Add simple recipe for survey results (Observation, QuestionnaireResponse, Questionnaire)

Right now, we don't have Questionnaire or QuestionnaireResponse. Each of these have to be merged with the appropriate Observation resources in order to have a nice frame of the results with the survey names and versions.

[ ] phc.Questionnaire
[ ] phc.Survey
[ ] phc.QuestionnaireResponse
[ ] phc.SurveyObservation (or SurveyResults, SurveyResponse, etc)

Example usage:

phc.SurveyObservation.get_data_frame() # => Returns observations that have the survey code

phc.Survey.get_data_frame() # => Returns surveys (questionnaires) and then you pick an ID
phc.SurveyObservation.get_data_frame(questionnaire_id="...", join_survey=True) # => (Allow multiple ids)

Here's some rough code of what's needed right now to accomplish this.

import pandas as pd

questionnaires_raw = phc.Query.execute_fhir_dsl({
    "type": "select",
    "columns": [
        {"expr": {"type": "column_ref", "column": c}}
        for c in ["id", "title", "meta", "version", "status", "date",
                  "subjectType", "identifier", "description", "contained"]
    ],
    "from": [{"table": "questionnaire"}],
}, page_size=100)

questionnaires = (
    phc.Frame
    .expand(pd.DataFrame([r["_source"] for r in questionnaires_raw]))
    .sort_values("version", ascending=False)
)

questionnaire_responses_raw = phc.Query.execute_fhir_dsl({
    "type": "select",
    "columns": [
        {"expr": {"type": "column_ref", "column": c}}
        for c in ["id", "status", "questionnaire"]
    ],
    "from": [{"table": "questionnaire_response"}],
}, all_results=True)

questionnaire_responses = phc.Frame.expand(
    pd.DataFrame([r["_source"] for r in questionnaire_responses_raw]),
    code_columns=["questionnaire"]
)

responses = phc.Observation.get_data_frame(
    code="...",
    system="http://lifeomic.com/fhir/primary-survey-id",
#     all_results=True
)

def join_observation_responses(
    observation_df: pd.DataFrame,
    questionnaire_response_df: pd.DataFrame,
    questionnaire_df: pd.DataFrame
):
    return observation_df.assign(**{
        "related.target_reference": observation_df["related.target_reference"].str.replace("QuestionnaireResponse/", "")
    }).join(
        questionnaire_response_df.set_index("id"),
        on="related.target_reference",
        rsuffix=".questionnaire_response"
    ).pipe(
        lambda df: df.assign(**{
            "questionnaire.reference": df["questionnaire.reference"].str.replace("Questionnaire/", "")
        })
    ).join(
        questionnaire_df.set_index("id"),
        on="questionnaire.reference",
        rsuffix=".questionnaire"
    )

join_observation_responses(responses, questionnaire_responses, questionnaires)[[
    "id",
    "subject.display",
    "status", # ?
    "title",
    "version",
    "status.questionnaire",
    "description",
    "status.questionnaire_response",
    "code.coding_system__lifeomic.com/fhir/questionnaire/item__code",
    "code.coding_system__lifeomic.com/fhir/questionnaire/item__display",
    "code.coding_system__lifeomic.com/fhir__code",
    "code.coding_system__lifeomic.com/fhir__display",
    "code.coding_system__lifeomic.com/fhir__userSelected",
    "valueCodeableConcept.coding_display",
    "valueCodeableConcept.coding_code",
    "valueString",
    "valueQuantity.value",
    "effectiveDateTime.local"
]].rename(columns={
    "code.coding_system__lifeomic.com/fhir/questionnaire/item__code": "item_code",
    "code.coding_system__lifeomic.com/fhir/questionnaire/item__display": "item", 
})

lifeomic / phc-sdk-py

Add simple recipe for survey results (Observation, QuestionnaireResponse, Questionnaire) #142