Fix user log for medal v1.2.0

tom-tan · Apr 16, 2021 · a973ebb · a973ebb
1 parent e1c347f
commit a973ebb
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Showing 7 changed files with 73 additions and 71 deletions.
diff --git a/ep3-runner b/ep3-runner
@@ -23,13 +23,15 @@ def run_cmd(cmd, loglevel)
     pid = spawn(cmd)
     _, status = Process.wait2 pid
     pid = nil
+    succ = status.exited? && status.exitstatus == 0
+    lv = if succ then 'info' else 'error' end
     hash = {
-      'log-level' => 'info',
-      'success' => status.exited?,
+      'log-level' => lv,
+      'success' => succ,
       'commmand' => cmd, 'return' => status.exitstatus,
       'tag' => 'ep3.system', 'timestamp' => Time.now.iso8601(7),
     }
-    if loglevel >= Verbose
+    if lv == 'error' || loglevel >= Verbose
       warn JSON.dump hash
     end
     hash

diff --git a/lib/ep3/ep3-run.rb b/lib/ep3/ep3-run.rb
@@ -62,8 +62,8 @@ def ep3_run(args)
   }
 
   lopt = case loglevel
-         when Quiet       then '--quiet'
-         when Normal      then '--sys-quiet'
+         when Quiet       then '--sys-silent --app-quiet'
+         when Normal      then '--sys-silent'
          when Verbose     then '--app-verbose'
          when VeryVerbose then '--verbose'
          end
@@ -87,8 +87,10 @@ def ep3_run(args)
       }
     ensure
       rest = io.read
-      warn rest
-      log.puts rest
+      unless rest.empty?
+        warn rest
+        log.puts rest
+      end
       log.flush
     end
   }

diff --git a/lib/ep3/init/cwl2wfnet.rb b/lib/ep3/init/cwl2wfnet.rb
@@ -120,7 +120,7 @@ def cmdnet(cwl)
                         out: [Place.new('StageIn', 'success'),
                               Place.new('cwl.input.json', '~(tr.stdout)'), Place.new('StageIn.err', '~(tr.stderr)')],
                         command: %q!mkdir -p $MEDAL_TMPDIR/outputs; stage-in.rb --outdir=$MEDAL_TMPDIR/outputs job.cwl ~(in.input.json)!,
-                        failureLog: LogEntry.new(level: 'critical', command: 'generalFailureLog stage-in ~(tr.stdout) ~(tr.stderr) ~(tr.return) ~(tag)'),
+                        failureLog: 'generalFailureLog stage-in ~(tr.stdout) ~(tr.stderr) ~(tr.return) ~(tag) ~(interrupted)',
                         name: 'stage-in')
 
   net << Transition.new(in_: [Place.new('CommandGeneration', 'not-started'), Place.new('StageIn', 'success'),
@@ -129,14 +129,14 @@ def cmdnet(cwl)
                               Place.new('CommandGeneration.command', '~(tr.stdout)'),
                               Place.new('CommandGeneration.err', '~(tr.stderr)')],
                         command: %Q!inspector.rb job.cwl commandline -i ~(in.cwl.input.json) --outdir=$MEDAL_TMPDIR/outputs!,
-                        failureLog: LogEntry.new(level: 'critical', command: 'generalFailureLog command-generation ~(tr.stdout) ~(tr.stderr) ~(tr.return) ~(tag)'),
+                        failureLog: 'generalFailureLog command-generation ~(tr.stdout) ~(tr.stderr) ~(tr.return) ~(tag) ~(interrupted)',
                         name: 'generate-command')
 
   net << Transition.new(in_: [Place.new('Execution', 'not-started'), Place.new('CommandGeneration', 'success'),
                               Place.new('CommandGeneration.command', any)],
                         out: [Place.new('Execution.return', '~(tr.return)'), Place.new('Execution.out', '~(tr.stdout)'), Place.new('Execution.err', '~(tr.stderr)')],
                         command: %Q!executor ~(in.CommandGeneration.command)!,
-                        failureLog: LogEntry.new(level: 'critical', command: 'commandFailureLog ~(in.CommandGeneration.command) ~(tr.stdout) ~(tr.stderr) ~(tr.return) ~(tag)'),
+                        failureLog: 'commandFailureLog ~(in.CommandGeneration.command) ~(tr.stdout) ~(tr.stderr) ~(tr.return) ~(tag) ~(interrupted)',
                         name: 'execute')
 
   successCodes = case cwl.class_
@@ -190,7 +190,7 @@ def cmdnet(cwl)
                         out: [Place.new('StageOut', 'success'), Place.new('ExecutionState', 'success'),
                               Place.new('cwl.output.json', '~(tr.stdout)'), Place.new('StageOut.err', '~(tr.stderr)')],
                         command: %Q!inspector.rb job.cwl list -i ~(in.cwl.input.json) --json --outdir=$MEDAL_TMPDIR/outputs!,
-                        failureLog: LogEntry.new(level: 'critical', command: 'generalFailureLog stage-out ~(tr.stdout) ~(tr.stderr) ~(tr.return) ~(tag)'),
+                        failureLog: 'generalFailureLog stage-out ~(tr.stdout) ~(tr.stderr) ~(tr.return) ~(tag) ~(interrupted)',
                         name: 'stage-out')
   net
 end
@@ -216,7 +216,7 @@ def expnet(cwl)
                               Place.new('CommandGeneration.command', '~(tr.stdout)'),
                               Place.new('CommandGeneration.err', '~(tr.stderr)')],
                         command: %Q!inspector.rb job.cwl commandline -i ~(in.cwl.input.json) --outdir=$MEDAL_TMPDIR/outputs!,
-                        failureLog: LogEntry.new(level: 'critical', command: 'generalFailureLog command-generation ~(tr.stdout) ~(tr.stderr) ~(tr.return) ~(tag)'),
+                        failureLog: 'generalFailureLog command-generation ~(tr.stdout) ~(tr.stderr) ~(tr.return) ~(tag) ~(interrupted)',
                         name: 'generate-command')
 
   net << Transition.new(in_: [Place.new('Execution', 'not-started'), Place.new('CommandGeneration', 'success'),
@@ -276,7 +276,7 @@ def expnet(cwl)
                         out: [Place.new('StageOut', 'success'), Place.new('ExecutionState', 'success'),
                               Place.new('cwl.output.json', '~(tr.stdout)'), Place.new('StageOut.err', '~(tr.stderr)')],
                         command: %Q!inspector.rb job.cwl list -i ~(in.cwl.input.json) --json --outdir=$MEDAL_TMPDIR/outputs!,
-                        failureLog: LogEntry.new(level: 'critical', command: 'generalFailureLog stage-out ~(tr.stdout) ~(tr.stderr) ~(tr.return) ~(tag)'),
+                        failureLog: 'generalFailureLog stage-out ~(tr.stdout) ~(tr.stderr) ~(tr.return) ~(tag) ~(interrupted)',
                         name: 'stage-out')
   net
 end

diff --git a/lib/ep3/init/workflownet.rb b/lib/ep3/init/workflownet.rb
@@ -46,9 +46,9 @@ def to_h
       'out' => @out.map{ |o| o.to_h },
       'command' => cmd,
       'log' => {
-        'pre' => @preLog.to_h,
-        'success' => @successLog.to_h,
-        'failure' => @failureLog.to_h,  
+        'pre' => @preLog,
+        'success' => @successLog,
+        'failure' => @failureLog,
       }.compact,
     }.compact
   end
@@ -101,30 +101,14 @@ def to_h
       'in' => @in.map{ |i| i.to_h },
       'out' => @out.map{ |o| o.to_h },
       'log' => {
-        'pre' => @preLog.to_h,
-        'success' => @successLog.to_h,
-        'failure' => @failureLog.to_h
-      }.compact
+        'pre' => @preLog,
+        'success' => @successLog,
+        'failure' => @failureLog,
+      }.compact,
     }.compact
   end
 end
 
-class LogEntry
-  attr_reader :command, :level
-
-  def initialize(command:, level:)
-    @command = command
-    @level = level
-  end
-
-  def to_h
-    {
-      'command' => @command,
-      'level' => @level,
-    }
-  end
-end
-
 class PetriNet
   attr_reader :transitions, :tag, :name, :application
   attr_accessor :preLog, :successLog, :failureLog
@@ -176,18 +160,9 @@ def to_h
       ],
       'transitions' => @transitions.map{ |t| t.to_h },
       'log' => {
-        'pre' => {
-          'level' => 'info',
-          'command' => 'classStartLog job.cwl ~(in.entrypoint) ~(tag)',
-        },
-        'success' => {
-          'level' => 'info',
-          'command' => 'classSuccessLog ~(out.cwl.output.json) ~(tag)',
-        },
-        'failure' => {
-          'level' => 'critical',
-          'command' => 'classFailureLog ~(tag)',
-        }
+        'pre' => 'classStartLog job.cwl ~(in.entrypoint) ~(tag)',
+        'success' => 'classSuccessLog ~(out.cwl.output.json) ~(tag)',
+        'failure' => 'classFailureLog ~(tag) ~(interrupted)',
       },
     }.compact
   end

diff --git a/lib/ep3/runtime/classFailureLog b/lib/ep3/runtime/classFailureLog
@@ -4,21 +4,28 @@ require 'optparse'
 
 if $0 == __FILE__
     opt = OptionParser.new
-    opt.banner = "#{$0} [options] <tag>"
+    opt.banner = "#{$0} [options] <tag> <interrupted>"
 
     opt.parse!(ARGV)
-    unless ARGV.length == 1
+    unless ARGV.length == 2
         puts opt.help
         exit
     end
 
-    tag = ARGV.first
+    tag, interrupted = *ARGV
 
+    level = if interrupted == 'true'
+                'warning'
+            else
+                'error'
+            end
 
     ret = {
-        tag: tag,
-        message: "Finished #{tag.split('.')[2..-1].join('.')}",
-        result: 'permanentFailure',
+        'log-level' => level,
+        'interrupted' => interrupted == 'true',
+        'tag' => tag,
+        'message' => "Finished #{tag.split('.')[2..-1].join('.')}",
+        'result' => 'permanentFailure',
     }
 
     puts JSON.dump(ret)

diff --git a/lib/ep3/runtime/commandFailureLog b/lib/ep3/runtime/commandFailureLog
@@ -4,15 +4,15 @@ require 'optparse'
 
 if $0 == __FILE__
     opt = OptionParser.new
-    opt.banner = "#{$0} [options] <comfile> <outfile> <errfile> <return> <tag>"
+    opt.banner = "#{$0} [options] <comfile> <outfile> <errfile> <return> <tag> <interrupted>"
 
     opt.parse!(ARGV)
-    unless ARGV.length == 5
+    unless ARGV.length == 6
         puts opt.help
         exit
     end
 
-    comfile, outfile, errfile, code, tag = *ARGV
+    comfile, outfile, errfile, code, tag, interrupted = *ARGV
 
     unless File.exist? comfile
         raise "File not found: #{comfile}"
@@ -29,13 +29,21 @@ if $0 == __FILE__
     end
     err = open(errfile).read(1024)
 
+    level = if interrupted == 'true'
+                'warning'
+            else
+                'error'
+            end
+
     ret = {
-        tag: tag,
-        message: "#{tag.split('.')[2..-1].join('.')} failed in command-execution",
-        command: com,
-        stdout: out,
-        stderr: err,
-        return: code.to_i,
+        'log-level' => level,
+        'interrupted' => interrupted == 'true',
+        'tag' => tag,
+        'message' => "#{tag.split('.')[2..-1].join('.')} failed in command-execution",
+        'command' => com,
+        'stdout' => out,
+        'stderr' => err,
+        'return' => code.to_i,
     }
 
     puts JSON.dump(ret)

diff --git a/lib/ep3/runtime/generalFailureLog b/lib/ep3/runtime/generalFailureLog
@@ -4,15 +4,15 @@ require 'optparse'
 
 if $0 == __FILE__
     opt = OptionParser.new
-    opt.banner = "#{$0} [options] <com> <outfile> <errfile> <return> <tag>"
+    opt.banner = "#{$0} [options] <com> <outfile> <errfile> <return> <tag> <interrupted>"
 
     opt.parse!(ARGV)
-    unless ARGV.length == 5
+    unless ARGV.length == 6
         puts opt.help
         exit
     end
 
-    com, outfile, errfile, code, tag = *ARGV
+    com, outfile, errfile, code, tag, interrupted = *ARGV
 
     unless File.exist? outfile
         raise "File not found: #{outfile}"
@@ -24,12 +24,20 @@ if $0 == __FILE__
     end
     err = open(errfile).read
 
+    level = if interrupted == 'true'
+                'warning'
+            else
+                'error'
+            end
+
     ret = {
-        tag: tag,
-        message: "#{tag.split('.')[2..-1].join('.')} failed in #{com}",
-        stdout: out,
-        stderr: err,
-        return: code.to_i,
+        'log-level' => level,
+        'interrupted' => interrupted == 'true',
+        'tag' => tag,
+        'message' => "#{tag.split('.')[2..-1].join('.')} failed in #{com}",
+        'stdout' => out,
+        'stderr' => err,
+        'return' => code.to_i,
     }
 
     puts JSON.dump(ret)