diff --git a/CHANGELOG b/CHANGELOG
index 852874c6df11e3764d8885047c1849089f040410..9e131afa95861b8d35620c527af4bc3becf624db 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,8 @@
+minerva (13.1.4) stable; urgency=medium
+ * Bug fix:search by drugs didn't check synonyms in chembl database
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Wed, 21 Aug 2019 17:00:00 +0200
+
minerva (13.1.3) stable; urgency=medium
* Bug fix: refreshing list of projects or list of users doesn't change active
page (#870)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
index 3a7519a5f3488d30759204fd1921b528424e0625..3d85947424392f8c46f4c03955785188a71e77a8 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
@@ -64,6 +64,11 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
*/
private static final String DRUG_NAME_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule?pref_name__exact=";
+ /**
+ * Url that access data of drug identified by name.
+ */
+ private static final String DRUG_SYNONYM_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule?molecule_synonyms__molecule_synonym__iexact=";
+
/**
* Url that access target by identifier.
*/
@@ -366,29 +371,22 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
String page = getWebPageContent(accessUrl);
Document document = XmlParser.getXmlDocumentFromString(page);
- Node response = XmlParser.getNode("response", document.getChildNodes());
- Node molecules = XmlParser.getNode("molecules", response.getChildNodes());
-
- NodeList list = molecules.getChildNodes();
-
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("molecule")) {
- if (drug == null) {
- drug = parseDrug(node);
- } else {
- logger.warn("More drugs than one found for query: " + query);
- }
- }
- }
+ List<Drug> drugs = extractDrugsFromDocument(document);
+ if (drugs.size()==0) {
+ accessUrl = DRUG_SYNONYM_API_URL + name;
+ page = getWebPageContent(accessUrl);
+ document = XmlParser.getXmlDocumentFromString(page);
+ drugs = extractDrugsFromDocument(document);
+ }
+ if (drugs.size()>1) {
+ logger.warn("More drugs than one found for query: " + query);
}
- if (drug == null) {
+ if (drugs.size() == 0) {
return null;
}
- setCacheValue(query, getDrugSerializer().objectToString(drug));
- return drug;
+ setCacheValue(query, getDrugSerializer().objectToString(drugs.get(0)));
+ return drugs.get(0);
} catch (IOException e) {
throw new DrugSearchException("Problem with accessing CHEMBL database", e);
} catch (InvalidXmlSchemaException e) {
@@ -396,6 +394,24 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
}
}
+ private List<Drug> extractDrugsFromDocument(Document document) throws DrugSearchException {
+ List<Drug> result = new ArrayList<>();
+ Node response = XmlParser.getNode("response", document.getChildNodes());
+ Node molecules = XmlParser.getNode("molecules", response.getChildNodes());
+
+ NodeList list = molecules.getChildNodes();
+
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("molecule")) {
+ result.add(parseDrug(node));
+ }
+ }
+ }
+ return result;
+ }
+
/**
* Parse xml node repesenting drug and returns drug with information obtained
* from there and other places in chembl API.
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
index 8fa920f651688e85b50daf5a607e0493b1b367f7..81975207903a0b61a29086e0714ba1114ca33c3a 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
@@ -1,20 +1,11 @@
package lcsb.mapviewer.annotation.services;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.ArgumentMatchers.anyString;
-import static org.mockito.ArgumentMatchers.nullable;
+import static org.junit.Assert.*;
+import static org.mockito.ArgumentMatchers.*;
import static org.mockito.Mockito.when;
import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
import org.apache.log4j.Logger;
import org.junit.Test;
@@ -23,22 +14,11 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.w3c.dom.Node;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.cache.XmlSerializer;
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargetType;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.UniprotSearchException;
+import lcsb.mapviewer.annotation.cache.*;
+import lcsb.mapviewer.annotation.data.*;
+import lcsb.mapviewer.annotation.services.annotators.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.*;
public class ChEMBLParserTest extends AnnotationTestFunctions {
Logger logger = Logger.getLogger(ChEMBLParserTest.class);
@@ -349,7 +329,8 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
fail("Exception expected");
@@ -411,7 +392,8 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn("<target><unk/></target>");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenReturn("<target><unk/></target>");
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
assertEquals(1, getWarnings().size());
@@ -842,7 +824,8 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
// simulate problem with downloading
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
@@ -866,7 +849,8 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
// simulate problem with downloading
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getDrugsByChemblTarget(new MiriamData());
@@ -920,7 +904,8 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
// simulate problem with downloading
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.refreshCacheQuery(query);
fail("Exception expected");
@@ -949,7 +934,8 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = chemblParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, chemblParser.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -984,9 +970,10 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
// valid xml but with empty data
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn("<response><molecules>"
- + "<molecule><pref_name/><max_phase/><molecule_chembl_id/><molecule_synonyms/></molecule>"
- + "</molecules><mechanisms/><molecule_forms/></response>");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenReturn("<response><molecules>"
+ + "<molecule><pref_name/><max_phase/><molecule_chembl_id/><molecule_synonyms/></molecule>"
+ + "</molecules><mechanisms/><molecule_forms/></response>");
chemblParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, chemblParser.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -1043,7 +1030,8 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetsByDrugId(new MiriamData(MiriamType.CHEMBL_COMPOUND, "123"));
fail("Exception expected");
@@ -1063,7 +1051,8 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getDrugListByTarget(new MiriamData(MiriamType.UNIPROT, "O60391"));
fail("Exception expected");
@@ -1165,7 +1154,8 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getDrugById(new MiriamData(MiriamType.CHEMBL_COMPOUND, ""));
fail("Exception expected");
@@ -1199,7 +1189,8 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetsForChildElements(new MiriamData());
fail("Exception expected");
@@ -1253,4 +1244,16 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
}
}
+ @Test
+ public void testFindDrugBryBrandName() throws Exception {
+ try {
+ Drug drug = chemblParser.findDrug("picato");
+ assertNotNull(drug);
+ assertEquals("CHEMBL1863513", drug.getSources().get(0).getResource());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/persist/src/main/resources/db/migration/13.1.4/V13.1.4.20190821__remove_chembl_cache.sql b/persist/src/main/resources/db/migration/13.1.4/V13.1.4.20190821__remove_chembl_cache.sql
new file mode 100644
index 0000000000000000000000000000000000000000..6aea6b38443948a2f8999010f401d3a6f41cb16a
--- /dev/null
+++ b/persist/src/main/resources/db/migration/13.1.4/V13.1.4.20190821__remove_chembl_cache.sql
@@ -0,0 +1 @@
+delete from cache_query_table where type in (select id from cache_type_table where class_name ='lcsb.mapviewer.annotation.services.ChEMBLParser');
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java
index af680065bee15cff9a415671b649f1d7828f0407..073367df2bc8d263fdf3686dab6a3c141a76e7f6 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java
@@ -1,11 +1,6 @@
package lcsb.mapviewer.services.search.drug;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
@@ -14,21 +9,14 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.Drug;
import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.services.ChEMBLParser;
-import lcsb.mapviewer.annotation.services.DrugSearchException;
-import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
+import lcsb.mapviewer.annotation.services.*;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.DbSearchCriteria;
@@ -185,9 +173,15 @@ public class DrugService extends DbSearchService implements IDrugService {
if (name.trim().equals("")) {
return null;
}
+ DrugAnnotation secondParser = chEMBLParser;
Drug drug = null;
try {
drug = drugBankParser.findDrug(name);
+
+ if (drug==null) {
+ drug = chEMBLParser.findDrug(name);
+ secondParser = drugBankParser;
+ }
if (drug != null) {
removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
}
@@ -201,13 +195,13 @@ public class DrugService extends DbSearchService implements IDrugService {
// * search for name
searchNames.add(name);
if (drug != null && drug.getName() != null) {
- // * search for name of a drug in drugbanke
+ // * search for name of a drug in drugbank
searchNames.add(drug.getName());
// * search for all synonyms found in drugbank
// searchNames.addAll(drug.getSynonyms());
}
for (String string : searchNames) {
- Drug drug2 = chEMBLParser.findDrug(string);
+ Drug drug2 = secondParser.findDrug(string);
if (drug2 != null) {
removeUnknownOrganisms(drug2, searchCriteria.getOrganisms());
// don't add drugs that were already found
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java
index c93d8dd442397f807d16878070eea849be05fb61..186339ba0c729e6c7c521e0774357c24d2fd8074 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java
@@ -57,6 +57,17 @@ public class DrugServiceTest extends ServiceTestFunctions {
}
}
+ @Test
+ public void testGetIstodax() throws Exception {
+ try {
+ Drug drug = drugService.getByName("istodax", new DbSearchCriteria());
+ assertEquals(2, drug.getSources().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testGetTargets() throws Exception {
try {