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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 getCNBP, postCNBP, is_response_success |
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logging.basicConfig(stream=sys.stdout, level=logging.INFO) |
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#logger = logging.getLogger('LORISQuery') |
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def check_DCCID(DCCID): |
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""" |
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Check if DCCID id conform. |
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:param DCCID: |
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:return: |
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""" |
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if not len(str(DCCID)) == 6: |
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return False |
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elif not str(DCCID).isnumeric(): |
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return False |
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elif DCCID > 999999: |
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return False |
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elif DCCID < 0: |
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return False |
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else: |
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return True |
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def createCandidateCNBP(token, proposded_PSCID): |
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""" |
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Create a candidate using the given PSCID |
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:param proposded_PSCID: |
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:return: DCCID |
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""" |
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logger = logging.getLogger('LORIS_CreateCNBPCandidates') |
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logger.info("Creating CNBP Candidates") |
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logger.info(proposded_PSCID) |
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PSCID_exist = checkPSCIDExist(token, proposded_PSCID) |
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if PSCID_exist: |
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return False |
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Candidate = {} |
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Candidate['Project'] = 'loris' |
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Candidate['PSCID'] = proposded_PSCID |
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Candidate['DoB'] = '2018-05-04' |
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Candidate['Gender'] = 'Female' |
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data = {"Candidate":Candidate} |
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data_json = json.dumps(data) |
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response_code, response = postCNBP(token, "candidates/", data_json) |
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if not is_response_success(response_code, 201): |
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return False, None |
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elif response is not None: # only try to decode if response is not empty! |
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response_json = response.json() |
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meta = response_json.get('Meta') |
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CandID = meta.get('CandID') |
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return True, CandID |
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else: |
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return False, None |
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def checkPSCIDExist(token, proposed_PSCID): |
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''' |
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Check if Site/Study already contain the PSCID |
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:param site: |
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:param study: |
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:return: bool for connection, bool on if such PSCID (INSTITUTIONID + PROJECTID + SUBJECTID) exist already. |
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''' |
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logger = logging.getLogger('LORIS_checkPSCIDExist') |
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logger.info("Checking if PSCID exist: "+proposed_PSCID) |
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load_dotenv() |
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institution_check = os.getenv("institutionID") |
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#Get list of projects |
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response_success, loris_project = getCNBP(token, r"projects/loris") |
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if not response_success: |
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return response_success, None |
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#Get list of candidates (Candidates in v0.0.1) |
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candidates = loris_project.get("Candidates") |
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logger.info(candidates) |
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for DCCID in candidates: #these candidates should really be only from the same ID regions. |
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response_success, candidate_json = getCNBP(token, r"candidates/"+DCCID) |
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if not response_success: |
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return response_success, False |
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# Each site following the naming convention should have SITE prefix and PI prefix and PROJECT prefix to avoid collision |
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# A site check here. |
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candidate_meta = candidate_json.get("Meta") |
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candidate_pscID = candidate_meta.get("PSCID") |
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# Not gonna check is institution ID doesn't even match. |
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if candidate_pscID[0:3] != institution_check: |
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continue |
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elif candidate_pscID == proposed_PSCID: |
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return response_success, True |
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#latest_timepoint = findLatestTimePoint(DCCID) |
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return False |
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def checkDCCIDExist(token, proposed_DCCID): |
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""" |
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Check if Site/Study already contain the PSCID |
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:param token: |
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:param proposed_DCCID: |
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:return: |
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""" |
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logger = logging.getLogger('LORIS_checkDCCIDExist') |
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logger.info("Checking if DCCID exist: "+str(proposed_DCCID)) |
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load_dotenv() |
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institution_check = os.getenv("institutionID") |
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assert (check_DCCID(proposed_DCCID)) |
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#Get list of projects |
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response, loris_project = getCNBP(token, r"projects/loris") |
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response_success = is_response_success(response, 200) |
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if not response_success: |
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logger.info("FAILED log response: " + str(response)) |
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return response_success, None |
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#Get list of candidates (Candidates in v0.0.1) |
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candidates = loris_project.get("Candidates") |
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logger.info(candidates) |
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for DCCID in candidates: |
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if str(proposed_DCCID) == DCCID: |
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return response_success, True |
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else: |
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continue |
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return response_success, False |
CNBP /
DICOMTransit
