rbbt-util 2.1.0 → 3.0.2

data/test/test_helper.rb

@@ -1,6 +1,8 @@
 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 'rbbt/util/log'
 require 'fileutils'
@@ -8,6 +10,14 @@ require 'fileutils'
 class Test::Unit::TestCase
   include FileUtils
 
+  def setup
+    Persistence.cachedir = Rbbt.tmp.test.persistence.find :user
+  end
+
+  def teardown
+    FileUtils.rm_rf Rbbt.tmp.test.find :user
+  end
+
   def test_datafile(file)
     File.join(File.dirname(__FILE__), 'data', file)
   end

data/test/test_rbbt.rb

@@ -4,42 +4,7 @@ require 'rbbt/util/misc'
 require 'rbbt/util/open'
 
 class TestRbbt < Test::Unit::TestCase
-  def test_url
-    Rbbt.claim :test_url, 'http://google.com'
-    assert Rbbt.files.test_url.read =~ /html/
-    FileUtils.rm Rbbt.files.test_url
+  def test_true
+    assert true
   end
-
-  def test_xclip
-    sharedir = PKGData.sharedir_for_file(__FILE__)
-  
-    File.open(File.join(sharedir, 'install', 'software', 'xclip'), 'w') do |f|
-      f.puts '#!/bin/bash
-
-INSTALL_HELPER_FILE="$1"
-RBBT_SOFTWARE_DIR="$2"
-source "$INSTALL_HELPER_FILE"
-
-name="xclip:0.12"
-url="http://downloads.sourceforge.net/project/xclip/xclip/0.12/xclip-0.12.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fxclip%2F&ts=1286472387&use_mirror=sunet"
-
-install_src "$name" "$url"
-      '
-    end
-    FileUtils.chmod 0774, File.join(sharedir, 'install', 'software', 'xclip')
-
-    Rbbt.add_software :xclip => ['','']
-    Rbbt.find_software :xclip
-    assert File.exists? File.join(Rbbt.bin_dir, 'xclip')
-
-    FileUtils.rm_rf  File.join(sharedir, 'install', 'software', 'xclip')
-    Dir.glob(File.join(Rbbt.datadir, 'software', 'opt', 'xclip','bin/*')).each do |exe|
-      FileUtils.rm_rf  File.join(Rbbt.datadir, 'software', 'opt', 'bin', File.basename(exe))
-    end
-    Dir.glob(File.join(Rbbt.datadir, 'software', 'opt', 'xclip','current', 'bin/*')).each do |exe|
-      FileUtils.rm_rf  File.join(Rbbt.datadir, 'software', 'opt', 'bin', File.basename(exe))
-    end
-    FileUtils.rm_rf  File.join(Rbbt.datadir, 'software', 'opt', 'xclip')
-  end
-
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-util
 version: !ruby/object:Gem::Version 
-  hash: 11
+  hash: 3
   prerelease: 
   segments: 
-  - 2
-  - 1
+  - 3
   - 0
-  version: 2.1.0
+  - 2
+  version: 3.0.2
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-02-10 00:00:00 +01:00
+date: 2011-03-19 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -94,6 +94,7 @@ executables:
 - tsv.rb
 - tchash.rb
 - workflow.rb
+- rbbt_query.rb
 extensions: []
 
 extra_rdoc_files: 
@@ -106,21 +107,18 @@ files:
 - lib/rbbt/util/bed.rb
 - lib/rbbt/util/cachehelper.rb
 - lib/rbbt/util/cmd.rb
-- lib/rbbt/util/data_module.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/path.rb
 - lib/rbbt/util/persistence.rb
-- lib/rbbt/util/pkg_config.rb
-- lib/rbbt/util/pkg_data.rb
-- lib/rbbt/util/pkg_software.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/tc_hash.rb
 - lib/rbbt/util/tmpfile.rb
 - lib/rbbt/util/tsv.rb
@@ -129,24 +127,24 @@ files:
 - lib/rbbt/util/tsv/index.rb
 - lib/rbbt/util/tsv/manipulate.rb
 - lib/rbbt/util/tsv/parse.rb
+- lib/rbbt/util/tsv/resource.rb
 - lib/rbbt/util/workflow.rb
 - share/install/software/lib/install_helpers
 - share/lib/R/util.R
 - test/rbbt/util/test_R.rb
 - test/rbbt/util/test_bed.rb
 - test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_data_module.rb
 - test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_fix_width_table.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
-- test/rbbt/util/test_path.rb
 - test/rbbt/util/test_persistence.rb
-- test/rbbt/util/test_pkg_data.rb
 - test/rbbt/util/test_rake.rb
+- test/rbbt/util/test_resource.rb
 - test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_task.rb
 - test/rbbt/util/test_tc_hash.rb
 - test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_tsv.rb
@@ -156,12 +154,13 @@ files:
 - test/rbbt/util/tsv/test_index.rb
 - test/rbbt/util/tsv/test_manipulate.rb
 - test/rbbt/util/tsv/test_parse.rb
+- test/rbbt/util/tsv/test_resource.rb
 - test/test_helper.rb
-- test/test_pkg.rb
 - test/test_rbbt.rb
 - bin/tsv.rb
 - bin/tchash.rb
 - bin/workflow.rb
+- bin/rbbt_query.rb
 has_rdoc: true
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses: []
@@ -200,18 +199,17 @@ test_files:
 - test/rbbt/util/test_R.rb
 - test/rbbt/util/test_bed.rb
 - test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_data_module.rb
 - test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_fix_width_table.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
-- test/rbbt/util/test_path.rb
 - test/rbbt/util/test_persistence.rb
-- test/rbbt/util/test_pkg_data.rb
 - test/rbbt/util/test_rake.rb
+- test/rbbt/util/test_resource.rb
 - test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_task.rb
 - test/rbbt/util/test_tc_hash.rb
 - test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_tsv.rb
@@ -221,6 +219,6 @@ test_files:
 - test/rbbt/util/tsv/test_index.rb
 - test/rbbt/util/tsv/test_manipulate.rb
 - test/rbbt/util/tsv/test_parse.rb
+- test/rbbt/util/tsv/test_resource.rb
 - test/test_helper.rb
-- test/test_pkg.rb
 - test/test_rbbt.rb

data/lib/rbbt/util/data_module.rb

@@ -1,93 +0,0 @@
-module DataModule
-
-  def self.rakefiles(sharedir, data_module)
-    Dir.glob(File.join(sharedir, 'install', data_module.to_s, '**','Rakefile')).collect{|f| File.expand_path f}
-  end
-
-  attr_accessor :sharedir, :rakefile, :pkg_module
-  def self.extended(data_module)
-    if defined? data_module::PKG and data_module::PKG
-      data_module.pkg_module = data_module::PKG
-    else
-      data_module.pkg_module = Rbbt
-    end
-
-    data_module.sharedir = PKGData.get_caller_sharedir 
-    
-    install_dir = File.join(data_module.sharedir, 'install')
-    rake_sharedir  = File.join(data_module.sharedir, 'install')
-
-    rakefiles(data_module.sharedir, data_module).each do |rakefile|
-      rakefile_dir = File.dirname(rakefile)
-
-      RakeHelper.files(rakefile).each do |file|
-        file_path = Misc.path_relative_to(File.join(File.dirname(rakefile), file), rakefile_dir)
-        get       = :Rakefile
-        subdir    = Misc.path_relative_to(File.dirname(rakefile), install_dir)
-        namespace = data_module.to_s.gsub('/', '::')
-
-        data_module.pkg_module.claim file_path, get, subdir, namespace, rake_sharedir
-      end
-    end
-  end
-
-  def files
-    DataModule.rakefiles(sharedir, self).collect do |rakefile|
-      RakeHelper.files(rakefile).collect
-    end.flatten
-  end
-
-  def datadir
-    File.join(pkg_module.datadir, self.to_s)
-  end
-
-  module WithKey
-    def klass=(klass)
-      @klass = klass
-    end
-   
-    def klass
-      @klass
-    end
-
-    def key=(key)
-      @key = key
-    end
-
-    def key
-      @key
-    end
-
-    def method_missing(name, *args)
-      if key
-        klass.send(name, key, *args)
-      else
-        klass.send(name, *args)
-      end
-    end
-  end
-
-  def with_key(key)
-    klass = self
-    o = Object.new
-    o.extend WithKey
-    o.klass = self
-    o.key = key
-    o
-  end
-
-  alias old_method_missing method_missing
-  def method_missing(name, *args, &block)
-    begin
-      if args.any?
-        pkg_module.files[self.to_s][args.first][name] 
-      else
-        pkg_module.files[self.to_s][name] 
-      end
-    rescue
-      Log.debug $!.message
-      Log.debug $!.backtrace * "\n"
-      old_method_missing name, *args, &block
-    end
-  end
-end

data/lib/rbbt/util/path.rb

@@ -1,155 +0,0 @@
-require 'rbbt/util/misc'
-require 'rbbt/util/tsv'
-
-module Path
-  attr_accessor :pkg_module, :datadir
-
-  def self.find_files_back_to(path, target, subdir)
-    return [] if path.nil?
-    raise "Path #{ path } not in directory #{ subdir }" if not Misc.in_directory? path, subdir
-
-    pkg_module = path.pkg_module
-
-    files = []
-    while path != subdir
-      path = File.dirname(path)
-      path.extend Path
-      path.pkg_module = pkg_module
-      path.datadir    = path.datadir
-      if path[target].exists? 
-        files << path[target]
-      end
-    end
-
-    files
-  end
-
-  def self.path(string, datadir = nil, pkg_module = nil)
-    string.extend Path
-    string.datadir = datadir
-    string.pkg_module = case
-                        when pkg_module.nil?
-                          nil
-                        when String === pkg_module
-                          Misc.string2const pkg_module
-                        else
-                          pkg_module
-                        end
-    string
-  end
-
-  def method_missing(name, *args, &block)
-    new = File.join(self.dup, name.to_s)
-    new.extend Path
-    new.pkg_module = pkg_module
-    new.datadir    = datadir
-    new
-  end
-
-  def [](name)
-    new = File.join(self.dup, name.to_s)
-    new.extend Path
-    new.pkg_module = pkg_module
-    new.datadir    = datadir
-    new
-  end
-
-  def namespace
-    return nil if self.nil? or self.empty? or (not datadir.nil? and (self == datadir or File.dirname(self) == datadir))
-    if File.directory? self
-      File.basename(self)
-    else
-      File.basename(File.dirname(self))
-    end
-  end
-
-  def identifier_files
-    if datadir.nil?
-      path = File.join(File.dirname(self), 'identifiers')
-      path.extend Path
-      path.pkg_module = pkg_module
-      if path.exists?
-        [path]
-      else
-        []
-      end
-    else
-      identifier_files = Path.find_files_back_to(self, 'identifiers', datadir)
-      return identifier_files.collect{|f| Path.path(f, datadir, pkg_module)}
-    end
-  end
-
-  def tsv(key = nil, options = {})
-    if options.empty? and Hash === key
-      options, key = key, nil
-    end
-
-    produce
-    TSV.new self, key, options.merge(:datadir => datadir)
-  end
-
-  def index(options = {})
-    produce
-    TSV.index self, options
-  end
-
-  def open(options = {})
-    produce
-    Open.open(self, options)
-  end
-
-  def read(options = {})
-    produce
-    Open.read(self, options)
-  end
-
-  def fields(sep = nil, header_hash = nil)
-    produce
-    TSV.parse_header(self.open, sep, header_hash)[1].collect{|f| f.extend TSV::Field; f.namespace = namespace ;f}
-  end
-
-  def all_fields(sep = nil, header_hash = nil)
-    produce
-    key_field, fields = TSV.parse_header(self.open, sep, header_hash).values_at(0, 1).flatten.collect{|f| f.extend TSV::Field; f.namespace = namespace; f}
-  end
-
-  def fields_in_namespace(sep = nil, header_hash = nil)
-    produce
-    TSV.parse_header(self.open, sep, header_hash)[1].collect{|f| f.extend TSV::Field; f.namespace = namespace ;f}.select{|f| f.namespace == namespace}
-  end
-
-  def all_namespace_fields(sep = nil, header_hash = nil)
-    produce
-    key_field, fields = TSV.parse_header(self.open, sep, header_hash).values_at(0, 1).flatten.collect{|f| f.extend TSV::Field; f.namespace = namespace; f}.select{|f| f.namespace == namespace}
-  end
-
-  def filename
-    self.to_s
-  end 
-
-  def exists?
-    begin
-      produce
-      true
-    rescue
-      false
-    end
-  end
-
-  def produce
-    return self if File.exists? self
-
-    raise "No especified pkg_data for file #{ self }, cannot produce" if pkg_data.nil?
-
-    Log.debug("Trying to produce '#{ self }'")
-    file, producer = pkg_module.reclaim self
-
-    raise "File #{self} has not been claimed, cannot produce" if file.nil? or producer.nil?
-
-    pkg_module.produce(self, producer[:get], producer[:subdir], producer[:sharedir])
-
-    self
-  end
-end
-
-

data/lib/rbbt/util/pkg_config.rb

@@ -1,78 +0,0 @@
-require 'yaml'
-
-module PKGConfig
-  class NoConfig < Exception; end
-  class NoVariables < Exception; end
-
-  class RootdirNotFoundError < StandardError; end
-
-  def self.rootdir_for_file(file = __FILE__)
-    dir = File.expand_path(File.dirname file)
-
-    while not File.exists?(File.join(dir, 'lib')) and dir != '/'
-      dir = File.dirname(dir)
-    end
-
-    if File.exists? File.join(dir, 'lib')
-      dir
-    else
-      raise RootdirNotFoundError
-    end
-  end
-
-  def self.get_caller_rootdir
-    caller.each do |line|
-      next if line =~ /\/pkg_config\.rb/ 
-        begin
-          return PKGConfig.rootdir_for_file(line)
-        rescue RootdirNotFoundError
-        end
-    end
-    raise RootdirNotFoundError
-  end
-
-
-  def self.extended(base)
-    base.module_eval{ @@rootdir = PKGConfig.get_caller_rootdir}
-  end
-
-  def rootdir
-    @@rootdir
-  end
-
-  def load_config(file, pkg_variables)
-    config = YAML.load_file(file)
-
-    pkg_variables.each do |variable|
-      self.send("#{variable}=", config[variable])
-    end
-  end
-
-  def load_cfg(pkg_variables, default = nil)
-    pkg_cfg_files = [ ENV['RBBT_CONFIG'] || "", 
-      File.join(ENV["HOME"], '.' + self.to_s), 
-      File.join('/etc/', '.' +  self.to_s)]
-
-    pkg_variables.each do |variable|
-      self.class_eval %{
-        def self.#{variable} 
-          @#{variable}
-        end
-        def self.#{variable}=(value)
-          @#{variable} = value
-        end
-      }
-    end
-
-    file = pkg_cfg_files.select{|file| File.exists? file}.first
-    if file.nil?
-      if default
-        file = pkg_cfg_files[1]
-        Open.write(file, default)
-      else
-        raise NoConfig, "No config file found. [#{pkg_cfg_files * ", "}]" if file.nil?
-      end
-    end
-    load_config file, pkg_variables
-  end
-end