From aa2f032b71a9e2eafbf7c7b6834f59fcdaddce8f Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 28 Oct 2016 17:12:48 +0200
Subject: [PATCH] model annotation are model scope (not project)
---
.../annotation/services/ModelAnnotator.java | 72 ++++++++-----------
.../services/ModelAnnotatorTest.java | 5 +-
.../java/lcsb/mapviewer/run/BellExport.java | 5 +-
.../java/lcsb/mapviewer/run/Statistics.java | 7 +-
.../services/impl/ProjectService.java | 2 +-
5 files changed, 35 insertions(+), 56 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index 1dadb9b071..a29e3d25ba 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -25,15 +25,12 @@ import lcsb.mapviewer.annotation.services.annotators.GoAnnotator;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -167,13 +164,13 @@ public class ModelAnnotator {
/**
* Performs all possible and automatic annotations on the model.
*
- * @param project
- * project to update
+ * @param model
+ * model to update
* @param progressUpdater
* callback function used for updating progress of the function
*/
- public void performAnnotations(Project project, final IProgressUpdater progressUpdater) {
- performAnnotations(project, progressUpdater, null);
+ public void performAnnotations(Model model, final IProgressUpdater progressUpdater) {
+ performAnnotations(model, progressUpdater, null);
}
/**
@@ -182,48 +179,37 @@ public class ModelAnnotator {
* @param annotators
* this map contains lists of {@link ElementAnnotator} objects that
* should be used for a given classes
- * @param project
- * project with models to update
+ * @param model
+ * model to update
* @param progressUpdater
* callback function used for updating progress of the function
*/
- public void performAnnotations(Project project, final IProgressUpdater progressUpdater, Map<Class<?>, List<ElementAnnotator>> annotators) {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- try {
- Logger.getRootLogger().addAppender(appender);
- progressUpdater.setProgress(0);
- List<Model> models = new ArrayList<>();
- for (ModelData model: project.getModels()) {
- models.add(model.getModel());
- models.addAll(model.getModel().getSubmodels());
- }
- final double size = models.size();
- double counter = 0;
- for (Model m : models) {
- final double ratio = counter / size;
+ public void performAnnotations(Model model, final IProgressUpdater progressUpdater, Map<Class<?>, List<ElementAnnotator>> annotators) {
+ progressUpdater.setProgress(0);
+ List<Model> models = new ArrayList<Model>();
+ models.add(model);
+ models.addAll(model.getSubmodels());
+ final double size = models.size();
+ double counter = 0;
+ for (Model m : models) {
+ final double ratio = counter / size;
- copyAnnotationFromOtherSpecies(m, new IProgressUpdater() {
- @Override
- public void setProgress(final double progress) {
- progressUpdater.setProgress(ratio * IProgressUpdater.MAX_PROGRESS + (progress * COPYING_RATIO) / size);
- }
- });
- annotateModel(m, new IProgressUpdater() {
+ copyAnnotationFromOtherSpecies(m, new IProgressUpdater() {
+ @Override
+ public void setProgress(final double progress) {
+ progressUpdater.setProgress(ratio * IProgressUpdater.MAX_PROGRESS + (progress * COPYING_RATIO) / size);
+ }
+ });
+ annotateModel(m, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- progressUpdater
- .setProgress(ratio * IProgressUpdater.MAX_PROGRESS + (COPYING_RATIO * IProgressUpdater.MAX_PROGRESS + progress * ANNOTATING_RATIO) / size);
- }
- }, annotators);
- counter++;
- }
- Logger.getRootLogger().removeAppender(appender);
- project.addLoggingInfo(appender);
- } finally {
- Logger.getRootLogger().removeAppender(appender);
+ @Override
+ public void setProgress(double progress) {
+ progressUpdater
+ .setProgress(ratio * IProgressUpdater.MAX_PROGRESS + (COPYING_RATIO * IProgressUpdater.MAX_PROGRESS + progress * ANNOTATING_RATIO) / size);
+ }
+ }, annotators);
+ counter++;
}
-
}
/**
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
index 0402014d42..b920636e1d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -29,7 +29,6 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -312,9 +311,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
final MutableDouble maxProgress = new MutableDouble(0.0);
- Project project = new Project();
- project.addModel(model);
- modelAnnotator.performAnnotations(project, new IProgressUpdater() {
+ modelAnnotator.performAnnotations(model, new IProgressUpdater() {
@Override
public void setProgress(double progress) {
maxProgress.setValue(Math.max(progress, maxProgress.getValue()));
diff --git a/console/src/main/java/lcsb/mapviewer/run/BellExport.java b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
index b70a0b9423..f3c63406f7 100644
--- a/console/src/main/java/lcsb/mapviewer/run/BellExport.java
+++ b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
@@ -7,7 +7,6 @@ import lcsb.mapviewer.annotation.services.ModelAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.ApplicationContextLoader;
@@ -82,10 +81,8 @@ public class BellExport {
// version = "1.1.38";
dbUtils.createSessionForCurrentThread();
Model model = p.createModel(new ConverterParams().filename(filename));
- Project project = new Project();
- project.addModel(model);
- modelAnnotator.performAnnotations(project, new IProgressUpdater() {
+ modelAnnotator.performAnnotations(model, new IProgressUpdater() {
@Override
public void setProgress(double progress) {
}
diff --git a/console/src/main/java/lcsb/mapviewer/run/Statistics.java b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
index 661ba6db47..600a4ba8a0 100644
--- a/console/src/main/java/lcsb/mapviewer/run/Statistics.java
+++ b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
@@ -20,7 +20,6 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -113,11 +112,9 @@ public class Statistics {
try {
// String modelName = PdMapAnnotations.getLastPdFilename();
CellDesignerXmlParser parser = new CellDesignerXmlParser();
- Project project = new Project();
for (String name : fileNames) {
Model model = parser.createModel(new ConverterParams().filename(name));
models.add(model);
- project.addModel(model);
}
IProgressUpdater updater = new IProgressUpdater() {
@@ -126,7 +123,9 @@ public class Statistics {
logger.debug("Progress: " + progress);
}
};
- modelAnnotator.performAnnotations(project, updater);
+ for (Model model : models) {
+ modelAnnotator.performAnnotations(model, updater);
+ }
// modelAnnotator.removeIncorrectAnnotations(model, updater);
printStatistics(models);
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 46a9e71f11..04fd199662 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -735,7 +735,7 @@ public class ProjectService implements IProjectService {
}
}
logger.debug("Updating annotations");
- modelAnnotator.performAnnotations(project, new IProgressUpdater() {
+ modelAnnotator.performAnnotations(model, new IProgressUpdater() {
@Override
public void setProgress(final double progress) {
--
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