresults'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = query_pars.get_parameter_dict
  unless statuses.empty?
    query_params['Statuses'] = statuses.join(",")
  end
  header_params  = {}
  verbose        = false
  return list_request(my_model, resource_path, method, query_params, header_params, verbose)
end

#get_app_session(id = nil) ⇒ Object

Returns an AppSession instance containing user and data-type the app was triggered by/on.

id

The AppSessionId, ID not supplied the AppSessionId used for instantiating the BaseSpaceAPI instance.



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# File 'lib/basespace/api/basespace_api.rb', line 123

def get_app_session(id = nil)
  if (not @app_session_id) and (not id)
    raise "This BaseSpaceAPI instance has no app_session_id set and no alternative id was supplied for method get_app_session"
  end

  # if (not id) and (not @key)
  #   raise "This BaseSpaceAPI instance has no client_secret (key) set and no alternative id was supplied for method get_app_session"
  # end
  
  resource_path = @api_server + '/appsessions/{AppSessionId}'
  if id
    resource_path = resource_path.sub('{AppSessionId}', id)
  else
    resource_path = resource_path.sub('{AppSessionId}', @app_session_id)
  end
  if $DEBUG
    $stderr.puts "    # ----- BaseSpaceAPI#get_app_session ----- "
    $stderr.puts "    # resource_path: #{resource_path}"
    $stderr.puts "    # "
  end
  uri = URI.parse(resource_path)
  uri.user = @key
  uri.password = @secret
  #response = Net::HTTP.get(uri)
  http_opts = {}
  if uri.scheme == "https"
    http_opts[:use_ssl] = true
  end
  response = Net::HTTP.start(uri.host, uri.port, http_opts) { |http|
    case RUBY_VERSION
    when /^1.9/
      if uri.query and not uri.query.empty?
        request = Net::HTTP::Get.new(uri.path + '?' + uri.query)
      else
        request = Net::HTTP::Get.new(uri.path)
      end
    else
      request = Net::HTTP::Get.new(uri)
    end
    request.basic_auth uri.user, uri.password
    http.request(request)
  }
  obj = JSON.parse(response.body)
  # TODO add exception if response isn't OK, e.g. incorrect server gives path not recognized
  return get_trigger_object(obj)
end

#get_app_session_by_id(id) ⇒ Object

Returns the AppSession instance identified by the given ID.

id

The ID of the AppSession.



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# File 'lib/basespace/api/basespace_api.rb', line 115

def get_app_session_by_id(id)
  # TO_DO make special case for access-token only retrieval
  return get_app_session(id)
end

#get_available_genomes(qp = {}) ⇒ Object

Returns a list of all available genomes.

qp

An object of type QueryParameters for custom sorting and filtering.



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# File 'lib/basespace/api/basespace_api.rb', line 455

def get_available_genomes(qp = {})
  query_pars     = qp.kind_of?(Hash) ? QueryParameters.new(qp) : qp
  query_pars.validate
  my_model       = 'GenomeV1'
  resource_path  = '/genomes'
  resource_path  = resource_path.sub('{format}', 'json')
  method         = 'GET'
  query_params   = query_pars.get_parameter_dict
  header_params  = {}
  verbose        = false
  return list_request(my_model, resource_path, method, query_params, header_params, verbose)
end

#get_coverage_meta_info(id, chrom) ⇒ Object

Returns Metadata about coverage as a CoverageMetadata instance.

id

ID of a BAM file.

chrom

Chromosome to query.



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# File 'lib/basespace/api/basespace_api.rb', line 539

def get_coverage_meta_info(id, chrom)
  my_model       = 'CoverageMetaResponse'
  resource_path  = '/coverage/{Id}/{Chrom}/meta'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Chrom}', chrom)
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = {}
  header_params  = {}
  post_data      = nil
  verbose        = false
  return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose)
end

#get_file_by_id(id) ⇒ Object

Returns a file object by ID.

id

The ID of the file.



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# File 'lib/basespace/api/basespace_api.rb', line 425

def get_file_by_id(id)
  my_model       = 'FileResponse'
  resource_path  = '/files/{Id}'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = {}
  header_params  = {}
  post_data      = nil
  verbose        = false
  return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose)
end

#get_files_by_sample(id, qp = {}) ⇒ Object

Returns a list of File objects associated with sample with ID.

id

Sample ID.

qp

An object of type QueryParameters for custom sorting and filtering.



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# File 'lib/basespace/api/basespace_api.rb', line 408

def get_files_by_sample(id, qp = {})
  query_pars     = qp.kind_of?(Hash) ? QueryParameters.new(qp) : qp
  query_pars.validate
  my_model       = 'File'
  resource_path  = '/samples/{Id}/files'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = query_pars.get_parameter_dict
  header_params  = {}
  verbose        = false
  return list_request(my_model, resource_path, method, query_params, header_params, verbose)
end

#get_genome_by_id(id) ⇒ Object

Returns an instance of Genome with the specified ID.

id

The genome ID.



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# File 'lib/basespace/api/basespace_api.rb', line 441

def get_genome_by_id(id)
  my_model       = 'GenomeResponse'
  resource_path  = '/genomes/{Id}'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = {}
  header_params  = {}
  return single_request(my_model, resource_path, method, query_params, header_params)
end

#get_interval_coverage(id, chrom, start_pos = nil, end_pos = nil) ⇒ Object

Mean coverage levels over a sequence interval. Returns an instance of CoverageResponse.

id

Chromosome to query.

chrom

The ID of the resource.

start_pos

Get coverage starting at this position. Default is 1.

end_pos

Get coverage up to and including this position. Default is start_pos + 1280.



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# File 'lib/basespace/api/basespace_api.rb', line 519

def get_interval_coverage(id, chrom, start_pos = nil, end_pos = nil)
  my_model       = 'CoverageResponse'
  resource_path  = '/coverage/{Id}/{Chrom}'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Chrom}', chrom)
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = {}
  header_params  = {}
  query_params['StartPos']  = @api_client.to_path_value(start_pos)
  query_params['EndPos']    = @api_client.to_path_value(end_pos)
  post_data      = nil
  verbose        = false
  return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose)
end

#get_project_by_id(id) ⇒ Object

Request a project object by ID.

id

The ID of the project.



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# File 'lib/basespace/api/basespace_api.rb', line 303

def get_project_by_id(id)
  my_model       = 'ProjectResponse'
  resource_path  = '/projects/{Id}'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = {}
  header_params  = {}
  return single_request(my_model, resource_path, method, query_params, header_params)
end

#get_project_by_user(id, qp = {}) ⇒ Object

Returns a list available projects for a User with the specified ID.

id

The ID of the user.

qp

An object of type QueryParameters for custom sorting and filtering.



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# File 'lib/basespace/api/basespace_api.rb', line 318

def get_project_by_user(id, qp = {})
  query_pars     = qp.kind_of?(Hash) ? QueryParameters.new(qp) : qp
  query_pars.validate
  my_model       = 'Project'
  resource_path  = '/users/{Id}/projects'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id) if id != nil
  method         = 'GET'
  query_params   = query_pars.get_parameter_dict
  header_params  = {}
  return list_request(my_model, resource_path, method, query_params, header_params)
end

#get_sample_by_id(id) ⇒ Object

Returns a Sample object.

id

The ID of the sample.



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# File 'lib/basespace/api/basespace_api.rb', line 391

def get_sample_by_id(id)
  my_model       = 'SampleResponse'
  resource_path  = '/samples/{Id}'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = {}
  header_params  = {}
  post_data      = nil
  verbose        = false
  return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose)
end

#get_samples_by_project(id, qp = {}) ⇒ Object

Returns a list of samples associated with a project with ID.

id

The ID of the project.

qp

An object of type QueryParameters for custom sorting and filtering.



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# File 'lib/basespace/api/basespace_api.rb', line 374

def get_samples_by_project(id, qp = {})
  query_pars     = qp.kind_of?(Hash) ? QueryParameters.new(qp) : qp
  query_pars.validate
  my_model       = 'Sample'
  resource_path  = '/projects/{Id}/samples'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = query_pars.get_parameter_dict
  header_params  = {}
  verbose        = false
  return list_request(my_model, resource_path, method, query_params, header_params, verbose)
end

#get_trigger_object(obj) ⇒ Object

This method is not for general use and should only be called from ‘get_app_session’.

obj

Application trigger JSON.



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# File 'lib/basespace/api/basespace_api.rb', line 76

def get_trigger_object(obj)
  if obj['ResponseStatus'].has_key?('ErrorCode')
    raise 'BaseSpace error: ' + obj['ResponseStatus']['ErrorCode'].to_s + ": " + obj['ResponseStatus']['Message']
  end
  #access_token = nil  # '' is false in Python but APIClient.new only raises when the value is None (not '')
  access_token = ''
  temp_api = APIClient.new(access_token, @api_server)
  response = temp_api.deserialize(obj, 'AppSessionResponse')
  # AppSessionResponse object has a response method which returns a AppSession object
  app_sess = response.get_attr('Response')
  # AppSession object has a serialize_references method which converts an array of
  # AppSessionLaunchObject objects by calling serialize_object method in each object.
  # The method in turn calls the serialize_object method of the given BaseSpaceAPI object
  # with @content ('dict') and @type ('str') arguments. Returns an array of serialized objects.
  res = app_sess.serialize_references(self)
  return res
end

#get_user_by_id(id) ⇒ Object

Returns the User object corresponding to ID.

id

The ID of the user.



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# File 'lib/basespace/api/basespace_api.rb', line 257

def get_user_by_id(id)
  my_model       = 'UserResponse'
  resource_path  = '/users/{Id}'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = {}
  header_params  = {}
  return single_request(my_model, resource_path, method, query_params, header_params)
end

#get_variant_metadata(id, format) ⇒ Object

Returns a VariantMetadata object for a variant file.

id

ID of the VCF file.

format

Set to ‘vcf’ to get the results as lines in VCF format.



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# File 'lib/basespace/api/basespace_api.rb', line 474

def get_variant_metadata(id, format)
  my_model       = 'VariantsHeaderResponse'
  resource_path  = '/variantset/{Id}'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'GET'
  query_params   = {}
  query_params['Format'] = @api_client.to_path_value(format)
  header_params  = {}
  verbose        = false
  return single_request(my_model, resource_path, method, query_params, header_params, verbose)
end

#get_verification_code(scope) ⇒ Object

Returns the BaseSpace dictionary containing the verification code and verification URL for the user to approve access to a specific data scope.

Corresponding curl call: curlCall = ‘curl -d “response_type=device_code” -d “client_id=’ + client_key + ‘” -d “scope=’ + scope + ‘” ’ + DEVICE_URL

For details see: developer.basespace.illumina.com/docs/content/documentation/authentication/obtaining-access-tokens

scope

The scope that access is requested for.



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# File 'lib/basespace/api/basespace_api.rb', line 196

def get_verification_code(scope)
  #curlCall = 'curl -d "response_type=device_code" -d "client_id=' + @key + '" -d "scope=' + scope + '" ' + @api_server + DEVICE_URL
  #puts curlCall
  unless @key
    raise "This BaseSpaceAPI instance has no client_secret (key) set and no alternative id was supplied for method get_verification_code."
  end
  data = {'client_id' => @key, 'scope' => scope, 'response_type' => 'device_code'}
  return make_curl_request(data, @api_server + DEVICE_URL)
end

#get_web_verification_code(scope, redirect_url, state = nil) ⇒ Object

Generates the URL the user should be redirected to for web-based authentication.

scope: The scope that access is requested for.

redirect_url

The redirect URL.

state

An optional state parameter that will passed through to the redirect response.



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# File 'lib/basespace/api/basespace_api.rb', line 211

def get_web_verification_code(scope, redirect_url, state = nil)
  if (not @key)
    raise "This BaseSpaceAPI instance has no client_id (key) set and no alternative id was supplied for method get_verification_code."
  end
  data = {'client_id' => @key, 'redirect_uri' => redirect_url, 'scope' => scope, 'response_type' => 'code', "state" => state}
  return @weburl + WEB_AUTHORIZE + '?' + hash2urlencode(data)
end

#obtain_access_token(device_code) ⇒ Object

Returns a user specific access token.

device_code

The device code returned by the verification code method.



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# File 'lib/basespace/api/basespace_api.rb', line 222

def obtain_access_token(device_code)
  if (not @key) or (not @secret)
    raise "This BaseSpaceAPI instance has either no client_secret or no client_id set and no alternative id was supplied for method get_verification_code."
  end
  data = {'client_id' => @key, 'client_secret' => @secret, 'code' => device_code, 'grant_type' => 'device', 'redirect_uri' => 'google.com'}
  dict = make_curl_request(data, @api_server + TOKEN_URL)
  return dict['access_token']
end

#serialize_object(d, type) ⇒ Object 



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# File 'lib/basespace/api/basespace_api.rb', line 94

def serialize_object(d, type)
  # [TODO] None (nil) or '' ?
  #access_token = nil
  access_token = ''
  temp_api = APIClient.new(access_token, @api_server)
  if type.downcase == 'project'
    return temp_api.deserialize(d, 'Project')
  end
  if type.downcase == 'sample'
    return temp_api.deserialize(d, 'Sample')
  end
  if type.downcase == 'appresult'
    return temp_api.deserialize(d, 'AppResult')
  end
  return d
end

#set_app_session_state(id, status, summary) ⇒ Object

Set the status of an AppResult object.

id

The id of the AppResult.

status

Status assignment string.

summary

Summary string.



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# File 'lib/basespace/api/basespace_api.rb', line 784

def set_app_session_state(id, status, summary)
  my_model       = 'AppSessionResponse'
  resource_path  = '/appsessions/{Id}'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  method         = 'POST'
  query_params   = {}
  header_params  = {}
  post_data      = {}
  verbose        = false

  status_allowed = ['running', 'complete', 'needsattention', 'aborted', 'error']
  unless status_allowed.include?(status.downcase)
    raise "AppResult state must be in #{status_allowed.inspect}"
  end
  post_data['status']         = status.downcase
  post_data['statussummary']  = summary
  return single_request(my_model, resource_path, method, query_params, header_params, post_data, verbose)
end

#update_privileges(code) ⇒ Object 



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# File 'lib/basespace/api/basespace_api.rb', line 231

def update_privileges(code)
  token = obtain_access_token(code)
  set_access_token(token)
end

#upload_multipart_unit(id, part_number, md5, data) ⇒ Object

Helper method for uploading multipart files, do not call directly.

id

File ID.

part_number

File part to be uploaded.

md5

MD5 sum of datastream.

data

The data-stream to be uploaded.



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# File 'lib/basespace/api/basespace_api.rb', line 730

def upload_multipart_unit(id, part_number, md5, data)
  resource_path  = '/files/{Id}/parts/{partNumber}'
  resource_path  = resource_path.sub('{format}', 'json')
  resource_path  = resource_path.sub('{Id}', id)
  resource_path  = resource_path.sub('{partNumber}', part_number.to_s)
  method         = 'PUT'
  query_params   = {}
  header_params  = {'Content-MD5' => md5.strip()}
  force_post     = false
  out = @api_client.call_api(resource_path, method, query_params, data, header_params, force_post)
  return out
  # curl -v -H "x-access-token: {access token}" \
  #   -H "Content-MD5: 9mvo6qaA+FL1sbsIn1tnTg==" \
  #   -T reportarchive.zipaa \
  #   -X PUT https://api.cloud-endor.illumina.com/v1pre2/files/7094087/parts/1
end