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Track input json filename in workflows table (new column) #130

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Track input json filename in workflows table (new column) #130

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db4bbd3
add input json column to tracked fields
ericsong Jun 9, 2020
55dd16a
update cromshell headers if needed
ericsong Jun 9, 2020
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22 changes: 13 additions & 9 deletions cromshell
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Original file line number Diff line number Diff line change
Expand Up @@ -42,15 +42,15 @@ DOOMED_LOGO_b64gz="H4sIAOfW3l0AA6WUwXHEIAxF767i35yDQQUkTiWeYcvIgUPa2GbSwHaRSiIJA
CROMSHELL_CONFIG_DIR=${HOME}/.cromshell
mkdir -p ${CROMSHELL_CONFIG_DIR}
CROMWELL_SUBMISSIONS_FILE="${CROMSHELL_CONFIG_DIR}/all.workflow.database.tsv"
[[ ! -f ${CROMWELL_SUBMISSIONS_FILE} ]] && echo -e "DATE\tCROMWELL_SERVER\tRUN_ID\tWDL_NAME\tSTATUS\tALIAS" > ${CROMWELL_SUBMISSIONS_FILE}
[[ ! -f ${CROMWELL_SUBMISSIONS_FILE} ]] && echo -e "DATE\tCROMWELL_SERVER\tRUN_ID\tWDL_NAME\tSTATUS\tALIAS\tINPUT_JSON" > ${CROMWELL_SUBMISSIONS_FILE}

# Update cromshell submissions file if it needs updating:
grep -q 'ALIAS$' ${CROMWELL_SUBMISSIONS_FILE}
grep -q 'INPUT_JSON$' ${CROMWELL_SUBMISSIONS_FILE}
r=$?
if [[ $r -ne 0 ]] ; then
echo "Upgrading cromshell config file..." 1>&2
cp ${CROMWELL_SUBMISSIONS_FILE} ${CROMSHELL_CONFIG_DIR}/tmp.tmptmp
echo -e "DATE\tCROMWELL_SERVER\tRUN_ID\tWDL_NAME\tSTATUS\tALIAS" > ${CROMWELL_SUBMISSIONS_FILE}
echo -e "DATE\tCROMWELL_SERVER\tRUN_ID\tWDL_NAME\tSTATUS\tALIAS\tINPUT_JSON" > ${CROMWELL_SUBMISSIONS_FILE}
tail -n+2 ${CROMSHELL_CONFIG_DIR}/tmp.tmptmp >> ${CROMWELL_SUBMISSIONS_FILE}
rm ${CROMSHELL_CONFIG_DIR}/tmp.tmptmp
fi
Expand Down Expand Up @@ -478,7 +478,7 @@ function populateLastWorkflowId()

function aliasExists(){
alias_name=${1}
grep -q "\\t${alias_name}\$" ${CROMWELL_SUBMISSIONS_FILE}
cut -d$'\t' -f6 ${CROMWELL_SUBMISSIONS_FILE} | grep -q ${alias_name}
}

function alias_workflow()
Expand Down Expand Up @@ -522,8 +522,9 @@ function alias_workflow()
function populateWorkflowIdAndServerFromAlias()
{
local alias_name=${1}
WORKFLOW_ID=$(grep "\\t${alias_name}\$" ${CROMWELL_SUBMISSIONS_FILE} | head -n1 | awk '{print $3}')
WORKFLOW_SERVER_URL=$(grep "\\t${alias_name}\$" ${CROMWELL_SUBMISSIONS_FILE} | head -n1 | awk '{print $2}')
WORKFLOW_ID=$(cat ${CROMWELL_SUBMISSIONS_FILE} | awk -F "\t" "{if (\$6 == \"$alias_name\") print \$3}" | head -n1)
WORKFLOW_SERVER_URL=$(cat ${CROMWELL_SUBMISSIONS_FILE} | awk -F "\t" "{if (\$6 == \"$alias_name\") print \$2}" | head -n1)

if [[ -z ${WORKFLOW_ID} ]]; then
error "Invalid workflow/alias: ${alias_name}"
exit 5
Expand Down Expand Up @@ -825,7 +826,7 @@ 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" >> ${CROMWELL_SUBMISSIONS_FILE}
echo -e "$(date +%Y%m%d_%H%M%S)\t${CROMWELL_URL}\t${id}\t$(basename ${1})\tSubmitted\t\t$(basename ${json})" >> ${CROMWELL_SUBMISSIONS_FILE}

# Now that we've submitted our task, we should see if we have to wait:
if ${doWait} ; then
Expand Down Expand Up @@ -1200,11 +1201,14 @@ function list()
error "The following cromwell servers cannot be reached and were skipped\n${pretty_ugly}\n"
fi

# Indexes correspond to order within the CROMWELL_SUBMISSIONS_FILE
PRINT_COLUMN_ORDER='$1"\t"$2"\t"$3"\t"$4"\t"$7"\t"$5"\t"$6'

# If we have to colorize the output, we do so:
if ${doColor} ; then

local tmpFile=$( makeTemp )
cat ${CROMWELL_SUBMISSIONS_FILE} | column -t > ${tmpFile}
cat ${CROMWELL_SUBMISSIONS_FILE} | awk -F "\t" "{print $PRINT_COLUMN_ORDER}" | column -n -t -s $'\t' > ${tmpFile}

while read line ; do

Expand Down Expand Up @@ -1241,7 +1245,7 @@ function list()
echo "${line}"
done < ${tmpFile}
else
cat ${CROMWELL_SUBMISSIONS_FILE} | column -t
cat ${CROMWELL_SUBMISSIONS_FILE} | awk -F "\t" "{print $PRINT_COLUMN_ORDER}" | column -n -t -s $'\t'
fi
return $?
}
Expand Down