extended sparql tests;factors,genes,pvalue,qvalue,foldchange

1 files changed, 131 insertions, 63 deletions

diff --git a/test/toxbank-investigation-sparql.rb b/test/toxbank-investigation-sparql.rb
index 6b07418..7a5b75b 100644
--- a/test/toxbank-investigation-sparql.rb
+++ b/test/toxbank-investigation-sparql.rb
@@ -107,112 +107,181 @@ class TBSPARQLTest < MiniTest::Test
     assert_equal 200, response.code
   end
 
-  #TODO assertions
+  def test_13_investigation_by_characteristic_value
+    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_characteristic_value", {:value => "Saccharomyces cerevisiae (Baker's yeast)"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    result = JSON.parse(response)
+    char_value = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["propname"]["value"]}:::#{n["ontoURI"]["value"]}"}
+    assert char_value.include?("#{@@uri}:::organism:::http://purl.obolibrary.org/obo/NEWT_4932")
+    assert_equal 200, response.code
+  end
+
+  def test_14_investigation_by_characteristic_name
+    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_characteristic_name", {:value => "organism"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    result = JSON.parse(response)
+    char_name = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["value"]["value"]}:::#{n["ontoURI"]["value"]}"}
+    assert char_name.include?("#{@@uri}:::Saccharomyces cerevisiae (Baker's yeast):::http://purl.obolibrary.org/obo/NEWT_4932")
+    assert_equal 200, response.code
+  end
+
+  def test_15_investigation_by_characteristic
+    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_characteristic", {:value => "http://purl.obolibrary.org/obo/NEWT_4932"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    result = JSON.parse(response)
+    inv_char = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["propname"]["value"]}:::#{n["value"]["value"]}"}
+    assert inv_char.include?("#{@@uri}:::organism:::Saccharomyces cerevisiae (Baker's yeast)")
+    assert_equal 200, response.code
+  end
+
+  def test_30_empty_factorValues_search
+    assert_raises OpenTox::BadRequestError do
+      response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_factors", {:factorValues => ""}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    end
+  end
+
+  def test_31_empty_value_search
+    assert_raises OpenTox::BadRequestError do
+      response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_characteristic", {:value => ""}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    end
+  end
+
+  # delete investigation/{id}
+  # @note expect code 200
+  def test_90_delete_investigation
+    result = OpenTox::RestClientWrapper.delete @@uri.to_s, {}, {:subjectid => $pi[:subjectid]}
+    assert_equal 200, result.code
+  end
+
+end
+
+class TBSPARQLTestExtended < MiniTest::Test
+
+  i_suck_and_my_tests_are_order_dependent!
+
+  # login as pi and create a test investigation
+  def test_00_create_investigation
+    OpenTox::RestClientWrapper.subjectid = $pi[:subjectid] # set pi as the logged in user
+    @@uri = ""
+    file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", "IST_test_sparql.zip"
+    response = OpenTox::RestClientWrapper.post $investigation[:uri], {:file => File.open(file)}, { :subjectid => $pi[:subjectid] }
+    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} ."
+    @@uri = URI(uri)
+    OpenTox::RestClientWrapper.put @@uri.to_s, { :published => "true", :summarySearchable => "true"}, { :subjectid => $pi[:subjectid] }
+  end  
+  
+  # Retrieves all factors (name, value, ontology URI of the value) given an investigation URI
+  def test_04_factors_by_investigation
+    response = OpenTox::RestClientWrapper.get "#{@@uri}/sparql/factors_by_investigation", {}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    result = JSON.parse(response)
+    headvars = result["head"]["vars"]
+    assert headvars.include?("factorname")
+    assert headvars.include?("value")
+    assert headvars.include?("ontouri")
+    assert headvars.include?("unitOnto")
+    assert headvars.include?("unit")
+    assert headvars.include?("unitID")
+    factors = result["results"]["bindings"].map{|n| "#{n["factorname"]["value"]}:::#{n["value"]["value"]}:::#{n["ontouri"]["value"]}:::#{n["unitOnto"]["value"]}:::#{n["unit"]["value"]}:::#{n["unitID"]["value"]}"}
+    #puts factors
+    assert factors.include?("sample TimePoint:::8::::::::::::")
+    assert factors.include?("dose:::0::::::http://purl.obolibrary.org/obo/UO_0000064:::micromolar:::UO:0000064")
+    assert factors.include?("compound:::DOXORUBICIN:::http://purl.obolibrary.org/chebi/CHEBI:28748:::::::::")
+  end
+  
   # Retrieves investigation URI and factors (name, value, ontology URI of the value)
   def test_09_investigations_and_factors
     response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigations_and_factors", {}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
-    #puts response
+    result = JSON.parse(response)
+    inv_factors = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["factorname"]["value"]}:::#{n["ontouri"]["value"]}:::#{n["value"]["value"]}"}
+    #puts inv_factors
     assert_equal 200, response.code
+    assert inv_factors.include?("#{@@uri}:::compound:::http://purl.obolibrary.org/chebi/CHEBI:28748:::DOXORUBICIN")
   end
 
-  #TODO assertions
   # Retrieves protocol URI containing any of the factor value URI (e.g. two compound URIs)
   def test_10_protocols_by_factors
     response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/protocols_by_factors", {:factorValues => "[]"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
     #puts response
+    result = JSON.parse(response)
+    protocol_factors = result["results"]["bindings"].map{|n| "#{n["protocol"]["value"]}:::#{n["label"]["value"]}:::#{n["factorname"]["value"]}:::#{n["value"]["value"]}"}
+    #puts protocol_factors
     assert_equal 200, response.code
+    assert protocol_factors.include?("#{@@uri}/P4:::labeling:::dose:::0")
+    assert protocol_factors.include?("#{@@uri}/P3:::RNA extraction:::dose:::0")
+    assert protocol_factors.include?("#{@@uri}/P2:::normalization data transformation:::dose:::0")
+    assert protocol_factors.include?("#{@@uri}/P1:::data transformation:::dose:::0")
+    assert protocol_factors.include?("#{@@uri}/P5:::data collection:::dose:::0")
+    assert protocol_factors.include?("#{@@uri}/P6:::nucleic acid hybridization:::dose:::0")
+    assert protocol_factors.include?("#{@@uri}/P4:::labeling:::sample TimePoint:::8")
+    assert protocol_factors.include?("#{@@uri}/P3:::RNA extraction:::sample TimePoint:::8")
+    assert protocol_factors.include?("#{@@uri}/P2:::normalization data transformation:::sample TimePoint:::8")
+    assert protocol_factors.include?("#{@@uri}/P1:::data transformation:::sample TimePoint:::8")
+    assert protocol_factors.include?("#{@@uri}/P5:::data collection:::sample TimePoint:::8")
+    assert protocol_factors.include?("#{@@uri}/P6:::nucleic acid hybridization:::sample TimePoint:::8")
+    assert protocol_factors.include?("#{@@uri}/P4:::labeling:::compound:::DOXORUBICIN")
+    assert protocol_factors.include?("#{@@uri}/P3:::RNA extraction:::compound:::DOXORUBICIN")
+    assert protocol_factors.include?("#{@@uri}/P2:::normalization data transformation:::compound:::DOXORUBICIN")
+    assert protocol_factors.include?("#{@@uri}/P1:::data transformation:::compound:::DOXORUBICIN")
+    assert protocol_factors.include?("#{@@uri}/P5:::data collection:::compound:::DOXORUBICIN")
+    assert protocol_factors.include?("#{@@uri}/P6:::nucleic acid hybridization:::compound:::DOXORUBICIN")
   end
 
-  #TODO assertions
   # Retrieves investigation URI containing any of the factor value URI (e.g. two compound URIs)
   def test_11_investigation_by_factors
-    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_factors", {:factorValues => "[]"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_factors", {:factorValues => "['http://purl.obolibrary.org/chebi/CHEBI:28748']"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
     #puts response
+    result = JSON.parse(response)
+    inv_factors = result["results"]["bindings"].map{|n| "#{n["inv"]["value"]}:::#{n["factorname"]["value"]}:::#{n["value"]["value"]}"}
     assert_equal 200, response.code
+    assert inv_factors.include?("#{@@uri}:::compound:::DOXORUBICIN")
   end
 
-  #TODO assertions
   # Retrieves investigation URI given a factor value URI (e.g. compound URI)
   def test_12_investigation_by_factor
-    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_factor", {:value => "http://factor.value/uri"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_factor", {:value => "http://purl.obolibrary.org/chebi/CHEBI:28748"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
     #puts response
-    assert_equal 200, response.code
-  end
-
-  def test_13_investigation_by_characteristic_value
-    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_characteristic_value", {:value => "Saccharomyces cerevisiae (Baker's yeast)"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
-    result = JSON.parse(response)
-    char_value = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["propname"]["value"]}:::#{n["ontoURI"]["value"]}"}
-    assert char_value.include?("#{@@uri}:::organism:::http://purl.obolibrary.org/obo/NEWT_4932")
-    assert_equal 200, response.code
-  end
-
-  def test_14_investigation_by_characteristic_name
-    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_characteristic_name", {:value => "organism"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
     result = JSON.parse(response)
-    char_name = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["value"]["value"]}:::#{n["ontoURI"]["value"]}"}
-    assert char_name.include?("#{@@uri}:::Saccharomyces cerevisiae (Baker's yeast):::http://purl.obolibrary.org/obo/NEWT_4932")
-    assert_equal 200, response.code
-  end
-
-  def test_15_investigation_by_characteristic
-    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_characteristic", {:value => "http://purl.obolibrary.org/obo/NEWT_4932"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
-    result = JSON.parse(response)
-    inv_char = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["propname"]["value"]}:::#{n["value"]["value"]}"}
-    assert inv_char.include?("#{@@uri}:::organism:::Saccharomyces cerevisiae (Baker's yeast)")
+    inv_factor = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["factorname"]["value"]}:::#{n["value"]["value"]}"}
     assert_equal 200, response.code
+    assert inv_factor.include?("#{@@uri}:::compound:::DOXORUBICIN")
   end
   
-  #TODO assertions
   def test_16_investigation_by_pvalue
-    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_pvalue", {:value => "0.05"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_pvalue", {:value => "0.65614"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
     result = JSON.parse(response)
-    #puts result
-    #inv_pvalue = result["results"]["bindings"].map{|n| ""}
-    #assert inv_pvalue.include?("")
+    #puts response
+    result = JSON.parse(response)
+    inv_pvalue = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["gene"]["value"]}"}
     assert_equal 200, response.code
+    assert inv_pvalue.include?("#{@@uri}:::http://onto.toxbank.net/isa/Entrez/3075")
   end
   
-  #TODO assertions
   def test_17_investigation_by_qvalue
-    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_qvalue", {:value => "0.05"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_qvalue", {:value => "0.805517"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    #puts response
     result = JSON.parse(response)
-    #puts result
-    #inv_qvalue = result["results"]["bindings"].map{|n| ""}
-    #assert inv_qvalue.include?("")
+    inv_qvalue = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["gene"]["value"]}"}
     assert_equal 200, response.code
+    assert inv_qvalue.include?("#{@@uri}:::http://onto.toxbank.net/isa/Entrez/3075")
   end
   
-  #TODO assertions
   def test_18_investigation_by_foldchange
-    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_foldchange", {:value => "1.5"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_foldchange", {:value => "0.035"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
     result = JSON.parse(response)
-    #puts result
-    #inv_foldchange = result["results"]["bindings"].map{|n| ""}
-    #assert inv_foldchange.include?("")
+    #puts response
+    inv_foldchange = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["gene"]["value"]}"}
     assert_equal 200, response.code
+    assert inv_foldchange.include?("#{@@uri}:::http://onto.toxbank.net/isa/Entrez/3075")
   end
   
-  #TODO assertions
   def test_19_investigation_by_genes
-    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_genes", {:geneIdentifiers => "[uniprot:P10809,genesymbol:HSPD1,unigene:Hs.595053,refseq:NM_002156,entrez:3329]"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
+    response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_genes", {:geneIdentifiers => "['entrez:3075']"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
     result = JSON.parse(response)
-    #puts result
-    #inv_genes = result["results"]["bindings"].map{|n| ""}
-    #assert inv_genes.include?("")
+    #puts response
+    inv_genes = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["datatype"]["value"]}:::#{n["title"]["value"]}:::#{n["valuetype"]["value"]}:::#{n["value"]["value"]}"}
     assert_equal 200, response.code
-  end
-
-  def test_30_empty_factorValues_search
-    assert_raises OpenTox::BadRequestError do
-      response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_factors", {:factorValues => ""}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
-    end
-  end
-
-  def test_31_empty_value_search
-    assert_raises OpenTox::BadRequestError do
-      response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_characteristic", {:value => ""}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
-    end
+    assert inv_genes.include?("#{@@uri}:::http://onto.toxbank.net/isa/bii/data_types/microarray_derived_data:::q-value[Low.8hr-Control.8hr]:::http://onto.toxbank.net/isa/qvalue:::0.911237")
   end
 
   # delete investigation/{id}
@@ -221,5 +290,4 @@ class TBSPARQLTest < MiniTest::Test
     result = OpenTox::RestClientWrapper.delete @@uri.to_s, {}, {:subjectid => $pi[:subjectid]}
     assert_equal 200, result.code
   end
-
 end