toxbank tests fixed and renamed

1 files changed, 151 insertions, 0 deletions

diff --git a/test/toxbank-investigation-curl.rb b/test/toxbank-investigation-curl.rb
new file mode 100644
index 0000000..8b73434
--- /dev/null
+++ b/test/toxbank-investigation-curl.rb
@@ -0,0 +1,151 @@
+require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb")
+
+#TODO: check 4store entries/errors
+
+class UploadTest < Test::Unit::TestCase
+
+  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 "subjectid:#{@@subjectid}" -i #{$toxbank_investigation[:uri]}`
+    assert_match /200/, response
+  end
+
+  def test_02_get_inexisting
+    response = `curl -Lk -H "Accept:text/uri-list" -i -H "subjectid:#{@@subjectid}" #{$toxbank_investigation[:uri]}/foo`.chomp
+    assert_match /404/, response
+    response = `curl -Lk -H "Accept:application/rdf+xml" -i -H "subjectid:#{@@subjectid}" #{$toxbank_investigation[:uri]}/999999/metadata`.chomp
+    assert_match /404/, response
+  end
+
+  def test_03_valid_zip_upload
+    # upload
+    #["isa-tab-renamed.zip"].each do |f|
+    ["BII-I-1.zip","isa-tab-renamed.zip"].each do |f|
+      file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", f
+      response = `curl -Lk -X POST -i -F file="@#{file};type=application/zip" -H "subjectid:#{@@subjectid}" #{$toxbank_investigation[:uri]}`.chomp
+      assert_match /202/, response
+=begin
+<<<<<<< Updated upstream
+      # task
+      puts taskuri = response.split("\n")[-1]
+      #t = OpenTox::Task.new(taskuri)
+      #assert t.running?
+      #assert_match t.hasStatus, "Running"
+      #t.wait
+      #assert t.completed?
+      #assert_match t.hasStatus, "Completed"
+      #uri = t.resultURI
+      count = `curl -Lk -H accept:text/uri-list #{$toxbank_investigation[:uri]}`.split("\n").count-1
+      puts uri = "#{$toxbank_investigation[:uri]}\/#{count}"
+      # metadata
+      metadata = `curl -Lk -H accept:application/rdf+xml "subjectid:#{@@subjectid}" #{uri}/metadata`
+      urii = uri.gsub("https", "http")
+      assert_match /#{urii}/, metadata
+      # zip
+=======
+=end
+      uri = response.split("\n")[-1]
+      t = OpenTox::Task.new(uri)
+      t.wait
+      assert_equal true, t.completed?
+      assert_match t.hasStatus, "Completed"
+      uri = t.resultURI
+      metadata = `curl -Lk -H accept:application/rdf+xml -H "subjectid:#{@@subjectid}" #{uri}/metadata`
+      assert_match /#{uri}/, metadata
+      zip = File.join @tmpdir,"tmp.zip"
+      `curl -Lk -H "Accept:application/zip" -H "subjectid:#{@@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:#{@@subjectid}" -H "Accept:text/uri-list" #{$toxbank_investigation[:uri]}`.split("\n")
+      urilist.each do |uri|    
+        unless uri.match(/[n3|zip]$/)
+          response = `curl -Lk -i -H "Accept:text/tab-separated-values" -H "subjectid:#{@@subjectid}" #{uri}`
+          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:#{@@subjectid}" #{uri}`
+      assert_match /200/, response
+      response = `curl -Lk -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`
+      assert_match /404/, response
+    end
+  end
+  def test_04_invalid_zip_upload
+    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:#{@@subjectid}" #{$toxbank_investigation[:uri]}`.chomp
+    assert_match /202/, response
+    uri = response.split("\n")[-1]
+    t = OpenTox::Task.new(uri)
+    t.wait
+    assert_match t.hasStatus, "Error"
+    # TODO: test errorReport, rdf output of tasks has to be fixed for that purpose
+  end
+
+=begin
+
+  def test_rest_client_wrapper
+    ["BII-I-1.zip","isa-tab-renamed.zip"].each do |f|
+      file = File.join File.dirname(__FILE__), "toxbank-investigation","data/toxbank-investigation/valid", f
+      investigation_uri = OpenTox::RestClientWrapper.post $toxbank_investigation[:uri], {:file => File.read(file),:name => file}, {:content_type => "application/zip", :subjectid => @@subjectid}
+      puts investigation_uri
+      zip = File.join @tmpdir,"tmp.zip"
+      #puts "curl -Lk -H 'Accept:application/zip' -H 'subjectid:#{@@subjectid}' #{uri} > #{zip}"
+      `curl -Lk -H "Accept:application/zip" -H "subjectid:#{@@subjectid}" #{uri} > #{zip}`
+      `unzip -o #{zip} -d #{@tmpdir}`
+      files = `unzip -l toxbank-investigation/data/toxbank-investigation/valid/#{f}|grep txt|cut -c 31- | sed 's#^.*/##'`.split("\n")
+      files.each{|f| assert_equal true, File.exists?(File.join(File.expand_path(@tmpdir),f)) }
+
+      # get isatab files
+      `curl -Lk -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`.split("\n").each do |u|
+        unless u.match(/n3$/)
+          response = `curl -Lk -i -H Accept:text/tab-separated-values -H "subjectid:#{@@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:#{@@subjectid}" #{uri}`
+      assert_match /200/, response
+      response = `curl -Lk -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`
+      assert_match /404/, response
+    end
+  end
+=end
+
+=begin
+  def test_ruby_api
+    ["BII-I-1.zip","isa-tab-renamed.zip"].each do |f|
+      file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", f
+      investigation = OpenTox::Investigation.create $toxbank_investigation[:uri], :file => file, :headers => {:content_type => "application/zip", :subjectid => @@subjectid}
+      zip = File.join @tmpdir,"tmp.zip"
+      #puts "curl -Lk -H 'Accept:application/zip' -H 'subjectid:#{@@subjectid}' #{uri} > #{zip}"
+      `curl -Lk -H "Accept:application/zip" -H "subjectid:#{@@subjectid}" #{uri} > #{zip}`
+      `unzip -o #{zip} -d #{@tmpdir}`
+      files = `unzip -l data/toxbank-investigation/valid/#{f}|grep txt|cut -c 31- | sed 's#^.*/##'`.split("\n")
+      files.each{|f| assert_equal true, File.exists?(File.join(File.expand_path(@tmpdir),f)) }
+
+      # get isatab files
+      `curl -Lk -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`.split("\n").each do |u|
+        unless u.match(/n3$/)
+          response = `curl -Lk -i -H Accept:text/tab-separated-values -H "subjectid:#{@@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:#{@@subjectid}" #{uri}`
+      assert_match /200/, response
+      response = `curl -Lk -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`
+      assert_match /404/, response
+    end
+  end
+=end
+
+end