miga-base 0.2.0.6 → 0.2.0.7

data/lib/miga/gui.rb

@@ -1,289 +1,366 @@
-#
 # @package MiGA
-# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license artistic license 2.0
-# @update Jul-11-2015
-#
+# @license Artistic-2.0
 
-require 'miga/project'
-require 'shoes'
-require 'shoes/swt'
+require "miga/common"
+require "miga/project"
+require "shoes"
+require "shoes/swt"
 
 Shoes::Swt.initialize_backend
 
-module MiGA
-   class MiGA
-      @@STATUS = "Initializing MiGA..."
-      def self.STATUS=(status) @@STATUS = status ; end
-      def self.STATUS() @@STATUS; end
-      def self.RESET_STATUS() @@STATUS="MiGA is ready to go!" ; end
-   end
-   class GUI < Shoes
-      url '/', :index
-      url '/project', :project
-      url '/datasets', :datasets
-      url '/dataset-(.*)', :dataset
-      url '/report', :report
-      $miga_path = File.expand_path(File.dirname(__FILE__) + "/../../")
+##
+# Graphical User Interface for MiGA using Shoes.
+class MiGA::GUI < Shoes
+  
+  # Class-level
+  
+  ##
+  # Set system status for MiGA::GUI.
+  def self.status=(status) @@STATUS = status ; end
 
-      def self.init (&block)
-	 Shoes.app title: "MiGA | Microbial Genomes Atlas", width: 750, height: 400, &block
+  ##
+  # System status for MiGA::GUI.
+  def self.status() @@STATUS; end
+  @@STATUS = "Initializing MiGA..."
+
+  ##
+  # Reset the system status for MiGA::GUI.
+  def self.reset_status() @@STATUS="MiGA is ready to go!" ; end
+
+  url "/",		:index
+  url "/project",	:project
+  url "/datasets",	:datasets
+  url "/dataset-(.*)",	:dataset
+  url "/report",	:report
+  $miga_gui_path = File.expand_path("../../../gui", __FILE__)
+
+  ##
+  # Initialize GUI.
+  def self.init (&block)
+    Shoes.app title: "MiGA | Microbial Genomes Atlas",
+      width: 750, height: 400, &block
+  end
+  
+  # =====================[ View : Windows ]
+  
+  ##
+  # Main window.
+  def index
+    header("Microbial Genomes Atlas")
+    stack(margin:40) do
+      menu_bar [:open_project, :new_project, :help]
+      box alpha: 0.0 do
+        para "Welcome to the MiGA GUI. If you use MiGA in your research, ",
+          "please consider citing:\n", MiGA::MiGA.CITATION
       end
-      
-      # =====================[ View : Windows ]
-      # Main window
-      def index
-	 status_bar
-	 stack(margin:40) do
-	    title "Welcome to MiGA!", align:"center"
-	    para ""
-	    flow{ menu_bar [:open_project, :new_project, :help] }
-	    para ""
-	    stack do
-	       image $miga_path + "/gui/img/MiGA.png", width:150, height:50
-	       para ""
-	       para "If you use MiGA in your research, please consider citing:"
-	       para MiGA.CITATION
-	       para ""
-	    end
-	 end
-	 MiGA.RESET_STATUS
-	 keypress do |key|
-	    if [:control_o, "o"].include? key
-	       MiGA.STATUS = "Calling open_project..."
-	       open_project
-	    elsif [:control_n, "n"].include? key
-	       MiGA.STATUS = "Calling new_project..."
-	       new_project
-	    end
-	 end
+    end
+    MiGA::GUI.reset_status
+    status_bar
+  end
+
+  ##
+  # Project window.
+  def project
+    header("» " + $project.name.unmiga_name)
+    stack(margin:40) do
+      menu_bar [:list_datasets, :new_dataset, :progress_report, :help]
+      stack(margin_top:10) do
+        para strong("Path"), ": ", $project.path
+        para strong("Datasets"), ": ", $project.metadata[:datasets].size
+        $project.metadata.each do |k,v|
+          para(strong(k.to_s.capitalize), ": ", v) unless k==:datasets
+        end
       end
+    end
+    MiGA::GUI.reset_status
+  end
 
-      # Project window
-      def project
-	 stack(margin:40) do
-	    title $project.name.unmiga_name, align:"center"
-	    caption $project.path, align:"center"
-	    para ""
-	    stack{ menu_bar [:list_datasets, :new_dataset, :progress_report, :help] }
-	    para ""
-	    stack do
-	       para strong("Datasets"), ": ", $project.metadata[:datasets].size
-	       $project.metadata.each { |k,v| para(strong(k), ": ", v) unless k==:datasets }
-	    end
-	    para ""
-	 end
-	 MiGA.RESET_STATUS
-	 keypress do |key|
-	    if [:control_r, "r"].include? key
-	       MiGA.STATUS = "Calling progress_report..."
-	       progress_report
-	    elsif [:control_d, "d"].include? key
-	       MiGA.STATUS = "Calling list_datasets..."
-	       list_datasets
-	    end
-	 end
+  ##
+  # Datasets list window.
+  def datasets
+    header("» " + $project.name.unmiga_name)
+    stack(margin:40) do
+      para "#{$project.metadata[:datasets].size} datasets:"
+      para ""
+      flow(width: 1.0) do
+        $project.metadata[:datasets].each do |name|
+          stack(width:150) do
+            para "> ", link(name.unmiga_name){ show_dataset(name) }
+          end
+        end
       end
+    end
+    MiGA::GUI.reset_status
+  end
 
-      # Datasets list window
-      def datasets
-	 stack(margin:40) do
-	    title $project.name.unmiga_name, align:"center"
-	    caption $project.path, align:"center"
-	    para ""
-	    stack do
-	       para "Displaying #{$project.metadata[:datasets].size} datasets:"
-	       para ""
-	       $project.metadata[:datasets].each do |name|
-		  para link(name, :click=>"/dataset-#{name}")
-	       end
-	    end
-	    para ""
-	    MiGA.RESET_STATUS
-	 end
+  ##
+  # Dataset details window.
+  def dataset(name)
+    header("» " + $project.name.unmiga_name + " » " + name.unmiga_name)
+    stack(margin:40) do
+      ds = $project.dataset(name)
+      stack do
+        ds.metadata.each { |k,v| para strong(k.to_s.capitalize), ": ", v }
+      end
+      flow(margin_top:10) do
+        w = 40+30*MiGA::Dataset.PREPROCESSING_TASKS.size
+        stack(width:w) do
+          subtitle "Advance"
+          done = graphic_advance(ds)
+          para sprintf("%.1f%% Complete", done*100)
+        end
+        stack(width:-w) do
+          subtitle "Task"
+          $task_name_field = stack { para "" }
+          animate do
+            $task_name_field.clear{ para $task }
+          end
+        end
       end
+      MiGA::GUI.reset_status
+    end
+  end
 
-      # Dataset details window
-      def dataset(name)
-	 stack(margin:40) do
-	    ds = $project.dataset(name)
-	    title ds.name.unmiga_name, align:"center"
-	    caption "A dataset in ", strong(link($project.name.unmiga_name, :click=>"/datasets")), align:"center"
-	    para ""
-	    stack{ ds.metadata.each { |k,v| para strong(k), ": ", v } }
-	    para ""
-	    flow do
-	       w = 40+30*Dataset.PREPROCESSING_TASKS.size
-	       stack(width:w) do
-		  subtitle "Advance"
-		  done = self.graphic_advance(ds)
-		  para sprintf("%.1f%% Complete", done*100)
-	       end
-	       stack(width:-w) do
-		  subtitle "Task"
-		  $task_name_field = stack { para "" }
-		  animate do
-		     $task_name_field.clear{ para $task }
-		  end
-	       end
-	    end
-	    para ""
-	    MiGA.RESET_STATUS
-	 end
+  ##
+  # Project report window.
+  def report
+    header("» " + $project.name.unmiga_name)
+    stack(margin:40) do
+      $done_para = subtitle "Dataset tasks advance: "
+      $done = 0.0
+      w = 40+30*MiGA::Dataset.PREPROCESSING_TASKS.size
+      stack(width:w) do
+        stack(margin_top:10) do
+          $done = $project.datasets.map{ |ds| graphic_advance(ds, 7) }.inject(:+)
+          motion { |_,y| show_report_hover(w, y) }
+          click { show_dataset($dataset) }
+        end
+        $done /= $project.metadata[:datasets].size
+        $done_para.text += sprintf("%.1f%% Complete.", $done*100)
       end
+      $task_ds_box = stack(width:-w)
+      stack(margin_top:10) do
+        subtitle "Project-wide tasks:"
+        tasks = MiGA::Project.DISTANCE_TASKS
+        tasks += MiGA::Project.INCLADE_TASK if $project.metadata[:type]==:clade
+        tasks.each do |t|
+          para strong(t), ": ",
+            ($project.add_result(t, false).nil? ? "Pending" : "Done")
+        end
+      end if $done==1.0
+    end
+  end
+
+  private
+    
+    ##
+    # The MiGA GUI's blue.
+    def miga_blue(alpha=1.0)
+      rgb(0,121,166,alpha)
+    end
 
-      # Project report window
-      def report
-	 stack(margin:40) do
-	    title $project.name.unmiga_name, align:"center"
-	    $done = 0.0
-	    $me = self
-	    flow do
-	       para ""
-	       w = 40+30*Dataset.PREPROCESSING_TASKS.size
-	       stack(width:w) do
-		  para ""
-		  subtitle "Dataset tasks advance:"
-		  caption link("toggle"){ $adv_logo.toggle }
-		  para ""
-		  $adv_logo = stack do
-		     $project.each_dataset do |ds|
-			$done += $me.graphic_advance(ds, 1)
-		     end
-		     motion do |x,y|
-			unless $task.nil?
-			   $task_ds_box.clear do
-			      subtitle "Task"
-			      para $task
-			      subtitle "Dataset"
-			      para $dataset
-			   end
-			   $task_ds_box.show
-			   $task_ds_box.move(w,y-150)
-			end
-		     end
-		     click do
-			GUI.init{ visit "/dataset-#{$dataset}" } unless $dataset.nil?
-		     end
-		     leave do
-			$task = nil
-			$dataset = nil
-			$task_ds_box.hide
-		     end
-		  end
-		  $done /= $project.metadata[:datasets].size
-		  para sprintf("%.1f%% Complete", $done*100)
-	       end
-	       $task_ds_box = stack(width:-w)
-	    end
-	    if $done==1.0
-	       para ""
-	       stack do
-		  subtitle "Project-wide tasks:"
-		  Project.DISTANCE_TASKS.each { |t| para strong(t), ": ", ($project.add_result(t).nil? ? "Pending" : "Done") }
-		  if $project.metadata[:type]==:clade
-		     Project.INCLADE_TASKS.each { |t| para strong(t), ": ", ($project.add_result(t).nil? ? "Pending" : "Done") }
-		  end
-	       end
-	    end
-	    para ""
-	    MiGA.RESET_STATUS
-	 end
+    ##
+    # The MIGA GUI's red.
+    def miga_red(alpha=1.0)
+      rgb(179,0,3,alpha)
+    end  
+
+    # =====================[ View : Elements ]
+    
+    ##
+    # Header in all windows
+    def header(msg="")
+      # workaround to shoes/shoes4#1212:
+      $clicky ||= []
+      $clicky.each{ |i| i.hide }
+      $clicky = []
+      # Keyboard support
+      key_shortcuts = {
+        :control_o => :open_project,    :super_o => :open_project,
+        :control_n => :new_project,     :super_n => :new_project,
+        :control_l => :list_datasets,   :super_l => :list_datasets,
+        :control_r => :progress_report, :super_r => :progress_report
+      }
+      keypress do |key|
+        funct = key_shortcuts[key]
+        send(funct) unless funct.nil?
       end
+      # Graphical header
+      flow(margin:[40,10,40,0]) do
+        image $miga_gui_path + "/img/MiGA-sm.png", width: 120, height: 50
+        title msg, margin_top: 5, margin_left: 5
+      end
+    end
+
+    ##
+    # General-purpose box
+    def box(opts={}, &blk)
+      flow(margin_bottom:5) do
+        opts[:alpha] ||= 0.2
+        opts[:side_line] ||= miga_blue
+        opts[:background] ||= miga_blue(opts[:alpha])
+        stack(width: 5, height: 1.0) do
+          background opts[:side_line]
+        end unless opts[:right]
+        stack(width: -5) do
+          background opts[:background]
+          stack{ background rgb(0,0,0,1.0) } # workaround to shoes/shoes4#1190
+          s = stack(margin:5, &blk)
+          unless opts[:click].nil?
+            s.click{ visit opts[:click] }
+          end
+        end
+        stack(width: 5, height: 1.0) do
+          background opts[:side_line]
+        end if opts[:right]
+      end
+    end
+    
+    ##
+    # Menu bar.
+    def menu_bar actions
+      box do
+        flow do
+          img = {
+            open_project: "iconmonstr-archive-5-icon-40",
+            new_project: "iconmonstr-plus-5-icon-40",
+            list_datasets: "iconmonstr-note-10-icon-40",
+            new_dataset: "iconmonstr-note-25-icon-40",
+            progress_report: "iconmonstr-bar-chart-2-icon-40",
+            help: "iconmonstr-help-3-icon-40"}
+          actions.each do |k|
+            flow(margin:0, width:200) do
+              image $miga_gui_path + "/img/#{img[k]}.png", margin: 2
+              button(k.to_s.unmiga_name.capitalize, top:5){ send(k) }
+            end
+          end
+        end
+      end
+    end
       
-      # =====================[ View : Elements ]
-      # Menu bar
-      def menu_bar actions
-	 flow do
-	    b = {
-	       open_project:["Open project", "iconmonstr-archive-5-icon-256"],
-	       new_project:["New project","iconmonstr-plus-5-icon-256"],
-	       list_datasets:["List datasets", "iconmonstr-note-10-icon-256"],
-	       new_dataset:["New dataset", "iconmonstr-note-25-icon-256"],
-	       progress_report:["Progress report", "iconmonstr-bar-chart-2-icon-256"],
-	       help:["Help", "iconmonstr-help-3-icon-256"]
-	    }
-	    actions.each do |k|
-	       v = b[k]
-	       flow(margin:0, width:200) do
-		  image $miga_path + "/gui/img/#{v[1]}.png", width:40, height:40, margin:2
-		  button v[0], top:5 do
-		     MiGA.STATUS = "Calling #{k}..."
-		     eval k.to_s
-		  end
-	       end
-	    end
-	 end
-      end # menu_bar
-      
-      # Status bar
-      def status_bar
-	 stack(bottom:0) do
-	    flow bottom:0, height:20, margin:0 do
-	       background "#CCC"
-	       stack(width:50)
-	       $status_cont = stack(width:-300, height:1.0)
-	       every do |i|
-		  $status_cont.clear { inscription MiGA.STATUS, margin:5 }
-	       end
-	       stack(width:250, height:1.0) do
-		  inscription MiGA.LONG_VERSION, align:"right", margin:5
-	       end
-	    end
-	    image $miga_path + "/gui/img/MiGA-sq.png", left:0, bottom:0, width:30, height:32
-	 end
-      end # status_bar
+    ##
+    # Status bar.
+    def status_bar
+      stack(bottom:0) do
+        flow bottom:0, height:20, margin:0 do
+          background "#CCC"
+          $status_cont = stack(width:-300, height:1.0, margin_left:45)
+          every do
+            $status_cont.clear { inscription MiGA::GUI.status, margin:5 }
+          end
+          stack(width:250, height:1.0, right: 5) do
+            inscription MiGA::MiGA.LONG_VERSION, align:"right", margin:5
+          end
+        end
+        image "#{$miga_gui_path}/img/MiGA-sq.png",
+          left:10, bottom:5, width:30, height:32
+      end
+    end
 
-      def graphic_advance(ds, h=10)
-	 ds_adv = ds.profile_advance
-	 flow(width:30*Dataset.PREPROCESSING_TASKS.size) do
-	    nostroke
-	    i = 0
-	    col = ["#CCC", rgb(119,130,61), rgb(160,41,50)]
-	    ds_adv.each do |j|
-	       stack(width:28,margin:0,top:0,left:i*30,height:h) do
-		  background col[j]
-		  t = Dataset.PREPROCESSING_TASKS[i]
-		  hover do
-		     $task = t
-		     $dataset = ds.name.unmiga_name
-		  end
-	       end
-	       i += 1
-	    end
-	    nofill
-	 end
-	 return 0.0 if ds_adv.count{|i| i>0} <= 1
-	 (ds_adv.count{|i| i==1}.to_f - 1.0)/(ds_adv.count{|i| i>0}.to_f - 1.0)
-      end # graphic_advance
+    ##
+    # Display processing status of a dataset as a horizontal bar, as reported
+    # by MiGA::Dataset#profile_advance.
+    def graphic_advance(ds, h=10)
+      ds_adv = ds.profile_advance
+      flow(width:30*MiGA::Dataset.PREPROCESSING_TASKS.size) do
+        nostroke
+        col = ["#CCC", rgb(119,130,61), rgb(160,41,50)]
+        ds_adv.each_index do |i|
+          stack(width:28,margin:0,top:0,left:i*30,height:h) do
+            background col[ ds_adv[i] ]
+            t = MiGA::Dataset.PREPROCESSING_TASKS[i]
+            hover do
+              $task = t
+              $dataset = ds.name.unmiga_name
+            end
+            leave do
+              $task = nil
+              $dataset = nil
+              $task_ds_box.hide unless $task_ds_box.nil?
+            end
+          end
+        end
+        nofill
+      end
+      return 0.0 if ds_adv.count{|i| i>0} <= 1
+      (ds_adv.count{|i| i==1}.to_f - 1.0)/(ds_adv.count{|i| i>0}.to_f - 1.0)
+    end
 
-      # =====================[ Controller : Projects ]
-      def open_project
-	 GUI.init do
-	    folder = ask_open_folder
-	    if folder.nil? or not Project.exist? folder
-	       alert "Cannot find a MiGA project at #{folder}!" unless folder.nil?
-	       return
-	    else
-	       $project = Project.new folder
-	       visit '/project'
-	    end
-	 end
-      end # open_project
-      def new_project
-	 GUI.init do
-	    folder = ask_save_folder
-	    if folder.nil? or Project.exist? folder
-	       alert "Cannot overwrite existent MiGA project at #{folder}!" unless folder.nil?
-	       return
-	    else
-	       $project = Project.new folder
-	       visit "/project"
-	    end
-	 end
-      end # new_project
-      def list_datasets ; GUI.init{ visit "/datasets" } ; end # list_datasets
-      def progress_report ; GUI.init{ visit "/report" } ; end # progress_report
-   end
-end
+    ##
+    # Show floating window with additional information on report cells.
+    def show_report_hover(w, y)
+      unless $task.nil?
+        $task_ds_box.clear do
+          para strong("Task: "), $task, "\n", strong("Dataset: "), $dataset
+        end
+        $task_ds_box.show
+        $task_ds_box.move(w-20, y-115)
+      end
+    end
+
+    # =====================[ Controller : Projects ]
+
+    ##
+    # Load a project.
+    def open_project
+      open_window("Opening project...") do
+        folder = ask_open_folder
+        if folder.nil? or not MiGA::Project.exist?(folder)
+          alert "Cannot find a MiGA project at #{folder}!" unless folder.nil?
+        else
+          $project = MiGA::Project.new(folder)
+          visit "/project"
+        end
+      end
+    end
+    
+    ##
+    # Create a project.
+    def new_project
+      open_window("Creating project...") do
+        if MiGA::MiGA.initialized?
+          folder = ask_save_folder
+          if folder.nil? or MiGA::Project.exist?(folder)
+            alert "Cannot overwrite existent MiGA project at #{folder}!" unless
+              folder.nil?
+          else
+            $project = MiGA::Project.new(folder)
+            visit "/project"
+          end
+        else
+          # FIXME Add a way to initialize MiGA from the GUI
+          alert "MiGA is currently uninitialized, no projects can be created."
+        end
+      end
+    end
+    
+    ##
+    # Open a window on #datasets.
+    def list_datasets
+      open_window("Listing all datasets..."){
+        visit "/datasets" } unless $project.nil?
+    end
+
+    ##
+    # Open a window on #dataset +name+.
+    def show_dataset(name)
+      open_window("Showing dataset details..."){
+        visit "/dataset-#{name}" } unless name.nil?
+    end
 
+    ##
+    # Open a window on #report.
+    def progress_report
+      open_window("Creating progress report..."){
+        visit "/report" } unless $project.nil?
+    end
+
+    ##
+    # Open a window sending +msg+ to the status, the yields +blk+.
+    def open_window(msg, &blk)
+      MiGA::GUI.status = msg
+      MiGA::GUI.init(&blk)
+      MiGA::GUI.reset_status
+    end
+
+end