Merge remote-tracking branch 'origin/master' into...

Merge remote-tracking branch 'origin/master' into 566-merge-rest-api-services-into-main-service-module

CHANGELOG

@@ -38,7 +38,7 @@ minerva (16.0.0~beta.1) stable; urgency=medium
   * Bug fix: search tab becomes active when drug/chemical/mirna result are
     available (#1491)
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 9 Jun 2021 15:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 25 Jun 2021 08:00:00 +0200
 
 minerva (16.0.0~beta.0) stable; urgency=medium
   * Backward incompatibility: debian package cannot be upgraded from version

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java

 package lcsb.mapviewer.annotation.services.annotators;
 
 import java.io.IOException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -12,15 +16,23 @@ import org.springframework.stereotype.Service;
 
 import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
 import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.services.*;
+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.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.LogMarker;
 import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.*;
-import lcsb.mapviewer.model.user.annotator.*;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.user.annotator.AnnotatorData;
+import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
+import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
 
 /**
  * This is a class that implements a backend to CAZy.
@@ -120,7 +132,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
 
   @Override
   public MiriamData getExampleValidAnnotation() {
-    return new MiriamData(MiriamType.UNIPROT, "Q9SG95");
+    return new MiriamData(MiriamType.UNIPROT, "Q00012");
   }
 
   /**
@@ -143,7 +155,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
    * @return CAZy family identifier found on the page
    */
   private Collection<MiriamData> parseCazy(String pageContent) {
-    Collection<MiriamData> result = new HashSet<MiriamData>();
+    Collection<MiriamData> result = new HashSet<>();
     Matcher m = cazyIdMatcher.matcher(pageContent);
     if (m.find()) {
       result.add(new MiriamData(MiriamType.CAZY, m.group(1)));
@@ -176,12 +188,16 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
       if (collection.size() > 0) {
         return collection.iterator().next();
       } else {
-        marker.getEntry().setType(ProjectLogEntryType.INVALID_IDENTIFIER);
+        if (marker != null) {
+          marker.getEntry().setType(ProjectLogEntryType.INVALID_IDENTIFIER);
+        }
         logger.warn(marker, "Cannot find CAZy data for UniProt id: " + uniprot.getResource());
         return null;
       }
     } catch (WrongResponseCodeIOException exception) {
-      marker.getEntry().setType(ProjectLogEntryType.OTHER);
+      if (marker != null) {
+        marker.getEntry().setType(ProjectLogEntryType.OTHER);
+      }
       logger.warn(marker, "Wrong response code when retrieving CAZy data for UniProt id: " + uniprot.getResource());
       return null;
     } catch (IOException exception) {

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java

@@ -36,14 +36,14 @@ public class CazyAnnotatorTest extends AnnotationTestFunctions {
   @Test
   public void testUniprotToCazy() throws Exception {
     assertEquals(new MiriamData(MiriamType.CAZY, "GH5_7"),
-        cazyAnnotator.uniprotToCazy(new MiriamData(MiriamType.UNIPROT, "Q9SG95"), null));
+        cazyAnnotator.uniprotToCazy(new MiriamData(MiriamType.UNIPROT, "Q00012"), null));
   }
 
   @Test
   public void testAnnotateFromUniprot() throws Exception {
     Species protein = new GenericProtein("id");
     protein.setName("bla");
-    protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q9SG95"));
+    protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q00012"));
 
     cazyAnnotator.annotateElement(protein);
 
@@ -85,8 +85,8 @@ public class CazyAnnotatorTest extends AnnotationTestFunctions {
   public void testAnnotateMultipleUniprots() throws Exception {
     Species protein = new GenericProtein("id");
     protein.setName("bla");
-    protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q9SG95"));
-    protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q12540"));
+    protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q00012"));
+    protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "A8MCI6"));
 
     cazyAnnotator.annotateElement(protein);
 
@@ -98,7 +98,7 @@ public class CazyAnnotatorTest extends AnnotationTestFunctions {
       }
     }
 
-    assertTrue("Wrong number of CAZy identifiers extracted from CAZy annotator", cntMDs == 2);
+    assertEquals("Wrong number of CAZy identifiers extracted from CAZy annotator", 2, cntMDs);
   }
 
   @Test