Fix cwl-metrics extension

lib/ep3/extensions/cwl-metrics/bin/sendMetricsFailureLog

@@ -0,0 +1,53 @@
+#!/usr/bin/env ruby
+require 'json'
+require 'optparse'
+
+if $0 == __FILE__
+    opt = OptionParser.new
+    opt.banner = "#{$0} [options] <response> <err> <tag> <interrupted>"
+
+    opt.parse!(ARGV)
+    unless ARGV.length == 4
+        puts opt.help
+        exit
+    end
+
+    resfile, errfile, tag, interrupted = *ARGV
+
+    unless File.exist? resfile
+        raise "File not found: #{resfile}"
+    end
+    res_str = open(resfile).read
+    begin
+        response = JSON.load(res_str)
+        message = 'Failed to send metrics'
+    rescue JSON::ParserError
+        response = res_str
+        message = 'Invalid response from metrics server'
+    end
+
+    unless File.exist? errfile
+        raise "File not found: #{errfile}"
+    end
+    err = open(errfile).read
+
+    level = if interrupted == 'true'
+        'warning'
+    else
+        'error'
+    end
+
+    ret = {
+        'log-level' => level,
+        'interrupted' => interrupted == 'true',
+        'tag' => tag,
+        'message' => message,
+        'response' => response,
+        'stderr' => err,
+        'metrics_server' => ENV['ES_HOST'],
+        'metrics_port' => ENV['ES_PORT'],
+    }
+
+    puts JSON.dump(ret)
+end
+

lib/ep3/extensions/cwl-metrics/extension.yml

@@ -39,6 +39,8 @@ hooks:
               out:
                 - place: uuid
                   pattern: ~(newfile)
+                - place: es_response
+                  pattern: ~(newfile)
               command: |
                 uuid=$(uuidgen)
                 echo $uuid > ~(out.uuid)
@@ -47,7 +49,11 @@ hooks:
                   -H "Content-Type: application/json" \
                   -X POST \
                   "${ES_HOST}:${ES_PORT}/workflow/_doc/${uuid}?pretty" \
-                  --data-binary @"~(in.cwl.metrics.json)" > /dev/null
+                  --data-binary @"~(in.cwl.metrics.json)" > ~(out.es_response)
+                result=$(jq -r .result ~(out.es_response))
+                test "$result" = 'created'
+              log:
+                failure: sendMetricsFailureLog ~(tr.newfile.es_response) ~(tr.stderr) ~(tag) ~(interrupted)
         transitions:
           - name: prepare-metrics-directory
             type: shell
@@ -246,7 +252,7 @@ hooks:
               - place: cid
                 pattern: ~(in.cid)
             command: |
-              mem=$(docker info 2> /dev/null | grep "Total Memory" | awk '{ print $3 }')
+              mem=$(docker info | grep "Total Memory" | awk '{ print $3 }')
               docker info --format '{{json .}}' | jq "{ running_containers: .ContainersRunning, server_version: .ServerVersion, storage_driver: .Driver, number_of_cpu: .NCPU, total_memory: \"$mem\" }" > ~(out.metrics.runtime.json)
               cid=$(cat ~(in.cid))
               docker inspect $cid | jq "{ id: \"$cid\", image: .[0].Config.Image, cmd: .[0].Config.Cmd | join(\" \"), status: .[0].State.Status, start_time: .[0].State.StartedAt, end_time: .[0].State.FinishedAt, exit_code: .[0].State.ExitCode }" > ~(out.metrics.process.json)