conceptql 0.1.1 → 0.2.0

data/lib/conceptql/nodes/count.rb

@@ -1,23 +0,0 @@
-require_relative 'pass_thru'
-
-module ConceptQL
-  module Nodes
-    class Count < PassThru
-      def query(db)
-        db.from(unioned(db))
-          .group(*COLUMNS)
-          .select(*(COLUMNS - [:value_as_numeric]))
-          .select_append{count(1).as(:value_as_numeric)}
-          .from_self
-      end
-
-      def unioned(db)
-        children.map { |c| c.evaluate(db) }.inject do |uni, q|
-          uni.union(q)
-        end
-      end
-    end
-  end
-end
-
-

data/lib/conceptql/nodes/cpt.rb

@@ -1,20 +0,0 @@
-require_relative 'standard_vocabulary_node'
-
-module ConceptQL
-  module Nodes
-    class Cpt < StandardVocabularyNode
-      def table
-        :procedure_occurrence
-      end
-
-      def vocabulary_id
-        4
-      end
-
-      def concept_column
-        :procedure_concept_id
-      end
-    end
-  end
-end
-

data/lib/conceptql/nodes/death.rb

@@ -1,19 +0,0 @@
-require_relative 'casting_node'
-
-module ConceptQL
-  module Nodes
-    class Death < CastingNode
-      def my_type
-        :death
-      end
-
-      def i_point_at
-        [ :person ]
-      end
-
-      def these_point_at_me
-        []
-      end
-    end
-  end
-end

data/lib/conceptql/nodes/define.rb

@@ -1,96 +0,0 @@
-require_relative 'node'
-
-module ConceptQL
-  module Nodes
-    # Mimics creating a variable name that stores an itermediate result as
-    # part of a larger concept
-    #
-    # The idea is that a concept might be very complex and it helps to break
-    # that complex concept into a set of sub-concepts to better understand it.
-    #
-    # Also, sometimes a particular piece of a concept is used in many places,
-    # so it makes sense to write that piece out once, store it as a "variable"
-    # and then insert that variable into the concept as needed.
-    # run the query once and subsequent calls
-    class Define < Node
-      def initialize(*args)
-        super
-      end
-      # Create a temporary table and store the stream of  results in that table.
-      # This "caches" the results so we only have to execute stream's query
-      # once.
-      #
-      # The logic here is that if something is assigned to a variable, chances
-      # are that it will be used more than once, so why run the query more than
-      # once?
-      #
-      # ConceptQL's SQL generator normally translates the entire statement into
-      # one, large query that can be executed later.
-      #
-      # Unfortunately, Sequel's "create_table" function actually executes the
-      # 'CREATE TABLE' SQL right away, meaning that the "define" node will
-      # execute immediately _during_ the processing of the ConceptQL statement.
-      # We'll see what kinds of problems this causes
-      #
-      # Lastly, this node does NOT pass its results to the next node.  The
-      # reason for this exception is to allow us to return the SQL that
-      # generates the temp table.  This is done so that the ConceptQL sandbox
-      # can return the entire set of SQL statements needed to run a query.
-      #
-      # Perhaps in the future we can find a way around this.
-      #
-      # Also, things will blow up if you try to use a variable that hasn't been
-      # defined yet.
-      def query(db)
-        # We'll wrap the creation of the temp table in memoization
-        # That way we can call #query multiple times, but only suffer the
-        # cost of creating the temp table just once
-        @_run ||= begin
-          if tree.opts[:sql_only]
-            db.create_table!(table_name, temp: true, as: fake_row(db))
-          else
-            db.create_table!(table_name, temp: true, as: stream.evaluate(db))
-          end
-          true
-        end
-        db.from(table_name)
-      end
-
-      def columns(query, local_type)
-        COLUMNS
-      end
-
-      def types
-        stream.types
-      end
-
-      def sql(db)
-        db[db.send(:create_table_as_sql, table_name, stream.evaluate(db).sql, temp: true)].sql
-      end
-
-      def tree=(tree)
-        super
-        tree.defined[table_name] = self
-      end
-
-      private
-
-      def table_name
-        @table_name ||= namify(arguments.first)
-      end
-
-      def fake_row(db)
-        db
-          .select(Sequel.cast(nil, Bignum).as(:person_id))
-          .select_append(Sequel.cast(nil, Bignum).as(:criterion_id))
-          .select_append(Sequel.cast(nil, String).as(:criterion_type))
-          .select_append(Sequel.cast(nil, Date).as(:start_date))
-          .select_append(Sequel.cast(nil, Date).as(:end_date))
-          .select_append(Sequel.cast(nil, Bignum).as(:value_as_numeric))
-          .select_append(Sequel.cast(nil, String).as(:value_as_string))
-          .select_append(Sequel.cast(nil, Bignum).as(:value_as_concept_id))
-      end
-    end
-  end
-end
-

data/lib/conceptql/nodes/drug_type_concept.rb

@@ -1,18 +0,0 @@
-require_relative 'node'
-
-module ConceptQL
-  module Nodes
-    class DrugTypeConcept < Node
-      def type
-        :drug_exposure
-      end
-
-      def query(db)
-        db.from(:drug_exposure)
-          .where(drug_type_concept_id: arguments)
-      end
-    end
-  end
-end
-
-

data/lib/conceptql/nodes/equal.rb

@@ -1,11 +0,0 @@
-require_relative 'temporal_node'
-
-module ConceptQL
-  module Nodes
-    class Equal < TemporalNode
-      def where_clause
-        { r__value_as_numeric: :l__value_as_numeric }
-      end
-    end
-  end
-end

data/lib/conceptql/nodes/except.rb

@@ -1,11 +0,0 @@
-require_relative 'binary_operator_node'
-
-module ConceptQL
-  module Nodes
-    class Except < BinaryOperatorNode
-      def query(db)
-        left.evaluate(db).except(right.evaluate(db))
-      end
-    end
-  end
-end

data/lib/conceptql/nodes/hcpcs.rb

@@ -1,20 +0,0 @@
-require_relative 'standard_vocabulary_node'
-
-module ConceptQL
-  module Nodes
-    class Hcpcs < StandardVocabularyNode
-      def table
-        :procedure_occurrence
-      end
-
-      def vocabulary_id
-        5
-      end
-
-      def concept_column
-        :procedure_concept_id
-      end
-    end
-  end
-end
-

data/lib/conceptql/nodes/icd10.rb

@@ -1,23 +0,0 @@
-require_relative 'source_vocabulary_node'
-
-module ConceptQL
-  module Nodes
-    class Icd10 < SourceVocabularyNode
-      def table
-        :condition_occurrence
-      end
-
-      def vocabulary_id
-        34
-      end
-
-      def source_column
-        :condition_source_value
-      end
-
-      def concept_column
-        :condition_concept_id
-      end
-    end
-  end
-end

data/lib/conceptql/nodes/icd9.rb

@@ -1,23 +0,0 @@
-require_relative 'source_vocabulary_node'
-
-module ConceptQL
-  module Nodes
-    class Icd9 < SourceVocabularyNode
-      def table
-        :condition_occurrence
-      end
-
-      def vocabulary_id
-        2
-      end
-
-      def source_column
-        :condition_source_value
-      end
-
-      def concept_column
-        :condition_concept_id
-      end
-    end
-  end
-end

data/lib/conceptql/nodes/icd9_procedure.rb

@@ -1,20 +0,0 @@
-require_relative 'standard_vocabulary_node'
-
-module ConceptQL
-  module Nodes
-    class Icd9Procedure < StandardVocabularyNode
-      def table
-        :procedure_occurrence
-      end
-
-      def vocabulary_id
-        3
-      end
-
-      def concept_column
-        :procedure_concept_id
-      end
-    end
-  end
-end
-

data/lib/conceptql/nodes/loinc.rb

@@ -1,20 +0,0 @@
-require_relative 'standard_vocabulary_node'
-
-module ConceptQL
-  module Nodes
-    class Loinc < StandardVocabularyNode
-      def table
-        :observation
-      end
-
-      def vocabulary_id
-        6
-      end
-
-      def concept_column
-        :observation_concept_id
-      end
-    end
-  end
-end
-

data/lib/conceptql/nodes/numeric.rb

@@ -1,40 +0,0 @@
-require_relative 'pass_thru'
-
-module ConceptQL
-  module Nodes
-    # Represents a node that will either:
-    # - create a value_as_numeric value for every person in the database
-    # - change the value_as_numeric value for every every result passed in
-    #   - either to a numeric
-    #   - or a value from a column in the origin row
-    #
-    # Accepts two params:
-    # - Either a numeric value or a symbol representing a column name
-    # - An optional stream
-    class Numeric < PassThru
-      def query(db)
-        stream.nil? ? as_criterion(db) : with_kids(db)
-      end
-
-      def types
-        stream.nil? ? [:person] : super
-      end
-
-      private
-      def with_kids(db)
-        db.from(stream.evaluate(db))
-          .select(*(COLUMNS - [:value_as_numeric]))
-          .select_append(Sequel.lit('?', arguments.first).cast(Float).as(:value_as_numeric))
-          .from_self
-      end
-
-      def as_criterion(db)
-        db.from(select_it(db.from(:person), :person))
-          .select(*(COLUMNS - [:value_as_numeric]))
-          .select_append(Sequel.lit('?', arguments.first).cast(Float).as(:value_as_numeric))
-          .from_self
-      end
-    end
-  end
-end
-

data/lib/conceptql/nodes/occurrence.rb

@@ -1,49 +0,0 @@
-require_relative 'node'
-
-module ConceptQL
-  module Nodes
-    # Represents a node that will grab the Nth occurrence of something
-    #
-    # Specify occurrences as integers, excluding O
-    # 1 => first
-    # 2 => second
-    # ...
-    # -1 => last
-    # -2 => second-to-last
-    #
-    # The node treats all streams as a single, large stream.  It partitions
-    # that larget stream by person_id, then sorts within those groupings
-    # by start_date and then select at most one row per person, regardless
-    # of how many different types of streams enter the node
-    #
-    # If two rows have the same start_date, the order of their ranking
-    # is arbitrary
-    #
-    # If we ask for the second occurrence of something and a person has only one
-    # occurrence, this node returns nothing for that person
-    class Occurrence < Node
-      def query(db)
-        stream.evaluate(db)
-          .from_self
-          .select_append { |o| o.row_number(:over, partition: :person_id, order: ordered_columns){}.as(:rn) }
-          .from_self
-          .where(rn: occurrence.abs)
-      end
-
-      def occurrence
-        @occurrence ||= arguments.first
-      end
-
-      private
-      def asc_or_desc
-        occurrence < 0 ? :desc : :asc
-      end
-
-      def ordered_columns
-        ordered_columns = [Sequel.send(asc_or_desc, :start_date)]
-        ordered_columns += [:criterion_type, :criterion_id]
-      end
-    end
-  end
-end
-

data/lib/conceptql/nodes/pass_thru.rb

@@ -1,11 +0,0 @@
-require_relative 'node'
-
-module ConceptQL
-  module Nodes
-    class PassThru < Node
-      def types
-        children.map(&:types).flatten.uniq
-      end
-    end
-  end
-end

data/lib/conceptql/nodes/person_filter.rb

@@ -1,12 +0,0 @@
-require_relative 'binary_operator_node'
-
-module ConceptQL
-  module Nodes
-    class PersonFilter < BinaryOperatorNode
-      def query(db)
-        db.from(left.evaluate(db))
-          .where(person_id: right.evaluate(db).select_group(:person_id))
-      end
-    end
-  end
-end

data/lib/conceptql/nodes/procedure_occurrence.rb

@@ -1,21 +0,0 @@
-require_relative 'casting_node'
-
-module ConceptQL
-  module Nodes
-    class ProcedureOccurrence < CastingNode
-      def my_type
-        :procedure_occurrence
-      end
-
-      def i_point_at
-        [ :person ]
-      end
-
-      def these_point_at_me
-        %i[
-          procedure_cost
-        ]
-      end
-    end
-  end
-end

data/lib/conceptql/nodes/recall.rb

@@ -1,50 +0,0 @@
-require_relative 'pass_thru'
-
-module ConceptQL
-  module Nodes
-    # Mimics using a variable that has been set via "define" node
-    #
-    # The idea is that a concept might be very complex and it helps to break
-    # that complex concept into a set of sub-concepts to better understand it.
-    #
-    # This node will look for a sub-concept that has been created through the
-    # "define" node and will fetch the results cached in the corresponding table
-    class Recall < Node
-      # Behind the scenes we simply fetch all rows from the temp table that
-      # corresponds to the name fed to "recall"
-      #
-      # We also set the @types variable by pulling the type information out
-      # of the hash piggybacking on the database connection.
-      #
-      # TODO: This might be an issue since we might need the type information
-      # before we call #query.  Probably time to reevaluate how we're caching
-      # the type information.
-      def query(db)
-        # We're going to call evaluate on definition to ensure the definition
-        # has been created.  We were running into odd timing issues when
-        # drawing graphs where the recall node was being drawn before definition
-        # was drawn.
-        definition.evaluate(db)
-        db.from(table_name)
-      end
-
-      def columns(query, local_type)
-        COLUMNS
-      end
-
-      def types
-        definition.types
-      end
-
-      private
-      def table_name
-        @table_name ||= namify(arguments.first)
-      end
-
-      def definition
-        tree.defined[table_name]
-      end
-    end
-  end
-end
-

data/lib/conceptql/nodes/rxnorm.rb

@@ -1,20 +0,0 @@
-require_relative 'standard_vocabulary_node'
-
-module ConceptQL
-  module Nodes
-    class Rxnorm < StandardVocabularyNode
-      def table
-        :drug_exposure
-      end
-
-      def vocabulary_id
-        8
-      end
-
-      def concept_column
-        :drug_concept_id
-      end
-    end
-  end
-end
-

data/lib/conceptql/nodes/snomed.rb

@@ -1,19 +0,0 @@
-require_relative 'standard_vocabulary_node'
-
-module ConceptQL
-  module Nodes
-    class Snomed < StandardVocabularyNode
-      def table
-        :condition_occurrence
-      end
-
-      def vocabulary_id
-        1
-      end
-
-      def concept_column
-        :condition_concept_id
-      end
-    end
-  end
-end

data/lib/conceptql/nodes/visit.rb

@@ -1,11 +0,0 @@
-require_relative 'node'
-
-module ConceptQL
-  module Nodes
-    class Visit < Node
-      def types
-        [:visit_occurrence]
-      end
-    end
-  end
-end

data/spec/conceptql/nodes/after_spec.rb

@@ -1,18 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/after'
-require_double('stream_for_temporal')
-
-describe ConceptQL::Nodes::After do
-  it 'behaves itself' do
-    ConceptQL::Nodes::After.new.must_behave_like(:temporal_node)
-  end
-
-  subject do
-    ConceptQL::Nodes::After.new(left: StreamForTemporalDouble.new, right: StreamForTemporalDouble.new)
-  end
-
-  it 'should use proper where clause' do
-    subject.query(Sequel.mock).sql.must_match 'l.start_date > r.end_date'
-  end
-end
-

data/spec/conceptql/nodes/before_spec.rb

@@ -1,18 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/before'
-require_double('stream_for_temporal')
-
-describe ConceptQL::Nodes::Before do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Before.new.must_behave_like(:temporal_node)
-  end
-
-  subject do
-    ConceptQL::Nodes::Before.new(left: StreamForTemporalDouble.new, right: StreamForTemporalDouble.new)
-  end
-
-  it 'should use proper where clause' do
-    subject.query(Sequel.mock).sql.must_match 'l.end_date < r.start_date'
-  end
-end
-

data/spec/conceptql/nodes/complement_spec.rb

@@ -1,15 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/complement'
-require_relative 'query_double'
-
-describe ConceptQL::Nodes::Complement do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Complement.new.must_behave_like(:evaluator)
-  end
-
-  it 'generates complement for single criteria' do
-    double1 = QueryDouble.new(1)
-    double1.must_behave_like(:evaluator)
-    ConceptQL::Nodes::Complement.new(double1).query(Sequel.mock).sql.must_equal "SELECT * FROM (SELECT person_id, visit_occurrence_id AS criterion_id, CAST('visit_occurrence' AS varchar(255)) AS criterion_type, CAST(visit_start_date AS date) AS start_date, CAST(visit_end_date AS date) AS end_date, CAST(NULL AS numeric) AS value_as_numeric, CAST(NULL AS varchar(255)) AS value_as_string, CAST(NULL AS integer) AS value_as_concept_id FROM visit_occurrence AS tab WHERE (visit_occurrence_id NOT IN (SELECT criterion_id FROM (SELECT * FROM table1) AS t1 WHERE ((criterion_id IS NOT NULL) AND (criterion_type = 'visit_occurrence'))))) AS t1"
-  end
-end

data/spec/conceptql/nodes/concept_spec.rb

@@ -1,34 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/concept'
-
-describe ConceptQL::Nodes::Concept do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Concept.new.must_behave_like(:evaluator)
-  end
-
-  class ConceptDouble < ConceptQL::Nodes::Concept
-    def arguments
-      [1]
-    end
-
-    def set_statement(value)
-      # Do Nothing
-    end
-
-    def stream
-      @stream ||= Minitest::Mock.new
-    end
-  end
-
-  describe '#query' do
-    it 'evaluates child' do
-      cd = ConceptDouble.new(1)
-      cd.stream.expect :evaluate, nil, [:db]
-      cd.query(:db)
-      cd.stream.verify
-    end
-  end
-end
-
-
-

data/spec/conceptql/nodes/cpt_spec.rb

@@ -1,31 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/cpt'
-
-describe ConceptQL::Nodes::Cpt do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Cpt.new.must_behave_like(:standard_vocabulary_node)
-  end
-
-  subject do
-    ConceptQL::Nodes::Cpt.new
-  end
-
-  describe '#table' do
-    it 'should be procedure_occurrence' do
-      subject.table.must_equal :procedure_occurrence
-    end
-  end
-
-  describe '#concept_column' do
-    it 'should be procedure_concept_id' do
-      subject.concept_column.must_equal :procedure_concept_id
-    end
-  end
-
-  describe '#vocabulary_id' do
-    it 'should be 4' do
-      subject.vocabulary_id.must_equal 4
-    end
-  end
-end
-