Error to warning

src/cript/api/api.py

@@ -258,6 +258,9 @@ def _init_logger(self, log_level=logging.INFO) -> None:
 
         logger.setLevel(log_level)
 
+        # Activate Warning handling
+        logging.captureWarnings(True)
+
         # Create a console handler
         console_handler = logging.StreamHandler()
 

src/cript/exceptions.py

@@ -10,3 +10,17 @@ class CRIPTException(Exception):
     @abstractmethod
     def __str__(self) -> str:
         pass
+
+
+class CRIPTWarning(Warning):
+    """
+    Parent CRIPT warning.
+    All CRIPT warning inherit this class.
+    """
+
+    @abstractmethod
+    def __str__(self) -> str:
+        pass
+
+    def __repr__(self):
+        return str(self)

src/cript/nodes/exceptions.py

@@ -1,7 +1,7 @@
 from abc import ABC, abstractmethod
 from typing import List
 
-from cript.exceptions import CRIPTException
+from cript.exceptions import CRIPTException, CRIPTWarning
 
 
 class CRIPTUUIDException(CRIPTException):
@@ -67,7 +67,7 @@ def __str__(self) -> str:
         return error_message
 
 
-class CRIPTMaterialIdentifierError(CRIPTException):
+class CRIPTMaterialIdentifierWarning(CRIPTWarning):
     """Every material node needs to have at least one identifier set."""
 
     def __init__(self, material_node):
@@ -281,14 +281,14 @@ def __str__(self):
         )
 
 
-class CRIPTOrphanedNodesError(CRIPTException, ABC):
+class CRIPTOrphanedNodesWarning(CRIPTWarning, ABC):
     """
     ## Definition
     This error is raised when a child node is not attached to the
     appropriate parent node. For example, all material nodes used
     within a project must belong to the project inventory or are explicitly listed as material of that project.
     If there is a material node that is used within a project but not a part of the
-    inventory and the validation code finds it then it raises an `CRIPTOrphanedNodeError`
+    inventory and the validation code finds it then it raises an `CRIPTOrphanedNodeWarning`
 
     ## Troubleshooting
     Fixing this is simple and easy, just take the node that CRIPT Python SDK
@@ -307,10 +307,10 @@ def __str__(self):
         pass
 
 
-class CRIPTOrphanedMaterialError(CRIPTOrphanedNodesError):
+class CRIPTOrphanedMaterialWarning(CRIPTOrphanedNodesWarning):
     """
     ## Definition
-    CRIPTOrphanedNodesError, but specific for orphaned materials.
+    CRIPTOrphanedNodesWarning, but specific for orphaned materials.
 
     ## Troubleshooting
     Handle this error by adding the orphaned materials into the parent project or its inventories.
@@ -327,10 +327,10 @@ def __str__(self):
         return ret_string
 
 
-class CRIPTOrphanedExperimentError(CRIPTOrphanedNodesError):
+class CRIPTOrphanedExperimentWarning(CRIPTOrphanedNodesWarning):
     """
     ## Definition
-    CRIPTOrphanedNodesError, but specific for orphaned nodes that should be listed in one of the experiments.
+    CRIPTOrphanedNodesWarning, but specific for orphaned nodes that should be listed in one of the experiments.
 
     ## Troubleshooting
     Handle this error by adding the orphaned node into one the parent project's experiments.
@@ -348,10 +348,10 @@ def __str__(self) -> str:
         return ret_string
 
 
-class CRIPTOrphanedDataError(CRIPTOrphanedExperimentError):
+class CRIPTOrphanedDataWarning(CRIPTOrphanedExperimentWarning):
     """
     ## Definition
-    CRIPTOrphanedExperimentError, but specific for orphaned Data node that should be listed in one of the experiments.
+    CRIPTOrphanedExperimentWarning, but specific for orphaned Data node that should be listed in one of the experiments.
 
     ## Troubleshooting
     Handle this error by adding the orphaned node into one the parent project's experiments `data` attribute.
@@ -361,10 +361,10 @@ def __init__(self, orphaned_node):
         super().__init__(orphaned_node)
 
 
-class CRIPTOrphanedProcessError(CRIPTOrphanedExperimentError):
+class CRIPTOrphanedProcessWarning(CRIPTOrphanedExperimentWarning):
     """
     ## Definition
-    CRIPTOrphanedExperimentError, but specific for orphaned Process node that should be
+    CRIPTOrphanedExperimentWarning, but specific for orphaned Process node that should be
     listed in one of the experiments.
 
     ## Troubleshooting
@@ -376,10 +376,10 @@ def __init__(self, orphaned_node):
         super().__init__(orphaned_node)
 
 
-class CRIPTOrphanedComputationError(CRIPTOrphanedExperimentError):
+class CRIPTOrphanedComputationWarning(CRIPTOrphanedExperimentWarning):
     """
     ## Definition
-    CRIPTOrphanedExperimentError, but specific for orphaned Computation node that should be
+    CRIPTOrphanedExperimentWarning, but specific for orphaned Computation node that should be
     listed in one of the experiments.
 
     ## Troubleshooting
@@ -391,10 +391,10 @@ def __init__(self, orphaned_node):
         super().__init__(orphaned_node)
 
 
-class CRIPTOrphanedComputationalProcessError(CRIPTOrphanedExperimentError):
+class CRIPTOrphanedComputationalProcessWarning(CRIPTOrphanedExperimentWarning):
     """
     ## Definition
-    CRIPTOrphanedExperimentError, but specific for orphaned ComputationalProcess
+    CRIPTOrphanedExperimentWarning, but specific for orphaned ComputationalProcess
     node that should be listed in one of the experiments.
 
     ## Troubleshooting

src/cript/nodes/primary_nodes/material.py

@@ -1,9 +1,10 @@
+import warnings
 from dataclasses import dataclass, field, replace
 from typing import Any, List, Optional, Union
 
 from beartype import beartype
 
-from cript.nodes.exceptions import CRIPTMaterialIdentifierError
+from cript.nodes.exceptions import CRIPTMaterialIdentifierWarning
 from cript.nodes.primary_nodes.primary_base_node import PrimaryBaseNode
 from cript.nodes.primary_nodes.process import Process
 from cript.nodes.util.json import UIDProxy
@@ -218,7 +219,7 @@ def validate(self, api=None, is_patch: bool = False, force_validation: bool = Fa
             and self.smiles is None
             and self.vendor is None
         ):
-            raise CRIPTMaterialIdentifierError(self)
+            warnings.warn(CRIPTMaterialIdentifierWarning(self))
 
     @property
     @beartype

src/cript/nodes/primary_nodes/project.py

@@ -1,3 +1,4 @@
+import warnings
 from dataclasses import dataclass, field, replace
 from typing import List, Optional, Union
 
@@ -106,7 +107,7 @@ def __init__(self, name: str, collection: Optional[List[Union[Collection, UIDPro
         self._update_json_attrs_if_valid(new_json_attrs)
 
     def validate(self, api=None, is_patch=False, force_validation: bool = False):
-        from cript.nodes.exceptions import CRIPTOrphanedMaterialError
+        from cript.nodes.exceptions import CRIPTOrphanedMaterialWarning
         from cript.nodes.util.core import get_orphaned_experiment_exception
 
         # First validate like other nodes
@@ -122,7 +123,7 @@ def validate(self, api=None, is_patch=False, force_validation: bool = False):
                 project_inventory_materials.append(material)
         for material in project_graph_materials:
             if material not in self.material and material not in project_inventory_materials:
-                raise CRIPTOrphanedMaterialError(material)
+                warnings.warn(CRIPTOrphanedMaterialWarning(material))
 
         # Check graph for orphaned nodes, that should be listed in the experiments
         project_experiments = self.find_children({"node": ["Experiment"]})
@@ -145,7 +146,7 @@ def validate(self, api=None, is_patch=False, force_validation: bool = False):
                     experiment_nodes.append(ex_node)
             for node in project_graph_nodes:
                 if node not in experiment_nodes:
-                    raise get_orphaned_experiment_exception(node)
+                    warnings.warn(get_orphaned_experiment_exception(node))
 
     @property
     @beartype

src/cript/nodes/util/core.py

@@ -1,12 +1,13 @@
 import uuid
+import warnings
 
 from cript.nodes.exceptions import (
-    CRIPTOrphanedComputationalProcessError,
-    CRIPTOrphanedComputationError,
-    CRIPTOrphanedDataError,
-    CRIPTOrphanedExperimentError,
-    CRIPTOrphanedMaterialError,
-    CRIPTOrphanedProcessError,
+    CRIPTOrphanedComputationalProcessWarning,
+    CRIPTOrphanedComputationWarning,
+    CRIPTOrphanedDataWarning,
+    CRIPTOrphanedExperimentWarning,
+    CRIPTOrphanedMaterialWarning,
+    CRIPTOrphanedProcessWarning,
 )
 
 
@@ -27,25 +28,28 @@ def add_orphaned_nodes_to_project(project, active_experiment, max_iteration: int
         raise RuntimeError(f"The provided active experiment {active_experiment} is not part of the project graph. Choose an active experiment that is part of a collection of this project.")
 
     counter = 0
-    while True:
-        if counter > max_iteration >= 0:
-            break  # Emergency stop
-        try:
-            project.validate()
-        except CRIPTOrphanedMaterialError as exc:
-            # because calling the setter calls `validate` we have to force add the material.
-            project._json_attrs.material.append(exc.orphaned_node)
-        except CRIPTOrphanedDataError as exc:
-            active_experiment.data += [exc.orphaned_node]
-        except CRIPTOrphanedProcessError as exc:
-            active_experiment.process += [exc.orphaned_node]
-        except CRIPTOrphanedComputationError as exc:
-            active_experiment.computation += [exc.orphaned_node]
-        except CRIPTOrphanedComputationalProcessError as exc:
-            active_experiment.computation_process += [exc.orphaned_node]
-        else:
-            break
-        counter += 1
+    # Convert Errors into exceptions, so we can catch and fix them
+    with warnings.catch_warnings():
+        warnings.simplefilter("error")
+        while True:
+            if counter > max_iteration >= 0:
+                break  # Emergency stop
+            try:
+                project.validate()
+            except CRIPTOrphanedMaterialWarning as exc:
+                # because calling the setter calls `validate` we have to force add the material.
+                project._json_attrs.material.append(exc.orphaned_node)
+            except CRIPTOrphanedDataWarning as exc:
+                active_experiment.data += [exc.orphaned_node]
+            except CRIPTOrphanedProcessWarning as exc:
+                active_experiment.process += [exc.orphaned_node]
+            except CRIPTOrphanedComputationWarning as exc:
+                active_experiment.computation += [exc.orphaned_node]
+            except CRIPTOrphanedComputationalProcessWarning as exc:
+                active_experiment.computation_process += [exc.orphaned_node]
+            else:
+                break
+            counter += 1
 
 
 def get_orphaned_experiment_exception(orphaned_node):
@@ -58,15 +62,15 @@ def get_orphaned_experiment_exception(orphaned_node):
     from cript.nodes.primary_nodes.process import Process
 
     if isinstance(orphaned_node, Data):
-        return CRIPTOrphanedDataError(orphaned_node)
+        return CRIPTOrphanedDataWarning(orphaned_node)
     if isinstance(orphaned_node, Process):
-        return CRIPTOrphanedProcessError(orphaned_node)
+        return CRIPTOrphanedProcessWarning(orphaned_node)
     if isinstance(orphaned_node, Computation):
-        return CRIPTOrphanedComputationError(orphaned_node)
+        return CRIPTOrphanedComputationWarning(orphaned_node)
     if isinstance(orphaned_node, ComputationProcess):
-        return CRIPTOrphanedComputationalProcessError(orphaned_node)
+        return CRIPTOrphanedComputationalProcessWarning(orphaned_node)
     # Base case raise the parent exception. TODO add bug warning.
-    return CRIPTOrphanedExperimentError(orphaned_node)
+    return CRIPTOrphanedExperimentWarning(orphaned_node)
 
 
 def iterate_leaves(obj):