organism_extract.py

import datetime
from lab import models
from opal.models import Patient
import csv

def get_demographics_dict(patient):
    result = {}
    demographics = patient.demographics_set.first()
    result["name"] = "{} {}".format(demographics.first_name, demographics.surname)
    result["hospital_number"] = demographics.hospital_number
    dob = demographics.date_of_birth
    if not dob:
        result["date_of_birth"] = ""
    else:
        dtob = datetime.datetime.combine(dob, datetime.datetime.min.time())
        result["date_of_birth"] = dtob.strftime('%d/%m/%Y')
        result["age"] = (datetime.datetime.now() - dtob).days/365
    return result


def get_lab_test_dict(patient):
    result = {}
    organisms = models.Organism.objects.filter(observation_type="Organism")
    organisms = organisms.filter(
        lab_test__patient=patient
    ).order_by("result").order_by("lab_test__datetime_ordered")
    for i, organism in enumerate(organisms):
        lab_test_number = "lab_test_{}_number".format(i)
        lab_test_ordered = "lab_test_{}_ordered".format(i)
        lab_test_organism = "lab_test_{}_organism".format(i)
        lab_test = organism.lab_test
        if "lab_number" in lab_test.extras and lab_test.extras["lab_number"]:
            result[lab_test_number] = lab_test.extras["lab_number"]
        else:
            result[lab_test_number] = ""
        if lab_test.datetime_ordered:
            result[lab_test_ordered] = lab_test.datetime_ordered.strftime('%d/%m/%Y')
        else:
            result[lab_test_ordered] = ""
        result[lab_test_organism] = organism.result
    return result

    observations = models.Observation.objects.filter(result__icontains="au").filter(observation_type="Organism")


def get_ward_dict(patient):
    return dict(ward=patient.episode_set.last().location_set.first().ward)


def get_result_dicts(patients):
    result = []
    for patient in patients:
        result_dict = {}
        result_dict.update(get_demographics_dict(patient))
        result_dict.update(get_ward_dict(patient))
        result_dict.update(get_lab_test_dict(patient))
        result.append(result_dict)
    return result

def get_keys(results):
    keys = list()
    for result in results:
        keys.extend(result.keys())
    keys = list(set(keys))
    keys = sorted(keys)
    keys.remove("ward")
    keys.remove("name")
    keys.insert(2, "ward")
    keys.insert(0, "name")
    for k in keys:
        if "10" in k:
            keys.remove(k)
            keys.append(k)
    return keys

def write_file(file_name, results, keys):
    with open(file_name, "w+") as e:
        dict_writer = csv.DictWriter(e, fieldnames=keys)
        dict_writer.writeheader()
        for row in results:
            dict_writer.writerow(row)

def get_patients(org_parital):
    observations = observations = models.Observation.objects.filter(result__icontains=org_parital).filter(observation_type="Organism")
    return Patient.objects.filter(labtest__observations__in=observations).distinct()

def get_csv(file_name, org_partial):
    patients = get_patients(org_partial)
    results_dicts = get_result_dicts(patients)
    keys = get_keys(results_dicts)
    write_file(file_name, results_dicts, keys)