rbbt-util 3.2.1 → 4.0.0

data/test/rbbt/workflow/test_task.rb

@@ -0,0 +1,84 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/workflow/task'
+require 'rbbt'
+
+class TEST
+  def self.times(str, times)
+    [str] * times 
+  end
+end
+
+class TestTask < Test::Unit::TestCase
+  def test_task_setup
+    a = [1,2]
+    p = Task.setup{|pos| self[pos]}
+
+    assert_equal 1, p.exec_in(a, 0)
+    assert_equal 2, p.exec_in(a, 1)
+  end
+
+  def test_task_exec
+    a = [1,2]
+    p = Proc.new{|pos| self[pos]}
+    p.extend Task
+    assert_equal 1, p.exec_in(a, 0)
+    assert_equal 2, p.exec_in(a, 1)
+  end
+
+  def test_task_named
+    t = Task.setup :inputs => %w(str times) do |str, times| [str] * times end
+    assert_equal %w(test test), t.exec(:str => "test", :times => 2)
+    assert_equal %w(test test), t.exec(:str => "test", :times => 2)
+  end
+
+  def test_task_persist
+    t = Task.setup :inputs => %w(str times) do |str, times| 
+      [str] * times 
+    end
+
+    TmpFile.with_file do |perfile|
+      assert_equal %w(test test), t.persist_exec_in(perfile, Object.new, :str => "test", :times => 2)
+      assert File.exist? perfile
+
+      t = Task.setup :inputs => %w(str times) do |str, times| 
+        raise "Persistence ignored"
+      end
+
+      assert_equal %w(test test), t.persist_exec_in(perfile, Object.new, :str => "test", :times => 2)
+    end
+  end
+
+  def test_task_unbound_method
+    t = TEST.method :times
+    t.extend Task
+    t.inputs = %w(str times) 
+
+    TmpFile.with_file do |perfile|
+      assert_equal %w(test test), t.persist_exec_in(perfile, Object.new, :str => "test", :times => 2)
+      assert File.exist? perfile
+
+      t = Task.setup :inputs => %w(str times) do |str, times| 
+        raise "Persistence ignored"
+      end
+
+      assert_equal %w(test test), t.persist_exec_in(perfile, Object.new, :str => "test", :times => 2)
+    end
+  end
+
+  def test_task_unbound_method2
+    t = Task.setup :inputs => %w(str times), &TEST.method(:times)
+
+    TmpFile.with_file do |perfile|
+      assert_equal %w(test test), t.persist_exec_in(perfile, Object.new, :str => "test", :times => 2)
+      assert File.exist? perfile
+
+      t = Task.setup :inputs => %w(str times) do |str, times| 
+        raise "Persistence ignored"
+      end
+
+      assert_equal %w(test test), t.persist_exec_in(perfile, Object.new, :str => "test", :times => 2)
+    end
+  end
+
+
+end

data/test/test_helper.rb

@@ -1,23 +1,23 @@
-require 'test/unit'
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'rbbt'
-require 'rbbt/util/persistence'
-require 'rbbt/util/tmpfile'
+require 'test/unit'
 require 'rbbt/util/log'
+require 'rbbt/util/tmpfile'
+require 'rbbt/resource/path'
 require 'fileutils'
 
 class Test::Unit::TestCase
   include FileUtils
 
   def setup
-    Persistence.cachedir = Rbbt.tmp.test.persistence.find :user
+    Persist.cachedir = Rbbt.tmp.test.persistence.find :user
   end
 
   def teardown
-    FileUtils.rm_rf Rbbt.tmp.test.find :user
-    TCHash::CONNECTIONS.values.each do |c| c.close end
-    TCHash::CONNECTIONS.clear
+    FileUtils.rm_rf Path.setup("", 'rbbt').tmp.test.find :user
+    Persist::TC_CONNECTIONS.values.each do |c| c.close end
+    Persist::TC_CONNECTIONS.clear
   end
 
   def datafile_test(file)

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-util
 version: !ruby/object:Gem::Version 
-  hash: 13
+  hash: 63
   prerelease: false
   segments: 
-  - 3
-  - 2
-  - 1
-  version: 3.2.1
+  - 4
+  - 0
+  - 0
+  version: 4.0.0
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-07-05 00:00:00 +02:00
+date: 2011-09-07 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -102,6 +102,20 @@ dependencies:
         version: "0"
   type: :runtime
   version_requirements: *id006
+- !ruby/object:Gem::Dependency 
+  name: RubyInline
+  prerelease: false
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id007
 description: Utilities for handling tsv files, caches, etc
 email: miguel.vazquez@fdi.ucm.es
 executables: 
@@ -115,65 +129,77 @@ extensions: []
 
 extra_rdoc_files: 
 - LICENSE
+- README.rdoc
 files: 
 - LICENSE
 - lib/rbbt-util.rb
 - lib/rbbt.rb
+- lib/rbbt/annotations.rb
+- lib/rbbt/fix_width_table.rb
+- lib/rbbt/persist.rb
+- lib/rbbt/persist/tsv.rb
+- lib/rbbt/resource.rb
+- lib/rbbt/resource/path.rb
+- lib/rbbt/resource/rake.rb
+- lib/rbbt/resource/util.rb
+- lib/rbbt/resource/with_key.rb
+- lib/rbbt/tsv.rb
+- lib/rbbt/tsv/accessor.rb
+- lib/rbbt/tsv/attach.rb
+- lib/rbbt/tsv/attach/util.rb
+- lib/rbbt/tsv/filter.rb
+- lib/rbbt/tsv/index.rb
+- lib/rbbt/tsv/manipulate.rb
+- lib/rbbt/tsv/parser.rb
+- lib/rbbt/tsv/serializers.rb
+- lib/rbbt/tsv/util.rb
 - lib/rbbt/util/R.rb
+- lib/rbbt/util/chain_methods.rb
 - lib/rbbt/util/cmd.rb
 - lib/rbbt/util/excel2tsv.rb
 - lib/rbbt/util/filecache.rb
-- lib/rbbt/util/fix_width_table.rb
 - lib/rbbt/util/log.rb
 - lib/rbbt/util/misc.rb
 - lib/rbbt/util/open.rb
 - lib/rbbt/util/persistence.rb
-- lib/rbbt/util/rake.rb
-- lib/rbbt/util/resource.rb
 - lib/rbbt/util/simpleDSL.rb
 - lib/rbbt/util/simpleopt.rb
-- lib/rbbt/util/task.rb
 - lib/rbbt/util/task/job.rb
-- lib/rbbt/util/tc_hash.rb
 - lib/rbbt/util/tmpfile.rb
-- lib/rbbt/util/tsv.rb
-- lib/rbbt/util/tsv/accessor.rb
-- lib/rbbt/util/tsv/attach.rb
-- lib/rbbt/util/tsv/filters.rb
-- lib/rbbt/util/tsv/index.rb
-- lib/rbbt/util/tsv/manipulate.rb
-- lib/rbbt/util/tsv/misc.rb
-- lib/rbbt/util/tsv/parse.rb
-- lib/rbbt/util/tsv/resource.rb
-- lib/rbbt/util/workflow.rb
-- lib/rbbt/util/workflow/soap.rb
+- lib/rbbt/workflow.rb
+- lib/rbbt/workflow/accessor.rb
+- lib/rbbt/workflow/annotate.rb
+- lib/rbbt/workflow/soap.rb
+- lib/rbbt/workflow/step.rb
+- lib/rbbt/workflow/task.rb
 - share/install/software/lib/install_helpers
 - share/lib/R/util.R
+- README.rdoc
 - test/test_helper.rb
 - test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_open.rb
-- test/rbbt/util/test_tsv.rb
+- test/rbbt/util/test_R.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_tc_hash.rb
 - test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/test_resource.rb
-- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/test_task.rb
-- test/rbbt/util/test_persistence.rb
-- test/rbbt/util/test_rake.rb
-- test/rbbt/util/test_workflow.rb
-- test/rbbt/util/tsv/test_parse.rb
-- test/rbbt/util/tsv/test_accessor.rb
-- test/rbbt/util/tsv/test_manipulate.rb
-- test/rbbt/util/tsv/test_index.rb
-- test/rbbt/util/tsv/test_attach.rb
-- test/rbbt/util/tsv/test_resource.rb
-- test/rbbt/util/tsv/test_filters.rb
-- test/rbbt/util/test_fix_width_table.rb
+- test/rbbt/resource/test_path.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/test_fix_width_table.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/workflow/test_soap.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_task.rb
 - test/test_rbbt.rb
 - bin/tsv.rb
 - bin/tchash.rb
@@ -220,25 +246,25 @@ test_files:
 - test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_open.rb
-- test/rbbt/util/test_tsv.rb
+- test/rbbt/util/test_R.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_tc_hash.rb
 - test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/test_resource.rb
-- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/test_task.rb
-- test/rbbt/util/test_persistence.rb
-- test/rbbt/util/test_rake.rb
-- test/rbbt/util/test_workflow.rb
-- test/rbbt/util/tsv/test_parse.rb
-- test/rbbt/util/tsv/test_accessor.rb
-- test/rbbt/util/tsv/test_manipulate.rb
-- test/rbbt/util/tsv/test_index.rb
-- test/rbbt/util/tsv/test_attach.rb
-- test/rbbt/util/tsv/test_resource.rb
-- test/rbbt/util/tsv/test_filters.rb
-- test/rbbt/util/test_fix_width_table.rb
+- test/rbbt/resource/test_path.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/test_fix_width_table.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/workflow/test_soap.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_task.rb
 - test/test_rbbt.rb

data/lib/rbbt/util/rake.rb

@@ -1,176 +0,0 @@
-require 'rake'
-require 'rbbt/util/tsv'
-require 'rbbt/util/open'
-require 'rbbt/util/log'
-
-module RakeHelper
-  def self.files(rakefile, task = :default, chdir = nil)
-    status = nil
-    files = nil
-    TmpFile.with_file do |f|
-      pid = Process.fork{
-        require 'rake'
-        FileUtils.chdir chdir if chdir
-
-        Rake::FileTask.module_eval do
-          if not self.respond_to? :old_define_task
-            class << self
-              alias_method :old_define_task, :define_task 
-            end 
-          end
-
-          def self.define_task(file, *args, &block)
-            @@files ||= []
-            if Hash === file
-              @@files << file.keys.first.to_s
-            else
-              @@files << file.to_s
-            end
-            old_define_task(file, *args, &block)
-          end
-
-          def self.files
-            if defined? @@files
-              @@files
-            else
-              @@file = []
-            end
-          end
-        end
-
-        load rakefile
-
-        Open.write(f, Rake::FileTask.files * "\n")
-        exit
-      }
-
-
-      pid, status = Process.waitpid2(pid)
-      files = Open.read(f).split("\n")
-    end
-    raise "Error getting files from Rake: #{ rakefile } " unless status.success?
-    files
-  end
-
-  def self.run(rakefile, task = :default, chdir = nil)
-    require 'rake'
-    old_pwd = FileUtils.pwd
-    FileUtils.chdir chdir if chdir
-
-    Rake::FileTask.module_eval do
-      if not self.respond_to? :old_define_task
-        class << self
-          alias_method :old_define_task, :define_task
-        end
-
-        def self.define_task(file, *args, &block)
-          @@files ||= []
-          @@files << file
-          old_define_task(file, *args, &block)
-        end
-      end
-
-      def self.files
-        @@files
-      end
-      
-      def self.clear_files
-        @@files = []
-      end
-    end
-
-    Rake::Task.clear
-    Rake::FileTask.clear_files
-    if block_given?
-      yield
-    else
-      load rakefile
-    end
-
-    task(:default) do |t|
-      Rake::FileTask.files.each do |file| Rake::Task[file].invoke end
-    end
-
-    Rake::Task[task].invoke
-
-    Rake::Task.clear
-    Rake::FileTask.clear_files
-
-    FileUtils.chdir old_pwd
-  end
-
-  module WorkFlow
-    attr_accessor :default_persistence, :stage_options, :run_options
-
-    def stage_options(stage = :next)
-      @stage_options ||= {}
-      @stage_options[stage] ||= []
-    end
-
-    def run_options
-      @run_options ||= {}
-    end
-
-    def stage(stage_name, options = nil)
-      dependencies, options = case
-                              when ((String === options or Symbol === options) and %w(string marshal yaml tsv tsv_string).include? options.to_s)
-                                [nil, {:persistence_type => options}]
-                              when Hash === options
-                                [nil, options]
-                              else
-                                [options, {}]
-                              end
-
-      @stage_options[stage_name] = @stage_options[:next]
-
-      options = Misc.add_defaults options, :persistence_type => default_persistence || :string
-      persistence_type = Misc.process_options options, :persistence_type
-      dependencies = Misc.process_options options, :dependencies if options.include? :dependencies
-
-      re = Regexp.new(/(?:^|\/)#{Regexp.quote stage_name.to_s}\/.*$/)
-
-      @last_step             = nil unless defined? @last_step
-      @last_persistence_type = nil unless defined? @last_persistence_type
-
-      if dependencies.nil? && ! @last_step.nil?
-        dependencies = @last_step
-      end
-      @last_step = stage_name
-
-      # Generate the Hash definition
-      rule_def = case 
-                 when dependencies.nil?
-                   re
-                 when String === dependencies 
-                   {re => dependencies}
-                 when Symbol === dependencies
-                   {re => lambda{|filename| filename.sub(stage_name.to_s, dependencies.to_s) }}
-                 when Array === dependencies
-                   {re => lambda{|filename| dependencies.collect{|dep| filename.sub(stage_name.to_s, dep.to_s) } }}
-                 when Proc === dependencies
-                   {re => dependencies}
-                 end
-
-      @last_step = stage_name
-      last_persistence_type, @last_persistence_type = @last_persistence_type, persistence_type
-
-      rule rule_def do |t|
-        Persistence.persist(t, "", persistence_type, :persistence_file => t.name) do |t, options|
-          data = case
-                 when (t.prerequisites.nil? or (Array === t.prerequisites and t.prerequisites.empty?))
-                   nil
-                 else
-                   Persistence.persist(t.prerequisites.first, "", last_persistence_type, :persistence_file => t.prerequisites.first) do
-                     raise "Error, this file should be produced already"
-                   end
-                 end
-          options = @run_options.values_at *stage_options
-          step stage_name, "Executing step [#{ stage_name }]"
-          yield t, *options
-        end
-      end
-    end
-  end
-end
-
-