class ConceptQL::Operators::SourceVocabularyOperator

A SourceVocabularyOperator is a superclass for a operator that represents a criterion whose column stores information associated with a source vocabulary.

If that seems confusing, then think of ICD-9 or NDC criteria. That type of criterion takes a set of values that are mapped via the source_to_concept_map table into a standard vocabulary.

This kind of criterion can have some interesting issues when we are searching for rows that match. Let's take ICD-9 286.53 for example. That code maps to concept_id 0, so if we try to pull all conditions that match just the concept_id of 0 we'll pull all condtions that have no match in the SNOMED standard vocabulary. That's not what we want! So we need to search the condition_source_value field for matches on this code instead.

But there's another, more complicated problem. Say we're looking for ICD-9 289.81. OMOP maps this to concept_id 432585. OMOP also maps 20 other conditions, 6 of which are other ICD-9 codes, to this same concept_id. So if we look for ICD-9s that have a non-zero condition_condept_id, we might pull up conditions that match on concept_id, but aren't the same exact code as the one we're looking for.

My coworker came up with a nice, gneralized query that checks for matching concept_ids and matching source_code values. This class encapsulates that query.

Subclasses must provide the following methods:

Public Instance Methods

conditions(db) click to toggle source
# File lib/conceptql/operators/source_vocabulary_operator.rb, line 54
def conditions(db)
  if omopv4?
    [[:scm__source_code, arguments_fix(db)], [:scm__source_vocabulary_id, vocabulary_id]]
  else
    conditions = { code_column => arguments_fix(db) }
    conditions[vocabulary_id_column] = vocabulary_id if vocabulary_id_column
    conditions
  end
end
describe_code(db, code) click to toggle source
# File lib/conceptql/operators/source_vocabulary_operator.rb, line 64
def describe_code(db, code)
  db[:source_to_concept_map].filter(:source_vocabulary_id => vocabulary_id).filter(:source_code => code).map(:source_code_description)[0]
end
query(db) click to toggle source
# File lib/conceptql/operators/source_vocabulary_operator.rb, line 30
def query(db)
  ds = db.from(table_name).where(conditions(db))
  if omopv4?
    ds = ds.join(:source_to_concept_map___scm, [[:scm__target_concept_id, table_concept_column], [:scm__source_code, table_source_column]])
  end
  ds
end
query_cols() click to toggle source
# File lib/conceptql/operators/source_vocabulary_operator.rb, line 38
def query_cols
  if omopv4?
    table_columns(table_name, :source_to_concept_map)
  else
    table_columns(table_name)
  end
end
union(other) click to toggle source
# File lib/conceptql/operators/source_vocabulary_operator.rb, line 50
def union(other)
  dup_values(values + other.values)
end
unionable?(other) click to toggle source
# File lib/conceptql/operators/source_vocabulary_operator.rb, line 46
def unionable?(other)
  other.is_a?(self.class)
end

Private Instance Methods

table_source_column() click to toggle source
# File lib/conceptql/operators/source_vocabulary_operator.rb, line 82
def table_source_column
  "tab__#{source_column}".to_sym
end
validate(db, opts = {}) click to toggle source
Calls superclass method
# File lib/conceptql/operators/source_vocabulary_operator.rb, line 70
def validate(db, opts = {})
  super
  if add_warnings?(db, opts)
    args = arguments.dup
    args -= bad_arguments
    missing_args = args - db[:source_to_concept_map].where(:source_vocabulary_id=>vocabulary_id, :source_code=>arguments_fix(db, args)).select_map(:source_code)
    unless missing_args.empty?
      add_warning("unknown source code", *missing_args)
    end
  end
end