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import sys |
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import os |
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import json |
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import argparse |
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import getpass |
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import logging |
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from dotenv import load_dotenv |
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from LORIS_query import number_extraction, getCNBP, putCNBP, login |
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from LORIS_candidates import check_DCCID, checkDCCIDExist |
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10
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logging.basicConfig(stream=sys.stdout, level=logging.INFO) |
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12
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def visit_number_extraction(string): |
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""" |
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A wrapper for number_extraction by calling it on a string and then return the latest one. |
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Used to deal with visitnumber list. |
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:param string: |
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:return: |
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""" |
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logger = logging.getLogger('visit_number_extraction') |
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number_extracted = number_extraction(string) |
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#return last number from the timepoint string: usually it should be V2 or T3 things like that. |
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if len(number_extracted) > 1: |
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return number_extracted[len(number_extracted)-1] |
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else: |
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return number_extracted[0] |
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def findLatestTimePoint(token, DCCID): |
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''' |
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Find and return the latest timepoint. Note that since DCCID exist, the record MUST ALREADY exist within the local SQLite database! |
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:param DCCID: |
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:return: |
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''' |
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logger = logging.getLogger('') |
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assert(check_DCCID(DCCID)) # Ensure it actually first exist. |
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response_success, candidate_json = getCNBP(token, r"candidates/" + str(DCCID)) # should exist as earlier check revealed. |
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# preliminary exit condition |
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if not response_success: |
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return response_success, None |
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candidate_visits_list = candidate_json.get("Visits") |
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if len(candidate_visits_list) > 0: |
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return candidate_visits_list[len(candidate_visits_list)-1] # return the LAST TIME POINT! |
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return None |
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def increaseTimepoint(token, DCCID): |
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""" |
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Increment the existing timepoint by check if DCCID existed, then get the latest one, then increment its number by creating a new timepoint. |
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:param token: auth token |
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:param DCCID: the DCCID of the existing subject. |
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:return: if creation request is successful, and what label is actually created. |
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""" |
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#todo: must handle the special edge case where timepoint reach V10 etc where two or three more digits are there! |
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# ensure valid input and subject actually exist. |
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assert (check_DCCID(DCCID)) |
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success, subject_exist = checkDCCIDExist(token, DCCID) |
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if not subject_exist or not success: |
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return False, None |
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latest_timepoint = findLatestTimePoint(token, DCCID) |
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if latest_timepoint is None: |
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success = createTimepoint(token, DCCID, "V1") |
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else: |
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visit_number = visit_number_extraction(latest_timepoint) |
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new_visit_number = int(visit_number) + 1 |
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load_dotenv() |
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prefix = os.getenv("timepoint_prefix") |
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timepoint_label = prefix + str(new_visit_number) |
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success = createTimepoint(token, DCCID, timepoint_label) |
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return success, timepoint_label |
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84
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85
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86
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def createTimepoint(token, DCCID, time_point): |
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""" |
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Create a timepoint of the given DCCID subject based on the timepoint provided. |
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:param token: |
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:param DCCID: |
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:param time_point: |
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:return: |
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""" |
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endpoint = r"/candidates/"+str(DCCID)+r"/"+time_point |
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MetaData = {"CandID": DCCID, "Visit": time_point, "Battery":"CNBP"} # default to CNBP for NOW |
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Meta = {"Meta": MetaData} |
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JSON = json.dumps(Meta) |
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success, response = putCNBP(token, endpoint, JSON) |
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# response should be null! |
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return success |
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102
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103
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# Only executed when running directly. |
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if __name__ == '__main__': |
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# print(login()) |
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# getCNBP("projects") |
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# assert(checkPSCIDExist("CNBP0020002")) |
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Success, token = login() |
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# createTimePoint(token, 559776, "V9") |
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success, latest_timepoint = increaseTimepoint(token, 635425) |
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print (success) |
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print (latest_timepoint) |
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113
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# print("Test complete") |
CNBP /
DICOMTransit
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