From e4b8601403cbab9bd08d3634bd0c01c2a0ce71ba Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 4 Jan 2019 10:31:03 +0100
Subject: [PATCH] export/import of model notes added
---
.../converter/model/sbml/NotesUtility.java | 32 +++++++++++++++++++
.../model/sbml/SbmlBioEntityParser.java | 23 +------------
.../converter/model/sbml/SbmlExporter.java | 7 ++++
.../converter/model/sbml/SbmlParser.java | 1 +
.../model/sbml/SbmlExporterTest.java | 10 ++++++
5 files changed, 51 insertions(+), 22 deletions(-)
create mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java
new file mode 100644
index 0000000000..7a0bac687e
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java
@@ -0,0 +1,32 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import javax.xml.stream.XMLStreamException;
+
+import org.sbml.jsbml.AbstractNamedSBase;
+
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+
+public class NotesUtility {
+ public static String extractNotes(AbstractNamedSBase sbmlElement) throws InvalidInputDataExecption {
+ String notes = "";
+ try {
+ notes = sbmlElement.getNotesString();
+ } catch (XMLStreamException e) {
+ throw new InvalidInputDataExecption(sbmlElement.getId() + " Invalid notes", e);
+ }
+ if (sbmlElement.getNotes() != null) {
+ if (sbmlElement.getNotes().getChildCount() > 1) {
+ if (sbmlElement.getNotes().getChild(1).getChildCount() > 1) {
+ if (sbmlElement.getNotes().getChild(1).getChild(1).getChildCount() > 0) {
+ notes = sbmlElement.getNotes().getChild(1).getChild(1).getChild(0).getCharacters();
+ } else {
+ notes = sbmlElement.getNotes().getChild(1).getChild(1).getCharacters();
+ }
+ }
+ }
+ }
+ return notes;
+ }
+
+
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
index acbffb2c09..b53c544c8b 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
@@ -95,7 +95,7 @@ public class SbmlBioEntityParser extends XmlParser {
if (result.getName() == null || result.getName().isEmpty()) {
result.setName(result.getElementId());
}
- String notes = extractNotes(sbmlElement);
+ String notes = NotesUtility.extractNotes(sbmlElement);
result.setNotes(notes);
if (result instanceof Element) {
@@ -104,27 +104,6 @@ public class SbmlBioEntityParser extends XmlParser {
}
}
- private String extractNotes(AbstractNamedSBase sbmlElement) throws InvalidInputDataExecption {
- String notes = "";
- try {
- notes = sbmlElement.getNotesString();
- } catch (XMLStreamException e) {
- throw new InvalidInputDataExecption(sbmlElement.getId() + " Invalid notes", e);
- }
- if (sbmlElement.getNotes() != null) {
- if (sbmlElement.getNotes().getChildCount() > 1) {
- if (sbmlElement.getNotes().getChild(1).getChildCount() > 1) {
- if (sbmlElement.getNotes().getChild(1).getChild(1).getChildCount() > 0) {
- notes = sbmlElement.getNotes().getChild(1).getChild(1).getChild(0).getCharacters();
- } else {
- notes = sbmlElement.getNotes().getChild(1).getChild(1).getCharacters();
- }
- }
- }
- }
- return notes;
- }
-
protected String getNextId() {
return (idCounter++) + "";
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 79d3012885..45d496c6ce 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -9,6 +9,7 @@ import java.util.Set;
import javax.xml.stream.XMLStreamException;
import org.apache.commons.io.output.ByteArrayOutputStream;
+import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBMLDocument;
@@ -78,6 +79,12 @@ public class SbmlExporter {
SBMLDocument doc = new SBMLDocument(3, 2);
Model result = doc.createModel(model.getIdModel());
result.setName(model.getName());
+ try {
+ result.setNotes(StringEscapeUtils.escapeXml(model.getNotes()));
+ } catch (XMLStreamException e) {
+ throw new InvalidStateException(e);
+ }
+
if (usedExtensions.contains(SbmlExtension.LAYOUT)) {
createSbmlLayout(model, result);
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 48f4e8d3ac..7bf2917282 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -68,6 +68,7 @@ public class SbmlParser implements IConverter {
org.sbml.jsbml.Model sbmlModel = sbmlDocument.getModel();
model.setIdModel(sbmlModel.getId());
model.setName(sbmlModel.getName());
+ model.setNotes(NotesUtility.extractNotes(sbmlModel));
checkAvailableExtensions(sbmlModel);
Layout layout = getSbmlLayout(sbmlModel);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
index 92b27dcc63..37a79998a3 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
@@ -614,4 +614,14 @@ public class SbmlExporterTest {
}
+ @Test
+ public void testExportNotes() throws Exception {
+ Model model = createEmptyModel();
+ model.setNotes("XX");
+ Model deserializedModel = getModelAfterSerializing(model);
+
+ assertEquals("Notes weren't exported/imported properly", model.getNotes(), deserializedModel.getNotes());
+
+ }
+
}
--
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