Python.Integration.DICOM_to_LORIS

Complexity

Total Complexity

6

Size/Duplication

Total Lines	44
Duplicated Lines	0 %

Importance

Changes

0

1 Method

Rating	Name	Duplication	Size	Complexity
B	Integration.step2_dicom2LORIS()	0	33	6

from DICOM.elements import DICOM_elements

The name DICOM_to_LORIS does not conform to the module naming conventions ((([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$).

This module should have a docstring.

Unable to import 'DICOM.elements'

from LocalDB.query import LocalDB_query

The name query does not seem to exist in module LocalDB.

Unable to import 'LocalDB.query'

from LocalDB.schema import CNBP_blueprint

The name schema does not seem to exist in module LocalDB.

Unable to import 'LocalDB.schema'

from dotenv import load_dotenv
import logging

standard import "import logging" should be placed before "from DICOM.elements import DICOM_elements"

from DICOM.validate import DICOM_validate

Unable to import 'DICOM.validate'

Imports from package DICOM are not grouped

#from LORIS.candidates import  LORIS_candidates

class Integration:

This class should have a docstring.

The variable __class__ seems to be unused.

    @staticmethod
    def step2_dicom2LORIS(folder_paths):

The name step2_dicom2LORIS does not conform to the method naming conventions ((([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$).

        """
        Within each folder, verify they all have the same PatientID.
        :param folder_paths:
        :return:
        """

        database_path = load_dotenv("LocalDatabase")

        logger = logging.getLogger(__name__)

The variable logger seems to be unused.

        for folder in folder_paths:
            success, DICOM_files = DICOM_validate.path(folder)

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

            if not success or DICOM_files is None:
                return False

            # At this point, we know all DICOM files from the folder has the same name.
            MRN = DICOM_elements.retrieveMRN(DICOM_files[0])

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

            # Store MRN in database.
            mrn_exist_in_database, _ = LocalDB_query.check_value(database_path, CNBP_blueprint.table_name, CNBP_blueprint.keyfield, MRN)

This line is too long as per the coding-style (136/100).

            # Continue to next subject if MRN already exist in the database.
            if mrn_exist_in_database:
                continue

            # else database the subject.
            elif not mrn_exist_in_database:

                # Create the subject
                LocalDB_query.create_entry(database_path, CNBP_blueprint.table_name, CNBP_blueprint.keyfield, MRN)

This line is too long as per the coding-style (114/100).

                # Retrieve the PSCID based on the scanner protocol
                #DICOM_elements.get_ResearchProtocol()

                #LORIS_candidates.check_PSCID_compliance(PSCID)

                # Contact LORIS to request new MRN number.