Merge branch '325-admin-panel-structured-log' into 'master'

Resolve "Admin panel: structured log"

Closes #325

See merge request minerva/core!983

CHANGELOG

 minerva (15.0.0~alpha.0) stable; urgency=medium
+  * Improvement: logs provided for validation data model are structurized (#325)
   * Small improvement: when downloading a map results in too big file (>1MB)
     the content is compressed and returned as a zip file (#348)
   * Small improvement: confirmation dialog when removing "general view"

annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java

@@ -3,10 +3,13 @@ package lcsb.mapviewer.annotation.services;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.apache.logging.log4j.Marker;
+
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 /**
  * Class describing improper annotation. All elements are annotated in the
@@ -35,7 +38,7 @@ public class ImproperAnnotations implements ProblematicAnnotation {
    * @param list
    *          list of improper {@link MiriamData}
    * @param bioEntity
-   *          bioentity
+   *          bio entity
    */
   public ImproperAnnotations(BioEntity bioEntity, List<MiriamData> list) {
     if (list.size() == 0) {
@@ -61,8 +64,7 @@ public class ImproperAnnotations implements ProblematicAnnotation {
 
   @Override
   public String getMessage() {
-    StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(bioEntity));
-    result.append("contains invalid annotations: ");
+    StringBuilder result = new StringBuilder("Invalid annotations found: ");
     for (MiriamData miriamData : wrongAnnotations) {
       result.append(miriamData.getDataType().getCommonName() + "(" + miriamData.getResource() + "), ");
     }
@@ -74,4 +76,9 @@ public class ImproperAnnotations implements ProblematicAnnotation {
     return getMessage();
   }
 
+  @Override
+  public Marker getLogMarker() {
+    return new LogMarker(ProjectLogEntryType.INVALID_ANNOTATION, bioEntity);
+  }
+
 }

annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java

 package lcsb.mapviewer.annotation.services;
 
+import org.apache.logging.log4j.Marker;
+
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
 
@@ -29,7 +33,7 @@ public class MissingAnnotation implements ProblematicAnnotation {
 
   @Override
   public String getMessage() {
-    return new ElementUtils().getElementTag(bioEntity) + "misses annotations.";
+    return "Missing annotations.";
   }
 
   @Override
@@ -37,4 +41,9 @@ public class MissingAnnotation implements ProblematicAnnotation {
     return getMessage();
   }
 
+  @Override
+  public Marker getLogMarker() {
+    return new LogMarker(ProjectLogEntryType.MISSING_ANNOTATION, bioEntity);
+  }
+
 }

annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java

@@ -2,7 +2,11 @@ package lcsb.mapviewer.annotation.services;
 
 import java.util.*;
 
+import org.apache.logging.log4j.Marker;
+
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.*;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
 
@@ -44,8 +48,7 @@ public class MissingRequiredAnnotations implements ProblematicAnnotation {
 
   @Override
   public String getMessage() {
-    StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(bioEntity));
-    result.append("misses one of the following annotations: ");
+    StringBuilder result = new StringBuilder("Missing one of the required annotations: ");
     for (MiriamType type : requiredMiriamType) {
       result.append(type.getCommonName() + ", ");
     }
@@ -57,4 +60,9 @@ public class MissingRequiredAnnotations implements ProblematicAnnotation {
     return getMessage();
   }
 
+  @Override
+  public Marker getLogMarker() {
+    return new LogMarker(ProjectLogEntryType.MISSING_REQUIRED_ANNOTATION, bioEntity);
+  }
+
 }

annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java

@@ -12,6 +12,7 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.LogMarker;
 import lcsb.mapviewer.model.map.*;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -244,7 +245,7 @@ public class ModelAnnotator {
   public Collection<ImproperAnnotations> findImproperAnnotations(Model m, IProgressUpdater updater,
       Map<Class<? extends BioEntity>, Set<MiriamType>> validAnnotations) {
     if (validAnnotations == null) {
-      logger.warn("List of valid annotations is missing. Using default.");
+      logger.warn(LogMarker.IGNORE, "List of valid annotations is missing. Using default.");
       validAnnotations = getDefaultValidClasses();
     }
     updater.setProgress(0.0);
@@ -310,14 +311,14 @@ public class ModelAnnotator {
    *          model where the search is performed
    * @param requestedAnnotations
    *          map that contains information which {@link MiriamType miriam types}
-   *          are obigatory for which class
+   *          are obligatory for which class
    * 
    * @return list of all elements that miss annotation
    */
   public Collection<ProblematicAnnotation> findMissingAnnotations(Model m,
       Map<Class<? extends BioEntity>, Set<MiriamType>> requestedAnnotations) {
     if (requestedAnnotations == null) {
-      logger.warn("List of requested annotations is missing. Using default.");
+      logger.warn(LogMarker.IGNORE, "List of requested annotations is missing. Using default.");
       requestedAnnotations = getDefaultRequiredClasses();
     }
     List<ProblematicAnnotation> result = new ArrayList<>();

annotation/src/main/java/lcsb/mapviewer/annotation/services/ProblematicAnnotation.java

 package lcsb.mapviewer.annotation.services;
 
+import org.apache.logging.log4j.Marker;
+
 /**
  * Interface that describes annotation that is problematic.
  * 
@@ -14,4 +16,6 @@ public interface ProblematicAnnotation {
    * @return problem error message
    */
   String getMessage();
+  
+  Marker getLogMarker(); 
 }

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

@@ -11,6 +11,7 @@ import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
 import lcsb.mapviewer.annotation.cache.WebPageDownloader;
 import lcsb.mapviewer.annotation.services.*;
 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.*;
@@ -96,7 +97,8 @@ public class BrendaAnnotator extends ElementAnnotator implements IExternalServic
           }
         }
       } catch (UniprotSearchException e) {
-        logger.warn("Cannot find EC data for UniProt id: " + mdUniprot.getResource());
+        logger.warn(object.getLogMarker(ProjectLogEntryType.CANNOT_FIND_INFORMATION),
+            "Cannot find EC data for UniProt id: " + mdUniprot.getResource());
       }
 
     }

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

@@ -15,6 +15,8 @@ import lcsb.mapviewer.annotation.cache.WebPageDownloader;
 import lcsb.mapviewer.annotation.services.*;
 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.*;
@@ -59,7 +61,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
     this.setCache(null);
 
     try {
-      MiriamData md = uniprotToCazy(getExampleValidAnnotation());
+      MiriamData md = uniprotToCazy(getExampleValidAnnotation(), new LogMarker(ProjectLogEntryType.OTHER, new GenericProtein("")));
 
       status.setStatus(ExternalServiceStatusType.OK);
       if (md == null || !md.getResource().equalsIgnoreCase("GH5_7")) {
@@ -86,7 +88,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
     }
     List<String> cazyIds = new ArrayList<String>();
     for (MiriamData mdUniprot : mdUniprots) {
-      MiriamData mdCazy = uniprotToCazy(mdUniprot);
+      MiriamData mdCazy = uniprotToCazy(mdUniprot, object.getLogMarker(ProjectLogEntryType.OTHER));
       if (mdCazy != null && cazyIds.indexOf(mdCazy.getResource()) == -1) {
         cazyIds.add(mdCazy.getResource());
         object.addMiriamData(mdCazy);
@@ -158,7 +160,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
    * @throws AnnotatorException
    *           thrown when there is a problem with accessing external database
    */
-  public MiriamData uniprotToCazy(MiriamData uniprot) throws AnnotatorException {
+  public MiriamData uniprotToCazy(MiriamData uniprot, LogMarker marker) throws AnnotatorException {
     if (uniprot == null) {
       return null;
     }
@@ -174,11 +176,13 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
       if (collection.size() > 0) {
         return collection.iterator().next();
       } else {
-        logger.warn("Cannot find CAZy data for UniProt id: " + uniprot.getResource());
+        marker.getEntry().setType(ProjectLogEntryType.INVALID_IDENTIFIER);
+        logger.warn(marker, "Cannot find CAZy data for UniProt id: " + uniprot.getResource());
         return null;
       }
     } catch (WrongResponseCodeIOException exception) {
-      logger.warn("Wrong response code when retrieving CAZy data for UniProt id: " + uniprot.getResource());
+      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) {
       throw new AnnotatorException(exception);

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

@@ -12,6 +12,7 @@ import lcsb.mapviewer.annotation.cache.*;
 import lcsb.mapviewer.annotation.data.Chebi;
 import lcsb.mapviewer.annotation.services.*;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.*;
 import lcsb.mapviewer.model.map.species.Chemical;
 import lcsb.mapviewer.model.user.annotator.*;
@@ -449,7 +450,8 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
         element.addMiriamData(chebi);
         return annotateElement(element, chebi, parameters);
       } else {
-        logger.warn(element.getElementTag() + "Chemical name cannot be found in chebi: " + name);
+        logger.warn(element.getLogMarker(ProjectLogEntryType.CANNOT_FIND_INFORMATION),
+            "Chemical name cannot be found in chebi: " + name);
         return false;
       }
     } catch (Exception e) {

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

@@ -10,13 +10,14 @@ import lcsb.mapviewer.common.comparator.StringSetComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerChemical;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.*;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.*;
 import lcsb.mapviewer.model.map.species.field.UniprotRecord;
 import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
 import lcsb.mapviewer.model.user.annotator.*;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 /**
  * Interface that allows to annotate {@link BioEntity elements} in the system.
@@ -132,12 +133,12 @@ public abstract class ElementAnnotator extends CachableInterface {
       AnnotatorData parameters)
       throws AnnotatorException;
 
-public boolean annotateElement(BioEntityProxy element, String name, AnnotatorData parameters)
+  public boolean annotateElement(BioEntityProxy element, String name, AnnotatorData parameters)
       throws AnnotatorException {
     throw new NotImplementedException();
   }
 
-    /**
+  /**
    * Returns a list of all classes that can be annotated using this annotator.
    *
    * @return a list of all classes that can be annotated using this annotator
@@ -353,8 +354,10 @@ public boolean annotateElement(BioEntityProxy element, String name, AnnotatorDat
       return originalBioEntity.getMiriamData().contains(copy) || originalBioEntity.getMiriamData().contains(copy2);
     }
 
-    public String getElementTag() {
-      return new ElementUtils().getElementTag(originalBioEntity, ElementAnnotator.this);
+    public LogMarker getLogMarker(ProjectLogEntryType type) {
+      LogMarker result = new LogMarker(type, originalBioEntity);
+      result.getEntry().setSource(ElementAnnotator.this.getClass().getSimpleName());
+      return result;
     }
 
     public boolean isElement() {
@@ -408,7 +411,8 @@ public boolean annotateElement(BioEntityProxy element, String name, AnnotatorDat
         set2.addAll(oldCollection);
 
         if (stringSetComparator.compare(set1, set2) != 0) {
-          logger.warn(getElementTag() + field.getCommonName() + " don't match: \"" + set1 + "\", \"" + set2 + "\"");
+          logger.warn(getLogMarker(ProjectLogEntryType.ANNOTATION_CONFLICT),
+              field.getCommonName() + " don't match: \"" + set1 + "\", \"" + set2 + "\"");
           return false;
         }
         return true;
@@ -440,7 +444,8 @@ public boolean annotateElement(BioEntityProxy element, String name, AnnotatorDat
       if (oldValue == null || oldValue.trim().equals("") || oldValue.equals(newValue)) {
         return true;
       } else {
-        logger.warn(getElementTag(field) + " doesn't match: \"" + newValue + "\", \"" + oldValue + "\"");
+        logger.warn(getLogMarker(ProjectLogEntryType.ANNOTATION_CONFLICT), field.getCommonName() +
+            " doesn't match: \"" + newValue + "\", \"" + oldValue + "\"");
         return false;
       }
     }
@@ -455,15 +460,12 @@ public boolean annotateElement(BioEntityProxy element, String name, AnnotatorDat
       if (oldValue == null || oldValue == 0 || oldValue.toString().equals(newValue)) {
         return true;
       } else {
-        logger.warn(getElementTag(field) + " doesn't match: \"" + newValue + "\", \"" + oldValue + "\"");
+        logger.warn(getLogMarker(ProjectLogEntryType.ANNOTATION_CONFLICT),
+            field.getCommonName() + " doesn't match: \"" + newValue + "\", \"" + oldValue + "\"");
         return false;
       }
     }
 
-    private String getElementTag(BioEntityField field) {
-      return getElementTag() + " " + field.getCommonName();
-    }
-
     public void setFormerSymbols(Collection<String> formerSymbols) {
       if (originalBioEntity instanceof Element) {
         Element element = (Element) originalBioEntity;
@@ -521,7 +523,7 @@ public boolean annotateElement(BioEntityProxy element, String name, AnnotatorDat
         try {
           md = MiriamType.getMiriamByUri("urn:miriam:" + generalIdentifier);
         } catch (InvalidArgumentException e1) {
-          logger.warn(getElementTag() + "Unknown miriam uri: " + generalIdentifier);
+          logger.warn(getLogMarker(ProjectLogEntryType.INVALID_IDENTIFIER), "Unknown miriam uri: " + generalIdentifier);
         }
       }
       addMiriamData(md);

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

@@ -15,6 +15,7 @@ import lcsb.mapviewer.annotation.services.*;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 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.*;
@@ -134,7 +135,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
             if (node.getNodeName().equals("data")) {
               String error = XmlParser.getNodeAttr("error", node);
               if (error != null && !error.isEmpty()) {
-                logger.warn(element.getElementTag() + error);
+                logger.warn(element.getLogMarker(ProjectLogEntryType.OTHER), error);
               }
               String dbname = XmlParser.getNodeAttr("dbname", node);
 
@@ -188,8 +189,8 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
         }
         return true;
       } catch (WrongResponseCodeIOException e) {
-        logger.warn(
-            element.getElementTag() + "Cannot find information for ensembl: " + identifier.getResource());
+        logger.warn(element.getLogMarker(ProjectLogEntryType.CANNOT_FIND_INFORMATION),
+            "Cannot find information for ensembl: " + identifier.getResource());
         return false;
       } catch (Exception e) {
         throw new AnnotatorException(e);

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

@@ -16,6 +16,8 @@ import lcsb.mapviewer.annotation.data.EntrezData;
 import lcsb.mapviewer.annotation.services.*;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.*;
+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.*;
@@ -125,8 +127,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
   public boolean annotateElement(BioEntityProxy element, MiriamData identifier, AnnotatorData parameters)
       throws AnnotatorException {
     if (identifier.getDataType().equals(MiriamType.ENTREZ)) {
-      String prefix = element.getElementTag();
-      EntrezData data = getEntrezForMiriamData(identifier, prefix);
+      EntrezData data = getEntrezForMiriamData(identifier, element.getLogMarker(ProjectLogEntryType.OTHER));
       if (data != null) {
         element.setSymbol(data.getSymbol());
 
@@ -185,7 +186,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
    *           thrown when there is a problem with obtaining data from entrez
    *           database
    */
-  EntrezData getEntrezForMiriamData(MiriamData entrezMiriamData, String prefix) throws AnnotatorException {
+  EntrezData getEntrezForMiriamData(MiriamData entrezMiriamData, LogMarker marker) throws AnnotatorException {
     EntrezData result = entrezSerializer
         .xmlToObject(super.getCacheNode(ENTREZ_DATA_PREFIX + entrezMiriamData.getResource()));
     if (result == null) {
@@ -199,13 +200,15 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
         if (response != null) {
           Node errorNode = XmlParser.getNode("Error", response.getChildNodes());
           if (errorNode != null) {
-            logger.warn(
-                prefix + " Invalid " + MiriamType.ENTREZ + " identifier: \"" + entrezMiriamData.getResource() + "\"");
+            LogMarker m = new LogMarker(marker);
+            m.getEntry().setType(ProjectLogEntryType.INVALID_IDENTIFIER);
+            logger.warn(m, " Invalid " + MiriamType.ENTREZ + " identifier: \"" + entrezMiriamData.getResource() + "\"");
             return null;
           }
         } else {
-          logger
-              .warn(prefix + "Problematic entrez response for identifier: \"" + entrezMiriamData.getResource() + "\"");
+          LogMarker m = new LogMarker(marker);
+          m.getEntry().setType(ProjectLogEntryType.OTHER);
+          logger.warn(m, "Problematic entrez response for identifier: \"" + entrezMiriamData.getResource() + "\"");
           return null;
         }
 
@@ -294,7 +297,9 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
         setCacheValue(ENTREZ_DATA_PREFIX + entrezMiriamData.getResource(), entrezSerializer.objectToString(result));
       } catch (WrongResponseCodeIOException e) {
         if (e.getResponseCode() == HttpURLConnection.HTTP_BAD_REQUEST) {
-          logger.warn(prefix + " Invalid " + MiriamType.ENTREZ.getCommonName() + " identifier found");
+          LogMarker m = new LogMarker(marker);
+          m.getEntry().setType(ProjectLogEntryType.INVALID_IDENTIFIER);
+          logger.warn(m, " Invalid " + MiriamType.ENTREZ.getCommonName() + " identifier found");
         } else {
           throw new AnnotatorException(e);
         }

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

@@ -14,6 +14,7 @@ import lcsb.mapviewer.annotation.cache.WebPageDownloader;
 import lcsb.mapviewer.annotation.services.*;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.*;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.species.*;
@@ -96,7 +97,8 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
       if (count == null || count.equals("") || count.equals("0")) {
         // print warn info when we have only hgnc identifiers (or no
         // identifiers at all)
-        logger.warn(element.getElementTag() + "Cannot find information for element.");
+        logger.warn(element.getLogMarker(ProjectLogEntryType.CANNOT_FIND_INFORMATION),
+            "Cannot find information for element.");
         return false;
       } else {
         Node entry = XmlParser.getNode("doc", result.getChildNodes());
@@ -173,7 +175,8 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
         return true;
       }
     } catch (WrongResponseCodeIOException e) {
-      logger.warn(element.getElementTag() + "Cannot find information for element.");
+      logger.warn(element.getLogMarker(ProjectLogEntryType.CANNOT_FIND_INFORMATION),
+          "Cannot find information for element.");
       return false;
     } catch (Exception e) {
       throw new AnnotatorException(e);

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

@@ -16,6 +16,7 @@ import lcsb.mapviewer.annotation.cache.WebPageDownloader;
 import lcsb.mapviewer.annotation.services.*;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.*;
 import lcsb.mapviewer.model.map.species.*;
 import lcsb.mapviewer.model.map.species.field.Structure;
@@ -107,7 +108,8 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
       try {
         Collection<Structure> structures = uniProtToPdb(identifier);
         if (structures.size() == 0) {
-          logger.warn(bioEntity.getElementTag() + " No PDB mapping for UniProt ID: " + identifier.getResource());
+          logger.warn(bioEntity.getLogMarker(ProjectLogEntryType.OTHER),
+              " No PDB mapping for UniProt ID: " + identifier.getResource());
           return false;
         } else {
           // add the annotations to the set of annotation irrespective on

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

@@ -15,6 +15,7 @@ import lcsb.mapviewer.annotation.cache.WebPageDownloader;
 import lcsb.mapviewer.annotation.services.*;
 import lcsb.mapviewer.common.MinervaLoggerAppender;
 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.reaction.Reaction;
@@ -286,17 +287,19 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
                 unknown = true;
               }
               if (unknown) {
-                logger.warn(element.getElementTag() + "Unknown field in recon annotation: \"" + key + "\" (value: "
-                    + value + ")");
+                logger.warn(element.getLogMarker(ProjectLogEntryType.OTHER),
+                    "Unknown field in recon annotation: \"" + key + "\" (value: " + value + ")");
               }
             }
             return true;
           } else {
-            logger.warn(element.getElementTag() + "No recon annotations \"" + identifier.getResource() + "\"");
+            logger.warn(element.getLogMarker(ProjectLogEntryType.CANNOT_FIND_INFORMATION),
+                "No recon annotations \"" + identifier.getResource() + "\"");
             return false;
           }
         } else {
-          logger.warn(element.getElementTag() + "No recon annotations \"" + identifier.getResource() + "\"");
+          logger.warn(element.getLogMarker(ProjectLogEntryType.CANNOT_FIND_INFORMATION),
+              "No recon annotations \"" + identifier.getResource() + "\"");
           return false;
         }
       } catch (IOException e) {
@@ -370,8 +373,8 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
     } else if (value.startsWith("K")) {
       md = new MiriamData(MiriamType.KEGG_ORTHOLOGY, value);
     } else {
-      logger.warn(element.getElementTag()
-          + "Unknown Kegg identifier type (only Kegg compounds and reactions are supported): \"" + value + "\"");
+      logger.warn(element.getLogMarker(ProjectLogEntryType.INVALID_IDENTIFIER),
+          "Unknown Kegg identifier type (only Kegg compounds and reactions are supported): \"" + value + "\"");
     }
     return md;
   }

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

@@ -14,6 +14,7 @@ import lcsb.mapviewer.annotation.cache.WebPageDownloader;
 import lcsb.mapviewer.annotation.services.*;
 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.*;
@@ -106,7 +107,8 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
         } else {
           // this means that entry with a given uniprot id doesn't exist
           if (object.contains(identifier)) {
-            logger.warn(object.getElementTag() + " Invalid uniprot id: " + identifier);
+            logger.warn(object.getLogMarker(ProjectLogEntryType.INVALID_IDENTIFIER),
+                " Invalid uniprot id: " + identifier);
           }
           return false;
         }

annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingAnnotationTest.java

@@ -23,7 +23,7 @@ public class MissingAnnotationTest {
   @Test
   public void test() {
     MissingAnnotation annotation = new MissingAnnotation(new GenericProtein("id"));
-    assertTrue(annotation.toString().contains("misses annotations"));
+    assertTrue(annotation.toString().contains("Missing annotations"));
   }
 
 }

annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotationsTest.java

@@ -36,14 +36,10 @@ public class MissingRequiredAnnotationsTest {
 
   @Test
   public void testGetMessage() {
-    try {
-      List<MiriamType> list = new ArrayList<>();
-      list.add(MiriamType.CAS);
-      MissingRequiredAnnotations mre = new MissingRequiredAnnotations(new GenericProtein("id"), list);
-      assertTrue(mre.toString().contains("misses one of the following annotations"));
-    } catch (InvalidArgumentException e) {
-      assertTrue(e.getMessage().contains("List of improper annotations cannot be null"));
-    }
+    List<MiriamType> list = new ArrayList<>();
+    list.add(MiriamType.CAS);
+    MissingRequiredAnnotations mre = new MissingRequiredAnnotations(new GenericProtein("id"), list);
+    assertTrue(mre.toString().contains("Missing one of the required annotations"));
   }
 
 }

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

@@ -36,7 +36,7 @@ public class CazyAnnotatorTest extends AnnotationTestFunctions {
   @Test
   public void