Merge branch '1520-drug-suggested-list' into 'devel_16.0.x'

Resolve "Autocomplete does not work"

See merge request !1384

CHANGELOG

@@ -20,8 +20,10 @@ minerva (16.0.1) stable; urgency=medium
     were projects with a lot of log entries (#1588)
   * Bug fix: complex target of chembl compounds (like ME-344) were not
     highligted on map (#1579)
+  * Bug fix: chembl drugs targeting RNA (like BEVASIRANIB) prevented providing
+    list of suggested drug queries (#1520)
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 2 Nov 2021 15:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 9 Nov 2021 15:00:00 +0200
 
 minerva (16.0.0) stable; urgency=medium
   * Backward incompatibility: debian package cannot be upgraded from version

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

 package lcsb.mapviewer.annotation.services.annotators;
 
 import java.io.IOException;
-import java.util.*;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.springframework.http.HttpStatus;
 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.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.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;
+import lcsb.mapviewer.model.user.annotator.BioEntityField;
 
 /**
  * This is a class that implements a backend to uniprot restfull API.
@@ -164,8 +177,8 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
   }
 
   /**
-   * Returns URL to UniProt result containing mapped UniProtIds for submitted TAIR
-   * entry.
+   * Returns URL to UniProt result containing mapped UniProtIds for submitted
+   * TAIR entry.
    *
    * @param tairId
    *          TAIR identifier
@@ -177,8 +190,8 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
   }
 
   /**
-   * Parse uniprot webpage to find information about {@link MiriamType#ENTREZ} and
-   * returns them.
+   * Parse uniprot webpage to find information about {@link MiriamType#ENTREZ}
+   * and returns them.
    *
    * @param pageContent
    *          uniprot info page
@@ -254,6 +267,13 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
       } else {
         return null;
       }
+    } catch (WrongResponseCodeIOException e) {
+      if (e.getResponseCode() == HttpStatus.NOT_FOUND.value()) {
+        logger.warn("Unknown uniprot id: " + uniprot.getResource());
+        return null;
+      } else {
+        throw new UniprotSearchException("Problem with accessing uniprot webpage", e);
+      }
     } catch (IOException e) {
       throw new UniprotSearchException("Problem with accessing uniprot webpage", e);
     }

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

@@ -125,6 +125,11 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
     uniprotAnnotator.uniProtToHgnc(new MiriamData(MiriamType.WIKIPEDIA, "bla"));
   }
 
+  @Test
+  public void testUnknownUniprotId() throws Exception {
+    assertNull(uniprotAnnotator.uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, "bla")));
+  }
+
   @Test
   public void testAnnotate2() throws Exception {
     Species protein = new GenericProtein("id");