Proxy application logs are discarded when CATALINA_OUT is /dev/null

[jvendetti]

Problem

The sifr-bioportal-annotator-proxy servlet logs useful runtime information through SLF4J/Log4j, but the current Log4j setup only writes to a ConsoleAppender.

The relevant configuration is effectively:

log4j.rootLogger=info, STDERR
log4j.appender.STDERR=org.apache.log4j.ConsoleAppender

Despite the appender name STDERR, this is console output, not a dedicated application log file.

On servers where Tomcat is configured with:

CATALINA_OUT=/dev/null

... the proxy's application logs are discarded. Tomcat still writes container exceptions to files such as localhost.YYYY_MM_DD.log, but the app's own contextual logs are unavailable.

Impact

When the servlet fails, we may only see a Tomcat stack trace, without the proxy logs that would explain what happened.

For example, AnnotatorServlet logs the upstream annotator response before parsing it:

logger.info("Query output: {}", queryOutput);

... but that output is lost when console output is redirected to /dev/null.

This makes production incidents difficult to diagnose, especially when the upstream annotator returns invalid JSON, HTML, plaintext, or an empty response.

Expected behavior

The proxy should write application logs to a durable location independent of catalina.out.

Proposed fix

Add an explicit Log4j file or rolling-file appender for the proxy WAR, ideally configured under ${catalina.base}/logs.

For example, write proxy logs to something like:

${catalina.base}/logs/annotatorplus.log

or a date-rolling equivalent.

Acceptance criteria

• Proxy application logs are written to a dedicated file.
• Logs are still available when CATALINA_OUT=/dev/null.
• The log file includes servlet request handling errors and upstream annotator response status.
• Documentation notes where production logs are expected to appear.