Sign upLogin

KarrLab/datanator_query_python

View on GitHub
Star
datanator_query_python/query/query_protein.py

Summary

Maintainability
F
2 wks
Test Coverage
D
69%

File query_protein.py has 898 lines of code (exceeds 250 allowed). Consider refactoring.
Open

from datanator_query_python.util import mongo_util, file_util
from datanator_query_python.query import query_taxon_tree, query_kegg_orthology
from pymongo.collation import Collation, CollationStrength
from pymongo import ASCENDING
from collections import deque
Severity: Major
Found in datanator_query_python/query/query_protein.py - About 2 days to fix

    QueryProtein has 30 functions (exceeds 20 allowed). Consider refactoring.
    Open

    class QueryProtein(mongo_util.MongoUtil):

    def __init__(self, username=None, password=None, server=None, authSource='admin',
                 database='datanator', max_entries=float('inf'), verbose=True, collection_str='uniprot',
                 readPreference='nearest', replicaSet=None):
    Severity: Minor
    Found in datanator_query_python/query/query_protein.py - About 3 hrs to fix

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

          def get_equivalent_protein_with_anchor(self, _id, max_distance, max_depth=float('inf')):
        '''
            Get replacement abundance value by taxonomic distance
            with the same kegg_orthology number.
      Severity: Minor
      Found in datanator_query_python/query/query_protein.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_equivalent_kegg_with_anchor_obsolete has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
      Open

          def get_equivalent_kegg_with_anchor_obsolete(self, ko, anchor, max_distance, max_depth=float('inf')):
        '''
            Get replacement abundance value by taxonomic distance
            with the same kegg_orthology number.
      Severity: Minor
      Found in datanator_query_python/query/query_protein.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_equivalent_protein has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
      Open

          def get_equivalent_protein(self, _id, max_distance, max_depth=float('inf')):
        '''
            Get replacement abundance value by taxonomic distance
            with the same kegg_orthology number.
      Severity: Minor
      Found in datanator_query_python/query/query_protein.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 10 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__(self, username=None, password=None, server=None, authSource='admin',
      Severity: Major
      Found in datanator_query_python/query/query_protein.py - About 1 hr to fix

        Function get_all_ortho has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
        Open

            def get_all_ortho(self, ko, anchor, max_distance):
        '''Get replacement abundance value by taxonomic distance
            with the same OrthoDB group number.

        Args:
        Severity: Minor
        Found in datanator_query_python/query/query_protein.py - About 55 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

        Function get_all_kegg has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
        Open

            def get_all_kegg(self, ko, anchor, max_distance):
        '''Get replacement abundance value by taxonomic distance
            with the same kegg_orthology number.

        Args:
        Severity: Minor
        Found in datanator_query_python/query/query_protein.py - About 55 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

        Function _get_common_canon_anc has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
        Open

            def _get_common_canon_anc(self, org1, org2, canon_anc_1, canon_anc_2):
        """Get canon common ancestors between species.

        Args:
            org1(:obj:`str`): Name of species 1.
        Severity: Minor
        Found in datanator_query_python/query/query_protein.py - About 35 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

        Function get_proximity_abundance_taxon has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
        Open

            def get_proximity_abundance_taxon(self, _id, max_distance=3):
        '''
            Get replacement abundance value by taxonomic distance
            with the same kegg_orthology number.
        Severity: Minor
        Found in datanator_query_python/query/query_protein.py - About 35 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

        Function get_info_by_text_abundances has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
        Open

            def get_info_by_text_abundances(self, name):
        '''
            Get proteins whose name or kegg name contains string 'name'.

            Args:
        Severity: Minor
        Found in datanator_query_python/query/query_protein.py - About 35 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

        Function get_meta_by_id has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
        Open

            def get_meta_by_id(self, _id):
        '''
            Get protein's metadata given uniprot id

            Args:
        Severity: Minor
        Found in datanator_query_python/query/query_protein.py - About 35 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

        Avoid too many return statements within this function.
        Open

                return result
        Severity: Major
        Found in datanator_query_python/query/query_protein.py - About 30 mins to fix

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

                  for level in range(levels):
            cur_id = ancestor_ids[-(level+1)]

            if level == 0:
                common_ancestors = ancestor_ids
          Severity: Major
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 2 days to fix
          datanator_query_python/query/query_protein.py on lines 523..543

          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 237.

          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 level in range(levels):
            cur_id = ancestor_ids[-(level+1)]

            if level == 0:
                common_ancestors = ancestor_ids
          Severity: Major
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 2 days to fix
          datanator_query_python/query/query_protein.py on lines 803..823

          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 237.

          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_info_by_ko(self, ko):
        '''
            Find all proteins with the same kegg orthology id.

            Args:
          Severity: Major
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 1 day to fix
          datanator_query_python/query/query_protein.py on lines 1026..1048

          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 136.

          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_info_by_orthodb(self, orthodb):
        '''
            Find all proteins with the same kegg orthology id.

            Args:
          Severity: Major
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 1 day to fix
          datanator_query_python/query/query_protein.py on lines 298..320

          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 136.

          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 doc in docs:
            ko_number = doc.get('ko_number', 'no number')
            ko_name = doc.get('ko_name', ['no name'])
            uniprot_id = doc['uniprot_id']
            index = self.file_manager.search_dict_index(result, 'ko_number', ko_number)
          Severity: Major
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 1 day to fix
          datanator_query_python/query/query_protein.py on lines 255..264

          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 124.

          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 doc in docs:
            ko_number = doc.get('ko_number', 'no number')
            ko_name = doc.get('ko_name', ['no name'])
            uniprot_id = doc['uniprot_id']
            index = self.file_manager.search_dict_index(result, 'ko_number', ko_number)
          Severity: Major
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 1 day to fix
          datanator_query_python/query/query_protein.py on lines 190..199

          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 124.

          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 distance != -1 and distance <= max_distance:
                species_canon_ancestor = obj[species+'_canon_ancestors']
                doc['canon_ancestors'] = species_canon_ancestor
                result[distance-1]['documents'].append(doc)
          Severity: Major
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 4 hrs to fix
          datanator_query_python/query/query_protein.py on lines 979..982

          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 76.

          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 distance != -1 and distance <= max_distance:
                species_canon_ancestor = obj[species+'_canon_ancestors']
                doc['canon_ancestors'] = species_canon_ancestor
                result[distance-1]['documents'].append(doc)
          Severity: Major
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 4 hrs to fix
          datanator_query_python/query/query_protein.py on lines 899..902

          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 76.

          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 len(index) == 1:
                result[index[0]]['uniprot_ids'][uniprot_id] = abundance_status
            else:
                dic = {'ko_number': ko_number, 'ko_name': ko_name, 'uniprot_ids': {uniprot_id: abundance_status}}
                result.append(dic)
          Severity: Major
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 3 hrs to fix
          datanator_query_python/query/query_protein.py on lines 291..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 70.

          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 len(index) == 1:
                result[index[0]]['uniprot_ids'][uniprot_id] = abundance_status
            else:
                dic = {'ko_number': ko_number, 'ko_name': ko_name, 'uniprot_ids': {uniprot_id: abundance_status}}
                result.append(dic)
          Severity: Major
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 3 hrs to fix
          datanator_query_python/query/query_protein.py on lines 230..234

          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 70.

          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 canon_anc_1[-1] == org2:
            distance1 = 1
            distance2 = 0
        elif canon_anc_2[-1] == org1:
            distance1 = 0
          Severity: Major
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 3 hrs to fix
          datanator_query_python/query/query_taxon_tree.py on lines 432..440

          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 64.

          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 3 locations. Consider refactoring.
          Open

                  return {str(org1): distance1, str(org2): distance2, str(org1)+'_canon_ancestors':canon_anc_1,
        str(org2)+'_canon_ancestors':canon_anc_2}
          Severity: Major
          Found in datanator_query_python/query/query_protein.py and 2 other locations - About 1 hr to fix
          datanator_query_python/query/query_taxon_tree.py on lines 403..404
          datanator_query_python/query/query_taxon_tree.py on lines 453..454

          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 41.

          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

                  query = {'$and': [{'$text': { '$search': expression } },
                         {'ncbi_taxonomy_id': {'$in' :taxon_ids}},
                         {'abundances': {'$exists': True} }]}
          Severity: Minor
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 55 mins to fix
          datanator_query_python/query/query_taxon_tree.py on lines 221..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 37.

          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 doc in docs:
            doc = json.loads(json.dumps(doc, ignore_nan=True))
            result.append(doc)
          Severity: Minor
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 50 mins to fix
          datanator_query_python/query/query_protein.py on lines 142..144

          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 36.

          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 doc in docs:
            doc = json.loads(json.dumps(doc, ignore_nan=True))
            result.append(doc)
          Severity: Minor
          Found in datanator_query_python/query/query_protein.py and 1 other location - About 50 mins to fix
          datanator_query_python/query/query_protein.py on lines 117..119

          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 36.

          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

          There are no issues that match your filters.

          Category
          Status