Sbml model enhancements (#333)

* - allow to initialize from sbml str

* - disambiguate between warning and errors

Author: fbergmann

petab/v1/models/sbml_model.py

@@ -81,6 +81,22 @@ def from_file(filepath_or_buffer, model_id: str = None):
             model_id=model_id,
         )
 
+    @staticmethod
+    def from_string(sbml_string, model_id: str = None):
+        sbml_reader, sbml_document, sbml_model = load_sbml_from_string(
+            sbml_string
+        )
+
+        if not model_id:
+            model_id = sbml_model.getIdAttribute()
+
+        return SbmlModel(
+            sbml_model=sbml_model,
+            sbml_reader=sbml_reader,
+            sbml_document=sbml_document,
+            model_id=model_id,
+        )
+
     @property
     def model_id(self):
         return self._model_id

petab/v1/sbml.py

@@ -43,12 +43,18 @@ def is_sbml_consistent(
             libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, False
         )
 
-    has_problems = sbml_document.checkConsistency()
-    if has_problems:
+    has_issues = sbml_document.checkConsistency()
+
+    # we only have an issue with errors or fatals
+    has_problems = sbml_document.getNumErrors(
+        libsbml.LIBSBML_SEV_ERROR
+    ) + sbml_document.getNumErrors(libsbml.LIBSBML_SEV_FATAL)
+    if has_issues:
         log_sbml_errors(sbml_document)
-        logger.warning(
-            "WARNING: Generated invalid SBML model. Check messages above."
-        )
+        if has_problems:
+            logger.warning(
+                "WARNING: Generated invalid SBML model. Check messages above."
+            )
 
     return not has_problems