rbbt-util 5.2.0 → 5.2.2

data/bin/rbbt

@@ -29,7 +29,9 @@ while ARGV.any?
         load dir[command].find
         exit 0
     else
-        raise "Command not understood"
+        puts "Error: Command not understood"
+        puts
+        break
     end
 end
 

data/bin/run_workflow.rb

@@ -86,30 +86,6 @@ workflow = ARGV.first
 
 if options[:server]
 
-  #require 'rbbt/util/log'
-  #require 'rbbt/workflow'
-  #require 'rbbt/workflow/rest'
-  #require 'sinatra'
-  #require 'compass'
-
-  #if workflow
-  #  Workflow.require_workflow workflow
-  #  WorkflowREST.add_workflows *Workflow.workflows
-  #end
-
-  #WorkflowREST.setup
-
-  #Sinatra::Application.port = options[:port] || 4567
-  #Sinatra::Application.run = true
-
-  #if workflow and File.exists? workflow
-  #  Sinatra::Application.views = File.join(File.dirname(workflow), 'www/views')
-  #end
-
-  #sinatra_file = './lib/sinatra.rb'
-  #if File.exists? sinatra_file
-  #  require sinatra_file
-  #end
   require 'zurb-foundation'
   require 'modular-scale'
 

data/lib/rbbt-util.rb

@@ -10,4 +10,4 @@ require 'rbbt/util/misc'
 FileCache.cachedir   = Rbbt.var.cache.filecache.find :user
 Open.cachedir        = Rbbt.var.cache["open-remote"].find :user
 TmpFile.tmpdir       = Rbbt.tmp.find :user
-Persist.cachedir = Rbbt.var.cache.persistence.find :user
+Persist.cachedir = Rbbt.var.cache.persistence

data/lib/rbbt.rb

@@ -1,16 +1,19 @@
+require 'rbbt/resource'
 require 'rbbt/util/open'
+require 'rbbt/util/cmd'
 require 'rbbt/util/tmpfile'
 require 'rbbt/util/filecache'
 require 'rbbt/tsv'
 require 'rbbt/persist'
-require 'rbbt/resource'
+require 'rbbt/util/misc'
 
 module Rbbt
   extend Resource
   pkgdir = 'rbbt'
-
-  FileCache.cachedir   = var.cache.filecache.find :user
-  TmpFile.tmpdir       = tmp.find :user
-  Open.cachedir        = var.cache["open-remote"].find :user
-  Persist.cachedir     = var.cache.persistence.find :user
 end
+
+Open.cachedir        = Rbbt.var.cache["open-remote"].find :user
+TmpFile.tmpdir       = Rbbt.tmp.find :user
+FileCache.cachedir   = Rbbt.var.cache.filecache.find :user
+Persist.cachedir     = Rbbt.var.cache.persistence.find :user
+

data/lib/rbbt/persist.rb

@@ -6,20 +6,18 @@ require 'rbbt/persist/tsv'
 require 'set'
 
 module Persist
-  CACHEDIR = "/tmp/tsv_persistent_cache" unless defined? CACHEDIR
-  FileUtils.mkdir CACHEDIR unless File.exist? CACHEDIR
+  class << self
+    attr_accessor :cachedir
+    def self.cachedir=(cachedir)
+      @cachedir = Path === cachedir ? cachedir : Path.setup(cachedir)
+    end
+    def self.cachedir
+      @cachedir ||= Rbbt.var.cache.persistence 
+    end
+  end
 
   MEMORY = {} unless defined? MEMORY
 
-  def self.cachedir=(cachedir)
-    CACHEDIR.replace cachedir
-    FileUtils.mkdir_p CACHEDIR unless File.exist? CACHEDIR
-  end
-
-  def self.cachedir
-    CACHEDIR
-  end
- 
   def self.newer?(path, file)
     return true if not File.exists? file
     return true if File.mtime(path) < File.mtime(file)
@@ -60,7 +58,8 @@ module Persist
       end
     end
 
-    persistence_dir = Misc.process_options(persist_options, :dir) || CACHEDIR
+    persistence_dir = Misc.process_options(persist_options, :dir) || Persist.cachedir
+    Path.setup(persistence_dir) unless Path === persistence_dir
 
     filename = perfile.gsub(/\s/,'_').gsub(/\//,'>')
     clean_options = options
@@ -70,7 +69,7 @@ module Persist
     options_md5 = Misc.hash2md5 clean_options
     filename  << ":" << options_md5 unless options_md5.empty?
 
-    File.join(persistence_dir, filename)
+    persistence_dir[filename].find
   end
 
   TRUE_STRINGS = Set.new ["true", "True", "TRUE", "t", "T", "1", "yes", "Yes", "YES", "y", "Y", "ON", "on"] unless defined? TRUE_STRINGS

data/lib/rbbt/persist/tsv.rb

@@ -82,7 +82,8 @@ module Persist
         end
 
         def write_and_close
-          Misc.lock(persistence_path) do
+          lock_filename = Persist.persistence_path(persistence_path, {:dir => Rbbt.tmp.tsv_open_locks.find})
+          Misc.lock(lock_filename) do
             write if @closed or not write?
             res = begin
                     yield
@@ -154,7 +155,8 @@ module Persist
 
              if is_persisted? path
                Log.debug "TSV persistence up-to-date: #{ path }"
-               return Misc.lock(path) do open_tokyocabinet(path, false); end
+               lock_filename = Persist.persistence_path(path, {:dir => Rbbt.tmp.tsv_open_locks.find})
+               return Misc.lock(lock_filename) do open_tokyocabinet(path, false); end
              else
                Log.debug "TSV persistence creating: #{ path }"
              end

data/lib/rbbt/resource.rb

@@ -1,8 +1,7 @@
- require 'rbbt/util/open'
+require 'rbbt/util/open'
 require 'rbbt/util/log'
 require 'rbbt/util/chain_methods'
 require 'rbbt/resource/path'
-#require 'rbbt/resource/rake'
  
 module Resource
   extend ChainMethods

data/lib/rbbt/tsv/attach.rb

@@ -137,6 +137,12 @@ module TSV
     fields, one2one = Misc.process_options options, :fields, :one2one
     in_namespace = options[:in_namespace]
 
+    unless TSV === other
+      other_identifier_files = other.identifier_files if other.respond_to? :identifier_files
+      other = TSV.open(other, :persist => options[:persist_input] == true) unless TSV === other 
+      other.identifiers = other_identifier_files 
+    end
+
     fields = other.fields - [key_field].concat(self.fields) if fields.nil?  or fields == :all 
     if in_namespace
       fields = other.fields_in_namespace - [key_field].concat(self.fields) if fields.nil?
@@ -144,13 +150,8 @@ module TSV
       fields = other.fields - [key_field].concat(self.fields) if fields.nil?
     end
 
-    Log.medium("Attaching fields:#{fields.inspect} from #{other.filename.inspect}.")
-
-    unless TSV === other
-      other_identifier_files = other.identifier_files
-      other = other.tsv(:persist => options[:persist_input] == true) unless TSV === other 
-      other.identifiers = other_identifier_files 
-    end
+    other_filename = other.respond_to?(:filename) ? other.filename : other.inspect
+    Log.medium("Attaching fields:#{fields.inspect} from #{other_filename}.")
 
     case
     when key_field == other.key_field

data/lib/rbbt/tsv/attach/util.rb

@@ -173,7 +173,6 @@ module TSV
             current += all_new_values
 
             self[key] = current
-
           end
         end
       end

data/lib/rbbt/util/misc.rb

@@ -635,6 +635,17 @@ end
     res
   end
 
+  def self.do_once(&block)
+    return nil if $__did_once
+    $__did_once = true
+    yield
+    nil
+  end
+
+  def self.reset_do_once
+    $__did_once = false
+  end
+
   def self.insist(times = 3, sleep = nil)
     try = 0
     begin

data/lib/rbbt/util/named_array.rb

@@ -115,8 +115,10 @@ module NamedArray
   end
 
   def named_array_values_at(*keys)
-    keys = keys.collect{|k| Misc.field_position(fields, k) }
-    named_array_clean_values_at(*keys)
+    keys = keys.collect{|k| Misc.field_position(fields, k, true) }
+    keys.collect{|k|
+      named_array_get_brackets(k) unless k.nil?
+    }
   end
 
   def zip_fields

data/lib/rbbt/util/simpleopt.rb

@@ -32,18 +32,29 @@ module SOPT
 
     index = 0
     while index < ARGV.length do
-      arg = ARGV[index]
+      orig_arg = ARGV[index]
+
+      if orig_arg =~ /=/
+        arg, value = orig_arg.match(/(.*?)=(.*)/).values_at 1, 2
+      else
+        arg = orig_arg
+        value = nil
+      end
+
       if switches.include? arg
         name = switches[arg]
         i = info[name]
         if i[:arg]
-          options[name.to_sym] = ARGV[index + 1]
-          index += 1
+          if value.nil?
+            value = ARGV[index + 1]
+            index += 1
+          end
+          options[name.to_sym] = value
         else
           options[name.to_sym] = true
         end
       else
-        rest << arg
+        rest << orig_arg
       end
       index += 1
     end

data/lib/rbbt/workflow/accessor.rb

@@ -180,7 +180,7 @@ module Workflow
     description = task.description
     result_description = task.result_description
     result_type = task.result_type
-    inputs = rec_inputs(name)
+    inputs = rec_inputs(name).uniq
     input_types = rec_input_types(name)
     input_descriptions = rec_input_descriptions(name)
     input_defaults = rec_input_defaults(name)

data/lib/rbbt/workflow/usage.rb

@@ -13,7 +13,13 @@ module Task
       default = input_defaults[name]
       type = input_types[name]
 
-      puts "  * -#{short}, --#{name}=<#{ type }>#{default ? " (default: #{default})" : ""}:"
+
+      if type.to_sym == :boolean
+        puts "  * -#{short}, --#{name}[=<true|false>]#{default != nil ? " (default: #{default})" : ""}:"
+      else
+        puts "  * -#{short}, --#{name}=<#{ type }>#{default != nil ? " (default: #{default})" : ""}:"
+      end
+
       puts "    " << description if description and not description.empty?
       puts
     end
@@ -32,7 +38,12 @@ module Task
           default = dep.input_defaults[name]
           type = dep.input_types[name]
 
-          puts "  * -#{short}, --#{name}=<#{ type }>#{default ? " (default: #{default})" : ""}:"
+          if type.to_sym == :boolean
+            puts "  * -#{short}, --#{name}[=<true|false>]#{default != nil ? " (default: #{default})" : ""}:"
+          else
+            puts "  * -#{short}, --#{name}=<#{ type }>#{default != nil ? " (default: #{default})" : ""}:"
+          end
+
           puts "    " << description if description and not description.empty?
           puts
         end

data/share/rbbt_commands/app/start

@@ -0,0 +1,18 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+options = SOPT.get "-e--environment*:-p--port*:-s--server*"
+
+app = ARGV.shift
+
+app_dir = Rbbt.etc.app_dir.exists? ? Path.setup(Rbbt.etc.app_dir.read.strip) : Rbbt.apps.find
+
+app_dir = app_dir[app]
+
+server = options[:server] || 'thin'
+
+Misc.in_dir(app_dir) do
+  `#{options.include?(:environment)? "env RACK_ENV=#{options[:environment]}" : ""} #{server} start -p #{options[:port]} #{ARGV.collect{|a| "'#{a}'"} * " "}`
+end

data/share/rbbt_commands/tsv/info

@@ -0,0 +1,20 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+
+file = ARGV.shift
+
+header = TSV.parse_header(Open.open(file))
+
+puts "File: #{ file }"
+puts "Key: #{header.key_field}"
+puts "Fields: "
+header.fields.each_with_index do |f,i|
+  puts "  - #{i + 1}: " << f
+end
+puts "Rows: #{`wc -l #{ file }|cut -f 1 -d' '`}"
+puts "First line:"
+puts header.first_line
+

data/share/rbbt_commands/workflow/server

@@ -0,0 +1,70 @@
+#!/usr/bin/env ruby
+
+require 'rbbt/util/simpleopt'
+require 'rbbt/workflow'
+
+require 'zurb-foundation'
+require 'modular-scale'
+
+require 'rbbt/rest/main'
+require 'rbbt/rest/entity'
+require 'rbbt/rest/workflow'
+require 'rbbt/rest/file_server'
+require 'rbbt/rest/helpers'
+
+options = SOPT.get "--profile:-p--port*"
+
+workflow = ARGV.first
+
+YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler
+
+Workflow.require_workflow workflow
+
+class WorkflowRest < Sinatra::Base
+  get '/' do
+    redirect to(File.join('/', Workflow.workflows.last.to_s))
+  end
+end
+
+if options[:profile]
+  WorkflowRest.before File.join('/', Workflow.workflows.last.to_s, '*') do
+    @profile = true
+  end
+end
+
+class WorkflowRest < Sinatra::Base
+   
+  #{{{ MODULES AND HELPERS
+  register Sinatra::RbbtRESTMain
+  register Sinatra::RbbtRESTWorkflow
+  register Sinatra::RbbtRESTEntity
+  helpers Sinatra::RbbtMiscHelpers
+
+  #{{{ DIRECTORIES
+  local_var = Rbbt.var.find(:lib)
+  set :cache_dir           , local_var.sinatra.cache.find
+  set :file_dir            , local_var.sinatra.files.find
+  set :favourites_dir      , local_var.sinatra.favourites.find
+  set :favourite_lists_dir , local_var.sinatra.favourite_lists
+
+  #{{{ SESSIONS
+  use Rack::Session::Cookie, :key => 'rack.session',
+    :path => '/',
+    :expire_after => 2592000,
+    :secret => "Workflow #{Workflow.workflows.inspect} secret!!"
+
+  #{{{ FOUNDATION RESOURCES
+  add_sass_load_path "#{Gem.loaded_specs['compass'].full_gem_path}/frameworks/compass/stylesheets"
+  add_sass_load_path "#{Gem.loaded_specs['zurb-foundation'].full_gem_path}/scss/" 
+  add_sass_load_path "#{Gem.loaded_specs['modular-scale'].full_gem_path}/stylesheets/" 
+  RbbtRESTHelpers.javascript_resources << Path.setup("#{Gem.loaded_specs['zurb-foundation'].full_gem_path}/js/foundation")
+  RbbtRESTHelpers.javascript_resources << Path.setup("#{Gem.loaded_specs['zurb-foundation'].full_gem_path}/js/vendor")
+
+  $title = "Workflow Scout"
+  use Rack::Deflater
+end
+
+WorkflowRest.add_workflow Workflow.workflows.last, true
+
+WorkflowRest.port = options[:port] || 4567
+WorkflowRest.run!

data/share/rbbt_commands/workflow/task

@@ -54,14 +54,20 @@ def fix_options(workflow, task, job_options)
               if Array === value
                 value
               else
-                case
+                str = case
                 when value == '-'
                   STDIN.read
                 when (String === value and File.exists?(value))
                   Open.read(value)
                 else
                   value
-                end.split(/[,|\s]/)
+                end
+                
+                if $array_separator
+                  str.split(/#{$array_separator}/)
+                else
+                  str.split(/[,|\s]/)
+                end
               end
             when :tsv
               if TSV === value
@@ -86,7 +92,7 @@ def fix_options(workflow, task, job_options)
   job_options_cleaned
 end
 
-options = SOPT.get "-t--task*:--profile:-l--log*:-h--help:-n--name*:-cl--clean:-rcl-recursive_clean:-pn--printname"
+options = SOPT.get "-t--task*:--profile:-l--log*:-h--help:-n--name*:-cl--clean:-rcl-recursive_clean:-pn--printname:-as--array_separator*"
 
 workflow = ARGV.shift
 usage if workflow.nil?
@@ -100,6 +106,7 @@ help = !!options.delete(:help)
 do_fork = !!options.delete(:fork)
 clean = !!options.delete(:clean)
 recursive_clean = !!options.delete(:recursive_clean)
+$array_separator = options.delete(:array_separator)
 
 # Get workflow
 
@@ -156,7 +163,11 @@ if do_fork
     sleep 2
   end
   raise job.messages.last if job.error?
-  res = job.load
+  if $array_separator
+    res = job.load(:sep2 => $array_separator)
+  else
+    res = job.load
+  end
 else
   res = job.run
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.2.0
+  version: 5.2.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-05-08 00:00:00.000000000 Z
+date: 2013-05-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -236,12 +236,15 @@ files:
 - lib/rbbt/workflow/usage.rb
 - share/install/software/lib/install_helpers
 - share/lib/R/util.R
+- share/rbbt_commands/app/start
 - share/rbbt_commands/conf/web_user/add
 - share/rbbt_commands/conf/web_user/list
 - share/rbbt_commands/conf/web_user/remove
+- share/rbbt_commands/tsv/info
 - share/rbbt_commands/workflow/remote/add
 - share/rbbt_commands/workflow/remote/list
 - share/rbbt_commands/workflow/remote/remove
+- share/rbbt_commands/workflow/server
 - share/rbbt_commands/workflow/task
 - README.rdoc
 - test/rbbt/tsv/test_accessor.rb