toxbank-investigation 0.0.2pre → 1.0.0pre1

data/.gitignore

@@ -1,3 +1,4 @@
+Gemfile.lock
 *.gem
 .bundle
 pkg/*

data/ChangeLog

@@ -0,0 +1,26 @@
+v0.0.4 2012-07-
+- Address and IDs changed
+  - Service URI https://INVESTIGATIONSERVICE is now https://INVESTIGATIONSERVICE/investigation
+  - IDs changed to UUIDs e.G.: https://INVESTIGATIONSERVICE/123 changed to https://INVESTIGATIONSERVICE/investigation/1f6d584a-53aa-4c59-bae3-8c7ac9cb82ff
+    UUID is a v4 random UUID (Universally Unique IDentifier).
+- Policy/Access management
+  - allowReadByUser and allowReadByGroup parameters added to POST and PUT request (POST to service and PUT to a specific investigation).
+    both values are optional and can be empty or contain single or comma separated URIs of an existing ToxBank user or group (e.G.: allowReadByUser=http://USERSERVICE/toxbank/user/U2,http://USERSERVICE/toxbank/user/U124 )
+    as described here: http://api.toxbank.net/index.php/Protocol#Security.
+    Every user or group get read access to the specific investigation.
+  - The creator of a new investigation gets full REST access (GET/POST/PUT/DELETE). Creator is identified by its subjectid from login and should be member of the LDAP Public Investigator group (cn=PI_GROUP,ou=groups,dc=DOMAIN,dc=TLD).
+- isPublished flag
+  - New investigations get http://onto.toxbank.net/api/isPublished = false to its metadata RDF representation:
+    e.G.:
+      <rdf:Description rdf:about="https://INVESTIGATIONSERVICE/investigation/f0154c33-e27a-4683-b9cd-94473beccae3/">
+        <ns0:isPublished xmlns:ns0="http://onto.toxbank.net/api/" rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</ns0:isPublished>
+      </rdf:Description>
+  - published parameter added to PUT request to set isPublished in metadata to true:
+    curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://INVESTIGATIONSERVICE/investigation/UUID
+- isSummarySearchable flag
+  summarySearchable parameter added to POST and PUT request to set isSummarySearchable flag in metadata.
+- Add studies, assays or data to an investigation / Updating an investigation
+  - additions to or updating an investigation will be handled via PUT request
+
+v0.0.3 2012-05-07
+* switch from v0.0.2pre to v0.0.3

data/Gemfile

@@ -7,6 +7,6 @@ gemspec
 #gem 'rake', '~> 0.9.3.beta.1'
 gem 'opentox-server', :path => "~/opentox-server"
 gem "opentox-client", :path => "~/opentox-client"
-group :test do
-  gem "rack-test", :require => "rack/test"
-end
+#group :test do
+  #gem "rack-test", :require => "rack/test"
+#end

data/Rakefile

@@ -1,14 +1 @@
 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/VERSION

@@ -0,0 +1 @@
+1.0.0pre1

data/application.rb

@@ -1,19 +1,21 @@
-require "opentox-server"
-require File.join(ENV["HOME"],".opentox","config","toxbank-investigation.rb")
+require 'opentox-server'
+require "#{File.dirname(__FILE__)}/tbaccount.rb"
+require "#{File.dirname(__FILE__)}/pirewriter.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']}"
+      def investigation_uri
+        to("/investigation/#{params[:id]}") # new in Sinatra, replaces url_for
       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 = Dir[d].collect{|f| to(f.sub(/\.\//,'')) }
         uris.collect!{|u| u.sub(/(\/#{params[:id]}\/)/,'\1isatab/')} if params[:id]
+        uris.delete_if{|u| u.match(/_policies$/)}
         uris.compact.sort.join("\n") + "\n"
       end
 
@@ -33,22 +35,17 @@ module OpenTox
         "#{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?
+        #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}
+        FileUtils.cp params[:file][:tempfile], File.join(tmp, params[:file][:filename])
       end
 
       def extract_zip
@@ -58,6 +55,7 @@ module OpenTox
           `mv #{d}/* #{tmp}`
           `rmdir #{d}`
         end
+        replace_pi @subjectid
       end
 
       def extract_xls
@@ -83,95 +81,135 @@ module OpenTox
 
       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'}`
+          `cd #{File.dirname(__FILE__)}/java && java -jar isa2rdf-0.0.3-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
+          bad_request_error "ISA-TAB validation failed:\n#{log}", investigation_uri
         end
         # rewrite default prefix
-        `sed -i 's;http://onto.toxbank.net/isa/tmp/;#{uri}/;' #{File.join tmp,n3}`
+        `sed -i 's;http://onto.toxbank.net/isa/tmp/;#{investigation_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}`
+        `sed -i 's;#{investigation_id};:;' #{File.join tmp,n3}`
+        `echo "\n: a <#{RDF::OT.Investigation}> ." >>  #{File.join tmp,n3}`
+        #`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}'`
+        c_length = File.size(File.join dir,n3)
+        RestClient.put File.join(FourStore.four_store_uri,"data",investigation_uri), File.read(File.join(dir,n3)), {:content_type => "application/x-turtle", :content_length => c_length} # content-type not very consistent in 4store
         FileUtils.remove_entry tmp  # unlocks tmp
-        OpenTox::Authorization.check_policy(uri, @subjectid)
-        uri
+        # git commit
+        newfiles = `cd #{File.dirname(__FILE__)}/investigation; git ls-files --others --exclude-standard --directory #{params[:id]}`
+        `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}"`
+        investigation_uri
+      end
+
+      def create_policy ldaptype, uristring
+        begin
+          filename = File.join(dir, "#{ldaptype}_policies")
+          policyfile = File.open(filename,"w")
+          uriarray = uristring.split(",")
+          uriarray.each do |u|
+            tbaccount = OpenTox::TBAccount.new(u, @subjectid)
+            policyfile.puts tbaccount.get_policy(investigation_uri)
+          end
+          policyfile.close
+          policytext = File.read filename
+          replace = policytext.gsub!("</Policies>\n<!DOCTYPE Policies PUBLIC \"-//Sun Java System Access Manager7.1 2006Q3 Admin CLI DTD//EN\" \"jar://com/sun/identity/policy/policyAdmin.dtd\">\n<Policies>\n", "")
+          File.open(filename, "w") { |file| file.puts replace } if replace
+          Authorization.reset_policies investigation_uri, ldaptype, @subjectid
+          ret = Authorization.create_policy(File.read(policyfile), @subjectid)
+          File.delete policyfile if ret
+        rescue
+          $logger.warn "create policies error for Investigation URI: #{investigation_uri} for user/group uris: #{uristring}"
+        end
+      end
+
+      def set_flag flag, value, type = ""
+        flagtype = type == "boolean" ? "^^<#{RDF::XSD.boolean}>" : ""
+        FourStore.update "DELETE DATA { GRAPH <#{investigation_uri}> {<#{investigation_uri}/> <#{flag}> \"#{!value}\"#{flagtype}}}"
+        FourStore.update "INSERT DATA { GRAPH <#{investigation_uri}> {<#{investigation_uri}/> <#{flag}> \"#{value}\"#{flagtype}}}"
       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'
+      def qfilter(flag, uri)
+        qfilter = FourStore.query "SELECT ?s FROM <#{uri}> WHERE {?s <#{RDF::TB}#{flag}> ?o FILTER regex(?o, 'true', 'i')}", "application/sparql-results+xml"
+        qfilter.split("\n")[7].gsub(/<binding name="s"><uri>|\/<\/uri><\/binding>/, '').strip
+      end
+
+      def protected!(subjectid)
+        if !env["session"] && subjectid
+          unless authorized?(subjectid) || get_permission
+            $logger.debug ">-get_permission failed"
+            $logger.debug "URI not authorized: clean: " + clean_uri("#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}").sub("http://","https://").to_s + " full: #{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']} with request: #{request.env['REQUEST_METHOD']}"
+            unauthorized_error "Not authorized: #{request.env['REQUEST_URI']}"
+          end
         else
-          response['Content-type'] = "application/sparql-results+xml"
+          unauthorized_error "Not authorized: #{request.env['REQUEST_URI']}"
         end
-        `curl -H 'Accept:#{@accept}' -k -u #{$four_store[:user]}:#{$four_store[:password]} -d 'query=#{sparql}' '#{$four_store[:uri]}/sparql/'`
       end
       
+      def get_permission
+        # only for GET
+        return false if request.env['REQUEST_METHOD'] != "GET"
+        if request.env['REQUEST_URI'] =~ /metadata/
+          ruri = request.env['REQUEST_URI'].chomp("/metadata")
+          return true if qfilter("isSummarySearchable", to(ruri)) =~ /#{to(ruri)}/
+          return false
+        else
+          ruri = request.env['REQUEST_URI'].gsub(/\/isatab\/.*/,'')
+          return true if qfilter("isPublished", to(ruri)) =~ /#{to(ruri)}/
+          return false
+        end
+      end
+
+      def qlist
+        list = FourStore.list(to("/investigation"), "text/uri-list")
+        list.split.keep_if{|v| v =~ /#{$investigation[:uri]}/ || qfilter("isSummarySearchable", v)}.join("\n")
+      end
+
     end
 
     before do
-      not_found_error "Directory #{dir} does not exist."  unless File.exist? dir
+      resource_not_found_error "Directory #{dir} does not exist."  unless File.exist? dir
+      parse_input if request.request_method =~ /POST|PUT/
       @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
+    # uri-list of all investigations
     # @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
+    # include own and searchable
+    # TODO handle published for uri-list
+    get '/investigation/?' do
+      bad_request_error "Mime type #{@accept} not supported here. Please expect data as text/uri-list." unless @accept.to_s == "text/uri-list"
+      qlist
     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"]
+    # @return [text/uri-list] Task URI
+    post '/investigation/?' do
+      params[:id] = SecureRandom.uuid
+      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($task[:uri], :description => "#{params[:file][:filename]}: Uploding, validating and converting to RDF") do
+      if params[:file]
+        if params[:file][:type] == "application/zip"
+          bad_request_error "The zip #{params[:file][:filename]} contains no investigation file.", investigation_uri unless `unzip -Z -1 #{File.join(params[:file][:tempfile])}`.match('.txt')
+        end
+      end
+      task = OpenTox::Task.create($task[:uri], @subjectid, RDF::DC.description => "#{params[:file][:filename]}: Uploading, validating and converting to RDF") do
         prepare_upload
+        OpenTox::Authorization.create_pi_policy(investigation_uri, @subjectid)
         case params[:file][:type]
         when "application/vnd.ms-excel"
           extract_xls
@@ -182,6 +220,14 @@ module OpenTox
         #when  'text/tab-separated-values' # do nothing, file is already in tmp
         end
         isa2rdf
+        set_flag(RDF::TB.isPublished, false, "boolean")
+        set_flag(RDF::TB.isSummarySearchable, (params[:summarySearchable].to_s == "true" ? true : false), "boolean")
+        #set_flag(RDF.Type, RDF::OT.Investigation)
+        create_policy "user", params[:allowReadByUser] if params[:allowReadByUser]
+        create_policy "group", params[:allowReadByGroup] if params[:allowReadByGroup]
+        # TODO send notification to UI
+        # OpenTox::RestClientWrapper.put "https://www.leadscope.com/dev-toxbank-search/search/index/investigation?resourceUri=#{CGI.escape(investigation_uri)}",{},{:subjectid => @subjectid}
+        investigation_uri
       end
       response['Content-Type'] = 'text/uri-list'
       halt 202,task.uri+"\n"
@@ -190,8 +236,9 @@ module OpenTox
     # 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???
+    # include own and published
+    get '/investigation/:id' do
+      resource_not_found_error "Investigation #{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
@@ -199,82 +246,96 @@ module OpenTox
         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
+        FourStore.query "CONSTRUCT { ?s ?p ?o } FROM <#{investigation_uri}> WHERE {?s ?p ?o}", @accept
       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 .
-        }
-      "
+    # include own, pulished and searchable
+    get '/investigation/:id/metadata' do
+      resource_not_found_error "Investigation #{investigation_uri} does not exist."  unless File.exist? dir # not called in before filter???
+      FourStore.query "CONSTRUCT { ?s ?p ?o.  } FROM <#{investigation_uri}> WHERE { ?s <#{RDF.type}> <http://onto.toxbank.net/isa/Investigation>. ?s ?p ?o .  } ", @accept
     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
+    # include own and published
+    get '/investigation/:id/isatab/:filename'  do
+      resource_not_found_error "File #{File.join investigation_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 .
-        }
-      "
+    # include own and published
+    get '/investigation/:id/:resource' do
+      FourStore.query " CONSTRUCT {  <#{File.join(investigation_uri,params[:resource])}> ?p ?o.  } FROM <#{investigation_uri}> WHERE { <#{File.join(investigation_uri,params[:resource])}> ?p ?o .  } ", @accept
     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($task[:uri], :description => "#{params[:file][:filename]}: Uploding, validationg and converting to RDF") do
-        prepare_upload
-        isa2rdf
+    # @return [text/uri-list] Task URI
+    put '/investigation/:id' do
+      mime_types = ['application/zip','text/tab-separated-values', 'application/vnd.ms-excel']
+      bad_request_error "Mime type #{params[:file][:type]} not supported. Please submit data as zip archive (application/zip), Excel file (application/vnd.ms-excel) or as tab separated text (text/tab-separated-values)" unless mime_types.include?(params[:file][:type]) if params[:file] 
+      task = OpenTox::Task.create($task[:uri], @subjectid, RDF::DC.description => "#{investigation_uri}: Add studies, assays or data.") do
+        if params[:file]
+          prepare_upload
+          case params[:file][:type]
+          when 'application/zip'
+            extract_zip
+          end
+          isa2rdf
+        end
+        set_flag(RDF::TB.isPublished, (params[:published].to_s == "true" ? true : false), "boolean") if params[:file] || (!params[:file] && params[:published])
+        set_flag(RDF::TB.isSummarySearchable, (params[:summarySearchable].to_s == "true" ? true : false), "boolean") if params[:file] || (!params[:file] && params[:summarySearchable])
+        create_policy "user", params[:allowReadByUser] if params[:allowReadByUser]
+        create_policy "group", params[:allowReadByGroup] if params[:allowReadByGroup]
+        # TODO send notification to UI
+        # OpenTox::RestClientWrapper.put "https://www.leadscope.com/dev-toxbank-search/search/index/investigation?resourceUri=#{CGI.escape(investigation_uri)}",{},{:subjectid => @subjectid}
+        investigation_uri
       end
       response['Content-Type'] = 'text/uri-list'
       halt 202,task.uri+"\n"
     end
 
     # Delete an investigation
-    delete '/:id' do
+    delete '/investigation/: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}'`
+      FourStore.delete investigation_uri
+      if @subjectid and !File.exists?(dir) and investigation_uri
+        begin
+          res = OpenTox::Authorization.delete_policies_from_uri(investigation_uri, @subjectid)
+          $logger.debug "Policy deleted for Investigation URI: #{investigation_uri} with result: #{res}"
+        rescue
+          $logger.warn "Policy delete error for Investigation URI: #{investigation_uri}"
+        end
+      end
+      # TODO send notification to UI
+      # OpenTox::RestClientWrapper.delete "https://www.leadscope.com/dev-toxbank-search/search/index/investigation?resourceUri=#{CGI.escape(investigation_uri)}",{},{:subjectid => @subjectid}
       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($task[:uri], :description => "Deleting #{params[:file][:filename]} from investigation #{params[:id]}.") do
-        prepare_upload
-        File.delete File.join(tmp,params[:filename])
-        isa2rdf
-        "#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}"
+    delete '/investigation/:id/:filename'  do
+      if is_pi?(@subjectid)
+        task = OpenTox::Task.create($task[:uri], @subjectid, RDF::DC.description => "Deleting #{params[:file][:filename]} from investigation #{params[:id]}.") do
+          prepare_upload
+          File.delete File.join(tmp,params[:filename])
+          isa2rdf
+          # TODO send notification to UI (TO CHECK: if files will be indexed?)
+          # OpenTox::RestClientWrapper.put "https://www.leadscope.com/dev-toxbank-search/search/index/investigation?resourceUri=#{CGI.escape(investigation_uri)}",{},{:subjectid => @subjectid}
+          "#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}"
+        end
+      else
+        unauthorized_error "not authorized: #{investigation_uri}"
       end
       response['Content-Type'] = 'text/uri-list'
       halt 202,task.uri+"\n"

data/bin/toxbank-investigation-install

@@ -2,7 +2,7 @@
 # Main ToxBank-investigation install script
 # Author: Christoph Helma, Andreas Maunz, Denis Gebele.
 
-ISA2RDF=isa2rdf-0.0.1-SNAPSHOT.jar
+ISA2RDF=isa2rdf-0.0.3-SNAPSHOT.jar
 
 echo
 echo "This script will setup and configure the toxbank-investigation service."
@@ -32,6 +32,8 @@ then
   git init
   echo "*/*.zip" > .gitignore
   echo "*/tmp" >> .gitignore
+  echo "user_policies" >> .gitignore
+  echo "group_policies" >> .gitignore
   git add .gitignore
   git commit -am "Initial commit: .gitignore added"
 fi
@@ -39,11 +41,11 @@ cd $TB_HOME
 
 echo "Installing configuration files"
 
-mkdir -p "$HOME/.opentox/config/toxbank-investigation" 
+mkdir -p "$HOME/.opentox/config" 
 mkdir -p "$HOME/.opentox/log" 
 mkdir -p "$HOME/.opentox/tmp" 
 
-config="$HOME/.opentox/config/toxbank-investigation/production.rb" 
+config="$HOME/.opentox/config/investigation.rb" 
 
 if [ -f $config ]
 then

data/config.ru

@@ -1,3 +1,4 @@
+SERVICE = "investigation"
 require 'bundler'
 Bundler.require
 #Encoding.default_external = Encoding::UTF_8

data/java/config/isa_configurator/investigation.xml

@@ -0,0 +1,277 @@
+<?xml version="1.0" encoding="utf-8"?>
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#">
+  <isatab-configuration table-name="investigation" isatab-assay-type="generic_assay" isatab-conversion-target="generic">
+    <measurement term-label="[investigation]" term-accession="" source-abbreviation="" />
+    <technology term-label="" term-accession="" source-abbreviation="" />
+    <field header="Investigation Identifier" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION">
+      <description><![CDATA[A user defined identifier for the investigation.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Title" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION">
+      <description><![CDATA[A title for the Investigation.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Description" data-type="Long String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION">
+      <description><![CDATA[A brief description of the investigation aims.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Submission Date" data-type="Date" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION">
+      <description><![CDATA[The date the investigation was submitted.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Public Release Date" data-type="Date" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION">
+      <description><![CDATA[The date the investigation was release publicly.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Comment [Created with configuration]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="true" is-forced-ontology="false" section="INVESTIGATION">
+      <description><![CDATA[A field indicating which ISA configuration was used to create the ISAtab file.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Comment [Last Opened With Configuration]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="true" is-forced-ontology="false" section="INVESTIGATION">
+      <description><![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Comment [Owning Organisation URI]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION">
+      <description><![CDATA[Owning Organisation URI]]></description>
+      <default-value><![CDATA[]]></default-value>
+      <recommended-ontologies>
+        <ontology id="TBO" abbreviation="TBO" name="ToxBank organisation" version="0.1" />
+      </recommended-ontologies>
+    </field>
+    <field header="Comment [Consortium URI]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION">
+      <description><![CDATA[Consortium URI]]></description>
+      <default-value><![CDATA[]]></default-value>
+      <recommended-ontologies>
+        <ontology id="TBC" abbreviation="TBC" name="ToxBank consortium" version="0.1" />
+      </recommended-ontologies>
+    </field>
+    <field header="Comment [Principal Investigator URI]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION">
+      <description><![CDATA[Toxbank user URI]]></description>
+      <default-value><![CDATA[]]></default-value>
+      <recommended-ontologies>
+        <ontology id="TBU" abbreviation="TBU" name="ToxBank users" version="0.1" />
+      </recommended-ontologies>
+    </field>
+    <field header="Comment [Investigation keywords]" data-type="Ontology term" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false" is-forced-ontology="true" section="INVESTIGATION">
+      <description><![CDATA[Investigation keywords.]]></description>
+      <default-value><![CDATA[]]></default-value>
+      <recommended-ontologies>
+        <ontology id="TBK" abbreviation="TBK" name="ToxBank keywords" version="0.1" />
+      </recommended-ontologies>
+    </field>
+    <field header="Investigation PubMed ID" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION PUBLICATIONS">
+      <description><![CDATA[The PubMed ID related to this publication (if available).]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Publication DOI" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION PUBLICATIONS">
+      <description><![CDATA[The DOI related to this publication (if available).]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Publication Author List" data-type="Long String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION PUBLICATIONS">
+      <description><![CDATA[The authors who contributed to this publication.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Publication Title" data-type="Long String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION PUBLICATIONS">
+      <description><![CDATA[The title of the publication.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Publication Status" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION PUBLICATIONS">
+      <description><![CDATA[The status of this publication, e.g. Published, Submitted, etc.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Person Last Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION CONTACTS">
+      <description><![CDATA[The last name/surname of the contact.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Person First Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION CONTACTS">
+      <description><![CDATA[The first name/forename of the contact.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Person Mid Initials" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION CONTACTS">
+      <description><![CDATA[The mid initial of the contact.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Person Email" data-type="Long String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION CONTACTS">
+      <description><![CDATA[The email corresponding to this contact.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Person Phone" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION CONTACTS">
+      <description><![CDATA[A phone number for this contact, if available.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Person Fax" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION CONTACTS">
+      <description><![CDATA[A fax number for this contact, if available.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Person Address" data-type="Long String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION CONTACTS">
+      <description><![CDATA[The address for this contact, preferably, their institution.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Person Affiliation" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION CONTACTS">
+      <description><![CDATA[The affiliation for this contact.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Investigation Person Roles" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="INVESTIGATION CONTACTS">
+      <description><![CDATA[The role of the person in this investigation.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Comment [Investigation Person URI]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="true" section="INVESTIGATION CONTACTS">
+      <description><![CDATA[Toxbank User URI]]></description>
+      <default-value><![CDATA[]]></default-value>
+      <recommended-ontologies>
+        <ontology id="TBU" abbreviation="TBU" name="ToxBank users" version="0.1" />
+      </recommended-ontologies>
+    </field>
+    <field header="Study Identifier" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="STUDY">
+      <description><![CDATA[A user defined identifier for the study.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Title" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="STUDY">
+      <description><![CDATA[A title for the Study.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Description" data-type="Long String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="STUDY">
+      <description><![CDATA[A brief description of the study aims.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Submission Date" data-type="Date" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY">
+      <description><![CDATA[The date the study was submitted.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Public Release Date" data-type="Date" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY">
+      <description><![CDATA[The date the study was released publicly.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study File Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="true" is-forced-ontology="false" section="STUDY">
+      <description><![CDATA[The name of the study sample file linked to this Study]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study PubMed ID" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="STUDY PUBLICATIONS">
+      <description><![CDATA[The PubMed ID related to this publication (if available).]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Publication DOI" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="STUDY PUBLICATIONS">
+      <description><![CDATA[The DOI related to this publication (if available).]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Publication Author List" data-type="Long String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="STUDY PUBLICATIONS">
+      <description><![CDATA[The authors who contributed to this publication.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Publication Title" data-type="Long String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="STUDY PUBLICATIONS">
+      <description><![CDATA[The title of the publication.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Publication Status" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="STUDY PUBLICATIONS">
+      <description><![CDATA[The status of this publication, e.g. Published, Submitted, etc.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Person Last Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="STUDY CONTACTS">
+      <description><![CDATA[The last name/surname of the contact.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Person First Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="STUDY CONTACTS">
+      <description><![CDATA[The first name/forename of the contact.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Person Mid Initials" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="STUDY CONTACTS">
+      <description><![CDATA[The mid initial of the contact.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Person Email" data-type="Long String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY CONTACTS">
+      <description><![CDATA[The email corresponding to this contact.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Person Phone" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY CONTACTS">
+      <description><![CDATA[A phone number for this contact, if available.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Person Fax" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY CONTACTS">
+      <description><![CDATA[A fax number for this contact, if available.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Person Address" data-type="Long String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY CONTACTS">
+      <description><![CDATA[The address for this contact, preferably, their institution.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Person Affiliation" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY CONTACTS">
+      <description><![CDATA[The affiliation for this contact.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Person Roles" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY CONTACTS">
+      <description><![CDATA[The role of the person in this Study.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Factor Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY FACTORS">
+      <description><![CDATA[The name of the Factor driving this study, e.g. Dose, Collection Time Point, Compound, and so forth]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Factor Type" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY FACTORS">
+      <description><![CDATA[The type of the Factor driving this study, e.g. EFO:Dose (from Ontology), or Dose if the Factor name is something related to Dose as well, etc.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Design Type" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY DESIGN DESCRIPTORS">
+      <description><![CDATA[The type of study design being employed, e.g. Observation, Intervention, Cross-Over, etc.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Assay Measurement Type" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY ASSAYS">
+      <description><![CDATA[The measurement being observed in this assay, e.g. Transcription Profiling, Metabolite Profiling]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Assay Technology Type" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY ASSAYS">
+      <description><![CDATA[The technology being employed to observe this measurement, e.g. DNA microarray, NMR, Mass Spectrometry and so forth]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Assay Technology Platform" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY ASSAYS">
+      <description><![CDATA[The technology platform used, e.g. Affymetrix, Illumina, Solexa, SOLiD, Bruker, etc.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Assay File Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY ASSAYS">
+      <description><![CDATA[The name of the file which contains the information about this assay, the samples and pipeline used.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Protocol Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY PROTOCOLS">
+      <description><![CDATA[The name of the protocol, e.g. RNA Extraction Protocol]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Protocol Type" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="true" section="STUDY PROTOCOLS">
+      <description><![CDATA[The type of the protocol, preferably coming from an Ontology, e.g. Extraction Protocol]]></description>
+      <default-value><![CDATA[]]></default-value>
+      <recommended-ontologies>
+        <ontology id="TBP" abbreviation="TBP" name="ToxBank protocols" version="0.1" />
+      </recommended-ontologies>
+    </field>
+    <field header="Study Protocol Description" data-type="Long String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY PROTOCOLS">
+      <description><![CDATA[A description of the Protocol.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Protocol URI" data-type="Long String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false" section="STUDY PROTOCOLS">
+      <description><![CDATA[A URI to link out to a publication, web page, etc. describing the protocol.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Protocol Version" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY PROTOCOLS">
+      <description><![CDATA[The version of the protocol used, where applicable.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Protocol Parameters Name" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY PROTOCOLS">
+      <description><![CDATA[The parameters used when executing this protocol.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Protocol Components Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY PROTOCOLS">
+      <description><![CDATA[The components used when carrying out this protocol.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Study Protocol Components Type" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false" section="STUDY PROTOCOLS">
+      <description><![CDATA[The type of Components used in this Protocol.]]></description>
+      <default-value><![CDATA[]]></default-value>
+    </field>
+    <field header="Comment [Protocol URI]" data-type="Ontology term" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="true" section="STUDY PROTOCOLS">
+      <description><![CDATA[Toxbank Protocol URI]]></description>
+      <default-value><![CDATA[]]></default-value>
+      <recommended-ontologies>
+        <ontology id="TBP" abbreviation="TBP" name="ToxBank protocols" version="0.1" />
+      </recommended-ontologies>
+    </field>
+    <structured-field name="factors" />
+  </isatab-configuration>
+</isatab-config-file>

data/pirewriter.rb

@@ -0,0 +1,15 @@
+def replace_pi subjectid
+  begin
+    user = OpenTox::Authorization.get_user(subjectid)
+    accounturi = OpenTox::RestClientWrapper.get("http://toxbanktest1.opentox.org:8080/toxbank/user?username=#{user}", nil, {:Accept => "text/uri-list", :subjectid => subjectid}).sub("\n","")
+    account = OpenTox::TBAccount.new(accounturi, subjectid)
+    investigation_file = Dir["#{tmp}/i_*vestigation.txt"]
+    investigation_file.each do |inv_file|
+      text = File.read(inv_file, :encoding => "BINARY")
+      replace = text.gsub!(/TBU:U\d+/, account.ns_uri)
+      File.open(inv_file, "wb") { |file| file.puts replace } if replace
+    end
+  rescue
+    $logger.error "can not replace Principal Investigator to user: #{user} with subjectid: #{subjectid}"
+  end
+end

data/tbaccount.rb

@@ -0,0 +1,153 @@
+module OpenTox
+
+  # define RDF vocabularies
+  RDF::TB   = RDF::Vocabulary.new "http://onto.toxbank.net/api/"
+  RDF::TBU  = RDF::Vocabulary.new "http://toxbanktest1.opentox.org:8080/toxbank/user/"
+  RDF::TBO  = RDF::Vocabulary.new "http://toxbanktest1.opentox.org:8080/toxbank/organisation/"
+  RDF::TBPT = RDF::Vocabulary.new "http://toxbanktest1.opentox.org:8080/toxbank/project/"
+
+  CLASSES << "TBAccount"
+
+=begin
+  # TODO: this should not be necessary, class in initialized below
+  # add new OpenTox class
+  c = Class.new do
+    include OpenTox
+    #extend OpenTox::ClassMethods
+  end
+  OpenTox.const_set "TBAccount",c
+=end
+
+  # Get rdf representation for a user, organisation or project from the ToxBank service 
+  # @see http://api.toxbank.net/index.php/User ToxBank API User
+  # @see http://api.toxbank.net/index.php/Organisation ToxBank API Organisation
+  # @see http://api.toxbank.net/index.php/Project ToxBank API Project
+  # @see http://api.toxbank.net/index.php/Protocol#Security ToxBank API Security
+  # @example TBAccount
+  #   require "opentox-server"
+  #   User1 = OpenTox::TBAccount.new("http://uri_to_toxbankservice/toxbank/user/U123", subjectid)
+  #   puts User1.ldap_dn #=> "uid=username,ou=people,dc=opentox,dc=org"
+  #   User1.send_policy("http://uri_toprotect/bla/foo") #=> creates new read policy for http://uri_toprotect/bla/foo
+  class TBAccount
+    include OpenTox
+
+    # Get hasAccount value of a user,organisation or project from ToxBank service
+    # @return [String] username
+    def account
+      @account ||= get_account
+    end
+
+    # Generates LDAP Distinguished Name (DN)
+    # @return [String] LDAP Distinguished Name (DN)
+    def ldap_dn
+      @uri.match(RDF::TBU.to_s) ? "uid=#{self.account},ou=people,dc=opentox,dc=org" : "cn=#{self.account},ou=groups,dc=opentox,dc=org"
+    end
+
+    # Get LDAP type - returns 'LDAPUsers' if the TBAccount.uri is a user URI   
+    # @return [String] 'LDAPUsers' or 'LDAPGroups'
+    def ldap_type
+      @uri.match(RDF::TBU.to_s) ? "LDAPUsers" : "LDAPGroups"
+    end
+
+    # GET policy XML 
+    # @param [String,String] URI,Type URI to protect, Access-rights < "all", "readwrite", "read" (default) >
+    # @return [String] policy in XML 
+    def get_policy uri, type="read"
+      policy(uri, type)
+    end
+
+    # sends policy to opensso server
+    # @param (see #get_policy) 
+    def send_policy uri, type="read"
+      OpenTox::Authorization.create_policy(policy(uri, type), @subjectid)
+    end
+
+    # Change account URI into RDF prefixed Version e.G.: "http://toxbanktest1.opentox.org:8080/toxbank/user/U2" becomes "TBU:U2"
+    # @example 
+    #   user = OpenTox::TBAccount.new("http://uri_to_toxbankservice/toxbank/user/U2", subjectid)
+    #   puts user.ns_uri #=> "RDF::TBU:U2"
+    # @return [String] prefixed URI of a user/organisation/project
+    def ns_uri
+      out = "TBU:#{@uri.split('/')[-1]}"  if @uri.match(RDF::TBU.to_s)
+      out = "TBO:#{@uri.split('/')[-1]}"  if @uri.match(RDF::TBO.to_s)
+      out = "TBPT:#{@uri.split('/')[-1]}" if @uri.match(RDF::TBPT.to_s)
+      out
+    end
+
+    private
+
+    # Get rdf from user service and returns username
+    # @private 
+    def get_account
+      get "application/rdf+xml" # get rdfxml instead of ntriples
+      # do not catch errors as this will lead do follow up problems
+      # error handling is implemented at a lower level in opentox-client
+      self[RDF::TB.hasAccount]
+    end
+
+    # creates policy
+    def policy uri, type="read"
+      return <<-EOS
+<!DOCTYPE Policies PUBLIC "-//Sun Java System Access Manager7.1 2006Q3 Admin CLI DTD//EN" "jar://com/sun/identity/policy/policyAdmin.dtd">
+<Policies>
+  <Policy name="tbi-#{self.account}-#{self.ldap_type[4,6].downcase}-#{Time.now.strftime("%Y-%m-%d-%H-%M-%S-x") + rand(1000).to_s}" referralPolicy="false" active="true">
+    <Rule name="rule_name">
+      <ServiceName name="iPlanetAMWebAgentService" />
+      <ResourceName name="#{uri}"/>
+      #{get_permissions(type)}
+    </Rule>
+    <Subjects name="subjects_name" description="">
+      <Subject name="subject_name" type="#{self.ldap_type}" includeType="inclusive">
+        <AttributeValuePair>
+          <Attribute name="Values"/>
+          <Value>#{self.ldap_dn}</Value>
+        </AttributeValuePair>
+      </Subject>
+    </Subjects>
+  </Policy>
+</Policies>
+      EOS
+    end
+
+    # creates permission part of policy
+    def get_permissions type
+      requests = case type
+      when "all"
+        ["GET", "POST", "PUT", "DELETE"]
+      when "readwrite"
+        ["GET", "POST", "PUT"]
+      else
+        ["GET"]
+      end
+      out=""
+      requests.each{|r| out = "#{out}<AttributeValuePair><Attribute name=\"#{r}\" /><Value>allow</Value></AttributeValuePair>\n"}
+      return out
+    end
+
+  end
+
+  # ToxBank-investigation specific extension to OpenTox::Authorization in opentox-client 
+  # @see http://rubydoc.info/gems/opentox-client/frames opentox-client documentation
+  module Authorization
+
+    # Create policy for PI-user (owner of subjectid)
+    # @param [String, String] URI,subjectid URI to create a policy for, subjectid
+    def self.create_pi_policy uri, subjectid
+      user = get_user(subjectid)
+      piuri = RestClientWrapper.get("http://toxbanktest1.opentox.org:8080/toxbank/user?username=#{user}", nil, {:Accept => "text/uri-list", :subjectid => subjectid}).sub("\n","")
+      piaccount = TBAccount.new(piuri, subjectid)
+      piaccount.send_policy(uri, "all")
+    end
+
+    # Delete all policies for Users or Groups of an investigation except the policy of the PI (Principal Investigator) user. 
+    # @param [String, String, String] URI,LDAPtype,subjectid URI to protect, LDAPUsers or LDAPGroups, subjectid
+    def self.reset_policies uri, type, subjectid
+      policies = self.list_uri_policies(uri, subjectid)
+      user = get_user(subjectid)
+      policies.keep_if{|policy| policy =~ /^tbi-\w+-#{type}-*/ }
+      policies.delete_if{|policy| policy =~ /^tbi-#{user}-users-*/ }
+      policies.each{|policy| self.delete_policy(policy, subjectid) }
+    end
+
+  end
+end

data/toxbank-investigation.gemspec

@@ -3,7 +3,7 @@ $:.push File.expand_path("../lib", __FILE__)
 
 Gem::Specification.new do |s|
   s.name        = "toxbank-investigation"
-  s.version     = "0.0.2pre"
+  s.version     = File.read("./VERSION")
   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"
@@ -15,13 +15,11 @@ Gem::Specification.new do |s|
   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"
+  s.add_runtime_dependency 'roo'
 
   # external requirements
   ["git", "zip", "java", "curl", "wget"].each{|r| s.requirements << r}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: toxbank-investigation
 version: !ruby/object:Gem::Version
-  version: 0.0.2pre
+  version: 1.0.0pre1
   prerelease: 5
 platform: ruby
 authors:
@@ -11,11 +11,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-04-02 00:00:00.000000000 Z
+date: 2012-08-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: opentox-server
-  requirement: &78865690 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -23,23 +23,44 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *78865690
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: roo
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Toxbank investigation service
 email:
 - helma@in-silico.ch
 - gebele@in-silico.ch
 - rautenenberg@in-silico.ch
-executables:
-- toxbank-investigation-install
+executables: []
 extensions: []
 extra_rdoc_files: []
 files:
 - .gitignore
+- ChangeLog
 - Gemfile
-- Gemfile.lock
 - LICENSE
 - README
 - Rakefile
+- VERSION
 - application.rb
 - bin/toxbank-investigation-install
 - config.ru
@@ -56,6 +77,7 @@ files:
 - java/config/isa_configurator/heterozygosity_micro.xml
 - java/config/isa_configurator/histology.xml
 - java/config/isa_configurator/histonemodification_seq.xml
+- java/config/isa_configurator/investigation.xml
 - java/config/isa_configurator/metaboliteprofiling_ms.xml
 - java/config/isa_configurator/metaboliteprofiling_nmr.xml
 - java/config/isa_configurator/metagenome_seq.xml
@@ -74,6 +96,8 @@ files:
 - java/config/isa_configurator/transcription_micro.xml
 - java/config/isa_configurator/transcription_rtpcr.xml
 - java/config/isa_configurator/transcription_seq.xml
+- pirewriter.rb
+- tbaccount.rb
 - toxbank-investigation.gemspec
 homepage: http://github.com/ToxBank/toxbank-investigation
 licenses:
@@ -101,7 +125,7 @@ requirements:
 - curl
 - wget
 rubyforge_project: toxbank-investigation
-rubygems_version: 1.8.11
+rubygems_version: 1.8.18
 signing_key: 
 specification_version: 3
 summary: Toxbank investigation service

data/Gemfile.lock

@@ -1,111 +0,0 @@
-PATH
-  remote: .
-  specs:
-    toxbank-investigation (0.0.2pre)
-      opentox-server
-
-PATH
-  remote: ~/opentox-client
-  specs:
-    opentox-client (0.0.2pre)
-      bundler
-      open4
-      rdf
-      rdf-raptor
-      rest-client
-
-PATH
-  remote: ~/opentox-server
-  specs:
-    opentox-server (0.0.2pre)
-      emk-sinatra-url-for
-      opentox-client
-      rack
-      rack-contrib
-      roo
-      sinatra
-      sinatra-contrib
-      unicorn
-
-GEM
-  remote: http://rubygems.org/
-  specs:
-    addressable (2.2.7)
-    backports (2.3.0)
-    choice (0.1.5)
-    emk-sinatra-url-for (0.2.1)
-      sinatra (>= 0.9.1.1)
-    eventmachine (0.12.10)
-    faraday (0.7.6)
-      addressable (~> 2.2)
-      multipart-post (~> 1.1)
-      rack (~> 1.1)
-    ffi (1.0.11)
-    google-spreadsheet-ruby (0.1.8)
-      nokogiri (>= 1.4.3.1)
-      oauth (>= 0.3.6)
-      oauth2 (>= 0.5.0)
-    kgio (2.7.2)
-    log4r (1.1.10)
-    mime-types (1.17.2)
-    multi_json (1.1.0)
-    multipart-post (1.1.5)
-    nokogiri (1.5.2)
-    oauth (0.4.5)
-    oauth2 (0.5.2)
-      faraday (~> 0.7)
-      multi_json (~> 1.0)
-    open4 (1.3.0)
-    rack (1.4.1)
-    rack-contrib (1.1.0)
-      rack (>= 0.9.1)
-    rack-protection (1.2.0)
-      rack
-    rack-test (0.6.1)
-      rack (>= 1.0)
-    raindrops (0.8.0)
-    rdf (0.3.5)
-      addressable (>= 2.2.6)
-    rdf-raptor (0.4.1)
-      ffi (>= 1.0)
-      rdf (~> 0.3.0)
-    rest-client (1.6.7)
-      mime-types (>= 1.16)
-    roo (1.10.1)
-      choice (>= 0.1.4)
-      google-spreadsheet-ruby (>= 0.1.5)
-      nokogiri (>= 1.5.0)
-      rubyzip (>= 0.9.4)
-      spreadsheet (> 0.6.4)
-      todonotes (>= 0.1.0)
-    ruby-ole (1.2.11.3)
-    rubyzip (0.9.6.1)
-    sinatra (1.3.2)
-      rack (~> 1.3, >= 1.3.6)
-      rack-protection (~> 1.2)
-      tilt (~> 1.3, >= 1.3.3)
-    sinatra-contrib (1.3.1)
-      backports (>= 2.0)
-      eventmachine
-      rack-protection
-      rack-test
-      sinatra (~> 1.3.0)
-      tilt (~> 1.3)
-    spreadsheet (0.6.8)
-      ruby-ole (>= 1.0)
-    tilt (1.3.3)
-    todonotes (0.1.0)
-      log4r
-    unicorn (4.2.0)
-      kgio (~> 2.6)
-      rack
-      raindrops (~> 0.7)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  opentox-client!
-  opentox-server!
-  rack-test
-  toxbank-investigation!