If you have checked the main open tree of life repos out into a directory which you lovingly call OPEN_TREE_REPO_ROOT in your env, then this will run grep on the files that appear to be java, python, or shell scripts in those repos.

grep_ot_code

#!/bin/sh
for repo in api.opentreeoflife.org deployed-systems gcmdr opentree ot-base oti ott peyotl phylografter taxomachine reference-taxonomy treemachine ;
do
    for suffix in .java .py .sh
    do
        find "$OPEN_TREE_REPO_ROOT/$repo" -name "*$suffix" -exec grep -H $@ {} \; | sed -e "s+$OPEN_TREE_REPO_ROOT/++"
    done
done