Merge branch 'master' into images

Gemfile

@@ -1,7 +1,7 @@
 source 'https://rubygems.org'
 ruby '2.1.1'
 
-gem 'rails', '4.0.3'
+gem 'rails', '4.0.4'
 
 # PostgreSQL
 gem 'pg', '~> 0.17.0'
@@ -84,6 +84,7 @@ end
 group :test do
   gem "rspec"
   gem 'coveralls', '~> 0.7', require: false
+  gem 'capybara', '~> 2.1'
 end
 
 group :development do 

README.md

@@ -14,15 +14,15 @@ TaxonWorks is Ruby on Rails application that facilitates biodiversity informatic
 Installation
 ------------
 
-TaxonWorks is a Rails 4 application using Ruby 2.0 and rubygems.  It requires PostgreSQL with the postgis extension.  The core development team is using [rvm][16] and [brew][9] to configure their environment on OS X.  
+TaxonWorks is a Rails 4 application using Ruby 2.0 and rubygems.  It requires PostgreSQL with the postgis extension.  It uses ImageMagick.  The core development team is using [rvm][16] and [brew][9] to configure their environment on OS X.  
 
 Minimally, the following steps are required.  If you have postgres installed skip to 3. 
 
-1. Install Postgres and postgis.
+1. Install Postgres and postgis and image magick.
 
    ``` 
    brew install postgres
-   brew install postgis
+   brew install postgis 
    brew install imagemagick
    ```
 

app/assets/javascripts/sessions.js.coffee

@@ -0,0 +1,3 @@
+# Place all the behaviors and hooks related to the matching controller here.
+# All this logic will automatically be available in application.js.
+# You can use CoffeeScript in this file: http://coffeescript.org/

app/assets/javascripts/users.js.coffee

@@ -0,0 +1,3 @@
+# Place all the behaviors and hooks related to the matching controller here.
+# All this logic will automatically be available in application.js.
+# You can use CoffeeScript in this file: http://coffeescript.org/

app/assets/stylesheets/sessions.css.scss

@@ -0,0 +1,3 @@
+// Place all the styles related to the sessions controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/

app/assets/stylesheets/users.css.scss

@@ -0,0 +1,3 @@
+// Place all the styles related to the users controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/

app/controllers/application_controller.rb

@@ -2,4 +2,30 @@ class ApplicationController < ActionController::Base
   # Prevent CSRF attacks by raising an exception.
   # For APIs, you may want to use :null_session instead.
   protect_from_forgery with: :exception
+
+  layout 'basic'
+
+  include SessionsHelper
+
+  attr_writer   :meta_title, :meta_data, :site_name
+  attr_accessor :meta_description, :meta_keywords, :page_title
+
+  helper_method :meta_title, :meta_data, :site_name, :page_title
+
+  def meta_title
+    @meta_title ||= [@meta_title.presence || @page_title.presence, site_name].
+                    compact.join(' | ')
+  end
+
+  def meta_data
+    @meta_data ||= {
+      description: @meta_description,
+      keywords: @meta_keywords
+    }.delete_if{ |k, v| v.nil? }
+  end
+
+  def site_name
+    @site_name ||= 'TaxonWorks'
+  end
+
 end

app/controllers/dashboard_controller.rb

@@ -1,6 +1,9 @@
 class DashboardController < ApplicationController
 
+  # GET '/'
   def index
+    redirect_to signin_path, status: 301 and return unless sessions_signed_in?
+    @page_title = 'Your dashboard'
   end
 
 end

app/controllers/sessions_controller.rb

@@ -0,0 +1,28 @@
+class SessionsController < ApplicationController
+
+  # GET /signin
+  def new
+    @page_title = 'Sign in'
+    @user = User.new
+  end
+
+  # POST /sessions
+  def create
+    user = User.find_by(email: params[:session][:email].downcase)
+    if user && user.authenticate(params[:session][:password])
+      sessions_sign_in user
+      redirect_to root_path
+    else
+      @page_title = 'Sign in'
+      flash.now[:error] = 'Unrecognised email and password combination.'
+      render 'new'
+    end
+  end
+
+  # DELETE /signout
+  def destroy
+    sessions_sign_out
+    redirect_to root_url
+  end
+
+end

app/controllers/users_controller.rb

@@ -0,0 +1,68 @@
+class UsersController < ApplicationController
+
+  # GET /users
+  def index
+    @users = User.all
+    @page_title = 'Users'
+  end
+
+  # GET /signup
+  def new
+    @user = User.new
+    @page_title = 'Create account'
+  end
+
+  # GET /users/:id
+  def show
+    @user = User.find(params[:id])
+    @page_title = "User #{@user.id}"
+  end
+
+  # GET /users/:id/edit
+  def edit
+    @user = User.find(params[:id])
+    @page_title = "Edit user #{@user.id}"
+  end
+
+  # POST /users
+  def create
+    @user = User.new(user_params)
+    if @user.save
+      sessions_sign_in @user
+      flash[:success] = 'Thanks for signing up and welcome to TaxonWorks!'
+      redirect_to root_path
+    else
+      @page_title = 'Create account'
+      render 'new'
+    end
+  end
+
+  # PATCH or PUT /users/:id
+  def update
+    @user = User.find(params[:id])
+    if @user.update_attributes(user_params)
+      flash[:success] = 'Changes to your account information have been saved.'
+      redirect_to @user
+    else
+      @page_title = "Edit user #{@user.id}"
+      render 'edit'
+    end
+  end
+
+  # DELETE /users/:id
+  def destroy
+    User.find(params[:id]).destroy
+    flash[:success] = "Your account has been deleted."
+    redirect_to root_url
+  end
+
+  private
+
+    def user_params
+      params.require(:user).permit(:name,
+                                   :email,
+                                   :password,
+                                   :password_confirmation)
+    end
+
+end

app/helpers/sessions_helper.rb

@@ -0,0 +1,28 @@
+module SessionsHelper
+
+  def sessions_signed_in?
+    !sessions_current_user.nil?
+  end
+
+  def sessions_current_user=(user)
+    @sessions_current_user = user
+  end
+
+  def sessions_current_user
+    remember_token = User.encrypt(cookies[:remember_token])
+    @sessions_current_user ||= User.find_by(remember_token: remember_token)
+  end
+
+  def sessions_sign_in(user)
+    remember_token = User.secure_random_token
+    cookies.permanent[:remember_token] = remember_token
+    user.update_attribute(:remember_token, User.encrypt(remember_token))
+    self.sessions_current_user = user
+  end
+
+  def sessions_sign_out
+    self.sessions_current_user = nil
+    cookies.delete(:remember_token)
+  end
+
+end

app/helpers/users_helper.rb

@@ -0,0 +1,2 @@
+module UsersHelper
+end

app/models/collection_object/biological_collection_object.rb

@@ -1,10 +1,9 @@
 class CollectionObject::BiologicalCollectionObject < CollectionObject
+  has_many :biocuration_classes, through: :biocuration_classifications
+  has_many :biocuration_classifications
   has_many :otus, through: :taxon_determinations
   has_many :taxon_determinations
-
-  has_many :biocuration_classifications
-  has_many :biocuration_classes, through: :biocuration_classifications
-
+
   accepts_nested_attributes_for :biocuration_classes, :biocuration_classifications, :taxon_determinations, :otus
 
   def current_determination

app/models/concerns/shared/data_attributes.rb

@@ -11,7 +11,7 @@ def has_data_attributes?
   end
 
   def keyword_value_hash
-    self.data_attributes.inject({}) do |hsh, a| 
+    self.data_attributes.inject({}) do |hsh, a|   
       if a.class == ImportAttribute
         hsh.merge!(a.import_predicate => a.value)
       else # there are only two

app/models/concerns/shared/identifiable.rb

@@ -3,6 +3,7 @@ module Shared::Identifiable
   included do
 
     has_many :identifiers, as: :identified_object, validate: false
+    accepts_nested_attributes_for :identifiers
 
    #scope :creator_missing_first_name, -> { where(people: {first_name: nil}).joins(:creator)}
    #scope :created_by,  lambda {|person| where("created_by_id = ?", person) }