def upload_drive_api(upload_type):
file = request.files['file']
if not allowed_file(file.filename):
return error_response('invalid file')
if upload_type not in valid_types:
return error_response('invalid file type')
f = LocalFiles(file=file.read())
file_path = f.save()
try:
# upload file to drive
cloud_file_path = Drive().upload(file_path=file_path,
folder_id=folder_id,
share=True)
# delete file from local directory
f.delete()
# create patient account
uuid = Patient.create_new()
# add file url to patient file dict
obj = {"uuid": uuid, "type": upload_type, "url": cloud_file_path}
# if patient UUID is valid, add file it
if not Patient.add_file(**obj):
return error_response('uuid invalid')
return success_response(uuid)
except Exception as e:
return error_response(e)
def insert_profile():
if request.method == 'POST':
json = request.form.to_dict(flat=True)
result = check_json(
json,
['name', 'email', 'specialty', 'password', 'keywords', 'genes'])
if result:
return error_response("missing {}".format(result))
office_db = Office()
json['office_id'] = office_db.unique_id()
json['password'] = encrypt(json['password'])
json['keyword_genes'] = ast.literal_eval(json['genes'])
#remove key/value from json before insertion
del json['genes']
del json['keywords']
# TODO: check if email exists
office_db.insert(json)
return success_response(json['office_id'])
def search_genes():
keyword = request.args.get('keyword', default='', type=str)
limit = request.args.get('limit', default=100, type=int)
try:
result = Gene().search(unquote(keyword), limit)
return success_response(result)
except Exception as e:
return error_response(e)
def handle_report(report_id):
report_db_init = DB(collection='reports')
query = {"report_id": report_id}
if request.method == 'GET':
try:
report_dict = report_db_init.search_db_one(query)
if report_dict:
return success_response(report_dict)
else:
return error_response('none')
except Exception as e:
return error_response(e)
if request.method == 'DELETE':
try:
report_db_init.delete_one(query)
return success_response('ok')
except Exception as e:
print(e)
return error_response(e)
def profile_handler():
if request.method == 'POST':
json = request.form.to_dict(flat=True)
result = check_json(json, ['name', 'email', 'provider_name', 'provider_email', 'url'])
if result:
return error_response("missing {}".format(result))
User().add(json)
mailer = Mailer()
html = 'Name: {} \n Email: {} \n Provider: {} \n Provider Email: {}'.format(json['name'], json['email'], json['provider_name'], json['provider_email'])
mailer.sendMail(html=html, toaddr="*****@*****.**", subject="Meports: User provider request")
mailer.sendProviderEmail(provider_name=json['provider_name'], provider_email=json['provider_email'], client_name=json['name'], url=json['url'], client_email=json['email'])
return success_response('ok')
def generate_report():
# get office param
office_id = request.args.get('office', default=None, type=str)
source = request.args.get('source', default=None, type=str)
mag = 3
# if office param not passed use a test office_id
if office_id is None:
office_id = 'c4e482f6-e21f-11e8-9ada-d20785d6bfad'
if source is None:
return error_response('no source supplied')
# load file - if error then return such
# TODO: parser for other genome file types ( ancestry, etc. )
file = request.files['file']
report_id = REPORT_ID().generate()
temp_file_path = "{}/misc/tmp/{}".format(appConfig['ROOT_PATH'], report_id)
file.save(temp_file_path)
genome_file = REPORT_FILE(file=temp_file_path, source=source).load()
if not genome_file:
return error_response('invalid file')
# insert report ID if file parsed
REPORT_ID().insert(report_id)
report_build = REPORT_BUILD(genome_file=genome_file, mag=mag)
master_response_list = []
office = Office(office_id=office_id)
office_query = office.find_one()
filters = office.get_genes_and_keywords(query=office_query)
for filter in filters:
genes_list = filter['gene']
db_base_query = report_build.return_snps_from_genes(
genes_list=genes_list)
master_response_list += report_build.generate_report(
db_base_query, keyword=filter['keyword'])
report = {}
report['report_dict'] = report_build.uniquify(master_response_list)
report['timestamp'] = time()
report['report_id'] = report_id
report['office'] = {
"id": office_query['office_id'],
"name": office_query['name'],
"email": office_query['email']
}
session['report_id'] = report_id
os.remove(temp_file_path)
DB(collection='reports').update(query={"report_id": report_id},
updated_dict=report)
return success_response(report['report_id'])
def intake_submit_api(patient_uuid):
json = request.json
result = check_json(json, ['name', 'email', 'phone'])
if result:
return error_response("missing {}".format(result))