rbbt-util 5.9.2 → 5.9.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: f42669bd1035c8734f8425f317ce30f8a0aedbaa
+  metadata.gz: 29daeb012f3ce90b479f7b858abff79e166f936d
+  data.tar.gz: 78e6fd7422a46b33271de8c8f0eb81d0fc97d772
 SHA512:
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-  data.tar.gz: d617993ba70c9cb43a5aa9ba176da9994db0493aafc484831b68bb7c1804f34ffff3a7f88c2342d21d3b06cfd4a5db08014e033cd90915669e6cd7b56625f18f
+  metadata.gz: bcbb30fb3e53e872d6b2de2fce030f93a78fbe01b7d1a238d8dff243d602f2f42ba6d11e01de4f11ac9aead3d4a90c03779bdd8f1311aa72b4c62d2d320bfef5
+  data.tar.gz: 4e5faf9f1ac86e500fd9f5d747ed2c34ba31aabf2a8bbced66aa626bb7e2f1b7d3428cd5af714dfe09c7ae5990302409edfb691bafe1e7fa4bf99d64c01f4dcc

data/lib/rbbt/tsv/accessor.rb

@@ -199,6 +199,7 @@ module TSV
   end
 
   def zip_new(key, values)
+    values = [values] unless Array === values
     if self.include? key
       new = []
       self[key, true].each_with_index do |v,i|

data/lib/rbbt/util/misc.rb

@@ -43,7 +43,7 @@ module Misc
               word = words.shift
               while word
                 word = word[0..size-indent-offset-4] + '...' if word.length >= size - indent - offset
-                while word and line.length + word.length <= size - indent
+                while word and Log.uncolor(line).length + Log.uncolor(word).length <= size - indent
                   line << word << " "
                   word = words.shift
                 end
@@ -60,6 +60,7 @@ module Misc
   end
 
   def self.format_definition_list_item(dt, dd, size = 80, indent = 20, color = :yellow)
+    dd = "" if dd.nil?
     dt = dt.to_s + ":" unless dd.empty?
     dt = Log.color color, dt if color
     len = Log.uncolor(dt).length

data/lib/rbbt/workflow.rb

@@ -107,9 +107,21 @@ module Workflow
       remote_workflows = Rbbt.etc.remote_workflows.yaml
       if Hash === remote_workflows and remote_workflows.include?(wf_name)
         url = remote_workflows[wf_name]
-        require_remote_workflow(wf_name, url)
+        begin
+          return require_remote_workflow(wf_name, url)
+        ensure
+          Log.debug{"Workflow #{ wf_name } loaded remotely: #{ url }"}
+        end
+      end
+    end
+
+    if Open.remote? wf_name
+      url = wf_name
+      wf_name = File.basename(url)
+      begin
+        return require_remote_workflow(wf_name, url)
+      ensure
         Log.debug{"Workflow #{ wf_name } loaded remotely: #{ url }"}
-        return
       end
     end
 

data/lib/rbbt/workflow/accessor.rb

@@ -238,6 +238,29 @@ end
 
 module Workflow
 
+  def self.load_inputs(dir, input_names, input_types)
+    inputs = {}
+    dir = Path.setup(dir.dup)
+    input_names.each do |input|
+      file = dir[input].find
+      Log.debug "Trying #{ input }: #{file}"
+      next unless file.exists?
+
+      case input_types[input]
+      when :tsv, :array, :text
+        Log.debug "Pointing #{ input } to #{file}"
+        inputs[input.to_sym]  = file
+      when :boolean
+        inputs[input.to_sym]  = (file.read.strip == 'true')
+      else
+        Log.debug "Loading #{ input } from #{file}"
+        inputs[input.to_sym]  = file.read.strip
+      end
+
+    end
+    IndiferentHash.setup(inputs)
+  end
+
   def log(status, message = nil, &block)
     Step.log(status, message, nil, &block)
   end
@@ -264,7 +287,7 @@ module Workflow
                :none
              end
 
-    
+
     dependencies = task_dependencies[name].select{|dep| String === dep or Symbol === dep}
     { :id => File.join(self.to_s, name.to_s),
       :description => description,

data/share/rbbt_commands/workflow/cmd

@@ -38,14 +38,14 @@ begin
 end
 
 puts SOPT.doc
-
-puts "## COMMANDS"
 puts
-puts "Command:"
+puts Log.color :magenta, "## COMMANDS"
+puts
+puts Log.color :magenta, "Command:"
 puts 
-puts "  #{File.basename($0)} #{prev * " "}"
+puts "  #{File.basename($0)} #{$previous_commands * " "} cmd"
 puts 
-puts "Subcommands:"
+puts Log.color :magenta, "Subcommands:"
 puts 
 commands(prev).each do |command|
     puts "  " << command

data/share/rbbt_commands/workflow/task

@@ -4,25 +4,6 @@ require 'rbbt/util/simpleopt'
 require 'rbbt/workflow'
 require 'rbbt/workflow/usage'
 
-def load_inputs(dir, task)
-  inputs = {}
-  dir = Path.setup(dir.dup)
-  task.inputs.each do |input|
-    file = dir[input].find
-    Log.debug "Trying #{ input }: #{file}"
-    next unless file.exists?
-    case task.input_types[input]
-    when :tsv, :array, :text
-      Log.debug "Pointing #{ input } to #{file}"
-      inputs[input.to_sym]  = file
-    else
-      Log.debug "Loading #{ input } from #{file}"
-      inputs[input.to_sym]  = file.read.strip
-    end
-  end
-  IndiferentHash.setup(inputs)
-end
-
 def report_options(options)
   if options.nil? or options.empty?
     puts "No options"
@@ -73,14 +54,14 @@ def SOPT_options(workflow, task)
 end
 
 def fix_options(workflow, task, job_options)
-  option_types = workflow.rec_input_types(task.name)
+  option_types = IndiferentHash.setup workflow.rec_input_types(task.name)
 
   job_options_cleaned = {}
 
   job_options.each do |name, value|
     value = case option_types[name].to_sym
             when :boolean
-              TrueClass === true or %w(true TRUE T yes).include? value
+              TrueClass === value or %w(true TRUE T yes).include? value
             when :float
               value.to_f
             when :integer
@@ -195,14 +176,7 @@ else
   remote_workflows = {}
 end
 
-if remote_workflows.include? workflow
-  require 'rbbt/rest/client'
-  workflow = WorkflowRESTClient.new remote_workflows[workflow], workflow
-else
-  Workflow.require_workflow workflow
-  workflow = Workflow.workflows.select{|mod| Misc.snake_case(mod.to_s) == Misc.snake_case(workflow)}.first
-  workflow = Workflow.workflows.last if workflow.nil?
-end
+workflow = Workflow.require_workflow workflow
 
 # Set task
 namespace = nil, nil
@@ -235,7 +209,8 @@ name = options.delete(:jobname) || "Default"
 # get job args
 sopt_option_string = SOPT_options(workflow, task)
 if options[:load_inputs]
-  job_options = load_inputs(options[:load_inputs], task).merge(SOPT.get(sopt_option_string))
+  task_info = workflow.task_info(task_name)
+  job_options = Workflow.load_inputs(options[:load_inputs], task_info[:inputs], task_info[:input_types]).merge(SOPT.get(sopt_option_string))
 else
   job_options = SOPT.get sopt_option_string
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.9.2
+  version: 5.9.3
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-19 00:00:00.000000000 Z
+date: 2014-03-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake