toxbank-investigation 0.0.1pre-x86-linux

data/java/config/isa_configurator/transcription_micro.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="transcription_micro" isatab-assay-type="transcriptomics_assay" isatab-conversion-target="magetab"><measurement term-label="transcription profiling" term-accession="0000424" source-abbreviation="OBI"/><technology term-label="DNA microarray" term-accession="0400148" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="RNA extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Identifier for the labeled extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT]</generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Indicates a chemical or biological marker, such as a radioactive isotope or a fluorescent dye which is bound to a material in order to make it detectable by some assay technology (e.g. P33, biotin, GFP).]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="45788"/></recommended-ontologies></field><protocol-field protocol-type ="nucleic acid hybridization"/><field header="Hybridization Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].HYB-[HYB_COUNT]</generated-value-template></field><field header="Array Design REF" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Reference to the identifier (or accession number) of an existing array design]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[ARRAY_DESIGN]</generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Scan Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each scan event.]]></description><default-value><![CDATA[]]></default-value></field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the image files generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the raw array data matrix file.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="normalization data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the processed data matrix file resulting from data transformation or processing.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/transcription_rtpcr.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="transcription_rtpcr" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="transcription profiling" term-accession="0000424" source-abbreviation="OBI"/><technology term-label="real time PCR" term-accession="" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="nucleic acid extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Identifier for the labeled extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT]</generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Indicates a chemical or biological marker, such as a radioactive isotope or a fluorescent dye which is bound to a material in order to make it detectable by some assay technology (e.g. P33, biotin, GFP).]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="40664"/></recommended-ontologies></field><protocol-field protocol-type ="reverse transcribed pcr"/><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the raw data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/transcription_seq.xml

@@ -0,0 +1,6 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="transcription_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="transcription profiling" term-accession="0000424" source-abbreviation="OBI"/><technology term-label="nucleotide sequencing" term-accession="" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]
+            </generated-value-template></field><protocol-field protocol-type ="nucleic acid extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>
+                [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]
+            </generated-value-template></field><protocol-field protocol-type ="library construction"/><field header="Parameter Value[library layout]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[specifies whether to expect single, paired, or other configuration of reads.]]></description><default-value><![CDATA[]]></default-value><list-values>SINGLE,PAIRED</list-values></field><field header="Parameter Value[mid]" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA['mid' stands for 'multiplex identifier' (aka barcode tag). Use this field when performing a multiplexing procedure and indicate here the nucleic acid tag used to uniquely identify the sample if the pool.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="nucleic acid sequencing"/><field header="Parameter Value[sequencing instrument]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a parameter to report the sequencing instrument model and make]]></description><default-value><![CDATA[]]></default-value><list-values>454 GS,454 GS 20,454 GS FLX,454 GS FLX Titanium,454 GS Junior,GS 20,GS FLX,AB SOLiD System,AB SOLiD System 2.0,AB SOLiD System 3.0,AB SOLiD 4 System,AB SOLiD 4hq System,AB SOLiD PI System,Solexa 1G Genome Analyzer,Illumina Genome Analyzer,Illumina Genome Analyzer II,Illumina Genome Analyzer IIx,Illumina HiSeq 2000,Sanger sequencing instrument</list-values></field><field header="Parameter Value[base caller]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the base or color calling software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[quality score]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name and version of the quality scoring software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>
+                [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]
+            </generated-value-template></field><field header="Comment[Export]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Use this field to select/set which records should be exported for a submission to SRA/ENA]]></description><default-value><![CDATA[no]]></default-value><list-values>yes,no</list-values></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the raw data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="sequence analysis data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/test/Rakefile

@@ -0,0 +1,48 @@
+require 'rubygems'
+require 'opentox-server'
+#require File.join(File.dirname(__FILE__),"../lib/toxbank-investigation.rb")
+#['otlogger', 'environment', 'helper'].each do |lib|
+	#require '../lib/' + lib
+#end
+
+HOST = "http://localhost/"
+AA_SERVER = "https://opensso.in-silico.ch"
+TEST_USER = "guest"
+TEST_PW = "guest"
+
+=begin
+task ARGV[0] do
+  puts "Environment: #{ENV["RACK_ENV"]}"
+  ARGV[0] = ARGV[0].gsub(/\.rb$/,"")
+  puts "Test: "+ARGV[0]+".rb"
+  puts File.join(File.dirname(__FILE__),ARGV[0]+".rb")
+  #require File.join(File.dirname(__FILE__),ARGV[0]+".rb")
+  require "./"+ARGV[0]+".rb"
+end
+=end
+
+task ARGV[0] do
+  puts "Environment: #{ENV["RACK_ENV"]}"
+  ARGV[0] = ARGV[0].gsub(/\.rb$/,"")
+  puts "Test: "+ARGV[0]+".rb"
+  require "./"+ARGV[0]+".rb"
+end
+
+task :setup do
+  # setup code
+  if AA_SERVER
+    resource = RestClient::Resource.new("#{AA_SERVER}/auth/authenticate")
+    @@subjectid = resource.post(:username=>TEST_USER, :password => TEST_PW).sub("token.id=","").sub("\n","")
+  else
+    @@subjectid = ""
+  end
+end
+
+task :teardown do
+  # teardown code
+end
+
+[:all, :upload, :basic_rest, :xls_upload, :querytest, :authorization, :httpd].each do |t|
+  task :teardown => t
+  task t => :setup
+end

data/test/all.rb

@@ -0,0 +1,3 @@
+require 'rubygems'
+require 'test/unit'
+#Dir["*.rb"].each {|f| puts f; require File.join(File.dirname(__FILE__),f) }

data/test/authorization.rb

@@ -0,0 +1,112 @@
+require "rubygems"
+#require "opentox-ruby"
+require "test/unit"
+
+TEST_URI  = "http://only_a_test/test/" + rand(1000000).to_s
+unless AA_SERVER #overwrite turned off A&A server for testing
+  AA_SERVER = "https://opensso.in-silico.ch"
+  @@subjectid = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW)
+end
+
+class TestOpenToxAuthorizationBasic < Test::Unit::TestCase
+ 
+  def test_01_server
+    @aaserver = AA_SERVER
+    assert_equal(@aaserver, OpenTox::Authorization.server)
+  end
+ 
+  def test_02_get_token
+    assert_not_nil @@subjectid
+  end
+  
+  def test_03_is_valid_token
+    tok = login
+    assert_not_nil tok
+    assert OpenTox::Authorization.is_token_valid(tok)
+    logout(tok)
+  end
+  
+  def test_04_logout
+    tok = login  
+    assert logout(tok) 
+  end
+  
+  def test_05_list_policies
+    assert_kind_of Array, OpenTox::Authorization.list_policies(@@subjectid)
+  end
+  
+end
+
+class TestOpenToxAuthorizationLDAP < Test::Unit::TestCase
+
+  def test_01_list_groups
+    assert_kind_of Array, OpenTox::Authorization.list_groups(@@subjectid)
+  end  
+
+  def test_02_list_user_groups
+    assert_kind_of Array, OpenTox::Authorization.list_user_groups(TEST_USER, @@subjectid)
+  end
+  
+  def test_03_get_user
+    assert_equal TEST_USER, OpenTox::Authorization.get_user(@@subjectid)
+  end
+
+end
+
+class TestOpenToxAuthorizationLDAP < Test::Unit::TestCase
+
+  def test_01_create_check_delete_default_policies
+    res = OpenTox::Authorization.send_policy(TEST_URI, @@subjectid)
+    assert res
+    assert OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid)
+    policies = OpenTox::Authorization.list_uri_policies(TEST_URI, @@subjectid)
+    assert_kind_of Array, policies
+    policies.each do |policy|
+      assert OpenTox::Authorization.delete_policy(policy, @@subjectid)
+    end
+    assert_equal false, OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid)
+  end
+
+  def test_02_check_policy_rules
+    tok_anonymous = OpenTox::Authorization.authenticate("anonymous","anonymous")
+    assert_not_nil tok_anonymous
+    res = OpenTox::Authorization.send_policy(TEST_URI, @@subjectid)
+    assert res
+    assert OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid)
+    owner_rights = {"GET" => true, "POST" => true, "PUT" => true, "DELETE" => true}
+    groupmember_rights = {"GET" => true, "POST" => nil, "PUT" => nil, "DELETE" => nil}
+    owner_rights.each do |request, right|
+      assert_equal right, OpenTox::Authorization.authorize(TEST_URI, request, @@subjectid), "#{TEST_USER} requests #{request} to #{TEST_URI}"
+    end
+    groupmember_rights.each do |request, r|
+      assert_equal r, OpenTox::Authorization.authorize(TEST_URI, request, tok_anonymous), "anonymous requests #{request} to #{TEST_URI}"
+    end
+    
+    policies = OpenTox::Authorization.list_uri_policies(TEST_URI, @@subjectid)
+    assert_kind_of Array, policies
+    policies.each do |policy|
+      assert OpenTox::Authorization.delete_policy(policy, @@subjectid)
+    end
+    logout(tok_anonymous)
+  end
+
+  def test_03_check_different_uris
+    res = OpenTox::Authorization.send_policy(TEST_URI, @@subjectid)
+    assert OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid)
+    assert OpenTox::Authorization.authorize(TEST_URI, "GET", @@subjectid), "GET request"
+    policies = OpenTox::Authorization.list_uri_policies(TEST_URI, @@subjectid)
+    policies.each do |policy|
+      assert OpenTox::Authorization.delete_policy(policy, @@subjectid)
+    end
+ 
+  end  
+end
+
+
+def logout (token)
+   OpenTox::Authorization.logout(token)
+end
+
+def login
+  OpenTox::Authorization.authenticate(TEST_USER,TEST_PW)
+end 

data/test/basic_rest.rb

@@ -0,0 +1,98 @@
+require 'rubygems'
+require 'rest-client'
+require 'test/unit'
+require 'uri'
+
+HOST = "http://localhost/"
+AA_SERVER = "https://opensso.in-silico.ch"
+TEST_USER = "guest"
+TEST_PW = "guest"
+  resource = RestClient::Resource.new("#{AA_SERVER}/auth/authenticate")
+  @@subjectid = resource.post(:username=>TEST_USER, :password => TEST_PW).sub("token.id=","").sub("\n","")
+
+class BasicTest < Test::Unit::TestCase
+
+  # check response from service
+  def test_01_get_investigations_200
+    response = RestClient.get HOST,:subjectid => @@subjectid
+    assert_equal 200, response.code
+  end
+
+  # check if default response header is text/uri-list
+  def test_02_get_investigations_type
+    response = RestClient.get HOST, { :subjectid => @@subjectid }
+    assert_equal "text/uri-list", response.headers[:content_type]
+  end
+
+  # check sparql query call to all investigations
+  def test_03_get_investigations_query
+    response = nil
+    Net::HTTP.get_response(URI(File.join(HOST, "?query=bla&subjectid=#{CGI.escape(@@subjectid)}"))) {|http|
+      response = http
+    }
+    assert_equal 200, response.code.to_i
+  end
+
+end
+
+class BasicTestCRUDInvestigation < Test::Unit::TestCase
+
+  # check post to investigation service with wrong content type
+  def test_01_post_investigation_400
+    uri = URI(File.join(HOST, 'investigation'))
+    req = Net::HTTP::Post.new("#{uri.path}?subjectid=#{CGI.escape(@@subjectid)}")
+    req.content_type = "text/dummy"
+    res = Net::HTTP.start(uri.host, uri.port) do |http|
+      http.request(req)
+    end
+    assert_equal 400, res.code.to_i
+  end
+
+  # create an investigation by uploading a zip file
+  def test_02_post_investigation
+    @@uri = ""
+    result = `curl -X POST #{HOST} -H "Content-Type: multipart/form-data" -F "file=@data/valid/BII-I-1.zip;type=application/zip" -H "subjectid:#{@@subjectid}"`
+    puts result
+    @@uri = URI(result)
+    assert @@uri.host == URI(HOST).host
+  end
+
+  # get investigation/{id} as text/uri-list
+  def test_03_get_investigation_uri_list
+    result = RestClient.get @@uri.to_s, {:Accept => "text/uri-list", :subjectid => @@subjectid}
+    assert_equal "text/uri-list", result.headers[:content_type]
+  end
+
+  # get investigation/{id} as application/zip
+  def test_04_get_investigation_zip
+    result = RestClient.get @@uri.to_s, {:Accept => "application/zip", :subjectid => @@subjectid}
+    assert_equal "application/zip", result.headers[:content_type]
+  end
+
+  # get investigation/{id} as text/tab-separated-values
+  def test_05_get_investigation_tab
+    result = RestClient.get @@uri.to_s, {:Accept => "text/tab-separated-values", :subjectid => @@subjectid}
+    assert_equal "text/tab-separated-values;charset=utf-8", result.headers[:content_type]
+  end
+
+  # get investigation/{id} as application/sparql-results+json
+  def test_06_get_investigation_sparql
+    result = RestClient.get @@uri.to_s, {:Accept => "application/sparql-results+json", :subjectid => @@subjectid}
+    assert_equal "application/sparql-results+json", result.headers[:content_type]
+  end
+
+  # check if uri is in uri-list
+  def test_98_get_investigation
+    response = RestClient.get HOST, :subjectid => @@subjectid
+    assert response.index(@@uri.to_s) != nil, "URI: #{@@uri} is not in uri-list"
+  end
+
+  # delete investigation/{id}
+  def test_99_delete_investigation
+    result = RestClient.delete @@uri.to_s, :subjectid => @@subjectid
+    assert result.match(/^investigation.[0-9]*.deleted$/)
+  end
+
+end
+
+