Function files_sublist has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

def files_sublist(handler, container):
    """
    Files have slightly modified permissions centered around origin.
    Admin is required to remove files with an origin type other than engine or user.
    """

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Function handle_exception has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def handle_exception(self, exception, debug, return_json=False): # pylint: disable=arguments-differ
        """
        Send JSON response for exception

        For HTTP and other known exceptions, use its error code

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Function modify_info has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def modify_info(self, _id, query_params, payload):
        update = {}
        set_payload = payload.get('set')
        delete_payload = payload.get('delete')
        replace_payload = payload.get('replace')

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Consider simplifying this complex logical expression.

Open

            if handler.public_request:
                handler.abort(403, 'public request is not authorized')
            elif handler.superuser_request and not (method == 'DELETE' and _id == handler.uid):
                pass
            elif handler.user_is_admin and (method == 'DELETE' and not _id == handler.uid):

Function __init__ has 18 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def __init__(self, gear_id, inputs, destination=None, tags=None,

Function create_potential_jobs has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

def create_potential_jobs(db, container, container_type, file_):
    """
    Check all rules that apply to this file, and creates the jobs that should be run.
    Jobs are created but not enqueued.
    Returns list of potential job objects containing job ready to be inserted and rule.

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Function apply_env_variables has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

def apply_env_variables(config):
    # Overwrite default config values with SCITRAN env variables if available

    # Load auth config from file if available
    if 'SCITRAN_AUTH_CONFIG_FILE' in os.environ:

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Function create_el has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

    def create_el(self, analysis, parent_type, parent_id, origin, uid=None):
        """
        Create an analysis.
        * Fill defaults if not provided
        * Flatten input filerefs using `FileReference.get_file()`

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Function get_parent_tree has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

def get_parent_tree(cont_name, _id):
    """
    Given a contanier and an id, returns that container and its parent tree.

    For example, given `sessions`, `<session_id>`, it will return:

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File util.py has 260 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import datetime
import enum as baseEnum
import errno
import hashlib
import json

Function process_file_field has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def process_file_field(self, field, file_attrs):
        # Only create the hierarchy once
        if self.count == 0:
            # If not a superuser request, pass uid of user making the upload request
            targets = self.create_hierarchy(self.metadata, type_=self.match_type, user=self.context.get('uid'))

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Function parse_range_header has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

def parse_range_header(range_header_val, valid_units=('bytes',)):
    """
    Range header parser according to RFC7233

    https://tools.ietf.org/html/rfc7233

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Function create_or_recreate_ttl_index has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

def create_or_recreate_ttl_index(coll_name, index_name, ttl):
    if coll_name in db.collection_names():
        index_list = db[coll_name].index_information()
        if index_list:
            for index in index_list:

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Function recalc_sessions_compliance has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def recalc_sessions_compliance(self, project_id=None):
        if project_id is None:
            # Recalc all projects
            projects = self.get_all_el({'template': {'$exists': True}}, None, None)
        else:

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Function finalize has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def finalize(self):
        job = None
        job_ticket = None
        success = True

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File containerutil.py has 252 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import bson.objectid
import copy

from .. import config
from ..auth import has_access

Function _lintDuplicateNames has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

SchemaLinter.prototype._lintDuplicateNames = function(schema, filename) {
    var k, errors = [];

    if( schema.definitions ) {
        for( k in schema.definitions ) {

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Function _lintDefinitionNameStyle has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

SchemaLinter.prototype._lintDefinitionNameStyle = function(schema, filename) {
    var k, errors = [];

    if( schema.definitions ) {
        for( k in schema.definitions ) {

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Function put has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

    def put(self, cont_name, **kwargs):
        _id = kwargs.pop('cid')
        self.config = self.container_handler_configurations[cont_name]
        self.storage = self.config['storage']
        container = self._get_container(_id)

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Function upgrade_to_12 has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

def upgrade_to_12():
    """
    scitran/core PR #372

    Store job inputs on job-based analyses

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