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Serialization

Serialization of PhenEx classes allows for easy data transfer and storage. PhenEx classes can easily be serialized with the to_dict() method on the given class. However, PhenEx also duplicates the interface of the built-in python JSON library with the dump, dumps, load and loads methods found here.

dump(obj, fp, **kwargs)

Serialize PhenEx objects as a JSON formatted stream to fp (a .write()-supporting file-like object).

Example: 

from phenex.codelists import Codelist
from phenex.phenotypes import CodelistPhenotype
import phenex.util.serialization.json as pxjson


# Initialize with a list
cl = Codelist(
    ['x', 'y', 'z'],
    'mycodelist'
)
entry = CodelistPhenotype(
    return_date="first",
    codelist=cl,
    domain="DRUG_EXPOSURE",
    date_range=study_period,
)

cohort = Cohort(
    entry=entry
)

PATH = ''

# serialize the phenex object to file
with open(PATH, "w") as f:
    pxjson.dump(cohort, f, indent=4)

Source code in phenex/util/serialization/json.py 
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def dump(obj, fp, **kwargs):
    """
    Serialize PhenEx objects as a JSON formatted stream to `fp` (a `.write()`-supporting file-like object).

    Example:
    ```python
    from phenex.codelists import Codelist
    from phenex.phenotypes import CodelistPhenotype
    import phenex.util.serialization.json as pxjson


    # Initialize with a list
    cl = Codelist(
        ['x', 'y', 'z'],
        'mycodelist'
    )
    entry = CodelistPhenotype(
        return_date="first",
        codelist=cl,
        domain="DRUG_EXPOSURE",
        date_range=study_period,
    )

    cohort = Cohort(
        entry=entry
    )

    PATH = ''

    # serialize the phenex object to file
    with open(PATH, "w") as f:
        pxjson.dump(cohort, f, indent=4)
    ```

    """
    pyjson.dump(obj.to_dict(), fp, **kwargs)

dumps(obj, **kwargs)

Serialize a PhenEx object to a JSON formatted str.

Source code in phenex/util/serialization/json.py 
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def dumps(obj, **kwargs):
    """
    Serialize a PhenEx object to a JSON formatted `str`.
    """
    return pyjson.dumps(to_dict(obj), **kwargs)

load(fp, **kwargs)

Deserialize fp (a .read()-supporting file-like object containing a JSON document) to a PhenEx object.

Example: 

PATH = ''
# serialize the phenex object to file
with open(PATH, "r") as f:
    cohort = pxjson.load(f)

Source code in phenex/util/serialization/json.py 
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def load(fp, **kwargs):
    """
    Deserialize `fp` (a `.read()`-supporting file-like object containing a JSON document) to a PhenEx object.

    Example:
    ```python
    PATH = ''
    # serialize the phenex object to file
    with open(PATH, "r") as f:
        cohort = pxjson.load(f)
    ```
    """
    data = pyjson.load(fp, **kwargs)
    return from_dict(data)

loads(s, **kwargs)

Deserialize s (a str, bytes or bytearray instance containing a JSON document) to a PhenEx object.

Source code in phenex/util/serialization/json.py 
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def loads(s, **kwargs):
    """
    Deserialize `s` (a `str`, `bytes` or `bytearray` instance containing a JSON document) to a PhenEx object.
    """
    data = pyjson.loads(s, **kwargs)
    return from_dict(data)