Only check for the server when necessary (#25)

* Only test if we can connect to the server when running a command that requires a server connection.

Author: lbergelson

cromshell

@@ -190,6 +190,16 @@ function checkPrerequisites
   return 0
 }
 
+
+function assertCanCommunicateWithServer
+{
+  # Make sure we can talk to the cromwell server:
+  serverName=$( echo ${1}| sed 's#.*://##g' )
+  $PING_CMD $serverName &> /dev/null
+  r=$?
+  [[ $r -ne 0 ]] && error "Error: Cannot communicate with Cromwell server: $serverName" && exit 4
+}
+
 function assertHavePreviouslySubmittedAJob()
 {
   local nLines=$( wc -l ${CROMWELL_SUBMISSIONS_FILE} | awk '{print $1}' )
@@ -241,8 +251,9 @@ function populateWorkflowIdAndServerUrl()
 
 # Submit a workflow and arguments to the Cromwell Server
 
-function submit()
-{
+function submit() 
+{ 
+  assertCanCommunicateWithServer $CROMWELL_URL
 
   local response=$(curl --connect-timeout $CURL_CONNECT_TIMEOUT -s -F workflowSource=@${1}  ${2:+ -F workflowInputs=@${2}} ${3:+ -F workflowOptions=@${3}} ${4:+ -F workflowDependencies=@${4}} ${CROMWELL_URL}/api/workflows/v1)
   local r=$?
@@ -267,6 +278,7 @@ function status()
 {
   local retVal=0
 
+  assertCanCommunicateWithServer $2
   local f=$( makeTemp )
   curl --connect-timeout $CURL_CONNECT_TIMEOUT -s ${2}/api/workflows/v1/${1}/status > $f
   [[ $? -ne 0 ]] && error "Could not connect to Cromwell server." && return 2
@@ -286,32 +298,36 @@ function status()
 }
 
 # Get the logs of a Cromwell job UUID
-function logs()
+function logs() 
 {
+  assertCanCommunicateWithServer $2
   curl --connect-timeout $CURL_CONNECT_TIMEOUT -s ${2}/api/workflows/v1/${1}/logs | jq . 
   checkPipeStatus "Could not connect to Cromwell server." "Could not parse JSON output from cromwell server."
   return $?
 }
 
 # Get the metadata for a Cromwell job UUID
-function metadata()
+function metadata() 
 {
+  assertCanCommunicateWithServer $2
   curl --connect-timeout $CURL_CONNECT_TIMEOUT --compressed -s ${2}/api/workflows/v1/${1}/metadata?${CROMWELL_METADATA_PARAMETERS} | jq . 
   checkPipeStatus "Could not connect to Cromwell server." "Could not parse JSON output from cromwell server."
   return $?
 }
 
 # Get the metadata in condensed form for a Cromwell job UUID
-function slim-metadata()
+function slim-metadata() 
 {
+  assertCanCommunicateWithServer $2
   curl --connect-timeout $CURL_CONNECT_TIMEOUT --compressed -s "${2}/api/workflows/v1/$1/metadata?includeKey=executionStatus&includeKey=backendStatus" | jq .
   checkPipeStatus "Could not connect to Cromwell server." "Could not parse JSON output from cromwell server."
   return $?
 }
 
 # Get the status of the given job and how many times it was run
-function execution-status-count()
+function execution-status-count() 
 {
+  assertCanCommunicateWithServer $2
   f=$( makeTemp )
   curl --connect-timeout $CURL_CONNECT_TIMEOUT --compressed -s ${2}/api/workflows/v1/$1/metadata?${CROMWELL_METADATA_PARAMETERS} > $f
   [[ $? -ne 0 ]] && error "Could not connect to Cromwell server." && return 9
@@ -330,16 +346,17 @@ function execution-status-count()
 }
 
 # Bring up a browser window to view timing information on the job.
-function timing()
+function timing() 
 {
-  echo "Opeining timing information in a web browser for job ID: ${1}"
+  echo "Opening timing information in a web browser for job ID: ${1}"
   open ${2}/api/workflows/v1/${1}/timing
   return $?
 }
 
 # Cancel a running job.
-function abort()
+function abort() 
 {
+  assertCanCommunicateWithServer $2
   response=$(curl --connect-timeout $CURL_CONNECT_TIMEOUT -X POST --header "Content-Type: application/json" --header "Accept: application/json" "${2}/api/workflows/v1/${1}/abort")
   local r=$?
   echo $response  
@@ -430,8 +447,9 @@ function list()
 #     stderr
 #     script
 #     output
-function list-outputs()
+function list-outputs() 
 {
+  assertCanCommunicateWithServer $2
   local id=$1
   local cromwellServer=$2
 
@@ -456,8 +474,9 @@ function list-outputs()
 
 
 # Get the root log folder from the cloud and put it in the metadata folder for this run
-function fetch-logs()
+function fetch-logs() 
 {
+  assertCanCommunicateWithServer $2
   local id=$1
   local cromwellServer=$2
 
@@ -490,8 +509,9 @@ function fetch-logs()
 
 # Get the root log folder from the cloud and put it in the metadata folder for this run
 # Includes all logs and output files
-function fetch-all()
+function fetch-all() 
 {
+  assertCanCommunicateWithServer $2
   local id=$1
   local cromwellServer=$2
 
@@ -523,7 +543,8 @@ function notify()
   local id=$1
   local email=$2
   local cromwellServer=$3
-  
+
+  assertCanCommunicateWithServer ${cromwellServer}
   local separator="=================================================="
 
   while true ; do 
@@ -602,12 +623,6 @@ if ${ISCALLEDBYUSER} ; then
   r=$?
   [[ $r -ne 0 ]] && exit 6
 
-  # Make sure we can talk to the cromwell server:
-  serverName=$( echo ${CROMWELL_URL} | sed 's#.*://##g' )
-  $PING_CMD $serverName &> /dev/null
-  r=$?
-  [[ $r -ne 0 ]] && error "Error: Cannot communicate with Cromwell server: $serverName" && exit 4
-
   # Special case: submitting a job:
   if [[ "${SUB_COMMAND}" == "submit" ]] ; then
     ${SUB_COMMAND} $1 $2 $3 $4