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

      DataModel::GeneAttribute.where("name LIKE ' %' or name LIKE '% '").all.each do |a|
        clean_attribute = DataModel::GeneAttribute.where(name: a.name.strip, value: a.value.strip, gene_id: a.gene_id).first_or_create
        a.sources.each do |source|
          clean_attribute.sources << source unless clean_attribute.sources.include? source
          a.sources.delete(source)
Severity: Minor
Found in lib/utils/database.rb and 1 other location - About 1 hr to fix
lib/utils/database.rb on lines 334..340

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 47.

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

      DataModel::GeneAttribute.where("value LIKE ' %' or value LIKE '% '").all.each do |a|
        clean_attribute = DataModel::GeneAttribute.where(name: a.name.strip, value: a.value.strip, gene_id: a.gene_id).first_or_create
        a.sources.each do |source|
          clean_attribute.sources << source unless clean_attribute.sources.include? source
          a.sources.delete(source)
Severity: Minor
Found in lib/utils/database.rb and 1 other location - About 1 hr to fix
lib/utils/database.rb on lines 326..332

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 47.

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 combine_input_genes(params)
    bad_request("You must enter at least one gene name to search!") unless params[:genes]
    split_char = params[:genes].include?(',') ? ',' : "\n"
    gene_names = params[:genes].split(split_char)
    gene_names.delete_if{ |gene| gene.strip.empty? }
Severity: Minor
Found in app/controllers/application_controller.rb and 1 other location - About 45 mins to fix
app/controllers/application_controller.rb on lines 43..48

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

  def combine_input_drugs(params)
    bad_request("You must enter at least one drug name to search!") unless params[:drugs]
    split_char = params[:drugs].include?(',') ? ',' : "\n"
    drug_names = params[:drugs].split(split_char)
    drug_names.delete_if{ |drug| drug.strip.empty? }
Severity: Minor
Found in app/controllers/application_controller.rb and 1 other location - About 45 mins to fix
app/controllers/application_controller.rb on lines 35..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 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

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

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

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

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

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

    def create_new_source
      @source ||= DataModel::Source.create(
        {
          base_url:           'http://amigo.geneontology.org/amigo/gene_product/UniProtKB:',
          site_url:           'http://www.geneontology.org/',
Severity: Minor
Found in lib/genome/online_updaters/go/updater.rb and 1 other location - About 35 mins to fix
lib/genome/online_updaters/pharos/updater.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 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

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

    def create_new_source
      @source ||= DataModel::Source.create(
        {
          base_url:           'https://pharos-api.ncats.io/graphql',
          site_url:           'https://pharos.nih.gov/',
Severity: Minor
Found in lib/genome/online_updaters/pharos/updater.rb and 1 other location - About 35 mins to fix
lib/genome/online_updaters/go/updater.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 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

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

    def create_new_source
      @source ||= DataModel::Source.create(
        {
          source_db_name: 'JAX-CKB',
          source_db_version: new_version,
Severity: Minor
Found in lib/genome/online_updaters/ckb/updater.rb and 1 other location - About 35 mins to fix
lib/genome/online_updaters/oncokb/updater.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 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

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

    def create_new_source
      @source ||= DataModel::Source.create(
        {
          source_db_name: 'OncoKB',
          source_db_version: new_version,
Severity: Minor
Found in lib/genome/online_updaters/oncokb/updater.rb and 1 other location - About 35 mins to fix
lib/genome/online_updaters/ckb/updater.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 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

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

  def show
    @drug_claim = DrugClaimPresenter.new DataModel::DrugClaim.for_show
      .where(name: params[:name].upcase)
      .where('lower(sources.source_db_name) = ?',  params[:source_db_name].downcase)
      .first || not_found("No drug claim from #{params[:source_db_name]} with name #{params[:name]} found!")
Severity: Minor
Found in app/controllers/drug_claims_controller.rb and 1 other location - About 35 mins to fix
app/controllers/gene_claims_controller.rb on lines 2..7

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 35.

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 show
    @gene_claim = GeneClaimPresenter.new DataModel::GeneClaim.for_show
      .where(name: params[:name].upcase)
      .where('lower(sources.source_db_name) = ?', params[:source_db_name].downcase)
      .first || not_found("No gene claim from #{params[:source_db_name]} with name #{params[:name]} found!")
Severity: Minor
Found in app/controllers/gene_claims_controller.rb and 1 other location - About 35 mins to fix
app/controllers/drug_claims_controller.rb on lines 2..7

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 35.

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 perform()
    ActiveRecord::Base.transaction(joinable: false, requires_new: true) do
      import
      pre_grouper = PreGrouper.new
      pre_grouper.perform
Severity: Minor
Found in app/jobs/api_updater.rb and 1 other location - About 35 mins to fix
app/jobs/tsv_updater.rb on lines 7..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 34.

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 perform()
    ActiveRecord::Base.transaction(joinable: false, requires_new: true) do
      import
      pre_grouper = PreGrouper.new
      pre_grouper.perform
Severity: Minor
Found in app/jobs/tsv_updater.rb and 1 other location - About 35 mins to fix
app/jobs/api_updater.rb on lines 4..12

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 34.

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 self.print_gene_row(file_handle, gene_claim)
      gene_name = gene_claim.gene ? gene_claim.gene.name : ""
      entrez_id = gene_claim.gene ? gene_claim.gene.entrez_id : ""
      row = [
        gene_claim.name,
Severity: Minor
Found in lib/utils/tsv.rb and 1 other location - About 30 mins to fix
lib/utils/tsv.rb on lines 174..184

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 33.

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 self.print_drug_row(file_handle, drug_claim)
      drug_name = drug_claim.drug ? drug_claim.drug.name : ""
      concept_id = drug_claim.drug ? drug_claim.drug.concept_id : ""
      row = [
        drug_claim.name,
Severity: Minor
Found in lib/utils/tsv.rb and 1 other location - About 30 mins to fix
lib/utils/tsv.rb on lines 156..166

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 33.

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

              drug :pubchem_name, nomenclature: 'Primary Drug Name', primary_name: :pubchem_name, transform: upcase do
                name :drug_name, nomenclature: 'Drug Trade Name', unless: blank_filter
                name :cid, nomenclature: 'PubChem Drug ID', unless: blank_filter
                names :other_drug_names, nomenclature: 'Other Drug Name', unless: blank_filter
              end
Severity: Minor
Found in lib/genome/importers/my_cancer_genome_clinical_trial/my_cancer_genome_clinical_trial_tsv_importer.rb and 1 other location - About 30 mins to fix
lib/genome/importers/tdg_clinical_trial/tdg_clinical_trial_tsv_importer.rb on lines 31..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 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

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

            drug :drug_name, nomenclature: 'Drug Name', primary_name: :drug_name, transform: upcase do
              attributes :indication, name: 'Drug Indications', unless: blank_filter
              attribute :drug_class, name: 'Drug Class', unless: blank_filter
              attribute :fda_approval, name: 'FDA Approval', unless: blank_filter
            end
Severity: Minor
Found in lib/genome/importers/tdg_clinical_trial/tdg_clinical_trial_tsv_importer.rb and 1 other location - About 30 mins to fix
lib/genome/importers/my_cancer_genome_clinical_trial/my_cancer_genome_clinical_trial_tsv_importer.rb on lines 31..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 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

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

        elsif val == 'inhibitor, competitive' || val == 'gating inhibitor' || val == 'inhibitor; antagonist; blocker' || val == 'inhibitor (gating inhibitor)' || val == 'growth_inhibition' || val == 'inhibition' || val == 'weak inhibitor' || val == 'aggregation inhibitor' || val == 'inhibition of synthesis' || val == "translocation inhibitor" || val == 'inhibits downstream inflammation cascades' || val == 'inactivator'
          'inhibitor'
Severity: Minor
Found in lib/genome/normalizers/interaction_claim_type.rb and 2 other locations - About 25 mins to fix
lib/genome/normalizers/interaction_claim_type.rb on lines 74..75
lib/genome/normalizers/interaction_claim_type.rb on lines 90..91

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 31.

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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