Merge branch 'master' of https://github.com/evast/transmart-xnat-impo…

…rter-plugin

README.md

@@ -0,0 +1,18 @@
+The TranSMART-XNAT-Importer plugin can import clinical image-derived data from XNAT and store them in TranSMART.
+
+![alt tag](https://raw.github.com/evast/transmart-xnat-importer-plugin/master/docs/navigator.png)  
+XNAT Data hierarchy shown in TranSMART ontology. 
+
+TranSMART-XNAT Coupling
+----------
+
+TranSMART  (http://transmartfoundation.org) is a data integration and browsing platform for central statistical analysis in translational research.
+
+XNAT (www.xnat.org) is a framework to store, share and manage medical imaging data. This imaging archive can be connected to a computing cluster for further image analyses. After analyses of the images, the analysis results (e.g. grey matter volumes) can be stored back in XNAT. 
+
+To correlate the image-derived results with other medical data, such as demographic or genetic data, it would be useful to import the XNAT results in TranSMART. To this end, we developed the TranSMART-XNAT-Importer plugin. To configure which XNAT image-derived data is imported in TranSMART, an administrator can create a coupling configuration in the online administration panel and start the import process. The plugin uses the default ETL Importer for clinical data to import the XNAT results in TranSMART. 
+
+Documentation and Installation
+------------------------------
+
+More information about the plugin and installation instructions can be found in [TranSMART-XNAT-Importer-plugin-manual.pdf](https://github.com/evast/transmart-xnat-importer-plugin/blob/master/docs/TranSMART-XNAT-Importer-plugin-manual.pdf?raw=true) in the directory docs. A user-guide to import data with step-by-step instructions and screenshots can be found in the same document.

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"