tap-tasks 0.3.0 → 0.5.0

data/History

@@ -1,3 +1,17 @@
+== 0.5.0 / 2009-12-05
+
+Updates for Tap-0.19.0
+
+== 0.4.0
+
+* added short options to load/dump csv
+* added Gate join
+* added Null task
+* added Stream task for stream loading
+* updated load/yaml to only load a single document
+* added stream/yaml for stream loading documents
+* added Profiler middleware
+
 == 0.3.0 / 2009-06-17
 
 * added load/dump csv tasks

data/MIT-LICENSE

@@ -1,22 +1,21 @@
 Copyright (c) 2009, Regents of the University of Colorado.
 
-Permission is hereby granted, free of charge, to any person
-obtaining a copy of this software and associated documentation
-files (the "Software"), to deal in the Software without
-restriction, including without limitation the rights to use,
-copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the
-Software is furnished to do so, subject to the following
-conditions:
+Copyright (c) 2009, Simon Chiang.
 
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-OTHER DEALINGS IN THE SOFTWARE.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/README

@@ -12,7 +12,6 @@ is a part of the {Tap-Suite}[http://tap.rubyforge.org/tap-suite]. Check out
 these links for documentation, development, and bug tracking.
 
 * Website[http://tap.rubyforge.org] 
-* Lighthouse[http://bahuvrihi.lighthouseapp.com/projects/9908-tap-task-application/tickets]
 * Github[http://github.com/bahuvrihi/tap/tree/master] 
 * {Google Group}[http://groups.google.com/group/ruby-on-tap]
 
@@ -25,13 +24,11 @@ Usage is the same as for any tasks.
 
 == Installation
 
-Tap-Tasks is available as a gem on RubyForge[http://rubyforge.org/projects/tap].  Use:
+Tap-Tasks is available as a gem on Gemcutter[http://gemcutter.org/gems/tap-tasks].
 
   % gem install tap-tasks
   
 == Info
 
-Copyright (c) 2009, Regents of the University of Colorado.
-Developer:: {Simon Chiang}[http://bahuvrihi.wordpress.com], {Biomolecular Structure Program}[http://biomol.uchsc.edu/], {Hansen Lab}[http://hsc-proteomics.uchsc.edu/hansenlab/] 
-Support:: CU Denver School of Medicine Deans Academic Enrichment Fund
+Developer:: {Simon Chiang}[http://bahuvrihi.wordpress.com]
 License:: {MIT-Style}[link:files/MIT-LICENSE.html]

data/lib/tap/joins/gate.rb

@@ -0,0 +1,87 @@
+require 'tap/join'
+
+module Tap
+  module Joins
+    
+    # :startdoc::join collects results before the join
+    #
+    # Similar to a synchronized merge, but collects all results regardless of
+    # where they come from.  Gates enque themselves when called as a join, and
+    # won't let results pass until they get run as a node.
+    # 
+    #   % tap run -- load a -- load b -- inspect --[0,1][2].gate
+    #   ["a", "b"]
+    # 
+    # Gates are useful in conjunction with iteration where a single task may
+    # feed multiple results to a single join; in this case a sync merge doesn't
+    # produce the desired behavior of collecting the results.
+    # 
+    #   % tap run -- load/yaml "[1, 2, 3]" --:i inspect --:.gate inspect
+    #   1
+    #   2
+    #   3
+    #   [1, 2, 3]
+    # 
+    #   % tap run -- load/yaml "[1, 2, 3]" --:i inspect --:.sync inspect
+    #   1
+    #   [1]
+    #   2
+    #   [2]
+    #   3
+    #   [3]
+    # 
+    # When a limit is specified, the gate will collect results up to the limit
+    # and then pass the results.  Any leftover results are still passed at the
+    # end.
+    #
+    #   % tap run -- load/yaml "[1, 2, 3]" --:i inspect -- inspect --. gate 1 2 --limit 2
+    #   1
+    #   2
+    #   [1, 2]
+    #   3
+    #   [3]
+    #
+    class Gate < Join
+      
+      # An array of results collected thusfar.
+      attr_reader :results
+      
+      config :limit, nil, :short => :l, &c.integer_or_nil   # Pass results after limit
+      
+      def initialize(config={}, app=Tap::App.instance)
+        super
+        @results = nil
+      end
+      
+      def call(result)
+        if @results
+          # Results are set, so self is already enqued and collecting
+          # results.  If the input is the collection, then it's time
+          # to dispatch the results and reset.  Otherwise, just
+          # collect the input and wait.
+          
+          if result == @results
+            @results = nil
+            super(result)
+          else
+            @results << result
+            
+            if limit && @results.length >= limit
+              super(@results.dup)
+              @results.clear
+            end
+          end
+          
+        else
+          # No results are set, so this is a first call and self is
+          # not enqued.  Setup the collection.
+          
+          @results = [result]
+          app.enq(self, @results)
+        end
+        
+        self
+      end
+    end
+  end
+end

data/lib/tap/middlewares/profiler.rb

@@ -0,0 +1,72 @@
+require 'tap/middleware'
+
+module Tap
+  module Middlewares
+    
+    # :startdoc::middleware profile the workflow execution time
+    #
+    #
+    class Profiler < Tap::Middleware
+      
+      attr_reader :app_time
+      attr_reader :nodes
+      attr_reader :counts
+      
+      def initialize(stack, config={})
+        super
+        reset
+        at_exit { app.quiet = false; app.log(:profile, "\n" + summary.join("\n")) }
+      end
+      
+      def reset
+        @app_time = 0
+        @last = nil
+        @nodes = Hash.new(0)
+        @counts = Hash.new(0)
+      end
+      
+      def total_time
+        nodes.values.inject(0) {|sum, elapsed| sum + elapsed }
+      end
+      
+      def total_counts
+        counts.values.inject(0) {|sum, n| sum + n }
+      end
+      
+      def call(node, inputs=[])
+        @app_time += Time.now - @last if @last
+        
+        start = Time.now
+        result = super
+        elapsed = Time.now - start
+        
+        nodes[node] += elapsed
+        counts[node] += 1
+        
+        @last = Time.now
+        result
+      end
+      
+      def summary
+        lines = []
+        lines << "App Time: #{app_time}s"
+        lines << "Node Time: #{total_time}s"
+        lines << "Nodes Run: #{total_counts}"
+        lines << "Breakdown:"
+        
+        nodes_by_class = {}
+        nodes.each_key do |node|
+          (nodes_by_class[node.class.to_s] ||= []) << node
+        end
+        
+        nodes_by_class.keys.sort.each do |node_class|
+          nodes_by_class[node_class].each do |node|
+            lines << "- #{node_class}: [#{nodes[node]}, #{counts[node]}]"
+          end
+        end
+        
+        lines
+      end
+    end
+  end
+end

data/lib/tap/tasks/dump/csv.rb

@@ -16,8 +16,8 @@ module Tap
       #
       class Csv < Dump
         
-        config :col_sep, ",", &c.string    # The column separator (",")
-        config :row_sep, "\n", &c.string   # The row separator ("\n")
+        config :col_sep, ",", :short => :c, &c.string    # The column separator (",")
+        config :row_sep, "\n", :short => :r, &c.string   # The row separator ("\n")
         
         # Dumps the data to io as CSV.  Data is converted to an array using
         # to_ary.

data/lib/tap/tasks/load/csv.rb

@@ -19,11 +19,11 @@ module Tap
       #
       class Csv < Load
         
-        config :columns, nil, &c.range_or_nil   # Specify a range of columns
-        config :rows, nil, &c.range_or_nil      # Specify a range of rows
+        config :columns, nil, :short => :C, &c.range_or_nil   # Specify a range of columns
+        config :rows, nil, :short => :R, &c.range_or_nil      # Specify a range of rows
         
-        config :col_sep, nil, &c.string_or_nil  # The column separator (",")
-        config :row_sep, nil, &c.string_or_nil  # The row separator ("\r\n" or "\n")
+        config :col_sep, nil, :short => :c, &c.string_or_nil  # The column separator (",")
+        config :row_sep, nil, :short => :r, &c.string_or_nil  # The row separator ("\r\n" or "\n")
         
         # Loads the io data as CSV, into an array of arrays.
         def load(io)

data/lib/tap/tasks/load/yaml.rb

@@ -14,35 +14,9 @@ module Tap
       #
       class Yaml < Load
         
-        config :stream, false, &c.flag   # Load documents from a stream
-        
         # Loads data from io as YAML.
         def load(io)
-          if stream
-            load_stream(io)
-          else
-            YAML.load(io)
-          end
-        end
-        
-        def load_stream(io)          
-          lines = []
-          while !io.eof?
-            line = io.readline
-
-            if line =~ /^---/ && !lines.empty?
-              io.pos = io.pos - line.length
-              break
-            else
-              lines << line
-            end
-          end
-
-          YAML.load(lines.join)
-        end
-        
-        def complete?(io, last)
-          !stream || io.eof?
+          YAML.load(io)
         end
         
       end

data/lib/tap/tasks/null.rb

@@ -0,0 +1,27 @@
+require 'tap/task'
+
+module Tap
+  module Tasks
+    # :startdoc::task a dev/null task
+    #
+    # Null serves the same function as /dev/null, that is inputs directed
+    # to Null go nowhere.  Null does not accept joins and will not execute
+    # the default app joins.
+    #
+    #   % tap run -- load a --: null
+    #
+    class Null < Tap::Task 
+      def process(*args)
+        nil
+      end
+      
+      def joins
+        nil
+      end
+      
+      def on_complete
+        raise "cannot be participate in joins: #{self}"
+      end
+    end 
+  end
+end

data/lib/tap/tasks/stream.rb

@@ -0,0 +1,64 @@
+require 'tap/tasks/load'
+
+module Tap
+  module Tasks
+    
+    # Stream recurrently loads data from $stdin by requeing self until an
+    # end-of-file is reached.  This behavior is useful for creating tasks
+    # that load a bit of data from an IO, send it into a workflow, and then
+    # repeat.
+    #
+    # The eof cutoff can be modified using complete? method.  Streaming will
+    # stop when complete? returns true.  For instance, this is a prompt task:
+    #
+    #   class Prompt < Tap::Tasks::Stream
+    #     config :exit_seq, "\n"
+    #
+    #     def load(io)
+    #       if io.eof?
+    #         nil
+    #       else
+    #         io.readline
+    #       end
+    #     end
+    #
+    #     def complete?(io, line)
+    #       line == nil || line == exit_seq
+    #     end
+    #   end
+    #
+    class Stream < Load
+      
+      # Loads data from io.  Process will open the input io object, load
+      # a result, then check to see if the loading is complete (using the
+      # complete? method).  Unless loading is complete, process will enque
+      # io to self.  Process will close io when loading is complete, provided
+      # use_close or file is specified.
+      def process(io=$stdin)
+        io = open(io)
+        result = load(io)
+        
+        if complete?(io, result)
+          if use_close || file
+            close(io)
+          end
+        else
+          reque(io)
+        end
+        
+        result
+      end
+      
+      # Returns true by default.  Override in subclasses to allow recurrent 
+      # loading (see process).
+      def complete?(io, last)
+        io.eof?
+      end
+      
+      # Reques self with io to the top of the queue.
+      def reque(io)
+        app.queue.unshift(self, [io])
+      end
+    end
+  end
+end

data/lib/tap/tasks/stream/yaml.rb

@@ -0,0 +1,49 @@
+require 'tap/tasks/stream'
+
+module Tap
+  module Tasks
+    class Stream
+      
+      # :startdoc::task streams data as YAML
+      #
+      # Stream loads data from the input IO as YAML.
+      #
+      #   [example.yml]
+      #   --- 
+      #   :sym
+      #   --- 
+      #   - 1
+      #   - 2
+      #   - 3
+      #   --- 
+      #   key: value
+      # 
+      #   % tap run -- stream/yaml --file example.yml --: inspect
+      #   :sym
+      #   [1, 2, 3]
+      #   {"key"=>"value"}
+      #
+      class Yaml < Stream
+        
+        # Streams data from io as YAML.
+        def load(io)
+          lines = []
+          
+          while !io.eof?
+            line = io.readline
+
+            if line =~ /^---/ && !lines.empty?
+              io.pos = io.pos - line.length
+              break
+            else
+              lines << line
+            end
+          end
+
+          YAML.load(lines.join)
+        end
+        
+      end
+    end
+  end
+end

data/lib/tap/tasks/version.rb

@@ -0,0 +1,9 @@
+module Tap
+  module Tasks
+    MAJOR = 0
+    MINOR = 5
+    TINY = 0
+
+    VERSION="#{MAJOR}.#{MINOR}.#{TINY}"
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: tap-tasks
 version: !ruby/object:Gem::Version 
-  version: 0.3.0
+  version: 0.5.0
 platform: ruby
 authors: 
 - Simon Chiang
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-06-17 00:00:00 -06:00
+date: 2009-12-05 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -20,7 +20,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.18.0
+        version: 0.19.0
     version: 
 - !ruby/object:Gem::Dependency 
   name: tap-test
@@ -30,7 +30,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.2.0
+        version: 0.3.0
     version: 
 description: 
 email: simon.a.chiang@gmail.com
@@ -43,19 +43,26 @@ extra_rdoc_files:
 - README
 - MIT-LICENSE
 files: 
+- lib/tap/joins/gate.rb
+- lib/tap/middlewares/profiler.rb
 - lib/tap/tasks/dump/csv.rb
 - lib/tap/tasks/dump/inspect.rb
 - lib/tap/tasks/dump/yaml.rb
 - lib/tap/tasks/load/yaml.rb
 - lib/tap/tasks/load/csv.rb
+- lib/tap/tasks/null.rb
 - lib/tap/tasks/glob.rb
-- lib/tap/tasks/prompt.rb
+- lib/tap/tasks/stream.rb
+- lib/tap/tasks/stream/yaml.rb
+- lib/tap/tasks/version.rb
 - tap.yml
 - History
 - README
 - MIT-LICENSE
 has_rdoc: true
-homepage: http:/tap.rubyforge.org/tap-tasks/
+homepage: http://tap.rubyforge.org/tap-tasks/
+licenses: []
+
 post_install_message: 
 rdoc_options: 
 - --main
@@ -81,9 +88,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: tap
-rubygems_version: 1.3.1
+rubygems_version: 1.3.5
 signing_key: 
-specification_version: 2
+specification_version: 3
 summary: A set of standard Tap tasks
 test_files: []
 

data/lib/tap/tasks/prompt.rb

@@ -1,42 +0,0 @@
-require 'tap/tasks/load'
-
-module Tap
-  module Tasks
-    # :startdoc::task an input prompt
-    #
-    # Prompt reads lines from the input until the exit sequence is reached
-    # or the source io is closed.  This is effectively an echo:
-    #
-    #   % tap run -- prompt --: dump
-    #   >
-    #
-    class Prompt < Load
-      config :prompt, "> ", &c.string_or_nil    # The prompt sequence
-      config :exit_seq, "\n", &c.string_or_nil  # The prompt exit sequence
-      config :terminal, $stdout, &c.io_or_nil   # The terminal IO
-      
-      configurations[:use_close].default = true
-      
-      def load(io)
-        open_io(terminal) do |terminal|
-          terminal.print prompt
-        end if prompt
-        
-        if io.eof?
-          nil
-        else
-          io.readline
-        end
-      end
-  
-      def complete?(io, line)
-        line == nil || line == exit_seq
-      end
-      
-      def close(io)
-        super
-        app.terminate
-      end
-    end
-  end
-end