From 0882c2cd0de934d7377fc9d08c306be98612c88a Mon Sep 17 00:00:00 2001 From: "helma@in-silico.ch" Date: Fri, 16 Nov 2018 18:42:42 +0100 Subject: real datasets for testing, test data cleanup, Daphnia import, upper and lower similarity thresholds --- lib/download.rb | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) (limited to 'lib/download.rb') diff --git a/lib/download.rb b/lib/download.rb index 5467167..f17d060 100644 --- a/lib/download.rb +++ b/lib/download.rb @@ -249,11 +249,17 @@ module OpenTox # Download Daphnia dataset from http://www.michem.unimib.it/download/data/acute-aquatic-toxicity-to-daphnia-magna/ into the public folder # The original file requires an email request, this is a temporary workaround def self.daphnia - url = "https://raw.githubusercontent.com/opentox/lazar-public-data/master/regression/daphnia_magna_mmol_log10.csv" + #url = "https://raw.githubusercontent.com/opentox/lazar-public-data/master/regression/daphnia_magna_mmol_log10.csv" + src = File.join(DATA,"parts","toxicity_data.xlsx") name = "Acute_toxicity-Daphnia_magna" $logger.debug name File.open(File.join(DATA,name+".csv"),"w+") do |f| - f.puts RestClientWrapper.get(url).to_s + i = 0 + CSV.parse(`xlsx2csv #{src}`) do |row| + i == 0 ? v = "-log[LC50_mmol/L]" : v = -Math.log10(10**-row[3].to_f*1000) + f.puts [row[0],row[1],v].join(",") + i += 1 + end end meta = { "species": "Daphnia magna", "endpoint": "Acute toxicity", @@ -289,7 +295,7 @@ module OpenTox :qmrf => {:group => "QMRF 4.12. Carcinogenicity", :name => "OECD 451 Carcinogenicity Studies"} } ].each do |assay| - Download.pubchem_classification aid: assay[:aid], species: assay[:species], endpoint: assay[:endpoint], active: "carcinogen", inactive: "non-carcinogen", qmrf: assay[:qmrf] + Download.pubchem_classification aid: assay[:aid], species: assay[:species], endpoint: assay[:endpoint], active: "carcinogenic", inactive: "non-carcinogenic", qmrf: assay[:qmrf] end Download.mutagenicity Download.blood_brain_barrier -- cgit v1.2.3