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

.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 ="(;allCohorts\n(fn []\n(map :cohort\n  (query\n    {:select [[#sql/call [:distinct #sql/call [:ifnull :cohort \"(unassigned)\"]] :cohort]]\n    :from [:dataset]})))\n)\n  EOF\n\n  self.query query, hub\nend\n"

.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