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Commit b9d175da authored by Piotr Gawron's avatar Piotr Gawron
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annotators provide information about type and source

parent d231b8bd
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annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
View file @ b9d175da
......@@ -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
View file @ b9d175da
......@@ -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.
......@@ -132,7 +133,7 @@ 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();
}
......@@ -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
View file @ b9d175da
......@@ -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
View file @ b9d175da
......@@ -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
View file @ b9d175da
......@@ -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
View file @ b9d175da
......@@ -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
View file @ b9d175da
......@@ -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
View file @ b9d175da
......@@ -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/annotators/EntrezAnnotatorTest.java
View file @ b9d175da
......@@ -192,7 +192,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn(response);
entrezAnnotator.setWebPageDownloader(mockDownloader);
EntrezData data = entrezAnnotator.getEntrezForMiriamData(new MiriamData(), "");
EntrezData data = entrezAnnotator.getEntrezForMiriamData(new MiriamData(), null);
boolean ensembl = false;
boolean hgnc = false;
for (MiriamData md : data.getMiriamData()) {
......@@ -223,7 +223,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn(response);
entrezAnnotator.setWebPageDownloader(mockDownloader);
entrezAnnotator.getEntrezForMiriamData(new MiriamData(), "");
entrezAnnotator.getEntrezForMiriamData(new MiriamData(), null);
} finally {
entrezAnnotator.setWebPageDownloader(downloader);
entrezAnnotator.setCache(cache);
......@@ -241,7 +241,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
.thenThrow(new WrongResponseCodeIOException(null, 404));
entrezAnnotator.setWebPageDownloader(mockDownloader);
entrezAnnotator.getEntrezForMiriamData(new MiriamData(), "");
entrezAnnotator.getEntrezForMiriamData(new MiriamData(), null);
} finally {
entrezAnnotator.setWebPageDownloader(downloader);
entrezAnnotator.setCache(cache);
......
commons/src/main/java/lcsb/mapviewer/common/exception/NotImplementedException.java
View file @ b9d175da
......@@ -3,7 +3,7 @@ package lcsb.mapviewer.common.exception;
/**
* Exception that should be thrown when application/class/method entered to the
* part of code that wasn't implemented (for instance the class is not abstract,
* but method should be considered abstrac...).
* but method should be considered abstract...).
*
* @author Piotr Gawron
*
......
model/src/main/java/lcsb/mapviewer/model/LogMarker.java
View file @ b9d175da
......@@ -14,7 +14,7 @@ public class LogMarker implements Marker {
private ProjectLogEntry entry;
public LogMarker(String type, BioEntity bioEntity) {
public LogMarker(ProjectLogEntryType type, BioEntity bioEntity) {
entry = new ProjectLogEntry();
entry.setType(type);
if (bioEntity != null) {
......@@ -26,6 +26,10 @@ public class LogMarker implements Marker {
}
}
public LogMarker(LogMarker marker) {
entry = new ProjectLogEntry(marker.getEntry());
}
@Override
public Marker addParents(Marker... markers) {
throw new NotImplementedException();
......
model/src/main/java/lcsb/mapviewer/model/ProjectLogEntry.java
View file @ b9d175da
......@@ -20,7 +20,8 @@ public class ProjectLogEntry implements Serializable {
private String severity;
@Column(nullable = false)
private String type;
@Enumerated(EnumType.STRING)
private ProjectLogEntryType type;
private String objectIdentifier;
......@@ -28,6 +29,8 @@ public class ProjectLogEntry implements Serializable {
private String mapName;
private String source;
@Column(nullable = false)
private String content;
......@@ -35,6 +38,17 @@ public class ProjectLogEntry implements Serializable {
}
public ProjectLogEntry(ProjectLogEntry entry) {
this.project = entry.getProject();
this.severity = entry.getSeverity();
this.type = entry.getType();
this.objectIdentifier = entry.getObjectIdentifier();
this.objectClass = entry.getObjectClass();
this.mapName = entry.getMapName();
this.source = entry.getSource();
this.content = entry.getContent();
}
public String getContent() {
return content;
}
......@@ -75,14 +89,6 @@ public class ProjectLogEntry implements Serializable {
this.severity = severity;
}
public String getType() {
return type;
}
public void setType(String type) {
this.type = type;
}
public Project getProject() {
return project;
}
......@@ -91,4 +97,20 @@ public class ProjectLogEntry implements Serializable {
this.project = project;
}
public String getSource() {
return source;
}
public void setSource(String source) {
this.source = source;
}
public ProjectLogEntryType getType() {
return type;
}
public void setType(ProjectLogEntryType type) {
this.type = type;
}
}
model/src/main/java/lcsb/mapviewer/model/ProjectLogEntryType.java 0 → 100644
View file @ b9d175da
package lcsb.mapviewer.model;
public enum ProjectLogEntryType {
OTHER,
CANNOT_FIND_INFORMATION,
INVALID_IDENTIFIER,
ANNOTATION_CONFLICT,
OUT_OF_MEMORY,
DATABASE_PROBLEM
}
persist/src/main/resources/db/migration/15.0.0/V15.0.1.20191025_3__structured_log.sql
View file @ b9d175da
......@@ -29,3 +29,4 @@ insert into project_log_entry_table (content, project_id, severity, type) SELECT
insert into project_log_entry_table (content, project_id, severity, type) SELECT s.token, id, 'ERROR', 'OTHER' from project_table t, unnest(string_to_array(t.errors, E'\n')) s(token);
alter table project_table drop column warnings;
alter table project_table drop column errors;
alter table project_log_entry_table add column source varchar;
persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
View file @ b9d175da
......@@ -7,8 +7,7 @@ import org.apache.logging.log4j.Logger;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectLogEntry;
import lcsb.mapviewer.model.*;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewModelLink;
import lcsb.mapviewer.model.map.layout.*;
......@@ -205,7 +204,7 @@ public class ProjectDaoTest extends PersistTestFunctions {
ProjectLogEntry entry = new ProjectLogEntry();
entry.setContent("content");
entry.setSeverity("WARN");
entry.setType("OTHER");
entry.setType(ProjectLogEntryType.OTHER);
project.addLogEntry(entry);
project.setOwner(userDao.getUserByLogin(ADMIN_BUILT_IN_LOGIN));
assertEquals(1, project.getLogEntries().size());
......
service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
View file @ b9d175da
......@@ -23,6 +23,7 @@ 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;
......@@ -407,7 +408,7 @@ public class ProjectService implements IProjectService {
logger.error("Out of memory", oome);
if (project != null) {
ProjectLogEntry entry = new ProjectLogEntry();
entry.setType("OUT_OF_MEMORY");
entry.setType(ProjectLogEntryType.OUT_OF_MEMORY);
entry.setSeverity("ERROR");
entry.setContent("Out of memory: " + oome.getMessage());
project.addLogEntry(entry);
......@@ -608,7 +609,7 @@ public class ProjectService implements IProjectService {
Project project = getProjectByProjectId(originalProject.getProjectId());
ProjectLogEntry entry = new ProjectLogEntry();
entry.setType("OTHER");
entry.setType(ProjectLogEntryType.OTHER);
entry.setSeverity("ERROR");
entry.setContent("Severe problem with removing object. Underlaying eror:\n" + exception.getMessage()
+ "\nMore information can be found in log file.");
......@@ -1073,7 +1074,7 @@ public class ProjectService implements IProjectService {
Project project = getProjectByProjectId(params.getProjectId());
ProjectLogEntry entry = new ProjectLogEntry();
entry.setType("DATABASE_PROBLEM");
entry.setType(ProjectLogEntryType.DATABASE_PROBLEM);
entry.setSeverity("ERROR");
entry.setContent("Problem with uploading to database. "
+ "You might violated some unhandled constraints or you run out of memory. Underlaying eror:\n"
......@@ -1107,7 +1108,7 @@ public class ProjectService implements IProjectService {
Project p = projectDao.getProjectByProjectId(params.getProjectId());
if (p != null) {
ProjectLogEntry entry = new ProjectLogEntry();
entry.setType("OTHER");
entry.setType(ProjectLogEntryType.OTHER);
entry.setSeverity("ERROR");
entry.setContent("Problem with uploading map: " + e.getMessage() + ". More details can be found in log file.");
p.addLogEntry(entry);
......@@ -1187,7 +1188,7 @@ public class ProjectService implements IProjectService {
}
if (entry==null) {
entry = new ProjectLogEntry();
entry.setType("OTHER");
entry.setType(ProjectLogEntryType.OTHER);
}
entry.setSeverity(severity);
entry.setContent(event.getMessage().getFormattedMessage());
......
service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
View file @ b9d175da
......@@ -665,12 +665,12 @@ public class ProjectServiceTest extends ServiceTestFunctions {
appender.append(Log4jLogEvent.newBuilder()
.setLevel(Level.WARN)
.setMessage(new SimpleMessage("Hello world"))
.setMarker(new LogMarker("type", protein))
.setMarker(new LogMarker(ProjectLogEntryType.OTHER, protein))
.build());
appender.append(Log4jLogEvent.newBuilder()
.setLevel(Level.ERROR)
.setMessage(new SimpleMessage("Hello world 2"))
.setMarker(new LogMarker("type2", protein))
.setMarker(new LogMarker(ProjectLogEntryType.OTHER, protein))
.build());
appender.append(Log4jLogEvent.newBuilder()
.setLevel(Level.ERROR)
......
web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java
View file @ b9d175da
......@@ -137,7 +137,7 @@ public class StartupBean {
if (!ProjectStatus.DONE.equals(project.getStatus()) && !ProjectStatus.FAIL.equals(project.getStatus())) {
ProjectLogEntry entry = new ProjectLogEntry();
entry.setSeverity("ERROR");
entry.setType("OTHER");
entry.setType(ProjectLogEntryType.OTHER);
entry.setContent(
"Project uploading was interrupted by application restart (at the stage: " + project.getStatus() + ").");
project.setStatus(ProjectStatus.FAIL);
......
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