rorchado 0.0.5

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 74ca265d8406c125d26a78f7b9283db74adbc06f
+  data.tar.gz: b75eaf4af8592097f813266744bb1ec7c07af760
+SHA512:
+  metadata.gz: 8ce4f9898e3d2cace8b02dac2475b08ef5c44efae19ffba6bd038f7f3349bfc234003a657dc90fc8aef6eecdfcd008629bd5b71643d9bc897116988b38a3394f
+  data.tar.gz: 6fac5c0c0462b318958adbe6f6e8ed75780b5405817177f60182cc0ca1129db5f8d7ceca2511e852f246943211f004be887eab234e49d059ddd4a64ce4065455

data/lib/rails/generators/rorchado/USAGE

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+Description:
+    It provides the ability to install/unistall the modules of Chado.
+    It will create the Model,the Controller and the Views to manage via your RoR app
+    all the data that Chado can store.
+
+Example:
+    rails generate rorchado install --all
+
+    This will create:
+        all the models,controllers and views for all the modules of Chado
+
+Example:
+    rails generate rorchado uninstall --all
+
+    This will remove:
+        all the models,controllers and views for all the modules of Chado

data/lib/rails/generators/rorchado/rorchado_generator.rb

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+require 'rubygems'
+require "rails/generators"
+require 'active_support/core_ext/object/inclusion'
+require 'hpricot'
+
+class RorchadoGenerator < Rails::Generators::Base
+  source_root File.expand_path('../templates', __FILE__)
+  argument :command_name, :type => :string, :default => "install"
+  class_option :module, :type => :string, :default => "all", :description => "Define which module to install/uninstall. Default value is 'all'."
+
+  def init
+    # Read the available modules from the XML file
+    xml = File.read(self.class.source_root + '/db_schemas/chado_schema.xml')    
+    @docxml = Hpricot::XML(xml)
+    
+    @valid_modules = []
+
+    (@docxml/:modules/:module).each do |module_item|      
+      @valid_modules << (module_item.get_attribute :id)
+    end
+      
+    @valid_commands = [ "help" , "list" , "install" , "uninstall" ]  
+  end
+  
+  
+  def GeneratorHandler
+    command = "#{command_name}".downcase
+    module_name = "#{options.module}".downcase
+
+    #Debug
+    #puts "Command: #{command}" 
+    #puts "Modules: #{module_name}"
+
+    # Check if the command is valid
+    if !@valid_commands.include?( command ) then
+      puts "The command '#{command}' is not supported by RoRChado gem."
+    elsif command=="help" then
+      puts "List of available commands:"
+      @valid_commands.each do |command|
+        puts " - #{command} , e.g. rails g rorchado #{command} [OPTIONS]"
+      end
+    elsif command=="list" then
+      puts "List of available Chado modules:"
+      @valid_modules.each do |module_tmp|
+        puts " - #{module_tmp}"
+      end      
+    else
+      # Check which module to handle
+      if module_name == "all" then
+        # create an array with all the modules
+        @valid_modules.each do |module_tmp|
+          send("#{command.capitalize}Module" , module_tmp )
+        end
+      else
+        # handle the requested and valid module        
+        found = false
+        @valid_modules.each do |module_tmp|
+          if module_tmp == module_name then
+            found = true
+            break
+          end
+        end
+
+        if found then
+          send("#{command.capitalize}Module" , module_name )
+        else
+          # Check if requested to install/unistall the admin
+          if module_name == "admin"  then
+            send("#{command.capitalize}Admin")
+          else
+            puts "The module '#{module_name}' is not supported by RoRChado gem."
+          end
+        end
+
+      end
+    end   
+  end
+
+  private
+  def InstallModule(module_name)
+    puts "Installing the #{module_name.capitalize} Module"
+
+    # Loop through the tables of this module
+    (@docxml/:modules/:module/"##{module_name}"/:tables/:table ).each do |table_item|
+      @table_name = table_item.get_attribute :id
+      @table_key  = table_item.get_attribute :primary_key
+      @class_name = @table_name.camelize
+
+      # parse the fields of the table & the ORM relations
+      @column_items = ""
+      @field_items = ""
+      @orm_items = ""
+      (table_item/:fields/:field ).each do |field_item|
+        field_item_id = (field_item.get_attribute :id)
+        if @column_items == "" then
+          @column_items = ":#{field_item_id}"
+        else
+          @column_items = @column_items + ", :#{field_item_id}"
+        end
+        @field_items = @field_items + "\t\tt." + (field_item.get_attribute :type) + " :" + field_item_id
+        if (field_item.get_attribute :not_null) == "1" then
+          @field_items = @field_items + ",\t :null=> false"
+        end
+        if (field_item.get_attribute :default) != "" then
+          @field_items = @field_items + ",\t :default=> " + (field_item.get_attribute :default)
+        end
+
+        @field_items = @field_items + "\n"
+
+        foreign_key = (field_item.get_attribute :foreign_key)        
+        if foreign_key != nil && !foreign_key.empty? then
+          foreign_key_class = foreign_key.camelize
+          @orm_items = @orm_items + "\t\tbelongs_to :#{foreign_key}, :class_name => \'#{foreign_key_class}\', :foreign_key => :#{field_item_id}\n"
+        end
+
+      end
+      #--------------
+
+      #parse the indexes
+      @index_items = ""
+      @constraint_items = ""
+      # counters for auto naming
+      @unique_id = 1
+      @index_id = 1
+
+      (table_item/:indexes/:index ).each do |index_item|
+         
+        
+        #grab the columns from the XML
+        @columns = (index_item.get_attribute :columns).split(",")
+        @comun_names = ""
+        @columns.each do |column|
+          if @comun_names == "" then
+            @comun_names = "\"#{column}\""
+          else
+            @comun_names = @comun_names + ", \"#{column}\""
+          end
+        end
+
+        #+ (index_item.get_attribute :type) + " :" + (index_item.get_attribute :id)
+        if (index_item.get_attribute :unique) == "1" then
+          @constraint_items = @constraint_items + "\t\tsuppress_messages {execute \'alter table #{@table_name}  add constraint #{@table_name}_c#{@unique_id}  unique("
+          @constraint_items = @constraint_items + @comun_names
+          @constraint_items = @constraint_items + ")\'"
+          @constraint_items = @constraint_items + "}\n"
+          @constraint_items = @constraint_items + "\t\tsay \"Constraint for columns \'"+ (index_item.get_attribute :columns) + "\' created!\"\n"
+          
+          @unique_id = @unique_id + 1
+        else
+          @index_items = @index_items + "\t\tsuppress_messages {add_index \"#{@table_name}\", ["
+          @index_items = @index_items + @comun_names
+          @index_items = @index_items + "], :name=> \"#{@table_name}_idx#{@index_id}\""
+          @index_items = @index_items + "}\n"
+          @index_items = @index_items + "\t\tsay \"Index for columns \'"+ (index_item.get_attribute :columns) + "\' created!\"\n"
+
+          @index_id = @index_id + 1
+        end
+
+      end
+      #--------------      
+
+      template "models/generic_model.erb", "app/models/#{@table_name}.rb"
+      template "migrations/generic_migration_create.erb", "db/migrate/" + ((Time.now.to_f * 10000).round).to_s + "_create_#{@table_name}.rb"
+    end
+
+  end
+
+  private
+  def UninstallModule(module_name)
+    puts "Uninstalling the #{module_name.capitalize} Module"
+
+    # Loop through the tables of this module
+    (@docxml/:modules/:module/"##{module_name}"/:tables/:table ).each do |table_item|
+      table_name = (table_item.get_attribute :id).camelize
+
+      Rails::Generators.invoke "model", ["#{table_name}"], :behavior => :revoke, :destination_root => Rails.root
+      Rails::Generators.invoke "migration", ["Create#{table_name}"], :behavior => :revoke, :destination_root => Rails.root
+    end
+
+  end
+
+  private 
+  def InstallAdmin()
+    puts "Installing Basic Admin for Chado"
+    # Copy Cv Admin
+    copy_file "controllers/cv_controller.rb", "app/controllers/cv_controller.rb"    
+    copy_file "views/cv/index.html.erb", "app/views/cv/index.html.erb"    
+    copy_file "views/cv/new.html.erb", "app/views/cv/new.html.erb"   
+    copy_file "views/cv/edit.html.erb", "app/views/cv/edit.html.erb"    
+    copy_file "views/cv/show.html.erb", "app/views/cv/show.html.erb"    
+    copy_file "views/cv/_form.html.erb", "app/views/cv/_form.html.erb"   
+    copy_file "controllers/cvterm_controller.rb", "app/controllers/cvterm_controller.rb"    
+    copy_file "views/cvterm/index.html.erb", "app/views/cvterm/index.html.erb"    
+    copy_file "views/cvterm/new.html.erb", "app/views/cvterm/new.html.erb"   
+    copy_file "views/cvterm/edit.html.erb", "app/views/cvterm/edit.html.erb"    
+    copy_file "views/cvterm/show.html.erb", "app/views/cvterm/show.html.erb"    
+    copy_file "views/cvterm/_form.html.erb", "app/views/cvterm/_form.html.erb"   
+
+    # Copy Contact Admin
+    copy_file "controllers/contact_controller.rb", "app/controllers/contact_controller.rb"    
+    copy_file "views/contact/index.html.erb", "app/views/contact/index.html.erb"    
+    copy_file "views/contact/new.html.erb", "app/views/contact/new.html.erb"   
+    copy_file "views/contact/edit.html.erb", "app/views/contact/edit.html.erb"    
+    copy_file "views/contact/show.html.erb", "app/views/contact/show.html.erb"    
+    copy_file "views/contact/_form.html.erb", "app/views/contact/_form.html.erb"   
+
+    # Copy Stock Admin
+    copy_file "controllers/stock_controller.rb", "app/controllers/stock_controller.rb"    
+    copy_file "views/stock/index.html.erb", "app/views/stock/index.html.erb"    
+    copy_file "views/stock/new.html.erb", "app/views/stock/new.html.erb"   
+    copy_file "views/stock/edit.html.erb", "app/views/stock/edit.html.erb"    
+    copy_file "views/stock/show.html.erb", "app/views/stock/show.html.erb"    
+    copy_file "views/stock/_form.html.erb", "app/views/stock/_form.html.erb"   
+
+    # Add Route
+    route "resources :contact"
+    route "resources :cv"
+    route "resources :cvterm"
+    route "resources :stock"
+  end
+
+  private 
+  def UninstallAdmin()
+    puts "Uninstalling Basic Admin for Chado"
+
+      remove_file("app/controllers/cvterm_controller.rb")
+      remove_file("app/views/cvterm/index.html.erb") 
+      remove_file("app/views/cvterm/new.html.erb") 
+      remove_file("app/views/cvterm/edit.html.erb") 
+      remove_file("app/views/cvterm/show.html.erb") 
+      remove_file("app/views/cvterm/_form.html.erb") 
+      gsub_file "config/routes.rb" , "resources :cvterm" , ""
+
+      remove_file("app/controllers/cv_controller.rb")
+      remove_file("app/views/cv/index.html.erb") 
+      remove_file("app/views/cv/new.html.erb") 
+      remove_file("app/views/cv/edit.html.erb") 
+      remove_file("app/views/cv/show.html.erb") 
+      remove_file("app/views/cv/_form.html.erb") 
+      gsub_file "config/routes.rb" , "resources :cv" , ""
+
+      remove_file("app/controllers/contact_controller.rb")
+      remove_file("app/views/contact/index.html.erb") 
+      remove_file("app/views/contact/new.html.erb") 
+      remove_file("app/views/contact/edit.html.erb") 
+      remove_file("app/views/contact/show.html.erb") 
+      remove_file("app/views/contact/_form.html.erb") 
+      gsub_file "config/routes.rb" , "resources :contact" , ""
+
+      remove_file("app/controllers/stock_controller.rb")
+      remove_file("app/views/stock/index.html.erb") 
+      remove_file("app/views/stock/new.html.erb") 
+      remove_file("app/views/stock/edit.html.erb") 
+      remove_file("app/views/stock/show.html.erb") 
+      remove_file("app/views/stock/_form.html.erb") 
+      gsub_file "config/routes.rb" , "resources :stock" , ""      
+  end
+
+end

data/lib/rails/generators/rorchado/templates/controllers/contact_controller.rb

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+class ContactController < ApplicationController
+  # GET /contacts
+  # GET /contacts.json
+  def index
+    @contacts = Contact.all
+
+    respond_to do |format|
+      format.html # index.html.erb
+      format.json { render :json => @contacts }
+    end
+  end
+
+  # GET /contacts/1
+  # GET /contacts/1.json
+  def show
+    @contact = Contact.find(params[:id])
+
+    respond_to do |format|
+      format.html # show.html.erb
+      format.json { render :json => @contact }
+    end
+  end
+
+  # GET /contacts/new
+  # GET /contacts/new.json
+  def new
+    @contact = Contact.new
+
+    respond_to do |format|
+      format.html # new.html.erb
+      format.json { render :json => @contact }
+    end
+  end
+
+  # GET /contacts/1/edit
+  def edit
+    @contact = Contact.find(params[:id])
+  end
+
+  # POST /contacts
+  # POST /contacts.json
+  def create
+    @contact = Contact.new(params[:contact])
+
+    respond_to do |format|
+      if @contact.save
+        format.html { redirect_to "/contact/", :notice => 'Contact was successfully created.' }
+        format.json { render :json => @contact, :status => :created, :location => @contact }
+      else
+        format.html { render :action => "new" }
+        format.json { render :json => @contact.errors, :status => :unprocessable_entity }
+      end
+    end
+  end
+
+  # PUT /contacts/1
+  # PUT /contacts/1.json
+  def update
+    @contact = Contact.find(params[:id])
+
+    respond_to do |format|
+      if @contact.update_attributes(params[:contact])
+        format.html { redirect_to "/contact/", :notice => 'Contact was successfully updated.' }
+        format.json { head :no_content }
+      else
+        format.html { render :action => "edit" }
+        format.json { render :json => @contact.errors, :status => :unprocessable_entity }
+      end
+    end
+  end
+
+  # DELETE /contacts/1
+  # DELETE /contacts/1.json
+  def destroy
+    @contact = Contact.find(params[:id])
+    @contact.destroy
+
+    respond_to do |format|
+      format.html { redirect_to "/contact/" }
+      format.json { head :no_content }
+    end
+  end
+end

data/lib/rails/generators/rorchado/templates/controllers/contact_controller.rb~

@@ -0,0 +1,83 @@
+class ContactsController < ApplicationController
+  # GET /contacts
+  # GET /contacts.json
+  def index
+    @contacts = Contact.all
+
+    respond_to do |format|
+      format.html # index.html.erb
+      format.json { render :json => @contacts }
+    end
+  end
+
+  # GET /contacts/1
+  # GET /contacts/1.json
+  def show
+    @contact = Contact.find(params[:id])
+
+    respond_to do |format|
+      format.html # show.html.erb
+      format.json { render :json => @contact }
+    end
+  end
+
+  # GET /contacts/new
+  # GET /contacts/new.json
+  def new
+    @contact = Contact.new
+
+    respond_to do |format|
+      format.html # new.html.erb
+      format.json { render :json => @contact }
+    end
+  end
+
+  # GET /contacts/1/edit
+  def edit
+    @contact = Contact.find(params[:id])
+  end
+
+  # POST /contacts
+  # POST /contacts.json
+  def create
+    @contact = Contact.new(params[:contact])
+
+    respond_to do |format|
+      if @contact.save
+        format.html { redirect_to @contact, :notice => 'Contact was successfully created.' }
+        format.json { render :json => @contact, :status => :created, :location => @contact }
+      else
+        format.html { render :action => "new" }
+        format.json { render :json => @contact.errors, :status => :unprocessable_entity }
+      end
+    end
+  end
+
+  # PUT /contacts/1
+  # PUT /contacts/1.json
+  def update
+    @contact = Contact.find(params[:id])
+
+    respond_to do |format|
+      if @contact.update_attributes(params[:contact])
+        format.html { redirect_to @contact, :notice => 'Contact was successfully updated.' }
+        format.json { head :no_content }
+      else
+        format.html { render :action => "edit" }
+        format.json { render :json => @contact.errors, :status => :unprocessable_entity }
+      end
+    end
+  end
+
+  # DELETE /contacts/1
+  # DELETE /contacts/1.json
+  def destroy
+    @contact = Contact.find(params[:id])
+    @contact.destroy
+
+    respond_to do |format|
+      format.html { redirect_to contacts_url }
+      format.json { head :no_content }
+    end
+  end
+end

data/lib/rails/generators/rorchado/templates/controllers/cv_controller.rb

@@ -0,0 +1,83 @@
+class CvController < ApplicationController
+  # GET /cvs
+  # GET /cvs.json
+  def index
+    @cvs = Cv.all
+
+    respond_to do |format|
+      format.html # index.html.erb
+      format.json { render :json => @cvs }
+    end
+  end
+
+  # GET /cvs/1
+  # GET /cvs/1.json
+  def show
+    @cv = Cv.find(params[:id])
+
+    respond_to do |format|
+      format.html # show.html.erb
+      format.json { render :json => @cv }
+    end
+  end
+
+  # GET /cvs/new
+  # GET /cvs/new.json
+  def new
+    @cv = Cv.new
+
+    respond_to do |format|
+      format.html # new.html.erb
+      format.json { render :json => @cv }
+    end
+  end
+
+  # GET /cvs/1/edit
+  def edit
+    @cv = Cv.find(params[:id])
+  end
+
+  # POST /cvs
+  # POST /cvs.json
+  def create
+    @cv = Cv.new(params[:cv])
+
+    respond_to do |format|
+      if @cv.save
+        format.html { redirect_to @cv, :notice => 'Cv was successfully created.' }
+        format.json { render :json => @cv, :status => :created, :location => @cv }
+      else
+        format.html { render :action => "new" }
+        format.json { render :json => @cv.errors, :status => :unprocessable_entity }
+      end
+    end
+  end
+
+  # PUT /cvs/1
+  # PUT /cvs/1.json
+  def update
+    @cv = Cv.find(params[:id])
+
+    respond_to do |format|
+      if @cv.update_attributes(params[:cv])
+        format.html { redirect_to @cv, :notice => 'Cv was successfully updated.' }
+        format.json { head :no_content }
+      else
+        format.html { render :action => "edit" }
+        format.json { render :json => @cv.errors, :status => :unprocessable_entity }
+      end
+    end
+  end
+
+  # DELETE /cvs/1
+  # DELETE /cvs/1.json
+  def destroy
+    @cv = Cv.find(params[:id])
+    @cv.destroy
+
+    respond_to do |format|
+      format.html { redirect_to cvs_url }
+      format.json { head :no_content }
+    end
+  end
+end

data/lib/rails/generators/rorchado/templates/controllers/cv_controller.rb~

@@ -0,0 +1,83 @@
+class CvsController < ApplicationController
+  # GET /cvs
+  # GET /cvs.json
+  def index
+    @cvs = Cv.all
+
+    respond_to do |format|
+      format.html # index.html.erb
+      format.json { render :json => @cvs }
+    end
+  end
+
+  # GET /cvs/1
+  # GET /cvs/1.json
+  def show
+    @cv = Cv.find(params[:id])
+
+    respond_to do |format|
+      format.html # show.html.erb
+      format.json { render :json => @cv }
+    end
+  end
+
+  # GET /cvs/new
+  # GET /cvs/new.json
+  def new
+    @cv = Cv.new
+
+    respond_to do |format|
+      format.html # new.html.erb
+      format.json { render :json => @cv }
+    end
+  end
+
+  # GET /cvs/1/edit
+  def edit
+    @cv = Cv.find(params[:id])
+  end
+
+  # POST /cvs
+  # POST /cvs.json
+  def create
+    @cv = Cv.new(params[:cv])
+
+    respond_to do |format|
+      if @cv.save
+        format.html { redirect_to @cv, :notice => 'Cv was successfully created.' }
+        format.json { render :json => @cv, :status => :created, :location => @cv }
+      else
+        format.html { render :action => "new" }
+        format.json { render :json => @cv.errors, :status => :unprocessable_entity }
+      end
+    end
+  end
+
+  # PUT /cvs/1
+  # PUT /cvs/1.json
+  def update
+    @cv = Cv.find(params[:id])
+
+    respond_to do |format|
+      if @cv.update_attributes(params[:cv])
+        format.html { redirect_to @cv, :notice => 'Cv was successfully updated.' }
+        format.json { head :no_content }
+      else
+        format.html { render :action => "edit" }
+        format.json { render :json => @cv.errors, :status => :unprocessable_entity }
+      end
+    end
+  end
+
+  # DELETE /cvs/1
+  # DELETE /cvs/1.json
+  def destroy
+    @cv = Cv.find(params[:id])
+    @cv.destroy
+
+    respond_to do |format|
+      format.html { redirect_to cvs_url }
+      format.json { head :no_content }
+    end
+  end
+end