moved command.sh to plugin and corrected html typo

grails-app/controllers/ImportXnatController.groovy

@@ -172,8 +172,9 @@ class ImportXnatController {
 			def username = importXnatConfiguration.username
 			def project = importXnatConfiguration.project
 			def node = importXnatConfiguration.node
-			def kettledir = (getTransmartDataLocation() + "/env/data-integration/")
-			def datadir = getScriptsLocation() + "/xnattotransmartlink/"
+			//def kettledir = (getTransmartDataLocation() + "/env/data-integration/")
+			def kettledir = (getScriptsLocation() + "/xnattotransmartlink/")
+			def datadir = (getScriptsLocation() + "/xnattotransmartlink/")
 
 			def process = ("python " + getScriptsLocation() + "/xnattotransmartlink/downloadscript.py ${url} ${username} ${password} ${project} ${node} ${kettledir} ${datadir}").execute(null, new File(getScriptsLocation() + "/xnattotransmartlink"))
 			process.waitFor()

grails-app/views/importXnat/import_wizard.gsp

@@ -10,7 +10,7 @@
 			$(document).ready(function() {
 			  $("#import_wizard_form").submit(function(event) {
 			    $(".message").remove();
-			    $("#import_info").html("<br /><img src=\"/transmart/static/images/ajax-loader.gif\" />&nbsp;&nbsp;<p style=\"background-color:#FEC0C0; font-size:15px; display:inline; border-style:solid; border-color:FD4F4F; border-width:2px;\">The data is now imported in XNAT. This can take a few seconds to minutes, depending on the size of the dataset. Please wait until this message is updated.</p><br />");
+			    $("#import_info").html("<br /><img src=\"/transmart/static/images/ajax-loader.gif\" />&nbsp;&nbsp;<p style=\"background-color:#FEC0C0; font-size:15px; display:inline; border-style:solid; border-color:FD4F4F; border-width:2px;\">The data is now imported from XNAT. This can take a few seconds to minutes, depending on the size of the dataset. Please wait until this message is updated.</p><br />");
 			  })
 			});
 		</script>

scripts/xnattotransmartlink/command.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+export KETTLE_HOME="/home/jenkins/transmart-data/env/tranSMART-ETL/Postgres/GPL-1.0/Kettle/Kettle-ETL/"
+
+sh "/home/jenkins/transmart-data/env/data-integration/kitchen.sh" \
+-norep=N \
+-file="/home/jenkins/transmart-data/env/tranSMART-ETL/Kettle-GPL/Kettle-ETL/create_clinical_data.kjb" \
+-log=load_clinical_data.log \
+-param:LOAD_TYPE=I \
+-param:COLUMN_MAP_FILE=xnat.tmm \
+-param:DATA_LOCATION=$2 \
+-param:TOP_NODE="\\Public Studies\\$1\\" \
+-param:STUDY_ID=$1 \
+-param:SORT_DIR=/home/transmart/ETL \
+-logging=Rowlevel \
+-level=Rowlevel \
+> command.out