Merge branch 'develop' into v2_calculate

Author: dweindl

petab/petablint.py

@@ -6,6 +6,7 @@
 import logging
 import sys
 
+import pydantic
 from colorama import Fore
 from colorama import init as init_colorama
 from jsonschema.exceptions import ValidationError as SchemaValidationError
@@ -160,10 +161,23 @@ def main():
         try:
             validate(args.yaml_file_name)
         except SchemaValidationError as e:
+            path = ""
+            if e.absolute_path:
+                # construct a path to the error location inside the YAML file
+                path = list(e.absolute_path)
+                path = (
+                    f" at {path[0]}"
+                    + "".join(f"[{str(p)}]" for p in path[1:])
+                    + ": "
+                )
             logger.error(
-                f"Provided YAML file does not adhere to PEtab schema: {e}"
+                "Provided YAML file does not adhere to the PEtab schema"
+                f"{path}: {e.args[0]}"
             )
             sys.exit(1)
+        except ValueError as e:
+            logger.error(e)
+            sys.exit(1)
 
         if petab.is_composite_problem(args.yaml_file_name):
             # TODO: further checking:
@@ -179,12 +193,24 @@ def main():
             case 2:
                 from petab.v2.lint import lint_problem
 
-                validation_issues = lint_problem(args.yaml_file_name)
-                if validation_issues:
-                    validation_issues.log(logger=logger)
+                try:
+                    validation_issues = lint_problem(args.yaml_file_name)
+                    if validation_issues:
+                        # Handle petab.v2.lint.ValidationTask issues
+                        validation_issues.log(logger=logger)
+                        sys.exit(1)
+                    logger.info("PEtab format check completed successfully.")
+                    sys.exit(0)
+                except pydantic.ValidationError as e:
+                    # Handle Pydantic validation errors
+                    for err in e.errors():
+                        loc = ", ".join(str(loc) for loc in err["loc"])
+                        msg = err["msg"]
+                        # TODO: include model info here once available
+                        #  https://github.com/pydantic/pydantic/issues/7224
+                        logger.error(f"Error in field(s) `{loc}`: {msg}")
                     sys.exit(1)
-                logger.info("PEtab format check completed successfully.")
-                sys.exit(0)
+
             case _:
                 logger.error(
                     "The provided PEtab files are of unsupported version "

petab/v1/yaml.py

@@ -77,16 +77,14 @@ def validate_yaml_syntax(
         #  but let's still use the latest PEtab schema for full validation
         version = yaml_config.get(FORMAT_VERSION, None)
         version = (
-            parse_version(version)[:2]
-            if version
-            else list(SCHEMAS.values())[-1]
+            parse_version(version)[:2] if version else list(SCHEMAS.keys())[-1]
         )
 
         try:
             schema = SCHEMAS[version]
         except KeyError as e:
             raise ValueError(
-                "Unknown PEtab version given in problem "
+                "No or unknown PEtab version given in problem "
                 f"specification: {version}"
             ) from e
     schema = load_yaml(schema)

petab/v2/lint.py

@@ -39,7 +39,6 @@
     "CheckUnusedExperiments",
     "CheckObservablesDoNotShadowModelEntities",
     "CheckUnusedConditions",
-    "CheckAllObservablesDefined",
     "CheckPriorDistribution",
     "lint_problem",
     "default_validation_tasks",
@@ -261,8 +260,9 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         }
         if undefined_observables := (used_observables - defined_observables):
             return ValidationError(
-                f"Observables {undefined_observables} used in "
-                "measurement table but not defined in observable table."
+                f"Observable(s) {undefined_observables} are used in the "
+                "measurement table but are not defined in the observable "
+                "table."
             )
 
         return None
@@ -289,8 +289,8 @@ def run(self, problem: Problem) -> ValidationIssue | None:
                 expected = observable_parameters_count[m.observable_id]
             except KeyError:
                 messages.append(
-                    f"Observable {m.observable_id} used in measurement "
-                    f"table is not defined."
+                    f"Observable {m.observable_id} is used in the measurement "
+                    f"table but is not defined in the observable table."
                 )
                 continue
 
@@ -443,31 +443,6 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         return None
 
 
-class CheckAllObservablesDefined(ValidationTask):
-    """A task to validate that all observables in the measurement table are
-    defined in the observable table."""
-
-    def run(self, problem: Problem) -> ValidationIssue | None:
-        if problem.measurement_df is None:
-            return None
-
-        measurement_df = problem.measurement_df
-        observable_df = problem.observable_df
-        used_observables = set(measurement_df[OBSERVABLE_ID].values)
-        defined_observables = (
-            set(observable_df.index.values)
-            if observable_df is not None
-            else set()
-        )
-        if undefined_observables := (used_observables - defined_observables):
-            return ValidationError(
-                f"Observables {undefined_observables} are used in the"
-                "measurements table but are not defined in observables table."
-            )
-
-        return None
-
-
 class CheckUniquePrimaryKeys(ValidationTask):
     """Check that all primary keys are unique."""
 
@@ -1092,7 +1067,6 @@ def get_placeholders(
     # CheckVisualizationTable(),
     # TODO validate mapping table
     CheckValidParameterInConditionOrParameterTable(),
-    CheckAllObservablesDefined(),
     CheckAllParametersPresentInParameterTable(),
     CheckValidConditionTargets(),
     CheckPriorDistribution(),