From d231b8bd79bf81da09396b48e9a93021beca43af Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 25 Oct 2019 19:36:04 +0200
Subject: [PATCH] logger entries are translated to project log entries
---
.../java/lcsb/mapviewer/model/LogMarker.java | 72 +++++++++++++++++++
.../mapviewer/model/map/species/Element.java | 3 +
.../services/impl/ProjectService.java | 29 +++++++-
.../services/impl/ProjectServiceTest.java | 37 ++++++++--
4 files changed, 132 insertions(+), 9 deletions(-)
create mode 100644 model/src/main/java/lcsb/mapviewer/model/LogMarker.java
diff --git a/model/src/main/java/lcsb/mapviewer/model/LogMarker.java b/model/src/main/java/lcsb/mapviewer/model/LogMarker.java
new file mode 100644
index 0000000000..90379cee6d
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/LogMarker.java
@@ -0,0 +1,72 @@
+package lcsb.mapviewer.model;
+
+import org.apache.logging.log4j.Marker;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.BioEntity;
+
+public class LogMarker implements Marker {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ private ProjectLogEntry entry;
+
+ public LogMarker(String type, BioEntity bioEntity) {
+ entry = new ProjectLogEntry();
+ entry.setType(type);
+ if (bioEntity != null) {
+ entry.setObjectIdentifier(bioEntity.getElementId());
+ entry.setObjectClass(bioEntity.getClass().getSimpleName());
+ if (bioEntity.getModel() != null) {
+ entry.setMapName(bioEntity.getModel().getName());
+ }
+ }
+ }
+
+ @Override
+ public Marker addParents(Marker... markers) {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public String getName() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public Marker[] getParents() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public boolean hasParents() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public boolean isInstanceOf(Marker m) {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public boolean isInstanceOf(String name) {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public boolean remove(Marker marker) {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public Marker setParents(Marker... markers) {
+ throw new NotImplementedException();
+ }
+
+ public ProjectLogEntry getEntry() {
+ return entry;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index 77d6d22964..8cd0b748ae 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -815,6 +815,9 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
@XmlTransient
@Override
public Model getModel() {
+ if (model == null) {
+ return null;
+ }
return model.getModel();
}
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 71c3000adc..c73e0e47c9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -9,6 +9,7 @@ import javax.mail.MessagingException;
import org.apache.commons.io.FileUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.core.LogEvent;
import org.hibernate.HibernateException;
import org.primefaces.model.DefaultTreeNode;
import org.primefaces.model.TreeNode;
@@ -22,7 +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;
@@ -1167,8 +1167,31 @@ public class ProjectService implements IProjectService {
return project;
}
- private Set<ProjectLogEntry> createLogEntries(MinervaLoggerAppender appender) {
- throw new NotImplementedException();
+ Set<ProjectLogEntry> createLogEntries(MinervaLoggerAppender appender) {
+ Set<ProjectLogEntry> result = new HashSet<>();
+ for (LogEvent event : appender.getWarnings()) {
+ result.add(createLogEntry("WARNING", event));
+ }
+ for (LogEvent event : appender.getErrors()) {
+ result.add(createLogEntry("ERROR", event));
+ }
+ return result;
+ }
+
+ private ProjectLogEntry createLogEntry(String severity, LogEvent event) {
+ ProjectLogEntry entry = null;
+ if (event.getMarker() != null) {
+ if (event.getMarker() instanceof LogMarker) {
+ entry = ((LogMarker) event.getMarker()).getEntry();
+ }
+ }
+ if (entry==null) {
+ entry = new ProjectLogEntry();
+ entry.setType("OTHER");
+ }
+ entry.setSeverity(severity);
+ entry.setContent(event.getMessage().getFormattedMessage());
+ return entry;
}
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index 24281d4e6a..12182db251 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -8,8 +8,9 @@ import java.util.*;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.core.impl.Log4jLogEvent;
+import org.apache.logging.log4j.message.SimpleMessage;
import org.apache.poi.util.IOUtils;
import org.junit.*;
import org.mockito.Mockito;
@@ -18,20 +19,19 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.annotation.Rollback;
import lcsb.mapviewer.commands.CopyCommand;
+import lcsb.mapviewer.common.MinervaLoggerAppender;
import lcsb.mapviewer.converter.ComplexZipConverter;
import lcsb.mapviewer.converter.ComplexZipConverterParams;
import lcsb.mapviewer.converter.graphics.MapGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.zip.*;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.ProjectStatus;
+import lcsb.mapviewer.model.*;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.model.map.layout.DataOverlayImageLayer;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.*;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.user.*;
import lcsb.mapviewer.persist.dao.ProjectDao;
import lcsb.mapviewer.persist.dao.map.LayoutDao;
@@ -657,4 +657,29 @@ public class ProjectServiceTest extends ServiceTestFunctions {
assertEquals(ProjectStatus.FAIL, project.getStatus());
projectService.removeProject(project, null, false);
}
+
+ @Test
+ public void testCreateLogEntries() throws Exception {
+ Protein protein = new GenericProtein("id");
+ MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
+ appender.append(Log4jLogEvent.newBuilder()
+ .setLevel(Level.WARN)
+ .setMessage(new SimpleMessage("Hello world"))
+ .setMarker(new LogMarker("type", protein))
+ .build());
+ appender.append(Log4jLogEvent.newBuilder()
+ .setLevel(Level.ERROR)
+ .setMessage(new SimpleMessage("Hello world 2"))
+ .setMarker(new LogMarker("type2", protein))
+ .build());
+ appender.append(Log4jLogEvent.newBuilder()
+ .setLevel(Level.ERROR)
+ .setMessage(new SimpleMessage("Hello world 3"))
+ .build());
+
+ ProjectService service = Mockito.mock(ProjectService.class, Mockito.CALLS_REAL_METHODS);
+ Set<ProjectLogEntry> entries = service.createLogEntries(appender);
+ assertEquals(3, entries.size());
+ }
+
}
--
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