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require_relative "toxbank-setup.rb"
# Test API extension SPARQL templates
class TBSPARQLTest < 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", "BII-I-1-tb2_ftp.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
# initial tests to be changed
def test_01_nonexisting_template
assert_raises OpenTox::ResourceNotFoundError do
response = OpenTox::RestClientWrapper.get "#{@@uri}/sparql/not_existing_template", {}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
end
end
def test_02_existing_template
response = OpenTox::RestClientWrapper.get "#{@@uri}/sparql/investigation_details", {}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
assert_equal 200, response.code
end
def test_03_camelcase_template
response = OpenTox::RestClientWrapper.get "#{@@uri}/sparql/InvestigationDetails", {}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
assert_equal 200, response.code
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")
factorvalues = result["results"]["bindings"].map {|n| "#{n["factorname"]["value"]}:::#{n["value"]["value"]}"}
assert factorvalues.include?("limiting nutrient:::phosphorus")
assert factorvalues.include?("limiting nutrient:::glucose")
assert factorvalues.include?("limiting nutrient:::carbon")
assert factorvalues.include?("limiting nutrient:::sulfur")
assert factorvalues.include?("limiting nutrient:::nitrogen")
assert factorvalues.include?("limiting nutrient:::ethanol")
assert factorvalues.include?("rate:::0.1")
assert factorvalues.include?("rate:::0.2")
assert factorvalues.include?("rate:::0.07")
end
def test_05_characteristics_by_investigation
response = OpenTox::RestClientWrapper.get "#{@@uri}/sparql/characteristics_by_investigation", {}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
result = JSON.parse(response)
propnamevalues = result["results"]["bindings"].map {|n| "#{n["propname"]["value"]}:::#{n["value"]["value"]}:::#{n["ontouri"]["value"]}"}
assert propnamevalues.include?("organism:::Saccharomyces cerevisiae (Baker's yeast):::http://purl.obolibrary.org/obo/NEWT_4932")
assert propnamevalues.include?("Label:::biotin:::http://purl.obolibrary.org/chebi/15956")
assert propnamevalues.include?("organism:::Saccharomyces cerevisiae (Baker's yeast):::http://purl.obolibrary.org/obo/NEWT_4932")
end
def test_06_investigation_endpoint_technology
response = OpenTox::RestClientWrapper.get "#{@@uri}/sparql/investigation_endpoint_technology", {}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
result = JSON.parse(response)
endpointtechnologies = result["results"]["bindings"].map {|n| "#{n["endpoint"]["value"]}:::#{n["technology"]["value"]}"}
assert endpointtechnologies.include?("http://purl.org/obo/owl/OBI#0000424:::http://purl.org/obo/owl/OBI#0400148")
assert endpointtechnologies.include?("http://purl.org/obo/owl/OBI#0000366:::http://purl.org/obo/owl/OBI#OBI_0000470")
assert endpointtechnologies.include?("http://purl.org/obo/owl/OBI#OBI_0000615:::http://purl.org/obo/owl/OBI#OBI_0000470")
assert endpointtechnologies.include?("http://purl.org/obo/owl/OBI#0000424:::http://purl.org/obo/owl/OBI#0400148")
assert_equal endpointtechnologies.size, 4
end
def test_07_investigation_and_characteristics
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_and_characteristics", {}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
result = JSON.parse(response)
inv_chars = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["propname"]["value"]}:::#{n["propValue"]["value"]}:::#{n["ontouri"]["value"]}"}
assert inv_chars.include?("#{@@uri}:::Label:::#{@@uri}/CV2:::http://purl.obolibrary.org/chebi/15956")
assert inv_chars.include?("#{@@uri}:::organism:::#{@@uri}/CV4:::http://purl.obolibrary.org/obo/NEWT_4932")
assert_equal 200, response.code
end
def test_08_investigations_and_protocols
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigations_and_protocols", {}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
result = JSON.parse(response)
inv_protocols = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["protocol"]["value"]}:::#{n["label"]["value"]}"}
#puts inv_protocols
assert inv_protocols.include?("#{@@uri}:::#{@@uri}/P2:::biotin labeling")
assert inv_protocols.include?("#{@@uri}:::#{@@uri}/P6:::EukGE-WS4")
assert inv_protocols.include?("#{@@uri}:::#{@@uri}/P1:::metabolite extraction")
assert inv_protocols.include?("#{@@uri}:::#{@@uri}/P5:::mRNA extraction")
assert inv_protocols.include?("#{@@uri}:::#{@@uri}/P9:::biotin labeling")
assert inv_protocols.include?("#{@@uri}:::#{@@uri}/P8:::mRNA extraction")
assert inv_protocols.include?("#{@@uri}:::#{@@uri}/P4:::protein extraction")
assert inv_protocols.include?("#{@@uri}:::#{@@uri}/P3:::EukGE-WS4")
assert inv_protocols.include?("#{@@uri}:::#{@@uri}/P7:::ITRAQ labeling")
assert_equal 200, response.code
end
def test_09_files_by_investigation
response = OpenTox::RestClientWrapper.get "#{@@uri}/sparql/files_by_investigation", {}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
result = JSON.parse(response)
files = result["results"]["bindings"].map{|n| "#{n["file"]["value"]}"}
assert_equal 180, files.size
downloaduris = result["results"]["bindings"].map{|n| "#{n["downloaduri"]["value"]}"}
assert_match /#{@@uri}\/files\/JIC37_Ethanol_0\.07_Internal_1_3\.txt/, downloaduris.to_s
end
def test_13_investigation_by_characteristic_value
response = OpenTox::RestClientWrapper.get "#{$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 => $pi[:subjectid]}
result = JSON.parse(response)
inv_char = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["propname"]["value"]}:::#{n["value"]["value"]}"}
assert inv_char.include?("#{@@uri}:::organism:::Saccharomyces cerevisiae (Baker's yeast)")
assert_equal 200, response.code
end
def test_30_empty_factorValues_search
assert_raises OpenTox::BadRequestError do
response = OpenTox::RestClientWrapper.get "#{$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 => $pi[:subjectid]}
result = JSON.parse(response)
inv_factors = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["factorname"]["value"]}:::#{n["ontouri"]["value"]}:::#{n["value"]["value"]}"}
#puts inv_factors
assert_equal 200, response.code
assert inv_factors.include?("#{@@uri}:::compound:::http://purl.obolibrary.org/chebi/CHEBI:28748:::DOXORUBICIN")
end
# Retrieves protocol URI containing any of the factor value URI (e.g. two compound URIs)
def test_10_protocols_by_factors
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/protocols_by_factors", {:factorValues => "['http://purl.obolibrary.org/chebi/CHEBI:28748']"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
result = JSON.parse(response)
protocol_factors = result["results"]["bindings"].map{|n| "#{n["protocol"]["value"]}:::#{n["label"]["value"]}:::#{n["factorname"]["value"]}:::#{n["value"]["value"]}"}
#puts protocol_factors
assert_equal 200, response.code
assert protocol_factors.include?("#{@@uri}/P4:::labeling:::compound:::DOXORUBICIN")
assert protocol_factors.include?("#{@@uri}/P3:::RNA extraction:::compound:::DOXORUBICIN")
assert protocol_factors.include?("#{@@uri}/P2:::normalization data transformation:::compound:::DOXORUBICIN")
assert protocol_factors.include?("#{@@uri}/P1:::data transformation:::compound:::DOXORUBICIN")
assert protocol_factors.include?("#{@@uri}/P5:::data collection:::compound:::DOXORUBICIN")
assert protocol_factors.include?("#{@@uri}/P6:::nucleic acid hybridization:::compound:::DOXORUBICIN")
end
# Retrieves investigation URI containing any of the factor value URI (e.g. two compound URIs)
def test_11_investigation_by_factors
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_factors", {:factorValues => "['http://purl.obolibrary.org/chebi/CHEBI:28748']"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
#puts response
result = JSON.parse(response)
inv_factors = result["results"]["bindings"].map{|n| "#{n["inv"]["value"]}:::#{n["factorname"]["value"]}:::#{n["value"]["value"]}"}
assert_equal 200, response.code
assert inv_factors.include?("#{@@uri}:::compound:::DOXORUBICIN")
end
# Retrieves investigation URI given a factor value URI (e.g. compound URI)
def test_12_investigation_by_factor
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_factor", {:value => "http://purl.obolibrary.org/chebi/CHEBI:28748"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
#puts response
result = JSON.parse(response)
inv_factor = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["factorname"]["value"]}:::#{n["value"]["value"]}"}
assert_equal 200, response.code
assert inv_factor.include?("#{@@uri}:::compound:::DOXORUBICIN")
end
def test_16_investigation_by_pvalue
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_pvalue", {:value => "0.65614"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
result = JSON.parse(response)
#puts response
result = JSON.parse(response)
inv_pvalue = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["gene"]["value"]}"}
assert_equal 200, response.code
assert inv_pvalue.include?("#{@@uri}:::http://onto.toxbank.net/isa/Entrez/3075")
end
def test_17_investigation_by_qvalue
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_qvalue", {:value => "0.805517"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
#puts response
result = JSON.parse(response)
inv_qvalue = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["gene"]["value"]}"}
assert_equal 200, response.code
assert inv_qvalue.include?("#{@@uri}:::http://onto.toxbank.net/isa/Entrez/3075")
end
def test_18_investigation_by_foldchange
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_foldchange", {:value => "0.035"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
result = JSON.parse(response)
#puts response
inv_foldchange = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["gene"]["value"]}"}
assert_equal 200, response.code
assert inv_foldchange.include?("#{@@uri}:::http://onto.toxbank.net/isa/Entrez/3075")
end
def test_19_investigation_by_genes
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_genes", {:geneIdentifiers => "['entrez:3075']"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
result = JSON.parse(response)
#puts response
inv_genes = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}:::#{n["datatype"]["value"]}:::#{n["title"]["value"]}:::#{n["valuetype"]["value"]}:::#{n["value"]["value"]}"}
assert_equal 200, response.code
assert inv_genes.include?("#{@@uri}:::http://onto.toxbank.net/isa/bii/data_types/microarray_derived_data:::q-value[Low.8hr-Control.8hr]:::http://onto.toxbank.net/isa/qvalue:::0.911237")
end
def test_20_investigation_by_gene_and_pvalue
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_gene_and_pvalue", {:geneIdentifiers => "['entrez:3075', 'uniprot:P10809']", :value => "0.7"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
result = JSON.parse(response)
#puts response
inv = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}"}
assert_equal 200, response.code
assert inv.include?("#{@@uri}")
end
def test_21_investigation_by_gene_and_pvalue
response = OpenTox::RestClientWrapper.get "#{$investigation[:uri]}/sparql/investigation_by_gene_and_pvalue", {:geneIdentifiers => "['entrez:3075']", :value => "0.7"}, {:accept => "application/json", :subjectid => $pi[:subjectid]}
result = JSON.parse(response)
#puts response
inv = result["results"]["bindings"].map{|n| "#{n["investigation"]["value"]}"}
assert_equal 200, response.code
assert inv.include?("#{@@uri}")
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
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