Started on normalization

1 files changed, 0 insertions, 67 deletions

diff --git a/workflows/pull-data/genbank/sparql-fetch-ids b/workflows/pull-data/genbank/sparql-fetch-ids
deleted file mode 100755
index 19b2d82..0000000
--- a/workflows/pull-data/genbank/sparql-fetch-ids
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/usr/bin/env ruby
-#
-# Use a SPARQL query to fetch all IDs in the PubSeq database
-#
-#   sparql-fetch-ids > pubseq_ids.txt
-#
-# Note: requires Ruby 3.x. Older Ruby gives a syntax error
-
-require 'net/http'
-require 'json'
-require 'ostruct'
-require 'erb'
-require 'pp'
-
-MAX=5_000
-
-SPARQL_HEADER="
-prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-prefix dc: <http://purl.org/dc/terms/>
-prefix schema: <https://schema.org/>
-PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
-"
-
-# Build a SPARQL query, submit and return results. Apply transform
-# lambda when passed in
-def sparql query, transform = nil
-  api_url = "http://sparql.genenetwork.org/sparql/?default-graph-uri=&format=application%2Fsparql-results%2Bjson&timeout=0&debug=on&run=+Run+Query+&query=#{ERB::Util.url_encode(SPARQL_HEADER + query)}"
-
-  response = Net::HTTP.get_response(URI.parse(api_url))
-  data = JSON.parse(response.body,symbolize_names: true)
-  data => { head: { vars: }, results: { bindings: results} }
-  vars = vars.map { |v| v.to_sym }
-  results.map { |rec|
-    # return results after transforming to a Hash and applying the
-    # optional transform lambda. Note the transform can not only
-    # reduce results, or create an array, but also may transform into
-    # an OpenStruct.
-    res = {}
-    vars.each { |name| res[name] = rec[name][:value] }
-    if transform
-      transform.call(res)
-    else
-      res
-    end
-  }
-end
-
-start = 0
-num = MAX
-begin
-  query = "
-SELECT DISTINCT ?id
-FROM <http://covid-19.genenetwork.org/graph/metadata.ttl>
-WHERE {
-
-  ?arvid <http://biohackathon.org/bh20-seq-schema/original_fasta_label> ?id .
-
-} LIMIT #{num} OFFSET #{start}
-"
-  list = sparql(query, lambda { |rec| rec[:id] })
-  list.each do | l |
-    print(l,"\n")
-  end
-  $stderr.print("#{start}-#{start+list.size}:#{list.first}\n") # show progress
-  start += num
-end while list.size == MAX