From 9b8dfe6ba504239a586ed1b11f328a5743c7ebf7 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 31 Jul 2017 15:56:10 +0200
Subject: [PATCH] when matching other target there was problem when no gene was
defiend
---
.../services/search/ElementMatcher.java | 13 +-
.../services/search/AllSearchTests.java | 3 +-
...ctoryTest.java => ElementMatcherTest.java} | 128 ++++++++++--------
3 files changed, 81 insertions(+), 63 deletions(-)
rename service/src/test/java/lcsb/mapviewer/services/search/{SearchResultFactoryTest.java => ElementMatcherTest.java} (66%)
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java b/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
index c947104992..1e01f40e07 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
@@ -103,8 +103,17 @@ public class ElementMatcher {
return false;
case OTHER:
// in other case just compare names
- String name = target.getGenes().get(0).getResource();
- return element.getName().equalsIgnoreCase(name);
+ String targetName = null;
+ if (target.getGenes().size() > 0) {
+ targetName = target.getGenes().get(0).getResource();
+ }
+ if (targetName == null) {
+ targetName = target.getName();
+ }
+ if (targetName == null) {
+ return false;
+ }
+ return element.getName().equalsIgnoreCase(targetName);
default:
throw new InvalidArgumentException("Unknown drug target type: " + target.getType());
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java b/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java
index 0073cd477c..512a3b462c 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java
@@ -13,7 +13,8 @@ import lcsb.mapviewer.services.search.layout.AllSearchLayoutTests;
@SuiteClasses({ AllCommentTests.class, //
AllSearchDbTests.class, //
AllSearchDataTests.class, //
- AllSearchLayoutTests.class,//
+ AllSearchLayoutTests.class, //
+ ElementMatcherTest.class, //
})
public class AllSearchTests {
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/ElementMatcherTest.java
similarity index 66%
rename from service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
rename to service/src/test/java/lcsb/mapviewer/services/search/ElementMatcherTest.java
index 7a310be346..c34aa859e2 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/ElementMatcherTest.java
@@ -1,60 +1,68 @@
-package lcsb.mapviewer.services.search;
-
-import static org.junit.Assert.assertTrue;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.search.comment.FullCommentViewFactory;
-import lcsb.mapviewer.services.search.db.DbSearchCriteria;
-import lcsb.mapviewer.services.search.db.chemical.IChemicalService;
-
-public class SearchResultFactoryTest extends ServiceTestFunctions {
-
- Logger logger = Logger.getLogger(SearchResultFactoryTest.class);
-
- @Autowired
- FullCommentViewFactory factory;
-
- @Autowired
- IChemicalService chemicalService;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testElementMatch() {
- String geneName = "GDNF";
- Chemical view = chemicalService.getByName("Amphetamine", new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
- Target target = null;
- for (Target t : view.getInferenceNetwork()) {
- for (MiriamData row : t.getGenes()) {
- if (row.getResource().equals(geneName)) {
- target = t;
- }
- }
- }
-
- Element element = new Rna("id");
- element.setName(geneName);
-
- assertTrue(factory.elementMatch(target, element));
-
- }
-
-}
+package lcsb.mapviewer.services.search;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.data.Chemical;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargetType;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+
+public class ElementMatcherTest extends ServiceTestFunctions {
+
+ @Autowired
+ ElementMatcher elementMatcher;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testMatchOther() {
+ Target target = new Target();
+
+ target.setType(TargetType.OTHER);
+ assertFalse(elementMatcher.elementMatch(target, new GenericProtein("s1")));
+ }
+
+ @Test
+ public void testElementMatch() {
+ String geneName = "GDNF";
+ Chemical view = chemicalService.getByName("Amphetamine", new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
+ Target target = null;
+ for (Target t : view.getInferenceNetwork()) {
+ for (MiriamData row : t.getGenes()) {
+ if (row.getResource().equals(geneName)) {
+ target = t;
+ }
+ }
+ }
+
+ Element element = new Rna("id");
+ element.setName(geneName);
+
+ assertTrue(elementMatcher.elementMatch(target, element));
+
+ }
+
+}
--
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