Added python infix functionality

.github/workflows/on-release-main.yml

@@ -10,7 +10,7 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [macos-13, windows-latest, ubuntu-latest, macos-14]
+        os: [macos-15-intel, windows-latest, ubuntu-latest, macos-15]
       fail-fast: false
     runs-on: ${{ matrix.os }}
     defaults:

build.py

@@ -21,12 +21,37 @@ def main() -> None:
     libvcell_lib_dir.mkdir(parents=True, exist_ok=True)
 
     # Build VCell Java project from submodule
+    install_message_1: str = """
+/*  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  */
+ *                                                                                      *
+ *                             Building Original VCell...                               *
+ *                                                                                      *
+/*  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  */
+    """.strip()
+    print(install_message_1)
     run_command("mvn --batch-mode clean install -DskipTests", cwd=vcell_submodule_dir)
 
     # Build vcell-native as Java
+    install_message_2: str = """
+/*  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  */
+ *                                                                                      *
+ *                             Building Lib VCell...                                    *
+ *                                                                                      *
+/*  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  */
+    """.strip()
+    print(install_message_2)
     run_command("mvn --batch-mode clean install", cwd=vcell_native_dir)
 
     # Run with native-image-agent to record configuration for native-image
+    install_message_3: str = """
+/*  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  */
+ *                                                                                      *
+ *                              Run with native-image-agent...                          *
+ *                                                                                      *
+/*  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  */
+    """.strip()
+    print(install_message_3)
+    run_command("echo $(which java) ", cwd=vcell_native_dir)
     run_command(
         "java -agentlib:native-image-agent=config-output-dir=target/recording "
         "-jar target/vcell-native-1.0-SNAPSHOT.jar "
@@ -39,6 +64,14 @@ def main() -> None:
     )
 
     # Build vcell-native as native shared object library
+    install_message_4: str = """
+/*  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  */
+ *                                                                                      *
+ *                                 Rebuild as shared DLL...                             *
+ *                                                                                      *
+/*  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  */
+    """.strip()
+    print(install_message_4)
     run_command("mvn --batch-mode package -P shared-dll", cwd=vcell_native_dir)
 
     # Copy the shared library to libvcell/lib

libvcell/__init__.py

@@ -1,4 +1,11 @@
-from libvcell.model_utils import sbml_to_vcml, vcml_to_sbml, vcml_to_vcml
+from libvcell.model_utils import sbml_to_vcml, vcell_infix_to_python_infix, vcml_to_sbml, vcml_to_vcml
 from libvcell.solver_utils import sbml_to_finite_volume_input, vcml_to_finite_volume_input
 
-__all__ = ["vcml_to_finite_volume_input", "sbml_to_finite_volume_input", "sbml_to_vcml", "vcml_to_sbml", "vcml_to_vcml"]
+__all__ = [
+    "vcml_to_finite_volume_input",
+    "sbml_to_finite_volume_input",
+    "sbml_to_vcml",
+    "vcml_to_sbml",
+    "vcml_to_vcml",
+    "vcell_infix_to_python_infix",
+]

libvcell/_internal/native_calls.py

@@ -12,6 +12,11 @@ class ReturnValue(BaseModel):
     message: str
 
 
+class MutableString:
+    def __init__(self, value: str):
+        self.value: str = value
+
+
 class VCellNativeCalls:
     def __init__(self) -> None:
         self.loader = VCellNativeLibraryLoader()
@@ -122,3 +127,41 @@ def vcml_to_vcml(self, vcml_content: str, vcml_file_path: Path) -> ReturnValue:
         except Exception as e:
             logging.exception("Error in vcml_to_vcml()", exc_info=e)
             raise
+
+    def vcell_infix_to_python_infix(
+        self, vcell_infix: str, target_python_infix: MutableString, buffer_size: int | None = None
+    ) -> ReturnValue:
+        try:
+            needed_buffer_size = int(1.5 * len(vcell_infix)) if buffer_size is None else buffer_size
+            buff = ctypes.create_string_buffer(needed_buffer_size)
+            with IsolateManager(self.lib) as isolate_thread:
+                json_ptr = self.lib.vcellInfixToPythonInfix(
+                    isolate_thread, ctypes.c_char_p(vcell_infix.encode("utf-8")), buff, needed_buffer_size
+                )
+            value: bytes | None = ctypes.cast(json_ptr, ctypes.c_char_p).value
+            if value is None:
+                logging.error("Failed to regenerate vcml")
+                return ReturnValue(success=False, message="Failed to generate python infix")
+            json_str = value.decode("utf-8")
+            if "not enough room, need: `" in json_str:
+                if buffer_size is not None:
+                    logging.error("Failed to identify correct buffer size reported by previous error")
+                    return ReturnValue(
+                        success=False, message="Failed to identify correct buffer size reported by previous error"
+                    )
+                # get the size from the error
+                index = json_str.find("not enough room, need: `") + len("not enough room, need: `")
+                end_index = json_str.find("`", index)
+                size_as_string: str = json_str[index:end_index]
+                if not size_as_string.isnumeric():
+                    logging.error("Buffer size reported by previous error is not an integer!")
+                    return ReturnValue(
+                        success=False, message="Buffer size reported by previous error is not an integer!"
+                    )
+                return self.vcell_infix_to_python_infix(vcell_infix, target_python_infix, int(size_as_string))
+            # self.lib.freeString(json_ptr)
+            target_python_infix.value = buff.value.decode("utf-8")
+            return ReturnValue.model_validate_json(json_data=json_str)
+        except Exception as e:
+            logging.exception("Error in vcell_infix_to_python_infix()", exc_info=e)
+            raise

libvcell/_internal/native_utils.py

@@ -53,6 +53,14 @@ def _define_entry_points(self) -> None:
         self.lib.vcmlToVcml.restype = ctypes.c_char_p
         self.lib.vcmlToVcml.argtypes = [ctypes.c_void_p, ctypes.c_char_p, ctypes.c_char_p]
 
+        self.lib.vcellInfixToPythonInfix.restype = ctypes.c_char_p
+        self.lib.vcellInfixToPythonInfix.argtypes = [
+            ctypes.c_void_p,
+            ctypes.c_char_p,
+            ctypes.c_char_p,
+            ctypes.c_longlong,
+        ]
+
         self.lib.freeString.restype = None
         self.lib.freeString.argtypes = [ctypes.c_char_p]
 

libvcell/model_utils.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from libvcell._internal.native_calls import ReturnValue, VCellNativeCalls
+from libvcell._internal.native_calls import MutableString, ReturnValue, VCellNativeCalls
 
 
 def vcml_to_sbml(
@@ -57,3 +57,19 @@ def vcml_to_vcml(vcml_content: str, vcml_file_path: Path) -> tuple[bool, str]:
     native = VCellNativeCalls()
     return_value: ReturnValue = native.vcml_to_vcml(vcml_content=vcml_content, vcml_file_path=vcml_file_path)
     return return_value.success, return_value.message
+
+
+def vcell_infix_to_python_infix(vcell_infix: str) -> tuple[bool, str, str]:
+    """
+    Converts an infix string version of a VCell Native Expression, and converts it to a Python compatible version
+
+    Args:
+        vcell_infix (str): the infix to convert
+
+    Returns:
+        tuple[bool, str, str]: A tuple containing the success status, a message, and the converted infix
+    """
+    native = VCellNativeCalls()
+    target_python_infix = MutableString("")
+    return_value: ReturnValue = native.vcell_infix_to_python_infix(vcell_infix, target_python_infix)
+    return return_value.success, return_value.message, target_python_infix.value

scripts/local_build_native.sh

@@ -11,8 +11,6 @@ echo "ROOT_DIR: $ROOT_DIR"
 cd "$ROOT_DIR"/vcell_submodule || ( echo "'vcell' directory not found" && exit 1 )
 mvn clean install -DskipTests
 
-export JAVA_HOME=$(jenv javahome)
-
 # test if JAVA_HOME is set
 if [ -z "$JAVA_HOME" ]; then
   echo "JAVA_HOME is not set"

tests/test_libvcell.py

@@ -1,7 +1,14 @@
 import tempfile
 from pathlib import Path
 
-from libvcell import sbml_to_finite_volume_input, sbml_to_vcml, vcml_to_finite_volume_input, vcml_to_sbml, vcml_to_vcml
+from libvcell import (
+    sbml_to_finite_volume_input,
+    sbml_to_vcml,
+    vcell_infix_to_python_infix,
+    vcml_to_finite_volume_input,
+    vcml_to_sbml,
+    vcml_to_vcml,
+)
 
 
 def test_vcml_to_finite_volume_input(temp_output_dir: Path, vcml_file_path: Path, vcml_sim_name: str) -> None:
@@ -74,3 +81,18 @@ def test_vcml_to_vcml(vcml_file_path: Path) -> None:
         assert vcml_file_path.exists()
         assert success is True
         assert msg == "Success"
+
+
+def test_vcell_infix_to_python_infix() -> None:
+    vcell_infix = "id_1 * csc(id_0 ^ 2.2)"
+    success, msg, value = vcell_infix_to_python_infix(vcell_infix)
+    expectedResult = "(id_1 * (1.0/math.sin(((id_0)**(2.2)))))"
+    assert success is True
+    assert msg == "Success"
+    assert value == expectedResult
+
+
+def test_bad_vcell_infix() -> None:
+    vcellInfix = "id_1 / + / /-  cos(/ / /) id_2"
+    success, msg, value = vcell_infix_to_python_infix(vcellInfix)
+    assert success is False

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

@@ -1,22 +1,24 @@
 package org.vcell.libvcell;
 
+import cbit.vcell.parser.Expression;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.graalvm.nativeimage.IsolateThread;
 import org.graalvm.nativeimage.c.function.CEntryPoint;
 import org.graalvm.nativeimage.c.type.CCharPointer;
+import org.graalvm.nativeimage.c.type.CIntPointer;
 import org.graalvm.nativeimage.c.type.CTypeConversion;
+import org.graalvm.word.UnsignedWord;
+import org.graalvm.word.WordFactory;
 import org.json.simple.JSONValue;
 
 import java.io.File;
 import java.nio.file.Path;
 import java.util.concurrent.ConcurrentHashMap;
 
+import static org.vcell.libvcell.ModelUtils.*;
 import static org.vcell.libvcell.SolverUtils.sbmlToFiniteVolumeInput;
 import static org.vcell.libvcell.SolverUtils.vcmlToFiniteVolumeInput;
-import static org.vcell.libvcell.ModelUtils.vcml_to_sbml;
-import static org.vcell.libvcell.ModelUtils.sbml_to_vcml;
-import static org.vcell.libvcell.ModelUtils.vcml_to_vcml;
 
 
 public class Entrypoints {
@@ -201,4 +203,41 @@ public static CCharPointer entrypoint_vcmlToVcml(
         return createString(json);
     }
 
+	@CEntryPoint(
+			name = "vcellInfixToPythonInfix",
+			documentation = """
+                    converts a vcell infix into a python-safe version"""
+	)
+	public static CCharPointer entrypoint_vcellInfixToPythonInfix(
+			IsolateThread ignoredThread,
+			CCharPointer vcellInfixPtr,
+			CCharPointer targetBufferForPythonInfix,
+			long sizeOfBuffer
+	){
+		System.err.println("Entrypoint_vcellInfixToPythonInfix");
+		ReturnValue returnValue;
+		try {
+			String vcellInfix = CTypeConversion.toJavaString(vcellInfixPtr);
+			String pythonInfix = get_python_infix(vcellInfix);
+			if (pythonInfix.length() >= sizeOfBuffer){
+				// not enough room
+				returnValue = new ReturnValue(false, "not enough room, need: `" + pythonInfix.length() + 1 + "`");
+			} else {
+				CTypeConversion.toCString(
+						pythonInfix,
+						targetBufferForPythonInfix,
+						WordFactory.unsigned(pythonInfix.length() + 1)
+				);
+				returnValue = new ReturnValue(true, "Success");
+			}
+		} catch (Throwable t) {
+			logger.error("Error translating vcell infix to python infix", t);
+			returnValue = new ReturnValue(false, t.getMessage());
+		}
+		// return result as a json string
+		String json = returnValue.toJson();
+		logger.info("Returning from vcellInfixToPythonInfix: " + json);
+		return createString(json);
+	}
+
 }

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

@@ -11,6 +11,7 @@
 import cbit.vcell.mapping.MappingException;
 import cbit.vcell.mapping.SimulationContext;
 import cbit.vcell.mongodb.VCMongoMessage;
+import cbit.vcell.parser.Expression;
 import cbit.vcell.parser.ExpressionException;
 import cbit.vcell.xml.XMLSource;
 import cbit.vcell.xml.XmlHelper;
@@ -34,8 +35,8 @@ public static void sbml_to_vcml(String sbml_content, Path vcmlPath)
             throws VCLoggerException, XmlParseException, IOException, MappingException {
 
         GeometrySpec.avoidAWTImageCreation = true;
+	    XmlHelper.cloneUsingXML = true;
         VCMongoMessage.enabled = false;
-        XmlHelper.cloneUsingXML = true;
 
         record LoggerMessage(VCLogger.Priority priority, VCLogger.ErrorType errorType, String message) {};
         final ArrayList<LoggerMessage> messages = new ArrayList<>();
@@ -76,8 +77,8 @@ record LoggerMessage(VCLogger.Priority priority, VCLogger.ErrorType errorType, S
     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;
+	    XmlHelper.cloneUsingXML = true;
         VCMongoMessage.enabled = false;
-        XmlHelper.cloneUsingXML = true;
 
         BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcml_content));
         bioModel.updateAll(false);
@@ -116,13 +117,20 @@ public static void vcml_to_sbml(String vcml_content, String applicationName, Pat
 
     public static void vcml_to_vcml(String vcml_content, Path vcmlPath) throws XmlParseException, IOException, MappingException {
         GeometrySpec.avoidAWTImageCreation = true;
+	    XmlHelper.cloneUsingXML = true;
         VCMongoMessage.enabled = false;
-        XmlHelper.cloneUsingXML = true;
 
         BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcml_content));
         bioModel.updateAll(false);
         // write the BioModel to a VCML file
         String vcml_str = XmlHelper.bioModelToXML(bioModel);
         XmlUtil.writeXMLStringToFile(vcml_str, vcmlPath.toFile().getAbsolutePath(), true);
     }
+
+	public static String get_python_infix(String vcellInfix) throws ExpressionException {
+		GeometrySpec.avoidAWTImageCreation = true;
+		XmlHelper.cloneUsingXML = true;
+		VCMongoMessage.enabled = false;
+		return new Expression(vcellInfix).infix_Python();
+	}
 }

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

@@ -40,8 +40,8 @@ public class SolverUtils {
 
     public static void vcmlToFiniteVolumeInput(String vcml_content, String simulation_name, File parentDir, File outputDir) throws XmlParseException, MappingException, SolverException, ExpressionException, MathException {
         GeometrySpec.avoidAWTImageCreation = true;
+	    XmlHelper.cloneUsingXML = true;
         VCMongoMessage.enabled = false;
-        XmlHelper.cloneUsingXML = true;
 
         if (vcml_content.substring(0, 300).contains("<sbml xmlns=\"http://www.sbml.org/sbml")) {
             throw new IllegalArgumentException("expecting VCML content, not SBML");
@@ -135,8 +135,8 @@ private static FieldDataIdentifierSpec[] getFieldDataIdentifierSpecs(Simulation
 
     public static void sbmlToFiniteVolumeInput(String sbml_content, File outputDir) throws MappingException, PropertyVetoException, SolverException, ExpressionException, VCLoggerException {
         GeometrySpec.avoidAWTImageCreation = true;
+	    XmlHelper.cloneUsingXML = true;
         VCMongoMessage.enabled = false;
-        XmlHelper.cloneUsingXML = true;
 
         SBMLExporter.MemoryVCLogger vcl = new SBMLExporter.MemoryVCLogger();
         boolean bValidateSBML = true;

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

@@ -59,4 +59,32 @@ public void test_vcml_to_vcml() throws MappingException, IOException, XmlParseEx
         assert(vcml_temp_file.exists());
     }
 
+	@Test
+	public void test_get_python_infix(){
+		String vcellInfix = "id_1 * csc(id_0 ^ 2.2)";
+		String pythonInfix;
+		try {
+			pythonInfix = get_python_infix(vcellInfix);
+		} catch (ExpressionException e) {
+			System.err.println("get_python_infix exception: " + e.getMessage());
+			assert(false);
+			return;
+		}
+		String expected = "(id_1 * (1.0/math.sin(((id_0)**(2.2)))))";
+		assert expected.equals(pythonInfix);
+	}
+
+	@Test
+	public void test_bad_python_infix_attempt(){
+		String vcellInfix = "id_1 / + / /-  cos(/ / /) id_2";
+		String pythonInfix;
+		try {
+			pythonInfix = get_python_infix(vcellInfix);
+		} catch (ExpressionException e) {
+			return; // this is what we'd expect
+		}
+		System.err.println("test_bad_python_infix_attempt did not throw an exception");
+		assert(false);
+	}
+
 }