rbbt 1.1.5 → 1.1.6

data/lib/rbbt/util/open.rb

@@ -15,6 +15,7 @@ module Open
   end
 
   class DirectoryNotFoundError < StandardError; end
+  class OpenURLError < StandardError; end
 
   private 
 
@@ -42,13 +43,13 @@ module Open
       end
     end
   end
- 
+
   # Checks if +url+ is a remote file.
   def self.remote(url)
     url =~ /^(?:http|ssh|https|ftp):\/\//
   end
 
-   
+
   # Checks if +url+ is a gzip file.
   def self.gziped(url)
     if remote(url)
@@ -58,14 +59,27 @@ module Open
     end
   end
 
+
+  @@last_time = Time.now   
+  def self.wait(lag = 0)
+    time = Time.now   
+
+    if time < @@last_time + lag
+      sleep @@last_time + lag - time
+    end
+
+    @@last_time = Time.now   
+  end
+
   public
   # Reads the file specified by url. If the url es local it just opens
   # the file, if it is remote if checks the cache first. In any case, it
   # unzips gzip files automatically.
   #
   # Options: 
-  # * :quiet => Do not print the progress of downloads
+  # * :quiet    => Do not print the progress of downloads
   # * :nocache  => do not use the cache.
+  # * :nice     => secconds to wait between online queries
   #
   def self.read(url, options = {})
 
@@ -75,18 +89,24 @@ module Open
         return data
       end
 
+      wait(options[:nice]) if options[:nice]
       tmp = TmpFile.tmp_file("open-")
       `wget -O #{tmp} '#{url}' #{options[:quiet] ? '-q' : '' }`
-      if gziped(url)
-        `mv #{tmp} #{tmp}.gz; gunzip #{tmp}`
-      end
 
+      if $!.success?
+        if gziped(url)
+        `mv #{tmp} #{tmp}.gz; gunzip #{tmp}`
+        end
 
-      cache(url, File.open(tmp){|file| file.read}) unless options[:nocache]
+        cache(url, File.open(tmp){|file| file.read}) unless options[:nocache]
 
-      data = File.open(tmp){|file| file.read}
-      FileUtils.rm tmp
-      return data
+        data = File.open(tmp){|file| file.read}
+        FileUtils.rm tmp
+        return data
+      else
+        raise OpenURLError, "Error reading remote url: #{ url }"
+      end
+    
     when IO === url
       url.read
     else

data/lib/rbbt/util/rake.rb

@@ -1,67 +1,183 @@
 require 'rake'
 
+# Include the step_def and step methods to simplify Pipelines. Steps depend on
+# the step strictly above by default. The output of the step is save marshaled,
+# except for Strings which are save as text. The input of the step, the output
+# of the previous step if availabe is accessed with the input method
+#
+# Example::
+#
+#     step :text do 
+#       "Text to revert"
+#     end
+#
+#     step :revert do
+#       text = input
+#       text.reverse
+#     end
+#
 module Rake::Pipeline
 
-  def step_def(*args)
-    Rake::Pipeline::Step.step_def(*args)
+  module Rake::Pipeline::Step
+
+    class << self
+
+      @@step_descriptions = {}
+      def step_descriptions
+        @@step_descriptions
+      end
+
+      def add_description(re, step, message)
+        @@step_descriptions[re] = "#{ step }: #{ message }"                       
+      end
+
+      @@last_step = nil
+      def step_def(name, dependencies = nil)
+
+        re = Regexp.new(/(?:^|\/)#{name}\/.*$/)
+
+        # Take the last_description and associate it with the name
+        if Rake.application.last_description
+          add_description(re, name, Rake.application.last_description)
+        end
+
+        if dependencies.nil? && ! @@last_step.nil?
+          dependencies = @@last_step
+        end
+        @@last_step = name
+
+        # Generate the Hash definition
+        case 
+        when dependencies.nil?
+          re
+        when String === dependencies || Symbol === dependencies
+          {re => lambda{|filename| filename.sub(name.to_s,dependencies.to_s) }}
+        when Array === dependencies
+          {re => lambda{|filename| dependencies.collect{|dep| filename.sub(name.to_s, dep.to_s) } }}
+        when Proc === dependencies
+          {re => dependencies}
+        end
+
+      end
+
+    end
+  end
+
+  module Rake::Pipeline::Info
+
+    def self.info_file(filename)
+      filename.sub(/^(.*?)(?:[^\/]*)\/([^\/]*)$/, '\1.info/\2.yaml')
+    end
+
+    def self.load_info(t)
+      filename = t.name
+      info_filename = info_file(filename)
+
+      if File.exists? info_filename
+        YAML.load(File.open(info_filename))
+      else
+        {}
+      end
+    end
+
+    def self.save_info(t, info = {})
+      filename = t.name
+      info_filename = info_file(filename)
+
+      FileUtils.mkdir_p File.dirname(info_filename) unless File.exists? File.dirname(info_filename)
+      File.open(info_filename,'w'){|file|
+        file.write YAML.dump info
+      }
+    end
+
+  end
+
+
+  NON_ASCII_PRINTABLE = /[^\x20-\x7e\s]/
+  def is_binary?(file)
+    binary = file.read(1024) =~ NON_ASCII_PRINTABLE
+    file.rewind
+    binary
   end
 
   def step_descriptions
     Rake::Pipeline::Step.step_descriptions
   end
 
+
+  def step_def(*args)
+    Rake::Pipeline::Step.step_def(*args)
+  end
+
   def infile(t, &block)
-    File.open(t.prerequisites.first)do |f|
+    File.open(t.prerequisites.first) do |f|
       block.call(f)
     end
   end
 
   def outfile(t, &block)
-    File.open(t.name, 'w')do |f|
+    File.open(t.name, 'w') do |f|
       block.call(f)
     end
   end
 
+  def load_input(t)
+    return nil if t.prerequisites.first.nil?
+    infile(t){|f| 
+      if is_binary?(f)
+        Marshal.load(f) 
+      else
+        f.read
+      end
+    }
+  end
 
-end
-
-module Rake::Pipeline::Step
-
-  class << self
-    @@step_descriptions = {}
-    def step_descriptions
-      @@step_descriptions
-    end
-
-    def add_description(re, step, message)
-      @@step_descriptions[re] = "#{ step }: #{ message }"                       
+  def save_output(t, output)
+    case 
+    when output.nil?
+      nil
+    when String === output
+      outfile(t){|f| f.write output } 
+    else
+      outfile(t){|f| f.write Marshal.dump(output) } 
     end
 
-    def step_def(name, dependencies = nil)
+  end
 
-      re = Regexp.new(/(?:^|\/)#{name}\/.*$/)
-      re = Regexp.new(/#{name}\/.*/)
-
-        # Take the last_description and associate it with the name
-        if Rake.application.last_description
-          add_description(re, name, Rake.application.last_description)
-        end
+  # We cannot load the input variable before the block.call, so we need another method
 
+  # Load the input data from the previous step
+  def input
+    load_input(@@current_task) if @@current_task
+  end
 
-      # Generate the Hash definition
-      case 
-      when dependencies.nil?
-        re
-      when String === dependencies || Symbol === dependencies
-        {re => lambda{|filename| filename.sub(name.to_s,dependencies.to_s) }}
-      when Array === dependencies
-        {re => lambda{|filename| dependencies.collect{|dep| filename.sub(name.to_s, dep.to_s) } }}
-      when Proc === dependencies
-        {re => dependencies}
-      end
-    end
+  # Add values to the info file
+  def info(values = {})
+    info = Rake::Pipeline::Info.load_info(@@current_task)
+    info = info.merge values
+    Rake::Pipeline::Info.save_info(@@current_task, info)
+    info
   end
+  
+  
+  # Define a new step, it depends on the previously defined by default. It
+  # saves the output of the block so it can be loaded by the input method of
+  # the next step
+  def step(name, dependencies = nil, &block)
+    rule step_def(name, dependencies) do |t| 
+
+      # Save the task object to be able to load the input
+      @@current_task = t
+      
+      output = block.call(t)
+      
+      save_output(t, output)
+    end
 
+  end
 end
 
+if __FILE__ == $0
 
+  p Rake::Pipeline::Info.info_file('work/diseases/t')
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt
 version: !ruby/object:Gem::Version 
-  version: 1.1.5
+  version: 1.1.6
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-12-16 00:00:00 +01:00
+date: 2009-12-31 00:00:00 +01:00
 default_executable: rbbt_config
 dependencies: 
 - !ruby/object:Gem::Dependency