rbbt-util 5.5.32 → 5.5.33

checksums.yaml

@@ -1,15 +1,15 @@
 ---
 !binary "U0hBMQ==":
   metadata.gz: !binary |-
-    MmRkMzQwMzlmNjZkOTJiNTkwZThjNjRjNDRlZTkyYTRhNDk4MjJjZg==
+    ZWEwNDc0YzJmMjEzZTdmMDQzNTdiMzg0MTdiNWQ2OTA1ZTgzYTk3ZQ==
   data.tar.gz: !binary |-
-    ZmM5ZmVkNmQ4YTVkN2E5MzM3YzQyZTA1NTQ1OTI3YWJkYTU4MWZmMQ==
+    MWMzNGU3YTA5MGJiMzkyZDNkOGUyZjYyOTE5YTM0ZDkwYWM2Yzc3MA==
 SHA512:
   metadata.gz: !binary |-
-    Njc4YmFmY2MwMzRkMTE3N2E2YThmNmUwMWEyOTFjNDQ2NDFiZjUzM2QyZWE0
-    ODFjY2QwMTY4MGZlYWIyMDdkMmRjMDQ2NDFmODJjNmVkNTM4MDY3MDAzN2Rm
-    MWMzOTJmZGJjMGY0ZWIwNzE3YzAwYjE4Y2IyYTM0ZjVkNGQ5ZTQ=
+    MzMyM2RmMjRiMDkxMzIxMjQ0MmMxMjU4YWJmYTc4MThmNGJjOTZlZWI3YTNl
+    NGZjMGViMTFmOWRkN2FkYjIxODZlNjA1NmFhZGE3MTdhYmVmYzdiZmU2N2Ri
+    N2M2OGRkZTE1NmU3ODkyZWY2NjkyMmU2ZjlmZTJlN2UwMTk0ZGE=
   data.tar.gz: !binary |-
-    MWQxOGUwYTliMjFhODkwZGE0NTk1NTRmNjExOTIzMDEzM2UzMDJiZjE5OGI2
-    ZDQ0ZjBkMGI4NGY2MDgxY2NlMjkxOWNkNTA4ZGRmYzE3ZWRiNDA0ODY4ZGUz
-    NzNkNzk5NGE2MTgzOTc1M2U4NDI5MTBhM2YwOGY5YTYyOTJmZDk=
+    OGQ3MTI4Yzc2NjIzNjQ1NjFmNjI4YWUxMzZlOTViMWU0NWZmOWU5ZjQ1MWJi
+    ZjBkOWRiYjg4YWZkNmNmNGVmYTBmZDdmMGMwNmZiOTJmMDE0MDY0YzRmOTE0
+    Njc0N2FmZmMxZDQ0ODZjYzliYzFkZWIyNWFjY2VlYWY5YzMxM2I=

data/bin/rbbt_exec.rb

@@ -1,6 +1,5 @@
 #!/usr/bin/env ruby
 
-
 code_file = ARGV[0]
 output = ARGV[1]
 

data/etc/app.d/base.rb

@@ -1,11 +1,14 @@
 #{{{ MODULES AND HELPERS
+
 register Sinatra::RbbtRESTWorkflow
+
 if Rbbt.etc.workflows.find.exists?
  Rbbt.etc.workflows.find.read.split("\n").each do |workflow|
   Workflow.require_workflow workflow
   add_workflow Kernel.const_get(workflow), true
  end
 end
+
 register Sinatra::RbbtRESTMain
 register Sinatra::RbbtRESTEntity
 register Sinatra::RbbtRESTFileServer # Remove to prevent serving files
@@ -13,6 +16,7 @@ register Sinatra::RbbtRESTKnowledgeBase
 helpers Sinatra::RbbtMiscHelpers
 
 #{{{ SESSIONS
+
 use Rack::Session::Cookie, :key => 'rack.session',
   :path => '/',
   :expire_after => 2592000,

data/share/config.ru

@@ -1,6 +1,6 @@
+require 'rbbt'
 require 'rbbt/resource'
 
-require 'rbbt'
 load Rbbt.etc['app.d/init.rb'].find
 
 $class_name = class_name = File.basename(FileUtils.pwd)
@@ -9,16 +9,16 @@ $app = app = eval "class #{class_name} < Sinatra::Base; self end"
 
 $LOAD_PATH.unshift('lib')
 
-#{{{ POST
+#{{{ PRE
 Log.info{"Loading: " << Rbbt.etc['app.d/pre.rb'].find if Rbbt.etc['app.d/pre.rb'].exists?}
 load Rbbt.etc['app.d/pre.rb'].find if Rbbt.etc['app.d/pre.rb'].exists?
 
+#{{{ BASE
 app.class_eval do
   Log.info{"Loading: " << Rbbt.etc['app.d/base.rb'].find}
   eval Rbbt.etc['app.d/base.rb'].read, nil, Rbbt.etc['app.d/base.rb'].find
 end
 
-
 #{{{ RESOURCES
 Log.info{"Loading: " << Rbbt.etc['app.d/resources.rb'].find}
 load Rbbt.etc['app.d/resources.rb'].find

data/share/rbbt_commands/app/template

@@ -0,0 +1,66 @@
+#!/usr/bin/env ruby
+
+require 'rbbt'
+require 'rbbt/resource'
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+options = SOPT.get "-e--environment*:-p--port*:-s--server*:-h--host*:-f--finder"
+options[:Port] ||= options[:port]
+
+file = ARGV.shift
+
+load Rbbt.etc['app.d/init.rb'].find
+
+$class_name = class_name = "SingleTemplate"
+
+$app = app = eval "class #{class_name} < Sinatra::Base; self end"
+
+#$LOAD_PATH.unshift('lib')
+
+#{{{ PRE
+Log.info{"Loading: " << Rbbt.etc['app.d/pre.rb'].find if Rbbt.etc['app.d/pre.rb'].exists?}
+load Rbbt.etc['app.d/pre.rb'].find if Rbbt.etc['app.d/pre.rb'].exists?
+
+app.get '/' do
+  file = file.sub(/\.haml/,'')
+  template_render(file)
+end
+
+#{{{ BASE
+app.class_eval do
+  Log.info{"Loading: " << Rbbt.etc['app.d/base.rb'].find}
+  eval Rbbt.etc['app.d/base.rb'].read, nil, Rbbt.etc['app.d/base.rb'].find
+end
+
+#{{{ RESOURCES
+Log.info{"Loading: " << Rbbt.etc['app.d/resources.rb'].find}
+load Rbbt.etc['app.d/resources.rb'].find
+
+#{{{ ENTITIES
+Log.info{"Loading: " << Rbbt.etc['app.d/entities.rb'].find}
+load Rbbt.etc['app.d/entities.rb'].find
+
+#{{{ FINDER
+app.class_eval do
+  Log.info{"Loading: " << Rbbt.etc['app.d/finder.rb'].find}
+  eval Rbbt.etc['app.d/finder.rb'].read
+end
+
+#{{{ POST
+Log.info{"Loading: " << Rbbt.etc['app.d/post.rb'].find if Rbbt.etc['app.d/post.rb'].exists?}
+load Rbbt.etc['app.d/post.rb'].find if Rbbt.etc['app.d/post.rb'].exists?
+
+#{{{ RUN
+$title = class_name
+require 'rack'
+
+ENV["RBBT_FINDER"] = "true" if options.include?(:finder)
+ENV["RACK_ENV"] = options[:environment] if options.include?(:environment)
+
+RbbtRESTHelpers.template_resources.unshift Path.setup(File.expand_path(File.dirname(file)))
+
+app.port = options[:port] if options[:port]
+app.server = options[:server] if options[:server]
+app.environment = options[:environment] if options[:environment]
+app.run!

data/share/rbbt_commands/tsv/info

@@ -3,20 +3,26 @@
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
 
+options = SOPT.get("-tc--tokyocabinet")
 
 file = ARGV.shift
 
-header = TSV.parse_header(Open.open(file))
+if options[:tokyocabinet]
+  tsv = Persist.open_tokyocabinet(file, false)
+  puts tsv.summary
+else
+  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
+  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:"
+  parts = []
+  header.first_line.split(header.sep).each_with_index{|p,i| parts << "(#{i}) #{p}"}
+  puts parts * "\t"
 end
-puts "Rows: #{`wc -l #{ file }|cut -f 1 -d' '`}"
-puts "First line:"
-parts = []
-header.first_line.split(header.sep).each_with_index{|p,i| parts << "(#{i}) #{p}"}
-puts parts * "\t"
 

data/{bin/rbbt_monitor.rb → share/rbbt_commands/workflow/monitor}

@@ -8,7 +8,6 @@ require 'rbbt/util/misc'
 
 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

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.5.32
+  version: 5.5.33
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -69,13 +69,9 @@ dependencies:
 description: Utilities for handling tsv files, caches, etc
 email: miguel.vazquez@cnio.es
 executables:
-- tsv.rb
-- tchash.rb
-- run_workflow.rb
 - rbbt_query.rb
 - rbbt_exec.rb
 - rbbt_Rutil.rb
-- rbbt_monitor.rb
 - rbbt
 - rbbt_dangling_locks.rb
 extensions: []
@@ -89,11 +85,7 @@ files:
 - bin/rbbt_Rutil.rb
 - bin/rbbt_dangling_locks.rb
 - bin/rbbt_exec.rb
-- bin/rbbt_monitor.rb
 - bin/rbbt_query.rb
-- bin/run_workflow.rb
-- bin/tchash.rb
-- bin/tsv.rb
 - etc/app.d/base.rb
 - etc/app.d/entities.rb
 - etc/app.d/finder.rb
@@ -158,6 +150,7 @@ files:
 - share/install/software/lib/install_helpers
 - share/rbbt_commands/app/install
 - share/rbbt_commands/app/start
+- share/rbbt_commands/app/template
 - share/rbbt_commands/conf/web_user/add
 - share/rbbt_commands/conf/web_user/list
 - share/rbbt_commands/conf/web_user/remove
@@ -170,6 +163,7 @@ files:
 - share/rbbt_commands/tsv/info
 - share/rbbt_commands/workflow/cmd
 - share/rbbt_commands/workflow/install
+- share/rbbt_commands/workflow/monitor
 - share/rbbt_commands/workflow/remote/add
 - share/rbbt_commands/workflow/remote/list
 - share/rbbt_commands/workflow/remote/remove

data/bin/run_workflow.rb

@@ -1,240 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'rbbt'
-require 'rbbt/util/simpleopt'
-require 'rbbt/workflow'
-require 'pp'
-
-def usage(task)
-  puts task.usage
-  exit -1
-end
-
-def SOPT_options(workflow, task)
-  sopt_options = []
-  workflow.rec_inputs(task.name).each do |name|
-    short = name.to_s.chars.first
-    boolean = workflow.rec_input_types(task.name)[name].to_sym == :boolean
-    
-    sopt_options << "-#{short}--#{name}#{boolean ? '' : '*'}"
-  end
-
-  sopt_options * ":"
-end
-
-def fix_options(workflow, task, job_options)
-  option_types = workflow.rec_input_types(task.name)
-
-  #workflow.resolve_locals(job_options)
-
-  job_options_cleaned = {}
-
-  job_options.each do |name, value|
-    value = case option_types[name].to_sym
-            when :float
-              value.to_f
-            when :integer
-              value.to_i
-            when :string, :text
-              case
-              when value == '-'
-                STDIN.read
-              when (String === value and File.exists?(value))
-                Open.read(value)
-              else
-                value
-              end
-            when :array
-              if Array === value
-                value
-              else
-                case
-                when value == '-'
-                  STDIN.read
-                when (String === value and File.exists?(value))
-                  Open.read(value)
-                else
-                  value
-                end.split(/[,|\s]/)
-              end
-            when :tsv
-              if TSV === value
-                value
-              else
-                begin
-                  if value == '-'
-                    TSV.open(STDIN).to_s :sort
-                  else
-                    TSV.new(value).to_s :sort
-                  end
-                rescue
-                  value
-                end
-              end
-            else
-              value
-            end
-    job_options_cleaned[name] = value
-  end
-
-  job_options_cleaned
-end
-
-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 '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'
-
-  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!
-else
-
-  # Set log, fork, clean, recursive_clean and help
-  Log.severity = options[:log].to_i if options.include? :log
-  help = !!options.delete(:help)
-  do_fork = !!options.delete(:fork)
-  clean = !!options.delete(:clean)
-  recursive_clean = !!options.delete(:recursive_clean)
-
-
-  # Get workflow
-  
-  if Rbbt.etc.remote_workflows.exists?
-    remote_workflows = Rbbt.etc.remote_workflows.yaml
-  else
-    remote_workflows = {}
-  end
-
-  if remote_workflows.include? workflow
-    require 'rbbt/workflow/rest/client'
-    workflow = RbbtRestClient.new remote_workflows[workflow], workflow
-  else
-    Workflow.require_workflow workflow
-    workflow = Workflow.workflows.last
-  end
-
-  # Set task
-  namespace, task = nil, nil
-
-  case 
-  when (not options[:task])
-    usage if help
-    task = workflow.last_task
-    namespace = workflow
-  when (options[:task] =~ /\./)
-    namespace, task = options.delete(:task).split('.')
-    namespace = Misc.string2const(namespace)
-  else
-    task_name = options.delete(:task).to_sym
-    task = workflow.tasks[task_name]
-    raise "Task not found: #{ task_name }" if task.nil?
-  end
-
-
-  workflow.usage(task) if help
-
-  name = options.delete(:name) || "Default"
-
-  # get job args
-  sopt_option_string = SOPT_options(workflow,task)
-  job_options = SOPT.get sopt_option_string
-  job_options = fix_options(workflow,task, job_options)
-
-  #- get job
-  job = workflow.job(task.name, name, job_options)
-
-  # clean job
-  job.clean if clean
-  job.recursive_clean if recursive_clean
-
-  # run
-  if do_fork
-    job.fork
-    while not job.done?
-      Log.debug "#{job.step}: #{job.messages.last}"
-      sleep 2
-    end
-    raise job.messages.last if job.error?
-    res = job.load
-  else
-    res = job.run
-  end
-
-  if options.delete(:printname)
-    puts job.name
-    exit
-  else
-    Log.low "Job name: #{job.name}"
-  end
-
-  case
-  when Array === res
-    puts res * "\n"
-  when TSV === res
-    puts res
-  when Hash === res
-    puts res.to_yaml
-  else
-    puts res
-  end
-end

data/bin/tchash.rb

@@ -1,15 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'rbbt-util'
-require 'rbbt/util/simpleopt'
-
-options = SOPT.parse "-h--help"
-
-command = ARGV.shift
-file    = ARGV.shift
-
-case command
-when 'cat'
-  puts TSV.new(TCHash.get(file))
-end
-

data/bin/tsv.rb

@@ -1,14 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'rbbt/util/simpleopt'
-
-options = SOPT.get "-h--help:-to--tsv-options*:-p--persistence"
-
-command = ARGV.shift
-file    = ARGV.shift
-
-case command
-when 'cat'
-  puts TSV.new(file, options["tsv-options"].merge(options["persistence"]))
-when 
-