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KarrLab/datanator_rest_api

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Showing 272 of 273 total issues

Use of possibly insecure function - consider using safer ast.literal_eval.
Open

        projection = eval(projection)
Severity: Minor
Found in datanator_rest_api/routes/reactions.py by bandit

Method "get" has 9 parameters, which is greater than the 7 authorized.
Open

    def get(substrates, products, _from, size, bound, dof,
            taxon_distance=False, species='homo sapiens',
            projection="{'kegg_meta.gene_ortholog': 0, 'kegg_meta._id': 0, '_id': 0}"):
Severity: Major
Found in datanator_rest_api/routes/reactions.py by sonar-python

A long parameter list can indicate that a new structure should be created to wrap the numerous parameters or that the function is doing too many things.

Noncompliant Code Example

With a maximum number of 4 parameters:

def do_something(param1, param2, param3, param4, param5):
    ...

Compliant Solution

def do_something(param1, param2, param3, param4):
    ...

Remove this commented out code.
Open

            # docs = r_manager.collection.aggregate([
Severity: Major
Found in datanator_rest_api/routes/reactions.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

Remove this commented out code.
Open

            # docs = ey_manager.collection_ymdb.aggregate([
Severity: Major
Found in datanator_rest_api/routes/metabolites.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

Method "get" has 8 parameters, which is greater than the 7 authorized.
Open

    def get(substrates, products, _from, size, bound, taxon_distance=True, 
            species='homo sapiens', projection="{'kegg_meta.gene_ortholog': 0, 'kegg_meta._id': 0, '_id': 0}"):
Severity: Major
Found in datanator_rest_api/routes/reactions.py by sonar-python

A long parameter list can indicate that a new structure should be created to wrap the numerous parameters or that the function is doing too many things.

Noncompliant Code Example

With a maximum number of 4 parameters:

def do_something(param1, param2, param3, param4, param5):
    ...

Compliant Solution

def do_something(param1, param2, param3, param4):
    ...

Method "get_dist_object" has 8 parameters, which is greater than the 7 authorized.
Open

    def get_dist_object(self, doc, queried_species, distance_obj,
                    target_species, org_format='tax_id',
                    tax_field='species_name', obj_name='taxon_distance'):
Severity: Major
Found in datanator_rest_api/util/taxon_distance.py by sonar-python

A long parameter list can indicate that a new structure should be created to wrap the numerous parameters or that the function is doing too many things.

Noncompliant Code Example

With a maximum number of 4 parameters:

def do_something(param1, param2, param3, param4, param5):
    ...

Compliant Solution

def do_something(param1, param2, param3, param4):
    ...

Remove this commented out code.
Open

            # docs = ey_manager.collection_ecmdb.aggregate([
Severity: Major
Found in datanator_rest_api/routes/metabolites.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

Refactor this function to reduce its Cognitive Complexity from 21 to the 15 allowed.
Open

        def get(ko_number, _from=0, size=10, target_organism='Escherichia coli', taxon_distance=False):
Severity: Critical
Found in datanator_rest_api/routes/rna.py by sonar-python

Cognitive Complexity is a measure of how hard the control flow of a function is to understand. Functions with high Cognitive Complexity will be difficult to maintain.

See

Remove this commented out code.
Open

            # if parameter == 'k_is':
Severity: Major
Found in datanator_rest_api/routes/reactions.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

Remove this commented out code.
Open

    # gunicorn_logger = logging.getLogger('gunicorn.error')
Severity: Major
Found in datanator_rest_api/core.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

Remove this commented out code.
Open

            # pipeline = pipelines.Pipeline().aggregate_total_array_length("modifications.reference")
Severity: Major
Found in datanator_rest_api/routes/proteins.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

Remove this commented out code.
Open

# import logging
Severity: Major
Found in datanator_rest_api/core.py by sonar-python

Programmers should not comment out code as it bloats programs and reduces readability.

Unused code should be deleted and can be retrieved from source control history if required.

See

  • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
  • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
  • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
  • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"
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