rbbt-util 5.1.0 → 5.2.0

data/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2010-2011 Miguel Vázquez García
+Copyright (c) 2010-2013 Miguel Vázquez García
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.rdoc

@@ -45,7 +45,6 @@
 
    gem install specific_install hoe
    gem specific_install -l https://github.com/bensomers/png.git
-   gem specific_install -l https://github.com/felipec/soap4r.git
    gem specific_install -l https://github.com/mikisvaz/tokyocabinet_19_fix.git
 
 3.pre2 - A couple of gems are better installed beforehand, since they require some configuration
@@ -82,7 +81,8 @@
     git clone git@github.com:mikisvaz/rbbt-phgx.git
     git clone git@github.com:mikisvaz/rbbt-entities.git
     git clone git@github.com:mikisvaz/rbbt-dm.git
-    git clone git@github.com:mikisvaz/rbbt-views.git
+    git clone git@github.com:mikisvaz/rbbt-rest.git
+    git clone git@github.com:mikisvaz/rbbt-studies.git
     alias druby="env RBBT_LOG=0 ruby $(for d in $HOME/git/rbbt-*;do echo -n "-I$d/lib ";done)"
     alias drake="env RBBT_LOG=0 rake $(for d in $HOME/git/rbbt-*;do echo -n "-I$d/lib ";done)"
 

data/bin/rbbt

@@ -0,0 +1,45 @@
+#!/usr/bin/env ruby
+
+require 'rbbt'
+
+$rbbt_command_dir = Rbbt.share.rbbt_commands
+
+def commands(prev)
+    rbbt_command_dir = $rbbt_command_dir
+
+    prev.each do |previous_command|
+        rbbt_command_dir = rbbt_command_dir[previous_command]
+    end
+
+    command_file_dirs = rbbt_command_dir.find_all
+    command_files = command_file_dirs.collect{|d| d.glob('*') }.flatten
+    command_files.collect{|p| File.basename(p) }.uniq.reject{|p| p =~ /\.desc$/}.sort
+end
+
+dir = $rbbt_command_dir
+prev = []
+
+while ARGV.any?
+    command = ARGV.shift
+    case
+    when File.directory?(dir[command].find)
+        prev << command
+        dir = dir[command]
+    when dir[command].exists?
+        load dir[command].find
+        exit 0
+    else
+        raise "Command not understood"
+    end
+end
+
+puts "Command:"
+puts 
+puts "  #{File.basename($0)} #{prev * " "}"
+puts 
+puts "Subcommands:"
+puts 
+commands(prev).each do |command|
+    puts "  " << command
+end
+    

data/bin/rbbt_dangling_locks.rb

@@ -0,0 +1,9 @@
+require 'rbbt/util/open'
+require 'rbbt/util/misc'
+
+lockfiles= `find . -name *.lock`.split "\n"
+lockfiles.each do |file|
+  Open.read(file) =~ /^pid: (\d+)/
+  pid = $1
+  puts [file + " (#{ pid })", Misc.pid_exists?(pid) ? "Running" : "Missing"] * ": "
+end

data/bin/rbbt_monitor.rb

@@ -4,20 +4,19 @@ require 'rbbt-util'
 require 'fileutils'
 require 'rbbt/util/simpleopt'
 require 'rbbt/workflow/step'
+require 'rbbt/util/misc'
 
-options = SOPT.get("-l--list:-z--zombies:-e--errors:-c--clean:-n--name:-a--all:-w--wipe:-f--file*")
+options = SOPT.get("-l--list:-z--zombies:-e--errors:-c--clean:-n--name:-a--all:-w--wipe:-f--file*:-q--quick")
+
+
+YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler
 
 def info_files
   Dir.glob('**/*.info')
 end
 
 def running?(info)
-  begin
-    Process.kill 0, info[:pid]
-    true
-  rescue
-    false
-  end
+  Misc.pid_exists? info[:pid]
 end
 
 def print_job(file, info, severity_color = nil)
@@ -27,7 +26,8 @@ def print_job(file, info, severity_color = nil)
   else
     info ||= {:status => :missing_info_file}
     str = [clean_file, info[:status].to_s] * " [ STATUS = " + " ]" 
-    str += " (#{running?(info)? :running : :zombie} #{info[:pid]})" if info.include? :pid
+    str += " (#{running?(info)? :running : :dead} #{info[:pid]})" if info.include? :pid
+    str += " (children: #{info[:children_pids].collect{|pid| [pid, Misc.pid_exists?(pid) ? "R" : "D"] * ":"} * ", "})" if info.include? :children_pids
 
     str = "#{severity_color}" <<  str  << "\033[0m" if severity_color
     puts str
@@ -40,11 +40,12 @@ def list_jobs(options)
 
   info_files.each do |file|
     clean_file = file.sub('.info','')
-    next if File.exists? clean_file
     begin
+      next if File.exists? clean_file and $quick
       info = YAML.load(Open.read(file))
+      next if File.exists? clean_file and not running? info
     rescue Exception
-      Log.debug "Error parsing info file: #{ file }"
+      puts "Error parsing info file: #{ file }"
       info = nil
     end
 
@@ -100,6 +101,7 @@ end
 
 
 $name = options.delete :name
+$quick = options.delete :quick
 case
 when (options[:clean] and not options[:list])
   if options[:file]

data/bin/run_workflow.rb

@@ -25,7 +25,7 @@ end
 def fix_options(workflow, task, job_options)
   option_types = workflow.rec_input_types(task.name)
 
-  workflow.resolve_locals(job_options)
+  #workflow.resolve_locals(job_options)
 
   job_options_cleaned = {}
 
@@ -80,35 +80,97 @@ def fix_options(workflow, task, job_options)
   job_options_cleaned
 end
 
-options = SOPT.get "-t--task*:-l--log*:-h--help:-n--name*:-cl--clean:-rcl-recursive_clean:-pn--printname:-srv--server:-p--port*"
+options = SOPT.get "-t--task*:--profile:-l--log*:-h--help:-n--name*:-cl--clean:-rcl-recursive_clean:-pn--printname:-srv--server:-p--port*"
 
 workflow = ARGV.first
 
 if options[:server]
 
-  require 'rbbt/util/log'
-  require 'rbbt/workflow'
-  require 'rbbt/workflow/rest'
-  require 'sinatra'
-  require 'compass'
+  #require 'rbbt/util/log'
+  #require 'rbbt/workflow'
+  #require 'rbbt/workflow/rest'
+  #require 'sinatra'
+  #require 'compass'
 
-  Workflow.require_workflow workflow
-  WorkflowREST.add_workflows *Workflow.workflows
+  #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'
+
+  require 'rbbt/rest/main'
+  require 'rbbt/rest/entity'
+  require 'rbbt/rest/workflow'
+  require 'rbbt/rest/file_server'
+  require 'rbbt/rest/helpers'
 
-  WorkflowREST.setup
+  YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler
 
-  Sinatra::Application.port = options[:port] || 4567
-  Sinatra::Application.run = true
+  Workflow.require_workflow workflow
+
+  class WorkflowRest < Sinatra::Base
+    get '/' do
+      redirect to(File.join('/', Workflow.workflows.last.to_s))
+    end
+  end
 
-  if File.exists? workflow
-    Sinatra::Application.views = File.join(File.dirname(workflow), 'www/views')
+  if options[:profile]
+    WorkflowRest.before File.join('/', Workflow.workflows.last.to_s, '*') do
+      @profile = true
+    end
   end
 
-  sinatra_file = './lib/sinatra.rb'
-  if File.exists? sinatra_file
-    require sinatra_file
+  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!
 else
 
   # Set log, fork, clean, recursive_clean and help
@@ -147,7 +209,7 @@ else
     namespace, task = options.delete(:task).split('.')
     namespace = Misc.string2const(namespace)
   else
-    task_name = options.delete(:task)
+    task_name = options.delete(:task).to_sym
     task = workflow.tasks[task_name]
     raise "Task not found: #{ task_name }" if task.nil?
   end

data/lib/rbbt.rb

@@ -12,5 +12,5 @@ module 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
+  Persist.cachedir     = var.cache.persistence.find :user
 end

data/lib/rbbt/annotations.rb

@@ -209,7 +209,7 @@ module Annotation
 
     hash.each do |key, value|
       begin
-        next unless @annotations.include? (key = key.to_sym)
+        next unless @annotations.include?(key = key.to_sym)
       rescue
         next
       end
@@ -280,21 +280,3 @@ module Annotation
     mod.instance_variable_set(:@masked_annotations, self.masked_annotations.dup)
   end
 end
-
-
-if __FILE__ == $0
-
-  module Gene
-    extend Annotation
-    annotation :format, :organism
-  end
-
-  a = %w(1 2 3 4 5 6 6)
-  Gene.setup a, "Ensembl Gene ID", "Hsa"
-
-  puts a.reject{|a| a.to_i < 6}.collect{|e| e.format}
-
-  puts 
-
-  puts a.reject{|a| a.to_i < 6}.uniq.collect{|e| e.format}
-end

data/lib/rbbt/annotations/annotated_array.rb

@@ -1,4 +1,6 @@
 module AnnotatedArray
+  attr_accessor :list_id
+
   def double_array
     AnnotatedArray === self.send(:[], 0, true)
   end
@@ -153,6 +155,27 @@ module AnnotatedArray
     res
   end
 
+  def select_by(method, *args, &block)
+    return [] if self.empty? and not self.respond_to? :annotate
+
+    values = self.send(method, *args)
+    values = values.clean_annotations if values.respond_to? :clean_annotations
+
+    new = []
+    if block_given?
+      self.clean_annotations.each_with_index do |e,i|
+        new << e if yield(values[i])
+      end
+    else
+      self.clean_annotations.each_with_index do |e,i|
+        new << e if values[i]
+      end
+    end
+    self.annotate(new)
+    new.extend AnnotatedArray
+
+    new
+  end
 
   %w(compact uniq flatten reverse sort_by).each do |method|
 

data/lib/rbbt/fix_width_table.rb

@@ -116,14 +116,14 @@ class FixWidthTable
   #{{{ Adding data
 
   def add_point(data)
-    data.sort_by{|value, pos| pos}.each do |value, pos|
+    data.sort_by{|value, pos| pos }.each do |value, pos|
       add pos, value
     end
   end
 
   def add_range(data)
     latest = []
-    data.sort_by{|value, pos| pos[0]}.each do |value, pos|
+    data.sort_by{|value, pos| pos[0] }.each do |value, pos|
       while latest.any? and latest[0] < pos[0]
         latest.shift
       end

data/lib/rbbt/persist.rb

@@ -1,3 +1,4 @@
+require 'rbbt'
 require 'rbbt/util/misc'
 require 'rbbt/util/open'
 
@@ -5,10 +6,10 @@ require 'rbbt/persist/tsv'
 require 'set'
 
 module Persist
-  CACHEDIR="/tmp/tsv_persistent_cache"
+  CACHEDIR = "/tmp/tsv_persistent_cache" unless defined? CACHEDIR
   FileUtils.mkdir CACHEDIR unless File.exist? CACHEDIR
 
-  MEMORY = {}
+  MEMORY = {} unless defined? MEMORY
 
   def self.cachedir=(cachedir)
     CACHEDIR.replace cachedir
@@ -72,7 +73,7 @@ module Persist
     File.join(persistence_dir, filename)
   end
 
-  TRUE_STRINGS = Set.new ["true", "True", "TRUE", "t", "T", "1", "yes", "Yes", "YES", "y", "Y", "ON", "on"]
+  TRUE_STRINGS = Set.new ["true", "True", "TRUE", "t", "T", "1", "yes", "Yes", "YES", "y", "Y", "ON", "on"] unless defined? TRUE_STRINGS
   def self.load_file(path, type)
     case (type || "nil").to_sym
     when :nil
@@ -231,6 +232,7 @@ module Persist
               repo[subkey + entities.id << ":" << "SINGLE"] = tsv_values
             when (not Array === entities or (AnnotatedArray === entities and AnnotatedArray === entities.first))
               entities.each_with_index do |e,i|
+                next if e.nil?
                 tsv_values = e.tsv_values("literal", "annotation_types", "JSON") 
                 repo[subkey + e.id << ":ANNOTATED_DOUBLE_ARRAY:" << i.to_s] = tsv_values
               end
@@ -276,12 +278,18 @@ end
 module LocalPersist
 
   attr_accessor :local_persist_dir
+
+  def local_persist_dir
+    @local_persist_dir ||= Rbbt.var.cache.persistence.find(:lib) if defined? Rbbt
+    @local_persist_dir
+  end
+
   def local_persist(name, type = nil, options= {}, &block)
-    Persist.persist(name, type, options.merge({:dir => @local_persist_dir}), &block)
+    Persist.persist(name, type, options.merge({:dir => local_persist_dir}), &block)
   end
 
   def local_persist_tsv(source, name, opt = {}, options= {}, &block)
-    Persist.persist_tsv(source, name, opt, options.merge({:dir => @local_persist_dir}), &block)
+    Persist.persist_tsv(source, name, opt, options.merge({:dir => local_persist_dir}), &block)
   end
 
 end

data/lib/rbbt/persist/tsv.rb

@@ -138,6 +138,8 @@ module Persist
            when persist_options[:persist]
 
              filename ||= case
+                          when Path === source
+                            source
                           when source.respond_to?(:filename)
                             source.filename
                           when source.respond_to?(:cmd)

data/lib/rbbt/resource.rb

@@ -1,9 +1,9 @@
-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'
-
+#require 'rbbt/resource/rake'
+ 
 module Resource
   extend ChainMethods
   self.chain_prefix = :resource
@@ -53,7 +53,7 @@ module Resource
       if type == :install
         Log.debug "Preparing software: #{path}"
         path.produce
-        software_dir = path.resource.root.software.find :user
+        software_dir = path.resource.root.software
         set_software_env(software_dir)
       end
     end