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require_relative "toxbank-setup.rb"
begin
puts "Service URI is: #{$investigation[:uri]}"
rescue
puts "Configuration Error: $investigation[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb")
exit
end
#TODO: check 4store entries/errors
class UploadTest < MiniTest::Test
def setup
@tmpdir = File.join(File.dirname(__FILE__),"tmp")
FileUtils.mkdir_p @tmpdir
FileUtils.rm_r Dir[File.join @tmpdir, '*']
end
def test_01_get_all
response = `curl -Lk -H "Accept:text/uri-list" -H "subjectid:#{$pi[:subjectid]}" -i #{$investigation[:uri]}`
assert_match /200/, response
end
def test_02_get_inexisting
response = `curl -Lk -H "Accept:text/uri-list" -i -H "subjectid:#{$pi[:subjectid]}" #{$investigation[:uri]}/foo`.chomp
assert_match /401|404/, response
response = `curl -Lk -H "Accept:application/rdf+xml" -i -H "subjectid:#{$pi[:subjectid]}" #{$investigation[:uri]}/999999/metadata`.chomp
assert_match /401|404/, response
end
def test_03_valid_zip_upload
# upload
OpenTox::RestClientWrapper.subjectid = $pi[:subjectid]
["BII-I-1-tb2.zip","E-MTAB-798_philippe-tb2.zip"].each do |f|
puts f
file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", f
response = `curl -Lk -X POST -i -F file="@#{file};type=application/zip" -H "subjectid:#{$pi[:subjectid]}" #{$investigation[:uri]}`.chomp
assert_match /202/, response
taskuri = response.split("\n")[-1]
t = OpenTox::Task.new taskuri
t.wait
puts t.uri
assert_equal true, t.completed?
assert_match t.hasStatus, "Completed"
uri = t.resultURI
metadata = `curl -Lk -H accept:application/rdf+xml -H "subjectid:#{$pi[:subjectid]}" #{uri}/metadata`
assert_match /#{uri}/, metadata
zip = File.join @tmpdir,"tmp.zip"
`curl -Lk -H "Accept:application/zip" -H "subjectid:#{$pi[:subjectid]}" #{uri} > #{zip}`
`unzip -o #{zip} -d #{@tmpdir}`
files = `unzip -l #{File.join File.dirname(__FILE__),"data/toxbank-investigation/valid",f}|grep txt|cut -c 31- | sed 's#^.*/##'`.split("\n")
files.each{|f| assert_equal true, File.exists?(File.join(File.expand_path(@tmpdir),f)) }
# get isatab files
urilist = `curl -Lk -H "subjectid:#{$pi[:subjectid]}" -H "Accept:text/uri-list" #{uri}`.split("\n")
urilist.each do |u|
unless u.match(/[nt|zip]$/)
response = `curl -Lk -i -H "Accept:text/tab-separated-values" -H "subjectid:#{$pi[:subjectid]}" #{u}`
assert_match /HTTP\/1.1 200 OK/, response.to_s.encode!('UTF-8', 'UTF-8', :invalid => :replace)
end
end
# delete
response = `curl -Lk -i -X DELETE -H "subjectid:#{$pi[:subjectid]}" #{uri}`
assert_match /200/, response
response = `curl -Lk -i -H "Accept:text/uri-list" -H "subjectid:#{$pi[:subjectid]}" #{uri}`
assert_match /401|404/, response
end
end
def test_04_invalid_zip_upload
OpenTox::RestClientWrapper.subjectid = $pi[:subjectid]
file = File.join File.dirname(__FILE__), "data/toxbank-investigation/invalid/isa_TB_ACCUTOX.zip"
response = `curl -Lk -X POST -i -F file="@#{file};type=application/zip" -H "subjectid:#{$pi[:subjectid]}" #{$investigation[:uri]}`.chomp
assert_match /202/, response
uri = response.split("\n")[-1]
t = OpenTox::Task.new(uri)
t.wait
puts t.uri
assert_match t.hasStatus, "Error"
# TODO: test errorReport, rdf output of tasks has to be fixed for that purpose
end
end
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