Node Exceptions

Node Exceptions

CRIPTAttributeModificationError

Bases: CRIPTException

Exception that is thrown when a node attribute is modified, that wasn't intended to be modified.

Source code in src/cript/nodes/exceptions.py

class CRIPTAttributeModificationError(CRIPTException):
    """
    Exception that is thrown when a node attribute is modified, that wasn't intended to be modified.
    """

    def __init__(self, name, key, value):
        self.name = name
        self.key = key
        self.value = value

    def __str__(self):
        return (
            f"Attempt to modify an attribute of a node ({self.name}) that wasn't intended to be modified.\n"
            f"Here the non-existing attribute {self.key} of {self.name} was attempted to be modified.\n"
            "Most likely this is due to a typo in the attribute that was intended to be modified i.e. `project.materials` instead of `project.material`.\n"
            "To ensure compatibility with the underlying CRIPT data model we do not allow custom attributes.\n"
        )

CRIPTDeserializationUIDError

Bases: CRIPTException

Definition

This exception is raised when converting a node from JSON to Python class fails, because a node is specified with its UID only, but not part of the data graph elsewhere.

Error Example

Invalid JSON that cannot be deserialized to a CRIPT Python SDK Node

{
"node": ["Algorithm"],
"key": "mc_barostat",
"type": "barostat",
"parameter": {"node": ["Parameter"], "uid": "uid-string"}
}

Here the algorithm has a parameter attribute, but the parameter is specified as uid only.

Valid Example

Valid JSON that can be deserialized to a CRIPT Python SDK Node

{
   "node":["Algorithm"],
   "key":"mc_barostat",
   "type":"barostat",
   "parameter":{
      "node":["Parameter"],
      "uid":"uid-string",
      "key":"update_frequency",
      "value":1,
      "unit":"1/second"
   }
}

Now the node is fully specified.

Troubleshooting

Specify the full node instead. This error might appear if you try to partially load previously generated JSON.

Source code in src/cript/nodes/exceptions.py

class CRIPTDeserializationUIDError(CRIPTException):
    """
    ## Definition
    This exception is raised when converting a node from JSON to Python class fails,
    because a node is specified with its UID only, but not part of the data graph elsewhere.

    ### Error Example
    Invalid JSON that cannot be deserialized to a CRIPT Python SDK Node

    ```json
    {
    "node": ["Algorithm"],
    "key": "mc_barostat",
    "type": "barostat",
    "parameter": {"node": ["Parameter"], "uid": "uid-string"}
    }
    ```
    Here the algorithm has a parameter attribute, but the parameter is specified as uid only.

    ### Valid Example
    Valid JSON that can be deserialized to a CRIPT Python SDK Node

    ```json
    {
       "node":["Algorithm"],
       "key":"mc_barostat",
       "type":"barostat",
       "parameter":{
          "node":["Parameter"],
          "uid":"uid-string",
          "key":"update_frequency",
          "value":1,
          "unit":"1/second"
       }
    }
    ```
    Now the node is fully specified.

    ## Troubleshooting
    Specify the full node instead. This error might appear if you try to partially load previously generated JSON.
    """

    def __init__(self, node_type: str, uid: str) -> None:
        self.node_type = node_type
        self.uid = uid

    def __str__(self) -> str:
        return f"JSON deserialization failed for node type {self.node_type} with unknown UID: {self.uid}"

CRIPTJsonDeserializationError

Bases: CRIPTException

Definition

This exception is raised when converting a node from JSON to Python class fails. This process fails when the attributes within the JSON does not match the node's class attributes within the JsonAttributes of that specific node

Error Example

Invalid JSON that cannot be deserialized to a CRIPT Python SDK Node

Valid Example

Valid JSON that can be deserialized to a CRIPT Python SDK Node

Troubleshooting

Source code in src/cript/nodes/exceptions.py

class CRIPTJsonDeserializationError(CRIPTException):
    """
    ## Definition
    This exception is raised when converting a node from JSON to Python class fails.
    This process fails when the attributes within the JSON does not match the node's class
    attributes within the `JsonAttributes` of that specific node

    ### Error Example
    Invalid JSON that cannot be deserialized to a CRIPT Python SDK Node

    ```json
    ```


    ### Valid Example
    Valid JSON that can be deserialized to a CRIPT Python SDK Node

    ```json
    ```

    ## Troubleshooting
    """

    def __init__(self, node_type: str, json_str: str) -> None:
        self.node_type = node_type
        self.json_str = json_str

    def __str__(self) -> str:
        return f"JSON deserialization failed for node type {self.node_type} with JSON str: {self.json_str}"

CRIPTJsonNodeError

Bases: CRIPTJsonDeserializationError

Definition

This exception is raised if a node attribute is present in JSON, but the list has more or less than exactly one type of node type.

Note: It is expected that there is only a single node type per JSON object.

Example

Valid JSON representation of a Material node

{
  "node": [
    "Material"
  ],
  "name": "Whey protein isolate",
  "uid": "_:Whey protein isolate"
},

Invalid JSON representation of a Material node

{
  "node": [
    "Material",
    "Property"
  ],
  "name": "Whey protein isolate",
  "uid": "_:Whey protein isolate"
},

---

{
  "node": [],
  "name": "Whey protein isolate",
  "uid": "_:Whey protein isolate"
},

Troubleshooting

Debugging skills are most helpful here as there is no one-size-fits-all approach.

It is best to identify whether the invalid JSON was created in the Python SDK or if the invalid JSON was given from the API.

If the Python SDK created invalid JSON during serialization, then it is helpful to track down and identify the point where the invalid JSON was started.

You may consider, inspecting the python objects to see if the node type are written incorrectly in python and the issue is only being caught during serialization or if the Python node is written correctly and the issue is created during serialization.

If the problem is with the Python SDK or API, it is best to leave an issue or create a discussion within the Python SDK GitHub repository for one of the members of the CRIPT team to look into any issues that there could have been.

Source code in src/cript/nodes/exceptions.py

class CRIPTJsonNodeError(CRIPTJsonDeserializationError):
    """
    ## Definition
    This exception is raised if a `node` attribute is present in JSON,
    but the list has more or less than exactly one type of node type.

    > Note: It is expected that there is only a single node type per JSON object.

    ### Example
    !!! Example "Valid JSON representation of a Material node"
        ```json
        {
          "node": [
            "Material"
          ],
          "name": "Whey protein isolate",
          "uid": "_:Whey protein isolate"
        },
        ```

    ??? Example "Invalid JSON representation of a Material node"

        ```json
        {
          "node": [
            "Material",
            "Property"
          ],
          "name": "Whey protein isolate",
          "uid": "_:Whey protein isolate"
        },
        ```

        ---

        ```json
        {
          "node": [],
          "name": "Whey protein isolate",
          "uid": "_:Whey protein isolate"
        },
        ```


    ## Troubleshooting
    Debugging skills are most helpful here as there is no one-size-fits-all approach.

    It is best to identify whether the invalid JSON was created in the Python SDK
    or if the invalid JSON was given from the API.

    If the Python SDK created invalid JSON during serialization, then it is helpful to track down and
    identify the point where the invalid JSON was started.

    You may consider, inspecting the python objects to see if the node type are written incorrectly in python
    and the issue is only being caught during serialization or if the Python node is written correctly
    and the issue is created during serialization.

    If the problem is with the Python SDK or API, it is best to leave an issue or create a discussion within the
    [Python SDK GitHub repository](https://github.com/C-Accel-CRIPT/Python-SDK) for one of the members of the
    CRIPT team to look into any issues that there could have been.
    """

    def __init__(self, node_list: List, json_str: str) -> None:
        self.node_list = node_list
        self.json_str = json_str

    def __str__(self) -> str:
        error_message: str = f"The 'node' attribute in the JSON string must be a single element list with the node name " f" such as `'node: ['Material']`. The `node` attribute provided was: `{self.node_list}`" f"The full JSON was: {self.json_str}."

        return error_message

CRIPTJsonSerializationError

Bases: CRIPTException

Definition

This Exception is raised if serialization of node from JSON to Python Object fails.

Troubleshooting

Source code in src/cript/nodes/exceptions.py

class CRIPTJsonSerializationError(CRIPTException):
    """
    ## Definition
    This Exception is raised if serialization of node from JSON to Python Object fails.

    ## Troubleshooting
    """

    def __init__(self, node_type: str, json_dict: str) -> None:
        self.node_type = node_type
        self.json_str = str(json_dict)

    def __str__(self) -> str:
        return f"JSON Serialization failed for node type {self.node_type} with JSON dict: {self.json_str}"

CRIPTMaterialIdentifierError

Bases: CRIPTException

Every material node needs to have at least one identifier set.

Source code in src/cript/nodes/exceptions.py

class CRIPTMaterialIdentifierError(CRIPTException):
    """Every material node needs to have at least one identifier set."""

    def __init__(self, material_node):
        self.material_node = material_node

    def __str__(self) -> str:
        error_message = "Every Material node needs at least one identifier from "
        error_message += " [ 'amino_acid', 'bigsmiles', 'chem_formula', 'chem_repeat', 'chemical_id', 'inchi', 'lot_number', 'names', 'pubchem_cid', 'smiles','vendor'] set."
        error_message += f" This node {self.material_node} has none set."
        return error_message

CRIPTNodeSchemaError

Bases: CRIPTException

Definition

This error is raised when the CRIPT json database schema validation fails for a node.

Please keep in mind that the CRIPT Python SDK converts all the Python nodes inside the Project into a giant JSON and sends an HTTP POST or PATCH request to the API to be processed.

However, before a request is sent to the API, the JSON is validated against API database schema via the JSON Schema library, and if the database schema validation fails for whatever reason this error is shown.

Possible Reasons

1. There was a mistake in nesting of the nodes
2. There was a mistake in creating the nodes
3. Nodes are missing
4. Nodes have invalid vocabulary
   • The database schema wants something a different controlled vocabulary than what is provided
5. There was an error with the way the JSON was created within the Python SDK
   • The format of the JSON the CRIPT Python SDK created was invalid
6. There is something wrong with the database schema

Troubleshooting

The easiest way to troubleshoot this is to examine the JSON that the SDK created via printing out the Project node's JSON and checking the place that the schema validation says failed

Example

print(my_project.json)

Source code in src/cript/nodes/exceptions.py

class CRIPTNodeSchemaError(CRIPTException):
    """
    ## Definition
    This error is raised when the CRIPT [json database schema](https://json-schema.org/)
    validation fails for a node.

    Please keep in mind that the CRIPT Python SDK converts all the Python nodes inside the
    [Project](../../nodes/primary_nodes/project) into a giant JSON
    and sends an HTTP `POST` or `PATCH` request to the API to be processed.

    However, before a request is sent to the API, the JSON is validated against API database schema
    via the [JSON Schema library](https://python-jsonschema.readthedocs.io/en/stable/),
    and if the database schema validation fails for whatever reason this error is shown.

    ### Possible Reasons

    1. There was a mistake in nesting of the nodes
    1. There was a mistake in creating the nodes
    1. Nodes are missing
    1. Nodes have invalid vocabulary
        * The database schema wants something a different controlled vocabulary than what is provided
    1. There was an error with the way the JSON was created within the Python SDK
        * The format of the JSON the CRIPT Python SDK created was invalid
    1. There is something wrong with the database schema

    ## Troubleshooting
    The easiest way to troubleshoot this is to examine the JSON that the SDK created via printing out the
    [Project](../../nodes/primary_nodes/project) node's JSON and checking the place that the schema validation
    says failed

    ### Example
    ```python
    print(my_project.json)
    ```
    """

    node_type: str = ""
    json_schema_validation_error: str = ""

    def __init__(self, node_type: str, json_schema_validation_error: str) -> None:
        self.json_schema_validation_error: str = json_schema_validation_error
        self.node_type = node_type

    def __str__(self) -> str:
        error_message: str = f"JSON database schema validation for node {self.node_type} failed."
        error_message += f"Error: {self.json_schema_validation_error}"

        return error_message

CRIPTOrphanedComputationError

Bases: CRIPTOrphanedExperimentError

Definition

CRIPTOrphanedExperimentError, but specific for orphaned Computation 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 Computation attribute.

Source code in src/cript/nodes/exceptions.py

class CRIPTOrphanedComputationError(CRIPTOrphanedExperimentError):
    """
    ## Definition
    CRIPTOrphanedExperimentError, but specific for orphaned Computation 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
    `Computation` attribute.
    """

    def __init__(self, orphaned_node):
        super().__init__(orphaned_node)

CRIPTOrphanedComputationalProcessError

Bases: CRIPTOrphanedExperimentError

Definition

CRIPTOrphanedExperimentError, but specific for orphaned ComputationalProcess 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 ComputationalProcess attribute.

Source code in src/cript/nodes/exceptions.py

class CRIPTOrphanedComputationalProcessError(CRIPTOrphanedExperimentError):
    """
    ## Definition
    CRIPTOrphanedExperimentError, but specific for orphaned ComputationalProcess
    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
    `ComputationalProcess` attribute.
    """

    def __init__(self, orphaned_node):
        super().__init__(orphaned_node)

CRIPTOrphanedDataError

Bases: CRIPTOrphanedExperimentError

Definition

CRIPTOrphanedExperimentError, 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.

Source code in src/cript/nodes/exceptions.py

class CRIPTOrphanedDataError(CRIPTOrphanedExperimentError):
    """
    ## Definition
    CRIPTOrphanedExperimentError, 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.
    """

    def __init__(self, orphaned_node):
        super().__init__(orphaned_node)

CRIPTOrphanedExperimentError

Bases: CRIPTOrphanedNodesError

Definition

CRIPTOrphanedNodesError, 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.

Source code in src/cript/nodes/exceptions.py

class CRIPTOrphanedExperimentError(CRIPTOrphanedNodesError):
    """
    ## Definition
    CRIPTOrphanedNodesError, 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.
    """

    def __init__(self, orphaned_node):
        super().__init__(orphaned_node)

    def __str__(self) -> str:
        node_name = self.orphaned_node.node_type.lower()
        ret_string = f"While validating a project graph, an orphaned {node_name} node was found. "
        ret_string += f"This {node_name} node is present in the graph, but not listed in any of the experiments of the  project. "
        ret_string += f"Please add the node like: `your_experiment.{node_name} += [orphaned_{node_name}]`. "
        ret_string += f"The orphaned {node_name} was {self.orphaned_node}."
        return ret_string

CRIPTOrphanedMaterialError

Bases: CRIPTOrphanedNodesError

Definition

CRIPTOrphanedNodesError, but specific for orphaned materials.

Troubleshooting

Handle this error by adding the orphaned materials into the parent project or its inventories.

Source code in src/cript/nodes/exceptions.py

class CRIPTOrphanedMaterialError(CRIPTOrphanedNodesError):
    """
    ## Definition
    CRIPTOrphanedNodesError, but specific for orphaned materials.

    ## Troubleshooting
    Handle this error by adding the orphaned materials into the parent project or its inventories.
    """

    def __init__(self, orphaned_node):
        super().__init__(orphaned_node)

    def __str__(self):
        ret_string = "While validating a project graph, an orphaned material node was found. "
        ret_string += "This material is present in the graph, but not listed in the project. "
        ret_string += "Please add the node like: `my_project.material += [orphaned_material]`. "
        ret_string += f"The orphaned material was {self.orphaned_node}."
        return ret_string

CRIPTOrphanedNodesError

Bases: CRIPTException, 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

Troubleshooting

Fixing this is simple and easy, just take the node that CRIPT Python SDK found a problem with and associate it with the appropriate parent via

my_project.material += my_orphaned_material_node

Source code in src/cript/nodes/exceptions.py

class CRIPTOrphanedNodesError(CRIPTException, 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`

    ## Troubleshooting
    Fixing this is simple and easy, just take the node that CRIPT Python SDK
    found a problem with and associate it with the appropriate parent via

    ```
    my_project.material += my_orphaned_material_node
    ```
    """

    def __init__(self, orphaned_node):
        self.orphaned_node = orphaned_node

    @abstractmethod
    def __str__(self):
        pass

CRIPTOrphanedProcessError

Bases: CRIPTOrphanedExperimentError

Definition

CRIPTOrphanedExperimentError, but specific for orphaned Process 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 process attribute.

Source code in src/cript/nodes/exceptions.py

class CRIPTOrphanedProcessError(CRIPTOrphanedExperimentError):
    """
    ## Definition
    CRIPTOrphanedExperimentError, but specific for orphaned Process 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
    `process` attribute.
    """

    def __init__(self, orphaned_node):
        super().__init__(orphaned_node)