Class: ConceptQL::Operators::StandardVocabularyOperator

Inherits:
VocabularyOperator show all
Defined in:
lib/conceptql/operators/standard_vocabulary_operator.rb

Overview

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

If that seems confusing, then think of CPT or SNOMED criteria. That type of criterion takes a set of values that live in the OMOP concept table.

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

Subclasses must provide the following methods:

  • table

    • The CDM table name where the criterion will fetch its rows

    • e.g. for CPT, this would be procedure_occurrence

  • concept_column

    • Name of the column in the table that stores a concept_id related to the criterion

    • e.g. for CPT, this would be procedure_concept_id

  • vocabulary_id

    • The vocabulary ID of the source vocabulary for the criterion

    • e.g. for CPT, a value of 4 (for CPT-4)

Instance Attribute Summary

Attributes inherited from Operator

#arguments, #errors, #nodifier, #options, #upstreams, #values

Instance Method Summary collapse

Methods inherited from VocabularyOperator

#code_list, #domain

Methods inherited from Operator

#annotate, #cast_column, #code_list, codes_should_match, #columns, #create_upstreams, #data_model, #database_type, default_query_columns, #domains, #dup_values, #dynamic_columns, #evaluate, inherited, #initialize, #inspect, #label, new, #operator_name, #optimized, query_columns, register, require_column, #required_columns, #scope, #select_it, #setup_select, #sql, #stream, #to_op, #unionable?, #upstreams_valid?, #valid?

Methods included from Metadatable

#allows_many_upstreams, #allows_one_upstream, #argument, #auto_label, #basic_type, #category, #derive_metadata_from_validations, #desc, #domains, #get_desc, #humanized_class_name, #inherited, #just_class_name, #no_desc, #option, #predominant_domains, #pref_name, #preferred_name, #reset_categories, #standard_description, #to_metadata, #validate_at_least_one_upstream_to_metadata, #validate_at_most_one_upstream_to_metadata, #validate_no_arguments_to_metadata, #validate_no_upstreams_to_metadata, #validate_one_upstream_to_metadata, #validate_required_options_to_metadata, #warn_about_missing_metadata

Constructor Details

This class inherits a constructor from ConceptQL::Operators::Operator

Instance Method Details

#conditions(db) ⇒ Object 



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# File 'lib/conceptql/operators/standard_vocabulary_operator.rb', line 36

def conditions(db)
  if omopv4?
    {c__concept_code: arguments_fix(db), c__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) ⇒ Object 



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# File 'lib/conceptql/operators/standard_vocabulary_operator.rb', line 46

def describe_code(db, code)
  db[:concept].filter(:vocabulary_id => vocabulary_id).filter(:concept_code => code).map(:concept_name)[0]
end

#query(db) ⇒ Object 



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# File 'lib/conceptql/operators/standard_vocabulary_operator.rb', line 23

def query(db)
  ds = db.from(table_name)
    .where(conditions(db))
  if omopv4?
    ds = ds.join(:concept___c, c__concept_id: table_concept_column)
  end
  ds
end

#query_cols ⇒ Object 



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# File 'lib/conceptql/operators/standard_vocabulary_operator.rb', line 32

def query_cols
  table_columns(table_name, :concept)
end