diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
index 864f9225072c5693c82db3822dc39ecea7a94fd8..db69a3b4867cc2b9c80c02b7643aa4124180b85a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
+++ b/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());
}
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
index 7974a2a06bf3b0f4c75911982b5071746a18ee04..4abd6df377e30f97ef8870c5886df498f37bbfd3 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
+++ b/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(),null);
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);
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
index fe852a34f3e58cc87a5577fabaa1cc2055deb92c..c60fdf6afc3540e43f39e85c4e6f3d33ce9fc087 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
@@ -36,7 +36,7 @@ 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")));
+ cazyAnnotator.uniprotToCazy(new MiriamData(MiriamType.UNIPROT, "Q9SG95"), null));
}
@Test
@@ -132,12 +132,12 @@ public class CazyAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testInvalidUniprotToCazyNull() throws Exception {
- assertNull(cazyAnnotator.uniprotToCazy(null));
+ assertNull(cazyAnnotator.uniprotToCazy(null, null));
}
@Test(expected = InvalidArgumentException.class)
public void testInvalidUniprotToCazyWrongMd() throws Exception {
- cazyAnnotator.uniprotToCazy(new MiriamData(MiriamType.WIKIPEDIA, "bla"));
+ cazyAnnotator.uniprotToCazy(new MiriamData(MiriamType.WIKIPEDIA, "bla"), null);
}
@Test
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index 64a886593f04fc5811d002f35bf819b9e8a07c4f..842ad58ae24655d16d8aadcb3b226e643b91a467 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -437,7 +437,9 @@ public class Reaction implements BioEntity {
*/
public void removeModifier(Modifier modifier) {
nodes.remove(modifier);
- } @Override
+ }
+
+ @Override
public String getVisibilityLevel() {
return visibilityLevel;
}
@@ -450,7 +452,9 @@ public class Reaction implements BioEntity {
*/
public void removeNode(AbstractNode node) {
nodes.remove(node);
- } @Override
+ }
+
+ @Override
public void setVisibilityLevel(String visibilityLevel) {
this.visibilityLevel = visibilityLevel;
}
@@ -521,7 +525,9 @@ public class Reaction implements BioEntity {
*/
public String getIdReaction() {
return idReaction;
- } /**
+ }
+
+ /**
* Creates copy of the reaction.
*
* @return copy of the reaction
@@ -675,7 +681,9 @@ public class Reaction implements BioEntity {
*/
public ModelData getModelData() {
return model;
- } /**
+ }
+
+ /**
* Sets model where the reaction is located.
*
* @param model2
@@ -692,9 +700,14 @@ public class Reaction implements BioEntity {
*/
public void setModelData(ModelData model) {
this.model = model;
- } @XmlTransient
+ }
+
+ @XmlTransient
@Override
public Model getModel() {
+ if (model == null) {
+ return null;
+ }
return model.getModel();
}
@@ -738,7 +751,9 @@ public class Reaction implements BioEntity {
*/
public Double getUpperBound() {
return upperBound;
- } @Override
+ }
+
+ @Override
public String getFormula() {
return formula;
}
@@ -750,7 +765,9 @@ public class Reaction implements BioEntity {
*/
public void setUpperBound(Double upperBound) {
this.upperBound = upperBound;
- } @Override
+ }
+
+ @Override
public void setFormula(String formula) {
this.formula = formula;
}
@@ -838,7 +855,9 @@ public class Reaction implements BioEntity {
public void setLine(PolylineData line) {
this.line = line;
- } @Override
+ }
+
+ @Override
public void setVisibilityLevel(Integer zoomLevelVisibility) {
if (zoomLevelVisibility == null) {
this.visibilityLevel = null;
@@ -848,19 +867,4 @@ public class Reaction implements BioEntity {
}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 2b5757a80b5a1ac6ab76d28b4a893e703a1a3552..8f25e69f7696315f794ab4c306c54382706ca099 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -23,7 +23,6 @@ import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
import lcsb.mapviewer.commands.*;
import lcsb.mapviewer.common.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.*;
import lcsb.mapviewer.converter.graphics.DrawingException;
import lcsb.mapviewer.converter.graphics.MapGenerator;