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gorpipe / gor

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.
GNU Affero General Public License v3.0
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Suppress DEBUG messages #15

Open jimlund opened 3 years ago

jimlund commented 3 years ago

How can I suppress DEBUG messages from gor / gorpipe? I was able to turn off the INFO messages using log4j.properties.

Jim Lund

sigmarkarl commented 3 years ago

edit the logback.xml or logback-console.xml under the config directory. Change root level="warn" to root level="off"

gmagnu commented 3 years ago

logback-console.xml is the one used for gorpipe. The root level logger is set by default to "off" though.

gmagnu commented 3 years ago

There is though an audit logger that is set by default to DEBUG, it is possible that you seeing output from that logger. I was not awate that it was used in standard gorpipe usage. @jimlund to you have an example of the DEBUG output you are receiving?

gorfather commented 3 years ago

Hi Jim - can you send me your email?

jimlund commented 3 years ago

I am jlund256 :at: gmail.

jimlund commented 3 years ago

Thanks for the help. It turned out to be path issues--I am running in Cygwin on Windows with Oracle Java. Cygwin translates C:\Users paths to /cygwin/c/Users, but between bash, gor, and java, things get messed up.

I was getting messages like:

16:12:02.541 [main] DEBUG org.gorpipe.base.config.ConfigManager - Config path determined from code source location 16:12:02.541 [main] DEBUG org.gorpipe.base.config.ConfigManager - Using configuration root path: C:\Users\jim.lund\Downloads\gorscripts-3.11.2-dist\lib/../config/ 16:12:02.563 [main] DEBUG org.gorpipe.base.config.ConfigManager - Loaded configuration file C:\Users\jim.lund\Downloads\gorscripts-3.11.2-dist\lib/../config/gor.props.defaults 16:12:02.594 [main] DEBUG org.gorpipe.base.config.ConfigManager - Loaded configuration file C:\Users\jim.lund\Downloads\gorscripts-3.11.2-dist\lib/../config/gor.props.defaults 16:12:10.827 [main] DEBUG org.apache.commons.configuration.PropertiesConfiguration - FileName set to C:\Users\jim.lund\Downloads\gorscripts-3.11.2-dist\lib/../config/gor.props.defaults

I was able to suppress them by hard coding the path in the gorpipe script:

DEFAULT_JVM_OPTS='"-Djava.security.egd=file:/dev/./urandom" "-Dlogback.configurationFile=file:C:\Users\jim.lund\gorscripts-3.11.2-dist\config\logback.xml"'

It is a strange setup and not worth trying to support.

Cheers,

Jim