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The annotations plugin currently being used in the BioCatalogue codebase to allow the addition of arbitrary metadata to things
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README.rdoc

This is the Gem version of Annotations plugin

Annotations Gem

Install

Add the following line in the Gemfile:

gem 'annotations', :git => "git://github.com/quyen/annotations.git"

Setup

Please read the setup of the Annotations Plugin. The only differences are the loadpaths of some dependencies. For example:

  • Annotations Gem uses:

    require_dependency File.join(Gem.loaded_specs['annotations'].full_gem_path,'lib','app','controllers','application_controller')

  • Annotations Plugin uses:

    require_dependency File.join(Rails.root, 'vendor', 'plugins', 'annotations', 'lib', 'app', 'controllers', 'application_controller')

Annotations Plugin (for Ruby on Rails applications)

Original Author

Jiten Bhagat (mail@jits.co.uk)

Other Authors:: Stuart Owen, Quyen Nguyen

Copyright

© 2008-2013, the University of Manchester and the European Bioinformatics Institute (EMBL-EBI)

License

BSD

Version

0.5.0

IMPORTANT NOTE

In v0.2.0+ this plugin has been modified substantially to support polymorphic annotation values rather than just strings.

Overview

This plugin allows arbitrary metadata and relationships to be stored and retrieved, in the form of Annotations for any model objects in your Ruby on Rails (v2.2+) application.

Annotations are in the form:

Annotation = Annotatable (what thing are you talking about?) 
           + Attribute (what is the kind/class of annotation? [tag? description?]) 
           + Value (what is the data or other thing you want to associate with the annotatable)) 
           + Source (who/what made this annotation?)
           + Version Info (how many versions of this annotation are there?) 
           + Timestamps (when was this annotation created/updated?)

The idea is to provide a consistent and systematic way to abstract out and decouple annotations from your application's core data model and allow layering in of metadata/relationships easily.

Examples of things you can use the annotations plugin for:

  • Tags

  • Categories

  • Descriptions

  • Examples

  • Notes

  • Comments

A concrete example of a 'tag' Annotation:

Ann1 = <car SF8 JK0>      (Annotatable)
     + <tag>              (Attribute)
     + <dirty>            (Value)
     + <Autobot 3000>     (Source)
     + <v1>               (Version Info)
     + <2011-07-06 10:00> (Timestamps)

A concrete example of another kind of Annotation:

Ann1 = <dog jack>         (Annotatable)
     + <isBreed>          (Attribute)
     + <chihuahua>        (Value)
     + <Dave Elias>       (Source)
     + <v2>               (Version Info)
     + <2011-07-06 11:00> (Timestamps)

The main benefit is that annotations are stored and retrieved in a uniform manner with a common API. Parts of the plugin can also be extended and overridden in your application (see the Usage section for more info).

The annotations plugin is currently being used successfully in the BioCatalogue codebase to allow easy annotation of web services and their deployments/versions/operations/inputs/outputs/etc. Check out www.biocatalogue.org.

Features:

  • A complete set of ActiveRecord models for annotations, annotation attributes and annotation values and annotation value seeds.

  • acts_as_annotatable, acts_as_annotation_source and acts_as_annotation_value mixin modules for your models, complete with a number of advanced finders.

  • A basic CRUD controller that can be used out of the box to list, create, view, edit and delete annotations.

  • Versioning of annotations - all updates to annotations cause a new version of that annotation to be created.

  • Annotation Value Seeds can be used to set up some default/preliminary seed data for attributes without having to create annotations.

  • Lots of configuration options!

Full Documentation

To generate full documentation (including this readme and full API docs) do the following:

Install RDoc (v2.3.0 or above):

% [sudo] gem install rdoc

Install the darkfish-rdoc gem:

% [sudo] gem install darkfish-rdoc

Run the following command in the plugin's root directory (vendor/plugins/annotations):

% rdoc -SHNU -w 2 --title='Annotations Plugin' -m 'INDEX.rdoc' -x '(/doc|/tasks|/script|/test)'

The generated documentation will be in the doc folder of the annotations plugin.

Conceptual Data Model

At a conceptual level, an Annotation consists of:

  • a link to the thing being annotated - the Annotatable

  • a link to the attribute which specifies what kind of annotation this is - the Attribute

  • a link to the value of the annotation - the Value

  • a link to the source of the annotation - the Source

  • version information - *Version Info*

  • timestamps for event time info - Timestamps

This can be represented as:

Annotation = Annotatable + Attribute + Value + Source + Version Info + Timestamps

The database model for an Annotation is made up of the following fields:

| id | annotatable_type | annotatable_id | source_type | source_id | attribute_id | value_type | value_id | version | version_creator_id | created_at | updated_at |

This makes use of ActiveRecord polymorphic relationships to allow any ActiveRecord model to be an Annotatable, Source and Value.

Note: The version_creator_id field is only relevant when there are more than one version of an Annotation. I.e.: for the first version of the annotation the version_creator_id will be nil.

Annotation Attributes currently consist of a name and a unique identifier (in the form of a URI). This is the attribute or property you are describing for an Annotatable. Examples: 'tag', 'description', etc.

Versioning of Annotations

Whenever an Annotation is updated, a new AnnotationVersion entry is created in the db (corresponding model name = Annotation::Version).

This uses a library from the version_fu plugin. A customised version of this is embedded within the Annotations plugin (which won't conflict if version_fu is installed in the main codebase).

Installation and Setup

Important Requirements

  • Only works for Ruby on Rails v2.2 and above.

  • Your Application Controller MUST define (or have access to) the following methods:

    • login_required - a method that checks if the user is logged in and if not redirects to the login page.

    • logged_in? - a method to check if the user is logged_in.

    • current_user - a method to retrieve the currently logged in user. This MUST return nil if no user is currently logged in.

Installation

To install the plugin as a git cloned repo (this allows you to easily update the plugin in the future):

ruby script/plugin install git://github.com/myGrid/annotations.git

Note: this requires git to be installed.

To install the plugin the regular way:

ruby script/plugin install http://github.com/myGrid/annotations.git/

Setup

  • Generate the migration(s):

    ruby script/generate annotations_migration all
  • Create a config file - config/initializers/annotations.rb - for the plugin specific configuration (see Usage section for the available config options)

  • Modify your application to work with the plugin:

    • Add the following line to the top of your app/controllers/application_controller.rb file (or application.rb in older versions of Rails):

      require_dependency File.join(Rails.root, 'vendor', 'plugins', 'annotations', 'lib', 'app', 'controllers', 'application_controller')
    • Add the following line to the top of your app/helpers/application_helper.rb file:

      require_dependency File.join(Rails.root, 'vendor', 'plugins', 'annotations', 'lib', 'app', 'helpers', 'application_helper')

    Note: the require_dependency line is crucial in making your app work with the files in the plugin and allows for easy extension and overriding of the plugin parts. *However, this does mean that any file with the require_dependency line will not be automagically loaded by Rails in development mode when changes have been made - a server restart is required whenever any changes are made to these files.*

  • Create the following files in your application:

    • Annotation model:

      # app/models/annotation.rb
      #
      # This extends the Annotation model defined in the Annotations plugin.
      
      require_dependency File.join(Rails.root, 'vendor', 'plugins', 'annotations', 'lib', 'app', 'models', 'annotation')
      
      class Annotation < ActiveRecord::Base
      end
    • AnnotationAttribute model:

      # app/models/annotation_attribute.rb
      #
      # This extends the AnnotationAttribute model defined in the Annotations plugin.
      
      require_dependency File.join(Rails.root, 'vendor', 'plugins', 'annotations', 'lib', 'app', 'models', 'annotation_attribute')
      
      class AnnotationAttribute < ActiveRecord::Base
      end
    • AnnotationsController controller:

      # app/controllers/annotations_controller.rb
      #
      # This extends the AnnotationsController controller defined in the Annotations plugin.
      
      require_dependency File.join(Rails.root, 'vendor', 'plugins', 'annotations', 'lib', 'app', 'controllers', 'annotations_controller')
      
      class AnnotationsController < ApplicationController
      end

    These are used to extend/override the models and controller from the plugin with extra actions, filters, validations, processing and so on (see Usage section for more details and examples).

  • Specify which models in your codebase can be annotated by adding acts_as_annotatable in the model's definition. For example:

    class Service < ActiveRecord::Base
      ...
      acts_as_annotatable
      ...
    end
  • Specify which models in your codebase can be the source of annotations by adding acts_as_annotation_source in the model's definition. For example:

    class User < ActiveRecord::Base
      ...
      acts_as_annotation_source
      ...
    end

The Annotations plugin has now been installed and is ready for use. See the Usage section for further details.

Usage

Quick Use

  • To add a bunch of Annotations to a model instance:

    book = Book.find(1)
    data = {
      :description => "My bookie wookie",
      :rating => 5,
      :tag => [ "horror", "romance", "indiluted", "true story" ] }
    new_annotations = book.create_annotations(data, current_user)
  • Create an Annotation directly:

    book = Book.find(10)
    ann1 = Annotation.new(:attribute_name => "tag", 
                          :value => "hot", 
                          :source_type => "User", 
                          :source_id => 100,
                          :annotatable_type => book.class.name,
                          :annotatable_id => book.id)
  • Building a simple form for adding a single Annotation, like 'description', to a specified model object:

    <% form_tag annotations_url do %>
      <%= hidden_field_tag "annotation[annotatable_type]", "Book" -%>
      <%= hidden_field_tag "annotation[annotatable_id]", 100 -%>
      <%= hidden_field_tag "annotation[attribute_name]", "description" -%>
      <%= text_area_tag "annotation[value]" -%>			
      <%= submit_tag "Submit", :disable_with => "Submitting..." -%>
    <% end %>
  • Building a simple form for adding multiple Annotations from one field, like 'tags', to a specified model object:

    <% form_tag create_multiple_annotations_url do %>
      <%= hidden_field_tag "separator", "," -%>
      <%= hidden_field_tag "annotation[annotatable_type]", "Book" -%>
    	<%= hidden_field_tag "annotation[annotatable_id]", 100 -%>
      <%= hidden_field_tag "annotation[attribute_name]", "description" -%>
      <%= text_area_tag "annotation[value]" -%>			
      <%= submit_tag "Submit", :disable_with => "Submitting..." -%>
    <% end %>
  • Find all Annotations for a model instance (that has acts_annotatable specified in the model's class):

    book = Book.find(6806)
    annotations = book.annotations
  • Find all 'tag' Annotations for a model instance (that has acts_annotatable specified in the model's class):

    book = Book.find(23)
    tag_annotations = book.annotations_with_attribute("tag")
  • Find all Annotations for a model instance that have a number of different attribute names (that has acts_annotatable specified in the model's class):

    book = Book.find(22124)
    rating_annotations = book.annotations_with_attributes([ "rating-performance", "rating-usefulness", "rating-documentation" ])

See _More Examples_ below.

Important Usage Notes

  • When using the built in Annotations Controller to create annotations (as in the forms examples above), the default is to use the current_user as the Source. However, you can explicitly specify the source by adding fields for “annotations[source_type]” and “annotations[source_id]”.

  • Attributes are NOT case-sensitive. So 'description' and 'Description' will be the same AnnotationAttribute entity and therefore all annotations with that attribute will be the exact same type/class/kind of annotation).

  • When displaying the values of annotations, ALWAYS clean the data using methods like h (html escape), sanitize and white_list.

  • By default, duplicate annotations cannot be created (by “duplicate” we mean: same value for the same attribute, on an annotatable object, regardless of source). For example: a user cannot add a description to a service that matches an existing description for that service. You can override this behaviour for annotations with certain attributes, using the configuration option: attribute_names_to_allow_duplicates. NOTE: this is different to the limits_per_source config_ option, which isn't about duplicate annotations, but rather limiting the quantity of annotations of a specific attribute on a specific annotatable object by a specific source.

Config Options

All the config options can be found in lib/annotations/config.rb, listed below:

  • attribute_names_for_values_to_be_downcased

  • attribute_names_for_values_to_be_upcase

  • strip_text_rules

  • user_model_name

  • limits_per_source

  • attribute_names_to_allow_duplicates

  • value_restrictions

TODO: explain and document these.

More Examples

  • Create multiple 'tag' Annotations from a single string value:

    params = { :annotatable_type => "Book",
               :annotatable_id => 78,
               :attribute_name => "tag",
               :value => "workflow, taverna, brilliant",
               :source_type => "Group",
               :source_id => 4 }
    Annotation.create_multiple(params, ',')
  • Find all 'comment' Annotations, by a specified Source, for a model instance (that has acts_annotatable specified in the model's class):

    book = Book.find(67)
    user = User.find_by_name("jane")
    annotations = book.annotations_with_attribute_and_by_source("comment", user)
  • Find all Annotations, that don't have the specified attributes, for a model instance (that has acts_annotatable specified in the model's class):

    book = Book.find(56)
    annotations = book.all_annotations_excluding_attributes([ "tag", "note", "example" ])
  • Find Annotatable objects that have a specific attribute name AND value:

    • Gets all annotatables regardless of type:

      Annotation.find_annotatables_with_attribute_name_and_value("complexity", "O(x^2)")
    • Gets only annotatables that are Books:

      Book.with_annotations_with_attribute_name_and_value("Tag", "Amusing rhetoric")
  • Find Annotatable objects that have a combination of attribute names AND values:

    Annotation.find_annotatables_with_attribute_names_and_values([ "tag" ], [ "fiction", "sci-fi", "fantasy" ])
    
    Annotation.find_annotatables_with_attribute_names_and_values([ "tag", "keyword", "category" ], [ "fiction", "fantasy" ])
  • Count the number of Annotations, by any Source, for a model instance (that has acts_annotatable specified in the model's class):

    book = Book.find(90)
    count = book.count_annotations_by("all")
  • Count the number of Annotations, by Users, for a model instance (that has acts_annotatable specified in the model's class):

    book = Book.find(90)
    count = book.count_annotations_by("User")

TODO: add more advanced examples!

Extending the Plugin

Most of the aspects of this plugin can be extended/overridden in your codebase.

Examples:

  • To restrict the values for certain annotations, you can either use the Annotations::Config::value_restrictions setting and/or extend the Annotation model in your own codebase and use the ActiveRecord validates_inclusion_of validation. For the latter, an example is below:

    require_dependency RAILS_ROOT + '/vendor/plugins/annotations/lib/app/models/annotation'
    
    class Annotation < ActiveRecord::Base
      ...
    
      validates_inclusion_of :value, 
      	                     :in => [ "fruit", "nut", "fibre" ], 
      	                     :message => "Please select a valid category.",
      	                     :if => Proc.new { |ann| ann.attribute_name.downcase == "category" }
    
      ...
    end

TODO: add more!

See Also

The BioCatalogue codebase contains many examples of using the Annotations plugin successfully. Some pointers:

The prototype Shims Library also makes use of the Annotations plugin successfully and may provide some useful examples.

Updating the Plugin

Update the plugin code using the appropriate mechanism. Then:

ruby script/generate annotations_migration vX

… where X is the version of the migration you want to generate

Main Plugin Contents

TODO: list files and what the purpose of each is.

Known Issues

  • May not work with sqlite and sqlite3 databases.

  • Not tested with Postgres DB.

  • Doesn't work consistently well with Single Table Inheritance (STI).

Troubleshooting

  • Whilst running in development mode, if you get an error such as:

    A copy of ApplicationController has been removed from the module tree but is still active!

    … then restart your server. This is due to the way Rails autoloads files in development mode, which affects the plugin and any extensions in the main app.

Future Plans

In no particular order:

  • Allow curation assertions such as “Agree”, “Useful”, “Incomplete” to be made on annotations.

  • Allow values to be any model rather than free text and provide a basic set of annotation value models, such as AnnotationValueFreeText, AnnotationValueNumber, AnnotationValueUri, etc

  • Extend the AnnotationAttribute model to contain controlled vocabulary / ontology term information.

  • Update the versioning to a better version of version_fu. See: github.com/jmckible/version_fu/network

Appendix A: Data Model

Annotations

Table name: annotations

Fields:

  • id

  • source_type

  • source_id

  • annotatable_type

  • annotatable_id

  • attribute_id

  • value

  • value_type

  • created_at

  • updated_at

  • version

  • version_creator_id

Annotation Versions

Table name: annotation_versions

Fields:

  • id

  • annotation_id

  • version

  • version_creator_id

  • source_type

  • source_id

  • annotatable_type

  • annotatable_id

  • attribute_id

  • value

  • value_type

  • created_at

  • updated_at

Annotation Attributes

Table name: annotation_attributes

Fields:

  • id

  • name

  • created_at

  • updated_at

Annotation Value Seeds

Table name: annotation_value_seeds

Fields:

  • id

  • attribute_id

  • value

  • created_at

  • updated_at

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