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File placer.py has 532 lines of code (exceeds 250 allowed). Consider refactoring.
Open

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

    Function _preflight_archivestream has a Cognitive Complexity of 56 (exceeds 5 allowed). Consider refactoring.
    Open

        def _preflight_archivestream(self, req_spec, collection=None):
        data_path = config.get_item('persistent', 'data_path')
        arc_prefix = self.get_param('prefix', 'scitran')
        file_cnt = 0
        total_size = 0
    Severity: Minor
    Found in api/download.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 213 lines of code (exceeds 25 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: Major
    Found in swagger/support/tasks/simplify-swagger.js - About 1 day to fix

      File containerhandler.py has 509 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      import bson
import datetime
import dateutil

from .. import config
      Severity: Major
      Found in api/handlers/containerhandler.py - About 1 day to fix

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

                    if ticket:
                ticket = config.db.downloads.find_one({'_id': ticket_id})
                if not ticket.get('logged', False):
                    self.log_user_access(AccessType.download_file, cont_name=cont_name, cont_id=cid, filename=fileinfo['name'])
                    config.db.downloads.update_one({'_id': ticket_id}, {'$set': {'logged': True}})
        Severity: Major
        Found in api/handlers/refererhandler.py and 1 other location - About 7 hrs to fix
        api/handlers/listhandler.py on lines 508..515

        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 119.

        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

                    if ticket:
                # recheck ticket for logged flag
                ticket = config.db.downloads.find_one({'_id': ticket_id})
                if not ticket.get('logged', False):
                    self.log_user_access(AccessType.download_file, cont_name=cont_name, cont_id=_id, filename=fileinfo['name'])
        Severity: Major
        Found in api/handlers/listhandler.py and 1 other location - About 7 hrs to fix
        api/handlers/refererhandler.py on lines 414..420

        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 119.

        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 _parse_request has a Cognitive Complexity of 49 (exceeds 5 allowed). Consider refactoring.
        Open

            def _parse_request(self, request_type='search'):

        try:
            request = self.request.json_body
        except (ValueError):
        Severity: Minor
        Found in api/handlers/dataexplorerhandler.py - About 7 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

                    for r in results:
                month = str(r['_id']['month'])
                year = str(r['_id']['year'])
                key = year+month
        Severity: Major
        Found in api/handlers/reporthandler.py and 1 other location - About 7 hrs to fix
        api/handlers/reporthandler.py on lines 779..788

        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 116.

        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

                    for r in results:
                month = str(r['_id']['month'])
                year = str(r['_id']['year'])
                key = year+month
        Severity: Major
        Found in api/handlers/reporthandler.py and 1 other location - About 7 hrs to fix
        api/handlers/reporthandler.py on lines 804..813

        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 116.

        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 hierarchy.py has 475 lines of code (exceeds 250 allowed). Consider refactoring.
        Open

        import bson
import copy
import datetime
import dateutil.parser
import difflib
        Severity: Minor
        Found in api/dao/hierarchy.py - About 7 hrs to fix

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

                  for r in results:
            month = str(r['_id']['month'])
            year = str(r['_id']['year'])
            key = year+month
          Severity: Major
          Found in api/handlers/reporthandler.py and 1 other location - About 7 hrs to fix
          api/handlers/reporthandler.py on lines 745..754

          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 114.

          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 r in results:
            month = str(r['_id']['month'])
            year = str(r['_id']['year'])
            key = year+month
          Severity: Major
          Found in api/handlers/reporthandler.py and 1 other location - About 7 hrs to fix
          api/handlers/reporthandler.py on lines 722..731

          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 114.

          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 resolve has a Cognitive Complexity of 38 (exceeds 5 allowed). Consider refactoring.
          Open

              def resolve(self):
        """Resolve a path through the hierarchy."""

        if self.public_request:
            self.abort(403, 'Request requires login')
          Severity: Minor
          Found in api/handlers/resolvehandler.py - About 5 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

              for s in sessions:
        try:
            fixed_timestamp = dateutil.parser.parse(s['timestamp'])
        except:
            config.db.sessions.update_one({'_id': s['_id']}, {'$unset': {'timestamp': ''}})
          Severity: Major
          Found in bin/database.py and 1 other location - About 5 hrs to fix
          bin/database.py on lines 501..507

          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 95.

          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 a in acquisitions:
        try:
            fixed_timestamp = dateutil.parser.parse(a['timestamp'])
        except:
            config.db.sessions.update_one({'_id': a['_id']}, {'$unset': {'timestamp': ''}})
          Severity: Major
          Found in bin/database.py and 1 other location - About 5 hrs to fix
          bin/database.py on lines 492..498

          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 95.

          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 containerstorage.py has 406 lines of code (exceeds 250 allowed). Consider refactoring.
          Open

          import datetime

import bson
import copy
          Severity: Minor
          Found in api/dao/containerstorage.py - About 5 hrs to fix

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

                    if cid == 'site':
            if self.public_request:
                raise APIPermissionException('Viewing site-level rules requires login.')
            projection = {'project_id': 0}
        else:
            Severity: Major
            Found in api/jobs/handlers.py and 1 other location - About 5 hrs to fix
            api/jobs/handlers.py on lines 240..247

            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 94.

            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 cid == 'site':
            if self.public_request:
                raise APIPermissionException('Viewing site-level rules requires login.')
            projection = {'project_id': 0}
        else:
            Severity: Major
            Found in api/jobs/handlers.py and 1 other location - About 5 hrs to fix
            api/jobs/handlers.py on lines 197..204

            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 94.

            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 query and query.get('collections'):
            # Find acquisition ids in this collection, add to query
            collection_id = query.pop('collections')
            a_ids = AcquisitionStorage().get_all_el({'collections': bson.ObjectId(collection_id)}, None, {'session': 1})
            query['_id'] = {'$in': list(set([a['session'] for a in a_ids]))}
            Severity: Major
            Found in api/dao/containerstorage.py and 1 other location - About 5 hrs to fix
            api/dao/containerstorage.py on lines 276..280

            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 92.

            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 query and query.get('collections'):
            # Find acquisition ids in this collection, add to query
            collection_id = query.pop('collections')
            a_ids = AcquisitionStorage().get_all_el({'collections': bson.ObjectId(collection_id)}, None, {'session': 1})
            query['_id'] = {'$in': list(set([a['session'] for a in a_ids]))}
            Severity: Major
            Found in api/dao/containerstorage.py and 1 other location - About 5 hrs to fix
            api/dao/containerstorage.py on lines 144..148

            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 92.

            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

            Severity
            Category
            Status
            Source
            Language