Add --[no-]compute-checksum option

ep3-runner

@@ -67,6 +67,7 @@ end
 
 if $0 == __FILE__
   extensions = []
+  compute_checksum = true
   loglevel = Normal
   keep_tmpdir_level = nil
 
@@ -101,6 +102,9 @@ if $0 == __FILE__
   parser.on('--veryverbose', 'more verbose output') {
     loglevel = VeryVerbose
   }
+  parser.on('--[no-]compute-checksum', 'compute (or do not compute) checksum of contents (default: --compute-checksum)') { |cs|
+    compute_checksum = cs
+  }
   parser.on('--extension=EXT', 'specify extension') { |ext|
     extensions.push ext
   }
@@ -178,7 +182,13 @@ if $0 == __FILE__
       exit ret_run.fetch('return', 1)
     end
 
-    ret_list = run_cmd("#{basedir}/ep3 list #{target_arg} --copy #{dst_arg}", loglevel)
+    copt = if compute_checksum
+              '--compute-checksum'
+           else
+              '--no-compute-checksum'
+           end
+
+    ret_list = run_cmd("#{basedir}/ep3 list #{target_arg} #{copt} --copy #{dst_arg}", loglevel)
     if ret_list['success']
       tmpdir_will_be_removed = true unless keep_tmpdir_level == LeaveAlways
       exit 0

lib/ep3/ep3-list.rb

@@ -7,11 +7,15 @@
 require_relative 'runtime/stage-in'
 
 def ep3_list(args)
+  compute_checksum = true
   parser = OptionParser.new
   parser.banner = "Usage: ep3 list [options]"
   parser.on('--target-dir=DIR')
   parser.on('--copy')
   parser.on('--destination=DST')
+  parser.on('--[no-]compute-checksum') { |cs|
+    compute_checksum = cs
+  }
 
   opts = parser.getopts(args)
   unless args.empty?
@@ -44,7 +48,7 @@ def ep3_list(args)
     v.nil?
   }
   puts JSON.dump(stagein(to_be_skipped, {}, output, dst,
-                         opts.include?('copy')))
+                         opts.include?('copy'), compute_checksum))
   0
 end
 

lib/ep3/runtime/stage-in.rb

@@ -7,19 +7,19 @@
 require 'securerandom'
 require_relative 'inspector'
 
-def stagein(to_be_skipped, staged_inputs, job, outdir, force_stagein = false)
+def stagein(to_be_skipped, staged_inputs, job, outdir, force_stagein = false, compute_checksum = false)
   Hash[job.each.map{ |k, v|
          if to_be_skipped.call(k, v)
            nil
          elsif staged_inputs.include?(k)
            [k, staged_inputs[k].to_h]
          else
-           [k, stagein_(v, outdir, force_stagein).to_h]
+           [k, stagein_(v, outdir, force_stagein, compute_checksum).to_h]
          end
        }.compact]
 end
 
-def stagein_(obj, outdir, force_stagein = false)
+def stagein_(obj, outdir, force_stagein = false, compute_checksum = false)
   case obj
   when CWLFile
     if force_stagein or need_staging(obj)
@@ -38,9 +38,9 @@ def stagein_(obj, outdir, force_stagein = false)
                  end
       ret.location = 'file://'+ret.path
       ret.secondaryFiles = obj.secondaryFiles.map{ |sec|
-        stagein_(sec, outdir, true)
+        stagein_(sec, outdir, true, compute_checksum)
       }
-      ret.evaluate(nil)
+      ret.evaluate(nil, false, compute_checksum)
     else
       obj
     end
@@ -52,21 +52,21 @@ def stagein_(obj, outdir, force_stagein = false)
       ret.location = 'file://'+ret.path
       FileUtils.mkdir_p ret.path
       ret.listing = obj.listing.map{ |lst|
-        stagein_(lst, ret.path, true)
+        stagein_(lst, ret.path, true, compute_checksum)
       }
-      ret.evaluate(nil)
+      ret.evaluate(nil, false, compute_checksum)
     else
       obj
     end
   when CWLRecordValue
     obj.fields.transform_values{ |v|
-      stagein_(v, outdir, force_stagein).to_h
+      stagein_(v, outdir, force_stagein, compute_checksum).to_h
     }
   when CWLUnionValue
-    stagein_(obj.value, outdir, force_stagein)
+    stagein_(obj.value, outdir, force_stagein, compute_checksum)
   when Array
     obj.map{ |o|
-      stagein_(o, outdir, force_stagein).to_h
+      stagein_(o, outdir, force_stagein, compute_checksum).to_h
     }
   else
     obj