conceptql 0.1.1 → 0.2.0

data/spec/conceptql/nodes/date_range_spec.rb

@@ -1,35 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/date_range'
-
-describe ConceptQL::Nodes::DateRange do
-  it 'behaves itself' do
-    ConceptQL::Nodes::DateRange.new.must_behave_like(:evaluator)
-  end
-
-  describe '#types' do
-    it 'should be [:date]' do
-      ConceptQL::Nodes::DateRange.new(start: '2004-12-13', end: '2010-03-20').types.must_equal([:person])
-    end
-  end
-
-  describe '#query' do
-    it 'should be dates specified assigned to all persons' do
-      ConceptQL::Nodes::DateRange.new(start: '2004-12-13', end: '2010-03-20').query(Sequel.mock).sql.must_equal("SELECT * FROM (SELECT *, CAST('person' AS varchar(255)) AS criterion_type, person_id AS criterion_id, date '2004-12-13' AS start_date, date '2010-03-20' AS end_date FROM person) AS t1")
-    end
-
-    it 'should handle strings for option keys' do
-      ConceptQL::Nodes::DateRange.new('start' => '2004-12-13', 'end' => '2010-03-20').query(Sequel.mock).sql.must_equal("SELECT * FROM (SELECT *, CAST('person' AS varchar(255)) AS criterion_type, person_id AS criterion_id, date '2004-12-13' AS start_date, date '2010-03-20' AS end_date FROM person) AS t1")
-    end
-
-    it 'handles START as day before first recorded visit_occurrence' do
-      ConceptQL::Nodes::DateRange.new(start: 'START', end: '2010-03-20').query(Sequel.mock).sql.must_equal("SELECT * FROM (SELECT *, CAST('person' AS varchar(255)) AS criterion_type, person_id AS criterion_id, (SELECT min(start_date) FROM visit_occurrence) AS start_date, date '2010-03-20' AS end_date FROM person) AS t1")
-    end
-
-    it 'handles END as 2010-12-31' do
-      ConceptQL::Nodes::DateRange.new(start: '2004-12-13', end: 'END').query(Sequel.mock).sql.must_equal("SELECT * FROM (SELECT *, CAST('person' AS varchar(255)) AS criterion_type, person_id AS criterion_id, date '2004-12-13' AS start_date, (SELECT max(end_date) FROM visit_occurrence) AS end_date FROM person) AS t1")
-    end
-  end
-
-end
-
-

data/spec/conceptql/nodes/death_spec.rb

@@ -1,12 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/death'
-require_double('stream_for_casting')
-
-describe ConceptQL::Nodes::CastingNode do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Death.new.must_behave_like(:casting_node)
-  end
-end
-
-
-

data/spec/conceptql/nodes/during_spec.rb

@@ -1,32 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/during'
-require_double('stream_for_temporal')
-
-describe ConceptQL::Nodes::During do
-  it 'behaves itself' do
-    ConceptQL::Nodes::During.new.must_behave_like(:temporal_node)
-  end
-
-  describe 'when not inclusive' do
-    subject do
-      ConceptQL::Nodes::During.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.end_date'
-      subject.query(Sequel.mock).sql.must_match 'r.start_date <= l.start_date'
-    end
-  end
-
-  describe 'when inclusive' do
-    subject do
-      ConceptQL::Nodes::During.new(left: StreamForTemporalDouble.new, right: StreamForTemporalDouble.new, inclusive: true)
-    end
-
-    it 'should use proper where clause' do
-      subject.query(Sequel.mock).sql.must_match '(r.start_date <= l.end_date) AND (l.end_date <= r.end_date)'
-      subject.query(Sequel.mock).sql.must_match '(r.start_date <= l.start_date) AND (l.start_date <= r.end_date)'
-    end
-  end
-end
-

data/spec/conceptql/nodes/except_spec.rb

@@ -1,18 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/except'
-require_relative 'query_double'
-
-describe ConceptQL::Nodes::Except do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Except.new.must_behave_like(:evaluator)
-  end
-
-  describe '#query' do
-    it 'uses right stream as argument to EXCEPT against left stream' do
-      double1 = QueryDouble.new(1)
-      double2 = QueryDouble.new(2)
-      double1.must_behave_like(:evaluator)
-      ConceptQL::Nodes::Except.new(left: double1, right: double2).query(Sequel.mock).sql.must_equal "SELECT * FROM (SELECT * FROM table1 EXCEPT SELECT * FROM table2) AS t1"
-    end
-  end
-end

data/spec/conceptql/nodes/first_spec.rb

@@ -1,37 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/first'
-require_double('stream_for_occurrence')
-
-describe ConceptQL::Nodes::First do
-  it 'behaves itself' do
-    ConceptQL::Nodes::First.new.must_behave_like(:evaluator)
-  end
-
-  it 'should have occurrence pegged at 1' do
-    ConceptQL::Nodes::First.new.occurrence.must_equal(1)
-  end
-
-  describe 'occurrence set to 1' do
-    subject do
-      ConceptQL::Nodes::First.new(StreamForOccurrenceDouble.new).query(Sequel.mock).sql
-    end
-
-    it 'should order by ascending start_date' do
-      subject.must_match 'ORDER BY start_date ASC'
-    end
-
-    it 'should partition by person_id' do
-      subject.must_match 'PARTITION BY person_id'
-    end
-
-    it 'should assign a row number' do
-      subject.must_match 'row_number()'
-    end
-
-    it 'should find the all rows with rn = 1' do
-      subject.must_match 'rn = 1'
-    end
-  end
-end
-
-

data/spec/conceptql/nodes/from_spec.rb

@@ -1,15 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/from'
-require_relative 'query_double'
-
-describe ConceptQL::Nodes::From do
-  it 'behaves itself' do
-    ConceptQL::Nodes::From.new.must_behave_like(:evaluator)
-  end
-
-  describe '#query' do
-    it 'works for single criteria' do
-      ConceptQL::Nodes::From.new(:table1).query(Sequel.mock).sql.must_equal "SELECT * FROM table1"
-    end
-  end
-end

data/spec/conceptql/nodes/gender_spec.rb

@@ -1,29 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/gender'
-
-describe ConceptQL::Nodes::Gender do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Gender.new.must_behave_like(:evaluator)
-  end
-
-  describe '#query' do
-    it 'works for male/MALE/Male/M/m' do
-      correct_query = "SELECT * FROM person WHERE (gender_concept_id IN (8507))"
-      ConceptQL::Nodes::Gender.new('male').query(Sequel.mock).sql.must_equal correct_query
-      ConceptQL::Nodes::Gender.new('Male').query(Sequel.mock).sql.must_equal correct_query
-      ConceptQL::Nodes::Gender.new('MALE').query(Sequel.mock).sql.must_equal correct_query
-      ConceptQL::Nodes::Gender.new('M').query(Sequel.mock).sql.must_equal correct_query
-      ConceptQL::Nodes::Gender.new('m').query(Sequel.mock).sql.must_equal correct_query
-    end
-
-    it 'works for Female/FEMALE/female/F/f' do
-      correct_query = "SELECT * FROM person WHERE (gender_concept_id IN (8532))"
-      ConceptQL::Nodes::Gender.new('female').query(Sequel.mock).sql.must_equal correct_query
-      ConceptQL::Nodes::Gender.new('Female').query(Sequel.mock).sql.must_equal correct_query
-      ConceptQL::Nodes::Gender.new('FEMALE').query(Sequel.mock).sql.must_equal correct_query
-      ConceptQL::Nodes::Gender.new('F').query(Sequel.mock).sql.must_equal correct_query
-      ConceptQL::Nodes::Gender.new('f').query(Sequel.mock).sql.must_equal correct_query
-    end
-  end
-end
-

data/spec/conceptql/nodes/hcpcs_spec.rb

@@ -1,31 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/hcpcs'
-
-describe ConceptQL::Nodes::Hcpcs do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Hcpcs.new.must_behave_like(:standard_vocabulary_node)
-  end
-
-  subject do
-    ConceptQL::Nodes::Hcpcs.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 5' do
-      subject.vocabulary_id.must_equal 5
-    end
-  end
-end
-

data/spec/conceptql/nodes/icd10_spec.rb

@@ -1,36 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/icd10'
-
-describe ConceptQL::Nodes::Icd10 do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Icd10.new.must_behave_like(:source_vocabulary_node)
-  end
-
-  subject do
-    ConceptQL::Nodes::Icd10.new
-  end
-
-  describe '#table' do
-    it 'should be condition_occurrence' do
-      subject.table.must_equal :condition_occurrence
-    end
-  end
-
-  describe '#concept_column' do
-    it 'should be condition_concept_id' do
-      subject.concept_column.must_equal :condition_concept_id
-    end
-  end
-
-  describe '#source_column' do
-    it 'should be condition_source_valuej' do
-      subject.source_column.must_equal :condition_source_value
-    end
-  end
-
-  describe '#vocabulary_id' do
-    it 'should be 34' do
-      subject.vocabulary_id.must_equal 34
-    end
-  end
-end

data/spec/conceptql/nodes/icd9_procedure_spec.rb

@@ -1,31 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/icd9_procedure'
-
-describe ConceptQL::Nodes::Icd9Procedure do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Icd9Procedure.new.must_behave_like(:standard_vocabulary_node)
-  end
-
-  subject do
-    ConceptQL::Nodes::Icd9Procedure.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 3' do
-      subject.vocabulary_id.must_equal 3
-    end
-  end
-end
-

data/spec/conceptql/nodes/icd9_spec.rb

@@ -1,36 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/icd9'
-
-describe ConceptQL::Nodes::Icd9 do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Icd9.new.must_behave_like(:source_vocabulary_node)
-  end
-
-  subject do
-    ConceptQL::Nodes::Icd9.new
-  end
-
-  describe '#table' do
-    it 'should be condition_occurrence' do
-      subject.table.must_equal :condition_occurrence
-    end
-  end
-
-  describe '#concept_column' do
-    it 'should be condition_concept_id' do
-      subject.concept_column.must_equal :condition_concept_id
-    end
-  end
-
-  describe '#source_column' do
-    it 'should be condition_source_valuej' do
-      subject.source_column.must_equal :condition_source_value
-    end
-  end
-
-  describe '#vocabulary_id' do
-    it 'should be 2' do
-      subject.vocabulary_id.must_equal 2
-    end
-  end
-end

data/spec/conceptql/nodes/intersect_spec.rb

@@ -1,33 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/intersect'
-require_relative 'query_double'
-
-describe ConceptQL::Nodes::Intersect do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Intersect.new.must_behave_like(:evaluator)
-  end
-
-  describe '#query' do
-    it 'works for multiple criteria of same type' do
-      double1 = QueryDouble.new(1)
-      double2 = QueryDouble.new(2)
-      double3 = QueryDouble.new(3)
-      double1.must_behave_like(:evaluator)
-      ConceptQL::Nodes::Intersect.new(double1, double2, double3).query(Sequel.mock).sql.must_equal "SELECT * FROM (SELECT * FROM (SELECT * FROM table1 INTERSECT SELECT * FROM table2) AS t1 INTERSECT SELECT * FROM table3) AS t1"
-    end
-
-    it 'works for multiple criteria of different type' do
-      double1 = QueryDouble.new(1)
-      double2 = QueryDouble.new(2, :person)
-      double3 = QueryDouble.new(3)
-      double1.must_behave_like(:evaluator)
-      ConceptQL::Nodes::Intersect.new(double1, double2, double3).query(Sequel.mock).sql.must_equal "SELECT * FROM (SELECT * FROM (SELECT * FROM table1 INTERSECT SELECT * FROM table3) AS t1 UNION ALL SELECT * FROM table2) AS t1"
-    end
-
-    it 'works for single criteria' do
-      double1 = QueryDouble.new(1)
-      double1.must_behave_like(:evaluator)
-      ConceptQL::Nodes::Intersect.new(double1).query(Sequel.mock).sql.must_equal "SELECT * FROM table1"
-    end
-  end
-end

data/spec/conceptql/nodes/last_spec.rb

@@ -1,38 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/last'
-require_double('stream_for_occurrence')
-
-describe ConceptQL::Nodes::Last do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Last.new.must_behave_like(:evaluator)
-  end
-
-  it 'should have occurrence pegged at -1' do
-    ConceptQL::Nodes::Last.new.occurrence.must_equal(-1)
-  end
-
-  describe 'occurrence set to -1' do
-    subject do
-      ConceptQL::Nodes::Last.new(StreamForOccurrenceDouble.new).query(Sequel.mock).sql
-    end
-
-
-    it 'should order by descending start_date' do
-      subject.must_match 'ORDER BY start_date DESC'
-    end
-
-    it 'should partition by person_id' do
-      subject.must_match 'PARTITION BY person_id'
-    end
-
-    it 'should assign a row number' do
-      subject.must_match 'row_number()'
-    end
-
-    it 'should find the all rows with rn = 1' do
-      subject.must_match 'rn = 1'
-    end
-  end
-end
-
-

data/spec/conceptql/nodes/loinc_spec.rb

@@ -1,31 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/loinc'
-
-describe ConceptQL::Nodes::Loinc do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Loinc.new.must_behave_like(:standard_vocabulary_node)
-  end
-
-  subject do
-    ConceptQL::Nodes::Loinc.new
-  end
-
-  describe '#table' do
-    it 'should be observation' do
-      subject.table.must_equal :observation
-    end
-  end
-
-  describe '#concept_column' do
-    it 'should be procedure_concept_id' do
-      subject.concept_column.must_equal :observation_concept_id
-    end
-  end
-
-  describe '#vocabulary_id' do
-    it 'should be 6' do
-      subject.vocabulary_id.must_equal 6
-    end
-  end
-end
-

data/spec/conceptql/nodes/occurrence_spec.rb

@@ -1,89 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/occurrence'
-require_double('stream_for_occurrence')
-
-describe ConceptQL::Nodes::Occurrence do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Occurrence.new.must_behave_like(:evaluator)
-  end
-
-  describe 'occurrence set to 1' do
-    subject do
-      ConceptQL::Nodes::Occurrence.new(1, StreamForOccurrenceDouble.new).query(Sequel.mock).sql
-    end
-
-    it 'should order by ascending start_date' do
-      subject.must_match 'ORDER BY start_date ASC'
-    end
-
-    it 'should partition by person_id' do
-      subject.must_match 'PARTITION BY person_id'
-    end
-
-    it 'should assign a row number' do
-      subject.must_match 'row_number()'
-    end
-
-    it 'should find the all rows with rn = 1' do
-      subject.must_match 'rn = 1'
-    end
-  end
-
-  describe 'occurrence set to 2' do
-    subject do
-      ConceptQL::Nodes::Occurrence.new(2, StreamForOccurrenceDouble.new).query(Sequel.mock).sql
-    end
-
-    it 'should order by ascending start_date' do
-      subject.must_match 'ORDER BY start_date ASC'
-    end
-
-    it 'should find the all rows with rn = 2' do
-      subject.must_match 'rn = 2'
-    end
-  end
-
-  describe 'occurrence set to -1' do
-    subject do
-      ConceptQL::Nodes::Occurrence.new(-1, StreamForOccurrenceDouble.new).query(Sequel.mock).sql
-    end
-
-    it 'should order by ascending start_date' do
-      subject.must_match 'ORDER BY start_date DESC'
-    end
-
-    it 'should find the all rows with rn = 1' do
-      subject.must_match 'rn = 1'
-    end
-  end
-
-  describe 'occurrence set to -2' do
-    subject do
-      ConceptQL::Nodes::Occurrence.new(-2, StreamForOccurrenceDouble.new).query(Sequel.mock).sql
-    end
-
-    it 'should order by ascending start_date' do
-      subject.must_match 'ORDER BY start_date DESC'
-    end
-
-    it 'should find the all rows with rn = 2' do
-      subject.must_match 'rn = 2'
-    end
-  end
-
-  describe 'occurrence respects types' do
-    subject do
-      dub = StreamForOccurrenceDouble.new
-      def dub.types
-        [:condition_occurrence]
-      end
-      ConceptQL::Nodes::Occurrence.new(-2, dub).query(Sequel.mock).sql
-    end
-
-    it 'should order by ascending start_date' do
-      subject.must_match ', criterion_type, criterion_id'
-    end
-  end
-end
-
-

data/spec/conceptql/nodes/person_filter_spec.rb

@@ -1,18 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/person_filter'
-require_relative 'query_double'
-
-describe ConceptQL::Nodes::PersonFilter do
-  it 'behaves itself' do
-    ConceptQL::Nodes::PersonFilter.new.must_behave_like(:evaluator)
-  end
-
-  describe '#query' do
-    it 'uses right stream as argument to PERSON_FILTER against left stream' do
-      double1 = QueryDouble.new(1)
-      double2 = QueryDouble.new(2)
-      double1.must_behave_like(:evaluator)
-      ConceptQL::Nodes::PersonFilter.new(left: double1, right: double2).query(Sequel.mock).sql.must_equal "SELECT * FROM (SELECT * FROM table1) AS t1 WHERE (person_id IN (SELECT person_id FROM table2 GROUP BY person_id))"
-    end
-  end
-end

data/spec/conceptql/nodes/person_spec.rb

@@ -1,12 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/person'
-require_double('stream_for_casting')
-
-describe ConceptQL::Nodes::CastingNode do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Person.new.must_behave_like(:casting_node)
-  end
-end
-
-
-

data/spec/conceptql/nodes/procedure_occurrence_spec.rb

@@ -1,12 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/procedure_occurrence'
-require_double('stream_for_casting')
-
-describe ConceptQL::Nodes::CastingNode do
-  it 'behaves itself' do
-    ConceptQL::Nodes::ProcedureOccurrence.new.must_behave_like(:casting_node)
-  end
-end
-
-
-

data/spec/conceptql/nodes/query_double.rb

@@ -1,19 +0,0 @@
-require 'conceptql/nodes/node'
-class QueryDouble < ConceptQL::Nodes::Node
-  def initialize(num, type = :visit_occurrence)
-    @num = num
-    @type = type
-  end
-
-  def types
-    [@type]
-  end
-
-  def evaluate(db)
-    query(db)
-  end
-
-  def query(db)
-    db["table#{@num}".to_sym]
-  end
-end

data/spec/conceptql/nodes/race_spec.rb

@@ -1,23 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/race'
-
-describe ConceptQL::Nodes::Race do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Race.new.must_behave_like(:evaluator)
-  end
-
-  describe '#query' do
-    it 'works for white' do
-      correct_query = "SELECT * FROM person AS p INNER JOIN vocabulary.concept AS vc ON (vc.concept_id = p.race_concept_id) WHERE (lower(vc.concept_name) IN ('white'))"
-      ConceptQL::Nodes::Race.new('White').query(Sequel.mock).sql.must_equal correct_query
-      ConceptQL::Nodes::Race.new('white').query(Sequel.mock).sql.must_equal correct_query
-    end
-
-    it 'works for multiple values' do
-      correct_query = "SELECT * FROM person AS p INNER JOIN vocabulary.concept AS vc ON (vc.concept_id = p.race_concept_id) WHERE (lower(vc.concept_name) IN ('white', 'other'))"
-      ConceptQL::Nodes::Race.new('White', 'Other').query(Sequel.mock).sql.must_equal correct_query
-      ConceptQL::Nodes::Race.new('white', 'other').query(Sequel.mock).sql.must_equal correct_query
-    end
-  end
-end
-

data/spec/conceptql/nodes/rxnorm_spec.rb

@@ -1,31 +0,0 @@
-require 'spec_helper'
-require 'conceptql/nodes/rxnorm'
-
-describe ConceptQL::Nodes::Rxnorm do
-  it 'behaves itself' do
-    ConceptQL::Nodes::Rxnorm.new.must_behave_like(:standard_vocabulary_node)
-  end
-
-  subject do
-    ConceptQL::Nodes::Rxnorm.new
-  end
-
-  describe '#table' do
-    it 'should be drug_exposure' do
-      subject.table.must_equal :drug_exposure
-    end
-  end
-
-  describe '#concept_column' do
-    it 'should be drug_concept_id' do
-      subject.concept_column.must_equal :drug_concept_id
-    end
-  end
-
-  describe '#vocabulary_id' do
-    it 'should be 8' do
-      subject.vocabulary_id.must_equal 8
-    end
-  end
-end
-

data/spec/conceptql/nodes/snomed_spec.rb

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