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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 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://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 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

Method validate_search_request has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def validate_search_request(params)
    bad_request("Please enter at least one gene to search!") if params[:genes].blank?
    params[:gene_categories] = DataModel::GeneClaimCategory.all_category_names unless params[:gene_categories]
    params[:sources] = DataModel::Source.potentially_druggable_source_names unless params[:sources]
    params[:source_trust_levels] = DataModel::SourceTrustLevel.all_trust_levels unless params[:source_trust_levels]
Severity: Minor
Found in app/controllers/genes_controller.rb - About 35 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_entries_for_evidence_item has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def create_entries_for_evidence_item(variant, ei, source)
      ei['drugs'].select { |d| valid_drug?(d) }.each do |drug|
        gc = create_gene_claim(variant['entrez_name'], 'Entrez Gene Symbol')
        create_gene_claim_aliases(gc, variant)
        if ei['clinical_significance'] == 'Resistance'
Severity: Minor
Found in lib/genome/online_updaters/civic/updater.rb - About 35 mins to fix

Cognitive Complexity

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

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

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

Further reading

Function extract has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def extract(self, file):
        with gzip.open(file, 'rb') as rf:
            with open(os.path.join(self.download_path, file.rsplit('.', 1)[0] + '.human'), 'w') as wf:
                for i, line in enumerate(rf):
                    line_ascii = line.decode('utf-8')
Severity: Minor
Found in lib/genome/updaters/get_entrez.py - About 35 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_drug_claims has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def create_drug_claims(row, gene_claim, fusion_protein)
      if row['Drug'].include?(',')
        combination_therapy = row['Drug']
        row['Drug'].split(',').each do |drug|
          drug_claim = create_drug_claim(drug, drug, 'FDA Drug Name')
Severity: Minor
Found in lib/genome/importers/fda/fda.rb - About 35 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

  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 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 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_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

    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

Avoid too many return statements within this method.
Open

                return get_normalized_record_or_drug_for_chembl_id(get_min_chembl_id(chembl_ids_for_records(records_with_trade_name)))
Severity: Major
Found in lib/genome/groupers/drug_grouper.rb - About 30 mins to fix

    Avoid too many return statements within this method.
    Open

                    return records_with_highest_max_phase.first
    Severity: Major
    Found in lib/genome/groupers/drug_grouper.rb - About 30 mins to fix

      Avoid too many return statements within this method.
      Open

                        return nil
      Severity: Major
      Found in lib/genome/groupers/drug_grouper.rb - About 30 mins to fix

        Avoid too many return statements within this method.
        Open

                            return get_normalized_record_or_drug_for_chembl_id(get_min_chembl_id(chembl_ids_for_records(records_with_trade_name)))
        Severity: Major
        Found in lib/genome/groupers/drug_grouper.rb - About 30 mins to fix
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