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Similar blocks of code found in 2 locations. Consider refactoring.
Open

        if upgraded % 1000 == 0:
            logging.info('  Processed ' + str(upgraded) + ' jobs of ' + str(maximum) + '...')
Severity: Major
Found in bin/database.py and 1 other location - About 2 hrs to fix
bin/database.py on lines 854..855

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 57.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

def upgrade_to_42():
    """
    Change container flag "archived" to container tag "hidden"
    """
    for cont_name in ['groups', 'projects', 'sessions', 'acquisitions']:
Severity: Major
Found in bin/database.py and 1 other location - About 2 hrs to fix
bin/database.py on lines 1152..1158

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 57.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Function modify_info has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

    def modify_info(self, _id, payload, modify_subject=False):

        # Support modification of subject info
        # Can be removed when subject becomes a standalone container
        info_key = 'subject.info' if modify_subject else 'info'
Severity: Minor
Found in api/dao/basecontainerstorage.py - About 2 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function upgrade_to_2 has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

def upgrade_to_2():
    """
    scitran/core PR #236

    Set file.origin.name to id if does not exist
Severity: Minor
Found in bin/database.py - About 2 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        if upgraded % 1000 == 0:
            logging.info('  Processed ' + str(upgraded) + ' batch of ' + str(maximum) + '...')
Severity: Major
Found in bin/database.py and 1 other location - About 2 hrs to fix
bin/database.py on lines 832..833

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 57.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

File config.py has 272 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import os
import copy
import glob
import json
import logging
Severity: Minor
Found in api/config.py - About 2 hrs to fix

    Function exports has 63 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

    module.exports = function(grunt) {
    var fs = require('fs');
    var path = require('path');
    var yaml = require('js-yaml');
    var _ = require('lodash');
    Severity: Major
    Found in swagger/support/tasks/schemas-to-defs.js - About 2 hrs to fix

      Function exports has 61 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

      module.exports = function(grunt) {
    var path = require('path');
    var fs = require('fs');
    var yaml = require('js-yaml');
    var resolve = require('json-refs').resolveRefs;
      Severity: Major
      Found in swagger/support/tasks/flatten-swagger.js - About 2 hrs to fix

        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.
    """
        Severity: Minor
        Found in api/auth/listauth.py - About 2 hrs to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        Identical blocks of code found in 2 locations. Consider refactoring.
        Open

                    if sibling_session:
                payload['subject']['_id'] = sibling_session.get('subject').get('_id')
            else:
                payload['subject']['_id'] = bson.ObjectId()
        Severity: Major
        Found in api/dao/containerstorage.py and 1 other location - About 2 hrs to fix
        api/dao/containerstorage.py on lines 211..214

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 55.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        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')
        Severity: Minor
        Found in api/dao/liststorage.py - About 2 hrs to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        Identical blocks of code found in 2 locations. Consider refactoring.
        Open

                    if sibling_session:
                payload['subject']['_id'] = sibling_session.get('subject').get('_id')
            else:
                payload['subject']['_id'] = bson.ObjectId()
        Severity: Major
        Found in api/dao/containerstorage.py and 1 other location - About 2 hrs to fix
        api/dao/containerstorage.py on lines 230..233

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 55.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        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
        Severity: Minor
        Found in api/web/base.py - About 2 hrs to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        Identical blocks of code found in 2 locations. Consider refactoring.
        Open

                        prefix = self._path_from_container(self._path_from_container(project['group'] + '/' + project['label'], subject, ids_of_paths, subject["code"]), session, ids_of_paths, session['_id'])
        Severity: Major
        Found in api/download.py and 1 other location - About 2 hrs to fix
        api/download.py on lines 214..214

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 55.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Identical blocks of code found in 2 locations. Consider refactoring.
        Open

                        prefix = self._path_from_container(self._path_from_container(self._path_from_container(project['group'] + '/' + project['label'], subject, ids_of_paths, subject['code']), session, ids_of_paths, session["_id"]), acq, ids_of_paths, acq['_id'])
        Severity: Major
        Found in api/download.py and 1 other location - About 2 hrs to fix
        api/download.py on lines 188..188

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 55.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        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):
        Severity: Critical
        Found in api/auth/userauth.py - About 2 hrs to fix

          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.
          Severity: Minor
          Found in api/jobs/rules.py - About 2 hrs to fix

          Cognitive Complexity

          Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

          A method's cognitive complexity is based on a few simple rules:

          • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
          • Code is considered more complex for each "break in the linear flow of the code"
          • Code is considered more complex when "flow breaking structures are nested"

          Further reading

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

              def __init__(self, gear_id, inputs, destination=None, tags=None,
          Severity: Major
          Found in api/jobs/jobs.py - About 2 hrs to fix

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                for f in container.get('files', []):
        if f['origin']['type'] not in [str(Origin.user), str(Origin.job)]:
            return True
            Severity: Major
            Found in api/dao/containerutil.py and 1 other location - About 2 hrs to fix
            api/dao/containerutil.py on lines 195..198

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 53.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                    for c in container.get(child_cont_name, []):
            for f in c.get('files', []):
                if f['origin']['type'] not in [str(Origin.user), str(Origin.job)]:
                    return True
            Severity: Major
            Found in api/dao/containerutil.py and 1 other location - About 2 hrs to fix
            api/dao/containerutil.py on lines 191..193

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 53.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

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