Merged Data¶

merged_data ¶

MergedData Entity

Represents the result of merging the dataset with external databases.

Classes¶

MergedData `dataclass` ¶

MergedData(original_dataset: Dataset, biorempp_data: Optional[Dict[str, Any]] = None, kegg_data: Optional[Dict[str, Any]] = None, hadeg_data: Optional[Dict[str, Any]] = None, toxcsm_data: Optional[Dict[str, Any]] = None)

Entity that represents the result of the merge with databases.

This entity is immutable after creation to ensure consistency of the processed data. It contains the original dataset and the results of the merges with each of the 4 system databases.

Parameters:

Name	Type	Description	Default
`original_dataset`	`Dataset`	Original dataset before the merges	required
`biorempp_data`	`Optional[Dict[str, Any]]`	Data resulting from the merge with the BioRemPP database	`None`
`kegg_data`	`Optional[Dict[str, Any]]`	Data resulting from the merge with the KEGG database	`None`
`hadeg_data`	`Optional[Dict[str, Any]]`	Data resulting from the merge with the HADEG database	`None`
`toxcsm_data`	`Optional[Dict[str, Any]]`	Data resulting from the merge with the ToxCSM database	`None`

Raises:

Type	Description
`ValueError`	If validated without a mandatory merge (BioRemPP)

Notes

BioRemPP, KEGG, and HADEG are considered mandatory merges. ToxCSM is optional as it depends on the presence of compounds in the data.

Attributes¶

is_biorempp_merged `property` ¶

is_biorempp_merged: bool

Checks if the merge with BioRemPP was executed.

Returns:

Type	Description
`bool`	True if BioRemPP data is present and not empty.

is_kegg_merged `property` ¶

is_kegg_merged: bool

Checks if the merge with KEGG was executed.

Returns:

Type	Description
`bool`	True if KEGG data is present and not empty.

is_hadeg_merged `property` ¶

is_hadeg_merged: bool

Checks if the merge with HADEG was executed.

Returns:

Type	Description
`bool`	True if HADEG data is present and not empty.

is_toxcsm_merged `property` ¶

is_toxcsm_merged: bool

Checks if the merge with ToxCSM was executed.

Returns:

Type	Description
`bool`	True if ToxCSM data is present and not empty.

is_fully_merged `property` ¶

is_fully_merged: bool

Checks if all mandatory merges were executed.

Returns:

Type	Description
`bool`	True if BioRemPP, KEGG, and HADEG were merged.

Notes

ToxCSM is not considered mandatory as it depends on the presence of compounds in the data.

Functions¶

get_merge_status ¶

get_merge_status() -> Dict[str, bool]

Returns the status of all merges.

Returns:

Type	Description
`Dict[str, bool]`	Dictionary with the status of each database.

Examples:

>>> status = merged.get_merge_status()
>>> status
{
    'biorempp': True,
    'kegg': True,
    'hadeg': True,
    'toxcsm': False
}

Source code in src/domain/entities/merged_data.py

def get_merge_status(self) -> Dict[str, bool]:
    """
    Returns the status of all merges.

    Returns
    -------
    Dict[str, bool]
        Dictionary with the status of each database.

    Examples
    --------
    >>> status = merged.get_merge_status()
    >>> status
    {
        'biorempp': True,
        'kegg': True,
        'hadeg': True,
        'toxcsm': False
    }
    """
    return {
        "biorempp": self.is_biorempp_merged,
        "kegg": self.is_kegg_merged,
        "hadeg": self.is_hadeg_merged,
        "toxcsm": self.is_toxcsm_merged,
    }

validate ¶

validate() -> None

Validates the merge state.

Raises:

Type	Description
`ValueError`	If the BioRemPP merge was not executed (mandatory).

Notes

Only BioRemPP is validated as it is the fundamental database. KEGG and HADEG may be optional depending on the context of use.

Source code in src/domain/entities/merged_data.py

def validate(self) -> None:
    """
    Validates the merge state.

    Raises
    ------
    ValueError
        If the BioRemPP merge was not executed (mandatory).

    Notes
    -----
    Only BioRemPP is validated as it is the fundamental database.
    KEGG and HADEG may be optional depending on the context of use.
    """
    if not self.is_biorempp_merged:
        raise ValueError("BioRemPP merge is required")

str ¶

__str__() -> str

Returns the string representation of the merged data.

Returns:

Type	Description
`str`	Descriptive string of the merge status.

Source code in src/domain/entities/merged_data.py

def __str__(self) -> str:
    """
    Returns the string representation of the merged data.

    Returns
    -------
    str
        Descriptive string of the merge status.
    """
    status = self.get_merge_status()
    merged_count = sum(status.values())
    return f"MergedData ({merged_count}/4 databases merged)"

repr ¶

__repr__() -> str

Returns the debug representation of the merged data.

Returns:

Type	Description
`str`	Detailed representation.

Source code in src/domain/entities/merged_data.py

def __repr__(self) -> str:
    """
    Returns the debug representation of the merged data.

    Returns
    -------
    str
        Detailed representation.
    """
    return (
        f"MergedData("
        f"biorempp={self.is_biorempp_merged}, "
        f"kegg={self.is_kegg_merged}, "
        f"hadeg={self.is_hadeg_merged}, "
        f"toxcsm={self.is_toxcsm_merged})"
    )

Merged Data¶

merged_data ¶

Classes¶

MergedData dataclass ¶

Attributes¶

is_biorempp_merged property ¶

is_kegg_merged property ¶

is_hadeg_merged property ¶

is_toxcsm_merged property ¶

is_fully_merged property ¶

Functions¶

get_merge_status ¶

validate ¶

__str__ ¶

__repr__ ¶

MergedData `dataclass` ¶

is_biorempp_merged `property` ¶

is_kegg_merged `property` ¶

is_hadeg_merged `property` ¶

is_toxcsm_merged `property` ¶

is_fully_merged `property` ¶

str ¶

repr ¶