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

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

    # Load auth config from file if available
    if 'SCITRAN_AUTH_CONFIG_FILE' in os.environ:
Severity: Minor
Found in api/config.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

    def validate_code(self, code, **kwargs):
        uid = self.validate_user(code)
        return {
            'access_token': code,
            'uid': uid,
Severity: Major
Found in api/auth/authproviders.py and 1 other location - About 2 hrs to fix
api/auth/authproviders.py on lines 92..98

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

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

    def validate_code(self, code, **kwargs):
        uid = self.validate_user(code)
        return {
            'access_token': code,
            'uid': uid,
Severity: Major
Found in api/auth/authproviders.py and 1 other location - About 2 hrs to fix
api/auth/authproviders.py on lines 289..295

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

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

    def create_el(self, analysis, parent_type, parent_id, origin, uid=None):
        """
        Create an analysis.
        * Fill defaults if not provided
        * Flatten input filerefs using `FileReference.get_file()`
Severity: Minor
Found in api/dao/containerstorage.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 get_parent_tree has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

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

    For example, given `sessions`, `<session_id>`, it will return:
Severity: Minor
Found in api/dao/hierarchy.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

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

import datetime
import enum as baseEnum
import errno
import hashlib
import json
Severity: Minor
Found in api/util.py - About 2 hrs to fix

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

    for schema_filepath in glob.glob(schema_path + '/mongo/*.json'):
    schema_file = os.path.basename(schema_filepath)
    mongo_schemas.add(schema_file)
    with open(schema_filepath, 'rU') as f:
    Severity: Major
    Found in api/config.py and 1 other location - About 2 hrs to fix
    api/config.py on lines 205..208

    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 52.

    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 singularize(cont_name):
    if cont_name in PLURAL_TO_SINGULAR:
        return PLURAL_TO_SINGULAR[cont_name]
    elif cont_name in SINGULAR_TO_PLURAL:
        return cont_name
    Severity: Major
    Found in api/dao/containerutil.py and 1 other location - About 2 hrs to fix
    api/dao/containerutil.py on lines 319..324

    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 52.

    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 pluralize(cont_name):
    if cont_name in SINGULAR_TO_PLURAL:
        return SINGULAR_TO_PLURAL[cont_name]
    elif cont_name in PLURAL_TO_SINGULAR:
        return cont_name
    Severity: Major
    Found in api/dao/containerutil.py and 1 other location - About 2 hrs to fix
    api/dao/containerutil.py on lines 326..331

    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 52.

    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 schema_filepath in glob.glob(schema_path + '/input/*.json'):
    schema_file = os.path.basename(schema_filepath)
    input_schemas.add(schema_file)
    with open(schema_filepath, 'rU') as f:
    Severity: Major
    Found in api/config.py and 1 other location - About 2 hrs to fix
    api/config.py on lines 197..200

    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 52.

    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

            pipeline = [
            {'$match': job_q},
            {'$project': {'month': {'$month': '$created'}, 'year': {'$year': '$created'}}},
            {'$group': {'_id': {'month': '$month', 'year': '$year'}, 'jobs_completed': {'$sum':1}}}
    Severity: Major
    Found in api/handlers/reporthandler.py and 1 other location - About 2 hrs to fix
    api/handlers/reporthandler.py on lines 734..737

    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 51.

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

        def finalize(self):
        job = None
        job_ticket = None
        success = True
    Severity: Minor
    Found in api/placer.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 recalc_sessions_compliance has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
    Open

        def recalc_sessions_compliance(self, project_id=None):
        if project_id is None:
            # Recalc all projects
            projects = self.get_all_el({'template': {'$exists': True}}, None, None)
        else:
    Severity: Minor
    Found in api/dao/containerstorage.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 create_or_recreate_ttl_index has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
    Open

    def create_or_recreate_ttl_index(coll_name, index_name, ttl):
    if coll_name in db.collection_names():
        index_list = db[coll_name].index_information()
        if index_list:
            for index in index_list:
    Severity: Minor
    Found in api/config.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 parse_range_header has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
    Open

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

    https://tools.ietf.org/html/rfc7233
    Severity: Minor
    Found in api/util.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 process_file_field has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
    Open

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

            pipeline = [
            {'$match': base_query},
            {'$project': {'month': {'$month': '$created'}, 'year': {'$year': '$created'}}},
            {'$group': {'_id': {'month': '$month', 'year': '$year'}, 'session_count': {'$sum':1}}}
    Severity: Major
    Found in api/handlers/reporthandler.py and 1 other location - About 2 hrs to fix
    api/handlers/reporthandler.py on lines 711..714

    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 51.

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

    import bson.objectid
import copy

from .. import config
from ..auth import has_access
    Severity: Minor
    Found in api/dao/containerutil.py - About 2 hrs to fix

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

          def _get_group(self, _id):
        group = self.storage.get_container(_id)
        if group is not None:
            return group
        else:
      Severity: Major
      Found in api/handlers/grouphandler.py and 1 other location - About 2 hrs to fix
      api/handlers/userhandler.py on lines 199..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 50.

      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_user(self, _id):
        user = self.storage.get_container(_id)
        if user is not None:
            return user
        else:
      Severity: Major
      Found in api/handlers/userhandler.py and 1 other location - About 2 hrs to fix
      api/handlers/grouphandler.py on lines 98..103

      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 50.

      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
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