From 1669d630207299f58398a52a82ec181965e2c4e2 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 31 Jul 2017 16:34:26 +0200
Subject: [PATCH] search by database id implemented
---
.../services/impl/SearchService.java | 43 +++++++++++-
.../services/impl/SearchServiceTest.java | 66 ++++++++++++++-----
2 files changed, 92 insertions(+), 17 deletions(-)
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
index d202b0c4c8..34186d37bb 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -28,10 +28,10 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Degraded;
import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.model.map.species.Phenotype;
@@ -77,6 +77,12 @@ public class SearchService implements ISearchService {
*/
public static final String REACTION_SEARCH_PREFIX = "reaction";
+ /**
+ * Prefix used in search by name interface to limit results only to
+ * {@link Element}.
+ */
+ private static final String ELEMENT_SEARCH_PREFIX = "element";
+
/**
* Default class logger.
*/
@@ -240,6 +246,8 @@ public class SearchService implements ISearchService {
return getReactionById(model, query.replaceFirst(REACTION_SEARCH_PREFIX, "").toLowerCase());
} else if (query.startsWith(SPECIES_SEARCH_PREFIX)) {
result.add(fullAliasViewFactory.create(model.getElementByElementId(query.replaceFirst(SPECIES_SEARCH_PREFIX, ""))));
+ } else if (query.startsWith(ELEMENT_SEARCH_PREFIX)) {
+ return getElementById(model, query.replaceFirst(ELEMENT_SEARCH_PREFIX, "").toLowerCase());
} else {
Set<Element> aliases = model.getElements();
@@ -309,14 +317,45 @@ public class SearchService implements ISearchService {
private List<IHeavyView> getReactionById(Model model, String reactionId) {
Set<Reaction> reactions = model.getReactions();
for (Reaction reaction : reactions) {
-
if (searchIndexer.getQueryStringForIndex(reaction.getIdReaction().toLowerCase(), new ArrayList<>()).equals(reactionId)) {
return reactionToResultList(reaction);
}
+ if (Integer.toString(reaction.getId()).equals(reactionId)) {
+ return reactionToResultList(reaction);
+ }
}
return new ArrayList<>();
}
+ /**
+ * Returns list with the element with a given id. If element with such id
+ * doesn't exist then empty list is returned.
+ *
+ * @param topModel
+ * where the search is performed
+ * @param elementId
+ * id of the element
+ * @return list that contains element with given id (or empty list if such
+ * element doesn't exist)
+ */
+ private List<IHeavyView> getElementById(Model topModel, String elementId) {
+ List<IHeavyView> result = new ArrayList<>();
+
+ Set<Model> models = new HashSet<>();
+ models.add(topModel);
+ models.addAll(topModel.getSubmodels());
+ for (Model model : models) {
+ for (Element element : model.getElements()) {
+ if (searchIndexer.getQueryStringForIndex(element.getElementId().toLowerCase(), new ArrayList<>()).equals(elementId)) {
+ result.add(fullAliasViewFactory.create(element));
+ } else if (Integer.toString(element.getId()).equals(elementId)) {
+ result.add(fullAliasViewFactory.create(element));
+ }
+ }
+ }
+ return result;
+ }
+
/**
* Transform {@link Reaction} into set of result entries.
*
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
index c6d48d10ac..8dc37c8a7c 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -31,6 +31,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Degraded;
import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Ion;
@@ -50,7 +51,6 @@ import lcsb.mapviewer.services.utils.SearchIndexer;
public class SearchServiceTest extends ServiceTestFunctions {
static Logger logger = Logger.getLogger(SearchServiceTest.class);
- private Model model = null;
SearchIndexer indexer = new SearchIndexer();
Map<Class<?>, String> speciesSearchPrefix = new HashMap<Class<?>, String>();
@@ -75,9 +75,10 @@ public class SearchServiceTest extends ServiceTestFunctions {
speciesSearchReversePrefix.put(prefix, clazz);
}
- protected void createFullModel() throws Exception {
- model = getModelForFile("testFiles/searchModel.xml", false);
+ protected Model createFullModel() throws Exception {
+ Model model = getModelForFile("testFiles/searchModel.xml", false);
model.setProject(new Project("unknown project"));
+ return model;
}
@After
@@ -87,7 +88,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testSearchByName() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
long count = searchHistoryDao.getCount();
SearchElementResult result = searchService.searchByQuery(model, "reaction:re21", 50, null, "127.0.0.1");
@@ -109,7 +110,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testSearchByName2() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
SearchElementResult result = searchService.searchByQuery(model, "BAD:BCL-2", 50, null, "127.0.0.1");
assertNotNull(result);
@@ -126,7 +127,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testSearchById() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_HAS_VERSION, MiriamType.CAS, "123");
model.getElements().iterator().next().addMiriamData(md);
SearchElementResult global = searchService.searchByQuery(model, "CAS:123", 50, null, "127.0.0.1");
@@ -138,10 +139,25 @@ public class SearchServiceTest extends ServiceTestFunctions {
}
}
+ @Test
+ public void testSearchByElementId() throws Exception {
+ try {
+ Model model = createFullModel();
+ Element element =model.getElements().iterator().next();
+ element.setId(907);
+ SearchElementResult global = searchService.searchByQuery(model, "element:907", 50, null, "127.0.0.1");
+ assertNotNull(global);
+ assertEquals(1, global.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testSearchByName4() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
SearchElementResult result = searchService.searchByQuery(model, "BC", 50, true, "127.0.0.1");
assertNotNull(result);
@@ -166,7 +182,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testQueryName() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
SearchElementResult result = searchService.searchByQuery(model, indexer.getQueryStringForIndex("reaction:re21", new HashSet<>()), 50, null, "127.0.0.1");
assertNotNull(result);
@@ -185,7 +201,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testQueryReactionId() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
model.getReactions().iterator().next().setIdReaction("R_x1");
SearchElementResult result = searchService.searchByQuery(model, indexer.getQueryStringForIndex("reaction:r_x1", new HashSet<>()), 50, null, "127.0.0.1");
@@ -199,10 +215,30 @@ public class SearchServiceTest extends ServiceTestFunctions {
}
}
+ @Test
+ public void testQueryReactionId2() throws Exception {
+ try {
+ Model model = createFullModel();
+ Reaction reaction = model.getReactions().iterator().next();
+ reaction.setId(154);
+ reaction.setIdReaction("test-name");
+ SearchElementResult result = searchService.searchByQuery(model, indexer.getQueryStringForIndex("reaction:154", new HashSet<>()), 50, null, "127.0.0.1");
+
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ FullReactionView resultReaction = (FullReactionView) result.get(0);
+ logger.debug(resultReaction.getName());
+ assertTrue(resultReaction.getName().contains("test-name"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testQueryName2() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
model.getModelData().setId(-13);
SearchElementResult result = searchService
.searchByQuery(model, indexer.getQueryStringForIndex("BCL-2", speciesSearchReversePrefix.keySet()), 50, null, "127.0.0.1");
@@ -219,7 +255,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testQueryName3() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
SearchElementResult result = searchService.searchByQuery(model, "fdhgjkhdsfsdhfgfhsd", 50, null, "127.0.0.1");
assertNotNull(result);
@@ -233,7 +269,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testQueryName4() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
SearchElementResult result = searchService
.searchByQuery(model, indexer.getQueryStringForIndex("protein:BCL-2", speciesSearchReversePrefix.keySet()), 50, null, "127.0.0.1");
assertNotNull(result);
@@ -249,7 +285,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testSearchClosest() throws Exception {
try {
- model = getModelForFile("testFiles/graph_path_example3.xml", true);
+ Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
assertNotNull(elements);
assertEquals(5, elements.size());
@@ -278,7 +314,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testSearchClosest2() throws Exception {
try {
- model = new ModelFullIndexed(null);
+ Model model = new ModelFullIndexed(null);
GenericProtein protein1 = new GenericProtein("s1");
protein1.setWidth(20);
protein1.setHeight(20);
@@ -317,7 +353,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testSearchClosestWithEmptyModel() throws Exception {
try {
- model = new ModelFullIndexed(null);
+ Model model = new ModelFullIndexed(null);
List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
assertNotNull(elements);
assertEquals(0, elements.size());
--
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