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authorrautenberg <rautenberg@in-silico.ch>2012-05-07 19:52:12 +0200
committerrautenberg <rautenberg@in-silico.ch>2012-05-07 19:52:12 +0200
commit96916da933e1bc53db69b3d3e8b335de4e77c0aa (patch)
treeb25a4ff5246f5cdc755bc5196ff05f4d09470bc1
parent9d67e1c80b8854f45032c46aa8c21c8e3a236e54 (diff)
parent81346e1ba9624b57e476688167157e64e07c60fd (diff)
Merge branch 'release/v0.0.3'v0.0.3
Diffstat
-rw-r--r--.gitignore1
-rw-r--r--Gemfile1
-rw-r--r--test/authorization.rb6
-rw-r--r--test/compound.rb24
-rw-r--r--test/data/toxbank-investigation/valid/BII-I-1.n331669
-rw-r--r--test/data/toxbank-investigation/valid/BII-I-1.rdf31669
-rw-r--r--test/data/toxbank-investigation/valid/BII-I-1.zipbin13225 -> 13684 bytes
-rw-r--r--test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zipbin111567 -> 111835 bytes
-rw-r--r--test/data/toxbank-investigation/valid/isa-tab-renamed.zipbin15666 -> 0 bytes
-rw-r--r--test/dataset.rb25
-rw-r--r--test/feature.rb140
-rw-r--r--test/policy.rb16
-rw-r--r--test/setup.rb11
-rw-r--r--test/task.rb32
-rw-r--r--test/toxbank-investigation-curl.rb9
-rw-r--r--test/toxbank-investigation-rest.rb17
-rw-r--r--test/toxbank-investigation-xls.rb2
17 files changed, 34097 insertions, 29525 deletions
diff --git a/.gitignore b/.gitignore
index d87d4be..aaffbb3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,3 +15,4 @@ spec/reports
test/tmp
test/version_tmp
tmp
+/test/urilist.rb
diff --git a/Gemfile b/Gemfile
index 8d63ad8..9d9cd0e 100644
--- a/Gemfile
+++ b/Gemfile
@@ -3,3 +3,4 @@ source 'https://rubygems.org'
# Specify your gem's dependencies in opentox-test.gemspec
gemspec
gem "opentox-client", :path => "~/opentox-client"
+gem "opentox-server", :path => "~/opentox-server"
diff --git a/test/authorization.rb b/test/authorization.rb
index 1556187..f23fe02 100644
--- a/test/authorization.rb
+++ b/test/authorization.rb
@@ -1,12 +1,6 @@
require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb")
TEST_URI = "http://only_a_test/test/" + rand(1000000).to_s
-unless defined? $aa[:uri] #overwrite turned off A&A server for testing
- $aa[:uri] = "https://opensso.in-silico.ch"
- @@subjectid = OpenTox::Authorization.authenticate($aa[:user],$aa[:password])
-end
-
-@@subjectid ||= OpenTox::Authorization.authenticate($aa[:user],$aa[:password])
class TestOpenToxAuthorizationBasic < Test::Unit::TestCase
diff --git a/test/compound.rb b/test/compound.rb
index 7573f58..e1167d8 100644
--- a/test/compound.rb
+++ b/test/compound.rb
@@ -1,38 +1,42 @@
require 'test/unit'
require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb")
-class CompoundTest < Test::Unit::TestCase
+begin
+ @@service_uri = $compound[:uri]
+ puts "Service URI is: #{@@service_uri}"
+rescue
+ puts "Configuration Error: $compound[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb")
+ exit
+end
- def setup
- @service_uri = "http://ot-dev.in-silico.ch/compound"
- end
+class CompoundTest < Test::Unit::TestCase
def test_compound_from_smiles_0
- c = OpenTox::Compound.from_smiles @service_uri, "F[B-](F)(F)F.[Na+]"
+ c = OpenTox::Compound.from_smiles @@service_uri, "F[B-](F)(F)F.[Na+]"
assert_equal "InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1", c.to_inchi
assert_equal "[Na+].F[B-](F)(F)F", c.to_smiles # still does not work on 64bit machines
end
def test_compound_from_smiles_1
- c = OpenTox::Compound.from_smiles @service_uri, "CC(=O)CC(C)C#N"
+ c = OpenTox::Compound.from_smiles @@service_uri, "CC(=O)CC(C)C#N"
assert_equal "InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3", c.to_inchi
assert_equal "CC(CC(=O)C)C#N", c.to_smiles
end
def test_compound_from_name
- c = OpenTox::Compound.from_name @service_uri, "Benzene"
+ c = OpenTox::Compound.from_name @@service_uri, "Benzene"
assert_equal "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H", c.to_inchi
assert_equal "c1ccccc1", c.to_smiles
end
def test_compound_from_smiles_2
- c = OpenTox::Compound.from_smiles @service_uri, "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F"
+ c = OpenTox::Compound.from_smiles @@service_uri, "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F"
assert_equal "InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1", c.to_inchi
assert_equal "N#[N+]c1ccccc1.F[B-](F)(F)F", c.to_smiles
end
def test_compound_from_inchi
- c = OpenTox::Compound.from_inchi @service_uri, "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+ c = OpenTox::Compound.from_inchi @@service_uri, "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
assert_equal "c1ccccc1", c.to_smiles
end
@@ -44,7 +48,7 @@ class CompoundTest < Test::Unit::TestCase
=begin
def test_match_hits
- c = OpenTox::Compound.from_smiles @service_uri, "N=C=C1CCC(=F=FO)C1"
+ c = OpenTox::Compound.from_smiles @@service_uri, "N=C=C1CCC(=F=FO)C1"
assert_equal ({"FF"=>2, "CC"=>10, "C"=>6, "C1CCCC1"=>10, "C=C"=>2}), c.match_hits(['CC','F=F','C','C=C','FF','C1CCCC1','OO'])
end
=end
diff --git a/test/data/toxbank-investigation/valid/BII-I-1.n3 b/test/data/toxbank-investigation/valid/BII-I-1.n3
index 6c6fb4a..3ca1c0d 100644
--- a/test/data/toxbank-investigation/valid/BII-I-1.n3
+++ b/test/data/toxbank-investigation/valid/BII-I-1.n3
@@ -1,19648 +1,21871 @@
-@prefix : <http://onto.toxbank.net/isa/TEST/> .
+@prefix : <https://toxbank-dev.in-silico.ch/0/> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix tb: <http://onto.toxbank.net/api/> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix isa: <http://onto.toxbank.net/isa/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
-:MN1290
+:DAN405
+ a isa:DataAcquisition ;
+ isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.40" ;
+ isa:hasInputNode :MN2178 ;
+ isa:hasOutputNode :DN1834 ;
+ isa:hasStudy :S2 .
+
+:MN1878
+ a isa:MaterialNode ;
+ isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.29:out:0" ;
+ isa:hasMaterial :M2234 ;
+ isa:hasStudy :S2 .
+
+:M2495
+ a isa:Material ;
+ isa:hasAccessionID "BII-S-1:extract:a_transcriptome.P-0.07-aliquot1" .
+
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a isa:MaterialProcessing ;
- isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.43" ;
- isa:hasInputNode :MN735 ;
- isa:hasOutputNode :MN396 ;
+ isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.13" ;
+ isa:hasInputNode :MN1979 ;
+ isa:hasOutputNode :MN1835 ;
isa:hasProtocolApplication
- :PA2647 ;
- isa:hasStudy :S17 .
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+ isa:hasStudy :S1 .
-:MN2153
- a isa:MaterialProcessing ;
- isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.30" ;
- isa:hasInputNode :MN678 ;
- isa:hasOutputNode :MN789 ;
- isa:hasStudy :S17 .
+:OE3123
+ a isa:OntologyEntry .
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+:M3914
+ a isa:Material ;
+ isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.G-0.1-aliquot3" .
+
+:M3763
+ a isa:Material ;
+ isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.N-0.1-aliquot10" .
+
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a isa:MaterialNode ;
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- isa:hasMaterial :M2785 ;
- isa:hasStudy :S17 .
+ isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.13:in:0" ;
+ isa:hasMaterial :M3693 ;
+ isa:hasStudy :S2 .
-:M2764
+:MN1443
+ a isa:MaterialNode ;
+ isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.43:out:0" ;
+ isa:hasMaterial :M3423 ;
+ isa:hasStudy :S2 .
+
+:M3111
a isa:Material ;
- isa:hasAccessionID "BII-S-1:sample:G-0.1-aliquot3" .
+ isa:hasAccessionID "BII-S-1:ms_spec:a_metabolome.JIC55_Carbon_0.07_External_1_3" .
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a isa:DataProcessing ;
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- isa:hasStudy :S17 .
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+ isa:hasOutputNode :DN1896 ;
+ isa:hasStudy :S2 .
+
+:PA3786
+ a isa:ProtocolApplication ;
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+:MN2169
+ a isa:MaterialNode ;
+ isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.3:out:0" ;
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isa:hasProtocolApplication
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a isa:MaterialNode ;
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isa:hasProtocolApplication
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a isa:Material ;
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isa:hasProtocolApplication
- :PA2652 ;
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+5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water.
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+ 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" .
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+4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min.
+5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water.
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+7. After precipitation (20 C for 1 h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water.
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+ 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" .
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+ dcterms:abstract """Background
+Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking.
+Results
+Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth.
+Conclusion
+This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;
+ dcterms:created "29 Apr 2007 20:00:00 GMT" ;
+ dcterms:issued "9 Mar 2009 21:00:00 GMT" ;
+ dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .
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+5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water.
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a isa:MaterialProcessing ;
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isa:hasProtocolApplication
- :PA2475 ;
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+ :PA3404 ;
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-:MN1090
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- isa:hasMaterial :M2322 ;
- isa:hasStudy :S17 .
+ isa:hasAccessionID "BII-S-2:proc:a_microarray.0.2.13:out:0" ;
+ isa:hasMaterial :M2466 ;
+ isa:hasStudy :S1 .
+
+:PA2405
+ a isa:ProtocolApplication ;
+ isa:appliesProtocol :P_1109 .
+
+:M3894
+ a isa:Material ;
+ isa:hasAccessionID "BII-S-1:source:culture16" .
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diff --git a/test/data/toxbank-investigation/valid/BII-I-1.rdf b/test/data/toxbank-investigation/valid/BII-I-1.rdf
index 6c6fb4a..3ca1c0d 100644
--- a/test/data/toxbank-investigation/valid/BII-I-1.rdf
+++ b/test/data/toxbank-investigation/valid/BII-I-1.rdf
@@ -1,19648 +1,21871 @@
-@prefix : <http://onto.toxbank.net/isa/TEST/> .
+@prefix : <https://toxbank-dev.in-silico.ch/0/> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix tb: <http://onto.toxbank.net/api/> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix isa: <http://onto.toxbank.net/isa/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
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+ isa:hasOutputNode :DN1834 ;
+ isa:hasStudy :S2 .
+
+:MN1878
+ a isa:MaterialNode ;
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+ isa:hasMaterial :M2234 ;
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+
+:M2495
+ a isa:Material ;
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+
+:MN83
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- isa:hasInputNode :MN735 ;
- isa:hasOutputNode :MN396 ;
+ isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.13" ;
+ isa:hasInputNode :MN1979 ;
+ isa:hasOutputNode :MN1835 ;
isa:hasProtocolApplication
- :PA2647 ;
- isa:hasStudy :S17 .
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- isa:hasInputNode :MN678 ;
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+:M3914
+ a isa:Material ;
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+
+:M3763
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+:MN1443
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+:PA3786
+ a isa:ProtocolApplication ;
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+:MN2169
+ a isa:MaterialNode ;
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+5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water.
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+7. After precipitation (20 C for 1h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water.
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+ 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" .
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+3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorouslyor 15 s, then 5min incubation at room temperature.
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+4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min.
+5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water.
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+6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl bffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample.
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+ dcterms:abstract """Background
+Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking.
+Results
+Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth.
+Conclusion
+This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.""" ;
+ dcterms:created "29 Apr 2007 20:00:00 GMT" ;
+ dcterms:issued "9 Mar 2009 21:00:00 GMT" ;
+ dcterms:title "Growth control of the eukaryote cell: a systems biology study in yeast" .
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+2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5 min.
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+3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorouslyor 15 s, then 5 min incubation at room temperature.
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+4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min.
+5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water.
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+6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl bffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample.
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+7. After precipitation (20 C for 1h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water.
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+ 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).""" .
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+:M2293
a isa:Material ;
- isa:hasAccessionID "BII-S-1:labelled_extract:a_transcriptome.S-0.1-aliquot1" .
+ isa:hasAccessionID "BII-S-1:extract:a_transcriptome.S-0.1-aliquot1" .
-:MN663
- a isa:MaterialNode ;
- isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.45:out:0" ;
- isa:hasMaterial :M2335 ;
- isa:hasStudy :S17 .
+:M2415
+ a isa:Material ;
+ isa:hasAccessionID "BII-S-1:sample:C-0.2-aliquot11" .
-:MN510
- a isa:MaterialNode ;
- isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.123:out:0" ;
- isa:hasMaterial :M2500 ;
- isa:hasStudy :S17 .
+:FV3300
+ a isa:FactorValue .
-:DN426
- a isa:DataNode ;
- isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.103:out:0" ;
- isa:hasData :D3453 ;
- isa:hasStudy :S17 .
+:DPN678
+ a isa:DataProcessing ;
+ isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.13" ;
+ isa:hasInputNode :DN1811 ;
+ isa:hasOutputNode :DN1698 ;
+ isa:hasStudy :S2 .
-:MN1222
- a isa:MaterialProcessing ;
- isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.20" ;
- isa:hasInputNode :MN691 ;
- isa:hasOutputNode :MN701 ;
- isa:hasProtocolApplication
- :PA2472 ;
- isa:hasStudy :S17 .
+:M3895
+ a isa:Material ;
+ isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.G-0.1-aliquot6" .
-:PA2729
- a isa:MaterialProcessing ;
- isa:hasProtocol :P_1133 .
+:M3658
+ a isa:Material ;
+ isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.S-0.2-aliquot7" .
-:MN1091
- a isa:MaterialNode ;
- isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.93:out:0" ;
- isa:hasMaterial :M2814 ;
- isa:hasStudy :S17 .
+:DAN418
+ a isa:DataAcquisition ;
+ isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.37" ;
+ isa:hasInputNode :MN2124 ;
+ isa:hasOutputNode :DN1453 ;
+ isa:hasStudy :S2 .
-:PA3531
+:MN810
a isa:MaterialProcessing ;
- isa:hasProtocol :P_1137 .
+ isa:hasAccessionID "BII-S-1:proc:a_metabolome.3.4.58" ;
+ isa:hasInputNode :MN1845 ;
+ isa:hasOutputNode :MN1675 ;
+ isa:hasStudy :S2 .
-:MN927
- a isa:MaterialNode ;
- isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.45:out:0" ;
- isa:hasMaterial :M3186 ;
- isa:hasStudy :S17 .
+:PA2274
+ a isa:ProtocolApplication ;
+ isa:appliesProtocol :P_1105 .
-:MN664
- a isa:MaterialNode ;
- isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.11:out:0" ;
- isa:hasMaterial :M3156 ;
- isa:hasStudy :S17 .
+:DPN160
+ a isa:DataProcessing ;
+ isa:hasAccessionID "BII-S-1:proc:a_proteome.7.8.7" ;
+ isa:hasInputNode :DN1585 ;
+ isa:hasOutputNode :DN1399 ;
+ isa:hasStudy :S2 .
-:MN511
- a isa:MaterialNode ;
- isa:hasAccessionID "BII-S-1:proc:a_metabolome.0.2.72:out:0" ;
- isa:hasMaterial :M2748 ;
- isa:hasStudy :S17 .
+:PA3772
+ a isa:ProtocolApplication ;
+ isa:appliesProtocol :P_1111 .
-:MN926
- a isa:MaterialNode ;
- isa:hasAccessionID "BII-S-2:proc:a_microarray.4.6.12:out:0" ;
- isa:hasMaterial :M2424 ;
- isa:hasStudy :S16 .
+:ISA_3978
+ a foaf:Person , isa:Contact ;
+ foaf:family_name "Leo"^^xsd:string ;
+ foaf:givenname "Zeef"^^xsd:string .
-:DN427
- a isa:DataNode ;
- isa:hasAccessionID "BII-S-1:proc:a_metabolome.4.5.84:out:0" ;
- isa:hasData :D2931 ;
- isa:hasStudy :S17 .
+:MN963
+ a isa:MaterialProcessing ;
+ isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.64" ;
+ isa:hasInputNode :MN1967 ;
+ isa:hasOutputNode :MN1798 ;
+ isa:hasStudy :S2 .
-:M3223
- a isa:Material ;
- isa:hasAccessionID "BII-S-1:sample:N-0.2-aliquot3" .
+:DPN388
+ a isa:DataProcessing ;
+ isa:hasAccessionID "BII-S-1:proc:a_metabolome.5.6.55" ;
+ isa:hasInputNode :DN1532 ;
+ isa:hasOutputNode :DN1379 ;
+ isa:hasStudy :S2 .
-:MN1223
+:MN772
a isa:MaterialProcessing ;
- isa:hasAccessionID "BII-S-1:proc:a_transcriptome.2.4.29" ;
- isa:hasInputNode :MN404 ;
- isa:hasOutputNode :MN864 ;
+ isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.107" ;
+ isa:hasInputNode :MN1441 ;
+ isa:hasOutputNode :MN1908 ;
isa:hasProtocolApplication
- :PA2475 ;
- isa:hasStudy :S17 .
+ :PA3783 ;
+ isa:hasStudy :S2 .
-:M3449
- a isa:Material ;
- isa:hasAccessionID "BII-S-1:labelled_extract:a_metabolome.C-0.1-aliquot8" .
+:DPN739
+ a isa:DataProcessing ;
+ isa:hasAccessionID "BII-S-1:proc:a_transcriptome.7.8.32" ;
+ isa:hasInputNode :DN2051 ;
+ isa:hasOutputNode :DN1345 ;
+ isa:hasStudy :S2 .
-:MN860
+:MN549
+ a isa:MaterialProcessing ;
+ isa:hasAccessionID "BII-S-1:proc:a_transcriptome.0.2.8" ;
+ isa:hasInputNode :MN1386 ;
+ isa:hasOutputNode :MN1912 ;
+ isa:hasProtocolApplication
+ :PA3404 ;
+ isa:hasStudy :S2 .
+
+:MN1348
a isa:MaterialNode ;
- isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.71:out:0" ;
- isa:hasMaterial :M2497 ;
- isa:hasStudy :S17 .
+ isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.13:out:0" ;
+ isa:hasMaterial :M3644 ;
+ isa:hasStudy :S2 .
-:DPN1976
- a isa:DataProcessing ;
- isa:hasAccessionID "BII-S-1:proc:a_proteome.6.7.9" ;
- isa:hasInputNode :DN260 ;
- isa:hasOutputNode :DN487 ;
- isa:hasStudy :S17 .
+:MN179
+ a isa:MaterialProcessing ;
+ isa:hasAccessionID "BII-S-1:proc:a_transcriptome.4.6.25" ;
+ isa:hasInputNode :MN1540 ;
+ isa:hasOutputNode :MN1366 ;
+ isa:hasProtocolApplication
+ :PA2727 ;
+ isa:hasStudy :S2 .
-:MN712
- a isa:MaterialNode ;
- isa:hasAccessionID "BII-S-1:proc:a_metabolome.2.3.89:out:0" ;
- isa:hasMaterial :M3521 ;
- isa:hasStudy :S17 .
+:M2364
+ a isa:Material ;
+ isa:hasAccessionID "BII-S-1:sample:C-0.1-aliquot9" .
-:MN1090
+:MN1349
a isa:MaterialNode ;
- isa:hasAccessionID "BII-S-1:proc:s_BII-S-1.0.2.41:out:0" ;
- isa:hasMaterial :M2322 ;
- isa:hasStudy :S17 .
+ isa:hasAccessionID "BII-S-2:proc:a_microarray.0.2.13:out:0" ;
+ isa:hasMaterial :M2466 ;
+ isa:hasStudy :S1 .
+
+:PA2405
+ a isa:ProtocolApplication ;
+ isa:appliesProtocol :P_1109 .
+
+:M3894
+ a isa:Material ;
+ isa:hasAccessionID "BII-S-1:source:culture16" .
+: owl:sameAs :I1115 .
diff --git a/test/data/toxbank-investigation/valid/BII-I-1.zip b/test/data/toxbank-investigation/valid/BII-I-1.zip
index fa56e5a..fbe4cdf 100644
--- a/test/data/toxbank-investigation/valid/BII-I-1.zip
+++ b/test/data/toxbank-investigation/valid/BII-I-1.zip
Binary files differ
diff --git a/test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zip b/test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zip
index c1aa89c..d0d0ffe 100644
--- a/test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zip
+++ b/test/data/toxbank-investigation/valid/E-MTAB-798_philippe.zip
Binary files differ
diff --git a/test/data/toxbank-investigation/valid/isa-tab-renamed.zip b/test/data/toxbank-investigation/valid/isa-tab-renamed.zip
deleted file mode 100644
index b8130a8..0000000
--- a/test/data/toxbank-investigation/valid/isa-tab-renamed.zip
+++ /dev/null
Binary files differ
diff --git a/test/dataset.rb b/test/dataset.rb
index 8730154..54c9871 100644
--- a/test/dataset.rb
+++ b/test/dataset.rb
@@ -4,23 +4,30 @@ DATASET = "http://ot-dev.in-silico.ch/dataset"
DATA_DIR = File.join(File.dirname(__FILE__),"data")
# TODO: add subjectids
+begin
+ @@service_uri = $dataset[:uri]
+ puts "Service URI is: #{@@service_uri}"
+rescue
+ puts "Configuration Error: $dataset[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb")
+ exit
+end
class DatasetTest < Test::Unit::TestCase
def test_all
- datasets = OpenTox::Dataset.all DATASET, @@subjectid
+ datasets = OpenTox::Dataset.all @@service_uri, @@subjectid
assert_equal OpenTox::Dataset, datasets.first.class
end
def test_create_empty
- d = OpenTox::Dataset.create DATASET, @@subjectid
+ d = OpenTox::Dataset.create @@service_uri, @@subjectid
assert_equal OpenTox::Dataset, d.class
- assert_match /#{DATASET}/, d.uri.to_s
+ assert_match /#{@@service_uri}/, d.uri.to_s
d.delete :subjectid => @@subjectid
end
def test_create_from_file
- d = OpenTox::Dataset.from_file DATASET, File.join(DATA_DIR,"EPAFHM.mini.csv"), @@subjectid
+ d = OpenTox::Dataset.from_file @@service_uri, File.join(DATA_DIR,"EPAFHM.mini.csv"), @@subjectid
assert_equal OpenTox::Dataset, d.class
assert_equal d.uri, d[RDF::XSD.anyURI]
assert_equal "EPAFHM.mini", d.metadata[RDF::URI("http://purl.org/dc/elements/1.1/title")].first.to_s # DC.title is http://purl.org/dc/terms/title
@@ -32,7 +39,7 @@ class DatasetTest < Test::Unit::TestCase
end
def test_from_yaml
- @dataset = OpenTox::Dataset.from_file DATASET, File.join(DATA_DIR,"hamster_carcinogenicity.yaml"), @@subjectid
+ @dataset = OpenTox::Dataset.from_file @@service_uri, File.join(DATA_DIR,"hamster_carcinogenicity.yaml"), @@subjectid
assert_equal OpenTox::Dataset, @dataset.class
assert_equal "hamster_carcinogenicity", @dataset[RDF::URI("http://purl.org/dc/elements/1.1/title")]
hamster_carc?
@@ -42,7 +49,7 @@ class DatasetTest < Test::Unit::TestCase
=begin
# TODO: fix (mime type??0 and add Egons example
def test_sdf_with_multiple_features
- @dataset = OpenTox::Dataset.from_file DATASET, "#{DATA_DIR}/CPDBAS_v5c_1547_29Apr2008part.sdf"
+ @dataset = OpenTox::Dataset.from_file @@service_uri, "#{DATA_DIR}/CPDBAS_v5c_1547_29Apr2008part.sdf"
assert_equal OpenTox::Dataset, @dataset.class
puts @dataset.features.size
puts @dataset.compounds.size
@@ -51,14 +58,14 @@ class DatasetTest < Test::Unit::TestCase
=end
def test_multicolumn_csv
- @dataset = OpenTox::Dataset.from_file DATASET, "#{DATA_DIR}/multicolumn.csv", @@subjectid
+ @dataset = OpenTox::Dataset.from_file @@service_uri, "#{DATA_DIR}/multicolumn.csv", @@subjectid
assert_equal 5, @dataset.features.size
assert_equal 4, @dataset.compounds.size
@dataset.delete :subjectid => @@subjectid
end
def test_from_csv
- @dataset = OpenTox::Dataset.from_file DATASET, "#{DATA_DIR}/hamster_carcinogenicity.csv", @@subjectid
+ @dataset = OpenTox::Dataset.from_file @@service_uri, "#{DATA_DIR}/hamster_carcinogenicity.csv", @@subjectid
assert_equal OpenTox::Dataset, @dataset.class
hamster_carc?
@dataset.delete :subjectid => @@subjectid
@@ -66,7 +73,7 @@ class DatasetTest < Test::Unit::TestCase
=begin
def test_save
- d = OpenTox::Dataset.create DATASET
+ d = OpenTox::Dataset.create @@service_uri
d.metadata
d.metadata[RDF::DC.title] = "test"
d.save
diff --git a/test/feature.rb b/test/feature.rb
index f6ce128..bf49bea 100644
--- a/test/feature.rb
+++ b/test/feature.rb
@@ -1,27 +1,142 @@
require 'test/unit'
require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb")
-class FeatureTest < Test::Unit::TestCase
+class FeatureRestTest < Test::Unit::TestCase
- def setup
- @features = [
- #@@classification_training_dataset.features.keys.first,
- "http://apps.ideaconsult.net:8080/ambit2/feature/35796",
- #File.join(OpenTox::Model::Lazar.all.last,"predicted","value")
+ def serialize rdf, format
+ string = RDF::Writer.for(format).buffer do |writer|
+ rdf.each{|statement| writer << statement}
+ end
+ string
+ end
+
+ def parse string, format
+ rdf = RDF::Graph.new
+ RDF::Reader.for(format).new(string) do |reader|
+ reader.each_statement { |statement| rdf << statement }
+ end
+ rdf
+ end
+ # TODO: test supported accept/content-type formats
+ # TODO: test invalid rdfs
+ def test_01_create_feature
+ @@rdf = RDF::Graph.new
+ subject = RDF::Node.new
+ #subject = RDF::URI.new File.join($feature[:uri]), SecureRandom.uuid)
+ @@rdf << RDF::Statement.new(subject, RDF::DC.title, "test" )
+ @@rdf << RDF::Statement.new(subject, RDF.type, RDF::OT.Feature)
+
+ @@formats = [
+ [:ntriples, "text/plain"],
+ [:rdfxml, "application/rdf+xml"],
+ [:turtle, 'text/turtle']
]
+ @@uris = []
+
+ @@formats.each do |f|
+ @@uris << OpenTox::RestClientWrapper.post($feature[:uri], serialize(@@rdf, f[0]), :content_type => f[1]).chomp
+ assert_equal true, URI.accessible?(@@uris.last)
+ end
+ end
+
+ def test_02_list_features
+ r = OpenTox::RestClientWrapper.get($feature[:uri], {}, :accept => "text/uri-list")#.split("\n")
+ @@uris.each{ |uri| assert_equal true, r.include?(uri) }
+ @@formats.each do |f|
+ rdf = OpenTox::RestClientWrapper.get($feature[:uri], {}, :accept => f[1])
+ @@uris.each do |uri|
+ assert_match /#{uri}/, rdf
+ assert_match /test/, rdf
+ assert_match /Feature/, rdf
+ end
+ end
+ end
+
+ def test_03_get_feature
+ @@uris.each do |uri|
+ @@formats.each do |f|
+ rdf = OpenTox::RestClientWrapper.get(uri, {}, :accept => f[1])
+ # TODO compare with rdf serialization
+ assert_match /#{uri}/, rdf
+ end
+ end
+ end
+
+ def test_04_add_to_feature
+ uri = @@uris.first
+ new_rdf = RDF::Graph.new
+ new_rdf << RDF::Statement.new(RDF::Node.new, RDF::DC.author, "XYZ")
+ @@formats.each do |f|
+ OpenTox::RestClientWrapper.post(uri, serialize(new_rdf,f[0]), :content_type => f[1])
+ assert_match /XYZ/, OpenTox::RestClientWrapper.get(uri,{},:accept => f[1])
+ # TODO compare with rdf serialization
+ end
+ end
+
+ def test_05_replace_feature
+ @@formats.each do |f|
+ @@uris.each do |uri|
+ OpenTox::RestClientWrapper.put(uri, serialize(@@rdf,f[0]), :content_type => f[1])
+ assert_equal true, URI.accessible?(uri)
+ assert_no_match /XYZ/, OpenTox::RestClientWrapper.get(uri,{},:accept => f[1])
+ end
+ end
end
- def test_feature
- @features.each do |uri|
- f = OpenTox::Feature.new(uri)
- assert_equal RDF::OT1.TUM_CDK_nAtom, f[RDF::OWL.sameAs]
- assert_equal RDF::OT1.TUM_CDK_nAtom, f.metadata[RDF::OWL.sameAs].first.to_s
- assert_equal [RDF::OT1.Feature,RDF::OT1.NumericFeature].sort, f[RDF.type].sort
+ def test_06_delete_feature
+ @@uris.each do |uri|
+ OpenTox::RestClientWrapper.delete(uri)
+ assert_raise OpenTox::RestCallError do
+ OpenTox::RestClientWrapper.get(uri)
+ end
end
end
+end
+
=begin
+class FeatureCrudTest < Test::Unit::TestCase
+
+ def test_01_create_feature
+ @@feature = OpenTox::Feature.create $feature[:uri]
+ assert_equal true, URI.accessible?(@@feature.uri)
+ end
+
+ def test_02_list_features
+ r = OpenTox::Feature.all($feature[:uri])
+ assert_equal true, r.include?(@@feature)
+ end
+
+ def test_03_get_feature
+ @@rdf = @@feature.metadata
+ assert_match /#{@@feature.uri}/, @@rdf
+ end
+
+ def test_04_update_feature
+ @@feature[RDF::DC.title] = "test"
+ @@feature.save
+ assert_match "test", OpenTox::RestClientWrapper.get(@@uri)
+ end
+
+ def test_05_delete_feature
+ uri = @@feature.uri
+ @@feature.delete
+ r = OpenTox::RestClientWrapper.get($feature[:uri]).split("\n")
+ assert_equal false, r.include?(@@uri)
+ assert_equal false, URI.accessible?(@@uri)
+ end
+
+end
+
+
+ def test_ambit_feature
+ uri = "http://apps.ideaconsult.net:8080/ambit2/feature/35796",
+ f = OpenTox::Feature.new(uri)
+ assert_equal RDF::OT1.TUM_CDK_nAtom, f[RDF::OWL.sameAs]
+ assert_equal RDF::OT1.TUM_CDK_nAtom, f.metadata[RDF::OWL.sameAs].first.to_s
+ assert_equal [RDF::OT1.Feature,RDF::OT1.NumericFeature].sort, f[RDF.type].sort
+ end
def test_owl
#@features.each do |uri|
validate_owl @features.first, @@subjectid unless CONFIG[:services]["opentox-dataset"].match(/localhost/)
@@ -32,4 +147,3 @@ class FeatureTest < Test::Unit::TestCase
=end
-end
diff --git a/test/policy.rb b/test/policy.rb
index c69175d..6babcc6 100644
--- a/test/policy.rb
+++ b/test/policy.rb
@@ -11,12 +11,6 @@ POLICY_NAME = "test_policy_#{rand(100000)}"
RULE_NAME = "test_rule_#{rand(100000)}"
SUBJECT_NAME = "test_subject_#{rand(100000)}"
-AA ||= "https://opensso.in-silico.ch"
-AA_USER = "guest"
-AA_PASS = "guest"
-
-@@subjectid = OpenTox::Authorization.authenticate(AA_USER,AA_PASS)
-
class PolicyTest < Test::Unit::TestCase
def test_01_class
@@ -67,16 +61,16 @@ class PolicyTest < Test::Unit::TestCase
def test_04_group_user
policies = OpenTox::Policies.new()
- policies.load_default_policy(AA_USER, TEST_URI, "member")
+ policies.load_default_policy($aa[:user], TEST_URI, "member")
assert_equal "member", policies.policies["policy_group"].group
- assert_equal AA_USER, policies.policies["policy_user"].user
+ assert_equal $aa[:user], policies.policies["policy_user"].user
end
def test_05_DN
policies = OpenTox::Policies.new()
policies.new_policy(POLICY_NAME)
policy = policies.policies[policies.names[0]]
- policy.set_ot_user(AA_USER)
+ policy.set_ot_user($aa[:user])
assert_equal USER_VALUE, policy.value
assert_equal USER_TYPE, policy.type
policy.set_ot_group(USER_GROUP)
@@ -84,10 +78,9 @@ class PolicyTest < Test::Unit::TestCase
assert_equal GROUP_TYPE, policy.type
end
-=begin
def test_06_load_xml_and_check_defaults
policies = OpenTox::Policies.new()
- xml = File.read(File.join(File.dirname(__FILE__), "../lib/templates/default_policy.xml"))
+ xml = policies.get_xml_template("default_policy")
policies.load_xml(xml)
# check user policy
policy = policies.policies["policy_user"]
@@ -116,6 +109,5 @@ class PolicyTest < Test::Unit::TestCase
assert policy.subject.type == GROUP_TYPE
assert policy.subject.value == GROUP_VALUE
end
-=end
end
diff --git a/test/setup.rb b/test/setup.rb
index c63a17c..b035a80 100644
--- a/test/setup.rb
+++ b/test/setup.rb
@@ -4,8 +4,11 @@ Bundler.require
require 'opentox-client'
require File.join(ENV["HOME"],".opentox","config","test.rb")
-if defined? $aa
- @@subjectid = OpenTox::Authorization.authenticate($aa[:user], $aa[:password])
-else
- @@subjectid = ""
+begin
+ AA = $aa[:uri]
+ @@subjectid = OpenTox::Authorization.authenticate($aa[:user],$aa[:password])
+ raise if !OpenTox::Authorization.is_token_valid(@@subjectid)
+rescue
+ puts "Configuration Error: $aa[:uri], $aa[:user] or $aa[:password] are not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb")
+ exit
end
diff --git a/test/task.rb b/test/task.rb
index c45704b..dd80c5b 100644
--- a/test/task.rb
+++ b/test/task.rb
@@ -2,17 +2,18 @@ require 'test/unit'
require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb")
#require "./validate-owl.rb"
-TASK_SERVICE_URI = "http://ot-dev.in-silico.ch/task"
-#TASK_SERVICE_URI = "http://ot-test.in-silico.ch/task"
-#TASK_SERVICE_URI = "https://ambit.uni-plovdiv.bg:8443/ambit2/task" #not compatible
+begin
+ @@service_uri = $task[:uri]
+ puts "Service URI is: #{@@service_uri}"
+rescue
+ puts "Configuration Error: $task[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb")
+ exit
+end
class TaskTest < Test::Unit::TestCase
-
-=begin
-=end
def test_all
- all = OpenTox::Task.all(TASK_SERVICE_URI)
+ all = OpenTox::Task.all(@@service_uri)
assert_equal Array, all.class
t = all.last
assert_equal OpenTox::Task, t.class
@@ -20,23 +21,22 @@ class TaskTest < Test::Unit::TestCase
end
def test_create_and_complete
- task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test" do
+ task = OpenTox::Task.create @@service_uri, :description => "test" do
sleep 1
- TASK_SERVICE_URI
+ @@service_uri
end
assert task.running?
assert_equal "Running", task.hasStatus
task.wait
assert task.completed?
assert_equal "Completed", task.hasStatus
- assert_equal TASK_SERVICE_URI, task.resultURI
+ assert_equal @@service_uri, task.resultURI
end
-
def test_create_and_cancel
- task = OpenTox::Task.create TASK_SERVICE_URI do
+ task = OpenTox::Task.create @@service_uri do
sleep 2
- TASK_SERVICE_URI
+ @@service_uri
end
assert task.running?
task.cancel
@@ -44,7 +44,7 @@ class TaskTest < Test::Unit::TestCase
end
def test_create_and_fail
- task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test failure", :creator => "http://test.org/fake_creator" do
+ task = OpenTox::Task.create @@service_uri, :description => "test failure", :creator => "http://test.org/fake_creator" do
sleep 1
raise "A runtime error occured"
end
@@ -56,7 +56,7 @@ class TaskTest < Test::Unit::TestCase
end
def test_create_and_fail_with_opentox_error
- task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test failure", :creator => "http://test.org/fake_creator" do
+ task = OpenTox::Task.create @@service_uri, :description => "test failure", :creator => "http://test.org/fake_creator" do
sleep 1
raise OpenTox::Error.new 500, "An OpenTox::Error occured"
end
@@ -70,7 +70,7 @@ class TaskTest < Test::Unit::TestCase
=begin
# temporarily removed until uri checking from virtual machines has been fixed
def test_wrong_result_uri
- task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test wrong result uri", :creator => "http://test.org/fake_creator" do
+ task = OpenTox::Task.create @@service_uri, :description => "test wrong result uri", :creator => "http://test.org/fake_creator" do
sleep 1
"Asasadasd"
end
diff --git a/test/toxbank-investigation-curl.rb b/test/toxbank-investigation-curl.rb
index 1c6726c..2810103 100644
--- a/test/toxbank-investigation-curl.rb
+++ b/test/toxbank-investigation-curl.rb
@@ -24,8 +24,7 @@ class UploadTest < Test::Unit::TestCase
def test_03_valid_zip_upload
# upload
- #["isa-tab-renamed.zip"].each do |f|
- ["BII-I-1.zip","isa-tab-renamed.zip","E-MTAB-798_philippe.zip"].each do |f|
+ ["BII-I-1.zip","E-MTAB-798_philippe.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
@@ -54,6 +53,8 @@ class UploadTest < Test::Unit::TestCase
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 /401/, response
+ response = `curl -I -Lk -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`
assert_match /404/, response
end
end
@@ -71,7 +72,7 @@ class UploadTest < Test::Unit::TestCase
=begin
def test_rest_client_wrapper
- ["BII-I-1.zip","isa-tab-renamed.zip"].each do |f|
+ ["BII-I-1.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
@@ -101,7 +102,7 @@ class UploadTest < Test::Unit::TestCase
=begin
def test_ruby_api
- ["BII-I-1.zip","isa-tab-renamed.zip"].each do |f|
+ ["BII-I-1.zip"].each do |f|
file = File.join File.dirname(__FILE__), "data/toxbank-investigation/valid", f
investigation = OpenTox::Investigation.create $toxbank_investigation[:uri], :file => file, :headers => {:content_type => "application/zip", :subjectid => @@subjectid}
zip = File.join @tmpdir,"tmp.zip"
diff --git a/test/toxbank-investigation-rest.rb b/test/toxbank-investigation-rest.rb
index 8849d60..5421972 100644
--- a/test/toxbank-investigation-rest.rb
+++ b/test/toxbank-investigation-rest.rb
@@ -43,6 +43,16 @@ class BasicTestCRUDInvestigation < Test::Unit::TestCase
uri = task.resultURI
@@uri = URI(uri)
assert @@uri.host == URI($toxbank_investigation[:uri]).host
+ # check_rdf
+ response = `curl -i -k -H subjectid:#{@@subjectid} -H accept:application/rdf+xml #{uri}`.chomp
+ assert_match /[Term Source Name, OBI, DOID, BTO, NEWT, UO, CHEBI, PATO, TBP, TBC, TBO, TBU, TBK]/, response
+ assert_match /[Investigation Identifier, BII\-I\-1]/, response
+ assert_match /[Investigation Title, Growth control of the eukaryote cell\: a systems biology study in yeast]/, response
+ assert_match /[Investigation Description, Background Cell growth underlies many key cellular and developmental processes]/, response
+ assert_match /[Owning Organisation URI, TBO\:G176, Public]/, response
+ assert_match /[Consortium URI, TBC\:G2, Douglas Connect]/, response
+ assert_match /[Principal Investigator URI, TBU\:U115, Glenn Myatt]/, response
+ assert_match /[Investigation keywords, TBK\:Blotting, Southwestern;TBK\:Molecular Imaging;DOID\:primary carcinoma of the liver cells]/, response
end
# get investigation/{id} as text/uri-list
@@ -78,15 +88,12 @@ class BasicTestCRUDInvestigation < Test::Unit::TestCase
assert response.index(@@uri.to_s) != nil, "URI: #{@@uri} is not in uri-list"
end
-=begin
# delete investigation/{id}
def test_99_delete_investigation
result = OpenTox::RestClientWrapper.delete @@uri.to_s, {}, :subjectid => @@subjectid
- assert_raise OpenTox::NotFoundError do
- OpenTox::RestClientWrapper.get @@uri.to_s, {}, {:accept => "text/uri-list", :subjectid => @@subjectid}
- end
+ assert result.match(/^Investigation [\d]+ deleted$/)
+ assert !OpenTox::Authorization.uri_has_policy(@@uri.to_s, @@subjectid)
end
-=end
end
diff --git a/test/toxbank-investigation-xls.rb b/test/toxbank-investigation-xls.rb
index 492d990..9ce8b2a 100644
--- a/test/toxbank-investigation-xls.rb
+++ b/test/toxbank-investigation-xls.rb
@@ -56,6 +56,8 @@ class UploadTest < Test::Unit::TestCase
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 /401/, response
+ response = `curl -I -Lk -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`
assert_match /404/, response
end
generated by cgit v1.2.3 (git 2.25.1) at 2024-04-20 03:58:26 +0000