Merge pull request #8 from virtualcell/round-trip-validation

export SBML with compatable units and optional validation

Author: jcschaff

libvcell/_internal/native_calls.py

@@ -59,14 +59,17 @@ def sbml_to_finite_volume_input(self, sbml_content: str, output_dir_path: Path)
             logging.exception("Error in sbml_to_finite_volume_input()", exc_info=e)
             raise
 
-    def vcml_to_sbml(self, vcml_content: str, application_name: str, sbml_file_path: Path) -> ReturnValue:
+    def vcml_to_sbml(
+        self, vcml_content: str, application_name: str, sbml_file_path: Path, round_trip_validation: bool
+    ) -> ReturnValue:
         try:
             with IsolateManager(self.lib) as isolate_thread:
                 json_ptr: ctypes.c_char_p = self.lib.vcmlToSbml(
                     isolate_thread,
                     ctypes.c_char_p(vcml_content.encode("utf-8")),
                     ctypes.c_char_p(application_name.encode("utf-8")),
                     ctypes.c_char_p(str(sbml_file_path).encode("utf-8")),
+                    ctypes.c_int(int(round_trip_validation)),
                 )
 
             value: bytes | None = ctypes.cast(json_ptr, ctypes.c_char_p).value

libvcell/_internal/native_utils.py

@@ -42,7 +42,13 @@ def _define_entry_points(self) -> None:
         self.lib.sbmlToVcml.argtypes = [ctypes.c_void_p, ctypes.c_char_p, ctypes.c_char_p]
 
         self.lib.vcmlToSbml.restype = ctypes.c_char_p
-        self.lib.vcmlToSbml.argtypes = [ctypes.c_void_p, ctypes.c_char_p, ctypes.c_char_p, ctypes.c_char_p]
+        self.lib.vcmlToSbml.argtypes = [
+            ctypes.c_void_p,
+            ctypes.c_char_p,
+            ctypes.c_char_p,
+            ctypes.c_char_p,
+            ctypes.c_int,
+        ]
 
         self.lib.vcmlToVcml.restype = ctypes.c_char_p
         self.lib.vcmlToVcml.argtypes = [ctypes.c_void_p, ctypes.c_char_p, ctypes.c_char_p]

libvcell/model_utils.py

@@ -3,7 +3,9 @@
 from libvcell._internal.native_calls import ReturnValue, VCellNativeCalls
 
 
-def vcml_to_sbml(vcml_content: str, application_name: str, sbml_file_path: Path) -> tuple[bool, str]:
+def vcml_to_sbml(
+    vcml_content: str, application_name: str, sbml_file_path: Path, round_trip_validation: bool
+) -> tuple[bool, str]:
     """
     Convert VCML content to SBML file
 
@@ -16,7 +18,12 @@ def vcml_to_sbml(vcml_content: str, application_name: str, sbml_file_path: Path)
         tuple[bool, str]: A tuple containing the success status and a message
     """
     native = VCellNativeCalls()
-    return_value: ReturnValue = native.vcml_to_sbml(vcml_content, application_name, sbml_file_path)
+    return_value: ReturnValue = native.vcml_to_sbml(
+        vcml_content=vcml_content,
+        application_name=application_name,
+        sbml_file_path=sbml_file_path,
+        round_trip_validation=round_trip_validation,
+    )
     return return_value.success, return_value.message
 
 
@@ -32,7 +39,7 @@ def sbml_to_vcml(sbml_content: str, vcml_file_path: Path) -> tuple[bool, str]:
         tuple[bool, str]: A tuple containing the success status and a message
     """
     native = VCellNativeCalls()
-    return_value: ReturnValue = native.sbml_to_vcml(sbml_content, vcml_file_path)
+    return_value: ReturnValue = native.sbml_to_vcml(sbml_content=sbml_content, vcml_file_path=vcml_file_path)
     return return_value.success, return_value.message
 
 
@@ -48,5 +55,5 @@ def vcml_to_vcml(vcml_content: str, vcml_file_path: Path) -> tuple[bool, str]:
         tuple[bool, str]: A tuple containing the success status and a message
     """
     native = VCellNativeCalls()
-    return_value: ReturnValue = native.vcml_to_vcml(vcml_content, vcml_file_path)
+    return_value: ReturnValue = native.vcml_to_vcml(vcml_content=vcml_content, vcml_file_path=vcml_file_path)
     return return_value.success, return_value.message

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "libvcell"
-version = "0.0.10"
+version = "0.0.11"
 description = "This is a python package which wraps a subset of VCell Java code as a native python package."
 authors = ["Jim Schaff <[email protected]>", "Ezequiel Valencia <[email protected]>"]
 repository = "https://github.com/virtualcell/libvcell"

tests/test_libvcell.py

@@ -33,13 +33,32 @@ def test_sbml_to_vcml(sbml_file_path: Path) -> None:
         assert msg == "Success"
 
 
-def test_vcml_to_sbml(vcml_file_path: Path, vcml_app_name: str) -> None:
+def test_vcml_to_sbml_with_validation(vcml_file_path: Path, vcml_app_name: str) -> None:
     vcml_content = vcml_file_path.read_text()
     with tempfile.TemporaryDirectory() as temp_dir:
         temp_output_dir = Path(temp_dir)
         sbml_file_path = temp_output_dir / "test.sbml"
         success, msg = vcml_to_sbml(
-            vcml_content=vcml_content, application_name=vcml_app_name, sbml_file_path=sbml_file_path
+            vcml_content=vcml_content,
+            application_name=vcml_app_name,
+            sbml_file_path=sbml_file_path,
+            round_trip_validation=True,
+        )
+        assert sbml_file_path.exists()
+        assert success is True
+        assert msg == "Success"
+
+
+def test_vcml_to_sbml_without_validation(vcml_file_path: Path, vcml_app_name: str) -> None:
+    vcml_content = vcml_file_path.read_text()
+    with tempfile.TemporaryDirectory() as temp_dir:
+        temp_output_dir = Path(temp_dir)
+        sbml_file_path = temp_output_dir / "test.sbml"
+        success, msg = vcml_to_sbml(
+            vcml_content=vcml_content,
+            application_name=vcml_app_name,
+            sbml_file_path=sbml_file_path,
+            round_trip_validation=False,
         )
         assert sbml_file_path.exists()
         assert success is True

vcell-native/src/main/java/org/vcell/libvcell/Entrypoints.java

@@ -125,13 +125,15 @@ public static CCharPointer entrypoint_vcmlToSbml(
             IsolateThread ignoredThread,
             CCharPointer vcml_content,
             CCharPointer application_name,
-            CCharPointer sbml_file_path) {
+            CCharPointer sbml_file_path,
+            int roundTripValidation) {
         ReturnValue returnValue;
         try {
             String vcmlContentStr = CTypeConversion.toJavaString(vcml_content);
             String applicationName = CTypeConversion.toJavaString(application_name);
             Path sbmlFilePath = new File(CTypeConversion.toJavaString(sbml_file_path)).toPath();
-            vcml_to_sbml(vcmlContentStr, applicationName, sbmlFilePath);
+            boolean bRoundTripValidation = CTypeConversion.toBoolean(roundTripValidation);
+            vcml_to_sbml(vcmlContentStr, applicationName, sbmlFilePath, bRoundTripValidation);
             returnValue = new ReturnValue(true, "Success");
         }catch (Throwable t) {
             logger.error("Error translating vcml application to sbml", t);

vcell-native/src/main/java/org/vcell/libvcell/MainRecorder.java

@@ -70,7 +70,7 @@ public static void main(String[] args) {
 
                 // create a temporary file for the SBML output
                 File temp_sbml_file = new File(output_dir, "temp.vcml");
-                vcml_to_sbml(vcml_str, vcml_app_name, temp_sbml_file.toPath());
+                vcml_to_sbml(vcml_str, vcml_app_name, temp_sbml_file.toPath(), true);
                 // remove temporary file
                 if (temp_sbml_file.exists()) {
                     boolean deleted = temp_sbml_file.delete();

vcell-native/src/main/java/org/vcell/libvcell/ModelUtils.java

@@ -1,19 +1,25 @@
 package org.vcell.libvcell;
 
+import cbit.image.ImageException;
 import cbit.util.xml.VCLogger;
 import cbit.util.xml.VCLoggerException;
 import cbit.util.xml.XmlUtil;
 import cbit.vcell.biomodel.BioModel;
+import cbit.vcell.biomodel.ModelUnitConverter;
+import cbit.vcell.geometry.GeometryException;
 import cbit.vcell.geometry.GeometrySpec;
 import cbit.vcell.mapping.MappingException;
 import cbit.vcell.mapping.SimulationContext;
 import cbit.vcell.mongodb.VCMongoMessage;
+import cbit.vcell.parser.ExpressionException;
 import cbit.vcell.xml.XMLSource;
 import cbit.vcell.xml.XmlHelper;
 import cbit.vcell.xml.XmlParseException;
 import org.vcell.sbml.SbmlException;
+import org.vcell.sbml.vcell.SBMLAnnotationUtil;
 import org.vcell.sbml.vcell.SBMLExporter;
 import org.vcell.sbml.vcell.SBMLImporter;
+import org.vcell.util.Pair;
 
 import javax.xml.stream.XMLStreamException;
 import java.io.ByteArrayInputStream;
@@ -66,17 +72,43 @@ record LoggerMessage(VCLogger.Priority priority, VCLogger.ErrorType errorType, S
     }
 
 
-    public static void vcml_to_sbml(String vcml_content, String applicationName, Path sbmlPath)
-            throws XmlParseException, IOException, XMLStreamException, SbmlException, MappingException {
+    public static void vcml_to_sbml(String vcml_content, String applicationName, Path sbmlPath, boolean roundTripValidation)
+            throws XmlParseException, IOException, XMLStreamException, SbmlException, MappingException, ImageException, GeometryException, ExpressionException {
         GeometrySpec.avoidAWTImageCreation = true;
         VCMongoMessage.enabled = false;
 
         BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcml_content));
         bioModel.updateAll(false);
-        SimulationContext simContext = bioModel.getSimulationContext(applicationName);
-        boolean validateSBML = true;
-        SBMLExporter sbmlExporter = new SBMLExporter(simContext, 3, 1, validateSBML);
+
+        if (applicationName == null || applicationName.isEmpty()) {
+            throw new RuntimeException("Error: Application name is null or empty");
+        }
+
+        if (bioModel.getSimulationContext(applicationName) == null) {
+            throw new RuntimeException("Error: Simulation context not found for application name: " + applicationName);
+        }
+
+        // change the unit system to SBML preferred units if not already.
+        final BioModel sbmlPreferredUnitsBM;
+        if (!bioModel.getModel().getUnitSystem().compareEqual(ModelUnitConverter.createSbmlModelUnitSystem())) {
+            sbmlPreferredUnitsBM = ModelUnitConverter.createBioModelWithSBMLUnitSystem(bioModel);
+            if(sbmlPreferredUnitsBM == null) {
+                throw new RuntimeException("Unable to clone BioModel with SBML unit system");
+            }
+        } else {
+            sbmlPreferredUnitsBM = bioModel;
+        }
+
+        SimulationContext simContext = sbmlPreferredUnitsBM.getSimulationContext(applicationName);
+
+        int sbml_level = 3;
+        int sbml_version = 1;
+        SBMLExporter sbmlExporter = new SBMLExporter(simContext, sbml_level, sbml_version, roundTripValidation);
         String sbml_string = sbmlExporter.getSBMLString();
+
+        // cleanup the string of all the "sameAs" statements
+        sbml_string = SBMLAnnotationUtil.postProcessCleanup(sbml_string);
+
         XmlUtil.writeXMLStringToFile(sbml_string, sbmlPath.toFile().getAbsolutePath(), true);
     }
 

vcell-native/src/test/java/org/vcell/libvcell/ModelEntrypointsTest.java

@@ -1,7 +1,10 @@
 package org.vcell.libvcell;
 
+import cbit.image.ImageException;
 import cbit.util.xml.VCLoggerException;
+import cbit.vcell.geometry.GeometryException;
 import cbit.vcell.mapping.MappingException;
+import cbit.vcell.parser.ExpressionException;
 import cbit.vcell.xml.XmlParseException;
 import org.junit.jupiter.api.Test;
 import org.vcell.sbml.SbmlException;
@@ -26,13 +29,25 @@ public void test_sbml_to_vcml() throws MappingException, IOException, XmlParseEx
     }
 
     @Test
-    public void test_vcml_to_sbml() throws MappingException, IOException, XmlParseException, XMLStreamException, SbmlException {
+    public void test_vcml_to_sbml_with_round_trip() throws MappingException, IOException, XmlParseException, XMLStreamException, SbmlException, ImageException, GeometryException, ExpressionException {
         String vcmlContent = getFileContentsAsString("/TinySpatialProject_Application0.vcml");
         File parent_dir = Files.createTempDirectory("vcmlToSbml").toFile();
-        File sbml_temp_file = new File(parent_dir, "temp.sbml");
         String applicationName = "unnamed_spatialGeom";
-        vcml_to_sbml(vcmlContent, applicationName, sbml_temp_file.toPath());
-        assert(sbml_temp_file.exists());
+
+        File sbml_temp_file_true = new File(parent_dir, "temp_true.sbml");
+        vcml_to_sbml(vcmlContent, applicationName, sbml_temp_file_true.toPath(), true);
+        assert(sbml_temp_file_true.exists());
+    }
+
+    @Test
+    public void test_vcml_to_sbml_without_round_trip() throws MappingException, IOException, XmlParseException, XMLStreamException, SbmlException, ImageException, GeometryException, ExpressionException {
+        String vcmlContent = getFileContentsAsString("/TinySpatialProject_Application0.vcml");
+        File parent_dir = Files.createTempDirectory("vcmlToSbml").toFile();
+        String applicationName = "unnamed_spatialGeom";
+
+        File sbml_temp_file_false = new File(parent_dir, "temp_false.sbml");
+        vcml_to_sbml(vcmlContent, applicationName, sbml_temp_file_false.toPath(), false);
+        assert(sbml_temp_file_false.exists());
     }
 
     @Test