Module: Sylfy::CBioPortal::REST

Defined in:
lib/sylfy/service/cbioportal.rb

Constant Summary collapse

BASEURI = 
URI.parse('http://www.cbioportal.org')
HTTP =

BASEURI = URI.parse(‘www.cbioportal.org/public-portal/webservice.do?’)

Net::HTTP.new(BASEURI.host, BASEURI.port)

Class Method Summary collapse

Class Method Details

.getCancerStudies ⇒ array of Hash

internal method supporting all ENSEMBLREST service

Parameters:

Returns:

  • (array of Hash) —

    results



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# File 'lib/sylfy/service/cbioportal.rb', line 65

def getCancerStudies()
  get_path = "/public-portal/webservice.do?cmd=getCancerStudies"
  return Sylfy::CBioPortal::REST.service(get_path)
end

.getCaseLists(cancer_study_id) ⇒ array of Hash

internal method supporting all ENSEMBLREST service

Parameters:

  • cancer_study_id (String) —

    service get_path

Returns:

  • (array of Hash) —

    results



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# File 'lib/sylfy/service/cbioportal.rb', line 87

def getCaseLists(cancer_study_id)
  get_path = "/public-portal/webservice.do?cmd=getCaseLists&cancer_study_id=#{cancer_study_id}"
  return Sylfy::CBioPortal::REST.service(get_path)
end

.getClinicalData(case_set_id) ⇒ array of Hash

internal method supporting all ENSEMBLREST service

Parameters:

  • case_set_id (String) —

    case set ID (required)

Returns:

  • (array of Hash) —

    results



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# File 'lib/sylfy/service/cbioportal.rb', line 129

def getClinicalData(case_set_id)
  get_path = "/public-portal/webservice.do?cmd=getClinicalData&case_set_id=#{case_set_id}"
  return Sylfy::CBioPortal::REST.service(get_path)
end

.getGeneticProfiles(cancer_study_id) ⇒ array of Hash

internal method supporting all ENSEMBLREST service

Parameters:

  • cancer_study_id (String) —

    service get_path

Returns:

  • (array of Hash) —

    results



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# File 'lib/sylfy/service/cbioportal.rb', line 76

def getGeneticProfiles(cancer_study_id)
  get_path = "/public-portal/webservice.do?cmd=getGeneticProfiles&cancer_study_id=#{cancer_study_id}"
  return Sylfy::CBioPortal::REST.service(get_path)
end

.getMutationData(case_set_id, genetic_profile_id, gene_list) ⇒ array of Hash

internal method supporting all ENSEMBLREST service

Parameters:

  • case_set_id (String) —

    case set ID (required)

  • genetic_profile_id (String) —

    one or more genetic profile IDs (required). Multiple genetic profile IDs must be separated by comma (,) characters, or URL encoded spaces, e.g. +

  • gene_list (String) —

    one or more genes, specified as HUGO Gene Symbols or Entrez Gene IDs (required). Multiple genes must be separated by comma (,) characters, or URL encoded spaces, e.g. +

Returns:

  • (array of Hash) —

    results



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# File 'lib/sylfy/service/cbioportal.rb', line 118

def getMutationData(case_set_id, genetic_profile_id, gene_list)
  get_path = "/public-portal/webservice.do?cmd=getMutationData&case_set_id=#{case_set_id}&genetic_profile_id=#{genetic_profile_id}&gene_list=#{gene_list}"
  return Sylfy::CBioPortal::REST.service(get_path)
end

.getProfileData(case_set_id, genetic_profile_id, gene_list) ⇒ array of Hash

internal method supporting all ENSEMBLREST service

Parameters:

  • case_set_id (String) —

    case set ID (required)

  • genetic_profile_id (String) —

    one or more genetic profile IDs (required). Multiple genetic profile IDs must be separated by comma (,) characters, or URL encoded spaces, e.g. +

  • gene_list (String) —

    one or more genes, specified as HUGO Gene Symbols or Entrez Gene IDs (required). Multiple genes must be separated by comma (,) characters, or URL encoded spaces, e.g. +

Returns:

  • (array of Hash) —

    results



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# File 'lib/sylfy/service/cbioportal.rb', line 103

def getProfileData(case_set_id, genetic_profile_id, gene_list)
  get_path = "/public-portal/webservice.do?cmd=getProfileData&case_set_id=#{case_set_id}&genetic_profile_id=#{genetic_profile_id}&gene_list=#{gene_list}"
  return Sylfy::CBioPortal::REST.service(get_path)
end

.getTypesOfCancer ⇒ array of Hash

internal method supporting all ENSEMBLREST service

Parameters:

Returns:

  • (array of Hash) —

    results



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# File 'lib/sylfy/service/cbioportal.rb', line 50

def getTypesOfCancer()
  get_path = "/public-portal/webservice.do?cmd=getTypesOfCancer"
  return Sylfy::CBioPortal::REST.service(get_path)
end

.service(get_path, csv_opts = {}) ⇒ array of Hash

internal method supporting all ENSEMBLREST service

Parameters:

Returns:

  • (array of Hash) —

    results



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# File 'lib/sylfy/service/cbioportal.rb', line 29

def service(get_path, csv_opts = {})
  request = Net::HTTP::Get.new(get_path)
  response = HTTP.request(request)
  
  if response.code != "200"
    raise Sylfy::Service::ParameterError, "Invalid response: #{response.code}"
  else
                    return CSV.parse(response.body, {col_sep: "\t", skip_lines: /^#/, headers: true}.merge(csv_opts))
  end
end