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Function upgrade_to_16 has a Cognitive Complexity of 28 (exceeds 5 allowed). Consider refactoring.
Open

def upgrade_to_16():
    """
    Fixes file.size sometimes being a floating-point rather than integer.
    """
Severity: Minor
Found in bin/database.py - About 4 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 check has a Cognitive Complexity of 28 (exceeds 5 allowed). Consider refactoring.
Open

    def check(self):
        self.requireTarget()

        # Check that required state exists
        if self.context.get('job_id'):
Severity: Minor
Found in api/placer.py - About 4 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 3 locations. Consider refactoring.
Open

    for x in acquisitions:
        for y in x.get('files', []):
            if y.get('size'):
                y['size'] = int(y['size'])
        config.db.acquisitions.update({"_id": x['_id']}, x)
Severity: Major
Found in bin/database.py and 2 other locations - About 4 hrs to fix
bin/database.py on lines 522..526
bin/database.py on lines 529..533

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 74.

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 3 locations. Consider refactoring.
Open

    for x in sessions:
        for y in x.get('files', []):
            if y.get('size'):
                y['size'] = int(y['size'])
        config.db.sessions.update({"_id": x['_id']}, x)
Severity: Major
Found in bin/database.py and 2 other locations - About 4 hrs to fix
bin/database.py on lines 515..519
bin/database.py on lines 529..533

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 74.

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 3 locations. Consider refactoring.
Open

    for x in projects:
        for y in x.get('files', []):
            if y.get('size'):
                y['size'] = int(y['size'])
        config.db.projects.update({"_id": x['_id']}, x)
Severity: Major
Found in bin/database.py and 2 other locations - About 4 hrs to fix
bin/database.py on lines 515..519
bin/database.py on lines 522..526

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 74.

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 base.py has 333 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import base64
import datetime
import jsonschema
import os
import pymongo
Severity: Minor
Found in api/web/base.py - About 4 hrs to fix

    Function update_el has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.
    Open

        def update_el(self, _id, payload, unset_payload=None, recursive=False, r_payload=None, replace_metadata=False):
        session = self.get_container(_id)
        if session is None:
            raise APINotFoundException('Could not find session {}'.format(_id))
    Severity: Minor
    Found in api/dao/containerstorage.py - About 3 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

        def get_parent(self, _id, cont=None, projection=None):
        if not cont:
            cont = self.get_container(_id, projection=projection)

        ps = ContainerStorage.factory(cont['parent']['type'])
    Severity: Major
    Found in api/dao/containerstorage.py and 1 other location - About 3 hrs to fix
    api/dao/containerstorage.py on lines 434..440

    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 72.

    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 get_parent_tree(self, _id, cont=None, projection=None, add_self=False):
        if not cont:
            cont = self.get_container(_id, projection=projection)

        ps = ContainerStorage.factory(cont['parent']['type'])
    Severity: Major
    Found in api/dao/containerstorage.py and 1 other location - About 3 hrs to fix
    api/dao/containerstorage.py on lines 427..432

    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 72.

    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 draft4ToOpenApi2 has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.
    Open

    SchemaTranspiler.prototype.draft4ToOpenApi2 = function(schema, defs, id) {
    var ref, defname;

    // Drop the $schema property, and make a copy
    schema = _.omit(schema, OMITTED_PROPERTIES);
    Severity: Minor
    Found in swagger/support/schema-transpiler.js - About 3 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 log_user_access has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.
    Open

        def log_user_access(self, access_type, cont_name=None, cont_id=None, filename=None, multifile=False, origin_override=None):

        if not config.get_item('core', 'access_log_enabled'):
            return
    Severity: Minor
    Found in api/web/base.py - About 3 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

    File queue.py has 316 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    """
A simple FIFO queue for jobs.
"""

import bson
    Severity: Minor
    Found in api/jobs/queue.py - About 3 hrs to fix

      Function _append_targets has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.
      Open

          def _append_targets(self, targets, cont_name, container, prefix, total_size, total_cnt, data_path, filters):
        inputs = [('input', f) for f in container.get('inputs', [])]
        outputs = [('output', f) for f in container.get('files', [])]
        for file_group, f in inputs + outputs:
            if filters:
      Severity: Minor
      Found in api/download.py - About 3 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 resolveRefs has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
      Open

      Schemas.prototype.resolveRefs = function(relpath, obj, jsonpath) {
    var $ref, parts, curpath, actualpath, pathpart;
    // Ignore examples
    if( jsonpath && jsonpath[jsonpath.length-1] === 'example' ) {
        return obj;
      Severity: Minor
      Found in swagger/support/schemas.js - About 3 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 authenticate_user_token has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
      Open

          def authenticate_user_token(self, session_token):
        """
        AuthN for user accounts. Calls self.abort on failure.

        Returns the user's UID.
      Severity: Minor
      Found in api/web/base.py - About 3 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 exclude_params is None:
            query[self.list_name] = {'$elemMatch': query_params}
        else:
            query['$and'] = [
                {self.list_name: {'$elemMatch': query_params}},
      Severity: Major
      Found in api/dao/liststorage.py and 1 other location - About 3 hrs to fix
      api/dao/liststorage.py on lines 90..95

      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 66.

      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 fileinfo.get('size') is not None:
        if type(fileinfo['size']) != int:
            log.warn('Fileinfo passed with non-integer size')
            fileinfo['size'] = int(fileinfo['size'])
      Severity: Major
      Found in api/dao/hierarchy.py and 1 other location - About 3 hrs to fix
      api/dao/hierarchy.py on lines 274..277

      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 66.

      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 fileinfo.get('size') is not None:
        if type(fileinfo['size']) != int:
            log.warn('Fileinfo passed with non-integer size')
            fileinfo['size'] = int(fileinfo['size'])
      Severity: Major
      Found in api/dao/hierarchy.py and 1 other location - About 3 hrs to fix
      api/dao/hierarchy.py on lines 257..260

      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 66.

      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 exclude_params is None:
            query[self.list_name] = {'$elemMatch': query_params}
        else:
            query['$and'] = [
                {self.list_name: {'$elemMatch': query_params}},
      Severity: Major
      Found in api/dao/liststorage.py and 1 other location - About 3 hrs to fix
      api/dao/liststorage.py on lines 136..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 66.

      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_properties has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
      Open

          def _handle_properties(cls, properties, current_field_name):

        ignore_fields = [
            '_all', 'dynamic_templates', 'analysis_reference', 'file_reference',
            'parent', 'container_type', 'origin', 'permissions', '_id',
      Severity: Minor
      Found in api/handlers/dataexplorerhandler.py - About 3 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

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