Merge pull request diffblue#464 from diffblue/owen-jones-diffblue/fix/ginco-stage-3

SEC-493: Fix bug in Ginco stage 3

Author: owen-jones-diffblue

benchmarks/GENUINE/Ginco.sh

@@ -23,7 +23,7 @@ if [[ ! -d "Ginco" ]]; then
 
     patch -p1 -f < ../Ginco_files/0001-Reverting-XSS-issue-and-adding-generation-of-jar.patch
 
-    mvn package -DskipTests
+    mvn install -DskipTests
 
     # Now we create an artificial entry-point project and build it
     cp -r ../Ginco_files/__MAIN__/ .

benchmarks/GENUINE/Ginco_files/0001-Reverting-XSS-issue-and-adding-generation-of-jar.patch

@@ -1,39 +1,33 @@
-From ed369d182a223b53c9ff37bec44b391833b24c7b Mon Sep 17 00:00:00 2001
-From: marek-trtik <[email protected]>
-Date: Fri, 8 Jun 2018 17:41:23 +0100
-Subject: [PATCH] Reverting XSS issue and adding generation of jar
-
----
- ginco-admin/pom.xml                                                     | 2 +-
- .../src/main/java/fr/mcc/ginco/rest/services/ImportRestService.java     | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/ginco-admin/pom.xml b/ginco-admin/pom.xml
-index d4f91e5..5b7f18c 100644
---- a/ginco-admin/pom.xml
-+++ b/ginco-admin/pom.xml
-@@ -151,7 +151,7 @@
+diff -ur Ginco/ginco-admin/pom.xml Ginco-patched/ginco-admin/pom.xml
+--- Ginco/ginco-admin/pom.xml	2018-06-22 14:15:46.526321053 +0100
++++ Ginco-patched/ginco-admin/pom.xml	2018-06-22 14:17:11.262895281 +0100
+@@ -151,6 +151,8 @@
  						</resource>
  					</webResources>
  					<warSourceExcludes>*.js,app/**/*.js</warSourceExcludes>
--				</configuration>
-+<attachClasses>true</attachClasses><classesClassifier>classes</classesClassifier></configuration>
++					<attachClasses>true</attachClasses>
++					<classesClassifier>classes</classesClassifier>
+ 				</configuration>
  			</plugin>
  			<plugin>
- 				<groupId>com.googlecode.jslint4java</groupId>
-diff --git a/ginco-admin/src/main/java/fr/mcc/ginco/rest/services/ImportRestService.java b/ginco-admin/src/main/java/fr/mcc/ginco/rest/services/ImportRestService.java
-index 140a5c8..d2ddaf1 100644
---- a/ginco-admin/src/main/java/fr/mcc/ginco/rest/services/ImportRestService.java
-+++ b/ginco-admin/src/main/java/fr/mcc/ginco/rest/services/ImportRestService.java
-@@ -193,7 +193,7 @@ public class ImportRestService {
+diff -ur Ginco/ginco-admin/src/main/java/fr/mcc/ginco/rest/services/ImportRestService.java Ginco-patched/ginco-admin/src/main/java/fr/mcc/ginco/rest/services/ImportRestService.java
+--- Ginco/ginco-admin/src/main/java/fr/mcc/ginco/rest/services/ImportRestService.java	2018-06-22 14:23:12.009303325 +0100
++++ Ginco-patched/ginco-admin/src/main/java/fr/mcc/ginco/rest/services/ImportRestService.java	2018-06-22 14:19:42.219909086 +0100
+@@ -106,7 +106,7 @@
+ 
+ 	@Inject
+ 	@Named("skosImportService")
+-	private ISKOSImportService skosImportService;
++	public ISKOSImportService skosImportService;
+ 
+ 	@Inject
+ 	@Named("gincoImportService")
+@@ -193,7 +193,7 @@
  		response.setExternalConceptIds(externalConceptIds);
  		ObjectMapper mapper = new ObjectMapper();
  		String serialized = mapper.writeValueAsString(new ExtJsonFormLoadData(response));
--		return StringEscapeUtils.unescapeHtml4(serialized);
-+        return serialized;
+- 		return StringEscapeUtils.unescapeHtml4(serialized);
++ 		return serialized;
  	}
 
  	/**
--- 
-2.7.4
-

benchmarks/GENUINE/Ginco_files/__MAIN__/src/main/java/Main.java

@@ -1,3 +1,4 @@
+import fr.mcc.ginco.imports.ISKOSImportService;
 import org.cprover.CProver;
 import javax.servlet.http.HttpServletRequest;
 import org.apache.cxf.jaxrs.ext.multipart.MultipartBody;
@@ -16,6 +17,7 @@ public static void main(String[] args) {
         makeTainted(arg0);
         HttpServletRequest arg1 = CProver.nondetWithNull((HttpServletRequest)null);
         ImportRestService obj = CProver.nondetWithNull((ImportRestService)null);
+        obj.skosImportService = new SKOSImportService();
         try {
             sink(obj.uploadFile(arg0, arg1));
         }

benchmarks/GENUINE/Ginco_files/__MAIN__/src/main/java/SKOSImportService.java

@@ -0,0 +1,17 @@
+import fr.mcc.ginco.imports.ISKOSImportService;
+import fr.mcc.ginco.beans.Alignment;
+import fr.mcc.ginco.beans.Thesaurus;
+
+import java.io.File;
+import java.util.Map;
+import java.util.HashMap;
+import java.util.Set;
+import java.util.HashSet;
+
+class SKOSImportService implements ISKOSImportService {
+ public Map<Thesaurus, Set<Alignment>> importSKOSFile(String fileContent, String fileName, File tempDir) {
+   Map<Thesaurus, Set<Alignment>> m = new HashMap<Thesaurus, Set<Alignment>>();
+   m.put(new Thesaurus(), new HashSet<Alignment>());
+   return m;
+ }
+}