From 5dc66c1f7cab2a02a6a48b19b9e0e1230ff1f133 Mon Sep 17 00:00:00 2001
From: Erwin Vast <e.vast@erasmusmc.nl>
Date: Wed, 6 May 2015 13:02:18 +0200
Subject: [PATCH] moved command.sh to plugin and corrected html typo

---
 grails-app/controllers/ImportXnatController.groovy |  5 +++--
 grails-app/views/importXnat/import_wizard.gsp      |  2 +-
 scripts/xnattotransmartlink/command.sh             | 16 ++++++++++++++++
 3 files changed, 20 insertions(+), 3 deletions(-)
 create mode 100755 scripts/xnattotransmartlink/command.sh

diff --git a/grails-app/controllers/ImportXnatController.groovy b/grails-app/controllers/ImportXnatController.groovy
index 516530f..c1a72c5 100644
--- a/grails-app/controllers/ImportXnatController.groovy
+++ b/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()
diff --git a/grails-app/views/importXnat/import_wizard.gsp b/grails-app/views/importXnat/import_wizard.gsp
index 2bfc300..7cd3d37 100644
--- a/grails-app/views/importXnat/import_wizard.gsp
+++ b/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>
diff --git a/scripts/xnattotransmartlink/command.sh b/scripts/xnattotransmartlink/command.sh
new file mode 100755
index 0000000..69d1219
--- /dev/null
+++ b/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