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genome/dgi-db

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lib/genome/importers/pharmgkb/new_pharmgkb.rb

Summary

Maintainability
C
7 hrs
Test Coverage

Method create_interaction_claims has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
Open

    def create_interaction_claims
      CSV.foreach(file_path, :headers => true, :col_sep => "\t") do |row|
        next if row['Association'] == 'not associated' || row['Association'] == 'ambiguous'
        if row['Entity1_type'] == 'Gene' and row['Entity2_type'] == 'Chemical'
          gene_name = row['Entity1_name']
Severity: Minor
Found in lib/genome/importers/pharmgkb/new_pharmgkb.rb - 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

Method create_interaction_claims has 35 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    def create_interaction_claims
      CSV.foreach(file_path, :headers => true, :col_sep => "\t") do |row|
        next if row['Association'] == 'not associated' || row['Association'] == 'ambiguous'
        if row['Entity1_type'] == 'Gene' and row['Entity2_type'] == 'Chemical'
          gene_name = row['Entity1_name']
Severity: Minor
Found in lib/genome/importers/pharmgkb/new_pharmgkb.rb - About 1 hr to fix

    Method add_interaction_claim_publications has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
    Open

        def add_interaction_claim_publications(interaction_claim, source_string)
      if source_string.include?(';')
        source_string.split(';').each do |value|
          value.split(/[^\d]/).each do |pmid|
            unless pmid.nil? || pmid == ''
    Severity: Minor
    Found in lib/genome/importers/pharmgkb/new_pharmgkb.rb - 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

                drug_name = row['Entity1_name']
            pharmgkb_drug_id = row['Entity1_id']
            gene_name = row['Entity2_name']
            pharmgkb_gene_id = row['Entity2_id']
            drug_claim = create_drug_claim(drug_name, drug_name, 'PharmGKB Drug Name')
    Severity: Major
    Found in lib/genome/importers/pharmgkb/new_pharmgkb.rb and 1 other location - About 1 hr to fix
    lib/genome/importers/pharmgkb/new_pharmgkb.rb on lines 48..59

    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 58.

    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

              gene_name = row['Entity1_name']
          pharmgkb_gene_id = row['Entity1_id']
          drug_name = row['Entity2_name']
          pharmgkb_drug_id = row['Entity2_id']
          drug_claim = create_drug_claim(drug_name, drug_name, 'PharmGKB Drug Name')
    Severity: Major
    Found in lib/genome/importers/pharmgkb/new_pharmgkb.rb and 1 other location - About 1 hr to fix
    lib/genome/importers/pharmgkb/new_pharmgkb.rb on lines 63..74

    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 58.

    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

        def create_new_source
      @source ||= DataModel::Source.create(
          {
              base_url:          'http://www.pharmgkb.org',
              site_url:          'http://www.pharmgkb.org/',
    Severity: Minor
    Found in lib/genome/importers/pharmgkb/new_pharmgkb.rb and 2 other locations - About 35 mins to fix
    lib/genome/importers/cgi/new_cgi.rb on lines 27..41
    lib/genome/importers/dtc/dtc.rb on lines 27..41

    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

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