From a6d20bcb6d748252eaa8b213b8947ac9b05eb1ac Mon Sep 17 00:00:00 2001
From: David Hoksza <david.hoksza@uni.lu>
Date: Tue, 14 Nov 2017 15:24:59 +0100
Subject: [PATCH] Basic TAIR annotation implemented, including unit tests.
---
.../services/annotators/TairAnnotator.java | 206 +++++++++++++++
.../applicationContext-annotation.xml | 1 +
.../annotators/AllAnnotatorTests.java | 1 +
.../annotators/TairAnnotatorTest.java | 245 ++++++++++++++++++
persist/src/db/11.1.1/fix_db_20171114.sql | 2 +
5 files changed, 455 insertions(+)
create mode 100644 annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
create mode 100644 annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
create mode 100644 persist/src/db/11.1.1/fix_db_20171114.sql
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
new file mode 100644
index 0000000000..06bc49b4c8
--- /dev/null
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
@@ -0,0 +1,206 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+import java.io.IOException;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.log4j.Logger;
+import org.kohsuke.rngom.ast.builder.Annotations;
+
+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 TAIR.
+ *
+ * @author David Hoksza
+ *
+ */
+public class TairAnnotator extends ElementAnnotator implements IExternalService {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(TairAnnotator.class);
+
+ /**
+ * Pattern used for finding UniProt symbol from TAIR info page .
+ */
+ private Pattern tairToUniprot = Pattern.compile("UniProtKB=([^-\"]*)");
+
+ /**
+ * Default constructor.
+ */
+ public TairAnnotator() {
+ super(TairAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false); //TODO - check with Simone
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ MiriamData md = tairToUniprot(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
+
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (md == null || !md.getResource().equalsIgnoreCase("Q9MAN1")) {
+ 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)) {
+ boolean uniprotFound = false;
+ MiriamData mdTair = null;
+ for (MiriamData md : object.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.TAIR_LOCUS)) {
+ mdTair = md;
+ }
+ if (md.getDataType().equals(MiriamType.UNIPROT)) {
+ uniprotFound = true;
+ }
+ }
+
+ if (mdTair == null || uniprotFound) {
+ return;
+ }
+
+ MiriamData mdUniprot = tairToUniprot(mdTair);
+ if (mdUniprot != null) {
+ object.addMiriamData(mdUniprot);
+ }
+ }
+ }
+
+ /**
+ * Returns url to TAIR page about TAIR entry.
+ *
+ * @param tairId
+ * tair identifier
+ * @return url to TAIR page about the TAIR entry
+ */
+ private String getTairUrl(String tairId) {
+ return "http://arabidopsis.org/servlets/TairObject?type=locus&name=" + tairId;
+ }
+
+ /**
+ * Parse TAIR webpage to find information about
+ * {@link MiriamType#UNIPROT} and returns them.
+ *
+ * @param pageContent
+ * tair info page
+ * @return uniprot identifier found on the page
+ */
+ private Collection<MiriamData> parseUniprot(String pageContent) {
+ Collection<MiriamData> result = new HashSet<MiriamData>();
+ Matcher m = tairToUniprot.matcher(pageContent);
+ if (m.find()) {
+ result.add(new MiriamData(MiriamType.UNIPROT, 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 tair identifier into uniprot identifier.
+ *
+ * @param tair
+ * {@link MiriamData} with tair identifier
+ * @return {@link MiriamData} with uniprot identifier
+ * @throws UniprotSearchException
+ * thrown when there is a problem with accessing external database
+ */
+ public MiriamData tairToUniprot(MiriamData tair) throws AnnotatorException {
+ if (tair == null) {
+ return null;
+ }
+
+ if (!MiriamType.TAIR_LOCUS.equals(tair.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.TAIR_LOCUS + " expected.");
+ }
+
+ String accessUrl = getTairUrl(tair.getResource());
+ try {
+ String pageContent = getWebPageContent(accessUrl);
+ Collection<MiriamData> collection = parseUniprot(pageContent);
+ if (collection.size() > 0) {
+ return collection.iterator().next();
+ } else {
+ logger.warn("Cannot find tair data for id: " + tair.getResource());
+ return null;
+ }
+ } catch (WrongResponseCodeIOException exception) {
+ logger.warn("Cannot find tair data for id: " + tair.getResource());
+ return null;
+ } catch (IOException exception) {
+ throw new AnnotatorException(exception);
+ }
+
+ }
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.TAIR_LOCUS.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.TAIR_LOCUS.getDbHomepage();
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+}
diff --git a/annotation/src/main/resources/applicationContext-annotation.xml b/annotation/src/main/resources/applicationContext-annotation.xml
index a7fb40eb35..d93c9675f4 100644
--- a/annotation/src/main/resources/applicationContext-annotation.xml
+++ b/annotation/src/main/resources/applicationContext-annotation.xml
@@ -21,6 +21,7 @@
<bean id="HgncAnnotator" class="lcsb.mapviewer.annotation.services.annotators.HgncAnnotator"/>
<bean id="ReconAnnotator" class="lcsb.mapviewer.annotation.services.annotators.ReconAnnotator"/>
<bean id="PdbAnnotator" class="lcsb.mapviewer.annotation.services.annotators.PdbAnnotator"/>
+ <bean id="TairAnnotator" class="lcsb.mapviewer.annotation.services.annotators.TairAnnotator"/>
<bean id="UniprotAnnotator" class="lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator"/>
<bean id="ChEMBLParser" class="lcsb.mapviewer.annotation.services.ChEMBLParser"/>
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 218bd397ee..f49dd7668d 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
@@ -15,6 +15,7 @@ import org.junit.runners.Suite.SuiteClasses;
HgncAnnotatorTest.class, //
PdbAnnotatorTest.class, //
ReconAnnotatorTest.class, //
+ TairAnnotatorTest.class, //
UniprotAnnotatorTest.class, //
})
public class AllAnnotatorTests {
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
new file mode 100644
index 0000000000..1f9621829e
--- /dev/null
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
@@ -0,0 +1,245 @@
+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.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;
+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 TairAnnotatorTest extends AnnotationTestFunctions {
+
+ @Autowired
+ TairAnnotator tairAnnotator;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAnnotate1() throws Exception {
+ try {
+
+ Species protein = new GenericProtein("id");
+ protein.setName("bla");
+ protein.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
+
+ tairAnnotator.annotateElement(protein);
+
+ MiriamData mdUniprot = null;
+
+ for (MiriamData md : protein.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.UNIPROT)) {
+ mdUniprot = md;
+ }
+ }
+
+ assertTrue("No UNIPROT annotation extracted from TAIR annotator", mdUniprot != null);
+ assertTrue("Invalid UNIPROT annotation extracted from TAIR annotator", mdUniprot.getResource().equalsIgnoreCase("Q9MAN1") );
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testAnnotateInvalidTair() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("bla");
+ protein.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "bla"));
+ tairAnnotator.annotateElement(protein);
+
+ assertEquals(1, protein.getMiriamData().size());
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testInvalidTairToUniprot() throws Exception {
+ try {
+ assertNull(tairAnnotator.tairToUniprot(null));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidTairToUniprot2() throws Exception {
+ try {
+ tairAnnotator.tairToUniprot(new MiriamData(MiriamType.WIKIPEDIA, "bla"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testAnnotateInvalid() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("bla");
+ tairAnnotator.annotateElement(protein);
+
+ assertEquals(0, protein.getMiriamData().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testTairToUniprot() throws Exception {
+ try {
+ assertEquals(new MiriamData(MiriamType.UNIPROT, "Q9MAN1"),
+ tairAnnotator.tairToUniprot(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ tairAnnotator.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 {
+ tairAnnotator.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 = tairAnnotator.refreshCacheQuery("http://google.cz/");
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, tairAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = tairAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ tairAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, tairAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ tairAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+
+// @Test
+// public void testAnnotateWithUniprotServerError() throws Exception {
+// WebPageDownloader downloader = uniprotAnnotator.getWebPageDownloader();
+// GeneralCacheInterface cache = uniprotAnnotator.getCache();
+// uniprotAnnotator.setCache(new GeneralCacheWithExclusion(cache, 1));
+// try {
+// WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+// when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+// uniprotAnnotator.setWebPageDownloader(mockDownloader);
+// Species protein = new GenericProtein("id");
+// protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "P01308"));
+// uniprotAnnotator.annotateElement(protein);
+// fail("Exception expected");
+// } catch (AnnotatorException e) {
+// } catch (Exception e) {
+// e.printStackTrace();
+// throw e;
+// } finally {
+// uniprotAnnotator.setCache(cache);
+// uniprotAnnotator.setWebPageDownloader(downloader);
+// }
+// }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ WebPageDownloader downloader = tairAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("GN Name=ACSS2; Synonyms=ACAS2;");
+ tairAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, tairAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ tairAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+}
diff --git a/persist/src/db/11.1.1/fix_db_20171114.sql b/persist/src/db/11.1.1/fix_db_20171114.sql
new file mode 100644
index 0000000000..4eae7d939e
--- /dev/null
+++ b/persist/src/db/11.1.1/fix_db_20171114.sql
@@ -0,0 +1,2 @@
+DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.TairAnnotator';
+INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.TairAnnotator');
\ No newline at end of file
--
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