nera 0.4.0 → 0.5.0

data/History.txt

@@ -1,3 +1,10 @@
+== 0.5.0
+* 1 major enhancement:
+  * Routines to remove, dump, and import simulators are implemented.
+    Dumped data can be imported to another database.
+* 2 bug fixes:
+
+
 == 0.4.0
 * 1 major enhancement:
   * A new format is adopted in parameters_table.

data/lib/nera/nera_cui.rb

@@ -74,7 +74,7 @@ HEADER
         r[:name]
       end
       names.unshift("go to Jobs layer")
-      names += ["show logs", "exit"]
+      names += ["show logs", "remove a simulator", "dump a simulator", "import a simulator", "exit"]
       selected = 0
       Dir.chdir( slc.path_to_sim_layer) {
         selected = Dialog::select_one_or_return_string( names, "Select a simulator.")
@@ -83,12 +83,46 @@ HEADER
           return :simulator_layer
         end
       }
-      if names[selected] == "go to Jobs layer"
+      case names[selected]
+      when "go to Jobs layer"
         return :job_layer
-      elsif names[selected] == "show logs"
+      when "show logs"
         system "less #{slc.path_to_log_file}"
         return :simulator_layer
-      elsif names[selected] == "exit"
+      when "remove a simulator"
+        sim_names = ["Cancel"] + slc.list.map do |r| r[:name] end
+        selected = Dialog::select_one( sim_names, "Select a simulator to be removed.")
+        return :simulator_layer if selected == 0
+        flag = slc.remove_simulator( sim_names[selected])
+        if flag
+          Dialog::message("Simulator \"#{sim_names[selected]}\" have been successfully removed from the database.")
+        else
+          Dialog::message("Failed to remove the simulator \"#{sim_names[selected]}\". There are uncompleted jobs.")
+        end
+        return :simulator_layer
+      when "dump a simulator"
+        sim_names = ["Cancel"] + slc.list.map do |r| r[:name] end
+        selected = Dialog::select_one( sim_names, "Select a simulator to be dumped.")
+        return :simulator_layer if selected == 0
+        flag = slc.dump_simulator( sim_names[selected])
+        if flag
+          Dialog::message("Data for the simulator \"#{sim_names[selected]}\" have been successfully dumped.")
+        else
+          Dialog::message("Failed to dump the simulator \"#{sim_names[selected]}\". There are uncompleted jobs.")
+        end
+        return :simulator_layer
+      when "import a simulator"
+        list = ["Cancel"] + slc.importable_simulators
+        selected = Dialog::select_one( list, "Select a simulator to be dumped.")
+        return :simulator_layer if selected == 0
+        flag = slc.import_simulator( list[selected])
+        if flag
+          Dialog::message("Simulator \"#{list[selected]}\" have been successfully imported.")
+        else
+          Dialog::message("Failed to import the simulator \"#{sim_names[selected]}\".")
+        end
+        return :simulator_layer
+      when "exit"
         return :exit
       else
         @simulator_class = names[selected]

data/lib/nera/nera_simulator.rb

@@ -21,6 +21,18 @@ module NERA
     def self.inherited_simulators
       return @@inherited
     end
+
+    def self.remove_simulator( sim_class)
+      raise ArgumentError unless sim_class.is_a?(Class)
+      @@inherited -= [ sim_class ]
+    end
+
+    def self.add_simulator( sim_class)
+      raise ArgumentError unless sim_class.is_a?(Class)
+      @@inherited << sim_class
+      @@inherited.uniq!
+    end
+
   end
   
 end

data/lib/nera/nera_simulator_layer_controller.rb

@@ -1,6 +1,8 @@
 require 'nera_db_folders'
 require 'nera_simulator_records'
 require 'nera_parameter_records'
+require 'nera_job_records'
+require 'pathname'
 
 module NERA
   
@@ -21,22 +23,24 @@ module NERA
 
       NERA::Simulator.inherited_simulators.each do |sim|
         next if list.find do |rec| rec[:name] == sim.to_s end
+        mapped = NERA::ParameterRecords::ATTRIBUTES_PART.map do |att| att[0] end
         found = sim::Parameters.find do |p|
-            p[0] == :in_trashbox? or p[0] == :created_at or p[0] == :updated_at
+          mapped.include?(p[0])
+          # p[0] == :in_trashbox? or p[0] == :created_at or p[0] == :updated_at
         end
         next if found
         register_a_simulator( sim)
       end
     end
-
+    
     def list
       @sim_records.list
     end
-
+    
     def path_to_sim_layer
       @db_folders.path_to_simulator_layer
     end
-
+    
     def get_class_by_name( sim_name)
       raise ArgumentError unless sim_name.is_a?(String)
       found = NERA::Simulator.inherited_simulators.find do |sim|
@@ -68,6 +72,172 @@ module NERA
       @db_folders.path_to_log_file
     end
 
+    def remove_simulator( sim_name)
+      flag = true
+      sim_class = get_class_by_name( sim_name)
+      return nil unless sim_class
+      sim_id = (list.find do |rec| rec[:name] == sim_name end)[:id]
+      return nil unless sim_id
+      job_records = NERA::JobRecords.new( @db_folders.path_to_jobs_table )
+      job_records.transaction {
+        @sim_records.transaction {
+          # check uncompleted jobs
+          found = job_records.list_all.find do |rec| rec[:simulator] == sim_name end
+          if found
+            flag = nil
+            return
+          end
+          # destroy the record
+          f = @sim_records.destroy( sim_id)
+          raise "Couldn't destroy the record #{sim_id} in simulators table" unless f
+          # compression
+          path1 = @db_folders.path_to_parameter_layer( sim_class)
+          path2 = File.dirname( @db_folders.path_to_parameters_table( sim_class) )
+          path3 = File.join( @db_folders.path_to_simulator_layer, "Simulator_classes", "#{sim_name}.rb")
+          raise "Couldn't find #{path1}" unless File.directory?(path1)
+          raise "Couldn't find #{path2}" unless File.directory?(path2)
+          raise "Couldn't find #{path3}" unless File.exist?(path3)
+          base_path = Pathname.new( @db_folders.path_to_simulator_layer ).realpath
+          path1 = Pathname.new( path1).realpath.relative_path_from( base_path).to_s
+          path2 = Pathname.new( path2).realpath.relative_path_from( base_path).to_s
+          path3 = Pathname.new( path3).realpath.relative_path_from( base_path).to_s
+          Dir.chdir(base_path) {
+            tar_file = "#{sim_id}_#{sim_name}.tar"
+            cmd = "tar cf #{tar_file} #{path1} #{path2} #{path3}"
+            system cmd
+            raise "command \"#{cmd}\" failed." unless $? == 0
+            bz2_file = tar_file + '.bz2'
+            FileUtils.rm( bz2_file) if File.exist?( bz2_file )
+            cmd = "bzip2 #{tar_file}"
+            system cmd
+            raise "command \"#{cmd}\" failed." unless $? == 0
+            FileUtils.rm_r( path1)
+            FileUtils.rm_r( path2)
+            FileUtils.rm( path3)
+          }
+          # remove inherited classes
+          NERA::Simulator.remove_simulator( sim_class)
+          # keep a log
+          @db_folders.logger.info(self.class.to_s) {
+            "removed the simulator (#{sim_class.to_s})"
+          }
+        }
+      }
+      return flag
+    end
+
+    def dump_simulator( sim_name, job_records = nil)
+      flag = true
+      sim_class = get_class_by_name( sim_name)
+      return nil unless sim_class
+      sim_id = (list.find do |rec| rec[:name] == sim_name end)[:id]
+      return nil unless sim_id
+      job_records = NERA::JobRecords.new( @db_folders.path_to_jobs_table ) unless job_records.is_a?(NERA::JobRecords)
+      job_records.transaction {
+        @sim_records.transaction {
+          # check uncompleted jobs
+          found = job_records.list_all.find do |rec| rec[:simulator] == sim_name end
+          if found
+            flag = nil
+            return
+          end
+          # destroy the record
+          # f = @sim_records.destroy( sim_id)
+          # raise "Couldn't destroy the record #{sim_id} in simulators table" unless f
+          # compression
+          path1 = @db_folders.path_to_parameter_layer( sim_class)
+          path2 = File.dirname( @db_folders.path_to_parameters_table( sim_class) )
+          path3 = File.join( @db_folders.path_to_simulator_layer, "Simulator_classes", "#{sim_name}.rb")
+          raise "Couldn't find #{path1}" unless File.directory?(path1)
+          raise "Couldn't find #{path2}" unless File.directory?(path2)
+          raise "Couldn't find #{path3}" unless File.exist?(path3)
+          base_path = Pathname.new( @db_folders.path_to_simulator_layer ).realpath
+          path1 = Pathname.new( path1).realpath.relative_path_from( base_path).to_s
+          path2 = Pathname.new( path2).realpath.relative_path_from( base_path).to_s
+          path3 = Pathname.new( path3).realpath.relative_path_from( base_path).to_s
+          Dir.chdir(base_path) {
+            tar_file = "#{sim_id}_#{sim_name}.tar"
+            cmd = "tar cf #{tar_file} #{path1} #{path2} #{path3}"
+            system cmd
+            raise "command \"#{cmd}\" failed." unless $? == 0
+            bz2_file = tar_file + '.bz2'
+            FileUtils.rm( bz2_file) if File.exist?( bz2_file )
+            cmd = "bzip2 #{tar_file}"
+            system cmd
+            raise "command \"#{cmd}\" failed." unless $? == 0
+            # FileUtils.rm_r( path1)
+            # FileUtils.rm_r( path2)
+            # FileUtils.rm( path3)
+          }
+          # remove inherited classes
+          # NERA::Simulator.remove_simulator( sim_class)
+          # keep a log
+          @db_folders.logger.info(self.class.to_s) {
+            "dumped the simulator (#{sim_class.to_s})"
+          }
+        }
+      }
+      return flag
+    end
+
+    
+    def importable_simulators
+      sim_names = @sim_records.list.map do |rec| rec[:name] end
+
+      Dir.chdir( @db_folders.path_to_simulator_layer ) {
+        candidates = Dir.glob( "[0-9]*_[A-Z]*.tar.bz2").find_all do |file|
+          file =~ /^([0-9]+)_([A-Z]\w*)\.tar\.bz2/ and !(sim_names.include?($2))
+        end
+        # found = candidates.find_all do |file|
+        #   file =~ /^([0-9]+)_([A-Z]\w*)\.tar\.bz2/ and
+        #     !(@sim_records.list.include? do |rec| rec[:name] == $2 end)
+        # end
+        return candidates
+      }
+    end
+    
+    def import_simulator( sim_file)
+      flag = true
+      return nil unless sim_file =~ /^([0-9]+)_([A-Z]\w*)\.tar\.bz2/
+      return nil unless File.exist?( File.join(@db_folders.path_to_simulator_layer,sim_file) )
+      sim_name = $2
+      job_records = NERA::JobRecords.new( @db_folders.path_to_jobs_table )
+
+      job_records.transaction {
+        @sim_records.transaction {
+          # check name overlap
+          if @sim_records.list.find do |rec| rec[:name] == sim_name end
+            flag = nil
+            return
+          end
+          raise "must not happen" if File.directory?( File.join( @db_folders.path_to_simulator_layer, sim_name ) )
+          raise "must not happen" if File.directory?( File.join( File.dirname(@db_folders.path_to_simulators_table), sim_name) )
+          raise "must not happen" if File.exist?( File.join( @db_folders.path_to_simulator_layer, "Simulator_classes", "#{sim_name}.rb") )
+          # decompress the file
+          Dir.chdir(@db_folders.path_to_simulator_layer) {
+            # cmd = "bunzip2 #{sim_file}"
+            # system cmd
+            # raise "command \"#{cmd}\" failed." unless $? == 0
+            tar_file = sim_file.sub(/\.bz2$/,'')
+            cmd = "tar xjf #{sim_file}"
+            system cmd
+            raise "command \"#{cmd}\" failed." unless $? == 0
+          }
+          # load simulator definition
+          require File.join( @db_folders.path_to_simulator_layer, "Simulator_classes", "#{sim_name}.rb")
+          sim_class = sim_name.split(/::/).inject(Object) {|c,name| c.const_get(name) }
+          raise "invalid definition of simulator class #{sim_name}" unless sim_class.is_a?(Class)
+          NERA::Simulator.add_simulator( sim_class)
+          flag = @sim_records.add( sim_class)
+          # keep a log
+          @db_folders.logger.info(self.class.to_s) {
+            "imported the simulator (#{sim_class.to_s})"
+          }
+        }
+      }
+      return flag
+    end
+    
   end
 
 end

data/lib/nera.rb

@@ -22,5 +22,5 @@ require 'nera_simulator_records'
 require 'nera_remote_connector'
 
 module NERA
-  VERSION = '0.4.0'
+  VERSION = '0.5.0'
 end

data/test/test_nera_simulator.rb

@@ -23,4 +23,24 @@ class TC_NERA_SIMULATOR < Test::Unit::TestCase
     end
     assert(a)
   end
+
+  def test_remove_simulator
+    sim1 = NERA::Simulator.inherited_simulators
+    NERA::Simulator.remove_simulator( Ising)
+    sim2 = NERA::Simulator.inherited_simulators
+    assert_equal( [Heisenberg, XY], sim2)
+    assert_raise(ArgumentError) {
+      NERA::Simulator.remove_simulator( "Ising")
+    }
+  end
+
+  def test_add_simulator
+    NERA::Simulator.remove_simulator( Ising)
+    NERA::Simulator.add_simulator( Ising)
+    sim2 = NERA::Simulator.inherited_simulators
+    assert_equal( [Heisenberg, XY, Ising], sim2)
+    assert_raise(ArgumentError) {
+      NERA::Simulator.add_simulator( "Ising")
+    }
+  end    
 end

data/test/test_nera_simulator_layer_controller.rb

@@ -8,9 +8,13 @@ class TC_NERA_SIM_LAYER_CONTROLLER < Test::Unit::TestCase
     FileUtils.mkdir(@testdir)
     FileUtils.chdir(@testdir)
     @db_folder = "nera_db"
+    NERA::Simulator.add_simulator( Ising)
+    NERA::Simulator.add_simulator( Heisenberg)
     NERA::DbFolders.create_db( @db_folder)
     @dbf = NERA::DbFolders.new( @db_folder)
     @slc = NERA::SimulatorLayerController.new( @db_folder)
+    FileUtils.touch(File.join(@db_folder,"Simulator_classes","Ising.rb") )
+    FileUtils.touch(File.join(@db_folder,"Simulator_classes","Heisenberg.rb") )
   end
 
   def teardown
@@ -63,6 +67,112 @@ class TC_NERA_SIM_LAYER_CONTROLLER < Test::Unit::TestCase
   def test_path_to_log_file
     path = @slc.path_to_log_file
     assert_equal( @db_folder + "/Tables/logfile.txt", path)
+  end
+
+  def test_remove_simulator
+    assert( File.exist?( File.join(@db_folder,"Simulator_classes","Ising.rb") ) )
+    assert_nil( @slc.remove_simulator( "unknown_simulator") )
+
+    # create a job
+    plc = NERA::ParameterLayerController.new( @db_folder, "Ising")
+    pid = plc.create_a_new_parameter_set( {} )
+    rlc = NERA::RunLayerController.new( @db_folder, "Ising", pid)
+    jid = rlc.create_jobs( 1)
+    assert_nil( @slc.remove_simulator( "Ising") )
+    assert( @slc.list.find do |rec| rec[:name] == "Ising" end )
+    assert( rlc.cancel_jobs( jid ) )
+    
+    # check raise
+    FileUtils.rm( File.join(@db_folder,"Simulator_classes","Ising.rb") )
+    assert_raise(RuntimeError) {
+      @slc.remove_simulator("Ising")
+    }
+    assert( @slc.list.find do |rec| rec[:name] == "Ising" end )
+    FileUtils.touch( File.join(@db_folder,"Simulator_classes","Ising.rb") )
+            
+    # remove a simulator
+    assert( @slc.remove_simulator( "Ising") )
+    assert( !File.directory?( File.join(@db_folder,"Ising") ) )
+    assert( !File.directory?( File.join(@db_folder,"Tables","Ising") ) )
+    assert( !File.exist?( File.join(@db_folder,"Simulator_classes","Ising.rb") ) )
+    assert( Dir.glob("#{@db_folder}/[1-9]_Ising.tar.bz2").size > 0 )
+    assert_nil( @slc.list.find do |rec| rec[:name] == "Ising" end )
+    assert_nil( @slc.get_class_by_name("Ising") )
+
+    # dump before remove
+    assert( @slc.dump_simulator("Heisenberg") )
+    assert( @slc.remove_simulator("Heisenberg") )
+  end
 
+  def test_dump_simulator
+    assert_nil( @slc.dump_simulator( "unknown_simulator") )
+    
+    # create a job
+    plc = NERA::ParameterLayerController.new( @db_folder, "Ising")
+    pid = plc.create_a_new_parameter_set( {} )
+    rlc = NERA::RunLayerController.new( @db_folder, "Ising", pid)
+    jid = rlc.create_jobs( 1)
+    assert_nil( @slc.dump_simulator( "Ising") )
+    assert_equal( 0, Dir.glob("#{@db_folder}/[1-9]_Ising.tar.bz2").size)
+    assert( rlc.cancel_jobs( jid ) )
+    
+    # check raise
+    FileUtils.rm( File.join(@db_folder,"Simulator_classes","Ising.rb") )
+    assert_raise(RuntimeError) {
+      @slc.dump_simulator("Ising")
+    }
+    assert( @slc.list.find do |rec| rec[:name] == "Ising" end )
+    FileUtils.touch( File.join(@db_folder,"Simulator_classes","Ising.rb") )
+    
+    # remove a simulator
+    assert( @slc.dump_simulator( "Ising") )
+    assert( File.directory?( File.join(@db_folder,"Ising") ) )
+    assert( File.directory?( File.join(@db_folder,"Tables","Ising") ) )
+    assert( File.exist?( File.join(@db_folder,"Simulator_classes","Ising.rb") ) )
+    assert( Dir.glob("#{@db_folder}/[1-9]_Ising.tar.bz2").size > 0 )
+    assert( @slc.list.find do |rec| rec[:name] == "Ising" end )
+    assert( @slc.get_class_by_name("Ising") )
+    # dump again
+    assert( @slc.dump_simulator( "Ising") )
+  end
+  
+  def test_importable_simulators
+    assert_equal( [], @slc.importable_simulators)
+    @slc.remove_simulator( "Ising")
+    list = @slc.importable_simulators
+    assert_equal( 1, list.size )
+    assert_match( /^[1-2]_Ising\.tar\.bz2$/, list[0] )
+    @slc.remove_simulator( "Heisenberg")
+    list = @slc.importable_simulators
+    assert_equal( 2, list.size )
+    assert( list.find do |l| l =~ /^[1-2]_Ising\.tar\.bz2$/ end )
+    assert( list.find do |l| l =~ /^[1-2]_Heisenberg\.tar\.bz2$/ end) 
+    found = list.find do |l| l =~ /^[1-2]_Ising\.tar\.bz2$/ end
+    @slc.import_simulator( found)
+    list = @slc.importable_simulators
+    assert_equal( 1, list.size )
+    assert_match( /^[1-2]_Heisenberg\.tar\.bz2$/, list[0] )
+
+    FileUtils.touch( File.join(@db_folder,"3_Ising.tar.bz2") )
+    list2 = @slc.importable_simulators
+    assert_equal( list2, list)
+    FileUtils.rm( File.join(@db_folder,"3_Ising.tar.bz2") )
+  end
+  
+  def test_import_simulator
+    assert_nil( @slc.import_simulator("1_Unknown.tar.bz2") )
+    @slc.remove_simulator("Ising")
+    fname = @slc.importable_simulators[0]
+    assert( @slc.import_simulator(fname) )
+    assert( File.directory?( File.join(@db_folder,"Ising") ) )
+    assert( File.exist?( File.join(@db_folder,"Ising","parameters.yml") ) )
+    assert( File.directory?( File.join(@db_folder,"Tables","Ising") ) )
+    assert( File.exist?( File.join(@db_folder,"Tables","Ising","parameters.pstore") ) )
+    assert( File.exist?( File.join(@db_folder,"Simulator_classes","Ising.rb") ) )
+    assert( Dir.glob( File.join(@db_folder,"[1-9]_Ising.tar.bz2")).size > 0 )
+    found = @slc.list.find do |rec| rec[:name] == "Ising" end
+    assert_equal( 3, found[:id] )
+    assert_equal( Ising, @slc.get_class_by_name("Ising") )
   end
+  
 end

data/website/index.html

@@ -34,7 +34,7 @@
     <div class="sidebar">
       <div id="version" class="clickable" onclick='document.location = "http://rubyforge.org/projects/nera"; return false'>
         <p>Get Version</p>
-        <a href="http://rubyforge.org/projects/nera" class="numbers">0.4.0</a>
+        <a href="http://rubyforge.org/projects/nera" class="numbers">0.5.0</a>
       </div>
     </div>
     <h2>What</h2>
@@ -59,14 +59,14 @@ Classifying the result data into folders, keeping a note of what we have done, c
 <p>The trunk repository is <code>svn://rubyforge.org/var/svn/nera/trunk</code> for anonymous access.</p>
 <h3>Build and test instructions</h3>
 <pre>cd nera
-rake test
+ruby test/runner.rb
 rake install_gem</pre>
 <h2>License</h2>
 <p>This code is free to use under the terms of the <span class="caps">GPL</span> license.</p>
 <h2>Contact</h2>
 <p>Comments are welcome. Send an email to <a href="mailto:murase_at_serow.t.u-tokyo.ac.jp">Yohsuke Murase</a></p>
     <p class="coda">
-      <a href="murase@serow.t.u-tokyo.ac.jp">Yohsuke Murase</a>, 26th November 2009<br>
+      <a href="murase@serow.t.u-tokyo.ac.jp">Yohsuke Murase</a>, 28th November 2009<br>
       Theme extended from <a href="http://rb2js.rubyforge.org/">Paul Battley</a>
     </p>
 </div>

data/website/index.txt

@@ -41,7 +41,7 @@ The trunk repository is <code>svn://rubyforge.org/var/svn/nera/trunk</code> for
 h3. Build and test instructions
 
 <pre>cd nera
-rake test
+ruby test/runner.rb
 rake install_gem</pre>
 
 

data/website/temporary/temp.html

@@ -34,7 +34,7 @@
     <div class="sidebar">
       <div id="version" class="clickable" onclick='document.location = "http://rubyforge.org/projects/nera"; return false'>
         <p>Get Version</p>
-        <a href="http://rubyforge.org/projects/nera" class="numbers">0.4.0</a>
+        <a href="http://rubyforge.org/projects/nera" class="numbers">0.5.0</a>
       </div>
     </div>
     <p>The database created by nera is a hierarchical database which consists of three layers.<br />

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: nera
 version: !ruby/object:Gem::Version 
-  version: 0.4.0
+  version: 0.5.0
 platform: ruby
 authors: 
 - Yohsuke Murase
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-11-26 00:00:00 +09:00
+date: 2009-11-28 00:00:00 +09:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency