I have attached a test.sh to test 6 cases Test Case 1: no geneSymbol Test Case 2: with one gene Test Case 3: with multiple valid genes Test Case 4: with a invalid gene in the mix Test Case 5: with Glioblastoma TP53 Pathway (4 genes) Test Case 6: with Glioblastoma RTK/Ras/PI3K/AKT Signaling (17 genes) Please be sure to set execution permission for both test.sh and gbm_summarize.sh before running them. ./test.sh will run all 6 cases. I have also attached the result in testReport.txt for your reference. Since this is a simple application with a fixed set of data. I did not implement Apache Commons CLI. If this is want to would like me to do, please let me know so I can make corrections. I have compiled my application with java 1.8.0_40. If you do not have this version, please use recompile.sh to compile the code with your default java compiler. The class created will be located at out/production/gbm_summarize/com/daisyflemming/