Module: Xena

Extended by:
Resource
Defined in:
lib/rbbt/sources/Xena.rb

Constant Summary collapse

DEFAULT_XENA_HUB = 
"https://ucscpublic.xenahubs.net"
TCGA_HUB = 
"https://tcga.xenahubs.net/"

Class Method Summary collapse

Class Method Details

.cohort_dataset(cohort, hub = DEFAULT_XENA_HUB) ⇒ Object 



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# File 'lib/rbbt/sources/Xena.rb', line 52

def self.cohort_dataset(cohort, hub = DEFAULT_XENA_HUB)
  query =<<-EOF
(; datasetList
(fn [cohorts]
  (let [count-table {:select [[:dataset.name :dname] [:%count.value :count]]
                     :from [:dataset]
                     :join [:field [:= :dataset.id :dataset_id]
                     :code [:= :field.id :field_id]]
                     :group-by [:dataset.name]
                     :where [:= :field.name "sampleID"]}]
      (query {:select [:d.name :d.longtitle :count :d.type :d.datasubtype :d.probemap :d.text :d.status [:pm-dataset.text :pmtext]]
                 :from [[:dataset :d]]
                 :left-join [[:dataset :pm-dataset] [:= :pm-dataset.name :d.probemap]
                              count-table [:= :dname :d.name]]
                 :where [:in :d.cohort cohorts]})
))
 ["#{ cohort }"])
  EOF

  self.query(query, hub)
end

.cohorts(hub = DEFAULT_XENA_HUB) ⇒ Object 



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# File 'lib/rbbt/sources/Xena.rb', line 38

def self.cohorts(hub = DEFAULT_XENA_HUB)
  query =<<-EOF
(;allCohorts
(fn []
(map :cohort
  (query
    {:select [[#sql/call [:distinct #sql/call [:ifnull :cohort "(unassigned)"]] :cohort]]
    :from [:dataset]})))
)
  EOF

  self.query query, hub
end

.query(query, hub = DEFAULT_XENA_HUB) ⇒ Object

self.search_paths = {} self.search_paths = :lib



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# File 'lib/rbbt/sources/Xena.rb', line 18

def self.query(query, hub = DEFAULT_XENA_HUB)
  url = File.join(hub, 'data/')
  
  uri = URI.parse(url)
  http = Net::HTTP.new(uri.host, uri.port)
  http.use_ssl = true

  header = {'Content-Type': 'text/plain'}
  request = Net::HTTP::Post.new(uri.request_uri, header)
  request.body = query
  response = http.request(request)

  JSON.parse(response.body)
end

.tsv(file, hub = DEFAULT_XENA_HUB) ⇒ Object 



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# File 'lib/rbbt/sources/Xena.rb', line 33

def self.tsv(file, hub = DEFAULT_XENA_HUB)
  url = "#{hub}/download/#{file}"
  TSV.open(url, :monitor => true, :header_hash => '')
end