Merge pull request #1 from CTMM-TraIT/master

Changes made to make it work for test-1dot2

grails-app/controllers/ImportXnatController.groovy

@@ -1,4 +1,3 @@
-import org.springframework.util.StringUtils
 import org.transmart.searchapp.ImportXnatConfiguration;
 import org.transmart.searchapp.ImportXnatVariable;
 import groovy.xml.MarkupBuilder
@@ -8,7 +7,6 @@ import groovy.xml.MarkupBuilder
  */
 class ImportXnatController {
 
-	def springSecurityService
 	def grailsApplication
 
 	// the delete, save and update actions only accept POST requests
@@ -176,13 +174,22 @@ class ImportXnatController {
 			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"))
+			def cmd = "python " +
+					getScriptsLocation() +
+					"/xnattotransmartlink/downloadscript.py" +
+					" ${url} ${username} ${password} ${project} ${node} ${kettledir} ${datadir}"
+			log.debug(cmd)
+			def process = (cmd).execute(null, new File(getScriptsLocation() + "/xnattotransmartlink"))
 			process.waitFor()
-			if (process.err.text == "") {
-				flash.message = "${process.in.text}"
+			def inText = process.in.text
+			def errText = process.err.text
+			if (errText) {
+				log.error(errText)
+				flash.message = "${errText}</br>${inText}"
 			} else {
-				flash.message = "${process.err.text}</br>${process.in.text}"
-			}				
+				log.info(inText)
+				flash.message = inText
+			}
 			redirect action: import_wizard, id: importXnatConfiguration.id
 		}
 

grails-app/ddl/postgres/import_xnat_configuration.sql

@@ -13,7 +13,8 @@ CREATE TABLE searchapp.import_xnat_configuration (
 );
 ALTER TABLE searchapp.import_xnat_configuration OWNER TO searchapp;
 GRANT ALL ON TABLE searchapp.import_xnat_configuration TO searchapp;
-
+GRANT SELECT, UPDATE, INSERT, DELETE ON TABLE searchapp.import_xnat_configuration TO biomart_user;
+GRANT ALL ON TABLE searchapp.import_xnat_configuration TO tm_cz;
 --
 -- Name: pk_import_xnat_configuration; Type: CONSTRAINT; Schema: searchapp; Owner: -
 --

grails-app/ddl/postgres/import_xnat_variable.sql

@@ -10,7 +10,8 @@ CREATE TABLE searchapp.import_xnat_variable (
 );
 ALTER TABLE searchapp.import_xnat_variable OWNER TO searchapp;
 GRANT ALL ON TABLE searchapp.import_xnat_variable TO searchapp;
-
+GRANT SELECT, UPDATE, INSERT, DELETE ON TABLE searchapp.import_xnat_variable TO biomart_user;
+GRANT ALL ON TABLE searchapp.import_xnat_variable TO tm_cz;
 --
 -- Name: pk_import_xnat_var; Type: CONSTRAINT; Schema: searchapp; Owner: -
 --

scripts/xnattotransmartlink/command.sh

@@ -1,9 +1,10 @@
 #!/bin/bash
-export KETTLE_HOME="/home/jenkins/transmart-data/env/tranSMART-ETL/Postgres/GPL-1.0/Kettle/Kettle-ETL/"
+export TS_DATA="/home/transmart/transmart-data/"
+export KETTLE_HOME="${TS_DATA}samples/postgres/kettle-home/"
 
-sh "/home/jenkins/transmart-data/env/data-integration/kitchen.sh" \
+sh "${TS_DATA}env/data-integration/kitchen.sh" \
 -norep=N \
--file="/home/jenkins/transmart-data/env/tranSMART-ETL/Kettle-GPL/Kettle-ETL/create_clinical_data.kjb" \
+-file="${TS_DATA}env/tranSMART-ETL/Postgres/GPL-1.0/Kettle/Kettle-ETL/create_clinical_data.kjb" \
 -log=load_clinical_data.log \
 -param:LOAD_TYPE=I \
 -param:COLUMN_MAP_FILE=xnat.tmm \

scripts/xnattotransmartlink/downloadscript.py

@@ -3,7 +3,7 @@
 import pyxnat
 import subprocess
 import sys
-from elementtree.ElementTree import parse
+from xml.etree.ElementTree import parse
 
 CONFIG_PATH = './'
 CONFIG_EXTENSION = ".xml"