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Method create_gene_claims has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def create_gene_claims
      CSV.foreach(file_path, :headers => true, :col_sep => "\t") do |row|
        if row['tax_id'] == '9606'
          gene_claim = create_gene_claim(row['Symbol'], 'Gene Symbol')
          create_gene_claim_alias(gene_claim, row['GeneID'], 'Gene ID')
Severity: Minor
Found in lib/genome/importers/d_gene/dgene.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method links has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def links
    {}.tap do |links|
      links['next'] = if items.last_page?
                        nil
                      else
Severity: Minor
Found in app/presenters/pagination_presenter.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method create_gene_claim_for_entry has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def create_gene_claim_for_entry(gene, category)
      gene_claim = create_gene_claim(gene['bioentity_label'], 'Gene Symbol')
      unless gene['synonym'].nil?
        gene['synonym'].each do |synonym|
          if synonym.include? 'UniProtKB:'
Severity: Minor
Found in lib/genome/online_updaters/go/updater.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method parse_rows has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

      def parse_rows(rows)
        processed_rows = []
        gene_name = ''
        width = rows.first.xpath('td').count
        rows.each do |row|
Severity: Minor
Found in lib/genome/downloaders/my_cancer_genome.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method create_gene_claims has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def create_gene_claims
      api_client = ApiClient.new
      categories.each do |category, go_id|
        start = 0
        rows = 500
Severity: Minor
Found in lib/genome/online_updaters/go/updater.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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

  def gene_id_mapping
    validate_gene_id_mapping_request(params)
    gene_claim = DataModel::GeneClaim.for_gene_id_mapping
      .where(name: params[:gene_id]).first ||
      not_found("A gene with the ID #{params[:gene_id]} was not found!")
Severity: Minor
Found in app/controllers/services_v2_controller.rb and 1 other location - About 25 mins to fix
app/controllers/services_v1_controller.rb on lines 55..61

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 30.

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

  def render_format(obj)
    respond_to do |format|
      format.json { render json: obj.to_json }
      format.xml  { render xml: obj.to_xml }
      format.all  { render json: obj.to_json }
Severity: Minor
Found in app/controllers/services_v1_controller.rb and 1 other location - About 25 mins to fix
app/controllers/services_v2_controller.rb on lines 124..128

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 30.

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

  def render_format(obj)
    respond_to do |format|
      format.json { render json: obj.to_json }
      format.xml  { render xml: obj.to_xml }
      format.all  { render json: obj.to_json }
Severity: Minor
Found in app/controllers/services_v2_controller.rb and 1 other location - About 25 mins to fix
app/controllers/services_v1_controller.rb on lines 76..80

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 30.

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 create_new_source
      @source ||= DataModel::Source.create(
          {
              base_url:          'http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067980',
              site_url:          'http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067980',
Severity: Minor
Found in lib/genome/importers/d_gene/dgene.rb and 1 other location - About 25 mins to fix
lib/genome/importers/human_protein_atlas/human_protein_atlas.rb on lines 22..36

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 29.

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 create_new_source
      @source ||= DataModel::Source.create(
          {
              base_url: 'https://wiki.nci.nih.gov/display/cageneindex/The+Cancer+Gene+Index+Gene-Disease+and+Gene-Compound+XML+Documents',
              site_url: 'https://wiki.nci.nih.gov/display/cageneindex',
Severity: Minor
Found in lib/genome/importers/nci/nci.rb and 1 other location - About 25 mins to fix
lib/genome/importers/fda/fda.rb on lines 26..40

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 29.

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 sorted_claims
    gene_claims.sort_by{ |g| [(g.gene_claim_attributes.empty? ? 1 : 0), (GeneClaimPresenter.new(g).publications.empty? ? 1 : 0), (g.gene_claim_aliases.empty? ? 1 : 0), g.sort_value] }
Severity: Minor
Found in app/presenters/gene_presenter.rb and 1 other location - About 25 mins to fix
app/presenters/drug_presenter.rb on lines 34..35

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 29.

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 create_new_source
      @source ||= DataModel::Source.create(
        {
            base_url: 'https://www.proteinatlas.org/search/protein_class%3APotential+drug+targets',
            site_url: 'https://www.proteinatlas.org/',
Severity: Minor
Found in lib/genome/importers/human_protein_atlas/human_protein_atlas.rb and 1 other location - About 25 mins to fix
lib/genome/importers/d_gene/dgene.rb on lines 21..35

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 29.

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 sorted_claims
    drug_claims.sort_by{ |d| [(d.drug_claim_attributes.empty? ? 1 : 0), (DrugClaimPresenter.new(d).publications.empty? ? 1 : 0), (d.drug_claim_aliases.empty? ? 1 : 0), d.sort_value] }
Severity: Minor
Found in app/presenters/drug_presenter.rb and 1 other location - About 25 mins to fix
app/presenters/gene_presenter.rb on lines 30..31

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 29.

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 create_new_source
      @source ||= DataModel::Source.create(
          {
              base_url: 'https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling',
              site_url: 'https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling',
Severity: Minor
Found in lib/genome/importers/fda/fda.rb and 1 other location - About 25 mins to fix
lib/genome/importers/nci/nci.rb on lines 26..40

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 29.

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 10 locations. Consider refactoring.
Open

      def self.source_info
        {
          base_url:           'http://stm.sciencemag.org/content/9/383/eaag1166',
          site_url:           'http://stm.sciencemag.org/content/9/383/eaag1166',
          citation:           'The druggable genome and support for target identification and validation in drug development. Finan C, Gaulton A, Kurger F, Lumbers T, Shah T, Engmann J, Galver L, Kelly R, Karlsson A, Santos R, Overington J, Hingorani A, Casas JP.   Sci. Transl. Med. 2017 Mar 29;9(383):eaag1166 PMID: 28356508.',
Severity: Major
Found in lib/genome/importers/hingorani_casas/hingorani_casas_tsv_importer.rb and 9 other locations - About 20 mins to fix
lib/genome/importers/bader_lab/bader_lab_tsv_importer.rb on lines 5..16
lib/genome/importers/cancer_commons/cancer_commons_tsv_importer.rb on lines 5..16
lib/genome/importers/clearity_foundation_biomarker/clearity_foundation_biomarker_tsv_importer.rb on lines 5..16
lib/genome/importers/clearity_foundation_clinical_trial/clearity_foundation_clinical_trial_tsv_importer.rb on lines 5..16
lib/genome/importers/foundation_one_interactions/foundation_one_interactions_tsv_importer.rb on lines 5..16
lib/genome/importers/idg/idg_tsv_importer.rb on lines 5..16
lib/genome/importers/my_cancer_genome_clinical_trial/my_cancer_genome_clinical_trial_tsv_importer.rb on lines 4..15
lib/genome/importers/talc/talc_tsv_importer.rb on lines 4..15
lib/genome/importers/tempus/tempus_tsv_importer.rb on lines 5..16

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 28.

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 10 locations. Consider refactoring.
Open

      def self.source_info
        {
            base_url: 'https://www.ncbi.nlm.nih.gov/pubmed/24377743',
            site_url: 'https://www.ncbi.nlm.nih.gov/pubmed/24377743',
            citation: "Morgensztern,D., Campo,M.J., Dahlberg,S.E., Doebele,R.C., Garon,E., Gerber,D.E., Goldberg,S.B., Hammerman,P.S., Heist,R.S., Hensing,T., et al. (2015) Molecularly targeted therapies in non-small-cell lung cancer annual update 2014. J. Thorac. Oncol., 10, S1–63. PMID: 25535693",
Severity: Major
Found in lib/genome/importers/talc/talc_tsv_importer.rb and 9 other locations - About 20 mins to fix
lib/genome/importers/bader_lab/bader_lab_tsv_importer.rb on lines 5..16
lib/genome/importers/cancer_commons/cancer_commons_tsv_importer.rb on lines 5..16
lib/genome/importers/clearity_foundation_biomarker/clearity_foundation_biomarker_tsv_importer.rb on lines 5..16
lib/genome/importers/clearity_foundation_clinical_trial/clearity_foundation_clinical_trial_tsv_importer.rb on lines 5..16
lib/genome/importers/foundation_one_interactions/foundation_one_interactions_tsv_importer.rb on lines 5..16
lib/genome/importers/hingorani_casas/hingorani_casas_tsv_importer.rb on lines 4..15
lib/genome/importers/idg/idg_tsv_importer.rb on lines 5..16
lib/genome/importers/my_cancer_genome_clinical_trial/my_cancer_genome_clinical_trial_tsv_importer.rb on lines 4..15
lib/genome/importers/tempus/tempus_tsv_importer.rb on lines 5..16

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 28.

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 10 locations. Consider refactoring.
Open

        def self.source_info
          {
              base_url: 'http://www.mycancergenome.org/',
              citation: 'Jain,N., Mittendorf,K.F., Holt,M., Lenoue-Newton,M., Maurer,I., Miller,C., Stachowiak,M., Botyrius,M., Cole,J., Micheel,C., et al. (2020) The My Cancer Genome clinical trial data model and trial curation workflow. J. Am. Med. Inform. Assoc., 27, 1057–1066. PMID: 32483629',
              site_url: 'http://www.mycancergenome.org/',
Severity: Major
Found in lib/genome/importers/my_cancer_genome_clinical_trial/my_cancer_genome_clinical_trial_tsv_importer.rb and 9 other locations - About 20 mins to fix
lib/genome/importers/bader_lab/bader_lab_tsv_importer.rb on lines 5..16
lib/genome/importers/cancer_commons/cancer_commons_tsv_importer.rb on lines 5..16
lib/genome/importers/clearity_foundation_biomarker/clearity_foundation_biomarker_tsv_importer.rb on lines 5..16
lib/genome/importers/clearity_foundation_clinical_trial/clearity_foundation_clinical_trial_tsv_importer.rb on lines 5..16
lib/genome/importers/foundation_one_interactions/foundation_one_interactions_tsv_importer.rb on lines 5..16
lib/genome/importers/hingorani_casas/hingorani_casas_tsv_importer.rb on lines 4..15
lib/genome/importers/idg/idg_tsv_importer.rb on lines 5..16
lib/genome/importers/talc/talc_tsv_importer.rb on lines 4..15
lib/genome/importers/tempus/tempus_tsv_importer.rb on lines 5..16

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 28.

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 10 locations. Consider refactoring.
Open

      def self.source_info
        {
          base_url:           'https://www.tempus.com/clinical-validation-of-the-tempus-xt-next-generation-targeted-oncology-sequencing-assay/',
          site_url:           'https://www.tempus.com/',
          citation:           'Beaubier, N, Tell, R, Lau, D, Parsons, JR, Bush, S, Perera, J, Sorrells, S, Baker, T, Chang, A, Michuda, J, Iguartua, C, MacNeil, S, Shah, K, Ellis, P, Yeatts, K, Mahon, B, Taxter, T, Bontrager, M, Khan, A, Huether, R, Lefkofsky, E, & White, KP. Clinical validation of the tempus xT next-generation targeted oncology sequencing assay. Oncotarget 2019 Mar 22;10(24):2384-2396. PMID: 31040929.',
Severity: Major
Found in lib/genome/importers/tempus/tempus_tsv_importer.rb and 9 other locations - About 20 mins to fix
lib/genome/importers/bader_lab/bader_lab_tsv_importer.rb on lines 5..16
lib/genome/importers/cancer_commons/cancer_commons_tsv_importer.rb on lines 5..16
lib/genome/importers/clearity_foundation_biomarker/clearity_foundation_biomarker_tsv_importer.rb on lines 5..16
lib/genome/importers/clearity_foundation_clinical_trial/clearity_foundation_clinical_trial_tsv_importer.rb on lines 5..16
lib/genome/importers/foundation_one_interactions/foundation_one_interactions_tsv_importer.rb on lines 5..16
lib/genome/importers/hingorani_casas/hingorani_casas_tsv_importer.rb on lines 4..15
lib/genome/importers/idg/idg_tsv_importer.rb on lines 5..16
lib/genome/importers/my_cancer_genome_clinical_trial/my_cancer_genome_clinical_trial_tsv_importer.rb on lines 4..15
lib/genome/importers/talc/talc_tsv_importer.rb on lines 4..15

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 28.

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 10 locations. Consider refactoring.
Open

      def self.source_info
        {
          base_url:           'https://druggablegenome.net/IDGProteinList/',
          site_url:           'https://druggablegenome.net/',
          citation:           'Rodgers,G., Austin,C., Anderson,J., Pawlyk,A., Colvis,C., Margolis,R. and Baker,J. (2018) Glimmers in illuminating the druggable genome. Nat. Rev. Drug Discov., 17, 301–302. PMID: 29348682',
Severity: Major
Found in lib/genome/importers/idg/idg_tsv_importer.rb and 9 other locations - About 20 mins to fix
lib/genome/importers/bader_lab/bader_lab_tsv_importer.rb on lines 5..16
lib/genome/importers/cancer_commons/cancer_commons_tsv_importer.rb on lines 5..16
lib/genome/importers/clearity_foundation_biomarker/clearity_foundation_biomarker_tsv_importer.rb on lines 5..16
lib/genome/importers/clearity_foundation_clinical_trial/clearity_foundation_clinical_trial_tsv_importer.rb on lines 5..16
lib/genome/importers/foundation_one_interactions/foundation_one_interactions_tsv_importer.rb on lines 5..16
lib/genome/importers/hingorani_casas/hingorani_casas_tsv_importer.rb on lines 4..15
lib/genome/importers/my_cancer_genome_clinical_trial/my_cancer_genome_clinical_trial_tsv_importer.rb on lines 4..15
lib/genome/importers/talc/talc_tsv_importer.rb on lines 4..15
lib/genome/importers/tempus/tempus_tsv_importer.rb on lines 5..16

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 28.

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 10 locations. Consider refactoring.
Open

      def self.source_info
        {
          base_url: 'http://www.cancercommons.org/researchers-clinicians/',
          site_url: 'http://www.cancercommons.org/',
          citation: 'Cancer Commons: Biomedicine in the Internet Age. Shrager J, Tenenbaum JM, and Travers M. Collaborative Computational Technologies for Biomedical Research, (Sean Elkins, Maggie Hupcey, and Antony Williams Eds). Wiley, 2010.',
Severity: Major
Found in lib/genome/importers/cancer_commons/cancer_commons_tsv_importer.rb and 9 other locations - About 20 mins to fix
lib/genome/importers/bader_lab/bader_lab_tsv_importer.rb on lines 5..16
lib/genome/importers/clearity_foundation_biomarker/clearity_foundation_biomarker_tsv_importer.rb on lines 5..16
lib/genome/importers/clearity_foundation_clinical_trial/clearity_foundation_clinical_trial_tsv_importer.rb on lines 5..16
lib/genome/importers/foundation_one_interactions/foundation_one_interactions_tsv_importer.rb on lines 5..16
lib/genome/importers/hingorani_casas/hingorani_casas_tsv_importer.rb on lines 4..15
lib/genome/importers/idg/idg_tsv_importer.rb on lines 5..16
lib/genome/importers/my_cancer_genome_clinical_trial/my_cancer_genome_clinical_trial_tsv_importer.rb on lines 4..15
lib/genome/importers/talc/talc_tsv_importer.rb on lines 4..15
lib/genome/importers/tempus/tempus_tsv_importer.rb on lines 5..16

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 28.

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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