Python.LORIS.timepoint

Complexity

Total Complexity

12

Size/Duplication

Total Lines	112
Duplicated Lines	0 %

Importance

Changes

0

4 Functions

Rating	Name	Duplication	Size	Complexity
A	findLatestTimePoint()	0	20	4
A	visit_number_extraction()	0	16	2
A	createTimepoint()	0	15	1
A	increaseTimepoint()	0	31	5

import sys

This module should have a docstring.

import os
import json
import logging
from dotenv import load_dotenv
from LORIS.helper import number_extraction

Unable to import 'LORIS.helper'

from LORIS.query import getCNBP, putCNBP, login

Unable to import 'LORIS.query'

from LORIS.candidates import check_DCCID, checkDCCIDExist

Unable to import 'LORIS.candidates'

logging.basicConfig(stream=sys.stdout, level=logging.INFO)


def visit_number_extraction(string):
    """
    A wrapper for number_extraction by calling it on a string and then return the latest one.
    Used to deal with visitnumber list.
    :param string:
    :return:
    """
    logger = logging.getLogger('visit_number_extraction')

The variable logger seems to be unused.

    number_extracted = number_extraction(string)

    #return last number from the timepoint string: usually it should be V2 or T3 things like that.
    if len(number_extracted) > 1:

Unnecessary "else" after "return"

        return number_extracted[len(number_extracted)-1]
    else:
        return number_extracted[0]


def findLatestTimePoint(token, DCCID):

The name findLatestTimePoint does not conform to the function naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

The name DCCID does not conform to the argument naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

token is re-defining a name which is already available in the outer-scope (previously defined on line 107).

    '''
    Find and return the latest timepoint. Note that since DCCID exist, the record MUST ALREADY exist within the local SQLite database!

This line is too long as per the coding-style (134/100).

    :param DCCID:
    :return:
    '''
    logger = logging.getLogger('')

The variable logger seems to be unused.

    assert(check_DCCID(DCCID)) # Ensure it actually first exist.

There is an unnecessary parenthesis after assert.

    response_success, candidate_json = getCNBP(token, r"candidates/" + str(DCCID)) # should exist as earlier check revealed.

This line is too long as per the coding-style (124/100).

    # preliminary exit condition
    if not response_success:
        return response_success, None

    candidate_visits_list = candidate_json.get("Visits")

    if len(candidate_visits_list) > 0:

Do not use len(SEQUENCE) as condition value

        return candidate_visits_list[len(candidate_visits_list)-1] # return the LAST TIME POINT!
    return None

def increaseTimepoint(token, DCCID):

The name increaseTimepoint does not conform to the function naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

The name DCCID does not conform to the argument naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

token is re-defining a name which is already available in the outer-scope (previously defined on line 107).

    """
    Increment the existing timepoint by check if DCCID existed, then get the latest one, then increment its number by creating a new timepoint.

This line is too long as per the coding-style (143/100).

    :param token: auth token
    :param DCCID: the DCCID of the existing subject.
    :return: if creation request is successful, and what label is actually created.
    """
    #todo: must handle the special edge case where timepoint reach V10 etc where two or three more digits are there!

This line is too long as per the coding-style (116/100).

    # ensure valid input and subject actually exist.
    assert (check_DCCID(DCCID))

There is an unnecessary parenthesis after assert.

    success, subject_exist = checkDCCIDExist(token, DCCID)

success is re-defining a name which is already available in the outer-scope (previously defined on line 109).

    if not subject_exist or not success:
        return False, None

    latest_timepoint = findLatestTimePoint(token, DCCID)

latest_timepoint is re-defining a name which is already available in the outer-scope (previously defined on line 109).

    if latest_timepoint is None:
        success = createTimepoint(token, DCCID, "V1")
    else:
        visit_number = visit_number_extraction(latest_timepoint)
        new_visit_number = int(visit_number) + 1

        load_dotenv()
        prefix = os.getenv("timepoint_prefix")

        timepoint_label = prefix + str(new_visit_number)

        success = createTimepoint(token, DCCID, timepoint_label)

    return success, timepoint_label

The variable timepoint_label does not seem to be defined for all execution paths.

def createTimepoint(token, DCCID, time_point):

The name createTimepoint does not conform to the function naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

The name DCCID does not conform to the argument naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

token is re-defining a name which is already available in the outer-scope (previously defined on line 107).

    """
    Create a timepoint of the given DCCID subject based on the timepoint provided.
    :param token:
    :param DCCID:
    :param time_point:
    :return:
    """
    endpoint = r"/candidates/"+str(DCCID)+r"/"+time_point
    MetaData = {"CandID": DCCID, "Visit": time_point, "Battery":"CNBP"} # default to CNBP for NOW

The name MetaData does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

    Meta = {"Meta": MetaData}

The name Meta does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

    JSON = json.dumps(Meta)

The name JSON does not conform to the variable naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

    success, response = putCNBP(token, endpoint, JSON)

success is re-defining a name which is already available in the outer-scope (previously defined on line 109).

The variable response seems to be unused.

    # response should be null!
    return success


# Only executed when running directly.
if __name__ == '__main__':
    # print(login())
    # getCNBP("projects")
    # assert(checkPSCIDExist("CNBP0020002"))
    Success, token = login()

The name Success does not conform to the constant naming conventions ((([A-Z_][A-Z0-9_]*)|(__.*__))$).

The name token does not conform to the constant naming conventions ((([A-Z_][A-Z0-9_]*)|(__.*__))$).

    # createTimePoint(token, 559776, "V9")
    success, latest_timepoint = increaseTimepoint(token, 635425)

The name success does not conform to the constant naming conventions ((([A-Z_][A-Z0-9_]*)|(__.*__))$).

The name latest_timepoint does not conform to the constant naming conventions ((([A-Z_][A-Z0-9_]*)|(__.*__))$).

    print (success)

No space allowed before bracket

    print (latest_timepoint)

No space allowed before bracket

    # print("Test complete")

Final newline missing