added test for biosearch feature

1 files changed, 130 insertions, 0 deletions

diff --git a/test/toxbank-investigation-biosearch.rb b/test/toxbank-investigation-biosearch.rb
new file mode 100644
index 0000000..b1c7795
--- /dev/null
+++ b/test/toxbank-investigation-biosearch.rb
@@ -0,0 +1,130 @@
+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.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 $uri1.to_s, { :published => "true", :owningPro => "#{$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.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 $uri2.to_s, { :published => "true", :owningPro => "#{$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_03_post_investigation
+    $uri3 = ""
+    file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", "BII-I-1-tb2.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} ."
+    $uri3 = URI(uri)
+    # update
+    res = OpenTox::RestClientWrapper.put $uri3.to_s, { :published => "true", :owningPro => "#{$user_service[:uri]}/project/G2"}, { :subjectid => $pi[:subjectid] }
+    task_uri = res.chomp
+    task = OpenTox::Task.new task_uri
+    task.wait
+  end
+
+end
+
+class TBInvestigationBioSearch < MiniTest::Test
+  i_suck_and_my_tests_are_order_dependent!
+
+  def test_01_biosearch_owner
+    response = OpenTox::RestClientWrapper.get "#{$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:::#{$uri2}/CV4:::http://purl.obolibrary.org/obo/NEWT_4932")
+    assert inv_chars.include?("#{$uri3}:::Label:::#{$uri3}/CV2:::http://purl.obolibrary.org/chebi/15956")
+    assert inv_chars.include?("#{$uri3}:::organism:::#{$uri3}/CV4:::http://purl.obolibrary.org/obo/NEWT_4932")
+  end
+
+  def test_02_biosearch_user1
+    response = OpenTox::RestClientWrapper.get "#{$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:::#{$uri1}/CV4:::http://purl.obolibrary.org/obo/NEWT_4932")
+    assert inv_chars.include?("#{$uri2}:::Label:::#{$uri2}/CV2:::http://purl.obolibrary.org/chebi/15956")
+    assert inv_chars.include?("#{$uri2}:::organism:::#{$uri2}/CV4:::http://purl.obolibrary.org/obo/NEWT_4932")
+    assert inv_chars.include?("#{$uri3}:::Label:::#{$uri3}/CV2:::http://purl.obolibrary.org/chebi/15956")
+    assert inv_chars.include?("#{$uri3}:::organism:::#{$uri3}/CV4:::http://purl.obolibrary.org/obo/NEWT_4932")
+  end
+  
+  def test_03_biosearch_user2
+    assert_raises OpenTox::BadRequestError do
+      response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_and_characteristics", {}, {:accept => "application/json", :subjectid => $guestid}
+    end
+  end
+
+end
+
+class TBInvestigationDelete < MiniTest::Test
+
+  def test_00_delete
+    [$uri1, $uri2, $uri3].each do |uri|
+      response = OpenTox::RestClientWrapper.delete uri.to_s, {}, { :subjectid => $owner }
+      assert_equal 200, response.code
+    end
+  end
+
+end
+