Merge pull request #6 from virtualcell/sbml-import-export

jcschaff · web-flow · commit 3ae5e81716f9 · 2025-04-04T09:55:27.000-04:00
sbml and vcml file import/export/validation
diff --git a/build.py b/build.py
@@ -33,6 +33,7 @@ def main() -> None:
         "src/test/resources/TinySpatialProject_Application0.xml "
         "src/test/resources/TinySpatialProject_Application0.vcml "
         "Simulation0 "
+        "unnamed_spatialGeom "
         "target/sbml-input",
         cwd=vcell_native_dir,
     )
diff --git a/libvcell/__init__.py b/libvcell/__init__.py
@@ -1,3 +1,4 @@
+from libvcell.model_utils import sbml_to_vcml, 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"]
+__all__ = ["vcml_to_finite_volume_input", "sbml_to_finite_volume_input", "sbml_to_vcml", "vcml_to_sbml", "vcml_to_vcml"]
diff --git a/libvcell/_internal/native_calls.py b/libvcell/_internal/native_calls.py
@@ -58,3 +58,64 @@ def sbml_to_finite_volume_input(self, sbml_content: str, output_dir_path: Path)
         except Exception as e:
             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:
+        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")),
+                )
+
+            value: bytes | None = ctypes.cast(json_ptr, ctypes.c_char_p).value
+            if value is None:
+                logging.error("Failed to convert vcml application to sbml")
+                return ReturnValue(success=False, message="Failed to convert vcml to sbml")
+            json_str: str = value.decode("utf-8")
+            # self.lib.freeString(json_ptr)
+            return ReturnValue.model_validate_json(json_data=json_str)
+        except Exception as e:
+            logging.exception("Error in vcml_to_sbml()", exc_info=e)
+            raise
+
+    def sbml_to_vcml(self, sbml_content: str, vcml_file_path: Path) -> ReturnValue:
+        try:
+            with IsolateManager(self.lib) as isolate_thread:
+                json_ptr: ctypes.c_char_p = self.lib.sbmlToVcml(
+                    isolate_thread,
+                    ctypes.c_char_p(sbml_content.encode("utf-8")),
+                    ctypes.c_char_p(str(vcml_file_path).encode("utf-8")),
+                )
+
+            value: bytes | None = ctypes.cast(json_ptr, ctypes.c_char_p).value
+            if value is None:
+                logging.error("Failed to convert sbml to vcml")
+                return ReturnValue(success=False, message="Failed to convert sbml to vcml")
+            json_str: str = value.decode("utf-8")
+            # self.lib.freeString(json_ptr)
+            return ReturnValue.model_validate_json(json_data=json_str)
+        except Exception as e:
+            logging.exception("Error in sbml_to_vcml()", exc_info=e)
+            raise
+
+    def vcml_to_vcml(self, vcml_content: str, vcml_file_path: Path) -> ReturnValue:
+        try:
+            with IsolateManager(self.lib) as isolate_thread:
+                json_ptr: ctypes.c_char_p = self.lib.vcmlToVcml(
+                    isolate_thread,
+                    ctypes.c_char_p(vcml_content.encode("utf-8")),
+                    ctypes.c_char_p(str(vcml_file_path).encode("utf-8")),
+                )
+
+            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 regenerate vcml")
+            json_str: str = value.decode("utf-8")
+            # self.lib.freeString(json_ptr)
+            return ReturnValue.model_validate_json(json_data=json_str)
+        except Exception as e:
+            logging.exception("Error in vcml_to_vcml()", exc_info=e)
+            raise
diff --git a/libvcell/_internal/native_utils.py b/libvcell/_internal/native_utils.py
@@ -38,6 +38,15 @@ def _define_entry_points(self) -> None:
         self.lib.sbmlToFiniteVolumeInput.restype = ctypes.c_char_p
         self.lib.sbmlToFiniteVolumeInput.argtypes = [ctypes.c_void_p, ctypes.c_char_p, ctypes.c_char_p]
 
+        self.lib.sbmlToVcml.restype = ctypes.c_char_p
+        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.vcmlToVcml.restype = ctypes.c_char_p
+        self.lib.vcmlToVcml.argtypes = [ctypes.c_void_p, ctypes.c_char_p, ctypes.c_char_p]
+
         self.lib.freeString.restype = None
         self.lib.freeString.argtypes = [ctypes.c_char_p]
 
diff --git a/libvcell/model_utils.py b/libvcell/model_utils.py
@@ -0,0 +1,52 @@
+from pathlib import Path
+
+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]:
+    """
+    Convert VCML content to SBML file
+
+    Args:
+        vcml_content (str): VCML content
+        application_name (str): VCell Biomodel application name
+        sbml_file_path (Path): path to resulting SBML file
+
+    Returns:
+        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 return_value.success, return_value.message
+
+
+def sbml_to_vcml(sbml_content: str, vcml_file_path: Path) -> tuple[bool, str]:
+    """
+    Convert SBML content to finite volume input files
+
+    Args:
+        sbml_content (str): SBML content
+        vcml_file_path (Path): path to resulting VCML file
+
+    Returns:
+        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 return_value.success, return_value.message
+
+
+def vcml_to_vcml(vcml_content: str, vcml_file_path: Path) -> tuple[bool, str]:
+    """
+    Process VCML content to regenerated VCML file
+
+    Args:
+        vcml_content (str): VCML content
+        vcml_file_path (Path): path to resulting VCML file
+
+    Returns:
+        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 return_value.success, return_value.message
diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "libvcell"
-version = "0.0.8"
+version = "0.0.9"
 description = "This is a python package which wraps a subset of VCell Java code as a native python package."
 authors = ["Jim Schaff <schaff@uchc.edu>", "Ezequiel Valencia <evalencia@uchc.edu>"]
 repository = "https://github.com/virtualcell/libvcell"
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1 +1,7 @@
-from tests.fixtures.data_fixtures import sbml_file_path, temp_output_dir, vcml_file_path, vcml_sim_name  # noqa: F401
+from tests.fixtures.data_fixtures import (  # noqa: F401
+    sbml_file_path,
+    temp_output_dir,
+    vcml_app_name,
+    vcml_file_path,
+    vcml_sim_name,
+)
diff --git a/tests/fixtures/data_fixtures.py b/tests/fixtures/data_fixtures.py
@@ -18,6 +18,11 @@ def vcml_sim_name() -> str:
     return "Simulation0"
 
 
+@pytest.fixture
+def vcml_app_name() -> str:
+    return "unnamed_spatialGeom"
+
+
 @pytest.fixture
 def sbml_file_path() -> Path:
     return fixtures_dir / "TinySpatialProject_Application0.xml"
diff --git a/tests/test_libvcell.py b/tests/test_libvcell.py
@@ -1,6 +1,7 @@
+import tempfile
 from pathlib import Path
 
-from libvcell import sbml_to_finite_volume_input, vcml_to_finite_volume_input
+from libvcell import sbml_to_finite_volume_input, sbml_to_vcml, 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:
@@ -19,3 +20,38 @@ def test_sbml_to_finite_volume_input(temp_output_dir: Path, sbml_file_path: Path
     assert len(list(temp_output_dir.iterdir())) > 0
     assert success is True
     assert msg == "Success"
+
+
+def test_sbml_to_vcml(sbml_file_path: Path) -> None:
+    sbml_content = sbml_file_path.read_text()
+    with tempfile.TemporaryDirectory() as temp_dir:
+        temp_output_dir = Path(temp_dir)
+        vcml_file_path = temp_output_dir / "test.vcml"
+        success, msg = sbml_to_vcml(sbml_content=sbml_content, vcml_file_path=vcml_file_path)
+        assert vcml_file_path.exists()
+        assert success is True
+        assert msg == "Success"
+
+
+def test_vcml_to_sbml(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
+        )
+        assert sbml_file_path.exists()
+        assert success is True
+        assert msg == "Success"
+
+
+def test_vcml_to_vcml(vcml_file_path: Path) -> None:
+    vcml_content = vcml_file_path.read_text()
+    with tempfile.TemporaryDirectory() as temp_dir:
+        temp_output_dir = Path(temp_dir)
+        vcml_file_path = temp_output_dir / "test.vcml"
+        success, msg = vcml_to_vcml(vcml_content=vcml_content, vcml_file_path=vcml_file_path)
+        assert vcml_file_path.exists()
+        assert success is True
+        assert msg == "Success"
diff --git a/vcell-native/src/main/java/org/vcell/libvcell/Entrypoints.java b/vcell-native/src/main/java/org/vcell/libvcell/Entrypoints.java
@@ -9,10 +9,14 @@
 import org.json.simple.JSONValue;
 
 import java.io.File;
+import java.nio.file.Path;
 import java.util.concurrent.ConcurrentHashMap;
 
 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 {
@@ -52,6 +56,7 @@ public String toJson() {
             documentation = """
                     Converts VCML file into Finite Volume Input files.
                       vcml_content: text of VCML XML document
+                      simulation_name: name of the simulation to convert
                       output_dir_path: path to the output directory (expected to be subdirectory of the workspace)
                       Returns a JSON string with success status and message"""
     )
@@ -106,4 +111,92 @@ public static CCharPointer entrypoint_sbmlToFiniteVolumeInput(
         logger.info("Returning from sbmlToFiniteVolumeInput: " + json);
         return createString(json);
     }
- }
+
+    @CEntryPoint(
+            name = "vcmlToSbml",
+            documentation = """
+                    Converts VCML file into an SBML file.
+                      vcml_content: text of VCML XML document
+                      application_name: name of the application to export
+                      sbml_file_path: path to the SBML file to write
+                      Returns a JSON string with success status and message"""
+    )
+    public static CCharPointer entrypoint_vcmlToSbml(
+            IsolateThread ignoredThread,
+            CCharPointer vcml_content,
+            CCharPointer application_name,
+            CCharPointer sbml_file_path) {
+        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);
+            returnValue = new ReturnValue(true, "Success");
+        }catch (Throwable t) {
+            logger.error("Error translating vcml application to sbml", t);
+            returnValue = new ReturnValue(false, t.getMessage());
+        }
+        // return result as a json string
+        String json = returnValue.toJson();
+        logger.info("Returning from vcellToSbml: " + json);
+        return createString(json);
+    }
+
+    @CEntryPoint(
+            name = "sbmlToVcml",
+            documentation = """
+                    Converts SBML file into a VCML file.
+                      sbml_content: text of SBML XML document
+                      vcml_file_path: path to the VCML file to write
+                      Returns a JSON string with success status and message"""
+    )
+    public static CCharPointer entrypoint_sbmlToVcml(
+            IsolateThread ignoredThread,
+            CCharPointer sbml_content,
+            CCharPointer vcml_file_path) {
+        ReturnValue returnValue;
+        try {
+            String sbmlContentStr = CTypeConversion.toJavaString(sbml_content);
+            Path vcmlFilePath = new File(CTypeConversion.toJavaString(vcml_file_path)).toPath();
+            sbml_to_vcml(sbmlContentStr, vcmlFilePath);
+            returnValue = new ReturnValue(true, "Success");
+        }catch (Throwable t) {
+            logger.error("Error translating sbml to vcml", t);
+            returnValue = new ReturnValue(false, t.getMessage());
+        }
+        // return result as a json string
+        String json = returnValue.toJson();
+        logger.info("Returning from sbmlToVcell: " + json);
+        return createString(json);
+    }
+
+    @CEntryPoint(
+            name = "vcmlToVcml",
+            documentation = """
+                    Updates a VCML file into a fully populated VCML file.
+                      vcml_content: text of VCML XML document
+                      vcml_file_path: path to the VCML file to write
+                      Returns a JSON string with success status and message"""
+    )
+    public static CCharPointer entrypoint_vcmlToVcml(
+            IsolateThread ignoredThread,
+            CCharPointer vcml_content,
+            CCharPointer vcml_file_path) {
+        ReturnValue returnValue;
+        try {
+            String vcmlContentStr = CTypeConversion.toJavaString(vcml_content);
+            Path vcmlFilePath = new File(CTypeConversion.toJavaString(vcml_file_path)).toPath();
+            vcml_to_vcml(vcmlContentStr, vcmlFilePath);
+            returnValue = new ReturnValue(true, "Success");
+        }catch (Throwable t) {
+            logger.error("Error refreshing vcml", t);
+            returnValue = new ReturnValue(false, t.getMessage());
+        }
+        // return result as a json string
+        String json = returnValue.toJson();
+        logger.info("Returning from vcellToVcml: " + json);
+        return createString(json);
+    }
+
+}
diff --git a/vcell-native/src/main/java/org/vcell/libvcell/MainRecorder.java b/vcell-native/src/main/java/org/vcell/libvcell/MainRecorder.java
diff --git a/vcell-native/src/main/java/org/vcell/libvcell/ModelUtils.java b/vcell-native/src/main/java/org/vcell/libvcell/ModelUtils.java
diff --git a/vcell-native/src/test/java/org/vcell/libvcell/EntrypointsTest.java b/vcell-native/src/test/java/org/vcell/libvcell/EntrypointsTest.java

Original file line number	Diff line number	Diff line change
`@@ -33,6 +33,7 @@ def main() -> None:`
`33`	`33`	`"src/test/resources/TinySpatialProject_Application0.xml "`
`34`	`34`	`"src/test/resources/TinySpatialProject_Application0.vcml "`
`35`	`35`	`"Simulation0 "`
	`36`	`+ "unnamed_spatialGeom "`
`36`	`37`	`"target/sbml-input",`
`37`	`38`	`cwd=vcell_native_dir,`
`38`	`39`	`)`