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module OpenTox
class Download
def self.pubchem_classification aid: , active: , inactive: , species: , endpoint:, qmrf: nil
aid_url = File.join PUBCHEM_URI, "assay/aid/#{aid}"
# Get assay data in chunks
# Assay record retrieval is limited to 10000 SIDs
# https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest-tutorial$_Toc458584435
list = JSON.parse(RestClientWrapper.get(File.join aid_url, "sids/JSON?list_return=listkey").to_s)["IdentifierList"]
listkey = list["ListKey"]
size = list["Size"]
start = 0
csv = []
while start < size
url = File.join aid_url, "CSV?sid=listkey&listkey=#{listkey}&listkey_start=#{start}&listkey_count=10000"
csv += CSV.parse(RestClientWrapper.get(url).to_s).select{|r| r[0].match /^\d/} # discard header rows
start += 10000
end
warnings = []
name = endpoint+"-"+species
table = [["SID","SMILES",name]]
csv.each_slice(100) do |slice| # get SMILES in chunks
cids = slice.collect{|s| s[2]}
pubchem_cids = []
JSON.parse(RestClientWrapper.get(File.join(PUBCHEM_URI,"compound/cid/#{cids.join(",")}/property/CanonicalSMILES/JSON")).to_s)["PropertyTable"]["Properties"].each do |prop|
i = cids.index(prop["CID"].to_s)
value = slice[i][3]
if value == "Active"
table << [slice[i][1].to_s,prop["CanonicalSMILES"],active]
pubchem_cids << prop["CID"].to_s
elsif value == "Inactive"
table << [slice[i][1].to_s,prop["CanonicalSMILES"],inactive]
pubchem_cids << prop["CID"].to_s
else
warnings << "Ignoring CID #{prop["CID"]}/ SMILES #{prop["CanonicalSMILES"]}, because PubChem activity is '#{value}'."
end
end
(cids-pubchem_cids).each { |cid| warnings << "Could not retrieve SMILES for CID '#{cid}', all entries are ignored." }
end
File.open(File.join(File.dirname(__FILE__),"..","data",name+".csv"),"w+"){|f| f.puts table.collect{|row| row.join(",")}.join("\n")}
meta = {
:species => species,
:endpoint => endpoint,
:source => aid_url,
:qmrf => qmrf,
:warnings => warnings
}
File.open(File.join(File.dirname(__FILE__),"..","data",name+".json"),"w+"){|f| f.puts meta.to_json}
end
end
end
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