Showing 122 of 193 total issues
Avoid deeply nested control flow statements. Open
if isinstance(datum, tuple):
datum = ';'.join(str(x) for x in datum)
datum = str(datum).replace("\t", '')
Method initialize
has 6 arguments (exceeds 4 allowed). Consider refactoring. Open
def initialize(collection, request, item_presenter_type, pagination_presenter_type, additional_meta = {}, page_state_param_names = [])
Avoid deeply nested control flow statements. Open
if species == '9606': # Grab human only
wf.write(line_ascii)
Method import
has 6 arguments (exceeds 4 allowed). Consider refactoring. Open
def self.import(tsv_path, rowtype, source_info, header = true, row_delimiter = "\t", &block)
Method uniquify_gene_claims
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def self.uniquify_gene_claims
DataModel::GeneClaim.find_each do |gc|
all_matching_claims = DataModel::GeneClaim.where(name: gc.name, nomenclature: gc.nomenclature, source_id: gc.source_id).all
next if all_matching_claims.length == 1
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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 uniquify_drug_claims
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def self.uniquify_drug_claims
DataModel::DrugClaim.find_each do |dc|
all_matching_claims = DataModel::DrugClaim.where(name: dc.name, nomenclature: dc.nomenclature, source_id: dc.source_id).all
next if all_matching_claims.length == 1
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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_aliases
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def create_gene_claim_aliases (gene_claim, line)
create_gene_claim_alias(gene_claim, line['target'], 'GuideToPharmacology Name') unless blank?(line['target'])
unless blank?(line['target_ensembl_gene_id'])
line['target_ensembl_gene_id'].split('|').each do |ensembl_id|
create_gene_claim_alias(gene_claim, ensembl_id, 'Ensembl ID')
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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
Avoid deeply nested control flow statements. Open
if records_with_trade_name.size == 1
return records_with_trade_name.first
elsif records_with_trade_name.size == 0
return get_normalized_record_or_drug_for_chembl_id(get_min_chembl_id(chembl_ids_for_records(records_with_highest_max_phase)))
else
Avoid deeply nested control flow statements. Open
if identifier.find('entry:resource',ns).text == 'HUGO Gene Nomenclature Committee (HGNC)':
hgnc_gene_acc = identifier.find('entry:identifier', ns).text
# Some identifiers are incorrectly labeled by DrugBank
r = re.compile(r'^\d+$')
if hgnc_gene_acc.startswith('GNC:'):
Method parse_interaction_information
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def parse_interaction_information(variant)
return [] unless variant.include?('meta')
drug_data = variant['meta'].find { |table| table.include?('Drug Interaction Data') }
return [] unless drug_data.present?
fields = drug_data['Drug Interaction Data']['fields']
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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 add_interaction_claim_publications
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def add_interaction_claim_publications(interaction_claim, source_string)
if source_string.include?(';')
source_string.split(';').each do |value|
value.split(/[^\d]/).each do |pmid|
unless pmid.nil? || pmid == ''
- Read upRead up
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
Avoid deeply nested control flow statements. Open
if not datum or datum == 'None':
datum = 'N/A'
out.append(datum)
Method add_interaction_claim_publications
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def add_interaction_claim_publications(interaction_claim, source_string)
if source_string.include?(';')
source_string.split(';').each do |value|
value.split(/[^\d]/).each do |pmid|
unless pmid.nil? || pmid == ''
- Read upRead up
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
Consider simplifying this complex logical expression. Open
elsif val == 'incorporation into and destabilization' || val == 'intercalation' || val == 'desensitize the target' || val == 'disrupter' || val == 'intercalator' || val == 'downregulator'
'negative modulator'
elsif val == 'inhibitory immune response' || val == 'car-t-cell-therapy(dual specific)' || val == 'immunomodulator' || val == 'immunomodulator (immunostimulant)' || val == 'immune response agent' || val == 'car-t-cell-therapy' || val == 'immune response agent' || val == 'immunostimulant'
'immunotherapy'
elsif val == 'component of'
Consider simplifying this complex logical expression. Open
unless pmid.nil? || pmid == "" || pmid == '""' || pmid == "''" || pmid[0] =='-' || pmid =='15288657'
create_interaction_claim_publication(interaction_claim, pmid)
end
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]
- Read upRead up
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'
- Read upRead up
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')
- Read upRead up
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')
- Read upRead up
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
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)))