color in the output to screen from cromwell run

blueskypy

The output to screen from java -jar cromwell-28.jar run ... contains color for different type of info, making it easier to read. But those from java -Dconfig.file=cromwell.config.0.txt -jar cromwell-28.jar run does not have any color. How to add color to the output in this care?

Thanks!

jgentry

@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

mcovarr

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"

mcovarr

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.

jgentry

@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

blueskypy

@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.

mcovarr

-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.

blueskypy

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

mcovarr

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"

blueskypy

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.

mcovarr

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

blueskypy

Thanks @mcovarr ! Here is the file

mcovarr

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.

blueskypy

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'

mcovarr

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.

blueskypy

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

mcovarr

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.

blueskypy

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?

mcovarr

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.

ChrisL

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.

blueskypy

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.

ChrisL

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

kshakir

Thanks Chris!

blueskypy

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