missing timestamps in ROBOT verbose (-vv) logs #1091
Description
Looks like this has actually likely been an issue since v1.8.3, but I just noticed it today, when I updated from v1.8.1 to 1.9.2.
Previously, verbose ROBOT log (console) output included timestamps; now it doesn't. E.g.:
Before (v1.8.1)
2023-02-10 21:32:44,920 INFO org.obolibrary.robot.CommandLineHelper - Reasoner: hermit
2023-02-10 21:32:44,938 INFO org.obolibrary.robot.ReasonOperation - Ontology has 56843 axioms.
2023-02-10 21:32:46,492 INFO org.obolibrary.robot.ReasonOperation - Starting reasoning...
2023-02-10 21:32:46,493 INFO org.obolibrary.robot.ReasonerHelper - Checking for inconsistencies
2023-02-10 21:32:46,570 INFO org.obolibrary.robot.ReasonerHelper - Checking for unsatisfiable classes...
2023-02-10 21:37:30,172 INFO org.obolibrary.robot.ReasonerHelper - Checking for unsatisfiable object properties...
2023-02-10 22:02:53,083 INFO org.obolibrary.robot.ReasonOperation - Precomputing class hierarchy...
After (v1.9.2)
INFO Reasoner: hermit
INFO Ontology has 56843 axioms.
INFO Starting reasoning...
INFO Checking for inconsistencies
INFO Checking for unsatisfiable classes...
INFO Checking for unsatisfiable object properties...
INFO Precomputing class hierarchy...
Looks like the essential issue might be that logback.xml is not found by java. Further, looks like that file was removed from robot-command/src/main/resources at some point after @beckyjackson added it. I was able to "fix" the issue by copying the file that used to be there (https://github.com/ontodev/robot/blob/5c03178e563a24fe633609bd9c701f25e31b8df5/robot-command/src/main/resources/logback.xml) to my local machine and then updating the robot shell script locally, so that the 2nd-to-last line is now:
exec java $ROBOT_JAVA_ARGS -Dlogback.configurationFile="$DIR/logback.xml" -jar "$DIR/robot.jar" "$@"
that's a hack... is there a better way?