Add ep3-hook

.devcontainer/install-medal-hook.sh

@@ -0,0 +1,10 @@
+#!/bin/sh
+
+if [ $# -eq 1 ]; then
+    download_str="download/$1"
+else
+    download_str=latest/download
+fi
+
+curl -SL https://github.com/tom-tan/medal-hook/releases/${download_str}/medal-hook-linux-x86_64.tar.gz \
+    | tar xC /usr/bin

ep3

@@ -3,5 +3,6 @@
 basedir=$(cd $(dirname $0) && pwd -P)
 export EP3_LIBPATH=$basedir/lib/ep3
 export EP3_TEMPLATE_DIR=$basedir/share/ep3
+export EP3_EXT_PATH=$basedir/lib/ep3/extensions
 
 $EP3_LIBPATH/ep3.rb "$@"

ep3-runner

@@ -41,13 +41,18 @@ rescue => e
 end
 
 if $0 == __FILE__
+  extensions = []
+
   parser = OptionParser.new
   parser.banner = "Usage: #{$0} cwl [jobfile]"
   parser.on('--tmpdir=TMP', 'directory for temporary files')
   parser.on('--outdir=OUT', 'directory for output objects')
   parser.on('--leave-tmpdir', 'do not remove temporary directory')
   parser.on('--debug', 'enable debug output')
   parser.on('--quiet', 'disable information output')
+  parser.on('--extension', 'specify extension') { |ext|
+    extensions.push ext
+  }
   parser.on('--version', 'show version information') {
     system('git describe', :chdir => File.dirname($0))
     exit
@@ -84,6 +89,15 @@ if $0 == __FILE__
   end
 
   begin
+    unless extensions.empty?
+      ret_hook = run_cmd("#{basedir}/ep3 hook --extensions=#{extensions.join(',')} #{target_arg}")
+      if ret_hook.include? 'interrupted'
+        exit 1
+      elsif not ret_hook['success']
+        exit ret_hook.fetch('return', 1)
+      end
+    end
+
     qopt = quiet ? '--quiet ' : ''
     dopt = debug ? '--debug ' : ''
     ret_run = run_cmd("#{basedir}/ep3 run #{qopt}#{dopt}#{target_arg} #{job}", debug)

lib/ep3/ep3-hook.rb

@@ -0,0 +1,68 @@
+#!/usr/bin/env ruby
+require 'optparse'
+require 'fileutils'
+
+def ep3_hook(args)
+    extensions = []
+
+    parser = OptionParser.new
+    parser.banner = "Usage: ep3 list [options]"
+    parser.on('--target-dir=DIR')
+    parser.on('--extensions=EXTS') { |exts|
+        extensions = exts.split(',')
+    }
+
+    opts = parser.getopts(args)
+    unless args.empty?
+        puts parser.help
+        exit
+    end
+
+    dir = if opts.include? 'target-dir'
+            opts['target-dir']
+          else
+            raise '--target-dir is needed'
+          end
+    unless Dir.exist? dir
+        raise "Directory not found: #{dir}"
+    end
+
+    unless ENV.include? 'EP3_EXT_PATH'
+        raise 'EP3_EXT_PATH is necessary to apply extensions'
+    end
+    extPaths = ENV['EP3_EXT_PATH'].split(':')
+
+    extFiles = extensions.map{ |e|
+        ret = extPaths.find{ |path|
+            File.exist?(File.join(path, e))
+        }
+        if ret.nil?
+            raise "Extension #{e} not found"
+        end
+        File.join(ret, e, 'extension.yml')
+    }
+    extArgs = extFiles.map{ |e| "--hook=#{e}" }
+    apply(File.join(dir, 'workdir', 'job.yml'), extArgs)
+end
+
+def apply(network, exts)
+    orig = "#{network}.orig"
+    unless File.exist?(orig)
+        FileUtils.mv(network, orig)
+    end
+    ret = system("medal-hook #{orig} #{exts.join(' ')} > #{network}")
+    ret = 0
+    return 1 unless ret
+    stepdir = File.join(File.dirname(network), 'steps')
+    if Dir.exist?(stepdir)
+        Dir.glob("#{stepdir}/*") { |d|
+            r = apply(File.join(d, 'job.yml'), exts)
+            ret = (ret and r)
+        }
+    end
+    ret
+end
+
+if $0 == __FILE__
+  ep3_hook(ARGV)
+end

lib/ep3/ep3.rb

@@ -3,6 +3,7 @@
 require_relative 'ep3-init'
 require_relative 'ep3-run'
 require_relative 'ep3-list'
+require_relative 'ep3-hook'
 
 if $0 == __FILE__
   parser = OptionParser.new
@@ -13,7 +14,7 @@
         init          initialize a configuration for a given workflow
         run           run the workflow for a given input
         list          show the output object for the given workflow
-        stop          (stop running the workflow)
+        hook          apply extensions to Petri Nets for a given workflow
         resume        (not yet implemented)
 EOS
 
@@ -28,7 +29,7 @@
        when 'init'      then ep3_init(ARGV)
        when 'run'       then ep3_run(ARGV)
        when 'list'      then ep3_list(ARGV)
-       when 'stop'      then ep3_stop(ARGV)
+       when 'hook'      then ep3_hook(ARGV)
        when 'resume'    then ep3_resume(ARGV)
        else raise "No such subcommand: #{cmd}"
        end