Module phc.easy.abstract.fhir_service_patient_item

Classes

class FhirServicePatientItem

Provides an abstract class and/or static methods for retrieving items from a FSS table that relates to a patient

Expand source code

class FhirServicePatientItem(FhirServiceItem):
    """Provides an abstract class and/or static methods for retrieving items
    from a FSS table that relates to a patient
    """

    @staticmethod
    def patient_key() -> str:
        return "subject.reference"

    @staticmethod
    def patient_id_prefixes() -> List[str]:
        return ["Patient/"]

    @classmethod
    def get_data_frame(
        cls,
        all_results: bool = False,
        raw: bool = False,
        id: Optional[str] = None,
        ids: List[str] = [],
        patient_id: Union[None, str] = None,
        patient_ids: List[str] = [],
        device_id: Union[None, str] = None,
        device_ids: List[str] = [],
        page_size: Union[int, None] = None,
        max_pages: Union[int, None] = None,
        query_overrides: dict = {},
        auth_args=Auth.shared(),
        ignore_cache: bool = False,
        expand_args: dict = {},
        log: bool = False,
        # Terms
        term: Optional[dict] = None,
        terms: List[dict] = [],
        max_terms: int = DEFAULT_MAX_TERMS,
        # Codes
        code: Optional[Union[str, List[str]]] = None,
        display: Optional[Union[str, List[str]]] = None,
        system: Optional[Union[str, List[str]]] = None,
        code_fields: List[str] = [],
    ):
        """Retrieve records

        Attributes
        ----------
        all_results : bool = False
            Retrieve sample of results (10) or entire set of records

        raw : bool = False
            If raw, then values will not be expanded (useful for manual
            inspection if something goes wrong)

        id : None or str = None
            Find records for a given id

        ids : List[str]
            Find records for given ids

        patient_id : None or str = None
            Find records for a given patient_id

        patient_ids : List[str]
            Find records for given patient_ids

        device_id: None or str = None
            Find records for a given device_id

        device_ids: List[str]
            Find records for given device_ids

        page_size : int
            The number of records to fetch per page

        max_pages : int
            The number of pages to retrieve (useful if working with tons of records)

        query_overrides : dict = {}
            Override any part of the elasticsearch FHIR query

        auth_args : Any
            The authenication to use for the account and project (defaults to shared)

        ignore_cache : bool = False
            Bypass the caching system that auto-saves results to a CSV file.
            Caching only occurs when all results are being retrieved.

        expand_args : Any
            Additional arguments passed to phc.Frame.expand

        log : bool = False
            Whether to log some diagnostic statements for debugging

        max_terms : int
            Maximum terms per query clause before chunking into multiple requests

        term : dict
            Add an arbitrary ES term/s to the query (includes chunking)

        terms : dict
            Add multiple arbitrary ES term/s to the query (includes chunking)

        code : str | List[str]
            Adds where clause for code value(s)

        display : str | List[str]
            Adds where clause for code display value(s)

        system : str | List[str]
            Adds where clause for code system value(s)

        code_fields : List[str]
            A list of paths to find FHIR codes in (default: codes for the given entity)

        Examples
        --------
        >>> import phc.easy as phc
        >>> phc.Auth.set({'account': '<your-account-name>'})
        >>> phc.Project.set_current('My Project Name')
        >>>
        >>> phc.Observation.get_data_frame(patient_id='<patient-id>')
        >>>
        >>> phc.Goal.get_data_frame(patient_id='<patient-id>')
        """
        query = {
            "type": "select",
            "columns": "*",
            "from": [{"table": cls.table_name()}],
        }

        code_fields = [*cls.code_fields(), *code_fields]

        def transform(df: pd.DataFrame):
            return cls.transform_results(df, **expand_args)

        # TODO: As of Feb 2023, only observations with patient references are indexed.
        # So in order to query for observations associated with a device we have to set the
        # device_id to the patient_id.
        # This is a workaround and should be fixed once The Platform properly indexes devices.
        if device_id:
            patient_id = device_id

        if device_ids:
            patient_ids = device_ids

        return Query.execute_fhir_dsl_with_options(
            query,
            transform,
            all_results,
            raw,
            query_overrides,
            auth_args,
            ignore_cache,
            id=id,
            ids=ids,
            patient_id=patient_id,
            patient_ids=patient_ids,
            page_size=page_size,
            max_pages=max_pages,
            patient_key=cls.patient_key(),
            log=log,
            patient_id_prefixes=cls.patient_id_prefixes(),
            # Terms
            term=term,
            terms=terms,
            max_terms=max_terms,
            # Codes
            code_fields=code_fields,
            code=code,
            display=display,
            system=system,
        )

    @classmethod
    def get_count_by_patient(cls, **kwargs):
        """Count records by a given field

        See argments for :func:`~phc.easy.query.Query.get_count_by_field`

        Examples
        --------
        >>> import phc.easy as phc
        >>> phc.Auth.set({'account': '<your-account-name>'})
        >>> phc.Project.set_current('My Project Name')
        >>>
        >>> phc.Observation.get_count_by_patient()
        """
        patient_key = cls.patient_key()

        df = Query.get_count_by_field(
            table_name=cls.table_name(), field=cls.patient_key(), **kwargs
        )

        # Make keys consistent (some are prefixed while others are not)
        df[patient_key] = df[patient_key].str.replace("Patient/", "")

        return df.groupby(patient_key).sum()

Ancestors

• FhirServiceItem

Subclasses

• AuditEvent
• CarePlan
• Composition
• Condition
• Consent
• DiagnosticReport
• DocumentReference
• Encounter
• Goal
• ImagingStudy
• Immunization
• Media
• MedicationAdministration
• MedicationDispense
• MedicationRequest
• MedicationStatement
• Observation
• Person
• Procedure
• ProcedureRequest
• Provenance
• ReferralRequest
• Sequence
• Specimen

Static methods

def code_fields() ‑> List[str]

Inherited from: FhirServiceItem.code_fields

Returns the code keys (e.g. when searching for codes)

def get_codes(display_query: Optional[str] = None, sample_size: Optional[int] = None, exclude_meta_tag=True, **kwargs)

Inherited from: FhirServiceItem.get_codes

Find all codes …

def get_count(query_overrides: dict = {}, auth_args=<phc.easy.auth.Auth object>)

Inherited from: FhirServiceItem.get_count

Get the count for a given FSS query

def get_count_by_field(field: str, **kwargs)

Inherited from: FhirServiceItem.get_count_by_field

Count records by a given field …

def get_count_by_patient(**kwargs)

Count records by a given field

See argments for :func:~phc.easy.query.Query.get_count_by_field

Examples

>>> import phc.easy as phc
>>> phc.Auth.set({'account': '<your-account-name>'})
>>> phc.Project.set_current('My Project Name')
>>>
>>> phc.Observation.get_count_by_patient()

Expand source code

@classmethod
def get_count_by_patient(cls, **kwargs):
    """Count records by a given field

    See argments for :func:`~phc.easy.query.Query.get_count_by_field`

    Examples
    --------
    >>> import phc.easy as phc
    >>> phc.Auth.set({'account': '<your-account-name>'})
    >>> phc.Project.set_current('My Project Name')
    >>>
    >>> phc.Observation.get_count_by_patient()
    """
    patient_key = cls.patient_key()

    df = Query.get_count_by_field(
        table_name=cls.table_name(), field=cls.patient_key(), **kwargs
    )

    # Make keys consistent (some are prefixed while others are not)
    df[patient_key] = df[patient_key].str.replace("Patient/", "")

    return df.groupby(patient_key).sum()

def get_data_frame(all_results: bool = False, raw: bool = False, id: Optional[str] = None, ids: List[str] = [], patient_id: Optional[str] = None, patient_ids: List[str] = [], device_id: Optional[str] = None, device_ids: List[str] = [], page_size: Optional[int] = None, max_pages: Optional[int] = None, query_overrides: dict = {}, auth_args=<phc.easy.auth.Auth object>, ignore_cache: bool = False, expand_args: dict = {}, log: bool = False, term: Optional[dict] = None, terms: List[dict] = [], max_terms: int = 30000, code: Union[str, List[str], None] = None, display: Union[str, List[str], None] = None, system: Union[str, List[str], None] = None, code_fields: List[str] = [])

Retrieve records

Attributes

all_results : bool = False

Retrieve sample of results (10) or entire set of records

raw : bool = False

If raw, then values will not be expanded (useful for manual inspection if something goes wrong)

id : None or str = None

Find records for a given id

ids : List[str]

Find records for given ids

patient_id : None or str = None

Find records for a given patient_id

patient_ids : List[str]

Find records for given patient_ids

device_id : None or str = None

Find records for a given device_id

device_ids : List[str]

Find records for given device_ids

page_size : int

The number of records to fetch per page

max_pages : int

The number of pages to retrieve (useful if working with tons of records)

query_overrides : dict = {}

Override any part of the elasticsearch FHIR query

auth_args : Any

The authenication to use for the account and project (defaults to shared)

ignore_cache : bool = False

Bypass the caching system that auto-saves results to a CSV file. Caching only occurs when all results are being retrieved.

expand_args : Any

Additional arguments passed to phc.Frame.expand

log : bool = False

Whether to log some diagnostic statements for debugging

max_terms : int

Maximum terms per query clause before chunking into multiple requests

term : dict

Add an arbitrary ES term/s to the query (includes chunking)

terms : dict

Add multiple arbitrary ES term/s to the query (includes chunking)

code : str | List[str]

Adds where clause for code value(s)

display : str | List[str]

Adds where clause for code display value(s)

system : str | List[str]

Adds where clause for code system value(s)

code_fields : List[str]

A list of paths to find FHIR codes in (default: codes for the given entity)

Examples

>>> import phc.easy as phc
>>> phc.Auth.set({'account': '<your-account-name>'})
>>> phc.Project.set_current('My Project Name')
>>>
>>> phc.Observation.get_data_frame(patient_id='<patient-id>')
>>>
>>> phc.Goal.get_data_frame(patient_id='<patient-id>')

Expand source code

@classmethod
def get_data_frame(
    cls,
    all_results: bool = False,
    raw: bool = False,
    id: Optional[str] = None,
    ids: List[str] = [],
    patient_id: Union[None, str] = None,
    patient_ids: List[str] = [],
    device_id: Union[None, str] = None,
    device_ids: List[str] = [],
    page_size: Union[int, None] = None,
    max_pages: Union[int, None] = None,
    query_overrides: dict = {},
    auth_args=Auth.shared(),
    ignore_cache: bool = False,
    expand_args: dict = {},
    log: bool = False,
    # Terms
    term: Optional[dict] = None,
    terms: List[dict] = [],
    max_terms: int = DEFAULT_MAX_TERMS,
    # Codes
    code: Optional[Union[str, List[str]]] = None,
    display: Optional[Union[str, List[str]]] = None,
    system: Optional[Union[str, List[str]]] = None,
    code_fields: List[str] = [],
):
    """Retrieve records

    Attributes
    ----------
    all_results : bool = False
        Retrieve sample of results (10) or entire set of records

    raw : bool = False
        If raw, then values will not be expanded (useful for manual
        inspection if something goes wrong)

    id : None or str = None
        Find records for a given id

    ids : List[str]
        Find records for given ids

    patient_id : None or str = None
        Find records for a given patient_id

    patient_ids : List[str]
        Find records for given patient_ids

    device_id: None or str = None
        Find records for a given device_id

    device_ids: List[str]
        Find records for given device_ids

    page_size : int
        The number of records to fetch per page

    max_pages : int
        The number of pages to retrieve (useful if working with tons of records)

    query_overrides : dict = {}
        Override any part of the elasticsearch FHIR query

    auth_args : Any
        The authenication to use for the account and project (defaults to shared)

    ignore_cache : bool = False
        Bypass the caching system that auto-saves results to a CSV file.
        Caching only occurs when all results are being retrieved.

    expand_args : Any
        Additional arguments passed to phc.Frame.expand

    log : bool = False
        Whether to log some diagnostic statements for debugging

    max_terms : int
        Maximum terms per query clause before chunking into multiple requests

    term : dict
        Add an arbitrary ES term/s to the query (includes chunking)

    terms : dict
        Add multiple arbitrary ES term/s to the query (includes chunking)

    code : str | List[str]
        Adds where clause for code value(s)

    display : str | List[str]
        Adds where clause for code display value(s)

    system : str | List[str]
        Adds where clause for code system value(s)

    code_fields : List[str]
        A list of paths to find FHIR codes in (default: codes for the given entity)

    Examples
    --------
    >>> import phc.easy as phc
    >>> phc.Auth.set({'account': '<your-account-name>'})
    >>> phc.Project.set_current('My Project Name')
    >>>
    >>> phc.Observation.get_data_frame(patient_id='<patient-id>')
    >>>
    >>> phc.Goal.get_data_frame(patient_id='<patient-id>')
    """
    query = {
        "type": "select",
        "columns": "*",
        "from": [{"table": cls.table_name()}],
    }

    code_fields = [*cls.code_fields(), *code_fields]

    def transform(df: pd.DataFrame):
        return cls.transform_results(df, **expand_args)

    # TODO: As of Feb 2023, only observations with patient references are indexed.
    # So in order to query for observations associated with a device we have to set the
    # device_id to the patient_id.
    # This is a workaround and should be fixed once The Platform properly indexes devices.
    if device_id:
        patient_id = device_id

    if device_ids:
        patient_ids = device_ids

    return Query.execute_fhir_dsl_with_options(
        query,
        transform,
        all_results,
        raw,
        query_overrides,
        auth_args,
        ignore_cache,
        id=id,
        ids=ids,
        patient_id=patient_id,
        patient_ids=patient_ids,
        page_size=page_size,
        max_pages=max_pages,
        patient_key=cls.patient_key(),
        log=log,
        patient_id_prefixes=cls.patient_id_prefixes(),
        # Terms
        term=term,
        terms=terms,
        max_terms=max_terms,
        # Codes
        code_fields=code_fields,
        code=code,
        display=display,
        system=system,
    )

def patient_id_prefixes() ‑> List[str]

Expand source code

@staticmethod
def patient_id_prefixes() -> List[str]:
    return ["Patient/"]

def patient_key() ‑> str

Expand source code

@staticmethod
def patient_key() -> str:
    return "subject.reference"

def table_name() ‑> str

Inherited from: FhirServiceItem.table_name

Returns the FSS table name for retrieval

def transform_results(data_frame: pandas.core.frame.DataFrame, **_expand_args)

Inherited from: FhirServiceItem.transform_results

Transform data frame batch