Include vcml file into OMEX archive for VCell-CLI

virtualcell · Dec 1, 2020 · 49a3c4c · 49a3c4c
1 parent a866772
commit 49a3c4c
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diff --git a/vcell-client/src/main/java/org/vcell/util/gui/exporter/OmexExtensionFilter.java b/vcell-client/src/main/java/org/vcell/util/gui/exporter/OmexExtensionFilter.java
@@ -1,9 +1,11 @@
 package org.vcell.util.gui.exporter;
 
 import java.io.File;
+import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.Objects;
 
+import cbit.vcell.xml.XmlHelper;
 import org.vcell.sedml.SEDMLExporter;
 import org.vcell.util.FileUtils;
 
@@ -34,6 +36,12 @@ public void writeBioModel(DocumentManager documentManager, BioModel bioModel, Fi
 		if (bioModel != null) {
 			sedmlExporter = new SEDMLExporter(bioModel, sedmlLevel, sedmlVersion);
 			resultString = sedmlExporter.getSEDMLFile(sPath);
+
+			// convert biomodel to vcml and save to file.
+			String vcmlString = XmlHelper.bioModelToXML(bioModel);
+			String vcmlFileName = Paths.get(sPath, sFile + ".vcml").toString();
+			File vcmlFile = new File(vcmlFileName);
+			XmlUtil.writeXMLStringToFile(vcmlString, vcmlFile.getAbsolutePath(), true);
 		} else {
 			throw new RuntimeException("unsupported Document Type " + Objects.requireNonNull(bioModel).getClass().getName() + " for SedML export");
 		}

diff --git a/vcell-core/src/main/java/org/vcell/sedml/SEDMLExporter.java b/vcell-core/src/main/java/org/vcell/sedml/SEDMLExporter.java
@@ -1075,6 +1075,13 @@ public boolean createOmexArchive(String srcFolder, String sFileName) {
 			);
     	}
 
+		archive.addFile(
+				Paths.get(srcFolder, sFileName + ".vcml").toString(),
+				sFileName + ".vcml",
+				KnownFormats.lookupFormat("vcml"),
+				false
+		);
+
 
 		archive.writeToFile(Paths.get(srcFolder, sFileName + ".omex").toString());