comana 0.0.8 → 0.0.9

data/VERSION

@@ -1 +1 @@
-0.0.8
+0.0.9

data/comana.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "comana"
-  s.version = "0.0.8"
+  s.version = "0.0.9"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["ippei94da"]
-  s.date = "2012-05-18"
+  s.date = "2012-05-29"
   s.description = "Comana, COmputation MANAger,\n    is a software to provide a framework of\n    managing scientific computing.\n    Researchers on computing have to check calculation and\n    generate new calculation and execute, repeatedly.\n    The abstract class that this gem provide would help the work.\n  "
   s.email = "ippei94da@gmail.com"
   s.extra_rdoc_files = [

data/lib/comana/machineinfo.rb

@@ -31,5 +31,14 @@ class MachineInfo
     @data[series]
   end
 
+  #def has_info?(host)
+  #  series = host.sub(/\d*$/, "")
+  #  unless @data.has_key?(series)
+  #    raise NoEntryError,
+  #      "#{series}"
+  #  end
+  #  @data[series]
+  #end
+
 end
 

data/lib/comana/queuesubmitter.rb

@@ -4,7 +4,6 @@
 require "fileutils"
 require "comana/computationmanager.rb"
 require "comana/machineinfo.rb"
-require "optparse"
 
 #
 #
@@ -20,61 +19,64 @@ class QueueSubmitter < ComputationManager
   class InvalidArgumentError < Exception; end
 
   # opts is a hash includes data belows:
-  #   :command => command line.
-  #   :cluster => name of cluster.
-  #   :machineinfo => MachineInfo class instance.
-  #   :directory => calculation as ComputationManager subclass.
-  #     Note that this is not directory name, to check to be calculatable.
+  #   "command" => executable command line written in script.
+  #   "cluster" => name of cluster.
+  #   "target" => calculation as ComputationManager subclass.
+  #     Note that this is not target name, to check calculatable.
   def initialize(opts)
-    [:directory, :command, :number,  :cluster, :fileserver].each do |symbol|
-      raise InitializeError, "No #{symbol}"  unless opts.has_key?(symbol)
+    #opts = self.class.correct_options(opts)
+    ["target", "command", "number", "cluster"].each do |symbol|
+      raise InitializeError, "No #{symbol} in argument 'opts'"  unless opts.has_key?(symbol)
     end
 
-    super(opts[:directory].dir)
-    @command    = opts[:command]
-    @cluster    = opts[:cluster]
-    @number     = opts[:number]
-    @fileserver = opts[:fileserver]
+    super(opts["target"].dir)
+
+    @command    = opts["command"]
+    @cluster    = opts["cluster"]
+    @number     = opts["number"]
     @lockdir    = "lock_queuesubmitter"
   end
 
-  def self.parse_options(ary, machineinfo)
-    ## option analysis
-    opts = {}
-    op = OptionParser.new
-    op.on("-c cluster", "--cluster" , "Cluster name."){|v| opts[:cluster] = v }
-    op.on("-n number", "--number", "Indicate node number, or key in ~/.machineinfo."){|v|
-      opts[:number] = v
-    }
-    op.parse!(ary)
-
-    unless ary.size == 1
-      raise InitializeError, "Not one directory indicated: #{ary.join(", ")}."
-    end
-
-    opts[:fileserver] = machineinfo.get_info("fileserver")
-
-    unless opts[:cluster]
-      raise InvalidArgumentError,
-      "-c option not set."
-    end
-
-    # Number of nodes: number, key string, or default value(1).
-    if opts[:number].to_i > 0
-      opts[:number] = opts[:number].to_i 
-    else
-      number = machineinfo.get_info(opts[:cluster])[opts[:number]]
-      if number
-        opts[:number] = number
-      else
-        raise InvalidArgumentError,
-        "No entry '#{opts[:number]}' in machineinfo: #{machineinfo.inspect}."
-      end
-    end
-    opts[:number] ||= 1
-
-    opts
-  end
+  ## Check and correct options given as hash, 'opts', using machineinfo.
+  ## Return hash corrected.
+  ## 'opts' must have keys of
+  ##   "number"
+  ##   "cluster"
+  ##   "target"
+  ## machineinfo is a MachineInfo class instance.
+  #def self.correct_options(opts, machineinfo)
+  #  # option analysis
+  #  ["target", "number", "cluster"].each do |symbol|
+  #    raise InitializeError, "No #{symbol} in argument 'opts'"  unless opts.has_key?(symbol)
+  #  end
+
+
+  #  #unless ary.size == 1
+  #  #  raise InitializeError, "Not one target indicated: #{ary.join(", ")}."
+  #  #end
+
+  #  #unless opts["cluster"]
+  #  #  raise InvalidArgumentError,
+  #  #  "-c option not set."
+  #  #end
+
+  #  ## Number of nodes: number, key string, or default value(1).
+  #  #if opts["number"].to_i > 0
+  #  #  opts["number"] = opts["number"].to_i 
+  #  #else
+  #  #  number = machineinfo.get_info(opts["cluster"])[opts["number"]]
+  #  #  if number
+  #  #    opts["number"] = number
+  #  #  else
+  #  #    raise InvalidArgumentError,
+  #  #    "No entry '#{opts["number"]}' in machineinfo: #{machineinfo.inspect}."
+  #  #  end
+  #  #end
+  #  #opts["number"] ||= 1
+
+
+  #  opts
+  #end
 
   def calculate
     # prologue

data/memo.txt

@@ -4,6 +4,9 @@ Comana don't have information of output files.
 Because it is difficult to define final output and to deal systematically.
 e.g., repeated calculation till convergence.
 
+0.0.9 release
+  Change opts specification in QueueSubmitter; symbol to string
+
 0.0.8 release
   Changed queuesubmitter option. (long name symbol)
   Add prologue and epilogue to QueueSubmitter.

data/spec/queuesubmitter_spec.rb

@@ -15,13 +15,12 @@ end
 #describe QueueSubmitter, "with chars to be escaped" do
 describe QueueSubmitter do
   describe "#initialize" do
-    context "opts not have :directory" do
+    context "opts not have target" do
       opts = {
-        #:directory => "dir_name",
-        :command => "command_line",
-        :cluster => "Nodes",
-        :number  => 4,
-        :fileserver => "FS",
+        #"target" => "dir_name",
+        "command" => "command_line",
+        "cluster" => "Nodes",
+        "number"  => 4,
       }
       it {lambda{QueueSubmitter.new(opts)}.should raise_error(
         QueueSubmitter::InitializeError)}
@@ -29,23 +28,21 @@ describe QueueSubmitter do
 
     context "opts not have :command" do
       opts = {
-        :directory => ComputationManager.new("dir_name"),
-        #:command => "command_line",
-        :cluster => "Nodes",
-        :number  => 4,
-        :fileserver => "FS",
+        "target" => ComputationManager.new("dir_name"),
+        #"command" => "command_line",
+        "cluster" => "Nodes",
+        "number"  => 4,
       }
       it {lambda{QueueSubmitter.new(opts)}.should raise_error(
         QueueSubmitter::InitializeError)}
     end
 
-    context "opts not have :cluster" do
+    context "opts not have cluster" do
       opts = {
-        :directory => ComputationManager.new("dir_name"),
-        :command => "command_line",
-        #:cluster => "Nodes",
-        :number  => 4,
-        :fileserver => "FS",
+        "target" => ComputationManager.new("dir_name"),
+        "command" => "command_line",
+        #"cluster" => "Nodes",
+        "number"  => 4,
       }
       it {lambda{QueueSubmitter.new(opts)}.should raise_error(
         QueueSubmitter::InitializeError)}
@@ -53,61 +50,101 @@ describe QueueSubmitter do
 
     context "opts not have :command" do
       opts = {
-        :directory => ComputationManager.new("dir_name"),
-        #:command => "command_line",
-        :cluster => "Nodes",
-        :number  => 4,
-        :fileserver => "FS",
+        "target" => ComputationManager.new("dir_name"),
+        #"command" => "command_line",
+        "cluster" => "Nodes",
+        "number"  => 4,
       }
       it {lambda{QueueSubmitter.new(opts)}.should raise_error(
         QueueSubmitter::InitializeError)}
     end
   end
 
-  describe "#self.parse_options" do
-    before do
-      @machine_info = MachineInfo.new(
-        {
-          "fileserver" => "FS",
-          "CLUSTER" => {
-            "speed" => 2,
-            "economy" => 1,
-          },
-        }
-      )
-    end
+  #describe "#self.correct_options" do
+  #  before do
+  #    @machine_info = MachineInfo.new(
+  #      {
+  #        "CLUSTER" => {
+  #          "speed" => 2,
+  #          "economy" => 1,
+  #          "command" => "calc_command"
+  #        },
+  #      }
+  #    )
+  #  end
 
-    context "-c not indicated" do
-      ary = %w( a -n 1 )
-      it {lambda{QueueSubmitter.parse_options(ary, @machine_info)}.should raise_error(
-        QueueSubmitter::InvalidArgumentError)}
-    end
+  #  context "cluster not indicated" do
+  #    opts = {
+  #      "number" => 1,
+  #      #"cluster" => "CLUSTER",
+  #      "target" => "calc_dir",
+  #    }
+  #    it {lambda{QueueSubmitter.correct_options(opts, @machine_info)}.should
+  #      raise_error(QueueSubmitter::InvalidArgumentError)}
+  #  end
 
-    #context "-n not indicated" do
-    #  ary = %w( a -c CLUSTER_DUMMY )
-    #  it {lambda{QueueSubmitter.parse_options(ary, @machine_info)}.should raise_error(MachineInfo::NoEntryError)}
-    #end
+  #  context "target not indicated" do
+  #    opts = {
+  #      "number" => 1,
+  #      "cluster" => "CLUSTER",
+  #      #"target" => "calc_dir",
+  #    }
+  #    it {lambda{QueueSubmitter.correct_options(opts, @machine_info)}.should
+  #      raise_error(QueueSubmitter::InvalidArgumentError)}
+  #  end
 
-    context "-n not indicated" do
-      ary = %w( a -c CLUSTER )
-      it {lambda{QueueSubmitter.parse_options(ary, @machine_info)}.should raise_error(QueueSubmitter::InvalidArgumentError)}
-    end
+  #  context "number not indicated" do
+  #    opts = {
+  #      #"number" => 1,
+  #      "cluster" => "CLUSTER",
+  #      "target" => "calc_dir",
+  #    }
+  #    it {lambda{QueueSubmitter.correct_options(opts, @machine_info)}.should
+  #      raise_error(QueueSubmitter::InvalidArgumentError)}
+  #  end
 
-    context "-c and -n number indicated" do
-      ary = %w( a -c CLUSTER -n 1 )
-      it {lambda{QueueSubmitter.parse_options(ary, @machine_info)}.should_not raise_error}
-    end
+  #  context "orthodox indication" do
+  #    opts = {
+  #      "number" => 1,
+  #      "cluster" => "CLUSTER",
+  #      "target" => "calc_dir",
+  #    }
+  #    results = QueueSubmitter.correct_options(opts, @machine_info)
+  #    it {results.should == 
+  #      {
+  #        "target"  => "calc_dir",
+  #        "command" => "calc_command",
+  #        "number"  => 1,
+  #        "cluster" => "CLUSTER",
+  #      }
+  #    }
+  #  end
 
-  end
+  #  context "number indication as string in MachineInfo" do
+  #    opts = {
+  #      "cluster" => "CLUSTER",
+  #      "number" => "speed",
+  #      "target" => "calc_dir",
+  #    }
+  #    results = QueueSubmitter.correct_options(opts, @machine_info)
+  #    it {results.should == 
+  #      {
+  #        "cluster" => "CLUSTER",
+  #        "number"  => 2,
+  #        "target"  => "calc_dir",
+  #        "command" => "calc_command",
+  #      }
+  #    }
+  #  end
+  #end
 
   describe "#dump_prologue" do
     before do
       opts = {
-        :directory => ComputationManager.new("spec/not_started"),
-        :command => "command_line",
-        :cluster => "Nodes",
-        :number  => 4,
-        :fileserver => "FS",
+        "target" => ComputationManager.new("spec/not_started"),
+        "command" => "command_line",
+        "cluster" => "Nodes",
+        "number"  => 4,
       }
       @qs00 = QueueSubmitter.new(opts)
 
@@ -137,11 +174,10 @@ describe QueueSubmitter do
   describe "#dump_script" do
     before do
       opts = {
-        :directory => ComputationManager.new("spec/not_started"),
-        :command => "command_line",
-        :cluster => "Nodes",
-        :number  => 4,
-        :fileserver => "FS",
+        "target" => ComputationManager.new("spec/not_started"),
+        "command" => "command_line",
+        "cluster" => "Nodes",
+        "number"  => 4,
       }
       @qs00 = QueueSubmitter.new(opts)
 
@@ -164,11 +200,10 @@ describe QueueSubmitter do
   describe "#dump_epilogue" do
     before do
       opts = {
-        :directory => ComputationManager.new("spec/not_started"),
-        :command => "command_line",
-        :cluster => "Nodes",
-        :number  => 4,
-        :fileserver => "FS",
+        "target" => ComputationManager.new("spec/not_started"),
+        "command" => "command_line",
+        "cluster" => "Nodes",
+        "number"  => 4,
       }
       @qs00 = QueueSubmitter.new(opts)
 
@@ -200,11 +235,10 @@ describe QueueSubmitter do
     context "locked" do
       it do
         opts = {
-          :directory => ComputationManager.new("spec/queuesubmitter/locked"),
-          :command => "command_line",
-          :cluster => "Nodes",
-          :number  => 4,
-          :fileserver => "FS",
+          "target" => ComputationManager.new("spec/queuesubmitter/locked"),
+          "command" => "command_line",
+          "cluster" => "Nodes",
+          "number"  => 4,
         }
         @qs00 = QueueSubmitter.new(opts)
 
@@ -215,11 +249,10 @@ describe QueueSubmitter do
     context "unlocked" do
       it do
         opts = {
-          :directory => ComputationManager.new("spec/queuesubmitter/unlocked"),
-          :command => "command_line",
-          :cluster => "Nodes",
-          :number  => 4,
-          :fileserver => "FS",
+          "target" => ComputationManager.new("spec/queuesubmitter/unlocked"),
+          "command" => "command_line",
+          "cluster" => "Nodes",
+          "number"  => 4,
         }
         @qs00 = QueueSubmitter.new(opts)
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: comana
 version: !ruby/object:Gem::Version
-  version: 0.0.8
+  version: 0.0.9
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-18 00:00:00.000000000 Z
+date: 2012-05-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &71401920 !ruby/object:Gem::Requirement
+  requirement: &72264660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 2.10.0
   type: :development
   prerelease: false
-  version_requirements: *71401920
+  version_requirements: *72264660
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &71401380 !ruby/object:Gem::Requirement
+  requirement: &72264230 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *71401380
+  version_requirements: *72264230
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &71400960 !ruby/object:Gem::Requirement
+  requirement: &72263870 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: 1.1.3
   type: :development
   prerelease: false
-  version_requirements: *71400960
+  version_requirements: *72263870
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &71400540 !ruby/object:Gem::Requirement
+  requirement: &72263500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *71400540
+  version_requirements: *72263500
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &71399840 !ruby/object:Gem::Requirement
+  requirement: &72263070 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,7 +65,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *71399840
+  version_requirements: *72263070
 description: ! "Comana, COmputation MANAger,\n    is a software to provide a framework
   of\n    managing scientific computing.\n    Researchers on computing have to check
   calculation and\n    generate new calculation and execute, repeatedly.\n    The
@@ -125,7 +125,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 49117789
+      hash: 67223151
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: