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

    def data_from_mongo_protein(self, server, db, username, password, verbose=False,
                                readPreference='nearest', authSource='admin', projection={'_id': 0},
                                query={}):
        ''' Acquire documents from protein collection in datanator
Severity: Major
Found in datanator/elasticsearch_kl/batch_load.py and 1 other location - About 5 hrs to fix
datanator/elasticsearch_kl/batch_load.py on lines 135..162

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 96.

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 base26_triplet_2(a):
    b0 = a[1] & 0xc0
    b1 = a[2]
    b2 = a[3] & 0x0f
    h = (b0 | b1 << 8 | b2 << 16) >> 6
Severity: Major
Found in datanator/util/base26.py and 1 other location - About 5 hrs to fix
datanator/util/base26.py on lines 27..32

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

def base26_triplet_3(a):
    b0 = a[3] & 0xf0
    b1 = a[4]
    b2 = a[5] & 0x03
    h = (b0 | b1 << 8 | b2 << 16) >> 4
Severity: Major
Found in datanator/util/base26.py and 1 other location - About 5 hrs to fix
datanator/util/base26.py on lines 19..24

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

    def index_uniprot(self, collection_str='uniprot'):
        '''Index uniprot collection
        '''
        if self.verbose:
            print('Indexing uniprot ...')
Severity: Major
Found in datanator/util/index_collection.py and 1 other location - About 5 hrs to fix
datanator/util/index_collection.py on lines 82..92

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

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

    def index_intact_complex(self, collection_str='intact_complex'):
        '''Index intact_complex collection
        '''
        if self.verbose:
            print('Indexing intact_complex ... ')
Severity: Major
Found in datanator/util/index_collection.py and 1 other location - About 5 hrs to fix
datanator/util/index_collection.py on lines 112..122

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

            for column_name in data.columns[1:]:
                if column_name != "SeqID" and column_name != "PSortVersion":
                    values_dict = {}
                    values_dict["type"] = column_name
                    values_dict["value"] = data[column_name].iloc[i]
Severity: Major
Found in datanator/data_source/protein_localization/justin_parseGramPositiveJSONSchema.py and 1 other location - About 5 hrs to fix
datanator/data_source/protein_localization/justin_parse_subcellular_location.py on lines 99..104

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 91.

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 column_name in data.columns[1:]:
                if column_name != "SeqID" and column_name != "PSortVersion":
                    values_dict = {}
                    values_dict["type"] = column_name
                    values_dict["value"] = data[column_name].iloc[i]
Severity: Major
Found in datanator/data_source/protein_localization/justin_parse_subcellular_location.py and 1 other location - About 5 hrs to fix
datanator/data_source/protein_localization/justin_parseGramPositiveJSONSchema.py on lines 35..40

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 91.

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 fill_rna_half_life has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.
Open

    def fill_rna_half_life(self, df, column, species, quantification_method='Illumina GA-II'):
        """Load df into rna_halflife collection
        
        Args:
            df (:obj:`pandas.DataFrame`): dataframe to be loaded
Severity: Minor
Found in datanator/data_source/rna_halflife/doi_10_1186_gb_2012_13_4_r30.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

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

        if "blood" in description:
            environment["condition"] = "fractionated by centrifugation, depleted of red blood cells"
            environment["media"] = "1 ml blood, anticoagulant buffer"
        else:
            if "brain" in description:
Severity: Major
Found in datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py and 1 other location - About 5 hrs to fix
datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py on lines 203..211

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 87.

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 "blood" in description:
            environment["condition"] = "fractionated by centrifugation, depleted of red blood cells"
            environment["media"] = "1 ml blood, anticoagulant buffer"
        else:
            if "brain" in description:
Severity: Major
Found in datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py and 1 other location - About 5 hrs to fix
datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py on lines 129..137

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 87.

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 i_part in range(reactants.size()):
            part_sbml = reactants.get(i_part)
            compound, compartment = self.get_specie_reference_from_sbml(part_sbml.getSpecies())
            part = ReactionParticipant(
                compound=compound,
Severity: Major
Found in datanator/data_source/sabio_rk.py and 1 other location - About 5 hrs to fix
datanator/data_source/sabio_rk.py on lines 979..987

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 86.

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 i_part in range(products.size()):
            part_sbml = products.get(i_part)
            compound, compartment = self.get_specie_reference_from_sbml(part_sbml.getSpecies())
            part = ReactionParticipant(
                compound=compound,
Severity: Major
Found in datanator/data_source/sabio_rk.py and 1 other location - About 5 hrs to fix
datanator/data_source/sabio_rk.py on lines 967..975

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 86.

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 load_compounds has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

    def load_compounds(self, compounds=None):
        """ Download information from SABIO-RK about all of the compounds stored sabio_compounds
                collection
        Args:
            compounds (:obj:`list` of :obj:`obj`): list of compounds to download
Severity: Minor
Found in datanator/data_source/sabio_rk_nosql.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 upload_backups has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

    def upload_backups(self):
        """ Backup the local sqlite database to Quilt """

        # create temporary directory to checkout package
        tmp_dirname = tempfile.mkdtemp()
Severity: Minor
Found in datanator/core/data_source.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 2 locations. Consider refactoring.
Open

                if match.group(1) == '?':
                    start = None
                    errors.append('Unknown processing start position')
                else:
                    start = int(float(match.group(1)))
Severity: Major
Found in datanator/data_source/protein_modification/pro.py and 1 other location - About 4 hrs to fix
datanator/data_source/protein_modification/pro.py on lines 393..399

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 84.

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 match.group(2) == '?':
                    end = None
                    errors.append('Unknown processing end position')
                else:
                    end = int(float(match.group(2)))
Severity: Major
Found in datanator/data_source/protein_modification/pro.py and 1 other location - About 4 hrs to fix
datanator/data_source/protein_modification/pro.py on lines 386..392

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 84.

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 core.py has 365 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Machinery for parsing k_cats and K_ms from `BRENDA <https://www.brenda-enzymes.org/>`_.

#. Download BRENDA text file from https://www.brenda-enzymes.org/download_brenda_without_registration.php.
#. Extract brenda_download.txt from zip archive and save to `./brenda_download.txt`
#. Run the parser in this module::
Severity: Minor
Found in datanator/data_source/brenda/core.py - About 4 hrs to fix

    Function _run_rrna has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.
    Open

        def _run_rrna(self, session, modomics_short_code_to_monomer, monomer_codes, out_filename):
        response = session.get(self.ENDPOINT, params={
            'RNA_type': 'rRNA',
            'RNA_subtype': 'all',
            'organism': 'all species',
    Severity: Minor
    Found in datanator/data_source/modomics.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 fill_helper has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.
    Open

        def fill_helper(self, doi, field_name, start=0, species=None):
        """Method to fill new collection across different dois.
        
        Args:
            doi (:obj:`str`): DOI of publications.
    Severity: Minor
    Found in datanator/data_source/rna_halflife/order_by_ko.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

                if i==39:
                entity["identifiers"].append({"namespace": "gene_symbol",
                                              "value":"K-"+"\u03B1"+"-1"})
            else:
                entity["identifiers"].append({"namespace": "gene_symbol",
    Severity: Major
    Found in datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py and 2 other locations - About 4 hrs to fix
    datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py on lines 46..51
    datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py on lines 217..222

    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 80.

    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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    Status
    Source
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