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Track input json filename in workflows table (as alias) #129

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Track input json filename in workflows table (as alias) #129

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22 changes: 19 additions & 3 deletions cromshell
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Original file line number Diff line number Diff line change
Expand Up @@ -478,7 +478,7 @@ function populateLastWorkflowId()

function aliasExists(){
alias_name=${1}
grep -q "\\t${alias_name}\$" ${CROMWELL_SUBMISSIONS_FILE}
grep -P -q "\\t${alias_name}\$" ${CROMWELL_SUBMISSIONS_FILE}
}

function alias_workflow()
Expand Down Expand Up @@ -730,14 +730,18 @@ function waitOnSubmittedStatus()
function submit()
{
local doWait=false
local saveInputJsonAsAlias=false

# Handle Arguments:
local OPTIND
while getopts "w" opt ; do
while getopts "wa" opt ; do
case ${opt} in
w)
doWait=true
;;
a)
saveInputJsonAsAlias=true
;;
*)
invalidSubCommand submit flag ${OPTARG}
;;
Expand All @@ -763,6 +767,14 @@ function submit()
assertRequiredFileIsNonEmpty "${json}" "Input JSON"

# At this point, we should validate our inputs if we can:
if $saveInputJsonAsAlias; then
local workflowAlias=$(basename ${json})
if aliasExists ${workflowAlias}; then
echo -e "Alias ${workflowAlias} is already in use. Please pick a new alias."
exit 8
fi
fi

which womtool &> /dev/null
local r=$?
if [[ ${r} -eq 0 ]] ; then
Expand Down Expand Up @@ -825,7 +837,11 @@ function submit()

cp ${1} ${2} ${3} ${4} ${runDir}/

echo -e "$(date +%Y%m%d_%H%M%S)\t${CROMWELL_URL}\t${id}\t$(basename ${1})\tSubmitted" >> ${CROMWELL_SUBMISSIONS_FILE}
if $saveInputJsonAsAlias ; then
workflowAlias="\t${workflowAlias}"
fi

echo -e "$(date +%Y%m%d_%H%M%S)\t${CROMWELL_URL}\t${id}\t$(basename ${1})\tSubmitted${workflowAlias}" >> ${CROMWELL_SUBMISSIONS_FILE}

# Now that we've submitted our task, we should see if we have to wait:
if ${doWait} ; then
Expand Down