Regarding application.properties file and environment variable

You can put environment variables in your properties file, but Java will not automatically recognise them as environment variables and therefore will not resolve them.

In order to do this you will have to parse the values and resolve any environment variables you find.

You can get at environment variables from Java using various methods. For example: Map<String, String> env = System.getenv();

There's a basic tutorial here: http://java.sun.com/docs/books/tutorial/essential/environment/env.html

Hope that's of some help.

Tom Duckering's answer is correct. Java doesn't handle this for you.

Here's some code utilizing regular expressions that I wrote to handle environment variable substitution:

/*
 * Returns input string with environment variable references expanded, e.g. $SOME_VAR or ${SOME_VAR}
 */
private String resolveEnvVars(String input)
{
    if (null == input)
    {
        return null;
    }
    // match ${ENV_VAR_NAME} or $ENV_VAR_NAME
    Pattern p = Pattern.compile("\\$\\{(\\w+)\\}|\\$(\\w+)");
    Matcher m = p.matcher(input); // get a matcher object
    StringBuffer sb = new StringBuffer();
    while(m.find()){
        String envVarName = null == m.group(1) ? m.group(2) : m.group(1);
        String envVarValue = System.getenv(envVarName);
        m.appendReplacement(sb, null == envVarValue ? "" : envVarValue);
    }
    m.appendTail(sb);
    return sb.toString();
}

Have a look at Commons configuration

Or alternatively use relative paths in your properties file, and load the base directory via command line as a system property. That way the property files remain independent of where the application is actually deployed.

Apache Tomcat has an optional script for setting environment variables. In the documentation, it says "all environment variables can be specified in the "setenv" script" (.bat for Windows and .sh for Linux).

Section 3.4 in https://tomcat.apache.org/tomcat-9.0-doc/RUNNING.txt

Since it is a script and not a static configuration, the properties file can be created from it. This patterned works for me for an environment configured S3 connection, but here it is re-written for your example, along with the bonus of how to set the properties file's location:

cat > "${CATALINA_HOME}/conf/application.properties" <<EOF
pathToInputFile=${TOM_DATA}/data/incoming/ready/
pathToInputFileProcess=${TOM_DATA}/data/incoming/work/
EOF
CATALINA_OPTS="${CATALINA_OPTS} -DTOM_DATA=${TOM_DATA}"
CATALINA_OPTS="${CATALINA_OPTS} -Dapplication.properties.location=${CATALINA_HOME}/conf/application.properties"

export CATALINA_OPTS

You may already be using this file if you configure runtime things like memory constraints, headless mode, or which garbage collect to use.

NOTE: the documentation has caveats about when setenv would not be called and some exceptions as to a few environment variable that cannot configured in it.