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datanator/data_source/pax_nosql.py

Summary

Maintainability
F
4 days
Test Coverage
B
82%

Function parse_paxDB_files has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.
Open

    def parse_paxDB_files(self):
        """ This function parses pax DB files and adds them to the NoSQL database
        """
        file_path = self.data_files[self.file_id]
        entry = {}
Severity: Minor
Found in datanator/data_source/pax_nosql.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 __init__ has 9 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def __init__(self, cache_dirname, MongoDB, db, verbose=False,
Severity: Major
Found in datanator/data_source/pax_nosql.py - About 1 hr to fix

    Function load_content has 28 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def load_content(self):
        """ Collects and Parses all data from Pax DB website and adds to MongoDB

        """
        client, db_obj, collection = self.con_db(self.collection)
    Severity: Minor
    Found in datanator/data_source/pax_nosql.py - About 1 hr to fix

      Avoid too many return statements within this function.
      Open

                      return
      Severity: Major
      Found in datanator/data_source/pax_nosql.py - About 30 mins to fix

        Avoid too many return statements within this function.
        Open

                        return
        Severity: Major
        Found in datanator/data_source/pax_nosql.py - About 30 mins to fix

          Avoid too many return statements within this function.
          Open

                  return entry
          Severity: Major
          Found in datanator/data_source/pax_nosql.py - About 30 mins to fix

            Avoid too many return statements within this function.
            Open

                            return
            Severity: Major
            Found in datanator/data_source/pax_nosql.py - About 30 mins to fix

              Function load_content has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
              Open

                  def load_content(self):
        """ Collects and Parses all data from Pax DB website and adds to MongoDB

        """
        client, db_obj, collection = self.con_db(self.collection)
              Severity: Minor
              Found in datanator/data_source/pax_nosql.py - About 25 mins 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 6 locations. Consider refactoring.
              Open

                          if field_name == '#name':
                entry['species_name'] = species_name
            else:
                print('Error found, see reports.txt')
                self.report.write(
              Severity: Major
              Found in datanator/data_source/pax_nosql.py and 5 other locations - About 4 hrs to fix
              datanator/data_source/pax_nosql.py on lines 129..136
              datanator/data_source/pax_nosql.py on lines 146..153
              datanator/data_source/pax_nosql.py on lines 161..168
              datanator/data_source/pax_nosql.py on lines 176..183
              datanator/data_source/pax_nosql.py on lines 191..198

              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 78.

              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 6 locations. Consider refactoring.
              Open

                          if field_name == '#description':
                entry['publication'] = publication
            else:
                print('Error found, see reports.txt')
                self.report.write('Warning: invalid #description field, excluding file form DB (file_id=' +
              Severity: Major
              Found in datanator/data_source/pax_nosql.py and 5 other locations - About 4 hrs to fix
              datanator/data_source/pax_nosql.py on lines 115..122
              datanator/data_source/pax_nosql.py on lines 129..136
              datanator/data_source/pax_nosql.py on lines 146..153
              datanator/data_source/pax_nosql.py on lines 176..183
              datanator/data_source/pax_nosql.py on lines 191..198

              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 78.

              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 6 locations. Consider refactoring.
              Open

                          if field_name == '#weight':
                entry['weight'] = weight
            else:
                print('Error found, see reports.txt')
                self.report.write('Warning: invalid #weight field, excluding file form DB (file_id=' +
              Severity: Major
              Found in datanator/data_source/pax_nosql.py and 5 other locations - About 4 hrs to fix
              datanator/data_source/pax_nosql.py on lines 115..122
              datanator/data_source/pax_nosql.py on lines 129..136
              datanator/data_source/pax_nosql.py on lines 161..168
              datanator/data_source/pax_nosql.py on lines 176..183
              datanator/data_source/pax_nosql.py on lines 191..198

              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 78.

              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 6 locations. Consider refactoring.
              Open

                          if field_name == '#coverage':
                entry['coverage'] = coverage
            else:
                print('Error found, see reports.txt')
                self.report.write('Warning: invalid #coverage field, excluding file form DB (file_id=' +
              Severity: Major
              Found in datanator/data_source/pax_nosql.py and 5 other locations - About 4 hrs to fix
              datanator/data_source/pax_nosql.py on lines 115..122
              datanator/data_source/pax_nosql.py on lines 129..136
              datanator/data_source/pax_nosql.py on lines 146..153
              datanator/data_source/pax_nosql.py on lines 161..168
              datanator/data_source/pax_nosql.py on lines 176..183

              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 78.

              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 6 locations. Consider refactoring.
              Open

                          if field_name == '#organ':
                entry['organ'] = organ
            else:
                print('Error found, see reports.txt')
                self.report.write(
              Severity: Major
              Found in datanator/data_source/pax_nosql.py and 5 other locations - About 4 hrs to fix
              datanator/data_source/pax_nosql.py on lines 115..122
              datanator/data_source/pax_nosql.py on lines 129..136
              datanator/data_source/pax_nosql.py on lines 146..153
              datanator/data_source/pax_nosql.py on lines 161..168
              datanator/data_source/pax_nosql.py on lines 191..198

              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 78.

              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 6 locations. Consider refactoring.
              Open

                          if field_name == '#score':
                entry['score'] = score
            else:
                print('Error found, see reports.txt')
                self.report.write(
              Severity: Major
              Found in datanator/data_source/pax_nosql.py and 5 other locations - About 4 hrs to fix
              datanator/data_source/pax_nosql.py on lines 115..122
              datanator/data_source/pax_nosql.py on lines 146..153
              datanator/data_source/pax_nosql.py on lines 161..168
              datanator/data_source/pax_nosql.py on lines 176..183
              datanator/data_source/pax_nosql.py on lines 191..198

              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 78.

              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 7 locations. Consider refactoring.
              Open

                      super(PaxNoSQL, self).__init__(cache_dirname=cache_dirname, MongoDB=MongoDB,
              Severity: Major
              Found in datanator/data_source/pax_nosql.py and 6 other locations - About 1 hr to fix
              datanator/data_source/corum_nosql.py on lines 26..26
              datanator/data_source/intact_nosql.py on lines 23..23
              datanator/data_source/kegg_orthology.py on lines 26..26
              datanator/data_source/metabolites_meta_collection.py on lines 27..27
              datanator/data_source/taxon_tree.py on lines 27..27
              datanator/util/index_collection.py on lines 19..19

              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 40.

              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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