toxbank-investigation 0.0.1pre-x86-linux

data/test/httpd.rb

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+require 'rubygems'
+require 'fileutils'
+require 'test/unit'
+require 'uri'
+require 'net/http'
+require File.join('~/.toxbank/userpass.rb')
+
+
+class UploadTest < Test::Unit::TestCase
+
+  def setup
+  end
+  
+  def teardown
+  end
+  
+  def test_01_basic_response
+    response = `curl -i --user USER:PASS 'http://4store.in-silico.ch/status/'`.chomp
+    assert_match /401/, response
+    response = `curl -i --user #{USER}:#{PASS} 'http://4store.in-silico.ch/status/'`.chomp
+    assert_match /200/, response
+  end
+  
+  def test_02_add_data
+    # upload invalid data
+    response = `curl -0 -i -u guest:toxbank -T data/invalid/BII-invalid.n3 'http://4store.in-silico.ch/data/BII-I-1.n3'`.chomp
+    assert_match /400/, response
+    # upload valid data
+    response = `curl -0 -i -u #{USER}:#{PASS} -T data/valid/BII-I-1.n3 'http://4store.in-silico.ch/data/BII-I-1.n3'`.chomp
+    assert_match /201/, response
+  end
+  
+  def test_03_query_all
+    response = `curl -i -u #{USER}:#{PASS} 'http://4store.in-silico.ch/sparql/'`.chomp
+    assert_match /500/, response
+    response = `curl -i -u #{USER}:#{PASS} -d "query=SELECT * WHERE {?s ?p ?o} LIMIT 10" 'http://4store.in-silico.ch/sparql/'`.chomp
+    assert_match /200/, response
+  end
+  
+  def test_04_delete_data
+    response = `curl -i -u #{USER}:#{PASS} -X DELETE 'http://4store.in-silico.ch/data/BII-I-1.n3'`.chomp
+    assert_match /200/, response
+  end
+  
+  def test_05_simultaneous_uploads 
+    threads = []
+    5.times do |t|
+      threads << Thread.new(t) do |up|
+        #puts "Start Time >> " << (Time.now).to_s
+        response = `curl -0 -i -u #{USER}:#{PASS} -T data/valid/BII-I-1.n3 'http://4store.in-silico.ch/data/test#{t}.n3'`.chomp
+        assert_match /201/, response
+      end
+    end
+    threads.each {|aThread| aThread.join}
+  end
+  
+  def test_06_delete_simultaneous 
+    threads = []
+    5.times do |t|
+      threads << Thread.new(t) do |up|
+        #puts "Start Time >> " << (Time.now).to_s
+        response = `curl -i -u #{USER}:#{PASS} -X DELETE 'http://4store.in-silico.ch/data/test#{t}.n3'`.chomp
+        assert_match /200/, response
+      end
+    end
+    threads.each {|aThread| aThread.join}
+  end
+
+end

data/test/querytest.rb

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+require 'rubygems'
+require 'fileutils'
+require 'test/unit'
+require 'uri'
+
+#HOST="http://localhost/"
+
+class QueryTest < Test::Unit::TestCase
+
+  def setup
+    info = `4s-size ToxBank`
+    response = `curl -X POST -i -F file="@data/valid/BII-I-1.zip;type=application/zip" -H "subjectid:#{@@subjectid}" #{HOST}`.chomp
+    assert_match /200/, response
+  end
+
+  def teardown
+  end
+  
+
+  def test_01_get_list_of_investigations    
+
+    response = `curl "http://localhost/?subjectid=#{CGI.escape(@@subjectid)}"`.chomp 
+    uri = response.split("\n").last
+    
+    # query for all in all investigations
+    res = `curl -i -H "Accept:application/sparql-results+json" -H "subjectid:#{@@subjectid}" #{HOST}?query_all=`
+    assert_match /200/, res
+    assert_match /head/, res
+    assert_match /results/, res
+    assert_match /bindings/, res
+    
+    # delete Model in 4store
+    del = `4s-delete-model ToxBank #{uri}`  
+    # delete Investigation
+    response = `curl -i -X DELETE -H "subjectid:#{@@subjectid}" #{uri}`
+    puts assert_match /200/, response
+    response = `curl -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`
+    puts assert_match /404/, response
+    
+  end
+  
+end

data/test/upload.rb

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+require 'test/unit'
+require 'bundler'
+Bundler.require
+require 'opentox-client'
+
+#TODO: check 4store emtries/errors
+
+require File.join(ENV["HOME"],".opentox","config","toxbank-investigation","production.rb")
+HOST = "http://localhost:8080"
+class UploadTest < Test::Unit::TestCase
+
+  def setup
+    @tmpdir = File.join(File.dirname(__FILE__),"tmp")
+    @tmpdir = "./tmp"
+    FileUtils.mkdir_p @tmpdir
+    @isatab_files = [
+      "i_Investigation.txt",
+      "s_TB-ACCUTOX-acetaminophen.txt",
+      "a_TB-ACCUTOX-plate1.txt",
+      "a_TB-ACCUTOX-plate2.txt",
+      "a_TB-ACCUTOX-plate3.txt",
+      "acetaminophen-plate1-data.txt",
+      "acetaminophen-plate2-data.txt",
+      "acetaminophen-plate3-data.txt",
+      "ic50.txt",
+    ]
+  resource = RestClient::Resource.new("#{AA}/auth/authenticate")
+  @@subjectid = resource.post(:username=>AA_USER, :password => AA_PASS).sub("token.id=","").sub("\n","")
+  end
+
+  def teardown
+    FileUtils.remove_entry_secure @tmpdir
+  end
+
+  def test_get_all
+    response = `curl -i #{HOST}`
+    assert_match /200/, response
+  end
+
+  def test_get_inexisting
+    response = `curl -H "Accept:text/uri-list" -i -H "subjectid:#{@@subjectid}" #{HOST}/foo`.chomp
+    assert_match /404/, response
+  end
+
+  def test_valid_zip_upload
+
+    # upload
+    ["BII-I-1.zip","isa-tab-renamed.zip"].each do |f|
+      file = File.join File.dirname(__FILE__), "data/valid", f
+      response = `curl -X POST -i -F file="@#{file};type=application/zip" -H "subjectid:#{@@subjectid}" #{HOST}`.chomp
+      assert_match /202/, response
+      uri = response.split("\n")[-1]
+      t = OpenTox::Task.new(uri)
+      assert_match t.hasStatus, "Running"
+      t.wait
+      assert_match t.hasStatus, "Completed"
+      uri = t.resultURI
+      zip = File.join @tmpdir,"tmp.zip"
+      #puts "curl -H 'Accept:application/zip' -H 'subjectid:#{@@subjectid}' #{uri} > #{zip}"
+      `curl -H "Accept:application/zip" -H "subjectid:#{@@subjectid}" #{uri} > #{zip}`
+      `unzip -o #{zip} -d #{@tmpdir}`
+      files = `unzip -l data/valid/#{f}|grep txt|cut -c 31- | sed 's#^.*/##'`.split("\n")
+      files.each{|f| assert_equal true, File.exists?(File.join(File.expand_path(@tmpdir),f)) }
+
+      # get isatab files
+      `curl -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`.split("\n").each do |u|
+        unless u.match(/n3$/)
+          response = `curl -i -H Accept:text/tab-separated-values -H "subjectid:#{@@subjectid}" #{u}`
+          assert_match /HTTP\/1.1 200 OK/, response.to_s.encode!('UTF-8', 'UTF-8', :invalid => :replace) 
+        end
+      end
+
+      # delete
+      response = `curl -i -X DELETE -H "subjectid:#{@@subjectid}" #{uri}`
+      assert_match /200/, response
+      response = `curl -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`
+      assert_match /404/, response
+=begin
+=end
+    end
+  end
+
+  def test_invalid_zip_upload
+    file = File.join File.dirname(__FILE__), "data/invalid/isa_TB_ACCUTOX.zip"
+    response = `curl -X POST -i -F file="@#{file};type=application/zip" -H "subjectid:#{@@subjectid}" #{HOST}`.chomp
+    assert_match /202/, response
+    uri = response.split("\n")[-1]
+    t = OpenTox::Task.new(uri)
+    t.wait
+    assert_match t.hasStatus, "Error"
+  end
+
+=begin
+  def test_rest_client_wrapper
+    ["BII-I-1.zip","isa-tab-renamed.zip"].each do |f|
+      file = File.join File.dirname(__FILE__), "data/valid", f
+      investigation_uri = OpenTox::RestClientWrapper.post HOST, {:file => File.read(file),:name => file}, {:content_type => "application/zip", :subjectid => @@subjectid}
+      puts investigation_uri
+      zip = File.join @tmpdir,"tmp.zip"
+      #puts "curl -H 'Accept:application/zip' -H 'subjectid:#{@@subjectid}' #{uri} > #{zip}"
+      `curl -H "Accept:application/zip" -H "subjectid:#{@@subjectid}" #{uri} > #{zip}`
+      `unzip -o #{zip} -d #{@tmpdir}`
+      files = `unzip -l data/valid/#{f}|grep txt|cut -c 31- | sed 's#^.*/##'`.split("\n")
+      files.each{|f| assert_equal true, File.exists?(File.join(File.expand_path(@tmpdir),f)) }
+
+      # get isatab files
+      `curl -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`.split("\n").each do |u|
+        unless u.match(/n3$/)
+          response = `curl -i -H Accept:text/tab-separated-values -H "subjectid:#{@@subjectid}" #{u}`
+          assert_match /HTTP\/1.1 200 OK/, response.to_s.encode!('UTF-8', 'UTF-8', :invalid => :replace) 
+        end
+      end
+
+      # delete
+      response = `curl -i -X DELETE -H "subjectid:#{@@subjectid}" #{uri}`
+      assert_match /200/, response
+      response = `curl -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`
+      assert_match /404/, response
+    end
+  end
+=end
+
+=begin
+  def test_ruby_api
+    ["BII-I-1.zip","isa-tab-renamed.zip"].each do |f|
+      file = File.join File.dirname(__FILE__), "data/valid", f
+      investigation = OpenTox::Investigation.create HOST, :file => file, :headers => {:content_type => "application/zip", :subjectid => @@subjectid}
+      zip = File.join @tmpdir,"tmp.zip"
+      #puts "curl -H 'Accept:application/zip' -H 'subjectid:#{@@subjectid}' #{uri} > #{zip}"
+      `curl -H "Accept:application/zip" -H "subjectid:#{@@subjectid}" #{uri} > #{zip}`
+      `unzip -o #{zip} -d #{@tmpdir}`
+      files = `unzip -l data/valid/#{f}|grep txt|cut -c 31- | sed 's#^.*/##'`.split("\n")
+      files.each{|f| assert_equal true, File.exists?(File.join(File.expand_path(@tmpdir),f)) }
+
+      # get isatab files
+      `curl -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`.split("\n").each do |u|
+        unless u.match(/n3$/)
+          response = `curl -i -H Accept:text/tab-separated-values -H "subjectid:#{@@subjectid}" #{u}`
+          assert_match /HTTP\/1.1 200 OK/, response.to_s.encode!('UTF-8', 'UTF-8', :invalid => :replace) 
+        end
+      end
+
+      # delete
+      response = `curl -i -X DELETE -H "subjectid:#{@@subjectid}" #{uri}`
+      assert_match /200/, response
+      response = `curl -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`
+      assert_match /404/, response
+    end
+  end
+=end
+
+end

data/test/xls_upload.rb

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+require 'rubygems'
+require 'fileutils'
+require 'test/unit'
+require 'uri'
+
+
+class UploadTest < Test::Unit::TestCase
+
+  def setup
+    @tmpdir = "./tmp"
+    FileUtils.mkdir_p @tmpdir
+    @isatab_files = [
+      "i_Investigation.txt",
+      "s_BII-S-1.txt",
+      "s_BII-S-2.txt",
+      "a_metabolome.txt",
+      "a_microarray.txt",
+      "a_proteome.txt",
+      "a_transcriptome.txt",
+    ]
+    #@test_files = {"data/isa_TB_ACCUTOX.zip" => 400}
+  end
+
+  def teardown
+    FileUtils.remove_entry_secure @tmpdir
+  end
+
+  def test_01_invalid_xls_upload 
+    # upload
+    response = `curl -X POST -i -F file="@data/invalid/isa_TB_ACCUTOX.xls;type=application/vnd.ms-excel" -H "subjectid:#{@@subjectid}" #{HOST}`.chomp
+    assert_match /400/, response
+    uri = response.split("\n").last
+  end
+  
+  def test_02_valid_xls_upload
+    # upload
+    response = `curl -X POST -i -F file="@data/valid/isa_TB_BII.xls;type=application/vnd.ms-excel" -H "subjectid:#{@@subjectid}" #{HOST}`.chomp
+    assert_match /200/, response
+    uri = response.split("\n").last
+    
+    # get zip file
+    `curl -H "Accept:application/zip" -H "subjectid:#{@@subjectid}" #{uri} > #{@tmpdir}/tmp.zip`
+    `unzip -o #{@tmpdir}/tmp.zip -d #{@tmpdir}`
+    @isatab_files.each{|f| assert_equal true, File.exists?(File.join(File.expand_path(@tmpdir),f)) }
+
+    # get isatab files
+    `curl -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`.split("\n").each do |u|
+      puts u
+      response = `curl -i -H Accept:text/tab-separated-values -H "subjectid:#{@@subjectid}" #{u}`
+      assert_match /200/, response
+    end
+
+    # delete
+    response = `curl -i -X DELETE -H "subjectid:#{@@subjectid}" #{uri}`
+    assert_match /200/, response
+    response = `curl -i -H "Accept:text/uri-list" -H "subjectid:#{@@subjectid}" #{uri}`
+    assert_match /404/, response
+  end
+  
+end

data/toxbank-investigation.gemspec

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+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+
+Gem::Specification.new do |s|
+  s.name        = "toxbank-investigation"
+  s.version     = "0.0.1pre"
+  s.authors     = ["Christoph Helma","Denis Gebele","Micha Rautenberg"]
+  s.email       = ["helma@in-silico.ch","gebele@in-silico.ch","rautenenberg@in-silico.ch"]
+  s.homepage    = "http://github.com/ToxBank/toxbank-investigation"
+  s.summary     = %q{Toxbank investigation service}
+  s.description = %q{Toxbank investigation service}
+  s.license     = 'GPL-3'
+  s.platform    = Gem::Platform::CURRENT
+
+  s.rubyforge_project = "toxbank-investigation"
+
+  s.files         = `git ls-files`.split("\n")
+  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+  #s.require_paths = ["lib"]
+  s.required_ruby_version = '>= 1.9.2'
+
+  # specify any dependencies here; for example:
+  s.add_runtime_dependency "opentox-server"
+
+  # external requirements
+  ["git", "zip", "java", "curl", "wget"].each{|r| s.requirements << r}
+  s.post_install_message = "Run toxbank-investigation-install to set up your service"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: toxbank-investigation
+version: !ruby/object:Gem::Version
+  version: 0.0.1pre
+  prerelease: 5
+platform: x86-linux
+authors:
+- Christoph Helma
+- Denis Gebele
+- Micha Rautenberg
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-03-09 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: opentox-server
+  requirement: &78809930 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *78809930
+description: Toxbank investigation service
+email:
+- helma@in-silico.ch
+- gebele@in-silico.ch
+- rautenenberg@in-silico.ch
+executables:
+- toxbank-investigation-install
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- Gemfile.lock
+- LICENSE
+- README
+- Rakefile
+- application.rb
+- bin/toxbank-investigation-install
+- config.ru
+- config/production.rb
+- java/config/isa_configurator/cellcount_flowcytometry.xml
+- java/config/isa_configurator/cellsorting_flowcyt.xml
+- java/config/isa_configurator/clinical_chemistry.xml
+- java/config/isa_configurator/copynumvariation_micro.xml
+- java/config/isa_configurator/dnamethylation_micro.xml
+- java/config/isa_configurator/dnamethylation_seq.xml
+- java/config/isa_configurator/envgen_survey_seq.xml
+- java/config/isa_configurator/genome_seq.xml
+- java/config/isa_configurator/hematology.xml
+- java/config/isa_configurator/heterozygosity_micro.xml
+- java/config/isa_configurator/histology.xml
+- java/config/isa_configurator/histonemodification_seq.xml
+- java/config/isa_configurator/metaboliteprofiling_ms.xml
+- java/config/isa_configurator/metaboliteprofiling_nmr.xml
+- java/config/isa_configurator/metagenome_seq.xml
+- java/config/isa_configurator/nru_assay.xml
+- java/config/isa_configurator/ppi_detection_micro.xml
+- java/config/isa_configurator/protein_dna_binding_ident_micro.xml
+- java/config/isa_configurator/protein_dna_binding_ident_seq.xml
+- java/config/isa_configurator/protein_expression_ge.xml
+- java/config/isa_configurator/protein_expression_micro.xml
+- java/config/isa_configurator/protein_expression_ms.xml
+- java/config/isa_configurator/proteinident_ms.xml
+- java/config/isa_configurator/snpanalysis_micro.xml
+- java/config/isa_configurator/studySample.xml
+- java/config/isa_configurator/tfbsident_micro.xml
+- java/config/isa_configurator/tfbsident_seq.xml
+- java/config/isa_configurator/transcription_micro.xml
+- java/config/isa_configurator/transcription_rtpcr.xml
+- java/config/isa_configurator/transcription_seq.xml
+- test/Rakefile
+- test/all.rb
+- test/authorization.rb
+- test/basic_rest.rb
+- test/data/invalid/BII-invalid.n3
+- test/data/invalid/a_TB-ACCUTOX-plate1.txt
+- test/data/invalid/a_TB-ACCUTOX-plate2.txt
+- test/data/invalid/a_TB-ACCUTOX-plate3.txt
+- test/data/invalid/acetaminophen-plate1-data.txt
+- test/data/invalid/acetaminophen-plate2-data.txt
+- test/data/invalid/acetaminophen-plate3-data.txt
+- test/data/invalid/i_Investigation.txt
+- test/data/invalid/ic50.txt
+- test/data/invalid/isa_TB_ACCUTOX.xls
+- test/data/invalid/isa_TB_ACCUTOX.zip
+- test/data/invalid/s_TB-ACCUTOX-acetaminophen.txt
+- test/data/valid/BII-I-1.n3
+- test/data/valid/BII-I-1.rdf
+- test/data/valid/BII-I-1.zip
+- test/data/valid/isa-tab-renamed.zip
+- test/data/valid/isa_TB_BII.xls
+- test/httpd.rb
+- test/querytest.rb
+- test/upload.rb
+- test/xls_upload.rb
+- toxbank-investigation.gemspec
+homepage: http://github.com/ToxBank/toxbank-investigation
+licenses:
+- GPL-3
+post_install_message: Run toxbank-investigation-install to set up your service
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: 1.9.2
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>'
+    - !ruby/object:Gem::Version
+      version: 1.3.1
+requirements:
+- git
+- zip
+- java
+- curl
+- wget
+rubyforge_project: toxbank-investigation
+rubygems_version: 1.8.11
+signing_key: 
+specification_version: 3
+summary: Toxbank investigation service
+test_files: []