color in the output to screen from cromwell run

Answers

• jgentry Member, Broadie, Dev ✭✭✭

  August 2017 Accepted Answer

  @blueskypy What are the contents of cromwell.config.0.txt?

  The color highlighting comes from the PRETTY logging mode: https://github.com/broadinstitute/cromwell#logging

  5 · Share on Twitter Share on Google+
• blueskypy Member ✭✭

  August 2017

  @jgentry the cromwell.config.0.txt is the ref config file in the github site core/src/main/resources/reference.conf. I export LOG_MODE="pretty", but it doesn't make any difference.

  0 · Share on Twitter Share on Google+
• mcovarr Cambridge, MAMember, Broadie, Dev ✭✭

  August 2017

  -DLOG_MODE=pretty on the command line works for me.

  You shouldn't need to add -Dconfig.file=... if you're just using the reference config.

  0 · Share on Twitter Share on Google+
• blueskypy Member ✭✭

  September 2017

  Thanks @mcovarr ! but adding-DLOG_MODE=pretty doesn't make a difference either.

  0 · Share on Twitter Share on Google+
• mcovarr Cambridge, MAMember, Broadie, Dev ✭✭

  September 2017 Accepted Answer

  What's your command line? This works for me:

  java -DLOG_MODE=pretty -jar /path/to/cromwell.jar server
  

  or with sbt:

  sbt -J-DLOG_MODE=pretty "run server"
  

  5 · Share on Twitter Share on Google+
• blueskypy Member ✭✭

  September 2017 edited September 2017

  Thanks @mcovarr ! Here is my command line:
  java -Dconfig.file=cromwell.config.0.txt -DLOG_MODE=pretty -jar cromwell-29.jar run h2.wdl -i h2.json

  cromwell.config.0.txt is just the reference config file in the github. Without -Dconfig.file, the log is colored without setting -DLOG_MODE in my case.

  I'm just trying to find out how to make the log colored when -Dconfig.file is set.

  0 · Share on Twitter Share on Google+
• mcovarr Cambridge, MAMember, Broadie, Dev ✭✭

  September 2017

  Could you please link to exactly which conf file you're using in GitHub? Thanks.

  0 · Share on Twitter Share on Google+
• blueskypy Member ✭✭

  September 2017 edited September 2017

  Thanks @mcovarr ! Here is the file

  0 · Share on Twitter Share on Google+
• mcovarr Cambridge, MAMember, Broadie, Dev ✭✭

  September 2017

  Okay I think the problem is that pointing to the reference.conf explicitly cuts out the application.conf, which is where this setup happens:

  akka {
    loggers = ["akka.event.slf4j.Slf4jLogger"]
    logging-filter = "akka.event.slf4j.Slf4jLoggingFilter"
    . . .
  

  So if you need to use a custom config file, just have include "application" as the first line.

  0 · Share on Twitter Share on Google+
• blueskypy Member ✭✭

  September 2017

  Thanks @mcovarr ! I downloaded the application.conf

  In cromwell.config.0.txt, adding include "application" or include "application.conf" on the top does not give color to the logging; adding include required("application") leads to error

  java.io.FileNotFoundException: include was not found: 'application.conf'

  0 · Share on Twitter Share on Google+
• mcovarr Cambridge, MAMember, Broadie, Dev ✭✭

  September 2017

  If cromwell.config.0.txt is just the reference.conf, you shouldn't do the -Dconfig.file=cromwell.config.0.txt on the command line. If you do have your own overrides in a separate file, then you can have include "application" at the top.

  0 · Share on Twitter Share on Google+
• blueskypy Member ✭✭

  September 2017

  @mcovarr , cromwell.config.0.txt is the reference.conf with a few minor changes by me.

  0 · Share on Twitter Share on Google+
• mcovarr Cambridge, MAMember, Broadie, Dev ✭✭

  September 2017 Accepted Answer

  Okay. It's best to make the minor changes in a separate file and then include "application" at the top and then -Dconfig.file=... that file.

  5 · Share on Twitter Share on Google+
• blueskypy Member ✭✭

  September 2017

  Thanks @mcovarr ! Just a few more questions:
  1. what's the difference among include "application", include "application.conf", include required("application")?
  2. do I need to download and keep application.conf in the same dir?

  0 · Share on Twitter Share on Google+
• mcovarr Cambridge, MAMember, Broadie, Dev ✭✭

  September 2017

  1. The Typesafe Config docs say to do include "application"; I don't know what those other forms do.
  2. No you don't need to do anything special for application.conf, the one that's baked into the Cromwell jar should work fine from there.

  0 · Share on Twitter Share on Google+
• ChrisL Cambridge, MAMember, Broadie, Dev admin

  September 2017

  The Cromwell docs suggest the include required(classpath("application")) method. I'll poke @kshakir to give us the full details but I'd be inclined to follow the Cromwell docs unless there's a reason not to.

  0 · Share on Twitter Share on Google+
• blueskypy Member ✭✭

  September 2017

  Thanks @ChrisL for chipping in! The cromwell.examples.conf uses include required("application"). But based on my testing, it leads to error

  com.typesafe.config.ConfigException$IO: application.conf: java.io.FileNotFoundException: include was not found: 'application.conf'

  But include required(classpath("application")) does not have that error.

  0 · Share on Twitter Share on Google+
• ChrisL Cambridge, MAMember, Broadie, Dev admin

  September 2017

  Thanks @blueskypy - I'll fix that line in the cromwell.examples.conf

  0 · Share on Twitter Share on Google+
• kshakir Broadie, Dev ✭✭

  September 2017 edited September 2017

  Thanks Chris!

  Post edited by kshakir on September 2017

  0 · Share on Twitter Share on Google+
• blueskypy Member ✭✭

  September 2017 edited September 2017

  @ChrisL , same error also exists at line 7 of reference.conf

  0 · Share on Twitter Share on Google+