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Contents
require_relative 'node'
module ConceptQL
module Nodes
# A StandardVocabularyNode is a superclass for a node 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, gneralized 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)
class StandardVocabularyNode < Node
def query(db)
db.from(table_name)
.join(:vocabulary__concept___c, c__concept_id: table_concept_column)
.where(c__concept_code: values, c__vocabulary_id: vocabulary_id)
end
def type
table
end
private
def table_name
@table_name ||= make_table_name(table)
end
def table_concept_column
"tab__#{concept_column}".to_sym
end
end
end
end
Version data entries
8 entries across 8 versions & 1 rubygems