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datanator/data_source/protein_localization/victoria_insert_protein_atlas.py

Summary

Maintainability
F
6 days
Test Coverage

Function build_obs has a Cognitive Complexity of 44 (exceeds 5 allowed). Consider refactoring.
Open

    def build_obs(self, data):
        """Build observation objects from obj.
        Go into observations collection.
        Args:
            data (:obj:`Obj`): source object.
Severity: Minor
Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py - About 6 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 build_obs has 49 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    def build_obs(self, data):
        """Build observation objects from obj.
        Go into observations collection.
        Args:
            data (:obj:`Obj`): source object.
Severity: Minor
Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py - About 1 hr to fix

    Function build_entity has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
    Open

        def build_entity(self, data):
        """Build entity object from obj.
        Go into entity collection

        Args:
    Severity: Minor
    Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.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 8 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def __init__(self,
    Severity: Major
    Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py - About 1 hr to fix

      Identical blocks of code found in 4 locations. Consider refactoring.
      Open

          def __init__(self,
                 MongoDB=None,
                 db=None,
                 collection=None,
                 max_entries=float('inf'),
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 3 other locations - About 7 hrs to fix
      datanator/data_source/protein_localization/victoria_insert_archaea.py on lines 8..26
      datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 7..25
      datanator/data_source/protein_localization/victoria_insert_neg_wo_outer_membrane.py on lines 7..25

      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 114.

      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_localization/victoria_insert_protein_atlas.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_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/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

      def main():
    conf=config.Victoria()
    conf_main = config.Config()
    username = conf.USERNAME
    password = conf.PASSWORD
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 10 other locations - About 3 hrs to fix
      datanator/data_source/protein_half_lives/victoria_parse_mouse_global_quantification.py on lines 314..327
      datanator/data_source/protein_half_lives/victoria_parse_proteome_half_lives.py on lines 376..389
      datanator/data_source/protein_half_lives/victoria_parse_quantification_budding_yeast_proteome.py on lines 158..170
      datanator/data_source/protein_half_lives/victoria_parse_yeast_global_proteome_turnover.py on lines 316..329
      datanator/data_source/protein_localization/experimental.py on lines 63..74
      datanator/data_source/protein_localization/victoria_insert_archaea.py on lines 148..159
      datanator/data_source/protein_localization/victoria_insert_experimental_protein.py on lines 182..193
      datanator/data_source/protein_localization/victoria_insert_neg_wo_outer_membrane.py on lines 148..159
      datanator/data_source/rna_localization/victoria_parse_LncAtlas.py on lines 224..236
      datanator/parse_metabolite_concentration.py on lines 44..55

      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 73.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

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

                  values_p.append({"type":"RNA_"+rna+"_specificity_score","value":data["RNA "+rna.replace("_"," ")+" specificity score"]})
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 2 other locations - About 2 hrs to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 109..109
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 110..110

      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 52.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

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

                  values_p.append({"type":"RNA_"+rna+"_distribution","value":data["RNA "+rna.replace("_"," ")+" distribution"]})
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 2 other locations - About 2 hrs to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 109..109
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 111..111

      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 52.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

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

                  values_p.append({"type":"RNA_"+rna+"_specificity","value":data["RNA "+rna.replace("_"," ")+" specificity"]})
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 2 other locations - About 2 hrs to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 110..110
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 111..111

      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 52.

      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

                      values_p.append({"type":"p_val","value":data["Pathology prognostics - "+cancer.capitalize()+" cancer"]["p_val"],"description":cancer+" cancer"})
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 1 other location - About 2 hrs to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 162..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 51.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

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

                      values_p.append({"type":"prognostic type","value":data["Pathology prognostics - "+cancer.capitalize()+" cancer"]["prognostic type"],"description":cancer+" cancer"})
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 1 other location - About 2 hrs to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 164..164

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 51.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

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

              if data["Subcellular additional location"]!=None:
            for location in data["Subcellular additional location"]:
                values_p.append({"type":"subcellular location","value":location,"description":"additional"})
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 1 other location - About 1 hr to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 145..147

      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 45.

      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 data["Subcellular main location"]!=None:
            for location in data["Subcellular main location"]:
                values_p.append({"type":"subcellular location","value":location,"description":"main"})
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 1 other location - About 1 hr to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 148..150

      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 45.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

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

              for b in blood_RNA:
            values_p.append({"type":"blood_RNA_NX","value":data["Blood RNA - "+b+" [NX]"],"description":b})
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 2 other locations - About 1 hr to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 177..178
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 189..190

      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 3 locations. Consider refactoring.
      Open

              for brain in brain_RNA:
            values_p.append({"type":"brain_RNA_NX","value":data["Brain RNA - "+brain+" [NX]"],"description":brain})
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 2 other locations - About 1 hr to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 177..178
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 185..186

      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 3 locations. Consider refactoring.
      Open

              for tissue in tissue_rna:
            values_p.append({"type":"tissue_RNA_NX","value":data["Tissue RNA - "+tissue+" [NX]"],"description":tissue})
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 2 other locations - About 1 hr to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 185..186
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 189..190

      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

                      values_p.append({"type":"p_val","value":data["Pathology prognostics - "+d.capitalize()]["p_val"],"description":d})
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 1 other location - About 1 hr to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 172..172

      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 39.

      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

                      values_p.append({"type":"prognostic type","value":data["Pathology prognostics - "+d.capitalize()]["prognostic type"],"description":d})
      Severity: Major
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 1 other location - About 1 hr to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 174..174

      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 39.

      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

                          values_p.append({"type":"RNA_"+rna_data[i]+"_specific_NX","value":data["RNA "+rna_data[i].replace("_"," ")+" specific NX"][x],"description":x.replace("\\","")})
      Severity: Minor
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 2 other locations - About 30 mins to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 114..114
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 115..115

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 32.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

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

                  if data["RNA "+rna_data[i].replace("_"," ")+" specific NX"]!=None:
      Severity: Minor
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 2 other locations - About 30 mins to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 116..116
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 115..115

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 32.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

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

                      for x in data["RNA "+rna_data[i].replace("_"," ")+" specific NX"].keys():
      Severity: Minor
      Found in datanator/data_source/protein_localization/victoria_insert_protein_atlas.py and 2 other locations - About 30 mins to fix
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 114..114
      datanator/data_source/protein_localization/victoria_insert_protein_atlas.py on lines 116..116

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 32.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

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