load transfer histories

load_transfer_histories.py

import datetime
from django.utils import timezone
from django.db import transaction
from intrahospital_api.apis.prod_api import ProdApi as ProdAPI
from elcid.models import Demographics
from plugins.admissions import loader
import csv, os
from plugins.admissions.models import TransferHistory
from elcid.episode_categories import InfectionService
from intrahospital_api.loader import create_rfh_patient_from_hospital_number

# process 1
def get_mrns():
    query = """
    SELECT DISTINCT(LOCAL_PATIENT_IDENTIFIER) FROM INP.TRANSFER_HISTORY_EL_CID WITH (NOLOCK)
    """
    api = ProdAPI()
    result = api.execute_warehouse_query(query)
    return [i["LOCAL_PATIENT_IDENTIFIER"] for i in result]

def write_mrns():
    mrns = get_mrns()
    mrns = sorted([i for i in list(set(mrns)) if i])
    with open("mrns_to_process.csv" "w") as some_file:
        import csv
        writer = csv.DictWriter(some_file, fieldnames="MRN")
        writer.writeheader()
        to_write = [{"MRN": mrn} for mrn in mrns]
        writer.writerows(to_write)
        
# the in 1 shell
def load_patients():
  ## load patients in the mrns that don't exist
  pass



def load_history_for_patients(mrns):
    if len(mrns) < 20:
        histories = []
        for mrn in mrns:
            histories.extend(get_histories_for_mrn(mrn))
    else:
        histories = get_histories_for_mrns(mrns)
    return histories


def get_histories_for_mrns(mrns):
    api = ProdAPI()
    Q_GET_TRANSFERS_FOR_MRNS = """
        SELECT *
        FROM INP.TRANSFER_HISTORY_EL_CID WITH (NOLOCK)
        WHERE
        LOCAL_PATIENT_IDENTIFIER in (
            @mrn_0,
            @mrn_1,
            @mrn_2,
            @mrn_3,
            @mrn_4,
            @mrn_5,
            @mrn_6,
            @mrn_7,
            @mrn_8,
            @mrn_9,
            @mrn_10,
            @mrn_11,
            @mrn_12,
            @mrn_13,
            @mrn_14,
            @mrn_15,
            @mrn_16,
            @mrn_17,
            @mrn_18,
            @mrn_19,
            @mrn_20,
            @mrn_21,
            @mrn_22,
            @mrn_23,
            @mrn_24,
            @mrn_25,
            @mrn_26,
            @mrn_27,
            @mrn_28,
            @mrn_29,
            @mrn_30,
            @mrn_31,
            @mrn_32,
            @mrn_33,
            @mrn_34,
            @mrn_35,
            @mrn_36,
            @mrn_37,
            @mrn_38,
            @mrn_39,
            @mrn_40,
            @mrn_41,
            @mrn_42,
            @mrn_43,
            @mrn_44,
            @mrn_45,
            @mrn_46,
            @mrn_47,
            @mrn_48,
            @mrn_49
        )
    """
    params = {f"mrn_{i}": v for i, v in enumerate(mrns)}
    return api.execute_warehouse_query(
        Q_GET_TRANSFERS_FOR_MRNS, params=params
    )

def get_histories_for_mrn(mrn):
    api = ProdAPI()
    Q_GET_TRANSFERS_FOR_MRN = """
        SELECT *
        FROM INP.TRANSFER_HISTORY_EL_CID WITH (NOLOCK)
        WHERE
        LOCAL_PATIENT_IDENTIFIER = @mrn
    """
    return api.execute_warehouse_query(
        Q_GET_TRANSFERS_FOR_MRN, params={"mrn": mrn}
    )

def get_top_1():
    api = ProdAPI()
    Q_GET_TRANSFERS_FOR_MRN = """
        SELECT TOP(1) *
        FROM INP.TRANSFER_HISTORY_EL_CID WITH (NOLOCK)
    """
    return api.execute_warehouse_query(
        Q_GET_TRANSFERS_FOR_MRN
    )[0]


def load_history_for_mrns(mrns):
    if len(mrns) < 50:
        histories = []
        for mrn in mrns:
            histories.extend(get_histories_for_mrn(mrn))
    else:
        histories = get_histories_for_mrns(mrns)
    return histories


def load_all_by_patients():
    mrns = list(set(get_mrns()))
    for idx, mrn in enumerate(mrns):
        print(f'looking at {idx+1}/{len(mrns)}, {mrn}')
        result = load_for_patient(mrn)
        print(f'{len(result)} results')
        loader.create_transfer_histories_from_upstream_result(result)

@transaction.atomic
def save_histories(rows):
    demographics = Demographics.objects.filter(
        hospital_number__in=set([i["LOCAL_PATIENT_IDENTIFIER"] for i in rows])
    ).filter(patient__transferhistory=None).select_related('patient')
    mrn_to_patient = {i.hospital_number: i.patient for i in demographics}
    transfer_histories = []
    for history in rows:
        patient = mrn_to_patient.get(history["LOCAL_PATIENT_IDENTIFIER"])
        if not patient:
            continue
        hist = TransferHistory(patient=mrn_to_patient[history["LOCAL_PATIENT_IDENTIFIER"]])
        for k, v in history.items():
            if k in TransferHistory.UPSTREAM_FIELDS_TO_MODEL_FIELDS:
                if isinstance(v, datetime.datetime):
                    v = timezone.make_aware(v)
                setattr(
                    hist,
                    TransferHistory.UPSTREAM_FIELDS_TO_MODEL_FIELDS[k],
                    v
                )
        transfer_histories.append(hist)
    TransferHistory.objects.bulk_create(transfer_histories)

def filter_mrns(mrns):
    """
    Ignore MRNS already loaded or those for new patients
    """
    to_ignore = set(
        Demographics.objects.filter(hospital_number__in=mrns).exclude(
            patient__transferhistory=None
        ).values_list('hospital_number', flat=True)
    )
    return list(set(mrns) - to_ignore)

def get_mrns_to_process():
    with open("mrns_to_process.csv") as some_file:
        reader = csv.DictReader(some_file)
        rows = list([i["MRN"] for i in reader])
    return rows

def load_histories():
    rows = filter_mrns(get_mrns_to_process())
    print(f'starting to process with {len(rows)} rows')
    for i in range(0, len(rows), 50):
        to_process = rows[i:i+50]
        histories = load_history_for_mrns(to_process)
        save_histories(histories)