conceptql 0.2.0 → 0.3.0
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- checksums.yaml +4 -4
- data/.gitignore +2 -0
- data/CHANGELOG.md +32 -104
- data/Gemfile +2 -0
- data/README.md +43 -21
- data/Rakefile +34 -0
- data/conceptql.gemspec +3 -4
- data/config/provenance.yml +454 -0
- data/doc/converter.rb +33 -0
- data/doc/metadata.md +89 -0
- data/doc/spec.md +1775 -861
- data/doc/spec.md.cql +1930 -0
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- data/doc/spec/ff7d5b5573d09bd7c4cdd3aeda124d18bf82ec46673a62881b399a75d69f3f53.png +0 -0
- data/lib/conceptql.rb +21 -1
- data/lib/conceptql/annotate_grapher.rb +127 -0
- data/lib/conceptql/behaviors/drugish.rb +12 -0
- data/lib/conceptql/behaviors/labish.rb +13 -0
- data/lib/conceptql/behaviors/metadatable.rb +156 -71
- data/lib/conceptql/behaviors/provenanceable.rb +30 -0
- data/lib/conceptql/cli.rb +81 -37
- data/lib/conceptql/database.rb +42 -0
- data/lib/conceptql/date_adjuster.rb +22 -4
- data/lib/conceptql/fake_annotater.rb +129 -0
- data/lib/conceptql/knitter.rb +221 -0
- data/lib/conceptql/nodifier.rb +34 -23
- data/lib/conceptql/operators/after.rb +20 -3
- data/lib/conceptql/operators/any_overlap.rb +3 -1
- data/lib/conceptql/operators/before.rb +19 -3
- data/lib/conceptql/operators/binary_operator_operator.rb +24 -20
- data/lib/conceptql/operators/casting_operator.rb +39 -31
- data/lib/conceptql/operators/co_reported.rb +42 -0
- data/lib/conceptql/operators/complement.rb +21 -16
- data/lib/conceptql/operators/concurrent_within.rb +57 -0
- data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator.rb +34 -0
- data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator_union.rb +28 -0
- data/lib/conceptql/operators/condition_type.rb +12 -4
- data/lib/conceptql/operators/contains.rb +6 -2
- data/lib/conceptql/operators/count.rb +10 -2
- data/lib/conceptql/operators/cpt.rb +5 -2
- data/lib/conceptql/operators/cpt_or_hcpcs.rb +27 -0
- data/lib/conceptql/operators/date_range.rb +20 -8
- data/lib/conceptql/operators/death.rb +4 -2
- data/lib/conceptql/operators/drg.rb +42 -0
- data/lib/conceptql/operators/drug_type_concept.rb +11 -2
- data/lib/conceptql/operators/during.rb +4 -2
- data/lib/conceptql/operators/equal.rb +4 -1
- data/lib/conceptql/operators/except.rb +16 -4
- data/lib/conceptql/operators/filter.rb +6 -3
- data/lib/conceptql/operators/first.rb +3 -1
- data/lib/conceptql/operators/from.rb +32 -5
- data/lib/conceptql/operators/from_seer_visits.rb +11 -5
- data/lib/conceptql/operators/gender.rb +9 -2
- data/lib/conceptql/operators/hcpcs.rb +5 -2
- data/lib/conceptql/operators/icd10.rb +6 -15
- data/lib/conceptql/operators/icd10_pcs.rb +28 -0
- data/lib/conceptql/operators/icd9.rb +6 -15
- data/lib/conceptql/operators/icd9_procedure.rb +5 -2
- data/lib/conceptql/operators/intersect.rb +15 -10
- data/lib/conceptql/operators/invalid.rb +36 -0
- data/lib/conceptql/operators/last.rb +3 -1
- data/lib/conceptql/operators/loinc.rb +5 -2
- data/lib/conceptql/operators/medcode.rb +5 -16
- data/lib/conceptql/operators/medcode_procedure.rb +3 -2
- data/lib/conceptql/operators/ndc.rb +5 -2
- data/lib/conceptql/operators/numeric.rb +30 -11
- data/lib/conceptql/operators/observation_by_enttype.rb +5 -2
- data/lib/conceptql/operators/observation_period.rb +6 -4
- data/lib/conceptql/operators/occurrence.rb +47 -11
- data/lib/conceptql/operators/one_in_two_out.rb +96 -33
- data/lib/conceptql/operators/operator.rb +628 -95
- data/lib/conceptql/operators/overlapped_by.rb +8 -5
- data/lib/conceptql/operators/overlaps.rb +7 -5
- data/lib/conceptql/operators/pass_thru.rb +12 -2
- data/lib/conceptql/operators/person.rb +7 -5
- data/lib/conceptql/operators/person_filter.rb +5 -1
- data/lib/conceptql/operators/place_of_service_code.rb +12 -5
- data/lib/conceptql/operators/place_of_service_filter.rb +47 -0
- data/lib/conceptql/operators/procedure_occurrence.rb +4 -2
- data/lib/conceptql/operators/prodcode.rb +5 -2
- data/lib/conceptql/operators/provenance.rb +66 -0
- data/lib/conceptql/operators/provider_filter.rb +36 -0
- data/lib/conceptql/operators/race.rb +11 -4
- data/lib/conceptql/operators/read.rb +149 -0
- data/lib/conceptql/operators/recall.rb +42 -7
- data/lib/conceptql/operators/revenue_code.rb +40 -0
- data/lib/conceptql/operators/rxnorm.rb +5 -1
- data/lib/conceptql/operators/snomed.rb +3 -2
- data/lib/conceptql/operators/source_vocabulary_operator.rb +44 -14
- data/lib/conceptql/operators/standard_vocabulary_operator.rb +36 -15
- data/lib/conceptql/operators/started_by.rb +2 -1
- data/lib/conceptql/operators/sum.rb +7 -1
- data/lib/conceptql/operators/temporal_operator.rb +75 -9
- data/lib/conceptql/operators/time_window.rb +13 -23
- data/lib/conceptql/operators/to_seer_visits.rb +6 -1
- data/lib/conceptql/operators/trim_date_end.rb +20 -12
- data/lib/conceptql/operators/trim_date_start.rb +22 -12
- data/lib/conceptql/operators/union.rb +39 -2
- data/lib/conceptql/operators/visit_occurrence.rb +5 -3
- data/lib/conceptql/operators/vocabulary_operator.rb +45 -0
- data/lib/conceptql/query.rb +68 -22
- data/lib/conceptql/query_modifiers/drug_query_modifier.rb +45 -0
- data/lib/conceptql/query_modifiers/pos_query_modifier.rb +31 -0
- data/lib/conceptql/query_modifiers/query_modifier.rb +16 -0
- data/lib/conceptql/scope.rb +169 -31
- data/lib/conceptql/sql_formatter.rb +22 -0
- data/lib/conceptql/version.rb +1 -1
- data/test/all.rb +3 -0
- data/test/all_operations_test.rb +45 -0
- data/test/code_list_test.rb +23 -0
- data/test/data/omopv4/care_site.csv +0 -0
- data/test/data/omopv4/cohort.csv +0 -0
- data/test/data/omopv4/condition_era.csv +0 -0
- data/test/data/omopv4/condition_occurrence.csv +34044 -0
- data/test/data/omopv4/death.csv +1 -0
- data/test/data/omopv4/drug_cost.csv +0 -0
- data/test/data/omopv4/drug_era.csv +0 -0
- data/test/data/omopv4/drug_exposure.csv +2 -0
- data/test/data/omopv4/location.csv +0 -0
- data/test/data/omopv4/observation.csv +2 -0
- data/test/data/omopv4/observation_period.csv +1 -0
- data/test/data/omopv4/organization.csv +0 -0
- data/test/data/omopv4/payer_plan_period.csv +0 -0
- data/test/data/omopv4/person.csv +250 -0
- data/test/data/omopv4/procedure_cost.csv +0 -0
- data/test/data/omopv4/procedure_occurrence.csv +35099 -0
- data/test/data/omopv4/provider.csv +0 -0
- data/test/data/omopv4/visit_occurrence.csv +14931 -0
- data/test/data/omopv4_plus/care_site.csv +0 -0
- data/test/data/omopv4_plus/cohort.csv +0 -0
- data/test/data/omopv4_plus/concept.csv +352 -0
- data/test/data/omopv4_plus/condition_era.csv +0 -0
- data/test/data/omopv4_plus/condition_occurrence.csv +46673 -0
- data/test/data/omopv4_plus/death.csv +9 -0
- data/test/data/omopv4_plus/drug_cost.csv +13921 -0
- data/test/data/omopv4_plus/drug_era.csv +0 -0
- data/test/data/omopv4_plus/drug_exposure.csv +13921 -0
- data/test/data/omopv4_plus/headers/care_site.csv +1 -0
- data/test/data/omopv4_plus/headers/cohort.csv +1 -0
- data/test/data/omopv4_plus/headers/concept.csv +1 -0
- data/test/data/omopv4_plus/headers/condition_era.csv +1 -0
- data/test/data/omopv4_plus/headers/condition_occurrence.csv +1 -0
- data/test/data/omopv4_plus/headers/death.csv +1 -0
- data/test/data/omopv4_plus/headers/drug_cost.csv +1 -0
- data/test/data/omopv4_plus/headers/drug_era.csv +1 -0
- data/test/data/omopv4_plus/headers/drug_exposure.csv +1 -0
- data/test/data/omopv4_plus/headers/location.csv +1 -0
- data/test/data/omopv4_plus/headers/observation.csv +1 -0
- data/test/data/omopv4_plus/headers/observation_period.csv +1 -0
- data/test/data/omopv4_plus/headers/organization.csv +1 -0
- data/test/data/omopv4_plus/headers/payer_plan_period.csv +1 -0
- data/test/data/omopv4_plus/headers/person.csv +1 -0
- data/test/data/omopv4_plus/headers/procedure_cost.csv +1 -0
- data/test/data/omopv4_plus/headers/procedure_occurrence.csv +1 -0
- data/test/data/omopv4_plus/headers/provider.csv +1 -0
- data/test/data/omopv4_plus/headers/source_to_concept_map.csv +1 -0
- data/test/data/omopv4_plus/headers/visit_occurrence.csv +1 -0
- data/test/data/omopv4_plus/headers/vocabulary.csv +1 -0
- data/test/data/omopv4_plus/location.csv +0 -0
- data/test/data/omopv4_plus/observation.csv +0 -0
- data/test/data/omopv4_plus/observation_period.csv +147 -0
- data/test/data/omopv4_plus/organization.csv +736 -0
- data/test/data/omopv4_plus/payer_plan_period.csv +808 -0
- data/test/data/omopv4_plus/person.csv +250 -0
- data/test/data/omopv4_plus/procedure_cost.csv +20123 -0
- data/test/data/omopv4_plus/procedure_occurrence.csv +27273 -0
- data/test/data/omopv4_plus/provider.csv +10193 -0
- data/test/data/omopv4_plus/source_to_concept_map.csv +285 -0
- data/test/data/omopv4_plus/visit_occurrence.csv +45125 -0
- data/test/data/omopv4_plus/vocabulary.csv +60 -0
- data/test/db.rb +15 -0
- data/test/db_setup.rb +408 -0
- data/test/db_teardown.rb +33 -0
- data/test/fake_annotater_test.rb +31 -0
- data/test/helper.rb +129 -0
- data/test/knitter/conceptql.md.cql +39 -0
- data/test/knitter/conceptql.md.expect +43 -0
- data/test/knitter/empty.md.cql +0 -0
- data/test/knitter/except.md.cql +13 -0
- data/test/knitter/except.md.expect +14 -0
- data/test/knitter/fake.md.cql +10 -0
- data/test/knitter/fake.md.expect +13 -0
- data/test/knitter/many.md.cql +7 -0
- data/test/knitter/many.md.expect +14 -0
- data/test/knitter/no_conceptql.md.cql +36 -0
- data/test/knitter/title.md.cql +12 -0
- data/test/knitter/title.md.expect +15 -0
- data/test/knitter/union.md.cql +11 -0
- data/test/knitter/union.md.expect +14 -0
- data/test/knitter_test.rb +69 -0
- data/test/query_test.rb +36 -0
- data/test/results/omopv4/after/anno_1 +25 -0
- data/test/results/omopv4/after/anno_2 +48 -0
- data/test/results/omopv4/after/anno_3 +34 -0
- data/test/results/omopv4/after/anno_4 +60 -0
- data/test/results/omopv4/after/anno_5 +68 -0
- data/test/results/omopv4/after/anno_6 +60 -0
- data/test/results/omopv4/after/crit_at_least +7 -0
- data/test/results/omopv4/after/crit_basic +32 -0
- data/test/results/omopv4/after/crit_occurrences +12 -0
- data/test/results/omopv4/after/crit_within +6 -0
- data/test/results/omopv4/any_overlap/crit_basic1 +15 -0
- data/test/results/omopv4/any_overlap/crit_basic2 +15 -0
- data/test/results/omopv4/any_overlap/crit_occurrences1 +2 -0
- data/test/results/omopv4/any_overlap/crit_occurrences2 +15 -0
- data/test/results/omopv4/any_overlap/crit_within +8 -0
- data/test/results/omopv4/before/crit_at_least +6 -0
- data/test/results/omopv4/before/crit_basic1 +48 -0
- data/test/results/omopv4/before/crit_basic2 +7 -0
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- data/test/results/omopv4/before/crit_within +18 -0
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- data/test/statements/complex/anno_1 +29 -0
- data/test/statements/complex/crit_1 +278 -0
- data/test/statements/complex/crit_2 +43 -0
- data/test/statements/complex/crit_3 +54 -0
- data/test/statements/complex/crit_4 +17 -0
- data/test/statements/complex/crit_5 +17 -0
- data/test/statements/complex/crit_6 +20 -0
- data/test/statements/complex/crit_7 +14 -0
- data/test/statements/complex/crit_out_of_order_ctes +39 -0
- data/test/statements/complex/scanno_1 +1508 -0
- data/test/statements/concurrent_within/crit_icd9 +11 -0
- data/test/statements/concurrent_within/crit_icd9_and_place_of_service +15 -0
- data/test/statements/concurrent_within/crit_negative_start +15 -0
- data/test/statements/condition_type/anno_icd9 +7 -0
- data/test/statements/condition_type/count_condition_era +4 -0
- data/test/statements/condition_type/count_condition_era_30_day_window +4 -0
- data/test/statements/condition_type/count_ehr_problem_list +4 -0
- data/test/statements/condition_type/count_era_0 +4 -0
- data/test/statements/condition_type/count_inpatient +4 -0
- data/test/statements/condition_type/count_inpatient_detail +4 -0
- data/test/statements/condition_type/count_inpatient_header +4 -0
- data/test/statements/condition_type/count_inpatient_header_2 +4 -0
- data/test/statements/condition_type/count_inpatient_header_3 +4 -0
- data/test/statements/condition_type/count_inpatient_header_4 +4 -0
- data/test/statements/condition_type/count_inpatient_header_5 +4 -0
- data/test/statements/condition_type/count_inpatient_outpatient_detail +5 -0
- data/test/statements/condition_type/count_inpatient_primary +4 -0
- data/test/statements/condition_type/count_inpatient_primary_or_first +4 -0
- data/test/statements/condition_type/count_outpatient +4 -0
- data/test/statements/condition_type/count_outpatient_detail +4 -0
- data/test/statements/condition_type/count_outpatient_header +4 -0
- data/test/statements/condition_type/count_outpatient_primary +4 -0
- data/test/statements/condition_type/count_primary +4 -0
- data/test/statements/contains/crit_1 +16 -0
- data/test/statements/contains/crit_2 +16 -0
- data/test/statements/contains/crit_3 +16 -0
- data/test/statements/count/anno_multiple_upstreams +11 -0
- data/test/statements/count/anno_no_upstream1 +3 -0
- data/test/statements/count/anno_no_upstream2 +4 -0
- data/test/statements/count/crit_icd9_ndc +15 -0
- data/test/statements/count/crit_ndc +11 -0
- data/test/statements/count/crit_person +7 -0
- data/test/statements/cpt/anno_icd9_upstream +7 -0
- data/test/statements/cpt/anno_invalid_code +5 -0
- data/test/statements/cpt/count_1 +4 -0
- data/test/statements/cpt/crit_1 +4 -0
- data/test/statements/cpt/scanno_1 +4 -0
- data/test/statements/cpt_or_hcpcs/anno_bad_format +7 -0
- data/test/statements/cpt_or_hcpcs/count_1 +5 -0
- data/test/statements/cpt_or_hcpcs/crit_1 +5 -0
- data/test/statements/date_range/anno_1 +7 -0
- data/test/statements/date_range/anno_extra_argument +8 -0
- data/test/statements/date_range/anno_invalid_argument +7 -0
- data/test/statements/date_range/anno_missing_argument1 +6 -0
- data/test/statements/date_range/anno_missing_argument2 +6 -0
- data/test/statements/date_range/anno_no_upstreams +11 -0
- data/test/statements/date_range/count_1 +7 -0
- data/test/statements/date_range/count_2 +7 -0
- data/test/statements/death/anno_multiple_upstreams +10 -0
- data/test/statements/death/anno_no_upstreams +4 -0
- data/test/statements/death/crit_basic +3 -0
- data/test/statements/death/crit_person +7 -0
- data/test/statements/drug_type_concept/anno_has_upstreams +8 -0
- data/test/statements/drug_type_concept/anno_no_arguments +3 -0
- data/test/statements/drug_type_concept/crit_basic1 +4 -0
- data/test/statements/drug_type_concept/crit_basic2 +4 -0
- data/test/statements/during/crit_1 +16 -0
- data/test/statements/during/crit_2 +16 -0
- data/test/statements/equal/crit_1 +17 -0
- data/test/statements/equal/crit_2 +21 -0
- data/test/statements/except/anno_1 +13 -0
- data/test/statements/except/anno_2 +14 -0
- data/test/statements/except/count_complex +31 -0
- data/test/statements/except/crit_412_cpt +13 -0
- data/test/statements/except/crit_412_inpatient +13 -0
- data/test/statements/filter/crit_1 +15 -0
- data/test/statements/first/anno_argument +4 -0
- data/test/statements/first/anno_no_upstream +3 -0
- data/test/statements/first/crit_cpt +7 -0
- data/test/statements/first/crit_icd9 +7 -0
- data/test/statements/first/crit_union +14 -0
- data/test/statements/from/anno_has_upstreams +7 -0
- data/test/statements/from/anno_multiple_arguments +5 -0
- data/test/statements/from_seer_visits/anno_multiple_upstreams +17 -0
- data/test/statements/from_seer_visits/anno_no_upstream +3 -0
- data/test/statements/from_seer_visits/crit_1 +10 -0
- data/test/statements/from_seer_visits/crit_2 +11 -0
- data/test/statements/from_seer_visits/crit_3 +11 -0
- data/test/statements/from_seer_visits/crit_4 +12 -0
- data/test/statements/gender/anno_has_upstreams +7 -0
- data/test/statements/gender/crit_male +4 -0
- data/test/statements/hcpcs/anno_bad_format +6 -0
- data/test/statements/hcpcs/crit_A0382 +4 -0
- data/test/statements/icd10/anno_bad_format +5 -0
- data/test/statements/icd10/anno_has_upstreams +7 -0
- data/test/statements/icd10/crit_1 +4 -0
- data/test/statements/icd10pcs/anno_bad_format +6 -0
- data/test/statements/icd10pcs/anno_has_upstreams +7 -0
- data/test/statements/icd10pcs/crit_1 +4 -0
- data/test/statements/icd9/anno_empty_label +7 -0
- data/test/statements/icd9/anno_invalid_code +4 -0
- data/test/statements/icd9/anno_valid_code +4 -0
- data/test/statements/icd9/crit_1 +4 -0
- data/test/statements/icd9_procedure/crit_1 +4 -0
- data/test/statements/intersect/anno_412_inpatient +11 -0
- data/test/statements/intersect/anno_has_arguments +4 -0
- data/test/statements/intersect/anno_no_upstream +3 -0
- data/test/statements/intersect/crit_412_inpatient +11 -0
- data/test/statements/intersect/crit_412_male +11 -0
- data/test/statements/intersect/crit_complex +19 -0
- data/test/statements/invalid/anno_bad_op +13 -0
- data/test/statements/invalid/scanno_1 +7 -0
- data/test/statements/last/crit_icd9 +7 -0
- data/test/statements/loinc/crit_basic +4 -0
- data/test/statements/ndc/crit_basic +4 -0
- data/test/statements/ndc/results_1 +4 -0
- data/test/statements/numeric/anno_multiple_upstreams +11 -0
- data/test/statements/numeric/num_values_1 +4 -0
- data/test/statements/numeric/num_values_2 +8 -0
- data/test/statements/numeric/num_values_3 +8 -0
- data/test/statements/observation_period/anno_has_arguments +8 -0
- data/test/statements/observation_period/anno_multiple_upstreams +11 -0
- data/test/statements/observation_period/count_all_periods +4 -0
- data/test/statements/observation_period/crit_female +7 -0
- data/test/statements/observation_period/crit_icd9 +7 -0
- data/test/statements/observation_period/crit_male +7 -0
- data/test/statements/occurrence/anno_no_upstream +3 -0
- data/test/statements/occurrence/count_412_410 +17 -0
- data/test/statements/occurrence/crit_1 +8 -0
- data/test/statements/occurrence/crit_2 +11 -0
- data/test/statements/occurrence/crit_3 +11 -0
- data/test/statements/one_in_two_out/anno_has_arguments +8 -0
- data/test/statements/one_in_two_out/anno_multiple_upstreams +15 -0
- data/test/statements/one_in_two_out/anno_no_upstream +7 -0
- data/test/statements/one_in_two_out/count_1 +10 -0
- data/test/statements/one_in_two_out/count_same_as_1 +11 -0
- data/test/statements/one_in_two_out/crit_hcpcs +10 -0
- data/test/statements/one_in_two_out/crit_icd9 +11 -0
- data/test/statements/one_in_two_out/results_1 +9 -0
- data/test/statements/one_in_two_out/results_2 +9 -0
- data/test/statements/overlapped_by/crit_1 +16 -0
- data/test/statements/overlapped_by/crit_2 +16 -0
- data/test/statements/overlapped_by/crit_3 +16 -0
- data/test/statements/overlapped_by/crit_4 +16 -0
- data/test/statements/overlaps/crit_1 +16 -0
- data/test/statements/overlaps/crit_2 +16 -0
- data/test/statements/overlaps/crit_3 +16 -0
- data/test/statements/overlaps/crit_4 +16 -0
- data/test/statements/person/anno_has_arguments +4 -0
- data/test/statements/person/anno_multiple_upstreams +11 -0
- data/test/statements/person/count_2 +3 -0
- data/test/statements/person/crit_1 +7 -0
- data/test/statements/person_filter/count_1 +20 -0
- data/test/statements/person_filter/crit_1 +20 -0
- data/test/statements/person_filter/crit_2 +13 -0
- data/test/statements/person_filter/crit_3 +13 -0
- data/test/statements/person_filter/crit_4 +13 -0
- data/test/statements/place_of_service_code/anno_has_upstreams +8 -0
- data/test/statements/place_of_service_code/anno_no_arguments +3 -0
- data/test/statements/place_of_service_code/crit_basic +4 -0
- data/test/statements/place_of_service_filter/anno_1 +8 -0
- data/test/statements/procedure_occurrence/anno_has_arguments +8 -0
- data/test/statements/procedure_occurrence/anno_multiple_upstreams +11 -0
- data/test/statements/procedure_occurrence/count_gender +7 -0
- data/test/statements/procedure_occurrence/count_icd9 +7 -0
- data/test/statements/procedure_occurrence/count_started_by +19 -0
- data/test/statements/provenance/anno_1 +8 -0
- data/test/statements/provenance/anno_bad_keyword +10 -0
- data/test/statements/provenance/count_1 +8 -0
- data/test/statements/provenance/count_2 +8 -0
- data/test/statements/provider_filter/anno_1 +10 -0
- data/test/statements/race/anno_1 +8 -0
- data/test/statements/race/anno_2 +3 -0
- data/test/statements/race/crit_1 +4 -0
- data/test/statements/read/anno_1 +4 -0
- data/test/statements/read/crit_1 +8 -0
- data/test/statements/recall/anno_1 +16 -0
- data/test/statements/recall/anno_2 +18 -0
- data/test/statements/recall/anno_3 +4 -0
- data/test/statements/recall/anno_4 +3 -0
- data/test/statements/recall/anno_5 +5 -0
- data/test/statements/recall/anno_6 +107 -0
- data/test/statements/recall/crit_1 +17 -0
- data/test/statements/recall/crit_2 +14 -0
- data/test/statements/recall/crit_3 +16 -0
- data/test/statements/recall/crit_cte_1 +17 -0
- data/test/statements/recall/crit_cte_2 +17 -0
- data/test/statements/recall/crit_nested_perm_0 +28 -0
- data/test/statements/revenue_code/crit_1 +4 -0
- data/test/statements/revenue_code/crit_basic +4 -0
- data/test/statements/revenue_code/domains_1 +4 -0
- data/test/statements/revenue_code/domains_drg100 +4 -0
- data/test/statements/rxnorm/crit_1 +4 -0
- data/test/statements/snomed/crit_1 +4 -0
- data/test/statements/started_by/crit_1 +16 -0
- data/test/statements/started_by/crit_2 +16 -0
- data/test/statements/started_by/crit_3 +16 -0
- data/test/statements/sum/anno_1 +3 -0
- data/test/statements/sum/anno_2 +8 -0
- data/test/statements/sum/num_1 +11 -0
- data/test/statements/sum/num_2 +15 -0
- data/test/statements/sum/num_3 +7 -0
- data/test/statements/time_window/anno_1 +7 -0
- data/test/statements/time_window/anno_2 +11 -0
- data/test/statements/time_window/anno_3 +11 -0
- data/test/statements/time_window/anno_4 +12 -0
- data/test/statements/time_window/anno_5 +15 -0
- data/test/statements/time_window/crit_1 +11 -0
- data/test/statements/time_window/crit_2 +11 -0
- data/test/statements/time_window/crit_3 +11 -0
- data/test/statements/time_window/crit_4 +11 -0
- data/test/statements/trim_date_end/crit_1 +16 -0
- data/test/statements/trim_date_end/crit_2 +16 -0
- data/test/statements/trim_date_end/crit_3 +16 -0
- data/test/statements/trim_date_end/crit_at_least +17 -0
- data/test/statements/trim_date_end/crit_occurrences_1 +17 -0
- data/test/statements/trim_date_end/crit_occurrences_2 +17 -0
- data/test/statements/trim_date_end/crit_within +17 -0
- data/test/statements/trim_date_start/crit_1 +16 -0
- data/test/statements/trim_date_start/crit_2 +16 -0
- data/test/statements/trim_date_start/crit_3 +16 -0
- data/test/statements/trim_date_start/crit_at_least +17 -0
- data/test/statements/trim_date_start/crit_occurrences_1 +17 -0
- data/test/statements/trim_date_start/crit_occurrences_2 +17 -0
- data/test/statements/trim_date_start/crit_within +17 -0
- data/test/statements/union/anno_1 +11 -0
- data/test/statements/union/anno_2 +18 -0
- data/test/statements/union/anno_3 +3 -0
- data/test/statements/union/anno_4 +4 -0
- data/test/statements/union/anno_5 +7 -0
- data/test/statements/union/anno_6 +10 -0
- data/test/statements/union/count_1 +11 -0
- data/test/statements/union/count_2 +11 -0
- data/test/statements/union/count_3 +15 -0
- data/test/statements/union/count_4 +18 -0
- data/test/statements/union/count_5 +18 -0
- data/test/statements/union/scanno_1 +3 -0
- data/test/statements/union/scanno_2 +18 -0
- data/test/statements/visit_occurrence/anno_1 +11 -0
- data/test/statements/visit_occurrence/anno_2 +8 -0
- data/test/statements/visit_occurrence/crit_1 +7 -0
- data/test/statements/visit_occurrence/crit_2 +7 -0
- data/test/statements/visit_occurrence/crit_3 +3 -0
- metadata +2016 -150
- data/lib/conceptql/behaviors/debuggable.rb +0 -70
- data/lib/conceptql/behaviors/dottable.rb +0 -103
- data/lib/conceptql/behaviors/preppable.rb +0 -20
- data/lib/conceptql/converter.rb +0 -65
- data/lib/conceptql/debugger.rb +0 -48
- data/lib/conceptql/fake_grapher.rb +0 -20
- data/lib/conceptql/graph.rb +0 -52
- data/lib/conceptql/graph_nodifier.rb +0 -203
- data/lib/conceptql/operators/concept.rb +0 -70
- data/lib/conceptql/operators/snomed_condition.rb +0 -26
- data/lib/conceptql/operators/visit.rb +0 -15
- data/lib/conceptql/tree.rb +0 -53
- data/lib/conceptql/utils/temp_table.rb +0 -72
- data/spec/conceptql/behaviors/dottable_spec.rb +0 -99
- data/spec/conceptql/converter_spec.rb +0 -51
- data/spec/conceptql/date_adjuster_spec.rb +0 -68
- data/spec/conceptql/operators/after_spec.rb +0 -16
- data/spec/conceptql/operators/before_spec.rb +0 -16
- data/spec/conceptql/operators/casting_operator_spec.rb +0 -68
- data/spec/conceptql/operators/complement_spec.rb +0 -15
- data/spec/conceptql/operators/concept_spec.rb +0 -40
- data/spec/conceptql/operators/condition_type_spec.rb +0 -128
- data/spec/conceptql/operators/contains_spec.rb +0 -19
- data/spec/conceptql/operators/cpt_spec.rb +0 -29
- data/spec/conceptql/operators/date_range_spec.rb +0 -33
- data/spec/conceptql/operators/death_spec.rb +0 -10
- data/spec/conceptql/operators/during_spec.rb +0 -30
- data/spec/conceptql/operators/except_spec.rb +0 -15
- data/spec/conceptql/operators/first_spec.rb +0 -35
- data/spec/conceptql/operators/from_spec.rb +0 -13
- data/spec/conceptql/operators/gender_spec.rb +0 -27
- data/spec/conceptql/operators/hcpcs_spec.rb +0 -29
- data/spec/conceptql/operators/icd10_spec.rb +0 -34
- data/spec/conceptql/operators/icd9_procedure_spec.rb +0 -29
- data/spec/conceptql/operators/icd9_spec.rb +0 -34
- data/spec/conceptql/operators/intersect_spec.rb +0 -28
- data/spec/conceptql/operators/last_spec.rb +0 -36
- data/spec/conceptql/operators/loinc_spec.rb +0 -29
- data/spec/conceptql/operators/medcode_procedure_spec.rb +0 -34
- data/spec/conceptql/operators/medcode_spec.rb +0 -34
- data/spec/conceptql/operators/observation_period_spec.rb +0 -10
- data/spec/conceptql/operators/occurrence_spec.rb +0 -87
- data/spec/conceptql/operators/overlapped_by_spec.rb +0 -32
- data/spec/conceptql/operators/overlaps_spec.rb +0 -21
- data/spec/conceptql/operators/person_filter_spec.rb +0 -15
- data/spec/conceptql/operators/person_spec.rb +0 -10
- data/spec/conceptql/operators/place_of_service_code_spec.rb +0 -24
- data/spec/conceptql/operators/procedure_occurrence_spec.rb +0 -10
- data/spec/conceptql/operators/prodcode_spec.rb +0 -35
- data/spec/conceptql/operators/query_double.rb +0 -20
- data/spec/conceptql/operators/query_double_spec.rb +0 -7
- data/spec/conceptql/operators/race_spec.rb +0 -21
- data/spec/conceptql/operators/rxnorm_spec.rb +0 -29
- data/spec/conceptql/operators/snomed_spec.rb +0 -29
- data/spec/conceptql/operators/source_vocabulary_operator_spec.rb +0 -35
- data/spec/conceptql/operators/standard_vocabulary_operator_spec.rb +0 -35
- data/spec/conceptql/operators/started_by_spec.rb +0 -22
- data/spec/conceptql/operators/temporal_operator_spec.rb +0 -51
- data/spec/conceptql/operators/time_window_spec.rb +0 -77
- data/spec/conceptql/operators/union_spec.rb +0 -21
- data/spec/conceptql/operators/visit_occurrence_spec.rb +0 -10
- data/spec/conceptql/query_spec.rb +0 -22
- data/spec/conceptql/tree_spec.rb +0 -50
- data/spec/doubles/stream_for_casting_double.rb +0 -9
- data/spec/doubles/stream_for_occurrence_double.rb +0 -25
- data/spec/doubles/stream_for_temporal_double.rb +0 -6
- data/spec/spec_helper.rb +0 -102
@@ -3,13 +3,16 @@ require_relative 'temporal_operator'
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module ConceptQL
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module Operators
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class OverlappedBy < TemporalOperator
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register __FILE__
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desc <<-EOF
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-
Compares all results on a person-by-person basis between the left hand results (LHR) and the right hand
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-
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+
Compares all results on a person-by-person basis between the left hand results (LHR) and the right hand results (RHR).
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Any result in the LHR with a start_date that occurs between the start_date and end_date of a result in the RHR is passed through.
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All other results are discarded, including all results in the RHR.
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-
L
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-
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-
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L---N---L
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R-----R
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L---Y---L
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EOF
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def where_clause
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if inclusive?
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@@ -3,13 +3,15 @@ require_relative 'temporal_operator'
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module ConceptQL
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module Operators
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class Overlaps < TemporalOperator
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register __FILE__
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desc <<-EOF
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-
Compares all results on a person-by-person basis between the left hand results (LHR) and the right hand
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-
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+
Compares all results on a person-by-person basis between the left hand results (LHR) and the right hand results (RHR).
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Any result in the LHR with an end_date that occurs between the start_date and end_date of a result in the RHR is passed through.
|
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All other results are discarded, including all results in the RHR.
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L
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L
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L---Y---L
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R-----R
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L---N---L
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EOF
|
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def where_clause
|
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17
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[Proc.new { l__start_date <= r__start_date}, Proc.new { r__start_date <= l__end_date }, Proc.new { l__end_date <= r__end_date }]
|
@@ -3,8 +3,18 @@ require_relative 'operator'
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3
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module ConceptQL
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module Operators
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class PassThru < Operator
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-
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-
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register __FILE__
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basic_type :set
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no_desc
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def domains(db)
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doms = upstreams.compact.flat_map { |up| up.domains(db) }.uniq
|
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doms.empty? ? [:invalid] : doms
|
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end
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def query_cols
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upstreams.first.query_cols
|
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18
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end
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19
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end
|
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20
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end
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@@ -3,11 +3,13 @@ require_relative 'casting_operator'
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module ConceptQL
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module Operators
|
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5
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class Person < CastingOperator
|
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-
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register __FILE__
|
7
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+
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|
+
desc 'Generates all person records, or, if fed a stream, fetches all person records for the people represented in the incoming result set.'
|
7
9
|
allows_one_upstream
|
8
|
-
|
10
|
+
domains :person
|
9
11
|
|
10
|
-
def
|
12
|
+
def my_domain
|
11
13
|
:person
|
12
14
|
end
|
13
15
|
|
@@ -16,12 +18,12 @@ module ConceptQL
|
|
16
18
|
end
|
17
19
|
|
18
20
|
def these_point_at_me
|
19
|
-
# I could list ALL the
|
21
|
+
# I could list ALL the domains we use, but the default behavior of casting,
|
20
22
|
# when there is no explicit casting defined, is to convert everything to
|
21
23
|
# person IDs
|
22
24
|
#
|
23
25
|
# So by defining no known castable relationships in this operator, all
|
24
|
-
#
|
26
|
+
# domains will be converted to person
|
25
27
|
[]
|
26
28
|
end
|
27
29
|
end
|
@@ -3,7 +3,11 @@ require_relative 'binary_operator_operator'
|
|
3
3
|
module ConceptQL
|
4
4
|
module Operators
|
5
5
|
class PersonFilter < BinaryOperatorOperator
|
6
|
-
|
6
|
+
register __FILE__
|
7
|
+
|
8
|
+
desc 'If a result in the left hand results (LHR) matches a person in the right hand results (RHR), it is passed through.'
|
9
|
+
default_query_columns
|
10
|
+
|
7
11
|
def query(db)
|
8
12
|
db.from(left.evaluate(db))
|
9
13
|
.where(person_id: right.evaluate(db).select_group(:person_id))
|
@@ -9,15 +9,22 @@ module ConceptQL
|
|
9
9
|
# concept_name column of the concept table. If you misspell the place_of_service_code name
|
10
10
|
# you won't get any matches
|
11
11
|
class PlaceOfServiceCode < Operator
|
12
|
-
|
12
|
+
register __FILE__
|
13
|
+
|
13
14
|
argument :places_of_service, type: :codelist, vocab: 'Place of Service'
|
14
|
-
|
15
|
+
domains :visit_occurrence
|
16
|
+
category "Select by Property"
|
17
|
+
basic_type :selection
|
18
|
+
|
19
|
+
query_columns :visit_occurrence, :concept
|
20
|
+
validate_no_upstreams
|
21
|
+
validate_at_least_one_argument
|
15
22
|
|
16
23
|
def query(db)
|
17
24
|
db.from(:visit_occurrence___v)
|
18
|
-
.join(:
|
19
|
-
.where(
|
20
|
-
.where(
|
25
|
+
.join(:concept___c, { c__concept_id: Sequel.cast(:v__visit_source_concept_id, :bigint) })
|
26
|
+
.where(c__concept_code: arguments.map(&:to_s))
|
27
|
+
.where(c__vocabulary_id: 14)
|
21
28
|
end
|
22
29
|
end
|
23
30
|
end
|
@@ -0,0 +1,47 @@
|
|
1
|
+
require_relative 'operator'
|
2
|
+
|
3
|
+
module ConceptQL
|
4
|
+
module Operators
|
5
|
+
# Filters the incoming stream of events to only those that have a
|
6
|
+
# an associated visit_occurrence with the matching place_of_service
|
7
|
+
#
|
8
|
+
# Provenance related concepts are the ones found in the xxx_type_concept_id
|
9
|
+
# field.
|
10
|
+
#
|
11
|
+
# If the event has NULL for the provenance-related field, they are filtered
|
12
|
+
# out.
|
13
|
+
#
|
14
|
+
# Multiple provenances can be specified at once
|
15
|
+
class PlaceOfServiceFilter < Operator
|
16
|
+
register __FILE__
|
17
|
+
|
18
|
+
desc <<-EOF
|
19
|
+
Filters records to include only those that match one or more of the Medicare Place Of Service values.
|
20
|
+
|
21
|
+
Common values include 21 (inpatient hospital), 23 (emergency room), and 11 (office).
|
22
|
+
EOF
|
23
|
+
argument :places_of_service, type: :codelist, vocab: 'Place of Service'
|
24
|
+
category "Filter Single Stream"
|
25
|
+
basic_type :temporal
|
26
|
+
allows_one_upstream
|
27
|
+
validate_one_upstream
|
28
|
+
validate_at_least_one_argument
|
29
|
+
require_column :place_of_service_concept_id
|
30
|
+
default_query_columns
|
31
|
+
|
32
|
+
def query(db)
|
33
|
+
db.from(stream.evaluate(db))
|
34
|
+
.where(place_of_service_concept_id: place_of_service_concept_ids(db))
|
35
|
+
end
|
36
|
+
|
37
|
+
private
|
38
|
+
|
39
|
+
def place_of_service_concept_ids(db)
|
40
|
+
db.from(:concept)
|
41
|
+
.where(concept_code: arguments.map(&:to_s))
|
42
|
+
.where(vocabulary_id: 14)
|
43
|
+
.select(:concept_id)
|
44
|
+
end
|
45
|
+
end
|
46
|
+
end
|
47
|
+
end
|
@@ -3,11 +3,13 @@ require_relative 'casting_operator'
|
|
3
3
|
module ConceptQL
|
4
4
|
module Operators
|
5
5
|
class ProcedureOccurrence < CastingOperator
|
6
|
+
register __FILE__
|
7
|
+
|
6
8
|
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.'
|
7
|
-
|
9
|
+
domains :procedure_occurrence
|
8
10
|
allows_one_upstream
|
9
11
|
|
10
|
-
def
|
12
|
+
def my_domain
|
11
13
|
:procedure_occurrence
|
12
14
|
end
|
13
15
|
|
@@ -1,11 +1,14 @@
|
|
1
1
|
require_relative 'source_vocabulary_operator'
|
2
|
+
require_relative '../behaviors/drugish'
|
2
3
|
|
3
4
|
module ConceptQL
|
4
5
|
module Operators
|
5
6
|
class Prodcode < SourceVocabularyOperator
|
6
|
-
|
7
|
+
register __FILE__
|
8
|
+
|
7
9
|
argument :prodcodes, type: :codelist, vocab_id: '203'
|
8
|
-
|
10
|
+
predominant_domains :drug_exposure
|
11
|
+
include ConceptQL::Drugish
|
9
12
|
|
10
13
|
def table
|
11
14
|
:drug_exposure
|
@@ -0,0 +1,66 @@
|
|
1
|
+
require_relative 'operator'
|
2
|
+
require_relative '../behaviors/provenanceable'
|
3
|
+
require 'facets/kernel/present'
|
4
|
+
|
5
|
+
module ConceptQL
|
6
|
+
module Operators
|
7
|
+
# Filters the incoming stream of events to only those that have a
|
8
|
+
# provenance-related concept_id.
|
9
|
+
#
|
10
|
+
# Provenance related concepts are the ones found in the xxx_type_concept_id
|
11
|
+
# field.
|
12
|
+
#
|
13
|
+
# If the event has NULL for the provenance-related field, they are filtered
|
14
|
+
# out.
|
15
|
+
#
|
16
|
+
# Multiple provenances can be specified at once
|
17
|
+
class Provenance < Operator
|
18
|
+
register __FILE__
|
19
|
+
|
20
|
+
include ConceptQL::Provenanceable
|
21
|
+
|
22
|
+
desc <<-EOF
|
23
|
+
Filters incoming events to those with the indicated provenance.
|
24
|
+
|
25
|
+
Enter numeric concept id(s), or the corresponding text label(s)
|
26
|
+
(e.g., "inpatient", "outpatient", "carrier_claim").
|
27
|
+
EOF
|
28
|
+
argument :provenance_types, label: 'Provenance Types', type: :codelist
|
29
|
+
category "Filter Single Stream"
|
30
|
+
basic_type :temporal
|
31
|
+
allows_one_upstream
|
32
|
+
validate_one_upstream
|
33
|
+
require_column :provenance_type
|
34
|
+
default_query_columns
|
35
|
+
|
36
|
+
def query(db)
|
37
|
+
db.from(stream.evaluate(db))
|
38
|
+
.where(provenance_type: provenance_concept_ids)
|
39
|
+
end
|
40
|
+
|
41
|
+
private
|
42
|
+
|
43
|
+
def validate(db, opts = {})
|
44
|
+
super
|
45
|
+
bad_keywords = all_args.select { |arg| arg.to_i.zero? }
|
46
|
+
.reject { |arg| concept_ids.keys.include?(arg.to_sym) }
|
47
|
+
|
48
|
+
if bad_keywords.present?
|
49
|
+
add_error("unrecognized keywords", *bad_keywords)
|
50
|
+
end
|
51
|
+
end
|
52
|
+
|
53
|
+
def provenance_concept_ids
|
54
|
+
all_args.flat_map do |arg|
|
55
|
+
to_concept_id(arg)
|
56
|
+
end
|
57
|
+
end
|
58
|
+
|
59
|
+
def all_args
|
60
|
+
arguments.map(&:to_s).flat_map { |w| w.split(/\s*,\s*/) }.uniq
|
61
|
+
end
|
62
|
+
end
|
63
|
+
end
|
64
|
+
end
|
65
|
+
|
66
|
+
|
@@ -0,0 +1,36 @@
|
|
1
|
+
require_relative 'operator'
|
2
|
+
|
3
|
+
module ConceptQL
|
4
|
+
module Operators
|
5
|
+
# Filters incoming events to only those that have been associated with
|
6
|
+
# providers matching the given criteria.
|
7
|
+
class ProviderFilter < Operator
|
8
|
+
register __FILE__
|
9
|
+
|
10
|
+
desc "Filters incoming events to only those that match the associated providers based on provider specialty concept_ids."
|
11
|
+
option :specialties, type: :string
|
12
|
+
category "Filter Single Stream"
|
13
|
+
basic_type :temporal
|
14
|
+
allows_one_upstream
|
15
|
+
validate_one_upstream
|
16
|
+
validate_required_options :specialties
|
17
|
+
require_column :provider_id
|
18
|
+
default_query_columns
|
19
|
+
|
20
|
+
def query(db)
|
21
|
+
db.from(stream.evaluate(db))
|
22
|
+
.where(provider_id: matching_provider_ids(db))
|
23
|
+
end
|
24
|
+
|
25
|
+
private
|
26
|
+
def matching_provider_ids(db)
|
27
|
+
specialty_concept_ids = options[:specialties].split(/\s*,\s*/).map(&:to_i)
|
28
|
+
db.from(:provider)
|
29
|
+
.where(specialty_concept_id: specialty_concept_ids)
|
30
|
+
.select(:provider_id)
|
31
|
+
end
|
32
|
+
end
|
33
|
+
end
|
34
|
+
end
|
35
|
+
|
36
|
+
|
@@ -9,14 +9,21 @@ module ConceptQL
|
|
9
9
|
# concept_name column of the concept table. If you misspell the race name
|
10
10
|
# you won't get any matches
|
11
11
|
class Race < Operator
|
12
|
-
|
12
|
+
register __FILE__
|
13
|
+
|
14
|
+
desc 'Generates all person records that match the given set of Race codes.'
|
13
15
|
argument :races, type: :codelist, vocab: 'Race'
|
14
|
-
|
16
|
+
domains :person
|
17
|
+
category "Select by Property"
|
18
|
+
basic_type :selection
|
19
|
+
query_columns :person, :concept
|
20
|
+
validate_no_upstreams
|
21
|
+
validate_at_least_one_argument
|
15
22
|
|
16
23
|
def query(db)
|
17
24
|
db.from(:person___p)
|
18
|
-
.join(:
|
19
|
-
.where(Sequel.function(:lower, :
|
25
|
+
.join(:concept___c, { c__concept_id: :p__race_concept_id })
|
26
|
+
.where(Sequel.function(:lower, :c__concept_name) => arguments.map(&:downcase))
|
20
27
|
end
|
21
28
|
end
|
22
29
|
end
|
@@ -0,0 +1,149 @@
|
|
1
|
+
require 'sequel'
|
2
|
+
require 'sequel/adapters/mock'
|
3
|
+
|
4
|
+
module ConceptQL
|
5
|
+
module Operators
|
6
|
+
class Read < Operator
|
7
|
+
register __FILE__
|
8
|
+
|
9
|
+
preferred_name "READ"
|
10
|
+
desc "Selects results from the the condition_occurrence, procedure_occurrence, drug_exposure, and observation tables based on the READ codes provided."
|
11
|
+
argument :read_codes, type: :codelist, vocab: "Read"
|
12
|
+
basic_type :selection
|
13
|
+
category "Select by Clinical Codes"
|
14
|
+
default_query_columns
|
15
|
+
|
16
|
+
def query(db)
|
17
|
+
ops = codes_by_domain(db).map do |domain, codes|
|
18
|
+
klasses[domain].new(self.nodifier, *codes)
|
19
|
+
end
|
20
|
+
|
21
|
+
streams = ops.map { |op| op.evaluate(db) }
|
22
|
+
|
23
|
+
streams.inject { |q, query| q.union(query, all: true) }.from_self
|
24
|
+
end
|
25
|
+
|
26
|
+
def domains(db)
|
27
|
+
codes_by_domain(db).keys
|
28
|
+
end
|
29
|
+
|
30
|
+
private
|
31
|
+
|
32
|
+
def codes_by_domain(db)
|
33
|
+
@codes_by_domain ||= get_codes_by_domain(db)
|
34
|
+
end
|
35
|
+
|
36
|
+
def get_codes_by_domain(db)
|
37
|
+
return { observation: arguments } if db.is_a?(::Sequel::Mock)
|
38
|
+
codes_and_mapping_types = db[:source_to_concept_map]
|
39
|
+
.where(source_code: arguments, source_vocabulary_id: 17)
|
40
|
+
.select_map([:source_code, :mapping_type])
|
41
|
+
|
42
|
+
doms_and_codes = codes_and_mapping_types.group_by(&:last).each_with_object({}) do |(mapping_type, codes_and_maps), doms|
|
43
|
+
dom = mapping_type_to_domain(mapping_type)
|
44
|
+
doms[dom] ||= []
|
45
|
+
doms[dom] += codes_and_maps.map(&:first)
|
46
|
+
end
|
47
|
+
|
48
|
+
leftovers = arguments - doms_and_codes.flat_map { |k, v| v }
|
49
|
+
doms_and_codes[:observation] ||= []
|
50
|
+
doms_and_codes[:observation] += leftovers
|
51
|
+
doms_and_codes
|
52
|
+
end
|
53
|
+
|
54
|
+
def mapping_type_to_domain(mapping_type)
|
55
|
+
case mapping_type.downcase.to_sym
|
56
|
+
when :condition
|
57
|
+
:condition_occurrence
|
58
|
+
when :procedure
|
59
|
+
:procedure_occurrence
|
60
|
+
when :drug
|
61
|
+
:drug_exposure
|
62
|
+
else
|
63
|
+
:observation
|
64
|
+
end
|
65
|
+
end
|
66
|
+
|
67
|
+
def klasses
|
68
|
+
@klasses ||= {
|
69
|
+
condition_occurrence: ReadCondition,
|
70
|
+
procedure_occurrence: ReadProcedure,
|
71
|
+
drug_exposure: ReadDrug,
|
72
|
+
observation: ReadObservation
|
73
|
+
}
|
74
|
+
end
|
75
|
+
|
76
|
+
class ReadCondition < ConditionOccurrenceSourceVocabularyOperator
|
77
|
+
preferred_name "READ"
|
78
|
+
argument :read_codes, type: :codelist, vocab: "Read"
|
79
|
+
|
80
|
+
def vocabulary_id
|
81
|
+
17
|
82
|
+
end
|
83
|
+
end
|
84
|
+
|
85
|
+
class ReadProcedure < SourceVocabularyOperator
|
86
|
+
preferred_name "READ"
|
87
|
+
argument :read_codes, type: :codelist, vocab: "Read"
|
88
|
+
|
89
|
+
def table
|
90
|
+
:procedure_occurrence
|
91
|
+
end
|
92
|
+
|
93
|
+
def vocabulary_id
|
94
|
+
17
|
95
|
+
end
|
96
|
+
|
97
|
+
def source_column
|
98
|
+
:procedure_source_value
|
99
|
+
end
|
100
|
+
|
101
|
+
def concept_column
|
102
|
+
:procedure_concept_id
|
103
|
+
end
|
104
|
+
end
|
105
|
+
|
106
|
+
class ReadObservation < SourceVocabularyOperator
|
107
|
+
preferred_name "READ"
|
108
|
+
argument :read_codes, type: :codelist, vocab: "Read"
|
109
|
+
|
110
|
+
def table
|
111
|
+
:observation
|
112
|
+
end
|
113
|
+
|
114
|
+
def vocabulary_id
|
115
|
+
17
|
116
|
+
end
|
117
|
+
|
118
|
+
def source_column
|
119
|
+
:observation_source_value
|
120
|
+
end
|
121
|
+
|
122
|
+
def concept_column
|
123
|
+
:observation_concept_id
|
124
|
+
end
|
125
|
+
end
|
126
|
+
|
127
|
+
class ReadDrug < SourceVocabularyOperator
|
128
|
+
preferred_name "READ"
|
129
|
+
argument :read_codes, type: :codelist, vocab: "Read"
|
130
|
+
|
131
|
+
def table
|
132
|
+
:drug_exposure
|
133
|
+
end
|
134
|
+
|
135
|
+
def vocabulary_id
|
136
|
+
17
|
137
|
+
end
|
138
|
+
|
139
|
+
def source_column
|
140
|
+
:drug_source_value
|
141
|
+
end
|
142
|
+
|
143
|
+
def concept_column
|
144
|
+
:drug_concept_id
|
145
|
+
end
|
146
|
+
end
|
147
|
+
end
|
148
|
+
end
|
149
|
+
end
|