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datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py

Summary

Maintainability
F
1 wk
Test Coverage

File victoria_parse_column_k0_mouse_brain.py has 289 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import pandas as pd
from pymongo import MongoClient
from datanator_query_python.util import mongo_util
from datanator_query_python.config import config
Severity: Minor
Found in datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py - About 2 hrs to fix

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

        def build_obs_protein(self, data, i, description):
        """Build observation objects from obj.
        Go into observations collection.
        Args:
            data (:obj:`Obj`): source object.
    Severity: Minor
    Found in datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.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 __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def __init__(self,
    Severity: Major
    Found in datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py - About 50 mins to fix

      Function build_obs_peptide has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
      Open

          def build_obs_peptide(self, data, i, description):
        """Build observation objects from obj.
        Go into observations collection.
        Args:
            data (:obj:`Obj`): source object.
      Severity: Minor
      Found in datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py - About 45 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 2 locations. Consider refactoring.
      Open

                  for i in range(len(data)):
                #update entity collection
                entity = self.build_entity_peptide(data,i)
                query = {"identifiers":{"$elemMatch":{"namespace":"uniprot_id",
                                                      "value":entity["identifiers"][0]["value"]}}}
      Severity: Major
      Found in datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py and 1 other location - About 3 days to fix
      datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py on lines 268..302

      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 399.

      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 in range(len(data)):
                #update entity collection
                entity = self.build_entity_protein(data,i)
                query = {"identifiers":{"$elemMatch":{"namespace":"uniprot_id",
                                                      "value":entity["identifiers"][0]["value"]}}}
      Severity: Major
      Found in datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py and 1 other location - About 3 days to fix
      datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py on lines 228..261

      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 399.

      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 4 locations. Consider refactoring.
      Open

          def __init__(self,
                 MongoDB=None,
                 db=None,
                 collection=None,
                 username=None,
      Severity: Major
      Found in datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py and 3 other locations - About 6 hrs to fix
      datanator/data_source/protein_half_lives/victoria_parse_mouse_global_quantification.py on lines 8..24
      datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py on lines 7..23
      datanator/data_source/protein_half_lives/victoria_parse_yeast_global_proteome_turnover.py on lines 8..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 104.

      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 11 locations. Consider refactoring.
      Open

              if doc!=None:
            for j in range(len(doc["canon_anc_names"])):
                d = {}
                d["ncbi_taxonomy_id"] = doc["canon_anc_ids"][j]
                d["name"] = doc["canon_anc_names"][j]
      Severity: Major
      Found in datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py and 10 other locations - About 6 hrs to fix
      datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py on lines 121..126
      datanator/data_source/protein_half_lives/victoria_parse_mouse_global_quantification.py on lines 225..230
      datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py on lines 126..131
      datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py on lines 257..262
      datanator/data_source/protein_half_lives/victoria_parse_quantification_budding_yeast_proteome.py on lines 98..103
      datanator/data_source/protein_half_lives/victoria_parse_yeast_global_proteome_turnover.py on lines 139..144
      datanator/data_source/protein_half_lives/victoria_parse_yeast_global_proteome_turnover.py on lines 223..228
      datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 101..106
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 198..203
      datanator/data_source/rna_localization/victoria_parse_LncAtlas.py on lines 130..135

      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 102.

      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 11 locations. Consider refactoring.
      Open

              if doc!=None:
            for j in range(len(doc["canon_anc_names"])):
                d = {}
                d["ncbi_taxonomy_id"] = doc["canon_anc_ids"][j]
                d["name"] = doc["canon_anc_names"][j]
      Severity: Major
      Found in datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py and 10 other locations - About 6 hrs to fix
      datanator/data_source/protein_half_lives/victoria_parse_column_k0_mouse_brain.py on lines 195..200
      datanator/data_source/protein_half_lives/victoria_parse_mouse_global_quantification.py on lines 225..230
      datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py on lines 126..131
      datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py on lines 257..262
      datanator/data_source/protein_half_lives/victoria_parse_quantification_budding_yeast_proteome.py on lines 98..103
      datanator/data_source/protein_half_lives/victoria_parse_yeast_global_proteome_turnover.py on lines 139..144
      datanator/data_source/protein_half_lives/victoria_parse_yeast_global_proteome_turnover.py on lines 223..228
      datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 101..106
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 198..203
      datanator/data_source/rna_localization/victoria_parse_LncAtlas.py on lines 130..135

      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 102.

      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

      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

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