From 1f093f89a903a502fb9ac3eac44dd5f75decbb59 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 7 Jan 2019 10:34:35 +0100
Subject: [PATCH] export of initial concentration added
---
.../sbml/species/SbmlSpeciesExporter.java | 3 +
.../model/sbml/species/SbmlSpeciesParser.java | 3 +
.../model/sbml/AllSbmlConverterTests.java | 1 +
.../model/sbml/ElementPropertiesExport.java | 102 ++++++++++++++++++
4 files changed, 109 insertions(+)
create mode 100644 converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExport.java
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
index 304fc53dc4..ee081b42f4 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
@@ -77,6 +77,9 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
if (element.getInitialAmount() != null) {
result.setInitialAmount(element.getInitialAmount());
}
+ if (element.getInitialConcentration() != null) {
+ result.setInitialConcentration(element.getInitialConcentration());
+ }
if (element.hasOnlySubstanceUnits() != null) {
result.setHasOnlySubstanceUnits(element.hasOnlySubstanceUnits());
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
index d458857d6d..78fb7ca6c8 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
@@ -78,6 +78,9 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
if (!Double.isNaN(species.getInitialAmount())) {
result.setInitialAmount(species.getInitialAmount());
}
+ if (!Double.isNaN(species.getInitialConcentration())) {
+ result.setInitialConcentration(species.getInitialConcentration());
+ }
if (species.isSetHasOnlySubstanceUnits()) {
result.setOnlySubstanceUnits(species.hasOnlySubstanceUnits());
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
index d33aff584a..922a00eb38 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
@@ -13,6 +13,7 @@ import lcsb.mapviewer.converter.model.sbml.species.AllSbmlSpeciesTests;
GenericSbmlParserTest.class,
GenericSbmlToXmlParserTest.class,
CellDesignerToMultiExportTest.class,
+ ElementPropertiesExport.class,
ElementPropertiesExportToMultiTest.class,
ElementPropertiesExportToLayoutTest.class,
MultiParserTest.class,
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExport.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExport.java
new file mode 100644
index 0000000000..c4f3cf8c96
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExport.java
@@ -0,0 +1,102 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+@RunWith(Parameterized.class)
+public class ElementPropertiesExport {
+
+ static Logger logger = Logger.getLogger(ElementPropertiesExport.class.getName());
+
+ private Model model;
+
+ public ElementPropertiesExport(String propertyName, Model model) {
+ this.model = model;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ Collection<Object[]> data = new ArrayList<>();
+
+ data.add(createTestEntry("Empty", createElement()));
+
+ Species element = createElement();
+ element.setInitialConcentration(1.0);
+ data.add(createTestEntry("Initial concentration", element));
+
+ element = createElement();
+ element.setInitialAmount(2.0);
+ data.add(createTestEntry("Initial amount", element));
+
+ element = createElement();
+ element.setBoundaryCondition(true);
+ data.add(createTestEntry("Boundary condition", element));
+
+ element = createElement();
+ element.setConstant(true);
+ data.add(createTestEntry("Constatnt", element));
+
+ return data;
+ }
+
+ private static Object[] createTestEntry(String string, Element element) {
+ Model result = new ModelFullIndexed(null);
+ result.setIdModel("X");
+ result.setWidth(200);
+ result.setHeight(200);
+ result.addElement(element);
+ return new Object[] { string, result };
+ }
+
+ private static Species createElement() {
+ Species element = new GenericProtein("id");
+ element.setX(10);
+ element.setY(10);
+ element.setWidth(1000);
+ element.setHeight(30);
+ return element;
+ }
+
+ @Test
+ public void createModelTest() throws Exception {
+ try {
+ SbmlExporter sbmlExporter = new SbmlExporter();
+ SbmlParser sbmlParser = new SbmlParser();
+ String xmlString = sbmlExporter.toXml(model);
+ logger.debug(xmlString);
+
+ InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+ Model model2 = sbmlParser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ model2.setName(model.getName());
+
+ ModelComparator comparator = new ModelComparator();
+ assertEquals(0, comparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
--
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