rbbt-util 5.21.128 → 5.21.129

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 78800e637163f3ddfc6cee51ea06a19a58d9e47baa87ec73327268414c72c731236f49dd1f6d0a18b25eebaf1df6f4c7063ee52fbb626441ab41c55eb24e990e

data/lib/rbbt/util/misc/inspect.rb

@@ -1,6 +1,6 @@
 module Misc
   ARRAY_MAX_LENGTH = 1000
-  STRING_MAX_LENGTH = ARRAY_MAX_LENGTH * 10
+  STRING_MAX_LENGTH = ARRAY_MAX_LENGTH * 100
 
   def self.break_lines(text, char_size=80)
     text = text.gsub("\n", " ")

data/share/rbbt_commands/app/template

@@ -1,4 +1,36 @@
 #!/usr/bin/env ruby
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+
+Run a web server over a simgle template
+
+$ rbbt app template [options] <filename.haml>
+
+-e--environment*
+-p--port*
+-s--server*
+-b--bind*
+-e--environment*
+-R--RServe_session*
+--finder
+--views*
+-W--workflows*"
+-h--help Print this help
+
+EOF
+if options[:help]
+  if defined? rbbt_usage
+    rbbt_usage 
+  else
+    puts SOPT.doc
+  end
+  exit 0
+end
+
 
 require 'rbbt/util/simpleopt'
 require 'rbbt/workflow'
@@ -13,10 +45,11 @@ require 'rbbt/rest/knowledge_base'
 require 'rbbt/rest/helpers'
 require 'rbbt/rest/web_tool'
 
-options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*:-R--RServe_session*:--finder:--views*:-W--workflows*"
 
 template = ARGV.first
 
+raise ParameterException, "No template specified" if template.nil?
+
 template = File.expand_path(template)
 template = template.sub('.haml','')
 

data/share/rbbt_commands/stat/heatmap

@@ -44,13 +44,13 @@ positive = false if positive.nil?
 require 'rbbt/util/R'
 if png
     R.run <<-EOF
-data = rbbt.tsv('#{file}')
-rbbt.pheatmap('#{png}', data, positive=#{R.ruby2R positive})
+data = rbbt.tsv2matrix(rbbt.tsv('#{file}'))
+rbbt.pheatmap('#{png}', data, width=#{ width }, height=#{ height }, take_log=#{R.ruby2R logs}, positive=#{R.ruby2R positive})
     EOF
 else
     TmpFile.with_file(nil, :extension => 'png') do |png|
         R.run <<-EOF
-data = rbbt.tsv('#{file}')
+data = rbbt.tsv2matrix(rbbt.tsv('#{file}'))
 rbbt.pheatmap('#{png}', data, width=#{ width }, height=#{ height }, take_log=#{R.ruby2R logs}, positive=#{R.ruby2R positive})
         EOF
         `op #{png}`

data/share/rbbt_commands/workflow/cmd

@@ -1,16 +1,37 @@
 #!/usr/bin/env ruby
 
-require 'rbbt'
+require 'rbbt-util'
 require 'rbbt/util/simpleopt'
-require 'rbbt/workflow'
 
+$0 = "rbbt #{$previous_commands*" "} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+
+Run a workflow command
+
+$ rbbt workflow cmd <workflow> <command> [<subcommands>] [<options>] [<arg> ...]
+
+EOF
 workflow = ARGV.shift
 
+if workflow == '-h'
+  if defined? rbbt_usage
+    rbbt_usage 
+  else
+    puts SOPT.doc
+  end
+  exit 0
+end
+
+raise ParameterException, "No workflow specified" if workflow.nil?
+
+require 'rbbt/workflow'
+
 wf = Workflow.require_workflow workflow
-dir = $command_dir = wf.libdir.share.rbbt_commands
+dir = $command_dir = wf.libdir.share.rbbt_commands.find
 
 def prev_dir(prev)
-    rbbt_command_dir = $rbbt_command_dir
+    rbbt_command_dir = $command_dir
 
     prev.each do |previous_command|
         rbbt_command_dir = rbbt_command_dir[previous_command]
@@ -30,12 +51,16 @@ end
 
 prev = []
 
+$previous_commands << 'cmd'
+$previous_commands << workflow
+
 begin
   while ARGV.any?
     command = ARGV.shift
     case
     when File.directory?(dir[command].find)
       prev << command
+      $previous_commands << command
       dir = dir[command]
     when File.directory?(dir[command].find)
       prev << command
@@ -63,7 +88,7 @@ puts Log.color :magenta, "## COMMANDS"
 puts
 puts Log.color :magenta, "Command:"
 puts 
-puts "  #{File.basename($0)} #{$previous_commands * " "} cmd"
+puts " rbbt #{$previous_commands * " "} "
 puts 
 puts Log.color :magenta, "Subcommands:"
 puts 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.128
+  version: 5.21.129
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-05-04 00:00:00.000000000 Z
+date: 2018-05-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake