f898118e25b9d795f31f1839c87f0ed57fc44a3c mspeir Fri Jul 15 15:16:33 2016 -0700 Changes to argument structure. Database and tables are now required positional arugments, rather than options. Re-did usage message to reflect this. Changed verbose option, no longer outputs to file, just stdout. Added quotes around variables in different placesat Jonathan's recommendation, no redmine diff --git src/utils/qa/bigPush.sh src/utils/qa/bigPush.sh index 9423ea0..ef6a396 100755 --- src/utils/qa/bigPush.sh +++ src/utils/qa/bigPush.sh @@ -15,153 +15,141 @@ ################################ ##### Variables ##### dbList="" tableList="" verboseMode="" outputMode="" ##### Functions ##### showHelp() { cat << EOF -Usage: $0 [-h] [-d DATABASE(S)] [-t TABLE(S)] [-v VERBOSITY LEVEL] +Usage: `basename $0` [-hv] \$database(s) \$table(s) - -h Display this help and exit. - -d DATABASE(S) A single database or list of databases for which + Required arguments: + \$database(s) A single database or list of databases for which table(s) will be pushed. This list can be a file. - -t TABLE(S) A single table or list of tables to be pushed. + \$table(s) A single table or list of tables to be pushed. List of tables can be a file. - -v VERBOSITY LEVEL Output details of push; 1 for results to stdout, + + Optional arguments: + -h Display this help and exit. + -v VERBOSE MODE Output details of push; 1 for results to stdout, 2 for results to stdout and file. Push a table or list of tables from Dev to Beta for a single database or list of databases. If you have multiple databases (and/or tables), they can be input in a few different ways. They can be either in a file or in a space-separated list enclosed in quotes. For example: -$0 -d "ce11 hg19 gorGor3" -t refGene +`basename $0` "ce11 hg19 gorGor3" refGene A list of tables can be pushed in a similar way. -If verbose mode is set to "2" with -v 2, then the output will be sent to -stdout and to a file. The file name will be push.<YYYY-MM-DD_hhmm>, where -the part after "push." is Year-Month-Day_HourMinute. +If verbose mode is set, then the output will be sent to stdout. EOF } ##### Parse command-line input ##### OPTIND=1 # Reset is necessary if getopts was used previously in the script. It is a good idea to make this local in a function. -while getopts "hd:t:v:" opt +while getopts "hv" opt do case $opt in h) showHelp exit 0 ;; - d) - dbList=$OPTARG - ;; - t) - tableList=$OPTARG - ;; v) - # Validate verbose option input - # Fails if input is not one of two supported options - if [[ $OPTARG != 1 ]] && [[ $OPTARG != 2 ]] - then - echo -e "Verbose mode should be 1 or 2. Or if no output is wanted, not used at all." - exit 1 - else - verboseMode=$OPTARG - fi + verboseMode=true ;; '?') showHelp >&2 exit 1 ;; esac done -# Check if no command line options were supplied -if [ $OPTIND -eq 1 ] +shift "$((OPTIND-1))" # Shift off the options and optional --. + +# Check number of required arguments +if [ $# -ne 2 ] then + # Output usage message if number of required arguments is wrong showHelp >&2 exit 1 +else + # Set variables with required argument values + dbList=$1 + tableList=$2 fi -shift "$((OPTIND-1))" # Shift off the options and optional --. - ##### Main Program ##### # Adjust output mode based on specified verbose mode -if [[ $verboseMode == 1 ]] +if [[ "$verboseMode" == "true" ]] then # Will cause output to be sent to stdout outputMode="" -elif [[ $verboseMode == 2 ]] -then - # Output goes to stdout and file - outputMode=" | tee -a push.$(date +%F_%H%M)" else # if no verbose mode specified just send output to /dev/null outputMode="> /dev/null" fi # First check if dbList is a file. # If not, skips down to "# Here" -if [[ -e $dbList ]] +if [[ -e "$dbList" ]] then # Loop through our dbList file - for db in $(cat $dbList) + for db in $(cat "$dbList") do # Now check if tableList is a file - if [[ -e $tableList ]] + if [[ -e "$tableList" ]] then # If tableList was a file, loop through contents - for tbl in $(cat $tableList) + for tbl in $(cat "$tableList") do # Build command with proper database, table name, and output mode. - command="sudo mypush $db $tbl mysqlbeta $outputMode" + command="sudo mypush '$db' '$tbl' mysqlbeta $outputMode" # Run command using bash - echo $command | bash + echo "$command" | bash done # Or, if tableList was not a file, push table(s) to beta else - for tbl in $(echo $tableList) + for tbl in $(echo "$tableList") do - command="sudo mypush $db $tbl mysqlbeta $outputMode" - echo $command | bash + command="sudo mypush '$db' '$tbl' mysqlbeta $outputMode" + echo "$command" | bash done fi done # Here. # Conditional excutes if dbList input was not a file. else - for db in $(echo $dbList) + for db in $(echo "$dbList") do # Similar to above, following conditionals and for loops # push tables from dev to beta if dbList was not a file - if [[ -e $tableList ]] + if [[ -e "$tableList" ]] then - for tbl in $(cat $tableList) + for tbl in $(cat "$tableList") do - command="sudo mypush $db $tbl mysqlbeta $outputMode" - echo $command | bash + command="sudo mypush '$db' '$tbl' mysqlbeta $outputMode" + echo "$command" | bash done else - for tbl in $(echo $tableList) + for tbl in $(echo "$tableList") do - command="sudo mypush $db $tbl mysqlbeta $outputMode" - echo $command | bash + command="sudo mypush '$db' '$tbl' mysqlbeta $outputMode" + echo "$command" | bash done fi done fi