cleanup API error handling

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

@@ -59,11 +59,16 @@ jobs:
           mkdir -p dist
           cp wheelhouse/*.whl dist/
 
-      - name: Publish to PyPI
+      - name: Publish to PyPI (dry run)
         run: |
           poetry config pypi-token.pypi "${{ secrets.PYPI_TOKEN }}"
           poetry publish --dry-run
+
+      - name: Publish to PyPI (release-only - push to PyPI)
+        run: |
+          poetry config pypi-token.pypi "${{ secrets.PYPI_TOKEN }}"
           poetry publish --skip-existing
+        if: github.event_name == 'release'
 
       - name: Setup tmate
         if: failure()

build.py

@@ -30,7 +30,9 @@ def main() -> None:
     run_command(
         "java -agentlib:native-image-agent=config-output-dir=target/recording "
         "-jar target/vcell-native-1.0-SNAPSHOT.jar "
-        "src/test/resources/TinySpacialProject_Application0.xml "
+        "src/test/resources/TinySpatialProject_Application0.xml "
+        "src/test/resources/TinySpatialProject_Application0.vcml "
+        "Simulation0 "
         "target/sbml-input",
         cwd=vcell_native_dir,
     )

docs/modules.md

@@ -1,5 +1,21 @@
 # Modules
 
-## libvcell.libvcell
+## libvcell
 
-::: libvcell.libvcell
+::: libvcell
+
+# Modules
+
+## libvcell
+
+::: libvcell
+
+### Functions
+
+#### sbml_to_finite_volume_input
+
+::: libvcell.solver_utils.sbml_to_finite_volume_input
+
+#### vcml_to_finite_volume_input
+
+::: libvcell.solver_utils.vcml_to_finite_volume_input

libvcell/__init__.py

@@ -0,0 +1,3 @@
+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"]

libvcell/solver_utils.py

@@ -0,0 +1,36 @@
+from pathlib import Path
+
+from libvcell._internal.native_calls import ReturnValue, VCellNativeCalls
+
+
+def vcml_to_finite_volume_input(vcml_content: str, simulation_name: str, output_dir_path: Path) -> tuple[bool, str]:
+    """
+    Convert VCML content to finite volume input files
+
+    Args:
+        vcml_content (str): VCML content
+        simulation_name (str): simulation name
+        output_dir_path (Path): output directory path
+
+    Returns:
+        tuple[bool, str]: A tuple containing the success status and a message
+    """
+    native = VCellNativeCalls()
+    return_value: ReturnValue = native.vcml_to_finite_volume_input(vcml_content, simulation_name, output_dir_path)
+    return return_value.success, return_value.message
+
+
+def sbml_to_finite_volume_input(sbml_content: str, output_dir_path: Path) -> tuple[bool, str]:
+    """
+    Convert SBML content to finite volume input files
+
+    Args:
+        sbml_content (str): SBML content
+        output_dir_path (Path): output directory path
+
+    Returns:
+        tuple[bool, str]: A tuple containing the success status and a message
+    """
+    native = VCellNativeCalls()
+    return_value: ReturnValue = native.sbml_to_finite_volume_input(sbml_content, output_dir_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 = "0.0.4"
+version = "0.0.5"
 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"

scripts/build_native.sh → scripts/local_build_native.sh

@@ -33,7 +33,9 @@ mvn clean install
 # run with native-image-agent to record configuration for native-image
 java -agentlib:native-image-agent=config-output-dir=target/recording \
      -jar target/vcell-native-1.0-SNAPSHOT.jar \
-     "$ROOT_DIR/vcell-native/src/test/resources/TinySpacialProject_Application0.xml" \
+     "$ROOT_DIR/vcell-native/src/test/resources/TinySpatialProject_Application0.xml" \
+     "$ROOT_DIR/vcell-native/src/test/resources/TinySpatialProject_Application0.vcml" \
+     "Simulation0" \
      "$ROOT_DIR/vcell-native/target/sbml-input"
 
 # build vcell-native as native shared object library

tests/test_libvcell.py

@@ -1,17 +1,21 @@
 from pathlib import Path
 
-from libvcell.libvcell import libvcell
+from libvcell import sbml_to_finite_volume_input, vcml_to_finite_volume_input
 
 
 def test_vcml_to_finite_volume_input(temp_output_dir: Path, vcml_file_path: Path, vcml_sim_name: str) -> None:
     vcml_content = vcml_file_path.read_text()
-    libvcell.vcml_to_finite_volume_input(
+    success, msg = vcml_to_finite_volume_input(
         vcml_content=vcml_content, simulation_name=vcml_sim_name, output_dir_path=temp_output_dir
     )
     assert len(list(temp_output_dir.iterdir())) > 0
+    assert success is True
+    assert msg == "Success"
 
 
 def test_sbml_to_finite_volume_input(temp_output_dir: Path, sbml_file_path: Path, vcml_sim_name: str) -> None:
     sbml_content = sbml_file_path.read_text()
-    libvcell.sbml_to_finite_volume_input(sbml_content=sbml_content, output_dir_path=temp_output_dir)
+    success, msg = sbml_to_finite_volume_input(sbml_content=sbml_content, output_dir_path=temp_output_dir)
     assert len(list(temp_output_dir.iterdir())) > 0
+    assert success is True
+    assert msg == "Success"

vcell-native/pom.xml

@@ -23,7 +23,7 @@
     <maven.compiler.source>${java.specification.version}</maven.compiler.source>
     <maven.compiler.target>${java.specification.version}</maven.compiler.target>
     <imageName>libvcell</imageName>
-    <mainClass>org.vcell.libvcell.Entrypoints</mainClass>
+    <mainClass>org.vcell.libvcell.MainRecorder</mainClass>
 </properties>
 
 <dependencies>

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

@@ -1,38 +1,19 @@
 package org.vcell.libvcell;
 
-import cbit.util.xml.VCLoggerException;
-import cbit.vcell.biomodel.BioModel;
-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.resource.PropertyLoader;
-import cbit.vcell.solver.Simulation;
-import cbit.vcell.solver.SolverException;
-import cbit.vcell.solver.TimeBounds;
-import cbit.vcell.solver.UniformOutputTimeSpec;
-import cbit.vcell.xml.XMLSource;
-import cbit.vcell.xml.XmlHelper;
-import cbit.vcell.xml.XmlParseException;
 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.CTypeConversion;
 import org.json.simple.JSONValue;
-import org.vcell.sbml.FiniteVolumeRunUtil;
-import org.vcell.sbml.vcell.SBMLExporter;
-import org.vcell.sbml.vcell.SBMLImporter;
 
-import java.beans.PropertyVetoException;
-import java.io.ByteArrayInputStream;
 import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStream;
 import java.util.concurrent.ConcurrentHashMap;
 
+import static org.vcell.libvcell.SolverUtils.sbmlToFiniteVolumeInput;
+import static org.vcell.libvcell.SolverUtils.vcmlToFiniteVolumeInput;
+
 
 public class Entrypoints {
     private static final Logger logger = LogManager.getLogger(Entrypoints.class);
@@ -50,7 +31,7 @@ private static CCharPointer createString(String str) {
 
     @CEntryPoint(name = "freeString", documentation = "Release memory allocated for a string")
     public static void freeString(
-            IsolateThread thread,
+            IsolateThread ignoredThread,
             CCharPointer ptr) {
         if (ptr.isNonNull()) {
             allocatedMemory.remove(ptr.rawValue());
@@ -75,7 +56,7 @@ public String toJson() {
                       Returns a JSON string with success status and message"""
     )
     public static CCharPointer entrypoint_vcmlToFiniteVolumeInput(
-            IsolateThread thread,
+            IsolateThread ignoredThread,
             CCharPointer vcml_content,
             CCharPointer simulation_name,
             CCharPointer output_dir_path) {
@@ -105,7 +86,7 @@ public static CCharPointer entrypoint_vcmlToFiniteVolumeInput(
                       Returns a JSON string with success status and message"""
     )
     public static CCharPointer entrypoint_sbmlToFiniteVolumeInput(
-            IsolateThread thread,
+            IsolateThread ignoredThread,
             CCharPointer sbml_content,
             CCharPointer output_dir_path) {
         ReturnValue returnValue;
@@ -123,61 +104,4 @@ public static CCharPointer entrypoint_sbmlToFiniteVolumeInput(
         logger.info("Returning from sbmlToFiniteVolumeInput: " + json);
         return createString(json);
     }
-
-
-    public static void vcmlToFiniteVolumeInput(String vcml_content, String simulation_name, File outputDir) throws XmlParseException, MappingException, SolverException, ExpressionException {
-        GeometrySpec.avoidAWTImageCreation = true;
-        VCMongoMessage.enabled = false;
-        BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcml_content));
-        bioModel.updateAll(false);
-        Simulation sim = bioModel.getSimulation(simulation_name);
-        FiniteVolumeRunUtil.writeInputFilesOnly(outputDir, sim);
-    }
-
-
-    public static void sbmlToFiniteVolumeInput(String sbml_content, File outputDir) throws MappingException, PropertyVetoException, SolverException, ExpressionException, VCLoggerException {
-        GeometrySpec.avoidAWTImageCreation = true;
-        VCMongoMessage.enabled = false;
-        SBMLExporter.MemoryVCLogger vcl = new SBMLExporter.MemoryVCLogger();
-        boolean bValidateSBML = true;
-        // input stream from sbml_content String
-        InputStream is = new ByteArrayInputStream(sbml_content.getBytes());
-        SBMLImporter importer = new SBMLImporter(is, vcl, bValidateSBML);
-        BioModel bioModel = importer.getBioModel();
-        bioModel.updateAll(false);
-
-        final double duration = 5.0;  // endpoint arg
-        final double time_step = 0.1;  // endpoint arg
-        //final ISize meshSize = new ISize(10, 10, 10);  // future endpoint arg
-        SimulationContext simContext = bioModel.getSimulationContext(0);
-        Simulation sim = new Simulation(simContext.getMathDescription(), simContext);
-        sim.getSolverTaskDescription().setTimeBounds(new TimeBounds(0.0, duration));
-        sim.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(time_step));
-
-        FiniteVolumeRunUtil.writeInputFilesOnly(outputDir, sim);
-    }
-
-
-
-    // Input Goes as Follows: SBML Input, Output dir
-    //    "/Users/evalencia/Documents/VCell_Repositories/vcell/vcell-rest/src/test/resources/TinySpacialProject_Application0.xml"
-    //    "/Users/evalencia/Documents/VCell_Repositories/vcell/vcell-nativelib/target/sbml-input"
-    public static void main(String[] args) {
-        try {
-            logger.info("Logger logging");
-            PropertyLoader.setProperty(PropertyLoader.vcellServerIDProperty, "none");
-            PropertyLoader.setProperty(PropertyLoader.mongodbDatabase, "none");
-            File sbml_file = new File(args[0]);
-            // read sbml_file and create a string object
-            try (FileInputStream fis = new FileInputStream(sbml_file)) {
-                byte[] data = fis.readAllBytes();
-                logger.info("Read " + data.length + " bytes from " + sbml_file);
-                String sbml_str = new String(data);
-                sbmlToFiniteVolumeInput(sbml_str, new File(args[1]));
-            }
-        } catch (Exception e) {
-            System.out.println(e.getMessage());
-            logger.error("Error processing spatial model", e);
-        }
-    }
-}
+ }

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

@@ -0,0 +1,47 @@
+package org.vcell.libvcell;
+
+import cbit.vcell.resource.PropertyLoader;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.io.File;
+import java.io.FileInputStream;
+
+import static org.vcell.libvcell.SolverUtils.sbmlToFiniteVolumeInput;
+import static org.vcell.libvcell.SolverUtils.vcmlToFiniteVolumeInput;
+
+
+public class MainRecorder {
+    private static final Logger logger = LogManager.getLogger(MainRecorder.class);
+
+    public static void main(String[] args) {
+        try {
+            File sbml_file = new File(args[0]);
+            File vcml_file = new File(args[1]);
+            String vcml_sim_name = args[2];
+            File output_dir = new File(args[3]);
+            logger.info("Logger logging");
+            PropertyLoader.setProperty(PropertyLoader.vcellServerIDProperty, "none");
+            PropertyLoader.setProperty(PropertyLoader.mongodbDatabase, "none");
+
+
+            try (FileInputStream f_sbml = new FileInputStream(sbml_file)) {
+                byte[] data = f_sbml.readAllBytes();
+                logger.info("Read " + data.length + " bytes from " + sbml_file.getAbsolutePath());
+                String sbml_str = new String(data);
+                sbmlToFiniteVolumeInput(sbml_str, output_dir);
+                //vcmlToFiniteVolumeInput(vcml_str, sim_name, new File(args[1]));
+            }
+            // read sbml_file and create a string object
+            try (FileInputStream f_vcml = new FileInputStream(vcml_file)) {
+                byte[] data = f_vcml.readAllBytes();
+                logger.info("Read " + data.length + " bytes from " + vcml_file.getAbsolutePath());
+                String vcml_str = new String(data);
+                vcmlToFiniteVolumeInput(vcml_str, vcml_sim_name, output_dir);
+            }
+        } catch (Exception e) {
+            System.out.println(e.getMessage());
+            logger.error("Error processing spatial model", e);
+        }
+    }
+}