Added womtool validation for WDL/JSON if it's in your path. (#87)

* Added womtool validation for WDL/JSON if it's in your path.

Fixes #18

Author: jonn-smith

README.md

@@ -32,7 +32,7 @@ requires `column`, `curl`, `mail`, and [jq](https://stedolan.github.io/jq/)
 
 ### Supported Flags:
   * `-t` `TIMEOUT`
-	  * Set the curl connect timeout to `TIMEOUT` seconds.
+    * Set the curl connect timeout to `TIMEOUT` seconds.
     * Also sets the curl max timeout to `2*TIMEOUT` seconds.
     * `TIMEOUT` must be an integer.
 
@@ -41,37 +41,38 @@ requires `column`, `curl`, `mail`, and [jq](https://stedolan.github.io/jq/)
 
    ####  Start/Stop workflows
    * `submit` `[-w]` *`<wdl>`* *`<inputs_json>`* `[options_json]` `[included_wdl_zip_file]`
-     * Submit a new workflow
+     * Submit a new workflow.
+     * Will automatically validate the WDL and JSON file if `womtool` is in your path.
      * *`-w`*                     Wait for workflow to transition from 'Submitted' to some other status
                                   before ${SCRIPTNAME} exits
      * *`included_wdl_zip_file`*  Zip file containing any WDL files included in the input WDL
    * `abort` *`[workflow-id] [[workflow-id]...]`*                   
-     * Abort a running workflow
+     * Abort a running workflow.
    #### Query workflow status:
    * `status` *`[workflow-id] [[workflow-id]...]`*                   
-     * Check the status of a workflow
+     * Check the status of a workflow.
    * `metadata` *`[workflow-id] [[workflow-id]...]`*                
-     * Get the full metadata of a workflow
+     * Get the full metadata of a workflow.
    * `slim-metadata` *`[workflow-id] [[workflow-id]...]`*           
-     * Get a subset of the metadata from a workflow
+     * Get a subset of the metadata from a workflow.
    * `execution-status-count` *`[-p] [-x] [workflow-id] [[workflow-id]...]`*   
-     * Get the summarized status of all jobs in the workflow
+     * Get the summarized status of all jobs in the workflow.
      * `-p` prints a pretty summary of the execution status instead of JSON
      * `-x` expands sub-workflows for more detailed summarization
    * `timing` *`[workflow-id] [[workflow-id]...]`*                  
-     * Open the timing diagram in a browser
+     * Open the timing diagram in a browser.
 
    #### Logs
    * `logs` *`[workflow-id] [[workflow-id]...]`*                     
-     * List the log files produced by a workflow
+     * List the log files produced by a workflow.
    * `fetch-logs` *`[workflow-id] [[workflow-id]...]`*               
-     * Download all logs produced by a workflow
+     * Download all logs produced by a workflow.
 
    #### Job Outputs
    * `list-outputs` *`[workflow-id] [[workflow-id]...]`*           
-     *  List all output files produced by a workflow
+     *  List all output files produced by a workflow.
    * `fetch-all` *`[workflow-id] [[workflow-id]...]`*             
-     * Download all output files produced by a workflow
+     * Download all output files produced by a workflow.
 
    ####  Get email notification on job completion
    * `notify` *`[workflow-id]` `[daemon-server]` `email` `[cromwell-server]`*

cromshell

@@ -53,16 +53,11 @@ fi
 export CROMWELL_URL=${CROMWELL_URL:-"${CROMWELL_SERVER_FROM_FILE}"}
 FOLDER_URL=$( echo ${CROMWELL_URL} | sed -e 's#ht.*://##g' ) 
 CROMWELL_METADATA_PARAMETERS="excludeKey=submittedFiles&expandSubWorkflows=true"
- CROMWELL_SLIM_METADATA_PARAMETERS="includeKey=executionStatus&includeKey=backendStatus&includeKey=status&includeKey=callRoot&expandSubWorkflows=true"
+CROMWELL_SLIM_METADATA_PARAMETERS="includeKey=executionStatus&includeKey=backendStatus&includeKey=status&includeKey=callRoot&expandSubWorkflows=true"
 
 CURL_CONNECT_TIMEOUT=5
 let CURL_MAX_TIMEOUT=2*${CURL_CONNECT_TIMEOUT}
 
-PING_CMD='ping -c1 -W1 -w10'
-if [[ $( uname ) == "Darwin" ]] ; then
-  PING_CMD='ping -c1 -W1000 -t10'
-fi
-
 alias curl='curl --connect-timeout ${CURL_CONNECT_TIMEOUT} --max-time ${CURL_MAX_TIMEOUT}'
 
 ################################################################################
@@ -405,9 +400,9 @@ function getAnswerFromUser()
 function assertCanCommunicateWithServer
 {
   # Make sure we can talk to the cromwell server:
-	local f=$(makeTemp)
-  curl -s ${1}/api/workflows/v1/backends > ${f}
-	grep -q 'supportedBackends' ${f}
+  local f=$(makeTemp)
+  curl -s ${1}/api/workflows/v1/backends > ${f}  
+  grep -q 'supportedBackends' ${f}
   r=$?
   if [[ ${r} -ne 0 ]] ; then
     turtleDead 
@@ -664,13 +659,32 @@ function submit()
 
   assertRequiredFileIsNonEmpty "${wdl}" "WDL"
   assertRequiredFileIsNonEmpty "${json}" "Input JSON"
+
+  # At this point, we should validate our inputs if we can:
+  which womtool &> /dev/null
+  local r=$?
+  if [[ ${r} -eq 0 ]] ; then
+    echo -ne "Validating WDL and JSON before submission..."
+    local tmpValidationOutput=$( makeTemp )
+    womtool validate ${wdl} -i ${json} &> ${tmpValidationOutput}
+    if [[ $? -eq 0 ]] ; then
+      echo -e '\tWDL and JSON are valid.'
+    else
+      echo
+      echo
+      error "ERROR: WDL and JSON files do not validate:"  
+      cat ${tmpValidationOutput} 1>&2
+      exit 8
+    fi
+  fi
+
   assertOptionalFileIsNonEmpty "${optionsJson}" "Options JSON"
   assertOptionalFileIsNonEmpty "${dependenciesZip}" "Dependencies Zip"
 
   assertCanCommunicateWithServer ${CROMWELL_URL}
 
   local response=$(curl -s -F workflowSource=@${wdl}  ${2:+ -F workflowInputs=@${json}} ${3:+ -F workflowOptions=@${optionsJson}} ${4:+ -F workflowDependencies=@${dependenciesZip}} ${CROMWELL_URL}/api/workflows/v1)
-  local r=$?
+  r=$?
 
   # Check to make sure that we actually submitted the job correctly 
   # and the server ate it well: