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datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py

Summary

Maintainability
D
3 days
Test Coverage
C
74%

Function add_to_halflife has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

    def add_to_halflife(self, df, growth_medium='TMA'):
        """Add df to existing rna_halflife collection
        
        Args:
            df (:obj:`pandas.DataFrame`): dataframe to be added.
Severity: Minor
Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py - About 1 hr 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 load_halflife has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    def load_halflife(self, df, growth_medium='MeOH', start=0):
        df_json = json.loads(df.to_json(orient='records'))
        row_count = len(df.index)
        for i, doc in enumerate(df_json[start:]):
            if i == self.max_entries:
Severity: Minor
Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py - About 1 hr 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 __init__ has 11 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def __init__(self, cache_dir=None, server=None, db=None, collection_str=None,
Severity: Major
Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py - About 1 hr to fix

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

                to_add = {'halflife': doc['half_life'], 'std': doc['half_life_std'], 'std_over_avg': doc['std_over_avg'],
                    'unit': 's', 'reference': [{'doi': '10.1186/s12864-016-3219-8'}], 'growth_medium': growth_medium,
                    'ordered_locus_name': doc['gene_fragment'], 'ar_cog': doc['ar_cog'], 'cog_class': doc['cog_class'],
                    'cog': doc['cog'], 'species': 'Methanosarcina acetivorans', 'ncbi_taxonomy_id': 188937}
    Severity: Major
    Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py and 1 other location - About 4 hrs to fix
    datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py on lines 79..82

    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 75.

    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

                doc['halflives'] = [{'halflife': doc['half_life'], 'std': doc['half_life_std'], 'std_over_avg': doc['std_over_avg'],
                                'unit': 's', 'reference': [{'doi': '10.1186/s12864-016-3219-8'}], 'growth_medium': growth_medium,
                                'ordered_locus_name': doc['gene_fragment'], 'ar_cog': doc['ar_cog'], 'cog_class': doc['cog_class'],
                                'cog': doc['cog'], 'species': 'Methanosarcina acetivorans', 'ncbi_taxonomy_id': 188937}]
    Severity: Major
    Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py and 1 other location - About 4 hrs to fix
    datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py on lines 126..129

    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 75.

    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 uniprot_names(self, results, count):
        """Extract protein_name and gene_name from returned
        tuple of uniprot query function
        
        Args:
    Severity: Major
    Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py and 1 other location - About 3 hrs to fix
    datanator/util/rna_halflife_util.py on lines 28..45

    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 62.

    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 doc['function'] != '-':
                self.collection.update_one({'function': doc['function']},
                                        {'$addToSet': {'halflives': to_add},
                                        '$set': {'modified': datetime.datetime.utcnow()}}, 
                                        upsert=True, collation=self.collation)
    Severity: Major
    Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py and 1 other location - About 2 hrs to fix
    datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py on lines 130..134

    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

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

                if doc['gene_name'] != '-':
                self.collection.update_one({'gene_name': doc['gene_name']},
                                        {'$addToSet': {'halflives': to_add},
                                        '$set': {'modified': datetime.datetime.utcnow()}}, 
                                        upsert=True, collation=self.collation)
    Severity: Major
    Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py and 1 other location - About 2 hrs to fix
    datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py on lines 135..139

    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

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

                    self.collection.update_one({'function': doc['function']},
                                           {'$set': doc}, upsert=True, collation=self.collation)
    Severity: Major
    Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py and 2 other locations - About 45 mins to fix
    datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py on lines 91..93
    datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py on lines 100..101

    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 35.

    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

                    self.collection.update_one({'halflives.ordered_locus_name': doc['gene_fragment']},
                                        {'$set': doc}, upsert=True, collation=self.collation)
    Severity: Major
    Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py and 2 other locations - About 45 mins to fix
    datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py on lines 91..93
    datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py on lines 96..97

    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 35.

    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

                if doc['gene_name'] != '-':
                self.collection.update_one({'gene_name': doc['gene_name']},
                                    {'$set': doc}, upsert=True, collation=self.collation)
    Severity: Major
    Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py and 2 other locations - About 45 mins to fix
    datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py on lines 96..97
    datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py on lines 100..101

    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 35.

    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

            data['half_life_std'] = data['half_life_std'].apply(lambda x: x*60)
    Severity: Minor
    Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py and 1 other location - About 45 mins to fix
    datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py on lines 67..67

    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 35.

    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

            data['half_life'] = data['half_life'].apply(lambda x: x*60)
    Severity: Minor
    Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py and 1 other location - About 45 mins to fix
    datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py on lines 68..68

    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 35.

    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

                if self.verbose and i % 100 == 0:
                print('Processing {} row {} out of {}'.format(growth_medium, i, row_count))
    Severity: Major
    Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py and 2 other locations - About 40 mins to fix
    datanator/data_source/kegg_orthology.py on lines 59..61
    datanator/data_source/kegg_reaction_class.py on lines 62..64

    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 34.

    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

                self.collection.update_one({'_id': doc['_id']},
                                       {'$set': {'gene_name': gene_name,
                                                 'protein_name': protein_name}})
    Severity: Minor
    Found in datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py and 1 other location - About 30 mins to fix
    datanator/data_source/protein_aggregate.py on lines 111..113

    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 32.

    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

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