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 f3b3f463ed38de817bab82431aeaf074b9c4995e..3e0dcf48faf902e4611e9f6184de6f39e13ace14 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -27,6 +27,7 @@ import lcsb.mapviewer.annotation.services.annotators.GoAnnotator;
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.TairAnnotator;
import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
@@ -140,6 +141,12 @@ public class ModelAnnotator {
@Autowired
private EnsemblAnnotator ensemblAnnotator;
+ /**
+ * STITCH annotator.
+ */
+ @Autowired
+ private StitchAnnotator stitchAnnotator;
+
/**
* TAIR annotator.
*/
@@ -177,6 +184,7 @@ public class ModelAnnotator {
addAnnotator(reconAnnotator);
addAnnotator(entrezAnnotator);
addAnnotator(ensemblAnnotator);
+ addAnnotator(stitchAnnotator);
addAnnotator(tairAnnotator);
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
new file mode 100644
index 0000000000000000000000000000000000000000..37a36f9a530e5d3a739aa6820ac8a205fe6a9b7d
--- /dev/null
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
@@ -0,0 +1,120 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.data.Chebi;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+
+/**
+ * This is a class that implements STITCH annotation which is derived from existing ChEBI annotation.
+ *
+ * @author David Hoksza
+ *
+ */
+public class StitchAnnotator extends ElementAnnotator implements IExternalService {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(StitchAnnotator.class);
+
+ /**
+ * Service used for annotation of entities using {@link MiriamType#STITCH STITCH}.
+ */
+ @Autowired
+ private ChebiAnnotator chebiAnnotator;
+
+ /**
+ * Default constructor.
+ */
+ public StitchAnnotator() {
+ super(StitchAnnotator.class, new Class[] { SimpleMolecule.class }, false);
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ return chebiAnnotator.getServiceStatus();
+ }
+
+ /**
+ * Returns main layer of the InchKey, * i.e. everything
+ * before first hyphen: WBYWAXJHAXSJNI-VOTSOKGWSA-N -> WBYWAXJHAXSJNI
+ * @param inchiKey Full inchiKey
+ * @return Main layer of the InchiKey
+ */
+ private String inchiKeyExtractMainLayer(String inchiKey){
+ return inchiKey.replaceFirst("-.*", "");
+ }
+
+ @Override
+ public void annotateElement(BioEntity object) throws AnnotatorException {
+ if (isAnnotatable(object)) {
+
+ MiriamData mdChebi = null;
+
+ for (MiriamData md : object.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.CHEBI)) {
+ mdChebi = md;
+ }
+ else if (md.getDataType().equals(MiriamType.STITCH)) {
+ return;
+ }
+ }
+
+ if (mdChebi == null) {
+ return;
+ }
+
+ try {
+
+ Chebi chebi = chebiAnnotator.getChebiElementForChebiId(mdChebi);
+ if (chebi == null) {
+ return;
+ }
+ String inchiKey = chebi.getInchiKey();
+ if (inchiKey == null) {
+ return;
+ }
+
+ object.addMiriamData(new MiriamData(MiriamType.STITCH, inchiKeyExtractMainLayer(inchiKey)));
+ } catch(ChebiSearchException exception) {
+ logger.warn("No ChEBI element retrieved fro ChEBI ID: " + mdChebi.getResource());
+ }
+ }
+ }
+
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ return chebiAnnotator.refreshCacheQuery(query);
+ }
+
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.STITCH.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.STITCH.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/TairAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
index eda127b27e4d6ea31f1e3296c50379f2bec8749b..0388293b12b091d15b0bf127e63d69e47bb6bf46 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
@@ -123,7 +123,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
Matcher m = tairToUniprot.matcher(pageContent);
if (m.find()) {
result.add(new MiriamData(MiriamType.UNIPROT, m.group(1)));
- }
+ }
return result;
}
diff --git a/annotation/src/main/resources/applicationContext-annotation.xml b/annotation/src/main/resources/applicationContext-annotation.xml
index ee83e7e98773f7e9960b279350a44fc68b347db4..c7deed22f76b818d87aaba6db44bba30885af859 100644
--- a/annotation/src/main/resources/applicationContext-annotation.xml
+++ b/annotation/src/main/resources/applicationContext-annotation.xml
@@ -23,6 +23,7 @@
<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="StitchAnnotator" class="lcsb.mapviewer.annotation.services.annotators.StitchAnnotator"/>
<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 8325d7f57cb8d375914e660bbc7d11a942988730..84f29bbdce07283272d7431bcf2163fc5860f3f0 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
@@ -17,6 +17,7 @@ import org.junit.runners.Suite.SuiteClasses;
HgncAnnotatorTest.class, //
PdbAnnotatorTest.class, //
ReconAnnotatorTest.class, //
+ StitchAnnotatorTest.class, //
TairAnnotatorTest.class, //
UniprotAnnotatorTest.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
index 87711ddccc6d814c6baa43a1c955cdcf5f4c430b..963bc74fa59afa47bedd9e34a6df59dac490d5c4 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
@@ -40,7 +40,7 @@ public class BrendaAnnotatorTest extends AnnotationTestFunctions {
}
@Test
- public void testUniprotToCazy() throws Exception {
+ public void testUniprotToBrenda() throws Exception {
try {
Collection<MiriamData> mds = brendaAnnotator.uniprotToBrenda(new MiriamData(MiriamType.UNIPROT, "P12345"));
assertEquals(mds.size(), 2);
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
new file mode 100644
index 0000000000000000000000000000000000000000..4a20dea77209b369a6210a2bbf99211283f6c598
--- /dev/null
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
@@ -0,0 +1,112 @@
+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;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class StitchAnnotatorTest extends AnnotationTestFunctions {
+
+ @Autowired
+ StitchAnnotator testedAnnotator;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAnnotate() throws Exception {
+ try {
+
+ Species bioEntity = new SimpleMolecule("id");
+ bioEntity.addMiriamData(new MiriamData(MiriamType.CHEBI, "CHEBI:35697"));
+
+ testedAnnotator.annotateElement(bioEntity);
+
+ MiriamData mdStitch = null;
+
+ for (MiriamData md : bioEntity.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.STITCH)) {
+ mdStitch = md; //there should be only one EC number for that TAIR<->UNIPROT record
+ }
+ }
+
+ assertTrue("No STITCH annotation extracted from STITCH annotator", mdStitch != null);
+ assertTrue("Wrong number of annotations extract from STITCH annotator", bioEntity.getMiriamData().size() == 2);
+ assertTrue("Invalid STITCH annotation extracted from STITCH annotator based on CHEBI ID", mdStitch.getResource().equalsIgnoreCase("WBYWAXJHAXSJNI") );
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testExtractInchiMainLayer() throws Exception {
+ try {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateInvalidEmpty() throws Exception {
+ try {
+ Species bioEntity = new SimpleMolecule("id");
+ testedAnnotator.annotateElement(bioEntity);
+
+ assertEquals(0, bioEntity.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateInvalidChebi() throws Exception {
+ try {
+ Species bioEntity = new SimpleMolecule("id");
+ bioEntity.addMiriamData(new MiriamData(MiriamType.CHEBI, "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 STTICH annotator
+ //internally calls ChEBI 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 831ca861b81f656702683e6610727763b62db808..f3526282a58ffb6d252381973bd6d6f02f95c559 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -365,6 +365,14 @@ public enum MiriamType {
"http://www.yeastgenome.org/", //
"urn:miriam:sgd", //
new Class<?>[] {}, "MIR:00000023"),
+
+ /**
+ * STITCH: http://stitch.embl.de/.
+ */
+ STITCH("STITCH", //
+ "http://stitch.embl.de/", //
+ "urn:miriam:stitch", //
+ new Class<?>[] {}, "MIR:00100343"),
/**
* 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 771e3f42a9a340dd5f6c0def1693ce7e87f443f3..fdf19e1303b661764dd4b56cb1eb9fb84d1a6063 100644
--- a/persist/src/db/11.1.1/fix_db_20171114.sql
+++ b/persist/src/db/11.1.1/fix_db_20171114.sql
@@ -6,3 +6,7 @@ INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotat
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');
+
+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');
+