From c5d85910256c699ea9dedc96614f342b807b023e Mon Sep 17 00:00:00 2001 From: mr Date: Tue, 14 Dec 2010 16:40:18 +0100 Subject: rename token_id to subjectid --- application.rb | 22 +++++++++++----------- helper.rb | 18 +++++++++--------- model.rb | 6 +++--- views/create.haml | 2 +- views/fragment.haml | 2 +- views/login.haml | 4 ++-- views/predict.haml | 2 +- views/prediction.haml | 2 +- 8 files changed, 29 insertions(+), 29 deletions(-) diff --git a/application.rb b/application.rb index 30458bc..2790076 100644 --- a/application.rb +++ b/application.rb @@ -118,14 +118,14 @@ post '/models' do # create a new model redirect url_for('/create') end - @model = ToxCreateModel.create(:name => params[:file][:filename].sub(/\..*$/,""), :token_id => session[:token_id]) + @model = ToxCreateModel.create(:name => params[:file][:filename].sub(/\..*$/,""), :subjectid => session[:subjectid]) @model.update :web_uri => url_for("/model/#{@model.id}", :full) @model.save task = OpenTox::Task.create("Uploading dataset and creating lazar model",url_for("/models",:full)) do @model.update :status => "Uploading and saving dataset" begin - @dataset = OpenTox::Dataset.create(nil, session[:token_id]) + @dataset = OpenTox::Dataset.create(nil, session[:subjectid]) # check format by extension - not all browsers provide correct content-type]) case File.extname(params[:file][:filename]) when ".csv" @@ -140,8 +140,8 @@ post '/models' do # create a new model rescue => e error "Dataset creation failed with #{e.message}" end - token_id = session[:token_id] if session[:token_id] - @dataset.save(token_id) + subjectid = session[:subjectid] if session[:subjectid] + @dataset.save(subjectid) if @dataset.compounds.size < 10 error "Too few compounds to create a prediction model. Did you provide compounds in SMILES format and classification activities as described in the #{link_to "instructions", "/excel_format"}? As a rule of thumb you will need at least 100 training compounds for nongeneric datasets. A lower number could be sufficient for congeneric datasets." end @@ -158,7 +158,7 @@ post '/models' do # create a new model @model.update :status => "Creating prediction model" begin - lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :token_id => session[:token_id]) + lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :subjectid => session[:subjectid]) rescue => e error "Model creation failed with '#{e.message}'. Please check if the input file is in a valid #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} format." end @@ -181,7 +181,7 @@ post '/models' do # create a new model validation = OpenTox::Validation.create_crossvalidation( :algorithm_uri => OpenTox::Algorithm::Lazar.uri, :dataset_uri => lazar.parameter("dataset_uri"), - :token_id => session[:token_id], + :subjectid => session[:subjectid], :prediction_feature => lazar.parameter("prediction_feature"), :algorithm_params => "feature_generation_uri=#{lazar.parameter("feature_generation_uri")}" ) @@ -254,7 +254,7 @@ post '/predict/?' do # post chemical name to model title = nil db_activities = [] lazar = OpenTox::Model::Lazar.new model.uri - prediction_dataset_uri = lazar.run(:compound_uri => @compound.uri, :token_id => session[:token_id]) + prediction_dataset_uri = lazar.run(:compound_uri => @compound.uri, :subjectid => session[:subjectid]) prediction_dataset = OpenTox::LazarPrediction.find(prediction_dataset_uri) if prediction_dataset.metadata[OT.hasSource].match(/dataset/) @predictions << { @@ -321,7 +321,7 @@ post "/lazar/?" do # get detailed prediction @page = params[:page].to_i if params[:page] @model_uri = params[:model_uri] lazar = OpenTox::Model::Lazar.new @model_uri - prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :token_id => params[:token_id]) + prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :subjectid => params[:subjectid]) @prediction = OpenTox::LazarPrediction.find(prediction_dataset_uri) @compound = OpenTox::Compound.new(params[:compound_uri]) #@title = prediction.metadata[DC.title] @@ -352,7 +352,7 @@ post "/lazar/?" do # get detailed prediction end post '/login' do - if session[:token_id] != nil + if session[:subjectid] != nil flash[:notice] = "You are already logged in as user: #{session[:username]}. Please log out first." redirect url_for('/login') end @@ -376,12 +376,12 @@ end delete '/model/:id/?' do model = ToxCreateModel.get(params[:id]) begin - RestClient.delete(model.uri, :token_id => session[:token_id]) if model.uri + RestClient.delete(model.uri, :subjectid => session[:subjectid]) if model.uri RestClient.delete model.task_uri if model.task_uri model.destroy unless ToxCreateModel.get(params[:id]) begin - aa = OpenTox::Authorization.delete_policies_from_uri(model.web_uri, session[:token_id]) + aa = OpenTox::Authorization.delete_policies_from_uri(model.web_uri, session[:subjectid]) LOGGER.debug "Policy deleted for Dataset URI: #{uri} with result: #{aa}" rescue LOGGER.warn "Policy delete error for Dataset URI: #{uri}" diff --git a/helper.rb b/helper.rb index a660cc2..e892669 100644 --- a/helper.rb +++ b/helper.rb @@ -1,9 +1,9 @@ helpers do def login(username, password) - session[:token_id] = OpenTox::Authorization.authenticate(username, password) - LOGGER.debug "ToxCreate login user #{username} with token_id: " + session[:token_id].to_s - if session[:token_id] != nil + session[:subjectid] = OpenTox::Authorization.authenticate(username, password) + LOGGER.debug "ToxCreate login user #{username} with subjectid: " + session[:subjectid].to_s + if session[:subjectid] != nil session[:username] = username return true else @@ -13,8 +13,8 @@ helpers do end def logout - if session[:token_id] != nil - session[:token_id] = nil + if session[:subjectid] != nil + session[:subjectid] = nil session[:username] = "" return true end @@ -23,15 +23,15 @@ helpers do def logged_in() return true if !AA_SERVER - if session[:token_id] != nil - return OpenTox::Authorization.is_token_valid(session[:token_id]) + if session[:subjectid] != nil + return OpenTox::Authorization.is_token_valid(session[:subjectid]) end return false end def is_authorized(uri, action) - if session[:token_id] != nil - return OpenTox::Authorization.authorize(uri, action, session[:token_id]) + if session[:subjectid] != nil + return OpenTox::Authorization.authorize(uri, action, session[:subjectid]) end return false end diff --git a/model.rb b/model.rb index 82a0135..eb459b3 100644 --- a/model.rb +++ b/model.rb @@ -40,8 +40,8 @@ class ToxCreateModel property :web_uri, String, :length => 255 - attr_accessor :token_id - @token_id = nil + attr_accessor :subjectid + @subjectid = nil after :save, :check_policy @@ -190,7 +190,7 @@ def status private def check_policy - OpenTox::Authorization.check_policy(web_uri, token_id) + OpenTox::Authorization.check_policy(web_uri, subjectid) end end diff --git a/views/create.haml b/views/create.haml index d83d2b9..5aeac67 100644 --- a/views/create.haml +++ b/views/create.haml @@ -30,7 +30,7 @@ = link_to "CSV", '/help' format: %input{:type => 'file', :name => 'file', :id => 'file', :size => '41'} - %input{:type => 'hidden', :name => 'token_id', :id => 'token_id', :value => session[:token_id]} + %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]} %input{ :type => "submit", :value => "Create model"} = link_to "Cancel", '/create' diff --git a/views/fragment.haml b/views/fragment.haml index eae786c..3b9f68b 100644 --- a/views/fragment.haml +++ b/views/fragment.haml @@ -2,7 +2,7 @@ %input{:type => :hidden, :name => :compound_uri, :value => compound_uri} %input{:type => :hidden, :name => :model_uri, :value => model_uri} %input{:type => :hidden, :name => :highlight, :value => smarts} - %input{:type => :hidden, :name => :token_id, :value => session[:token_id]} + %input{:type => :hidden, :name => :subjectid, :value => session[:subjectid]} - if smarts.nil? %input{ :type => "submit", :value => "Reset"} - else diff --git a/views/login.haml b/views/login.haml index 4f45de3..747430e 100644 --- a/views/login.haml +++ b/views/login.haml @@ -26,7 +26,7 @@ %b= session[:username] - if LOGGER.level == Logger::DEBUG %br - = session[:token_id] + = session[:subjectid] %input{ :type => "submit", :value => "Logout"} = link_to "Cancel", '/login' - \ No newline at end of file + diff --git a/views/predict.haml b/views/predict.haml index 6337a5b..cd5c0d4 100644 --- a/views/predict.haml +++ b/views/predict.haml @@ -29,7 +29,7 @@ %input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => model.id} %br - %input{:type => 'hidden', :name => 'token_id', :id => 'token_id', :value => session[:token_id]} + %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]} %input{ :type => "submit", :value => "Predict", :onclick => "getsmiles();"} = link_to 'Cancel', '/predict' diff --git a/views/prediction.haml b/views/prediction.haml index f0b48e8..9bb3f76 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -44,7 +44,7 @@ %form{:name => "form", :action => url_for('/lazar'), :method => "post", :enctype => "multipart/form-data" } %input{:type => :hidden, :name => :compound_uri, :value => @compound.uri} %input{:type => :hidden, :name => :model_uri, :value => p[:model_uri]} - %input{:type => :hidden, :name => :token_id, :value => session[:token_id]} + %input{:type => :hidden, :name => :subjectid, :value => session[:subjectid]} %input{ :type => "submit", :value => "Details"} = haml :confidence, :layout => false -- cgit v1.2.3