From dddfad1dabe01f20cab642948ee8b65445df3bcb Mon Sep 17 00:00:00 2001
From: David Hoksza <david.hoksza@uni.lu>
Date: Wed, 22 Nov 2017 13:22:01 +0100
Subject: [PATCH] BRENDA annotator including unit tests.
---
.../annotation/services/ModelAnnotator.java | 8 +
.../services/annotators/BrendaAnnotator.java | 233 ++++++++++++++
.../services/annotators/CazyAnnotator.java | 2 +-
.../applicationContext-annotation.xml | 1 +
.../annotators/AllAnnotatorTests.java | 1 +
.../annotators/BrendaAnnotatorTest.java | 301 ++++++++++++++++++
.../annotators/TairAnnotatorTest.java | 4 -
.../lcsb/mapviewer/model/map/MiriamType.java | 27 +-
persist/src/db/11.1.1/fix_db_20171114.sql | 3 +
9 files changed, 566 insertions(+), 14 deletions(-)
create mode 100644 annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
create mode 100644 annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index a9eb813ceb..f3b3f463ed 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -16,6 +16,7 @@ import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.BrendaAnnotator;
import lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator;
import lcsb.mapviewer.annotation.services.annotators.CazyAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
@@ -69,6 +70,12 @@ public class ModelAnnotator {
* Default class logger.
*/
private static Logger logger = Logger.getLogger(ModelAnnotator.class);
+
+ /**
+ * BRENDA annotator.
+ */
+ @Autowired
+ private BrendaAnnotator brendaAnnotator;
/**
* Service accessing <a href= "http://biocompendium.embl.de/" >internal
@@ -159,6 +166,7 @@ public class ModelAnnotator {
availableAnnotators = new ArrayList<>();
defaultAnnotators = new ArrayList<>();
+ addAnnotator(brendaAnnotator);
addAnnotator(biocompendiumAnnotator);
addAnnotator(cazyAnnotator);
addAnnotator(chebiBackend);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
new file mode 100644
index 0000000000..cbd483007a
--- /dev/null
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
@@ -0,0 +1,233 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+
+/**
+ * This is a class that implements a backend to Brenda enzyme database.
+ *
+ * @author David Hoksza
+ *
+ */
+public class BrendaAnnotator extends ElementAnnotator implements IExternalService {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(BrendaAnnotator.class);
+
+ /**
+ * Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
+ * TAIR}.
+ */
+ @Autowired
+ private TairAnnotator tairAnnotator;
+
+ /**
+ * Pattern used for finding UniProt symbol from TAIR info page .
+ */
+ private Pattern uniprotECMatcher = Pattern.compile("EC=((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))");
+
+ /**
+ * Default constructor.
+ */
+ public BrendaAnnotator() {
+ super(BrendaAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ Collection<MiriamData> mds = uniprotToBrenda(new MiriamData(MiriamType.UNIPROT, "P12345"));
+
+ status.setStatus(ExternalServiceStatusType.OK);
+ List<String> ecs = new ArrayList<>();
+ if (mds != null) {
+ for (MiriamData md: mds) {
+ ecs.add(md.getResource());
+ }
+ }
+ if (mds == null || mds.size() != 2 || ecs.indexOf("2.6.1.1") < 0 || ecs.indexOf("2.6.1.7") < 0) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ @Override
+ public void annotateElement(BioEntity object) throws AnnotatorException {
+ if (isAnnotatable(object)) {
+
+ MiriamData mdTair = null;
+ for (MiriamData md : object.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.BRENDA)) {
+ return;
+ }
+ else if (md.getDataType().equals(MiriamType.TAIR_LOCUS)) {
+ mdTair = md;
+ }
+ }
+ if (mdTair != null) {
+ tairAnnotator.annotateElement(object);
+ }
+
+ List<MiriamData> mdUniprots = new ArrayList<MiriamData>();
+ for (MiriamData md : object.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.UNIPROT)) {
+ mdUniprots.add(md);
+ }
+ }
+
+ List<String> ecIds = new ArrayList<String>();
+ for (MiriamData mdUniprot: mdUniprots) {
+ Collection<MiriamData> mdBrendas = uniprotToBrenda(mdUniprot);
+ if (mdBrendas != null) {
+ for (MiriamData mdBrenda: mdBrendas) {
+ if (ecIds.indexOf(mdBrenda.getResource()) == -1) {
+ ecIds.add(mdBrenda.getResource());
+ object.addMiriamData(mdBrenda);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Returns URL to UniProt restfull API about UniProt entry.
+ *
+ * @param uniprotId
+ * UniProt identifier
+ * @return URL to UniProt restfull API about UniProt entry
+ */
+ private String getUniprotUrl(String uniprotId) {
+ return "http://www.uniprot.org/uniprot/" + uniprotId + ".txt";
+ }
+
+ /**
+ * Parse UniProt webpage to find information about
+ * {@link MiriamType#BRENDA}, i.e. EC, and returns them.
+ *
+ * @param pageContent
+ * UniProt info page
+ * @return BRENDA family identifier, i.e. EC, found on the page
+ */
+ private Collection<MiriamData> parseUniprot(String pageContent) {
+ Collection<MiriamData> result = new HashSet<MiriamData>();
+ Matcher m = uniprotECMatcher.matcher(pageContent);
+ while (m.find()) {
+ result.add(new MiriamData(MiriamType.BRENDA, m.group(1)));
+ }
+ return result;
+ }
+
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String name;
+ String result = null;
+ if (query instanceof String) {
+ name = (String) query;
+ if (name.startsWith("http")) {
+ try {
+ result = getWebPageContent(name);
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with query: " + query);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ return result;
+ }
+
+ /**
+ * Transform UniProt identifier to CAZy identifier.
+ *
+ * @param UniProt
+ * {@link MiriamData} with UniProt identifier
+ * @return Collection of {@link MiriamData} with BRENDA identifier
+ * @throws AnnotatorException
+ * thrown when there is a problem with accessing external database
+ */
+ public Collection<MiriamData> uniprotToBrenda(MiriamData uniprot) throws AnnotatorException {
+ if (uniprot == null) {
+ return null;
+ }
+
+ if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
+ }
+
+ String accessUrl = getUniprotUrl(uniprot.getResource());
+ try {
+ String pageContent = getWebPageContent(accessUrl);
+ Collection<MiriamData> collection = parseUniprot(pageContent);
+ if (collection.size() > 0) {
+ return collection;
+ } else {
+ logger.warn("Cannot find EC data for UniProt id: " + uniprot.getResource());
+ return null;
+ }
+ } catch (WrongResponseCodeIOException exception) {
+ logger.warn("Wrong response code when retrieving EC data for UniProt id: " + uniprot.getResource());
+ return null;
+ } catch (IOException exception) {
+ throw new AnnotatorException(exception);
+ }
+ }
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.BRENDA.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.BRENDA.getDbHomepage();
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
index 6fb6ef830a..a0fa95d515 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
@@ -59,7 +59,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public ExternalServiceStatus getServiceStatus() { //TODO
+ public ExternalServiceStatus getServiceStatus() {
ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
GeneralCacheInterface cacheCopy = getCache();
diff --git a/annotation/src/main/resources/applicationContext-annotation.xml b/annotation/src/main/resources/applicationContext-annotation.xml
index 4e0956e5d1..ee83e7e987 100644
--- a/annotation/src/main/resources/applicationContext-annotation.xml
+++ b/annotation/src/main/resources/applicationContext-annotation.xml
@@ -13,6 +13,7 @@
<!-- Annotation services -->
<!-- Annotators -->
+ <bean id="BrendaAnnotator" class="lcsb.mapviewer.annotation.services.annotators.BrendaAnnotator"/>
<bean id="BiocompendiumAnnotator" class="lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator"/>
<bean id="CazyAnnotator" class="lcsb.mapviewer.annotation.services.annotators.CazyAnnotator"/>
<bean id="ChebiAnnotator" class="lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator"/>
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
index 1f994c0d3c..8325d7f57c 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
@@ -6,6 +6,7 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ AnnotatorExceptionTest.class, //
+ BrendaAnnotatorTest.class, //
BiocompendiumAnnotatorTest.class, //
CazyAnnotatorTest.class, //
ChebiAnnotatorTest.class, //
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
new file mode 100644
index 0000000000..87711ddccc
--- /dev/null
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
@@ -0,0 +1,301 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+import static org.junit.Assert.assertEquals;
+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.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.util.Collection;
+import java.io.IOException;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class BrendaAnnotatorTest extends AnnotationTestFunctions {
+
+ @Autowired
+ BrendaAnnotator brendaAnnotator;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testUniprotToCazy() throws Exception {
+ try {
+ Collection<MiriamData> mds = brendaAnnotator.uniprotToBrenda(new MiriamData(MiriamType.UNIPROT, "P12345"));
+ assertEquals(mds.size(), 2);
+ MiriamData md1 = new MiriamData(MiriamType.BRENDA, "2.6.1.1");
+ MiriamData md2 = new MiriamData(MiriamType.BRENDA, "2.6.1.7");
+ for (MiriamData md: mds) {
+ assertTrue(md.compareTo(md1) == 0 || md.compareTo(md2) == 0);
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateFromUniprot() throws Exception {
+ try {
+
+ Species protein = new GenericProtein("id");
+ protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "P12345"));
+
+ brendaAnnotator.annotateElement(protein);
+
+ int cntMds = 0;
+
+ for (MiriamData md : protein.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.BRENDA)) {
+ cntMds++;
+ assertTrue("Invalid BRENDA annotation extracted from BRENDA annotator",
+ md.getResource().equals("2.6.1.1") || md.getResource().equals("2.6.1.7") );
+ }
+ }
+
+ assertTrue("Incorrect BRENDA annotations extracted from BRENDA annotator", cntMds == 2);
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateFromTair() throws Exception {
+ try {
+
+ Species protein = new GenericProtein("id");
+ protein.setName("bla");
+ protein.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "AT5G48930"));
+
+ brendaAnnotator.annotateElement(protein);
+
+ MiriamData mdBrenda = null;
+
+ for (MiriamData md : protein.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.BRENDA)) {
+ mdBrenda = md; //there should be only one EC number for that TAIR<->UNIPROT record
+ }
+ }
+
+ assertTrue("No BRENDA annotation extracted from BRENDA annotator", mdBrenda != null);
+ assertTrue("Invalid BRENDA annotation extracted from BRENDA annotator based on TAIR", mdBrenda.getResource().equals("2.3.1.133") );
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateMultipleUniprots() throws Exception {
+ try {
+
+ Species protein = new GenericProtein("id");
+ protein.setName("bla");
+ protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q9SG95"));
+ protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q12540"));
+
+ brendaAnnotator.annotateElement(protein);
+
+ assertTrue("Wrong number of BRENDA identifiers extracted from BRENDA annotator", protein.getMiriamData().size() == 4 );
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateMultipleUniprotsWithIdenticalEC() throws Exception {
+ try {
+
+ Species protein = new GenericProtein("id");
+ protein.setName("bla");
+ protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q9SG95"));
+ protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q8L5J1"));
+
+ brendaAnnotator.annotateElement(protein);
+
+ assertTrue("Wrong number of BRENDA identifiers extracted from BRENDA annotator", protein.getMiriamData().size() == 3 );
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateInvalidEmpty() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("bla");
+ brendaAnnotator.annotateElement(protein);
+
+ assertEquals(0, protein.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateInvalidUniprot() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "bla"));
+ brendaAnnotator.annotateElement(protein);
+
+ assertEquals(1, protein.getMiriamData().size());
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateInvalidTair() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "bla"));
+ brendaAnnotator.annotateElement(protein);
+
+ assertEquals(1, protein.getMiriamData().size());
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidUniprotToCazyNull() throws Exception {
+ try {
+ assertNull(brendaAnnotator.uniprotToBrenda(null));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidUniprotToCazyWrongMd() throws Exception {
+ try {
+ brendaAnnotator.uniprotToBrenda(new MiriamData(MiriamType.WIKIPEDIA, "bla"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ brendaAnnotator.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ brendaAnnotator.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery() throws Exception {
+ try {
+ Object res = brendaAnnotator.refreshCacheQuery("http://google.cz/");
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, brendaAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = brendaAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ brendaAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, brendaAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ brendaAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ WebPageDownloader downloader = brendaAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("GN Name=ACSS2; Synonyms=ACAS2;");
+ brendaAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, brendaAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ brendaAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
index b2df54d225..10d1bb10e7 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
@@ -10,17 +10,13 @@ import static org.mockito.Mockito.when;
import java.io.IOException;
-import org.apache.http.client.HttpResponseException;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
-import javassist.NotFoundException;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 1644e64526..831ca861b8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -22,15 +22,24 @@ import lcsb.mapviewer.model.map.species.Rna;
*/
@SuppressWarnings("unchecked")
public enum MiriamType {
- /**
- * Chemical Abstracts Service database: http://commonchemistry.org.
- */
- CAS("Chemical Abstracts Service", //
- "http://commonchemistry.org", //
- new String[] { "urn:miriam:cas" }, //
- new Class<?>[] {}, "MIR:00000237"), //
-
- /**
+ /**
+ * Brenda enzyme database: http://www.brenda-enzymes.org.
+ */
+ BRENDA("BRENDA", //
+ "http://www.brenda-enzymes.org", //
+ new String[] { "urn:miriam:brenda" }, //
+ new Class<?>[] {}, "MIR:00100101"), //
+
+ /**
+ * Chemical Abstracts Service database: http://commonchemistry.org.
+ */
+ CAS("Chemical Abstracts Service", //
+ "http://commonchemistry.org", //
+ new String[] { "urn:miriam:cas" }, //
+ new Class<?>[] {}, "MIR:00000237"), //
+
+ /**
+
* The Carbohydrate-Active Enzyme (CAZy) database: http://www.cazy.org/.
*/
CAZY("CAZy", //
diff --git a/persist/src/db/11.1.1/fix_db_20171114.sql b/persist/src/db/11.1.1/fix_db_20171114.sql
index 8dd8092a16..771e3f42a9 100644
--- a/persist/src/db/11.1.1/fix_db_20171114.sql
+++ b/persist/src/db/11.1.1/fix_db_20171114.sql
@@ -3,3 +3,6 @@ INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotat
DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.CazyAnnotator';
INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.CazyAnnotator');
+
+DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.BrendaAnnotator';
+INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.BrendaAnnotator');
--
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