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require_relative "toxbank-setup.rb"
require File.join(File.expand_path(File.dirname(__FILE__)),".." ,".." ,"toxbank-investigation", "util.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
class TBInvestigationUploadBio < MiniTest::Test
i_suck_and_my_tests_are_order_dependent!
# define different users
$owner = $pi[:subjectid]
$user1 = $secondpi[:subjectid]
$user2 = $guestid
def test_00_select_user
OpenTox::RestClientWrapper.subjectid = $owner
end
# create a new investigation by uploading a zip file,
# Summary is not searchable, but published. { access=ToxBank group }
def test_01_post_investigation
$uri1 = ""
file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", "BII-I-1-tb2_ftp.zip"
response = OpenTox::RestClientWrapper.post $investigation[:uri], {:file => File.open(file)}, { :subjectid => $owner }
task_uri = response.chomp
task = OpenTox::Task.new task_uri
task.wait
uri = task.resultURI
assert_equal "Completed", task.hasStatus, "Task should be completed but is: #{task.hasStatus}. Task URI is #{task_uri} ."
$uri1 = URI(uri)
# update
res = OpenTox::RestClientWrapper.put $uri1.to_s, { :published => "true", :allowReadByGroup => "#{$user_service[:uri]}/project/G2"}, { :subjectid => $pi[:subjectid] }
task_uri = res.chomp
task = OpenTox::Task.new task_uri
task.wait
end
# create a new investigation by uploading a zip file,
# Summary is not searchable, but published. { access=ToxBank group }
def test_02_post_investigation
$uri2 = ""
file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", "BII-I-1-tb2_ftp.zip"
response = OpenTox::RestClientWrapper.post $investigation[:uri], {:file => File.open(file)}, { :subjectid => $owner }
task_uri = response.chomp
task = OpenTox::Task.new task_uri
task.wait
uri = task.resultURI
assert_equal "Completed", task.hasStatus, "Task should be completed but is: #{task.hasStatus}. Task URI is #{task_uri} ."
$uri2 = URI(uri)
# update
res = OpenTox::RestClientWrapper.put $uri2.to_s, { :published => "true"}, { :subjectid => $pi[:subjectid] }
task_uri = res.chomp
task = OpenTox::Task.new task_uri
task.wait
end
def test_04_biosearch_owner
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_and_characteristics", {}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
assert_equal 200, response.code
result = JSON.parse(response)
inv_chars = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["propname"]["value"]}:::#{n["propValue"]["value"]}:::#{n["ontouri"]["value"]}"}
assert inv_chars.include?("#{$uri1}:::Label:::#{$uri1}/CV2:::http://purl.obolibrary.org/chebi/15956")
assert inv_chars.include?("#{$uri1}:::organism:::#{$uri1}/CV4:::http://purl.obolibrary.org/obo/NEWT_4932")
assert inv_chars.include?("#{$uri2}:::Label:::#{$uri2}/CV2:::http://purl.obolibrary.org/chebi/15956")
assert inv_chars.include?("#{$uri2}:::organism:::#{$uri2}/CV4:::http://purl.obolibrary.org/obo/NEWT_4932")
end
def test_05_biosearch_user1
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_and_characteristics", {}, {:accept => "application/json", :subjectid => $secondpi[:subjectid]}
assert_equal 200, response.code
result = JSON.parse(response)
inv_chars = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["propname"]["value"]}:::#{n["propValue"]["value"]}:::#{n["ontouri"]["value"]}"}
assert inv_chars.include?("#{$uri1}:::Label:::#{$uri1}/CV2:::http://purl.obolibrary.org/chebi/15956")
assert inv_chars.include?("#{$uri1}:::organism:::#{$uri1}/CV4:::http://purl.obolibrary.org/obo/NEWT_4932")
refute inv_chars.include?("#{$uri2}:::Label:::#{$uri2}/CV2:::http://purl.obolibrary.org/chebi/15956")
refute inv_chars.include?("#{$uri2}:::organism:::#{$uri2}/CV4:::http://purl.obolibrary.org/obo/NEWT_4932")
end
def test_06_biosearch_user2
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_and_characteristics", {}, {:accept => "application/json", :subjectid => $guestid}
result = JSON.parse(response)
inv_chars = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["propname"]["value"]}:::#{n["propValue"]["value"]}:::#{n["ontouri"]["value"]}"}
refute inv_chars.include?("#{$uri1}:::Label:::#{$uri1}/CV2:::http://purl.obolibrary.org/chebi/15956")
refute inv_chars.include?("#{$uri1}:::organism:::#{$uri1}/CV4:::http://purl.obolibrary.org/obo/NEWT_4932")
refute inv_chars.include?("#{$uri2}:::Label:::#{$uri2}/CV2:::http://purl.obolibrary.org/chebi/15956")
refute inv_chars.include?("#{$uri2}:::organism:::#{$uri2}/CV4:::http://purl.obolibrary.org/obo/NEWT_4932")
end
def test_99_delete
[$uri1, $uri2].each do |uri|
response = OpenTox::RestClientWrapper.delete uri.to_s, {}, { :subjectid => $owner }
assert_equal 200, response.code
end
end
end
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