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Commit 1669d630 authored by Piotr Gawron's avatar Piotr Gawron
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search by database id implemented

parent 9d1f1ab0
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1 merge request!99Resolve "Link from literature file to the related reaction in the map does not work"
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service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+ 41
− 2
View file @ 1669d630
......@@ -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.
*
......
service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+ 51
− 15
View file @ 1669d630
......@@ -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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