Python.LORIS.candidates.checkPSCIDExist() - Code Metrics - Inspection of "Dicom Anonymization" - CNBP/DICOMTransit - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — master (#2)

by Yang

created 2018-08-01 16:20 UTC

Python.LORIS.candidates.checkPSCIDExist() B

↳ Parent: Python.LORIS.candidates

Complexity

Conditions

Size

Total Lines	42
Code Lines	21

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	21
dl	0
loc	42
rs	8.4426
c	0
b	0
f	0
cc	6
nop	2

import sys
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
import os
import json
import logging
from dotenv import load_dotenv
from LORIS.query import getCNBP, postCNBP, is_response_success


logging.basicConfig(stream=sys.stdout, level=logging.INFO)
#logger = logging.getLogger('LORISQuery')


def check_DCCID(DCCID):

    """
    Check if DCCID id conform.
    :param DCCID:
    :return:
    """
    if not len(str(DCCID)) == 6:

        return False
    elif not str(DCCID).isnumeric():
        return False
    elif DCCID > 999999:
        return False
    elif DCCID < 0:
        return False
    else:
        return True


def createCandidateCNBP(token, proposded_PSCID):

    """
    Create a candidate using the given PSCID
    :param proposded_PSCID:
    :return: DCCID
    """
    logger = logging.getLogger('LORIS_CreateCNBPCandidates')
    logger.info("Creating CNBP Candidates")
    logger.info(proposded_PSCID)
    PSCID_exist = checkPSCIDExist(token, proposded_PSCID)

    if PSCID_exist:
        return False

    Candidate = {}

    Candidate['Project'] = 'loris'
    Candidate['PSCID'] = proposded_PSCID
    Candidate['DoB'] = '2018-05-04'
    Candidate['Gender'] = 'Female'

    data = {"Candidate":Candidate}

    data_json = json.dumps(data)

    response_code, response = postCNBP(token, "candidates/", data_json)
    if not is_response_success(response_code, 201):

        return False, None
    elif response is not None:  # only try to decode if response is not empty!
        response_json = response.json()
        meta = response_json.get('Meta')
        CandID = meta.get('CandID')

        return True, CandID
    else:
        return False, None


def checkPSCIDExist(token, proposed_PSCID):

    '''
    Check if Site/Study already contain the PSCID
    :param site:
    :param study:
    :return: bool for connection, bool on if such PSCID (INSTITUTIONID + PROJECTID + SUBJECTID) exist already.

    '''
    logger = logging.getLogger('LORIS_checkPSCIDExist')
    logger.info("Checking if PSCID exist: "+proposed_PSCID)
    load_dotenv()
    institution_check = os.getenv("institutionID")


    #Get list of projects
    response_success, loris_project = getCNBP(token, r"projects/loris")
    if not response_success:
        return response_success, None

    #Get list of candidates (Candidates in v0.0.1)
    candidates = loris_project.get("Candidates")
    logger.info(candidates)

    for DCCID in candidates: #these candidates should really be only from the same ID regions.

        response_success, candidate_json = getCNBP(token, r"candidates/"+DCCID)
        if not response_success:
            return response_success, False
        # Each site following the naming convention should have SITE prefix and PI prefix and PROJECT prefix to avoid collision


        # A site check here.
        candidate_meta = candidate_json.get("Meta")
        candidate_pscID = candidate_meta.get("PSCID")


        # Not gonna check is institution ID doesn't even match.
        if candidate_pscID[0:3] != institution_check:
            continue

        elif candidate_pscID == proposed_PSCID:
            return response_success, True

            #latest_timepoint = findLatestTimePoint(DCCID)

    return False


def checkDCCIDExist(token, proposed_DCCID):

    """
    Check if Site/Study already contain the PSCID
    :param token: 

    :param proposed_DCCID: 

    :return: 

    """
    logger = logging.getLogger('LORIS_checkDCCIDExist')
    logger.info("Checking if DCCID exist: "+str(proposed_DCCID))
    load_dotenv()
    institution_check = os.getenv("institutionID")


    assert (check_DCCID(proposed_DCCID))


    #Get list of projects
    response, loris_project = getCNBP(token, r"projects/loris")
    response_success = is_response_success(response, 200)

    if not response_success:
        logger.info("FAILED log response: " + str(response))
        return response_success, None

    #Get list of candidates (Candidates in v0.0.1)
    candidates = loris_project.get("Candidates")
    logger.info(candidates)

    for DCCID in candidates:

        if str(proposed_DCCID) == DCCID:
            return response_success, True
        else:
            continue
    return response_success, False


1			import sys
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This module should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
2			import os
3			import json
4			import logging
5			from dotenv import load_dotenv
6			from LORIS.query import getCNBP, postCNBP, is_response_success
			0 ignored issues – show introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Unable to import 'LORIS.query' Loading history...
7
8			logging.basicConfig(stream=sys.stdout, level=logging.INFO)
9			#logger = logging.getLogger('LORISQuery')
10
11
12			def check_DCCID(DCCID):
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `check_DCCID` does not conform to the function naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `DCCID` does not conform to the argument naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
13			"""
14			Check if DCCID id conform.
15			:param DCCID:
16			:return:
17			"""
18			if not len(str(DCCID)) == 6:
			0 ignored issues – show unused-code introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Unnecessary "else" after "return" Loading history... Unused Code introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Consider changing "not len(str(DCCID)) == 6" to "len(str(DCCID)) != 6" Loading history...
19			return False
20			elif not str(DCCID).isnumeric():
21			return False
22			elif DCCID > 999999:
23			return False
24			elif DCCID < 0:
25			return False
26			else:
27			return True
28
29
30			def createCandidateCNBP(token, proposded_PSCID):
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `createCandidateCNBP` does not conform to the function naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `proposded_PSCID` does not conform to the argument naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
31			"""
32			Create a candidate using the given PSCID
33			:param proposded_PSCID:
34			:return: DCCID
35			"""
36			logger = logging.getLogger('LORIS_CreateCNBPCandidates')
37			logger.info("Creating CNBP Candidates")
38			logger.info(proposded_PSCID)
39			PSCID_exist = checkPSCIDExist(token, proposded_PSCID)
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `PSCID_exist` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
40			if PSCID_exist:
41			return False
42
43			Candidate = {}
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `Candidate` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
44			Candidate['Project'] = 'loris'
45			Candidate['PSCID'] = proposded_PSCID
46			Candidate['DoB'] = '2018-05-04'
47			Candidate['Gender'] = 'Female'
48
49			data = {"Candidate":Candidate}
50
51			data_json = json.dumps(data)
52
53			response_code, response = postCNBP(token, "candidates/", data_json)
54			if not is_response_success(response_code, 201):
			0 ignored issues – show unused-code introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Unnecessary "else" after "return" Loading history...
55			return False, None
56			elif response is not None: # only try to decode if response is not empty!
57			response_json = response.json()
58			meta = response_json.get('Meta')
59			CandID = meta.get('CandID')
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `CandID` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
60			return True, CandID
61			else:
62			return False, None
63
64
65			def checkPSCIDExist(token, proposed_PSCID):
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `checkPSCIDExist` does not conform to the function naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `proposed_PSCID` does not conform to the argument naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
66			'''
67			Check if Site/Study already contain the PSCID
68			:param site:
69			:param study:
70			:return: bool for connection, bool on if such PSCID (INSTITUTIONID + PROJECTID + SUBJECTID) exist already.
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (110/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
71			'''
72			logger = logging.getLogger('LORIS_checkPSCIDExist')
73			logger.info("Checking if PSCID exist: "+proposed_PSCID)
74			load_dotenv()
75			institution_check = os.getenv("institutionID")
76
77
78			#Get list of projects
79			response_success, loris_project = getCNBP(token, r"projects/loris")
80			if not response_success:
81			return response_success, None
82
83			#Get list of candidates (Candidates in v0.0.1)
84			candidates = loris_project.get("Candidates")
85			logger.info(candidates)
86
87			for DCCID in candidates: #these candidates should really be only from the same ID regions.
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `DCCID` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
88			response_success, candidate_json = getCNBP(token, r"candidates/"+DCCID)
89			if not response_success:
90			return response_success, False
91			# Each site following the naming convention should have SITE prefix and PI prefix and PROJECT prefix to avoid collision
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (127/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
92
93			# A site check here.
94			candidate_meta = candidate_json.get("Meta")
95			candidate_pscID = candidate_meta.get("PSCID")
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `candidate_pscID` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
96
97			# Not gonna check is institution ID doesn't even match.
98			if candidate_pscID[0:3] != institution_check:
99			continue
100
101			elif candidate_pscID == proposed_PSCID:
102			return response_success, True
103
104			#latest_timepoint = findLatestTimePoint(DCCID)
105
106			return False
107
108
109			def checkDCCIDExist(token, proposed_DCCID):
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `checkDCCIDExist` does not conform to the function naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `proposed_DCCID` does not conform to the argument naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
110			"""
111			Check if Site/Study already contain the PSCID
112			:param token:
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Trailing whitespace Loading history...
113			:param proposed_DCCID:
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Trailing whitespace Loading history...
114			:return:
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Trailing whitespace Loading history...
115			"""
116			logger = logging.getLogger('LORIS_checkDCCIDExist')
117			logger.info("Checking if DCCID exist: "+str(proposed_DCCID))
118			load_dotenv()
119			institution_check = os.getenv("institutionID")
			0 ignored issues – show Unused Code introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The variable `institution_check` seems to be unused. Loading history...
120
121			assert (check_DCCID(proposed_DCCID))
			0 ignored issues – show Unused Code Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report There is an unnecessary parenthesis after `assert`. Loading history...
122
123			#Get list of projects
124			response, loris_project = getCNBP(token, r"projects/loris")
125			response_success = is_response_success(response, 200)
126
127			if not response_success:
128			logger.info("FAILED log response: " + str(response))
129			return response_success, None
130
131			#Get list of candidates (Candidates in v0.0.1)
132			candidates = loris_project.get("Candidates")
133			logger.info(candidates)
134
135			for DCCID in candidates:
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `DCCID` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
136			if str(proposed_DCCID) == DCCID:
137			return response_success, True
138			else:
139			continue
140			return response_success, False
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Final newline missing Loading history...

CNBP / DICOMTransit

Pull Request — master (#2)

Python.LORIS.candidates.checkPSCIDExist() B

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

Filter issues like