From 21763fe012e9d0fb62a6920e03eff6a9b2c42774 Mon Sep 17 00:00:00 2001
From: David Hoksza <david.hoksza@uni.lu>
Date: Thu, 23 Nov 2017 14:56:38 +0100
Subject: [PATCH] STRING annotator including unit tests.
---
.../annotation/services/ModelAnnotator.java | 8 ++
.../services/annotators/StringAnnotator.java | 110 ++++++++++++++++
.../applicationContext-annotation.xml | 1 +
.../annotators/AllAnnotatorTests.java | 1 +
.../annotators/StitchAnnotatorTest.java | 10 --
.../annotators/StringAnnotatorTest.java | 119 ++++++++++++++++++
.../lcsb/mapviewer/model/map/MiriamType.java | 8 ++
persist/src/db/11.1.1/fix_db_20171114.sql | 3 +
8 files changed, 250 insertions(+), 10 deletions(-)
create mode 100644 annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
create mode 100644 annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotatorTest.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 3e0dcf48fa..60ece88325 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -28,6 +28,7 @@ import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.annotation.services.annotators.PdbAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
import lcsb.mapviewer.annotation.services.annotators.StitchAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.StringAnnotator;
import lcsb.mapviewer.annotation.services.annotators.TairAnnotator;
import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
@@ -147,6 +148,12 @@ public class ModelAnnotator {
@Autowired
private StitchAnnotator stitchAnnotator;
+ /**
+ * STRING annotator.
+ */
+ @Autowired
+ private StringAnnotator stringAnnotator;
+
/**
* TAIR annotator.
*/
@@ -185,6 +192,7 @@ public class ModelAnnotator {
addAnnotator(entrezAnnotator);
addAnnotator(ensemblAnnotator);
addAnnotator(stitchAnnotator);
+ addAnnotator(stringAnnotator);
addAnnotator(tairAnnotator);
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
new file mode 100644
index 0000000000..70e9d34d2a
--- /dev/null
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
@@ -0,0 +1,110 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.IExternalService;
+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 mapping to STRING database.
+ *
+ * @author David Hoksza
+ *
+ */
+public class StringAnnotator extends ElementAnnotator implements IExternalService {
+
+ /**
+ * Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
+ * TAIR}.
+ */
+ @Autowired
+ private TairAnnotator tairAnnotator;
+
+ /**
+ * Default constructor.
+ */
+ public StringAnnotator() {
+ super(StringAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ return tairAnnotator.getServiceStatus();
+ }
+
+ @Override
+ public void annotateElement(BioEntity object) throws AnnotatorException {
+ if (isAnnotatable(object)) {
+
+ MiriamData mdTair = null;
+ for (MiriamData md : object.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.STRING)) {
+ return;
+ }
+ 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> stringIds = new ArrayList<String>();
+ for (MiriamData mdUniprot: mdUniprots) {
+ MiriamData mdString = uniprotToString(mdUniprot);
+ if (mdString != null && stringIds.indexOf(mdString.getResource()) < 0) {
+ stringIds.add(mdString.getResource());
+ object.addMiriamData(mdString);
+ }
+ }
+ }
+ }
+
+ /**
+ * Transform UniProt {@link MiriamData} data to STRING {@link MiriamData}.
+ *
+ * @param UniProt
+ * {@link MiriamData} with UniProt identifier
+ * @return {@link MiriamData} with STRING identifier
+ * @throws AnnotatorException
+ * thrown when there is a problem with accessing external database
+ */
+ public MiriamData uniprotToString(MiriamData uniprot) throws AnnotatorException {
+ if (uniprot == null) {
+ return null;
+ }
+
+ if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
+ }
+
+ return new MiriamData(MiriamType.STRING, uniprot.getResource());
+ }
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.STRING.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.STRING.getDbHomepage();
+ }
+}
diff --git a/annotation/src/main/resources/applicationContext-annotation.xml b/annotation/src/main/resources/applicationContext-annotation.xml
index c7deed22f7..15b0210a0f 100644
--- a/annotation/src/main/resources/applicationContext-annotation.xml
+++ b/annotation/src/main/resources/applicationContext-annotation.xml
@@ -24,6 +24,7 @@
<bean id="ReconAnnotator" class="lcsb.mapviewer.annotation.services.annotators.ReconAnnotator"/>
<bean id="PdbAnnotator" class="lcsb.mapviewer.annotation.services.annotators.PdbAnnotator"/>
<bean id="StitchAnnotator" class="lcsb.mapviewer.annotation.services.annotators.StitchAnnotator"/>
+ <bean id="StringAnnotator" class="lcsb.mapviewer.annotation.services.annotators.StringAnnotator"/>
<bean id="TairAnnotator" class="lcsb.mapviewer.annotation.services.annotators.TairAnnotator"/>
<bean id="UniprotAnnotator" class="lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator"/>
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 84f29bbdce..0bd9c6f3f8 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
@@ -18,6 +18,7 @@ import org.junit.runners.Suite.SuiteClasses;
PdbAnnotatorTest.class, //
ReconAnnotatorTest.class, //
StitchAnnotatorTest.class, //
+ StringAnnotatorTest.class, //
TairAnnotatorTest.class, //
UniprotAnnotatorTest.class, //
})
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
index 4a20dea772..2016f4875e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
@@ -1,24 +1,14 @@
package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
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.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.SimpleMolecule;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotatorTest.java
new file mode 100644
index 0000000000..1264c71c81
--- /dev/null
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotatorTest.java
@@ -0,0 +1,119 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+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 StringAnnotatorTest extends AnnotationTestFunctions {
+
+ @Autowired
+ StringAnnotator testedAnnotator;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAnnotateUniprot() throws Exception {
+ try {
+
+ Species bioEntity = new GenericProtein("id");
+ bioEntity.addMiriamData(new MiriamData(MiriamType.UNIPROT, "P53350"));
+
+ testedAnnotator.annotateElement(bioEntity);
+
+ MiriamData mdString = null;
+
+ for (MiriamData md : bioEntity.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.STRING)) {
+ mdString = md; //there should be only one EC number for that TAIR<->UNIPROT record
+ }
+ }
+
+ assertTrue("No STRING annotation extracted from STRING annotator", mdString != null);
+ assertTrue("Wrong number of annotations extract from STRING annotator", bioEntity.getMiriamData().size() == 2);
+ assertTrue("Invalid STRING annotation extracted from STRING annotator based on the UniProt annotation", mdString.getResource().equalsIgnoreCase("P53350") );
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateTair() throws Exception {
+ try {
+
+ Species bioEntity = new GenericProtein("id");
+ bioEntity.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
+
+ testedAnnotator.annotateElement(bioEntity);
+
+ MiriamData mdString = null;
+
+ for (MiriamData md : bioEntity.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.STRING)) {
+ mdString = md; //there should be only one EC number for that TAIR<->UNIPROT record
+ }
+ }
+
+ assertTrue("No STRING annotation extracted from STRING annotator", mdString != null);
+ assertTrue("Wrong number of annotations extract from STRING annotator", bioEntity.getMiriamData().size() == 3);
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+
+ @Test
+ public void testAnnotateInvalidEmpty() throws Exception {
+ try {
+ Species bioEntity = new GenericProtein("id");
+ testedAnnotator.annotateElement(bioEntity);
+
+ assertEquals(0, bioEntity.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateInvalidTair() throws Exception {
+ try {
+ Species bioEntity = new GenericProtein("id");
+ bioEntity.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "bla"));
+ testedAnnotator.annotateElement(bioEntity);
+
+ assertEquals(1, bioEntity.getMiriamData().size());
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ //All the service status tests are not necessary, since STRING annotator
+ //internally calls TAIR annotator which has it own set of tests
+}
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 9b9740197b..155ec768e4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -364,6 +364,14 @@ public enum MiriamType {
"http://stitch.embl.de/", //
"urn:miriam:stitch", //
new Class<?>[] {}, "MIR:00100343"),
+
+ /**
+ * STRING: http://string-db.org/.
+ */
+ STRING("STRING", //
+ "http://string-db.org/", //
+ "urn:miriam:string", //
+ new Class<?>[] {}, "MIR:00000265"),
/**
* The Arabidopsis Information Resource (TAIR) maintains a database of genetic
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 fdf19e1303..c5481fe2fd 100644
--- a/persist/src/db/11.1.1/fix_db_20171114.sql
+++ b/persist/src/db/11.1.1/fix_db_20171114.sql
@@ -10,3 +10,6 @@ INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotat
DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.StitchAnnotator';
INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.StitchAnnotator');
+DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.StringAnnotator';
+INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.StringAnnotator');
+
--
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