conceptql 0.1.1 → 0.2.0

data/spec/conceptql/operators/date_range_spec.rb

@@ -0,0 +1,33 @@
+require 'spec_helper'
+require 'conceptql/operators/date_range'
+
+describe ConceptQL::Operators::DateRange do
+  it_behaves_like(:evaluator)
+
+  describe '#types' do
+    it 'should be [:date]' do
+      expect(ConceptQL::Operators::DateRange.new(start: '2004-12-13', end: '2010-03-20').types).to eq([:person])
+    end
+  end
+
+  describe '#query' do
+    it 'should be dates specified assigned to all persons' do
+      expect(ConceptQL::Operators::DateRange.new(start: '2004-12-13', end: '2010-03-20').query(Sequel.mock).sql).to eq("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
+      expect(ConceptQL::Operators::DateRange.new('start' => '2004-12-13', 'end' => '2010-03-20').query(Sequel.mock).sql).to eq("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 observation_period' do
+      expect(ConceptQL::Operators::DateRange.new(start: 'START', end: '2010-03-20').query(Sequel.mock).sql).to eq("SELECT * FROM (SELECT *, CAST('person' AS varchar(255)) AS criterion_type, person_id AS criterion_id, (SELECT min(observation_period_start_date) FROM observation_period) AS start_date, date '2010-03-20' AS end_date FROM person) AS t1")
+    end
+
+    it 'handles END as last date of recorded observation_period' do
+      expect(ConceptQL::Operators::DateRange.new(start: '2004-12-13', end: 'END').query(Sequel.mock).sql).to eq("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(observation_period_end_date) FROM observation_period) AS end_date FROM person) AS t1")
+    end
+  end
+
+end
+
+

data/spec/conceptql/operators/death_spec.rb

@@ -0,0 +1,10 @@
+require 'spec_helper'
+require 'conceptql/operators/death'
+require_double('stream_for_casting')
+
+describe ConceptQL::Operators::Death do
+  it_behaves_like(:casting_operator)
+end
+
+
+

data/spec/conceptql/operators/during_spec.rb

@@ -0,0 +1,30 @@
+require 'spec_helper'
+require 'conceptql/operators/during'
+require_double('stream_for_temporal')
+
+describe ConceptQL::Operators::During do
+  it_behaves_like(:temporal_operator)
+
+  describe 'when not inclusive' do
+    subject do
+      described_class.new(left: StreamForTemporalDouble.new, right: StreamForTemporalDouble.new)
+    end
+
+    it 'should use proper where clause' do
+      expect(subject.query(Sequel.mock).sql).to match('l.end_date <= r.end_date')
+      expect(subject.query(Sequel.mock).sql).to match('r.start_date <= l.start_date')
+    end
+  end
+
+  describe 'when inclusive' do
+    subject do
+      described_class.new(left: StreamForTemporalDouble.new, right: StreamForTemporalDouble.new, inclusive: true)
+    end
+
+    it 'should use proper where clause' do
+      expect(subject.query(Sequel.mock).sql).to match(/\(r.start_date <= l.end_date\) AND \(l.end_date <= r.end_date\)/)
+      expect(subject.query(Sequel.mock).sql).to match(/\(r.start_date <= l.start_date\) AND \(l.start_date <= r.end_date\)/)
+    end
+  end
+end
+

data/spec/conceptql/operators/except_spec.rb

@@ -0,0 +1,15 @@
+require 'spec_helper'
+require 'conceptql/operators/except'
+require_relative 'query_double'
+
+describe ConceptQL::Operators::Except do
+  it_behaves_like(:evaluator)
+
+  describe '#query' do
+    it 'uses right stream as argument to EXCEPT against left stream' do
+      double1 = QueryDouble.new(1)
+      double2 = QueryDouble.new(2)
+      expect(ConceptQL::Operators::Except.new(left: double1, right: double2).query(Sequel.mock).sql).to eq("SELECT * FROM (SELECT * FROM table1 EXCEPT SELECT * FROM table2) AS t1")
+    end
+  end
+end

data/spec/conceptql/operators/first_spec.rb

@@ -0,0 +1,35 @@
+require 'spec_helper'
+require 'conceptql/operators/first'
+require_double('stream_for_occurrence')
+
+describe ConceptQL::Operators::First do
+  it_behaves_like(:evaluator)
+
+  it 'should have occurrence pegged at 1' do
+    expect(described_class.new.occurrence).to eq(1)
+  end
+
+  describe 'occurrence set to 1' do
+    subject do
+      described_class.new(StreamForOccurrenceDouble.new).query(Sequel.mock(host: 'postgres')).sql
+    end
+
+    it 'should order by ascending start_date' do
+      expect(subject).to match('ORDER BY "start_date" ASC')
+    end
+
+    it 'should partition by person_id' do
+      expect(subject).to match('PARTITION BY "person_id"')
+    end
+
+    it 'should assign a row number' do
+      expect(subject).to match('row_number()')
+    end
+
+    it 'should find the all rows with rn = 1' do
+      expect(subject).to match('"rn" = 1')
+    end
+  end
+end
+
+

data/spec/conceptql/operators/from_spec.rb

@@ -0,0 +1,13 @@
+require 'spec_helper'
+require 'conceptql/operators/from'
+require_relative 'query_double'
+
+describe ConceptQL::Operators::From do
+  it_behaves_like(:evaluator)
+
+  describe '#query' do
+    it 'works for single criteria' do
+      expect(ConceptQL::Operators::From.new(:table1).query(Sequel.mock).sql).to eq("SELECT * FROM table1")
+    end
+  end
+end

data/spec/conceptql/operators/gender_spec.rb

@@ -0,0 +1,27 @@
+require 'spec_helper'
+require 'conceptql/operators/gender'
+
+describe ConceptQL::Operators::Gender do
+  it_behaves_like(:evaluator)
+
+  describe '#query' do
+    it 'works for male/MALE/Male/M/m' do
+      correct_query = "SELECT * FROM person WHERE (gender_concept_id IN (8507))"
+      expect(ConceptQL::Operators::Gender.new('male').query(Sequel.mock).sql).to eq(correct_query)
+      expect(ConceptQL::Operators::Gender.new('Male').query(Sequel.mock).sql).to eq(correct_query)
+      expect(ConceptQL::Operators::Gender.new('MALE').query(Sequel.mock).sql).to eq(correct_query)
+      expect(ConceptQL::Operators::Gender.new('M').query(Sequel.mock).sql).to eq(correct_query)
+      expect(ConceptQL::Operators::Gender.new('m').query(Sequel.mock).sql).to eq(correct_query)
+    end
+
+    it 'works for Female/FEMALE/female/F/f' do
+      correct_query = "SELECT * FROM person WHERE (gender_concept_id IN (8532))"
+      expect(ConceptQL::Operators::Gender.new('female').query(Sequel.mock).sql).to eq(correct_query)
+      expect(ConceptQL::Operators::Gender.new('Female').query(Sequel.mock).sql).to eq(correct_query)
+      expect(ConceptQL::Operators::Gender.new('FEMALE').query(Sequel.mock).sql).to eq(correct_query)
+      expect(ConceptQL::Operators::Gender.new('F').query(Sequel.mock).sql).to eq(correct_query)
+      expect(ConceptQL::Operators::Gender.new('f').query(Sequel.mock).sql).to eq(correct_query)
+    end
+  end
+end
+

data/spec/conceptql/operators/hcpcs_spec.rb

@@ -0,0 +1,29 @@
+require 'spec_helper'
+require 'conceptql/operators/hcpcs'
+
+describe ConceptQL::Operators::Hcpcs do
+  it_behaves_like(:standard_vocabulary_operator)
+
+  subject do
+    described_class.new
+  end
+
+  describe '#table' do
+    it 'should be procedure_occurrence' do
+      expect(subject.table).to eq(:procedure_occurrence)
+    end
+  end
+
+  describe '#concept_column' do
+    it 'should be procedure_concept_id' do
+      expect(subject.concept_column).to eq(:procedure_concept_id)
+    end
+  end
+
+  describe '#vocabulary_id' do
+    it 'should be 5' do
+      expect(subject.vocabulary_id).to eq(5)
+    end
+  end
+end
+

data/spec/conceptql/operators/icd10_spec.rb

@@ -0,0 +1,34 @@
+require 'spec_helper'
+require 'conceptql/operators/icd10'
+
+describe ConceptQL::Operators::Icd10 do
+  it_behaves_like(:source_vocabulary_operator)
+
+  subject do
+    described_class.new
+  end
+
+  describe '#table' do
+    it 'should be condition_occurrence' do
+      expect(subject.table).to eq(:condition_occurrence)
+    end
+  end
+
+  describe '#concept_column' do
+    it 'should be condition_concept_id' do
+      expect(subject.concept_column).to eq(:condition_concept_id)
+    end
+  end
+
+  describe '#source_column' do
+    it 'should be condition_source_valuej' do
+      expect(subject.source_column).to eq(:condition_source_value)
+    end
+  end
+
+  describe '#vocabulary_id' do
+    it 'should be 34' do
+      expect(subject.vocabulary_id).to eq(34)
+    end
+  end
+end

data/spec/conceptql/operators/icd9_procedure_spec.rb

@@ -0,0 +1,29 @@
+require 'spec_helper'
+require 'conceptql/operators/icd9_procedure'
+
+describe ConceptQL::Operators::Icd9Procedure do
+  it_behaves_like(:standard_vocabulary_operator)
+
+  subject do
+    described_class.new
+  end
+
+  describe '#table' do
+    it 'should be procedure_occurrence' do
+      expect(subject.table).to eq(:procedure_occurrence)
+    end
+  end
+
+  describe '#concept_column' do
+    it 'should be procedure_concept_id' do
+      expect(subject.concept_column).to eq(:procedure_concept_id)
+    end
+  end
+
+  describe '#vocabulary_id' do
+    it 'should be 3' do
+      expect(subject.vocabulary_id).to eq(3)
+    end
+  end
+end
+

data/spec/conceptql/operators/icd9_spec.rb

@@ -0,0 +1,34 @@
+require 'spec_helper'
+require 'conceptql/operators/icd9'
+
+describe ConceptQL::Operators::Icd9 do
+  it_behaves_like(:source_vocabulary_operator)
+
+  subject do
+    ConceptQL::Operators::Icd9.new
+  end
+
+  describe '#table' do
+    it 'should be condition_occurrence' do
+      expect(subject.table).to eq(:condition_occurrence)
+    end
+  end
+
+  describe '#concept_column' do
+    it 'should be condition_concept_id' do
+      expect(subject.concept_column).to eq(:condition_concept_id)
+    end
+  end
+
+  describe '#source_column' do
+    it 'should be condition_source_valuej' do
+      expect(subject.source_column).to eq(:condition_source_value)
+    end
+  end
+
+  describe '#vocabulary_id' do
+    it 'should be 2' do
+      expect(subject.vocabulary_id).to eq(2)
+    end
+  end
+end

data/spec/conceptql/operators/intersect_spec.rb

@@ -0,0 +1,28 @@
+require 'spec_helper'
+require 'conceptql/operators/intersect'
+require_relative 'query_double'
+
+describe ConceptQL::Operators::Intersect do
+  it_behaves_like(:evaluator)
+
+  describe '#query' do
+    it 'works for multiple criteria of same type' do
+      double1 = QueryDouble.new(1)
+      double2 = QueryDouble.new(2)
+      double3 = QueryDouble.new(3)
+      expect(ConceptQL::Operators::Intersect.new(double1, double2, double3).query(Sequel.mock).sql).to eq("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)
+      expect(ConceptQL::Operators::Intersect.new(double1, double2, double3).query(Sequel.mock).sql).to eq("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)
+      expect(ConceptQL::Operators::Intersect.new(double1).query(Sequel.mock).sql).to eq("SELECT * FROM table1")
+    end
+  end
+end

data/spec/conceptql/operators/last_spec.rb

@@ -0,0 +1,36 @@
+require 'spec_helper'
+require 'conceptql/operators/last'
+require_double('stream_for_occurrence')
+
+describe ConceptQL::Operators::Last do
+  it_behaves_like(:evaluator)
+
+  it 'should have occurrence pegged at -1' do
+    expect(described_class.new.occurrence).to eq(-1)
+  end
+
+  describe 'occurrence set to -1' do
+    subject do
+      described_class.new(StreamForOccurrenceDouble.new).query(Sequel.mock(host: 'postgres')).sql
+    end
+
+
+    it 'should order by descending start_date' do
+      expect(subject).to match('ORDER BY "start_date" DESC')
+    end
+
+    it 'should partition by person_id' do
+      expect(subject).to match('PARTITION BY "person_id"')
+    end
+
+    it 'should assign a row number' do
+      expect(subject).to match('row_number()')
+    end
+
+    it 'should find the all rows with rn = 1' do
+      expect(subject).to match('"rn" = 1')
+    end
+  end
+end
+
+

data/spec/conceptql/operators/loinc_spec.rb

@@ -0,0 +1,29 @@
+require 'spec_helper'
+require 'conceptql/operators/loinc'
+
+describe ConceptQL::Operators::Loinc do
+  it_behaves_like(:standard_vocabulary_operator)
+
+  subject do
+    described_class.new
+  end
+
+  describe '#table' do
+    it 'should be observation' do
+      expect(subject.table).to eq(:observation)
+    end
+  end
+
+  describe '#concept_column' do
+    it 'should be procedure_concept_id' do
+      expect(subject.concept_column).to eq(:observation_concept_id)
+    end
+  end
+
+  describe '#vocabulary_id' do
+    it 'should be 6' do
+      expect(subject.vocabulary_id).to eq(6)
+    end
+  end
+end
+

data/spec/conceptql/operators/medcode_procedure_spec.rb

@@ -0,0 +1,34 @@
+require 'spec_helper'
+require 'conceptql/operators/medcode_procedure'
+
+describe ConceptQL::Operators::MedcodeProcedure do
+  it_behaves_like(:source_vocabulary_operator)
+
+  subject do
+    described_class.new
+  end
+
+  describe '#table' do
+    it 'should be procedure_occurrence' do
+      expect(subject.table).to eq(:procedure_occurrence)
+    end
+  end
+
+  describe '#concept_column' do
+    it 'should be procedure_concept_id' do
+      expect(subject.concept_column).to eq(:procedure_concept_id)
+    end
+  end
+
+  describe '#source_column' do
+    it 'should be procedure_source_valuej' do
+      expect(subject.source_column).to eq(:procedure_source_value)
+    end
+  end
+
+  describe '#vocabulary_id' do
+    it 'should be 204 (a J&J provided mapping as part of CPRD)' do
+      expect(subject.vocabulary_id).to eq(204)
+    end
+  end
+end

data/spec/conceptql/operators/medcode_spec.rb

@@ -0,0 +1,34 @@
+require 'spec_helper'
+require 'conceptql/operators/medcode'
+
+describe ConceptQL::Operators::Medcode do
+  it_behaves_like(:source_vocabulary_operator)
+
+  subject do
+    described_class.new
+  end
+
+  describe '#table' do
+    it 'should be condition_occurrence' do
+      expect(subject.table).to eq(:condition_occurrence)
+    end
+  end
+
+  describe '#concept_column' do
+    it 'should be condition_concept_id' do
+      expect(subject.concept_column).to eq(:condition_concept_id)
+    end
+  end
+
+  describe '#source_column' do
+    it 'should be condition_source_valuej' do
+      expect(subject.source_column).to eq(:condition_source_value)
+    end
+  end
+
+  describe '#vocabulary_id' do
+    it 'should be 203 (a J&J provided mapping as part of CPRD)' do
+      expect(subject.vocabulary_id).to eq(203)
+    end
+  end
+end

data/spec/conceptql/operators/observation_period_spec.rb

@@ -0,0 +1,10 @@
+require 'spec_helper'
+require 'conceptql/operators/observation_period'
+require_double('stream_for_casting')
+
+describe ConceptQL::Operators::ObservationPeriod do
+  it_behaves_like(:casting_operator)
+end
+
+
+

data/spec/conceptql/operators/occurrence_spec.rb

@@ -0,0 +1,87 @@
+require 'spec_helper'
+require 'conceptql/operators/occurrence'
+require_double('stream_for_occurrence')
+
+describe ConceptQL::Operators::Occurrence do
+  it_behaves_like(:evaluator)
+
+  describe 'occurrence set to 1' do
+    subject do
+      described_class.new(1, StreamForOccurrenceDouble.new).query(Sequel.mock(host: 'postgres')).sql
+    end
+
+    it 'should order by ascending start_date' do
+      expect(subject).to match('ORDER BY "start_date" ASC')
+    end
+
+    it 'should partition by person_id' do
+      expect(subject).to match('PARTITION BY "person_id"')
+    end
+
+    it 'should assign a row number' do
+      expect(subject).to match('row_number()')
+    end
+
+    it 'should find the all rows with "rn" = 1' do
+      expect(subject).to match('"rn" = 1')
+    end
+  end
+
+  describe 'occurrence set to 2' do
+    subject do
+      described_class.new(2, StreamForOccurrenceDouble.new).query(Sequel.mock(host: 'postgres')).sql
+    end
+
+    it 'should order by ascending start_date' do
+      expect(subject).to match('ORDER BY "start_date" ASC')
+    end
+
+    it 'should find the all rows with "rn" = 2' do
+      expect(subject).to match('"rn" = 2')
+    end
+  end
+
+  describe 'occurrence set to -1' do
+    subject do
+      described_class.new(-1, StreamForOccurrenceDouble.new).query(Sequel.mock(host: 'postgres')).sql
+    end
+
+    it 'should order by ascending start_date' do
+      expect(subject).to match('ORDER BY "start_date" DESC')
+    end
+
+    it 'should find the all rows with "rn" = 1' do
+      expect(subject).to match('"rn" = 1')
+    end
+  end
+
+  describe 'occurrence set to -2' do
+    subject do
+      described_class.new(-2, StreamForOccurrenceDouble.new).query(Sequel.mock(host: 'postgres')).sql
+    end
+
+    it 'should order by ascending start_date' do
+      expect(subject).to match('ORDER BY "start_date" DESC')
+    end
+
+    it 'should find the all rows with "rn" = 2' do
+      expect(subject).to match('"rn" = 2')
+    end
+  end
+
+  describe 'occurrence respects types' do
+    subject do
+      dub = StreamForOccurrenceDouble.new
+      def dub.types
+        [:condition_occurrence]
+      end
+      described_class.new(-2, dub).query(Sequel.mock(host: 'postgres')).sql
+    end
+
+    it 'should order by ascending start_date' do
+      expect(subject).to match(', "criterion_type", "criterion_id"')
+    end
+  end
+end
+
+

data/spec/conceptql/operators/overlapped_by_spec.rb

@@ -0,0 +1,32 @@
+require 'spec_helper'
+require 'conceptql/operators/overlapped_by'
+require_double('stream_for_temporal')
+
+describe ConceptQL::Operators::OverlappedBy do
+  it_behaves_like(:temporal_operator)
+
+  describe 'when not inclusive' do
+    subject do
+      described_class.new(left: StreamForTemporalDouble.new, right: StreamForTemporalDouble.new)
+    end
+
+    it 'should use proper where clause' do
+      expect(subject.query(Sequel.mock).sql).to match('l.start_date <= r.end_date')
+      expect(subject.query(Sequel.mock).sql).to match('r.start_date <= l.start_date')
+      expect(subject.query(Sequel.mock).sql).to match('r.end_date <= l.end_date')
+    end
+  end
+
+  describe 'when inclusive' do
+    subject do
+      described_class.new(inclusive: true, left: StreamForTemporalDouble.new, right: StreamForTemporalDouble.new)
+    end
+
+    it 'should use proper where clause' do
+      expect(subject.query(Sequel.mock).sql).to match('l.start_date <= r.end_date')
+      expect(subject.query(Sequel.mock).sql).to match('r.start_date <= l.start_date')
+    end
+  end
+end
+
+

data/spec/conceptql/operators/overlaps_spec.rb

@@ -0,0 +1,21 @@
+require 'spec_helper'
+require 'conceptql/operators/overlaps'
+require_double('stream_for_temporal')
+
+describe ConceptQL::Operators::Overlaps do
+  it_behaves_like(:temporal_operator)
+
+  describe 'when not inclusive' do
+    subject do
+      described_class.new(left: StreamForTemporalDouble.new, right: StreamForTemporalDouble.new)
+    end
+
+    it 'should use proper where clause' do
+      expect(subject.query(Sequel.mock).sql).to match('r.start_date <= l.end_date')
+      expect(subject.query(Sequel.mock).sql).to match('l.start_date <= r.start_date')
+      expect(subject.query(Sequel.mock).sql).to match('l.end_date <= r.end_date')
+    end
+  end
+end
+
+

data/spec/conceptql/operators/person_filter_spec.rb

@@ -0,0 +1,15 @@
+require 'spec_helper'
+require 'conceptql/operators/person_filter'
+require_relative 'query_double'
+
+describe ConceptQL::Operators::PersonFilter do
+  it_behaves_like(:evaluator)
+
+  describe '#query' do
+    it 'uses right stream as argument to PERSON_FILTER against left stream' do
+      double1 = QueryDouble.new(1)
+      double2 = QueryDouble.new(2)
+      expect(ConceptQL::Operators::PersonFilter.new(left: double1, right: double2).query(Sequel.mock).sql).to eq("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/operators/person_spec.rb

@@ -0,0 +1,10 @@
+require 'spec_helper'
+require 'conceptql/operators/person'
+require_double('stream_for_casting')
+
+describe ConceptQL::Operators::Person do
+  it_behaves_like(:casting_operator)
+end
+
+
+