- Upgraded codebase to use Rails 2.3.2. Main changes:

  - Updated the Annotations and Favourites plugins (to also use the latest plugin_test_helper).
  - WSDL parsing - loading XML into a Hash has changed now... <serviceType> is now x['service_type'].
  - Many other small tweaks to get things working properly.

I have carried out some extensive testing but we still need much more testing to ascertain stability. We especially need to test Soaplab Server submission and new user account signups.

- Integrated the “Better Logging” plugin for Rails (http://github.com/pauldowman/better_logging/tree/master) to provide better log outputs. (Unfortunately this has resulted in losing the rotated log files mechanism. This is necessary because ActiveSupport::BufferedLogger.new is the recommended logger, NOT Logger.new).

- Revamped the way the cache client is set up to make it more consistent and also easier to fix for Passenger. Also, we now use the latest memcache-client instead of the one supplied by Rails (as the former is significantly faster).

- Installed the geokit-rails plugin, in place of the old geokit plugin, which relies on the geokit gem (which has been vendored).

git-svn-id: svn+ssh://rubyforge.org/var/svn/biocatalogue/trunk@763 1acaf488-1b9d-4964-8077-0a2fdb83ef00

.loadpath

@@ -2,11 +2,11 @@
 <loadpath>
 	<pathentry path="" type="src"/>
 	<pathentry path="org.rubypeople.rdt.launching.RUBY_CONTAINER" type="con"/>
-	<pathentry path="GEM_LIB/rake-0.8.3/lib" type="var"/>
-	<pathentry path="GEM_LIB/activeresource-2.2.2/lib" type="var"/>
-	<pathentry path="GEM_LIB/rails-2.2.2/lib" type="var"/>
-	<pathentry path="GEM_LIB/actionmailer-2.2.2/lib" type="var"/>
-	<pathentry path="GEM_LIB/activesupport-2.2.2/lib" type="var"/>
-	<pathentry path="GEM_LIB/activerecord-2.2.2/lib" type="var"/>
-	<pathentry path="GEM_LIB/actionpack-2.2.2/lib" type="var"/>
+	<pathentry path="GEM_LIB/rake-0.8.7/lib" type="var"/>
+	<pathentry path="GEM_LIB/activeresource-2.3.2/lib" type="var"/>
+	<pathentry path="GEM_LIB/rails-2.3.2/lib" type="var"/>
+	<pathentry path="GEM_LIB/actionmailer-2.3.2/lib" type="var"/>
+	<pathentry path="GEM_LIB/activesupport-2.3.2/lib" type="var"/>
+	<pathentry path="GEM_LIB/activerecord-2.3.2/lib" type="var"/>
+	<pathentry path="GEM_LIB/actionpack-2.3.2/lib" type="var"/>
 </loadpath>

app/controllers/application.rb → app/controllers/application_controller.rb

@@ -1,4 +1,4 @@
-# BioCatalogue: app/controllers/application.rb
+# BioCatalogue: app/controllers/application_controller.rb
 #
 # Copyright (c) 2009, University of Manchester, The European Bioinformatics
 # Institute (EMBL-EBI) and the University of Southampton.
@@ -11,21 +11,19 @@
 # Need to do this so that we play nice with the annotations and favourites plugin.
 # THIS DOES UNFORTUNATELY MEAN THAT A SERVER RESTART IS REQUIRED WHENEVER CHANGES ARE MADE
 # TO THIS FILE, EVEN IN DEVELOPMENT MODE.
-require_dependency RAILS_ROOT + '/vendor/plugins/annotations/lib/app/controllers/application'
-require_dependency RAILS_ROOT + '/vendor/plugins/favourites/lib/app/controllers/application'
+require_dependency RAILS_ROOT + '/vendor/plugins/annotations/lib/app/controllers/application_controller'
+require_dependency RAILS_ROOT + '/vendor/plugins/favourites/lib/app/controllers/application_controller'
 #---
 
 class ApplicationController < ActionController::Base
   helper :all # include all helpers, all the time
 
-  # See ActionController::RequestForgeryProtection for details
-  # Uncomment the :secret if you're not using the cookie session store
-  protect_from_forgery :secret => 'bc5fa0462513829e6a733e8947c24994'
-
   # See ActionController::Base for details
   # Uncomment this to filter the contents of submitted sensitive data parameters
   # from your application log (in this case, all fields with names like "password").
   filter_parameter_logging :password
+
+  protect_from_forgery
 
   layout "application_wide"
 

app/controllers/search_controller.rb

@@ -33,7 +33,7 @@ def show
           @results = BioCatalogue::Search.search_all(@query)
         rescue Exception => ex
           flash.now[:error] = "Search failed. Possible bad search term. Please report this if it continues for other searches."
-          logger.error("ERROR: search failed for query: '#{@query}'. Exception:")
+          logger.error("Search failed for query: '#{@query}'. Exception:")
           logger.error(ex.message)
           logger.error(ex.backtrace.join("\n"))
         end

app/controllers/services_controller.rb

@@ -105,7 +105,7 @@ def search
         @results = BioCatalogue::Search.search(@query, @type)
       rescue Exception => ex
         flash.now[:error] = "Search failed. Possible bad search term. Please report this if it continues for other searches."
-        logger.error("ERROR: search failed for query: '#{@query}'. Exception:")
+        logger.error("Search failed for query: '#{@query}'. Exception:")
         logger.error(ex.message)
         logger.error(ex.backtrace.join("\n"))
       end

app/controllers/soap_services_controller.rb

@@ -162,7 +162,7 @@ def load_wsdl
         end
       rescue Exception => ex
         @error_message = "Failed to load the WSDL location provided."
-        logger.error("ERROR: failed to load WSDL from location - #{wsdl_location}. Exception:")
+        logger.error("Failed to load WSDL from location - #{wsdl_location}. Exception:")
         logger.error(ex.message)
         logger.error(ex.backtrace.join("\n"))
       end
@@ -220,7 +220,7 @@ def bulk_create
             end
           rescue Exception => ex
             @error_urls << url
-            logger.error("ERROR: failed to register service - #{url}. Bulk registration Exception:")
+            logger.error("Failed to register service - #{url}. Bulk registration Exception:")
             logger.error(ex)
           end
       end

app/controllers/soaplab_servers_controller.rb

@@ -118,7 +118,7 @@ def load_wsdl
         @wsdl_geo_location = BioCatalogue::Util.url_location_lookup(wsdl_location)
       rescue Exception => ex
         @error_message = "Failed to load the WSDL location provided."
-        logger.error("ERROR: failed to load WSDL from location - #{wsdl_location}. Exception:")
+        logger.error("Failed to load WSDL from location - #{wsdl_location}. Exception:")
         logger.error(ex)
       end
     end

app/models/rest_service.rb

@@ -94,7 +94,7 @@ def submit_service(endpoint, actual_submitter, annotations_data)
       end
     rescue Exception => ex
       #ActiveRecord::RecordNotSaved, ActiveRecord::RecordInvalid
-      logger.error("ERROR: failed to submit REST service - #{endpoint}. Exception:")
+      logger.error("Failed to submit REST service - #{endpoint}. Exception:")
       logger.error(ex.message)
       logger.error(ex.backtrace.join("\n"))
       success = false
@@ -104,7 +104,7 @@ def submit_service(endpoint, actual_submitter, annotations_data)
       begin
         self.process_annotations_data(annotations_data, actual_submitter)
       rescue Exception => ex
-        logger.error("ERROR: failed to process annotations after REST service creation. REST service ID: #{self.id}. Exception:")
+        logger.error("Failed to process annotations after REST service creation. REST service ID: #{self.id}. Exception:")
         logger.error(ex.message)
         logger.error(ex.backtrace.join("\n"))
       end

app/models/soap_service.rb

@@ -176,7 +176,7 @@ def submit_service(endpoint, actual_submitter, annotations_data)
       end
     rescue Exception => ex
       #ActiveRecord::RecordNotSaved, ActiveRecord::RecordInvalid
-      logger.error("ERROR: failed to submit SOAP service - #{endpoint}. Exception:")
+      logger.error("Failed to submit SOAP service - #{endpoint}. Exception:")
       logger.error(ex.message)
       logger.error(ex.backtrace.join("\n"))
       success = false
@@ -186,7 +186,7 @@ def submit_service(endpoint, actual_submitter, annotations_data)
       begin
         self.process_annotations_data(annotations_data, actual_submitter)
       rescue Exception => ex
-        logger.error("ERROR: failed to process annotations after SOAP service creation. SOAP service ID: #{self.id}. Exception:")
+        logger.error("Failed to process annotations after SOAP service creation. SOAP service ID: #{self.id}. Exception:")
         logger.error(ex.message)
         logger.error(ex.backtrace.join("\n"))
       end

app/models/soaplab_server.rb

@@ -48,15 +48,15 @@ def save_services(current_user)
               c_success = soap_service.submit_service( data["endpoint"], current_user, {} )  
               if c_success
                 new_wsdls << url
-                logger.info("INFO: registered service - #{url}. SUCCESS:")
+                logger.info("Registered service - #{url}. SUCCESS:")
               else
                 error_urls << url
-                logger.error("ERROR: post_create failed for service - #{url}. ")
+                logger.error("post_create failed for service - #{url}. ")
               end
             end
           rescue Exception => ex
             error_urls << url
-            logger.error("ERROR: failed to register service - #{url}. soaplab registration Exception:")
+            logger.error("failed to register service - #{url}. soaplab registration Exception:")
             logger.error(ex)
           end
         end
@@ -92,7 +92,7 @@ def get_soaplab1_data(proxy)
       }
       return data
     rescue Exception => ex
-      logger.error("ERROR: failed to get data from sooaplab server:")
+      logger.error("Failed to get data from sooaplab server:")
       logger.error(ex)
       return {}
     end
@@ -127,7 +127,7 @@ def get_soaplab2_data(proxy)
       }
       return data
     rescue Exception => ex
-      logger.error("ERROR: failed to get data from sooaplab server:")
+      logger.error("Failed to get data from sooaplab server:")
       logger.error(ex)
       return {}
     end

app/models/user.rb

@@ -59,7 +59,7 @@ def activate!
       self.save!
       return true
     rescue Exception => ex
-      logger.error("ERROR: failed to activate user #{self.id}. Exception:")
+      logger.error("Failed to activate user #{self.id}. Exception:")
       logger.error(ex)
       return false
     end
@@ -83,7 +83,7 @@ def generate_security_token!
       self.save!
       return true
     rescue Exception => ex
-      logger.error("ERROR: failed to generate the security token for user #{self.id}. Exception:")
+      logger.error("Failed to generate the security token for user #{self.id}. Exception:")
       logger.error(ex)
       return false
     end
@@ -97,7 +97,7 @@ def reset_password!(password = nil, password_confirmation = nil)
       self.save!
       return true
     rescue Exception => ex
-      logger.error("ERROR: failed to reset password for user #{self.id}. Exception:")
+      logger.error("Failed to reset password for user #{self.id}. Exception:")
       logger.error(ex)
       return false
     end

app/views/services/_listing.html.erb

@@ -30,11 +30,11 @@
 																:show_add_option => false,
 																:show_modify_options => false } -%>
 
-				<div style="margin: 0.8em 0">
+				<div style="margin: 1.1em 0 0.8em 0;">
 					<%= render :partial => "annotations/descriptions",
 								:locals => { :annotatable => service_version_instance,
 									:show_header => false,
-									:truncate_desc => 150,
+									:truncate_desc => 100,
 									:auto_link_desc => false,
 									:show_modify_options => false,
 									:show_none_text => false } -%>

config/boot.rb

@@ -44,6 +44,7 @@ class VendorBoot < Boot
     def load_initializer
       require "#{RAILS_ROOT}/vendor/rails/railties/lib/initializer"
       Rails::Initializer.run(:install_gem_spec_stubs)
+      Rails::GemDependency.add_frozen_gem_path
     end
   end
 

config/environment.rb

@@ -5,7 +5,7 @@
 # ENV['RAILS_ENV'] ||= 'production'
 
 # Specifies gem version of Rails to use when vendor/rails is not present
-RAILS_GEM_VERSION = '2.2.2' unless defined? RAILS_GEM_VERSION
+RAILS_GEM_VERSION = '2.3.2' unless defined? RAILS_GEM_VERSION
 
 # Bootstrap the Rails environment, frameworks, and default configuration
 require File.join(File.dirname(__FILE__), 'boot')
@@ -27,6 +27,8 @@
   # config.gem "aws-s3", :lib => "aws/s3"
   config.gem 'disqus', :version => '1.0.1'
   config.gem 'soap4r', :version => '1.5.8'
+  config.gem 'mperham-memcache-client', :version => '>= 1.7.3', :lib => 'memcache', :source => "http://gems.github.com"
+  config.gem 'geokit'
 
   # Only load the plugins named here, in the order given. By default, all plugins 
   # in vendor/plugins are loaded in alphabetical order.
@@ -38,7 +40,6 @@
 
 	# Rotate logs when they reach a size of 10M and keep no more than 10 of these
   #config.logger = Logger.new(config.log_path, 10, (1024**2)*10)
-  config.logger = Logger.new(config.log_path, 100, (1024**2)*10)
 
   # Force all environments to use the same logger level
   # (by default production uses :info, the others :debug)
@@ -80,7 +81,8 @@
     PhusionPassenger.on_event(:starting_worker_process) do |forked|
       if forked
         # We're in smart spawning mode.
-        CACHE.reset
+        # Reset caches..
+        BioCatalogue::CacheHelper.reset_caches
       else
         # We're in conservative spawning mode. We don't need to do anything.
       end

config/environments/production.rb

@@ -20,10 +20,4 @@
 # Disable delivery errors, bad email addresses will be ignored
 # config.action_mailer.raise_delivery_errors = false
 
-
-# From: http://www.whatcodecraves.com/articles/2009/03/17/rails_2.2.2_chicken_and_egg_migrations_headache/ -
-
-# kids, this is what an ugly hack looks like. Don't worry, Rails
-# 2.3 will fix this.
-config.cache_classes = (File.basename($0) == "rake" && !ARGV.grep(/db:/).empty?) ? false : true
-
+config.action_view.cache_template_loading = true

config/initializers/biocat_local.rb.pre

@@ -37,11 +37,3 @@ Disqus::defaults[:developer] = true # allows for threads to work on localhost du
 
 # Enable or disable endpoint status check icon in view
 DISABLE_STATUS_CHECK = true
-
-# ============
-# Cache config
-# ------------
-
-ActionController::Base.cache_store = :mem_cache_store, "127.0.0.1:11211", { :namespace => "BioCatalogue", :multithread => true }
-
-# ============

config/initializers/biocat_main.rb

@@ -18,11 +18,24 @@
 require 'object'
 require 'addressable/uri'
 require 'system_timer'
+require 'libxml'
+require 'dnsruby'
+
+# Never explicitly load the memcache-client library as we need to use 
+# the specific one vendored in our codebase.
+#require 'memcache'
+
+# Change XML backend that Rails uses to a faster one
+#XmlMini.backend = 'LibXML'   # Not working currently. TODO: set this up when implementing the XML REST API.
 
 # Initialise the country codes library
 CountryCodes
 
-# Set up loggers to STDOUT if in script/console (so now things like SQL queries etc are shown in the console).
+# Set up caches
+BioCatalogue::CacheHelper.setup_caches
+
+# Set up loggers to STDOUT if in script/console 
+# (so now things like SQL queries etc are shown in the console instead of the development/production/etc logs).
 if "irb" == $0
   ActiveRecord::Base.logger = Logger.new(STDOUT)
   ActionController::Base.logger = Logger.new(STDOUT)

config/initializers/geokit_config.rb

@@ -0,0 +1,61 @@
+if defined? Geokit
+
+	# These defaults are used in Geokit::Mappable.distance_to and in acts_as_mappable
+	Geokit::default_units = :miles
+	Geokit::default_formula = :sphere
+
+	# This is the timeout value in seconds to be used for calls to the geocoder web
+	# services.  For no timeout at all, comment out the setting.  The timeout unit
+	# is in seconds. 
+	Geokit::Geocoders::timeout = 3
+
+	# These settings are used if web service calls must be routed through a proxy.
+	# These setting can be nil if not needed, otherwise, addr and port must be 
+	# filled in at a minimum.  If the proxy requires authentication, the username
+	# and password can be provided as well.
+	Geokit::Geocoders::proxy_addr = nil
+	Geokit::Geocoders::proxy_port = nil
+	Geokit::Geocoders::proxy_user = nil
+	Geokit::Geocoders::proxy_pass = nil
+
+	# This is your yahoo application key for the Yahoo Geocoder.
+	# See http://developer.yahoo.com/faq/index.html#appid
+	# and http://developer.yahoo.com/maps/rest/V1/geocode.html
+	Geokit::Geocoders::yahoo = 'REPLACE_WITH_YOUR_YAHOO_KEY'
+
+	# This is your Google Maps geocoder key. 
+	# See http://www.google.com/apis/maps/signup.html
+	# and http://www.google.com/apis/maps/documentation/#Geocoding_Examples
+	Geokit::Geocoders::google = 'REPLACE_WITH_YOUR_GOOGLE_KEY'
+
+	# This is your username and password for geocoder.us.
+	# To use the free service, the value can be set to nil or false.  For 
+	# usage tied to an account, the value should be set to username:password.
+	# See http://geocoder.us
+	# and http://geocoder.us/user/signup
+	Geokit::Geocoders::geocoder_us = false 
+
+	# This is your authorization key for geocoder.ca.
+	# To use the free service, the value can be set to nil or false.  For 
+	# usage tied to an account, set the value to the key obtained from
+	# Geocoder.ca.
+	# See http://geocoder.ca
+	# and http://geocoder.ca/?register=1
+	Geokit::Geocoders::geocoder_ca = false
+
+	# Uncomment to use a username with the Geonames geocoder
+	#Geokit::Geocoders::geonames="REPLACE_WITH_YOUR_GEONAMES_USERNAME"
+
+	# This is the order in which the geocoders are called in a failover scenario
+	# If you only want to use a single geocoder, put a single symbol in the array.
+	# Valid symbols are :google, :yahoo, :us, and :ca.
+	# Be aware that there are Terms of Use restrictions on how you can use the 
+	# various geocoders.  Make sure you read up on relevant Terms of Use for each
+	# geocoder you are going to use.
+	Geokit::Geocoders::provider_order = [:google,:us]
+
+	# The IP provider order. Valid symbols are :ip,:geo_plugin.
+	# As before, make sure you read up on relevant Terms of Use for each
+	# Geokit::Geocoders::ip_provider_order = [:geo_plugin,:ip]
+
+end