merge -r 2449:2525 branches/v1.1.0 trunk

git-svn-id: svn+ssh://rubyforge.org/var/svn/biocatalogue/trunk@2526 1acaf488-1b9d-4964-8077-0a2fdb83ef00

app/controllers/annotations_controller.rb

@@ -18,7 +18,7 @@ class AnnotationsController < ApplicationController
 
   before_filter :add_use_tab_cookie_to_session, :only => [ :create, :create_multiple, :update, :destroy, :set_as_field ]
 
-  before_filter :login_or_oauth_required, :only => [ :new, :create, :edit, :update, :destroy, :edit_popup, :create_inline, :change_attribute, :bulk_create ]
+  before_filter :login_or_oauth_required, :only => [ :new, :create, :edit, :update, :destroy, :edit_popup, :create_inline, :promote_alternative_name, :bulk_create ]
 
   before_filter :parse_filtered_index_params, :only => :filtered_index
 
@@ -30,12 +30,12 @@ class AnnotationsController < ApplicationController
 
   before_filter :find_annotations, :only => [ :index, :filtered_index ]
 
-  before_filter :find_annotation, :only => [ :show, :edit, :update, :destroy, :edit_popup, :download, :change_attribute ]
+  before_filter :find_annotation, :only => [ :show, :edit, :update, :destroy, :edit_popup, :download, :promote_alternative_name ]
 
   before_filter :find_annotatable, :only => [ :new, :create, :new_popup, :create_inline ]
 
   skip_before_filter :authorise_action
-  before_filter :authorise, :only =>  [ :edit, :edit_popup, :update, :destroy, :change_attribute, :bulk_create ]
+  before_filter :authorise, :only =>  [ :edit, :edit_popup, :update, :destroy, :promote_alternative_name, :bulk_create ]
 
   def index
     respond_to do |format|
@@ -103,24 +103,29 @@ def edit_popup
   # PUT /annotations/1
   # PUT /annotations/1.xml
   def update
-    @annotation.value = params[:annotation][:value]
-    @annotation.version_creator_id = current_user.id
-    respond_to do |format|
-      if @annotation.save
-        flash[:notice] = 'Annotation was successfully updated.'
-
-        url_to_redirect_to = if @annotation.annotatable_type =~ /RestParameter|RestRepresentation/
-                               request.env["HTTP_REFERER"]
-                             else  
-                               url_for_web_interface(@annotation.annotatable) || home_url
-                             end
-
-        format.html { redirect_to url_to_redirect_to }
-        format.xml  { head :ok }
-      else
-        format.html { render :action => "edit" }
-        format.xml  { render :xml => @annotation.errors, :status => :unprocessable_entity }
+    # Only allow update for certain kind of annotation values
+    if [ 'TextValue', 'NumberValue' ].include?(@annotation.value_type)
+      @annotation.value.ann_content = params[:annotation][:value]
+      @annotation.version_creator_id = current_user.id
+      respond_to do |format|
+        if @annotation.save
+          flash[:notice] = 'Annotation was successfully updated.'
+
+          url_to_redirect_to = if @annotation.annotatable_type =~ /RestParameter|RestRepresentation/
+                                 request.env["HTTP_REFERER"]
+                               else  
+                                 url_for_web_interface(@annotation.annotatable) || home_url
+                               end
+
+          format.html { redirect_to url_to_redirect_to }
+          format.xml  { head :ok }
+        else
+          format.html { render :action => "edit" }
+          format.xml  { render :xml => @annotation.errors, :status => :unprocessable_entity }
+        end
       end
+    else
+      error_to_back_or_home "Cannot perform this action!"
     end
   end
 
@@ -145,35 +150,26 @@ def create_inline
   end
 
   def download
-    send_data(@annotation.value, :type => "text/plain", :disposition => 'inline')
+    send_data(@annotation.value_content, :type => "text/plain", :disposition => 'inline')
   end
 
-  def change_attribute
-    attribs_allowed_to_be_changed = %w( alternative_name )
-    attribs_allowed_to_be_changed_to = %w( display_name )
-
-    new_attrib = params[:new_attribute]
-
-    # Check that the attributes are allowed...
-    if attribs_allowed_to_be_changed.include?(@annotation.attribute_name.downcase) and
-       attribs_allowed_to_be_changed_to.include?(new_attrib.try(:downcase))
-
-      # Authorise and carry on... 
-      if BioCatalogue::Auth.allow_user_to_curate_thing?(current_user, @annotation.annotatable)
-        @annotation.attribute_name = new_attrib
-
-        if @annotation.save
-          respond_to do |format|
-            flash[:notice] = "#{new_attrib.humanize} successfully updated"
-            format.html { redirect_to :back }
-          end
-        else
-          error_to_back_or_home "Sorry, something went wrong. Please try again. If this problem persists we would appreciate it if you contacted us."
+  def promote_alternative_name
+    if @annotation.attribute_name.downcase == "alternative_name" &&
+      BioCatalogue::Auth.allow_user_to_curate_thing?(current_user, @annotation.annotatable)
+
+      annotatable = @annotation.annotatable
+      annotatable.name = @annotation.val_content
+
+      if annotatable.save && @annotation.destroy
+        respond_to do |format|
+          flash[:notice] = "Display name successfully updated"
+          format.html { redirect_to :back }
         end
       else
-        error_to_back_or_home "You are not allowed to do that!"
+        error_to_back_or_home "Sorry, something went wrong. Please try again. If this problem persists we would appreciate it if you contacted us."
       end
-
+    else
+      error_to_back_or_home "You are not allowed to do that!"
     end
   end
 

app/controllers/application_controller.rb

@@ -1,6 +1,6 @@
 # BioCatalogue: app/controllers/application_controller.rb
 #
-# Copyright (c) 2009-2010, University of Manchester, The European Bioinformatics
+# Copyright (c) 2008-2011, University of Manchester, The European Bioinformatics
 # Institute (EMBL-EBI) and the University of Southampton.
 # See license.txt for details.
 
@@ -20,17 +20,9 @@ class ApplicationController < ActionController::Base
   # Allow for SSL support
   include SslRequirement
   if ENABLE_SSL && Rails.env.production?
-    ssl_allowed :all
-    DEFAULT_PROTOCOL = 'https'
-  else
-    DEFAULT_PROTOCOL = 'http'
+    ssl_required :all
   end
 
-  def default_protocol
-    DEFAULT_PROTOCOL
-  end
-  helper_method :default_protocol
-
   # ============================================
 
   # OAuth support
@@ -182,7 +174,7 @@ def mine?(thing)
         return thing.source == current_user
       when Service
         return c_id == thing.submitter_id.to_i
-      when Favourite
+      when Favourite, ServiceResponsible
         return c_id == thing.user_id
       else
         return false
@@ -220,7 +212,7 @@ def base_host
     request.host_with_port
   end
 
-  protected
+protected
 
   def debug_messages
     BioCatalogue::Util.say ""
@@ -345,13 +337,12 @@ def error(messages, *args)
     end
 
     respond_to do |format|
-
-      if options[:back_first] && !session[:previous_url].blank?
+      if !options[:back_first].blank? && !session[:previous_url].blank? && session[:previous_url]!=request.env["REQUEST_URI"]
         format.html { redirect_to(session[:previous_url]) }
       else
         format.html { render "home/index", :status => options[:status] }
       end
-      
+
       if options[:forbidden]
         format.xml  { head :forbidden }
         format.json { head :forbidden }
@@ -362,7 +353,7 @@ def error(messages, *args)
         format.xml  { render "api/errors", :status => options[:status] }
         format.json { render :json => { "errors" => messages }.to_json, :status => options[:status] }
         format.atom { render :atom => "", :status => options[:status] }
-      end
+      end      
     end
   end
 
@@ -522,14 +513,42 @@ def generate_sort_url(resource, sort_by, sort_order)
   helper_method :generate_sort_url
 
   def is_sort_selected(sort_by, sort_order)
-    return params[:sort_by] == sort_by.downcase && params[:sort_order] == sort_order.downcase
+    return @sort_by == sort_by.downcase && @sort_order == sort_order.downcase
   end
   helper_method :is_sort_selected
 
   def get_filter_groups
     @filter_groups = BioCatalogue::Filtering.get_all_filter_groups_for(self.controller_name.underscore.to_sym, @limit || nil, params[:q])
   end
 
+  def include_archived?
+    unless defined?(@include_archived)
+      session_key = "#{self.controller_name.downcase}_#{self.action_name.downcase}_include_archived"
+      if !params[:include_archived].blank?
+        @include_archived = !%w(false no 0).include?(params[:include_archived].downcase)
+        session[session_key] = @include_archived.to_s
+      elsif !session[session_key].blank?
+        @include_archived = (session[session_key] == "true")
+      else
+        @include_archived = true
+        session[session_key] = @include_archived.to_s
+      end
+    end
+    return @include_archived
+  end
+  helper_method :include_archived?
+
+  def generate_include_archived_url(resource, should_include_archived)
+    params_dup = BioCatalogue::Util.duplicate_params(params)
+    params_dup[:include_archived] = should_include_archived.to_s
+
+    # Reset page param
+    params_dup.delete(:page)
+
+    return eval("#{resource}_url(params_dup)")
+  end
+  helper_method :generate_include_archived_url
+
   # ===============================
 
 
@@ -584,6 +603,11 @@ def log_event
               ActivityLog.create(@log_event_core_data.merge(:action => "view_services_index",
                                  :culprit => current_user,
                                  :data => { :query => params[:q], :filters => @current_filters, :page => @page, :per_page => @per_page }))
+            # Archive/unarchive services
+            when "archive", "unarchive"
+              ActivityLog.create(@log_event_core_data.merge(:action => a,
+                                 :culprit => current_user,
+                                 :activity_loggable => @service))
             else
               do_generic_log = true
           end

app/controllers/contact_controller.rb

@@ -8,10 +8,6 @@ class ContactController < ApplicationController
 
   before_filter :disable_action_for_api
 
-  if ENABLE_SSL && Rails.env.production?
-    ssl_required :all
-  end
-
   # GET /contact
   def index
     respond_to do |format|

app/controllers/curation_controller.rb

@@ -90,6 +90,13 @@ def annotation_level
     end
   end
 
+  def providers_without_services
+    @service_providers = BioCatalogue::Curation::Reports.providers_without_services
+
+    respond_to do |format|
+      format.html # providers_without_services.html.erb
+    end
+  end
 
   protected
 

app/controllers/oauth_clients_controller.rb

@@ -13,11 +13,7 @@ class OauthClientsController < ApplicationController
   before_filter :get_client_application, :only => [ :show, :edit, :update, :destroy ]
 
   before_filter :authorise, :only => [ :show, :edit, :update, :destroy ]
-
-  if ENABLE_SSL && Rails.env.production?
-    ssl_required :all
-  end
-
+
   def index
     @client_applications = current_user.client_applications
     @tokens = current_user.tokens.find :all, :conditions => 'oauth_tokens.invalidated_at is null and oauth_tokens.authorized_at is not null'
@@ -53,8 +49,16 @@ def update
   end
 
   def destroy
-    @client_application.destroy
-    flash[:notice] = "Destroyed the client application registration"
+    begin
+      ClientApplication.transaction do
+        @client_application.destroy
+      end
+
+      flash[:notice] = "Destroyed the client application registration"
+    rescue
+      flash[:error] = "Could not delete the application"
+    end
+
     redirect_to :action => "index"
   end
 

app/controllers/oauth_controller.rb

@@ -10,10 +10,6 @@ class OauthController < ApplicationController
 
   before_filter :disable_action_for_api
 
-  if ENABLE_SSL && Rails.env.production?
-    ssl_required :all
-  end
-
   # Override this to match your authorization page form
   # It currently expects a checkbox called authorize
   # def user_authorizes_token?