toxbank-investigation 0.0.2pre

data/README

@@ -0,0 +1,34 @@
+toxbank-investigation: Investigation service for ToxBank
+
+Installation:
+
+  Dependencies: ruby 1.9.x, git, zip, java, curl, wget
+
+  gem install toxbank-investigation
+  toxbank-investigation-install # service setup, configuration and webserver start
+
+Development:
+
+  git clone git@github.com:ToxBank/toxbank-investigation.git  
+  cd toxbank-investigation
+  git checkout development
+
+  # edit Gemfile
+  #
+  # uncomment and edit if you want to use github versions of opentox gems
+  # gem 'opentox-server', :git => "git://github.com/opentox/opentox-server", :branch => "development"
+  # gem 'opentox-client', :git => "git://github.com/opentox/opentox-client", :branch => "development"
+  # uncomment and edit if you want to use local installations of opentox gems
+  # gem 'opentox-server', :path => "~/opentox-server"
+  # gem "opentox-client", :path => "~/opentox-client"
+
+  bundle install
+  bin/toxbank-investigation-install
+  # Do you want to start the webserver? (y/n)
+  # Answer "n" 
+  unicorn # starts server in development mode at port 8080
+  # unicorn -h: more options
+
+  see also https://github.com/opentox/opentox-server
+  
+ 

data/Rakefile

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+require "bundler/gem_tasks"
+require 'bundler'
+Bundler.require
+Bundler.setup
+
+require 'rake/testtask'
+Rake::TestTask.new do |t|
+  t.libs << 'test'
+  t.test_files = FileList['test/*.rb'] - FileList["test/setup.rb"]
+  t.verbose = true
+end
+
+desc "Run tests"
+task :default => :test

data/application.rb

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+require "opentox-server"
+require File.join(ENV["HOME"],".opentox","config","toxbank-investigation.rb")
+
+module OpenTox
+  class Application < Service
+
+    helpers do
+
+      def uri
+        params[:id] ? url_for("/#{params[:id]}", :full).sub("http://","https://") : "https://#{request.env['HTTP_HOST']}"
+      end
+
+      def uri_list 
+        params[:id] ? d = "./investigation/#{params[:id]}/*" : d = "./investigation/*"
+        uris = Dir[d].collect{|f|  url_for(f.sub(/\.\/investigation/,''), :full).sub("http://","https://") }
+        uris.collect!{|u| u.sub(/(\/#{params[:id]}\/)/,'\1isatab/')} if params[:id]
+        uris.compact.sort.join("\n") + "\n"
+      end
+
+      def dir
+        File.join File.dirname(File.expand_path __FILE__), "investigation", params[:id].to_s
+      end
+
+      def tmp
+        File.join dir,"tmp"
+      end
+
+      def file
+        File.join dir, params[:filename]
+      end
+
+      def n3
+        "#{params[:id]}.n3"
+      end
+
+      def next_id
+        id = Dir["./investigation/*"].collect{|f| File.basename(f).to_i}.sort.last
+        id ? id + 1 : 0
+      end
+
+      def prepare_upload
+        # remove stale directories from failed tests
+        stale_files = `cd #{File.dirname(__FILE__)}/investigation && git ls-files --others --exclude-standard --directory`.chomp
+        `cd #{File.dirname(__FILE__)}/investigation && rm -rf #{stale_files}` unless stale_files.empty?
+        # lock tmp dir
+        locked_error "Processing investigation #{params[:id]}. Please try again later." if File.exists? tmp
+        bad_request_error "Please submit data as multipart/form-data" unless request.form_data?
+        # move existing ISA-TAB files to tmp
+        FileUtils.mkdir_p tmp
+        FileUtils.cp Dir[File.join(dir,"*.txt")], tmp
+        File.open(File.join(tmp, params[:file][:filename]), "w+"){|f| f.puts params[:file][:tempfile].read}
+      end
+
+      def extract_zip
+        # overwrite existing files with new submission
+        `unzip -o #{File.join(tmp,params[:file][:filename])} -d #{tmp}`
+        Dir["#{tmp}/*"].collect{|d| d if File.directory?(d)}.compact.each  do |d|
+          `mv #{d}/* #{tmp}`
+          `rmdir #{d}`
+        end
+      end
+
+      def extract_xls
+        # use Excelx.new instead of Excel.new if your file is a .xlsx
+        xls = Excel.new(File.join(tmp, params[:file][:filename])) if params[:file][:filename].match(/.xls$/)
+        xls = Excelx.new(File.join(tmp, params[:file][:filename])) if params[:file][:filename].match(/.xlsx$/)
+        xls.sheets.each_with_index do |sh, idx|
+          name = sh.to_s
+          xls.default_sheet = xls.sheets[idx]
+          1.upto(xls.last_row) do |ro|
+            1.upto(xls.last_column) do |co|
+              unless (co == xls.last_column)
+                File.open(File.join(tmp, name + ".txt"), "a+"){|f| f.print "#{xls.cell(ro, co)}\t"}
+              else
+                File.open(File.join(tmp, name + ".txt"), "a+"){|f| f.print "#{xls.cell(ro, co)}\n"}
+              end
+            end
+          end
+        end   
+      rescue
+        bad_request_error "Could not parse spreadsheet #{params[:file][:filename]}"
+      end
+
+      def isa2rdf
+        begin # isa2rdf returns correct exit code
+          `cd #{File.dirname(__FILE__)}/java && java -jar isa2rdf-0.0.1-SNAPSHOT.jar -d #{tmp} -o #{File.join tmp,n3} &> #{File.join tmp,'log'}`
+        rescue
+          log = File.read File.join(tmp,"log")
+          FileUtils.remove_entry dir
+          bad_request_error "ISA-TAB validation failed:\n#{log}", uri
+        end
+        # rewrite default prefix
+        `sed -i 's;http://onto.toxbank.net/isa/tmp/;#{uri}/;' #{File.join tmp,n3}`
+        # add owl:sameAs to identify investigation later
+        investigation_id = `grep ":I[0-9]" #{File.join tmp,n3}|cut -f1 -d ' '`.strip
+        `echo "\n: owl:sameAs #{investigation_id} ." >>  #{File.join tmp,n3}`
+        FileUtils.rm Dir[File.join(tmp,"*.zip")]
+        # if everything is fine move ISA-TAB files back to original dir
+        FileUtils.cp Dir[File.join(tmp,"*")], dir
+        # git commit
+        newfiles = `cd #{File.dirname(__FILE__)}/investigation; git ls-files --others --exclude-standard --directory`
+        `cd #{File.dirname(__FILE__)}/investigation && git add #{newfiles}`
+        ['application/zip', 'application/vnd.ms-excel'].include?(params[:file][:type]) ? action = "created" : action = "modified"
+        `cd #{File.dirname(__FILE__)}/investigation && git commit -am "investigation #{params[:id]} #{action} by #{request.ip}"`
+        # create new zipfile
+        zipfile = File.join dir, "investigation_#{params[:id]}.zip"
+        `zip -j #{zipfile} #{dir}/*.txt`
+        # store RDF
+        length = File.size(File.join dir,n3)
+        file = File.join(dir,n3)
+        `curl -0 -k -u #{$four_store[:user]}:#{$four_store[:password]} -T #{file} -H 'Content_Length => #{length}' '#{$four_store[:uri]}/data/?graph=#{$four_store[:uri]}/data/#{$four_store[:user]}/investigation#{n3}'`
+        FileUtils.remove_entry tmp  # unlocks tmp
+        OpenTox::Authorization.check_policy(uri, @subjectid)
+        uri
+      end
+
+      def query sparql
+        if @accept.match(/turtle/) and sparql.match(/CONSTRUCT/)
+          response['Content-type'] = @accept
+        elsif sparql.match(/CONSTRUCT/)
+          response['Content-type'] = 'application/rdf+xml'
+        else
+          response['Content-type'] = "application/sparql-results+xml"
+        end
+        `curl -H 'Accept:#{@accept}' -k -u #{$four_store[:user]}:#{$four_store[:password]} -d 'query=#{sparql}' '#{$four_store[:uri]}/sparql/'`
+      end
+      
+    end
+
+    before do
+      not_found_error "Directory #{dir} does not exist."  unless File.exist? dir
+      @accept = request.env['HTTP_ACCEPT']
+      response['Content-Type'] = @accept
+      # TODO: A+A
+    end
+
+    # Query all investigations or get a list of all investigations
+    # Requests with a query parameter will perform a SPARQL query on all investigations
+    # @return [application/sparql-results+json] Query result
+    # @return [text/uri-list] List of investigations
+    get '/?' do
+      if params[:query] # pass SPARQL query to 4store
+        query params[:query]
+      else
+        # Requests without a query parameter return a list of all investigations
+        case @accept
+        when 'text/uri-list'
+          uri_list
+        else
+          response['Content-Type'] = 'application/rdf+xml'
+          response['Content-Type'] = @accept if @accept == 'text/turtle'
+          query "
+            PREFIX isa: <http://onto.toxbank.net/isa/>
+            CONSTRUCT { ?s ?p ?o . }
+            WHERE {
+              ?s a isa:Investigation ;
+                ?p ?o .
+              }
+          "
+        end
+      end
+    end
+
+    # Create a new investigation from ISA-TAB files
+    # @param [Header] Content-type: multipart/form-data
+    # @param file Zipped investigation files in ISA-TAB format
+    # @return [text/uri-list] Investigation URI 
+    post '/?' do
+      params[:id] = next_id
+      mime_types = ['application/zip','text/tab-separated-values', "application/vnd.ms-excel"]
+      bad_request_error "No file uploaded." unless params[:file]
+      bad_request_error "Mime type #{params[:file][:type]} not supported. Please submit data as zip archive (application/zip), Excel file (application/vnd.ms-excel) or as tab separated text (text/tab-separated-values)" unless mime_types.include? params[:file][:type]
+      task = OpenTox::Task.create($task[:uri], :description => "#{params[:file][:filename]}: Uploding, validating and converting to RDF") do
+        prepare_upload
+        case params[:file][:type]
+        when "application/vnd.ms-excel"
+          extract_xls
+        when "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
+          extract_xls
+        when 'application/zip'
+          extract_zip
+        #when  'text/tab-separated-values' # do nothing, file is already in tmp
+        end
+        isa2rdf
+      end
+      response['Content-Type'] = 'text/uri-list'
+      halt 202,task.uri+"\n"
+    end
+
+    # Get an investigation representation
+    # @param [Header] Accept: one of text/tab-separated-values, text/uri-list, application/zip, application/sparql-results+json
+    # @return [text/tab-separated-values, text/uri-list, application/zip, application/sparql-results+json] Investigation in the requested format
+    get '/:id' do
+      not_found_error "Investigation #{uri} does not exist."  unless File.exist? dir # not called in before filter???
+      case @accept
+      when "text/tab-separated-values"
+        send_file Dir["./investigation/#{params[:id]}/i_*txt"].first, :type => @accept
+      when "text/uri-list"
+        uri_list
+      when "application/zip"
+        send_file File.join dir, "investigation_#{params[:id]}.zip"
+      when "application/rdf+xml"
+        query "CONSTRUCT { ?s ?p ?o } FROM <#{$four_store[:uri]}/data/#{$four_store[:user]}/investigation#{n3}> WHERE {?s ?p ?o } LIMIT 15000"
+      else
+        #$logger.debug request.to_yaml
+        #bad_request_error "Accept header #{@accept} not supported for #{uri}"
+        $logger.warn "Accept header #{@accept} not supported for #{uri}" # do not halt: strange requests from test, TODO: identify and fix
+      end
+    end
+
+    # Get investigation metadata in RDF
+    get '/:id/metadata' do
+      not_found_error "Investigation #{uri} does not exist."  unless File.exist? dir # not called in before filter???
+      query "
+        PREFIX : <#{uri}/>
+        PREFIX owl: <http://www.w3.org/2002/07/owl#>
+        CONSTRUCT { ?s ?p ?o.  }
+        WHERE {
+          : owl:sameAs ?s .
+          ?s ?p ?o .
+        }
+      "
+    end
+
+    # Get a study, assay, data representation
+    # @param [Header] one of text/tab-separated-values, application/sparql-results+json
+    # @return [text/tab-separated-values, application/sparql-results+json] Study, assay, data representation in ISA-TAB or RDF format
+    get '/:id/isatab/:filename'  do
+      not_found_error "File #{File.join uri,"isatab",params[:filename]} does not exist."  unless File.exist? file
+      # TODO: returns text/plain content type for tab separated files
+      send_file file, :type => File.new(file).mime_type
+    end
+
+    # Get RDF for an investigation resource
+    get '/:id/:resource' do
+      query "
+        PREFIX : <#{uri}/>
+        PREFIX owl: <http://www.w3.org/2002/07/owl#>
+        CONSTRUCT { :#{params[:resource]} ?p ?o.  }
+        WHERE {
+          :#{params[:resource]} ?p ?o .
+        }
+      "
+    end
+
+    # Add studies, assays or data to an investigation
+    # @param [Header] Content-type: multipart/form-data
+    # @param file Study, assay and data file (zip archive of ISA-TAB files or individual ISA-TAB files)
+    post '/:id' do
+      mime_types = ['application/zip','text/tab-separated-values', "application/vnd.ms-excel"]
+      bad_request_error "Mime type #{params[:file][:type]} not supported. Please submit data as zip archive (application/zip), Excel file (application/vnd.ms-excel) or as tab separated text (text/tab-separated-values)" unless mime_types.include? params[:file][:type]
+      task = OpenTox::Task.create($task[:uri], :description => "#{params[:file][:filename]}: Uploding, validationg and converting to RDF") do
+        prepare_upload
+        isa2rdf
+      end
+      response['Content-Type'] = 'text/uri-list'
+      halt 202,task.uri+"\n"
+    end
+
+    # Delete an investigation
+    delete '/:id' do
+      FileUtils.remove_entry dir
+      # git commit
+      `cd #{File.dirname(__FILE__)}/investigation; git commit -am "#{dir} deleted by #{request.ip}"`
+      # updata RDF
+      `curl -i -k -u #{$four_store[:user]}:#{$four_store[:password]} -X DELETE '#{$four_store[:uri]}/data/#{$four_store[:user]}/investigation#{n3}'`
+      response['Content-Type'] = 'text/plain'
+      "Investigation #{params[:id]} deleted"
+    end
+
+    # Delete an individual study, assay or data file
+    delete '/:id/:filename'  do
+      task = OpenTox::Task.create($task[:uri], :description => "Deleting #{params[:file][:filename]} from investigation #{params[:id]}.") do
+        prepare_upload
+        File.delete File.join(tmp,params[:filename])
+        isa2rdf
+        "#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}"
+      end
+      response['Content-Type'] = 'text/uri-list'
+      halt 202,task.uri+"\n"
+    end
+
+  end
+end

data/bin/toxbank-investigation-install

@@ -0,0 +1,76 @@
+#!/bin/sh
+# Main ToxBank-investigation install script
+# Author: Christoph Helma, Andreas Maunz, Denis Gebele.
+
+ISA2RDF=isa2rdf-0.0.1-SNAPSHOT.jar
+
+echo
+echo "This script will setup and configure the toxbank-investigation service."
+echo "You may have to run the script as root if the toxbank-invetigation gem has been installed as root (deprecated)"
+echo
+
+TB_HOME=`dirname $0`/..
+cd $TB_HOME
+TB_HOME=`pwd`
+mkdir -p investigation
+mkdir -p java
+mkdir -p public
+
+
+cd java
+if [ ! -f $ISA2RDF ]
+then
+  echo "Installing isa2rdf"
+  wget -v "https://github.com/downloads/ToxBank/isa2rdf/$ISA2RDF"
+fi
+cd $TB_HOME
+
+cd investigation
+if [ ! -d .git ]
+then
+  echo "Initializing git for investigations"
+  git init
+  echo "*/*.zip" > .gitignore
+  echo "*/tmp" >> .gitignore
+  git add .gitignore
+  git commit -am "Initial commit: .gitignore added"
+fi
+cd $TB_HOME
+
+echo "Installing configuration files"
+
+mkdir -p "$HOME/.opentox/config/toxbank-investigation" 
+mkdir -p "$HOME/.opentox/log" 
+mkdir -p "$HOME/.opentox/tmp" 
+
+config="$HOME/.opentox/config/toxbank-investigation/production.rb" 
+
+if [ -f $config ]
+then
+  echo "Configuration $config exists. Please check if the settings are correct."
+else
+  echo "Creating configuration"
+  echo -n "Please enter your 4store username: "
+  read user
+  echo -n "Please enter your 4store password: "
+  read pass
+
+  sed -e "s/ USER/ '$user'/;s/ PASS/ '$pass'/" config/production.rb > $config
+  echo "Configuration $config created. Please check if the settings are correct."
+fi
+
+echo
+echo "Installation finished and system configured."
+echo "Do you want to start the webserver? (y/n)"
+
+read answer
+if [ $answer = "y" ]
+then
+  last_ip=`ip addr show|grep -w inet|grep -v '127.0'|sed  's/ \+inet //'|cut -d '/' -f1|cut -d '.' -f4`
+  port=8`printf "%03d" $last_ip`
+  echo "Starting unicorn in production mode at port $port"
+  unicorn -p $port -E production -D 
+else
+  echo "Run 'unicorn -E production -D' to start the service. See 'unicorn -h' for more options"
+fi
+echo

data/config.ru

@@ -0,0 +1,6 @@
+require 'bundler'
+Bundler.require
+#Encoding.default_external = Encoding::UTF_8
+#Encoding.default_internal = Encoding::UTF_8
+require './application.rb'
+run OpenTox::Application

data/config/production.rb

@@ -0,0 +1,9 @@
+TASK = "http://webservices.in-silico.ch/task"
+
+FOUR_STORE = "https://4store.in-silico.ch"
+FOUR_STORE_USER = USER
+FOUR_STORE_PASS = PASS
+
+AA = "https://opensso.in-silico.ch"
+AA_USER = "guest"
+AA_PASS = "guest"

data/java/config/isa_configurator/cellcount_flowcytometry.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="cellcount_flowcytometry" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="cell counting" term-accession="1111111" source-abbreviation="OBI"/><technology term-label="flow cytometry" term-accession="2222222" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[the name identifying the sample]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Sample Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[a name identifying the labeled sample.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[a semi-colon separated value of dyes selected from CHEBI]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="40664"/></recommended-ontologies></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[the name identifying the assay]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Parameter Value[flow cytometry instrument]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[instrument]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[optical path]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the optical path]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[detector voltage]" data-type="Integer" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[detector voltage]]></description><default-value><![CDATA[]]></default-value></field><unit-field data-type="Ontology term" is-multiple-value="false" is-required="false"><description>unit"</description><recommended-ontologies><ontology id="1112" abbreviation="UO" name="Units of measurement" version="40305"/></recommended-ontologies></unit-field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[path to image file]]></description><default-value><![CDATA[]]></default-value></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[path to fcs datafile]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="gating"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a data transformation carried out on the raw data files]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[path to gating-ml file]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/cellsorting_flowcyt.xml

@@ -0,0 +1,5 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="cellsorting_flowcyt" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="cell sorting" term-accession="" source-abbreviation=""/><technology term-label="flow cytometry" term-accession="" source-abbreviation=""/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[the name identifying the sample]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]
+            </generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Sample Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[a labeled sample name]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]
+            </generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[a semi-colon separated value of dyes selected from CHEBI]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="40664"/></recommended-ontologies></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[the name identifying the assay]]></description><default-value><![CDATA[]]></default-value><generated-value-template>
+                [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]
+            </generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Parameter Value[flow cytometry instrument]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the name of the flow cytometer used]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[optical path]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the optical path]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[detector voltage]" data-type="Integer" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a voltage value]]></description><default-value><![CDATA[]]></default-value></field><unit-field data-type="Ontology term" is-multiple-value="false" is-required="false"><description>voltage"</description><recommended-ontologies><ontology id="1112" abbreviation="UO" name="Units of measurement" version="40305"/></recommended-ontologies></unit-field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a path to an image file]]></description><default-value><![CDATA[]]></default-value></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[fcs files]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="gating"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[the name identifying the sample]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[a derived data file (e.g gating.ml file)]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/clinical_chemistry.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="clinical_chemistry" isatab-assay-type="generic_assay" isatab-conversion-target="generic"><measurement term-label="clinical chemistry analysis" term-accession="" source-abbreviation="OBI"/><technology term-label="" term-accession="" source-abbreviation=""/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="clinical chemistry"/><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]</generated-value-template></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied.]]></description><default-value><![CDATA[]]></default-value></field><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>

data/java/config/isa_configurator/copynumvariation_micro.xml

@@ -0,0 +1 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="copynumvariation_micro" isatab-assay-type="transcriptomics_assay" isatab-conversion-target="magetab"><measurement term-label="copy number variation profiling" term-accession="" source-abbreviation="OBI"/><technology term-label="DNA microarray" term-accession="0400148" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]</generated-value-template></field><protocol-field protocol-type ="DNA extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]</generated-value-template></field><protocol-field protocol-type ="labeling"/><field header="Labeled Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Identifier for the labeled extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT]</generated-value-template></field><field header="Label" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Indicates a chemical or biological marker, such as a radioactive isotope or a fluorescent dye which is bound to a material in order to make it detectable by some assay technology (e.g. P33, biotin, GFP).]]></description><default-value><![CDATA[]]></default-value><recommended-ontologies><ontology id="1007" abbreviation="CHEBI" name="Chemical entities of biological interest" version="40664"/></recommended-ontologies></field><protocol-field protocol-type ="nucleic acid hybridization"/><field header="Hybridization Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].HYB-[HYB_COUNT]</generated-value-template></field><field header="Array Design REF" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Reference to the identifier (or accession number) of an existing array design]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[ARRAY_DESIGN]</generated-value-template></field><protocol-field protocol-type ="data collection"/><field header="Scan Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each scan event.]]></description><default-value><![CDATA[]]></default-value></field><field header="Image File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the image files generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><field header="Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the raw array data matrix file.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="normalization data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="data transformation"/><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Array Data Matrix File" data-type="String" is-file-field="true" is-multiple-value="true" is-required="false" is-hidden="false"><description><![CDATA[Name (or URI) of the processed data matrix file resulting from data transformation or processing.]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="Factors"/></isatab-configuration></isatab-config-file>