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File database.py has 1099 lines of code (exceeds 250 allowed). Consider refactoring.
Open

#!/usr/bin/env python

import argparse
import bson
import copy
Severity: Major
Found in bin/database.py - About 2 days to fix

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

    class SessionNode(Node):

    @staticmethod
    def get_children(parent):
        acqs = _get_docs('acquisitions', 'acquisition', {'session' : parent['_id']})
    Severity: Major
    Found in api/resolver.py and 1 other location - About 1 day to fix
    api/resolver.py on lines 118..141

    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 214.

    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

    class ProjectNode(Node):

    @staticmethod
    def get_children(parent):
        sessions = _get_docs('sessions', 'session', {'project' : parent['_id']})
    Severity: Major
    Found in api/resolver.py and 1 other location - About 1 day to fix
    api/resolver.py on lines 93..116

    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 214.

    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 is_session_compliant has a Cognitive Complexity of 96 (exceeds 5 allowed). Consider refactoring.
    Open

    def is_session_compliant(session, template):
    """
    Given a project-level session template and a session,
    returns True/False if the session is in compliance with the template
    """
    Severity: Minor
    Found in api/dao/hierarchy.py - About 1 day 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

                    elif self.get_param('member') is not None:
                    zip_member = self.get_param('member')
                    try:
                        with zipfile.ZipFile(filepath) as zf:
                            self.response.headers['Content-Type'] = util.guess_mimetype(zip_member)
    Severity: Major
    Found in api/handlers/refererhandler.py and 1 other location - About 1 day to fix
    api/handlers/listhandler.py on lines 425..441

    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 199.

    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

            elif self.get_param('member') is not None:
            zip_member = self.get_param('member')
            try:
                with zipfile.ZipFile(filepath) as zf:
                    self.response.headers['Content-Type'] = util.guess_mimetype(zip_member)
    Severity: Major
    Found in api/handlers/listhandler.py and 1 other location - About 1 day to fix
    api/handlers/refererhandler.py on lines 385..401

    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 199.

    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_44():
    """
    A rerun of scitran/core issue #263

    A rerun was necessary because a bug was found when moving a session to a new project:
    Severity: Major
    Found in bin/database.py and 1 other location - About 1 day to fix
    bin/database.py on lines 543..567

    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 189.

    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_17():
    """
    scitran/core issue #557

    Reassign subject ids after bug fix in packfile code that did not properly match subjects
    Severity: Major
    Found in bin/database.py and 1 other location - About 1 day to fix
    bin/database.py on lines 1382..1410

    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 189.

    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 dataexplorerhandler.py has 710 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    import copy
import json

from elasticsearch import ElasticsearchException, TransportError, RequestError, helpers
    Severity: Major
    Found in api/handlers/dataexplorerhandler.py - About 1 day to fix

      File reporthandler.py has 704 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      import bson
import copy
import unicodecsv as csv
import datetime
import dateutil
      Severity: Major
      Found in api/handlers/reporthandler.py - About 1 day to fix

        Function upgrade_to_21 has a Cognitive Complexity of 67 (exceeds 5 allowed). Consider refactoring.
        Open

        def upgrade_to_21():
    """
    scitran/core issue #189 - Data Model v2

    Field `metadata` renamed to `info`
        Severity: Minor
        Found in bin/database.py - About 1 day 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 get has a Cognitive Complexity of 65 (exceeds 5 allowed). Consider refactoring.
        Open

            def get(self, cont_name, list_name, **kwargs):
        _id = kwargs.pop('cid')
        permchecker, storage, _, _, keycheck = self._initialize_request(cont_name, list_name, _id)
        list_name = storage.list_name
        filename = kwargs.get('name')
        Severity: Minor
        Found in api/handlers/listhandler.py - About 1 day 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

        File listhandler.py has 561 lines of code (exceeds 250 allowed). Consider refactoring.
        Open

        import os
import bson
import copy
import datetime
import dateutil
        Severity: Major
        Found in api/handlers/listhandler.py - About 1 day to fix

          Function download has a Cognitive Complexity of 60 (exceeds 5 allowed). Consider refactoring.
          Open

              def download(self, **kwargs):
        """
        .. http:get:: /api/(cont_name)*/(cid)*/analyses/(analysis_id)/{filegroup:inputs|files}/(filename)*

            * - not required
          Severity: Minor
          Found in api/handlers/refererhandler.py - About 1 day 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 exports has a Cognitive Complexity of 59 (exceeds 5 allowed). Consider refactoring.
          Open

          module.exports = function(grunt) {
    var path = require('path');
    var fs = require('fs');
    var _ = require('lodash');
    var yaml = require('js-yaml');
          Severity: Minor
          Found in swagger/support/tasks/simplify-swagger.js - About 1 day 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

          def group_permissions_sublist(handler, container):
    """
    This is the customized permissions checker for group permissions operations.
    """
    access = _get_access(handler.uid, container)
          Severity: Major
          Found in api/auth/listauth.py and 1 other location - About 1 day to fix
          api/auth/listauth.py on lines 108..122

          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 136.

          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 permissions_sublist(handler, container):
    """
    the customized permissions checker for permissions operations.
    """
    access = _get_access(handler.uid, container)
          Severity: Major
          Found in api/auth/listauth.py and 1 other location - About 1 day to fix
          api/auth/listauth.py on lines 76..90

          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 136.

          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

                  if cont_name == 'groups' and self.request.params.get('propagate') =='true':
            self._propagate_permissions(cont_name, _id, query={'permissions._id' : payload['_id']}, update={'$set': {'permissions.$.access': payload['access']}})
            self._propagate_permissions(cont_name, _id, query={'permissions._id': {'$ne': payload['_id']}}, update={'$addToSet': {'permissions': payload}})
        elif cont_name != 'groups':
            self._propagate_permissions(cont_name, _id)
          Severity: Major
          Found in api/handlers/listhandler.py and 1 other location - About 1 day to fix
          api/handlers/listhandler.py on lines 230..234

          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 132.

          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

                  if cont_name == 'groups' and self.request.params.get('propagate') =='true':
            self._propagate_permissions(cont_name, _id, query={'permissions._id' : payload['_id']}, update={'$set': {'permissions.$.access': payload['access']}})
            self._propagate_permissions(cont_name, _id, query={'permissions._id': {'$ne': payload['_id']}}, update={'$addToSet': {'permissions': payload}})
        elif cont_name != 'groups':
            self._propagate_permissions(cont_name, _id)
          Severity: Major
          Found in api/handlers/listhandler.py and 1 other location - About 1 day to fix
          api/handlers/listhandler.py on lines 217..221

          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 132.

          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 handlers.py has 533 lines of code (exceeds 250 allowed). Consider refactoring.
          Open

          """
API request handlers for the jobs module
"""
import bson
import copy
          Severity: Major
          Found in api/jobs/handlers.py - About 1 day to fix
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