add from/to files and strings for VCML, SBML, Antimony

Author: jcschaff

pyvcell/vcml/__init__.py

@@ -70,7 +70,7 @@ def load_antimony_str(antimony_str: str) -> Biomodel:
         raise ValueError("Error loading model:", antimony.getLastError())
 
 
-def load_antimony_file(antimony_file: PathLike[str]) -> Biomodel:
+def load_antimony_file(antimony_file: PathLike[str] | str) -> Biomodel:
     import antimony  # ignore
 
     antimony_success = antimony.loadAntimonyFile(antimony_file)
@@ -81,12 +81,49 @@ def load_antimony_file(antimony_file: PathLike[str]) -> Biomodel:
         raise ValueError("Error loading model:", antimony.getLastError())
 
 
-def load_sbml_file(sbml_file: PathLike[str]) -> Biomodel:
+def to_antimony_str(
+    bio_model: Biomodel, application_name: str | None = None, round_trip_validation: bool = True
+) -> str:
+    sbml_str = to_sbml_str(bio_model, application_name, round_trip_validation=round_trip_validation)
+    import antimony
+
+    antimony_success = antimony.loadSBMLString(sbml_str)
+    if antimony_success != -1:
+        antimony_str = str(antimony.getAntimonyString())
+        return antimony_str
+    else:
+        raise ValueError("Error converting SBML to Antimony:", antimony.getLastError())
+
+
+def write_antimony_file(bio_model: Biomodel, antimony_file: PathLike[str] | str) -> None:
+    antimony_str = to_antimony_str(bio_model)
+    with open(antimony_file, "w") as f:
+        f.write(antimony_str)
+
+
+def load_vcml_str(vcml_str: str) -> Biomodel:
+    return VcmlReader.biomodel_from_str(vcml_str)
+
+
+def load_vcml_file(vcml_file: PathLike[str] | str) -> Biomodel:
+    return VcmlReader.biomodel_from_file(vcml_file)
+
+
+def to_vcml_str(bio_model: Biomodel) -> str:
+    vcml_document = VCMLDocument(biomodel=bio_model)
+    vcml_str: str = VcmlWriter().write_vcml(document=vcml_document)
+    return vcml_str
+
+
+def write_vcml_file(bio_model: Biomodel, vcml_file: PathLike[str] | str) -> None:
+    vcml_document = VCMLDocument(biomodel=bio_model)
+    VcmlWriter.write_to_file(vcml_document=vcml_document, file_path=vcml_file)
+
+
+def load_sbml_str(sbml_str: str) -> Biomodel:
     import libvcell
 
     with tempfile.TemporaryDirectory() as tempdir:
-        with open(sbml_file) as f:
-            sbml_str = f.read()
         vcml_path = Path(tempdir) / "model.vcml"
         vc_success, vc_errmsg = libvcell.sbml_to_vcml(sbml_content=sbml_str, vcml_file_path=vcml_path)
         if vc_success:
@@ -95,10 +132,12 @@ def load_sbml_file(sbml_file: PathLike[str]) -> Biomodel:
             raise ValueError("Error loading model:", vc_errmsg)
 
 
-def load_sbml_str(sbml_str: str) -> Biomodel:
+def load_sbml_file(sbml_file: PathLike[str] | str) -> Biomodel:
     import libvcell
 
     with tempfile.TemporaryDirectory() as tempdir:
+        with open(sbml_file) as f:
+            sbml_str = f.read()
         vcml_path = Path(tempdir) / "model.vcml"
         vc_success, vc_errmsg = libvcell.sbml_to_vcml(sbml_content=sbml_str, vcml_file_path=vcml_path)
         if vc_success:
@@ -107,15 +146,43 @@ def load_sbml_str(sbml_str: str) -> Biomodel:
             raise ValueError("Error loading model:", vc_errmsg)
 
 
-def write_vcml_file(bio_model: Biomodel, vcml_file: PathLike[str]) -> None:
-    vcml_document = VCMLDocument(biomodel=bio_model)
-    VcmlWriter.write_to_file(vcml_document=vcml_document, file_path=vcml_file)
-
+def to_sbml_str(bio_model: Biomodel, application_name: str | None = None, round_trip_validation: bool = True) -> str:
+    import libvcell
 
-def to_vcml_str(bio_model: Biomodel) -> str:
+    if application_name is None:
+        if len(bio_model.applications) == 0:
+            raise ValueError("sbml export from biomodel needs a biomodel application")
+        if len(bio_model.applications) > 1:
+            raise ValueError("Application must have exactly one application")
+        application_name = bio_model.applications[0].name
+    elif application_name not in [app.name for app in bio_model.applications]:
+        raise ValueError(f"Application '{application_name}' not found in biomodel")
     vcml_document = VCMLDocument(biomodel=bio_model)
     vcml_str: str = VcmlWriter().write_vcml(document=vcml_document)
-    return vcml_str
+    with tempfile.TemporaryDirectory() as tempdir:
+        sbml_path = Path(tempdir) / "model.sbml"
+        success, msg = libvcell.vcml_to_sbml(
+            vcml_content=vcml_str,
+            application_name=application_name,
+            sbml_file_path=sbml_path,
+            round_trip_validation=round_trip_validation,
+        )
+        if not success:
+            raise ValueError("Error converting VCML to SBML:", msg)
+        with open(sbml_path) as f:
+            sbml_str = f.read()
+        return sbml_str
+
+
+def write_sbml_file(
+    bio_model: Biomodel,
+    sbml_file: PathLike[str] | str,
+    application_name: str | None = None,
+    round_trip_validation: bool = True,
+) -> None:
+    sbml_str = to_sbml_str(bio_model, application_name, round_trip_validation)
+    with open(sbml_file, "w") as f:
+        f.write(sbml_str)
 
 
 def refresh_biomodel(bio_model: Biomodel) -> Biomodel: