From 19d4679433193ee3ad0c6a7c9cb6f92064f58329 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 19 Nov 2018 13:36:11 +0100
Subject: [PATCH] export of compartments fixed
---
.../model/sbgnml/SbgnmlXmlExporter.java | 13 ++++---
.../model/sbgnml/CellDesignerToSbgnTest.java | 37 +++++++++++++++++++
2 files changed, 45 insertions(+), 5 deletions(-)
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index 824664c47b..1b536d4ee9 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -161,11 +161,14 @@ public class SbgnmlXmlExporter {
map.setLanguage(Language.PD.getName());
Sbgn sbgnData = new Sbgn();
- List<Species> aliases = model.getSpeciesList();
-
- for (Species a : aliases) {
- if (a.getComplex() == null) {
- Glyph newGlyph = aliasToGlyph(a);
+ for (Element element : model.getElements()) {
+ if (element instanceof Species) {
+ if (((Species) element).getComplex() == null) {
+ Glyph newGlyph = aliasToGlyph(element);
+ map.getGlyph().add(newGlyph);
+ }
+ } else if (element instanceof Compartment) {
+ Glyph newGlyph = aliasToGlyph(element);
map.getGlyph().add(newGlyph);
}
}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
index edaea41e34..05fca1f6c7 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
@@ -14,10 +14,14 @@ import org.junit.Test;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
public class CellDesignerToSbgnTest {
Logger logger = Logger.getLogger(CellDesignerToSbgnTest.class);
+ ElementUtils eu = new ElementUtils();
@Before
public void setUp() throws Exception {
@@ -70,4 +74,37 @@ public class CellDesignerToSbgnTest {
}
}
+ @Test
+ public void testCompartmentsExport() throws Exception {
+ try {
+ IConverter converter = new CellDesignerXmlParser();
+ IConverter converter2 = new SbgnmlXmlConverter();
+
+ Model model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/neuron.xml"));
+
+ String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
+ converter2.exportModelToFile(model, output);
+
+ converter2.createModel(new ConverterParams().filename(output));
+
+ String fileContent;
+ try (FileInputStream inputStream = new FileInputStream(output)) {
+ fileContent = IOUtils.toString(inputStream, "UTF-8");
+ }
+
+ for (Element element : model.getElements()) {
+ if (element instanceof Compartment) {
+ assertTrue(eu.getElementTag(element) + " comparmtent is not exported",
+ fileContent.contains(element.getElementId()));
+ }
+ }
+
+ new File(output).delete();
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
}
--
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