Experiment

Experiment

Bases: PrimaryBaseNode

Definition

An Experiment node is nested inside a Collection node.

Attributes

attribute	type	description	required
collection	Collection	collection associated with the experiment	True
process	List[Process]	process nodes associated with this experiment	False
computations	List[Computation]	computation method nodes associated with this experiment	False
computation_process	List[Computational Process]	computation process nodes associated with this experiment	False
data	List[Data]	data nodes associated with this experiment	False
funding	List[str]	funding source for experiment	False
citation	List[Citation]	reference to a book, paper, or scholarly work	False
notes	str	miscellaneous information, or custom data structure	False

Sub-objects

An Experiment node can be thought as a folder/bucket that can hold:

• Process
• Computations
• Computation_Process
• Data
• Funding
• Citation

Warnings

Experiment names

Experiment names MUST be unique within a Collection

---

JSON Representation

{
   "name":"my experiment name",
   "node":["Experiment"],
   "uid":"_:886c4deb-2186-4f11-8134-a37111200b83",
   "uuid":"886c4deb-2186-4f11-8134-a37111200b83"
}

Source code in src/cript/nodes/primary_nodes/experiment.py

class Experiment(PrimaryBaseNode):
    """
    ## Definition
    An
    [Experiment node](https://pubs.acs.org/doi/suppl/10.1021/acscentsci.3c00011/suppl_file/oc3c00011_si_001.pdf#page=9)
    is nested inside a [Collection](../collection) node.

    ## Attributes

    | attribute           | type                         | description                                               | required |
    |---------------------|------------------------------|-----------------------------------------------------------|----------|
    | collection          | Collection                   | collection associated with the experiment                 | True     |
    | process             | List[Process]                | process nodes associated with this experiment             | False    |
    | computations        | List[Computation]            | computation method nodes associated with this experiment  | False    |
    | computation_process | List[Computational  Process] | computation process nodes associated with this experiment | False    |
    | data                | List[Data]                   | data nodes associated with this experiment                | False    |
    | funding             | List[str]                    | funding source for experiment                             | False    |
    | citation            | List[Citation]               | reference to a book, paper, or scholarly work             | False    |
    | notes               | str                          | miscellaneous information, or custom data structure       | False    |


    ## Sub-objects
    An
    [Experiment node](https://pubs.acs.org/doi/suppl/10.1021/acscentsci.3c00011/suppl_file/oc3c00011_si_001.pdf#page=9)
    can be thought as a folder/bucket that can hold:

    * [Process](../process)
    * [Computations](../computation)
    * [Computation_Process](../computation_process)
    * [Data](../data)
    * [Funding](./#cript.nodes.primary_nodes.experiment.Experiment.funding)
    * [Citation](../../subobjects/citation)


    Warnings
    --------
    !!! warning "Experiment names"
        Experiment names **MUST** be unique within a [Collection](../collection)

    ---

    ## JSON Representation
    ```json
    {
       "name":"my experiment name",
       "node":["Experiment"],
       "uid":"_:886c4deb-2186-4f11-8134-a37111200b83",
       "uuid":"886c4deb-2186-4f11-8134-a37111200b83"
    }
    ```

    """

    @dataclass(frozen=True)
    class JsonAttributes(PrimaryBaseNode.JsonAttributes):
        """
        all Collection attributes
        """

        process: List[Union[Any, UIDProxy]] = field(default_factory=list)
        computation: List[Union[Any, UIDProxy]] = field(default_factory=list)
        computation_process: List[Union[Any, UIDProxy]] = field(default_factory=list)
        data: List[Union[Any, UIDProxy]] = field(default_factory=list)
        funding: List[str] = field(default_factory=list)
        citation: List[Union[Any, UIDProxy]] = field(default_factory=list)

    _json_attrs: JsonAttributes = JsonAttributes()

    @beartype
    def __init__(
        self,
        name: str,
        process: Optional[List[Union[Any, UIDProxy]]] = None,
        computation: Optional[List[Union[Any, UIDProxy]]] = None,
        computation_process: Optional[List[Union[Any, UIDProxy]]] = None,
        data: Optional[List[Union[Any, UIDProxy]]] = None,
        funding: Optional[List[str]] = None,
        citation: Optional[List[Union[Any, UIDProxy]]] = None,
        notes: str = "",
        **kwargs
    ):
        """
        create an Experiment node

        Examples
        --------
        >>> import cript
        >>> my_experiment = cript.Experiment(name="my experiment name")

        Parameters
        ----------
        name: str
            name of Experiment
        process: List[Process]
            list of Process nodes for this Experiment
        computation: List[Computation]
            list of computation nodes for this Experiment
        computation_process: List[ComputationalProcess]
            list of computational_process nodes for this Experiment
        data: List[Data]
            list of data nodes for this experiment
        funding: List[str]
            list of the funders names for this Experiment
        citation: List[Citation]
            list of Citation nodes for this experiment
        notes: str default=""
            notes for the experiment node

        Returns
        -------
        None
            Instantiate an Experiment node
        """

        if process is None:
            process = []
        if computation is None:
            computation = []
        if computation_process is None:
            computation_process = []
        if data is None:
            data = []
        if funding is None:
            funding = []
        if citation is None:
            citation = []

        super().__init__(name=name, notes=notes, **kwargs)

        new_json_attrs = replace(
            self._json_attrs,
            name=name,
            process=process,
            computation=computation,
            computation_process=computation_process,
            data=data,
            funding=funding,
            citation=citation,
            notes=notes,
        )

        self._update_json_attrs_if_valid(new_json_attrs)

    @property
    @beartype
    def process(self) -> List[Any]:
        """
        List of process for experiment

        Examples
        --------
        >>> import cript
        >>> my_experiment = cript.Experiment(name="my experiment name")
        >>> my_process = cript.Process(name="my process name", type="affinity_pure")
        >>> my_experiment.process = [my_process]

        Returns
        -------
        List[Process]
            List of process that were performed in this experiment
        """
        return self._json_attrs.process.copy()

    @process.setter
    @beartype
    def process(self, new_process_list: List[Any]) -> None:
        """
        set the list of process for this experiment

        Parameters
        ----------
        new_process_list: List[Process]
            new process list to replace the current process list

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, process=new_process_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def computation(self) -> List[Any]:
        """
        List of the [computations](../computation) in this experiment

        Examples
        --------
        >>> import cript
        >>> my_experiment = cript.Experiment(name="my experiment name")
        >>> my_computation = cript.Computation(name="my computation name", type="analysis")
        >>> my_experiment.computation = [my_computation]

        Returns
        -------
        List[Computation]
            List of [computations](../computation) for this experiment
        """
        return self._json_attrs.computation.copy()

    @computation.setter
    @beartype
    def computation(self, new_computation_list: List[Any]) -> None:
        """
        set the list of computations for this experiment

        Parameters
        ----------
        new_computation_list: List[Computation]
            new list of computations to replace the current list of experiments

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, computation=new_computation_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def computation_process(self) -> List[Any]:
        """
        List of [computation_process](../computation_process) for this experiment

        Examples
        --------
        >>> import cript
        >>> my_experiment = cript.Experiment(name="my experiment name")
        >>> my_file = cript.File(
        ...     name="my file node",
        ...     source="https://criptapp.org",
        ...     type="calibration",
        ...     extension=".csv",
        ...     data_dictionary="my file's data dictionary",
        ... )
        >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
        >>> my_material = cript.Material(
        ...     name="my material name", bigsmiles = "123456"
        ... )
        >>> my_quantity = cript.Quantity(
        ... key="mass", value=11.2, unit="kg", uncertainty=0.2, uncertainty_type="stdev"
        ... )
        >>> my_ingredient = cript.Ingredient(
        ... material=my_material, quantity=[my_quantity], keyword=["catalyst"]
        ... )
        >>> my_computation_process = cript.ComputationProcess(
        ...     name="my computational process name",
        ...     type="cross_linking",         # must come from CRIPT Controlled Vocabulary
        ...     input_data=[my_data],         # input data is another data node
        ...     ingredient=[my_ingredient],  # output data is another data node
        ... )
        >>> my_experiment.computation_process = [my_computation_process]

        Returns
        -------
        List[ComputationalProcess]
            computational process that were performed in this experiment
        """
        return self._json_attrs.computation_process.copy()

    @computation_process.setter
    @beartype
    def computation_process(self, new_computation_process_list: List[Any]) -> None:
        """
        set the list of computation_process for this experiment

        Parameters
        ----------
        new_computation_process_list: List[ComputationalProcess]
            new list of computations to replace the current for the experiment

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, computation_process=new_computation_process_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def data(self) -> List[Any]:
        """
        List of [data nodes](../data) for this experiment

        Examples
        --------
        >>> import cript
        >>> my_experiment = cript.Experiment(name="my experiment name")
        >>> my_file = cript.File(
        ...    name="my file node name",
        ...    source="https://criptapp.org",
        ...    type="calibration",
        ...    extension=".csv",
        ...    data_dictionary="my file's data dictionary",
        ... )
        >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
        >>> my_experiment.data = [my_data]

        Returns
        -------
        List[Data]
            list of [data nodes](../data) that belong to this experiment
        """
        return self._json_attrs.data.copy()

    @data.setter
    @beartype
    def data(self, new_data_list: List[Any]) -> None:
        """
        set the list of data for this experiment

        Parameters
        ----------
        new_data_list: List[Data]
            new list of data to replace the current list for this experiment

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, data=new_data_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def funding(self) -> List[str]:
        """
        List of strings of all the funders for this experiment

        Examples
        --------
        >>> import cript
        >>> my_experiment = cript.Experiment(name="my experiment name")
        >>> my_experiment.funding = ["National Science Foundation", "IRIS", "NIST"]

        Returns
        -------
        List[str]
            List of funders for this experiment
        """
        return self._json_attrs.funding.copy()

    @funding.setter
    @beartype
    def funding(self, new_funding_list: List[str]) -> None:
        """
        set the list of funders for this experiment

        Parameters
        ----------
        new_funding_list: List[str]
            replace the current list of funders

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, funding=new_funding_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def citation(self) -> List[Any]:
        """
        List of [citation](../../subobjects/citation) for this experiment

        Examples
        --------
        >>> import cript
        >>> my_experiment = cript.Experiment(name="my experiment name")
        >>> my_reference = cript.Reference(
        ...     type="journal_article",
        ...     title="title",
        ...     author=["Ludwig Schneider", "Marcus Müller"],
        ...     journal="Computer Physics Communications",
        ...     publisher="Elsevier",
        ...     year=2019,
        ...     pages=[463, 476],
        ...     doi="10.1016/j.cpc.2018.08.011",
        ...     issn="0010-4655",
        ...     website="https://www.sciencedirect.com/science/article/pii/S0010465518303072",
        ... )
        >>> my_citation = cript.Citation(type="derived_from", reference=my_reference)
        >>> my_experiment.citation = [my_citation]

        Returns
        -------
        List[Citation]
            list of citations of scholarly work that was used in this experiment
        """
        return self._json_attrs.citation.copy()

    @citation.setter
    @beartype
    def citation(self, new_citation_list: List[Any]) -> None:
        """
        set the list of citations for this experiment

        Parameters
        ----------
        new_citations_list: List[Citation]
            replace the list of citations for this experiment with a new list of citations

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, citation=new_citation_list)
        self._update_json_attrs_if_valid(new_attrs)

citation: List[Any] property writable

List of citation for this experiment

Examples:

>>> import cript
>>> my_experiment = cript.Experiment(name="my experiment name")
>>> my_reference = cript.Reference(
...     type="journal_article",
...     title="title",
...     author=["Ludwig Schneider", "Marcus Müller"],
...     journal="Computer Physics Communications",
...     publisher="Elsevier",
...     year=2019,
...     pages=[463, 476],
...     doi="10.1016/j.cpc.2018.08.011",
...     issn="0010-4655",
...     website="https://www.sciencedirect.com/science/article/pii/S0010465518303072",
... )
>>> my_citation = cript.Citation(type="derived_from", reference=my_reference)
>>> my_experiment.citation = [my_citation]

Returns:

Type	Description
List[Citation]	list of citations of scholarly work that was used in this experiment

computation: List[Any] property writable

List of the computations in this experiment

Examples:

>>> import cript
>>> my_experiment = cript.Experiment(name="my experiment name")
>>> my_computation = cript.Computation(name="my computation name", type="analysis")
>>> my_experiment.computation = [my_computation]

Returns:

Type	Description
List[Computation]	List of computations for this experiment

computation_process: List[Any] property writable

List of computation_process for this experiment

Examples:

>>> import cript
>>> my_experiment = cript.Experiment(name="my experiment name")
>>> my_file = cript.File(
...     name="my file node",
...     source="https://criptapp.org",
...     type="calibration",
...     extension=".csv",
...     data_dictionary="my file's data dictionary",
... )
>>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
>>> my_material = cript.Material(
...     name="my material name", bigsmiles = "123456"
... )
>>> my_quantity = cript.Quantity(
... key="mass", value=11.2, unit="kg", uncertainty=0.2, uncertainty_type="stdev"
... )
>>> my_ingredient = cript.Ingredient(
... material=my_material, quantity=[my_quantity], keyword=["catalyst"]
... )
>>> my_computation_process = cript.ComputationProcess(
...     name="my computational process name",
...     type="cross_linking",         # must come from CRIPT Controlled Vocabulary
...     input_data=[my_data],         # input data is another data node
...     ingredient=[my_ingredient],  # output data is another data node
... )
>>> my_experiment.computation_process = [my_computation_process]

Returns:

Type	Description
List[ComputationalProcess]	computational process that were performed in this experiment

data: List[Any] property writable

List of data nodes for this experiment

Examples:

>>> import cript
>>> my_experiment = cript.Experiment(name="my experiment name")
>>> my_file = cript.File(
...    name="my file node name",
...    source="https://criptapp.org",
...    type="calibration",
...    extension=".csv",
...    data_dictionary="my file's data dictionary",
... )
>>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
>>> my_experiment.data = [my_data]

Returns:

Type	Description
List[Data]	list of data nodes that belong to this experiment

funding: List[str] property writable

List of strings of all the funders for this experiment

Examples:

>>> import cript
>>> my_experiment = cript.Experiment(name="my experiment name")
>>> my_experiment.funding = ["National Science Foundation", "IRIS", "NIST"]

Returns:

Type	Description
List[str]	List of funders for this experiment

process: List[Any] property writable

List of process for experiment

Examples:

>>> import cript
>>> my_experiment = cript.Experiment(name="my experiment name")
>>> my_process = cript.Process(name="my process name", type="affinity_pure")
>>> my_experiment.process = [my_process]

Returns:

Type	Description
List[Process]	List of process that were performed in this experiment

JsonAttributes dataclass

Bases: JsonAttributes

all Collection attributes

Source code in src/cript/nodes/primary_nodes/experiment.py

@dataclass(frozen=True)
class JsonAttributes(PrimaryBaseNode.JsonAttributes):
    """
    all Collection attributes
    """

    process: List[Union[Any, UIDProxy]] = field(default_factory=list)
    computation: List[Union[Any, UIDProxy]] = field(default_factory=list)
    computation_process: List[Union[Any, UIDProxy]] = field(default_factory=list)
    data: List[Union[Any, UIDProxy]] = field(default_factory=list)
    funding: List[str] = field(default_factory=list)
    citation: List[Union[Any, UIDProxy]] = field(default_factory=list)

__init__(name, process=None, computation=None, computation_process=None, data=None, funding=None, citation=None, notes='', **kwargs)

create an Experiment node

Examples:

>>> import cript
>>> my_experiment = cript.Experiment(name="my experiment name")

Parameters:

Name	Type	Description	Default
name	str	name of Experiment	required
process	Optional[List[Union[Any, UIDProxy]]]	list of Process nodes for this Experiment	None
computation	Optional[List[Union[Any, UIDProxy]]]	list of computation nodes for this Experiment	None
computation_process	Optional[List[Union[Any, UIDProxy]]]	list of computational_process nodes for this Experiment	None
data	Optional[List[Union[Any, UIDProxy]]]	list of data nodes for this experiment	None
funding	Optional[List[str]]	list of the funders names for this Experiment	None
citation	Optional[List[Union[Any, UIDProxy]]]	list of Citation nodes for this experiment	None
notes	str	notes for the experiment node	''

Returns:

Type	Description
None	Instantiate an Experiment node

Source code in src/cript/nodes/primary_nodes/experiment.py

@beartype
def __init__(
    self,
    name: str,
    process: Optional[List[Union[Any, UIDProxy]]] = None,
    computation: Optional[List[Union[Any, UIDProxy]]] = None,
    computation_process: Optional[List[Union[Any, UIDProxy]]] = None,
    data: Optional[List[Union[Any, UIDProxy]]] = None,
    funding: Optional[List[str]] = None,
    citation: Optional[List[Union[Any, UIDProxy]]] = None,
    notes: str = "",
    **kwargs
):
    """
    create an Experiment node

    Examples
    --------
    >>> import cript
    >>> my_experiment = cript.Experiment(name="my experiment name")

    Parameters
    ----------
    name: str
        name of Experiment
    process: List[Process]
        list of Process nodes for this Experiment
    computation: List[Computation]
        list of computation nodes for this Experiment
    computation_process: List[ComputationalProcess]
        list of computational_process nodes for this Experiment
    data: List[Data]
        list of data nodes for this experiment
    funding: List[str]
        list of the funders names for this Experiment
    citation: List[Citation]
        list of Citation nodes for this experiment
    notes: str default=""
        notes for the experiment node

    Returns
    -------
    None
        Instantiate an Experiment node
    """

    if process is None:
        process = []
    if computation is None:
        computation = []
    if computation_process is None:
        computation_process = []
    if data is None:
        data = []
    if funding is None:
        funding = []
    if citation is None:
        citation = []

    super().__init__(name=name, notes=notes, **kwargs)

    new_json_attrs = replace(
        self._json_attrs,
        name=name,
        process=process,
        computation=computation,
        computation_process=computation_process,
        data=data,
        funding=funding,
        citation=citation,
        notes=notes,
    )

    self._update_json_attrs_if_valid(new_json_attrs)