conceptql 0.2.0 → 0.4.0

data/lib/conceptql/operators/condition_type.rb

@@ -1,71 +0,0 @@
-require_relative 'operator'
-
-module ConceptQL
-  module Operators
-    # Represents a operator that will grab all conditions that match the
-    # condition type passed in
-    #
-    # Condition Type represents which position the condition held in
-    # the raw data, e.g. primary inpatient header or 15th outpatient detail
-    #
-    # Multiple types can be specified at once
-    class ConditionType < Operator
-      desc 'Searches for conditions that match the given set of Condition Types'
-      argument :condition_types, type: :codelist, vocab: 'Condition Type'
-      category %(Occurrence Type)
-      predominant_types :condition_occurrence
-
-      def type
-        :condition_occurrence
-      end
-
-      def query(db)
-        db.from(:condition_occurrence)
-          .where(condition_type_concept_id: condition_occurrence_type_concept_ids)
-      end
-
-    private
-      def condition_occurrence_type_concept_ids
-        arguments.map do |arg|
-          to_concept_id(arg.to_s)
-        end.flatten
-      end
-
-      def to_concept_id(ctype)
-        ctype = ctype.to_s.downcase
-        position = nil
-        if ctype =~ /(\d|_primary)$/ && ctype.count('_') > 1
-          parts = ctype.split('_')
-          position = parts.pop.to_i
-          position -= 1 if ctype =~ /^outpatient/
-          ctype = parts.join('_')
-        end
-        retval = concept_ids[ctype.to_sym]
-        return retval[position] if position
-        return retval
-      end
-
-      def concept_ids
-        @concept_ids ||= begin
-          hash = {
-            inpatient_detail: (38000183..38000198).to_a,
-            inpatient_header: (38000199..38000214).to_a,
-            outpatient_detail: (38000215..38000229).to_a,
-            outpatient_header: (38000230..38000244).to_a,
-            ehr_problem_list: [38000245],
-            condition_era_0_day_window: [38000246],
-            condition_era_30_day_window: [38000247]
-          }
-          hash[:primary] = %w(inpatient_detail inpatient_header outpatient_detail outpatient_header).map { |w| hash[w.to_sym].first }
-          hash[:outpatient_primary] = %w(outpatient_detail outpatient_header).map { |w| hash[w.to_sym].first }
-          hash[:inpatient_primary] = %w(inpatient_detail inpatient_header).map { |w| hash[w.to_sym].first }
-          hash[:inpatient] = hash[:inpatient_detail] + hash[:inpatient_header]
-          hash[:outpatient] = hash[:outpatient_detail] + hash[:outpatient_header]
-          hash[:condition_era] = hash[:condition_era_0_day_window] + hash[:condition_era_30_day_window]
-          hash
-        end
-      end
-    end
-  end
-end
-

data/lib/conceptql/operators/cpt.rb

@@ -1,25 +0,0 @@
-require_relative 'standard_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class Cpt < StandardVocabularyOperator
-      preferred_name 'CPT'
-      desc 'Searches the procedure_occurrence table for all procedures with matching CPT codes'
-      argument :cpts, type: :codelist, vocab: 'CPT4'
-      predominant_types :procedure_occurrence
-
-      def table
-        :procedure_occurrence
-      end
-
-      def vocabulary_id
-        4
-      end
-
-      def concept_column
-        :procedure_concept_id
-      end
-    end
-  end
-end
-

data/lib/conceptql/operators/drug_type_concept.rb

@@ -1,21 +0,0 @@
-require_relative 'operator'
-
-module ConceptQL
-  module Operators
-    class DrugTypeConcept < Operator
-      desc 'Given a set of concept IDs in RxNorm, returns that set of drug exposures'
-      argument :concept_ids, type: :codelist, vocab: 'RxNorm'
-
-      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/operators/from_seer_visits.rb

@@ -1,23 +0,0 @@
-require_relative 'operator'
-
-module ConceptQL
-  module Operators
-    class FromSeerVisits < Operator
-      def type
-        :observation
-      end
-      def query(db)
-        visit_ids = stream.evaluate(db)
-          .from_self
-          .where(criterion_type: 'visit_occurrence')
-        query = db[:observation].where(visit_occurrence_id: visit_ids.select(:criterion_id))
-        arguments.inject(query) do |q, key|
-          q.where(observation_source_value: key.to_s.upcase)
-        end
-      end
-    end
-  end
-end
-
-
-

data/lib/conceptql/operators/hcpcs.rb

@@ -1,25 +0,0 @@
-require_relative 'standard_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class Hcpcs < StandardVocabularyOperator
-      preferred_name 'HCPCS'
-      desc 'Searches the procedure_occurrence table for all procedures with matching HCPCS codes'
-      argument :hcpcs, type: :codelist, vocab: 'HCPCS'
-      predominant_types :procedure_occurrence
-
-      def table
-        :procedure_occurrence
-      end
-
-      def vocabulary_id
-        5
-      end
-
-      def concept_column
-        :procedure_concept_id
-      end
-    end
-  end
-end
-

data/lib/conceptql/operators/icd10.rb

@@ -1,28 +0,0 @@
-require_relative 'source_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class Icd10 < SourceVocabularyOperator
-      preferred_name 'ICD-10 CM'
-      desc 'Searches the condition_occurrence table for the given set of ICD-10 codes.'
-      argument :icd10s, type: :codelist, vocab: 'ICD10CM'
-      predominant_types :condition_occurrence
-
-      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/operators/icd9.rb

@@ -1,28 +0,0 @@
-require_relative 'source_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class Icd9 < SourceVocabularyOperator
-      preferred_name 'ICD-9 CM'
-      desc 'Searches the condition_occurrence table for the given set of ICD-9 codes.'
-      argument :icd9s, type: :codelist, vocab: 'ICD9CM'
-      predominant_types :condition_occurrence
-
-      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/operators/icd9_procedure.rb

@@ -1,25 +0,0 @@
-require_relative 'standard_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class Icd9Procedure < StandardVocabularyOperator
-      preferred_name 'ICD-9 Proc'
-      desc 'Searches the procedure_occurrence table for the given set of ICD-9 codes.'
-      argument :icd9s, type: :codelist, vocab: 'ICD9Proc'
-      predominant_types :procedure_occurrence
-
-      def table
-        :procedure_occurrence
-      end
-
-      def vocabulary_id
-        3
-      end
-
-      def concept_column
-        :procedure_concept_id
-      end
-    end
-  end
-end
-

data/lib/conceptql/operators/intersect.rb

@@ -1,34 +0,0 @@
-require_relative 'pass_thru'
-
-module ConceptQL
-  module Operators
-    class Intersect < PassThru
-      desc 'Passes thru any result row that appears in all incoming result sets.'
-      allows_many_upstreams
-      category 'Set Logic'
-
-      def types
-        upstreams.map(&:types).flatten.uniq
-      end
-
-      def query(db)
-        exprs = {}
-        upstreams.each do |expression|
-          evaled = expression.evaluate(db)
-          expression.types.each do |type|
-            (exprs[type] ||= []) << evaled
-          end
-        end
-        typed_queries = exprs.map do |type, queries|
-          queries.inject do |q, query|
-            q.intersect(query)
-          end
-        end
-
-        typed_queries.inject do |q, query|
-          q.union(query, all: true)
-        end
-      end
-    end
-  end
-end

data/lib/conceptql/operators/loinc.rb

@@ -1,25 +0,0 @@
-require_relative 'standard_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class Loinc < StandardVocabularyOperator
-      preferred_name 'LOINC'
-      desc 'Searches the observation table for all observations with matching LOINC codes'
-      argument :loincs, type: :codelist, vocab: 'LOINC'
-      predominant_types :observation
-
-      def table
-        :observation
-      end
-
-      def vocabulary_id
-        6
-      end
-
-      def concept_column
-        :observation_concept_id
-      end
-    end
-  end
-end
-

data/lib/conceptql/operators/medcode.rb

@@ -1,28 +0,0 @@
-require_relative 'source_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class Medcode < SourceVocabularyOperator
-      desc 'Searches the condition_occurrence table for all conditions with matching Medcodes'
-      argument :medcodes, type: :codelist, vocab_id: '203'
-      predominant_types :condition_occurrence
-
-      def table
-        :condition_occurrence
-      end
-
-      def vocabulary_id
-        203
-      end
-
-      def source_column
-        :condition_source_value
-      end
-
-      def concept_column
-        :condition_concept_id
-      end
-    end
-  end
-end
-

data/lib/conceptql/operators/medcode_procedure.rb

@@ -1,27 +0,0 @@
-require_relative 'source_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class MedcodeProcedure < SourceVocabularyOperator
-      desc 'Searches the procedure_occurrence table for all procedures with matching Medcodes'
-      argument :medcodes, type: :codelist, vocab: '204'
-      predominant_types :procedure_occurrence
-
-      def table
-        :procedure_occurrence
-      end
-
-      def vocabulary_id
-        204
-      end
-
-      def source_column
-        :procedure_source_value
-      end
-
-      def concept_column
-        :procedure_concept_id
-      end
-    end
-  end
-end

data/lib/conceptql/operators/ndc.rb

@@ -1,29 +0,0 @@
-require_relative 'source_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class Ndc < SourceVocabularyOperator
-      preferred_name 'NDC'
-      desc 'Searches the drug_exposure table for all procedures with matching NDC codes'
-      argument :ndcs, type: :codelist, vocab: 'NDC'
-      predominant_types :drug_exposure
-
-      def table
-        :drug_exposure
-      end
-
-      def vocabulary_id
-        9
-      end
-
-      def source_column
-        :drug_source_value
-      end
-
-      def concept_column
-        :drug_concept_id
-      end
-    end
-  end
-end
-

data/lib/conceptql/operators/observation_by_enttype.rb

@@ -1,29 +0,0 @@
-require_relative 'source_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class ObservationByEnttype < SourceVocabularyOperator
-      desc 'Searches the observation table for all observations with matching Enttype'
-      argument :enttypes, type: :codelist, vocab_id: [206, 207]
-      predominant_types :observation
-
-      def table
-        :observation
-      end
-
-      def vocabulary_id
-        [206, 207]
-      end
-
-      def source_column
-        :observation_source_value
-      end
-
-      def concept_column
-        :observation_concept_id
-      end
-    end
-  end
-end
-
-

data/lib/conceptql/operators/observation_period.rb

@@ -1,30 +0,0 @@
-require_relative 'casting_operator'
-
-module ConceptQL
-  module Operators
-    class ObservationPeriod < CastingOperator
-      desc 'Generates all observation_period records, or, if fed a stream, fetches all observation_period records for the people represented in the incoming result set.'
-      types :observation_period
-      allows_one_upstream
-
-      def my_type
-        :observation_period
-      end
-
-      def i_point_at
-        []
-      end
-
-      def these_point_at_me
-        # I could list ALL the types we use, but the default behavior of casting,
-        # when there is no explicit casting defined, is to convert everything to
-        # person IDs
-        #
-        # So by defining no known castable relationships in this operator, all
-        # types will be converted to person
-        []
-      end
-    end
-  end
-end
-

data/lib/conceptql/operators/overlapped_by.rb

@@ -1,23 +0,0 @@
-require_relative 'temporal_operator'
-
-module ConceptQL
-  module Operators
-    class OverlappedBy < TemporalOperator
-      desc <<-EOF
-Compares all results on a person-by-person basis between the left hand results (LHR) and the right hand resuls (RHR).
-For any result in the LHR whose start_date occurs between the start_date and end_date of a result from the RHR, that result is passed through.
-All other results are discarded, including all results in the RHR.
-L-------N-------L
-         R-----R
-  L-----Y----L
-      EOF
-      def where_clause
-        if inclusive?
-          [Proc.new { r__start_date <= l__start_date}, Proc.new { l__start_date <= r__end_date }]
-        else
-          [Proc.new { r__start_date <= l__start_date}, Proc.new { l__start_date <= r__end_date }, Proc.new { r__end_date <= l__end_date }]
-        end
-      end
-    end
-  end
-end

data/lib/conceptql/operators/overlaps.rb

@@ -1,19 +0,0 @@
-require_relative 'temporal_operator'
-
-module ConceptQL
-  module Operators
-    class Overlaps < TemporalOperator
-      desc <<-EOF
-Compares all results on a person-by-person basis between the left hand results (LHR) and the right hand resuls (RHR).
-For any result in the LHR whose end_date occurs between the start_date and end_date of a result from the RHR, that result is passed through.
-All other results are discarded, including all results in the RHR.
-L-------Y-------L
-            R-----R
-L-----N----L
-      EOF
-      def where_clause
-        [Proc.new { l__start_date <= r__start_date}, Proc.new { r__start_date <= l__end_date }, Proc.new { l__end_date <= r__end_date }]
-      end
-    end
-  end
-end

data/lib/conceptql/operators/place_of_service_code.rb

@@ -1,24 +0,0 @@
-require_relative 'operator'
-
-module ConceptQL
-  module Operators
-    # Represents a operator that will grab all person rows that match the given place_of_service_codes
-    #
-    # PlaceOfServiceCode parameters are passed in as a set of strings.  Each string represents
-    # a single place_of_service_code.  The place_of_service_code string must match one of the values in the
-    # concept_name column of the concept table.  If you misspell the place_of_service_code name
-    # you won't get any matches
-    class PlaceOfServiceCode < Operator
-      desc 'Finds all visit_occurrences that match the Place of Service codes'
-      argument :places_of_service, type: :codelist, vocab: 'Place of Service'
-      types :visit_occurrence
-
-      def query(db)
-        db.from(:visit_occurrence___v)
-          .join(:vocabulary__concept___vc, { vc__concept_id: :v__place_of_service_concept_id })
-          .where(vc__concept_code: arguments.map(&:to_s))
-          .where(vc__vocabulary_id: 14)
-      end
-    end
-  end
-end

data/lib/conceptql/operators/procedure_occurrence.rb

@@ -1,25 +0,0 @@
-require_relative 'casting_operator'
-
-module ConceptQL
-  module Operators
-    class ProcedureOccurrence < CastingOperator
-      desc 'Generates all procedure_occurrence records, or, if fed a stream, fetches all procedure_occurrence records for the people represented in the incoming result set.'
-      types :procedure_occurrence
-      allows_one_upstream
-
-      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/operators/prodcode.rb

@@ -1,29 +0,0 @@
-require_relative 'source_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class Prodcode < SourceVocabularyOperator
-      desc 'Searches the drug_exposure table for all conditions with matching Prodcodes'
-      argument :prodcodes, type: :codelist, vocab_id: '203'
-      predominant_types :drug_exposure
-
-      def table
-        :drug_exposure
-      end
-
-      def vocabulary_id
-        200
-      end
-
-      def source_column
-        :drug_source_value
-      end
-
-      def concept_column
-        :drug_concept_id
-      end
-    end
-  end
-end
-
-

data/lib/conceptql/operators/rxnorm.rb

@@ -1,24 +0,0 @@
-require_relative 'standard_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class Rxnorm < StandardVocabularyOperator
-      preferred_name 'RxNorm'
-      desc 'Finds all drug_exposures by RxNorm codes'
-      argument :rxnorms, type: :codelist, vocab: 'RxNorm'
-
-      def table
-        :drug_exposure
-      end
-
-      def vocabulary_id
-        8
-      end
-
-      def concept_column
-        :drug_concept_id
-      end
-    end
-  end
-end
-

data/lib/conceptql/operators/snomed.rb

@@ -1,24 +0,0 @@
-require_relative 'standard_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class Snomed < StandardVocabularyOperator
-      preferred_name 'SNOMED'
-      desc 'Find all condition_occurrences by SNOMED codes'
-      argument :snomeds, type: :codelist, vocab: 'SNOMED'
-      predominant_types :condition_occurrence
-
-      def table
-        :condition_occurrence
-      end
-
-      def vocabulary_id
-        1
-      end
-
-      def concept_column
-        :condition_concept_id
-      end
-    end
-  end
-end

data/lib/conceptql/operators/snomed_condition.rb

@@ -1,26 +0,0 @@
-require_relative 'standard_vocabulary_operator'
-
-module ConceptQL
-  module Operators
-    class SnomedCondition < StandardVocabularyOperator
-      preferred_name 'SNOMED'
-      desc 'Find all condition_occurrences by SNOMED codes'
-      argument :snomeds, type: :codelist, vocab: 'SNOMED'
-      predominant_types :condition_occurrence
-
-      def table
-        :condition_occurrence
-      end
-
-      def vocabulary_id
-        1
-      end
-
-      def concept_column
-        :condition_concept_id
-      end
-    end
-  end
-end
-
-