conceptql 0.3.0 → 0.4.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +5 -5
- data/CHANGELOG.md +208 -27
- data/LICENSE +21 -0
- data/README.md +28 -98
- data/bin/conceptql +2 -1
- data/bin/conceptql_utils +6 -0
- data/config/multiple_vocabularies.csv +4 -0
- data/config/provenance.yml +471 -436
- data/config/race.yml +50 -0
- data/config/vocabularies.csv +87 -0
- data/lib/conceptql/behaviors/code_lister.rb +23 -0
- data/lib/conceptql/behaviors/drugish.rb +13 -8
- data/lib/conceptql/behaviors/labish.rb +15 -9
- data/lib/conceptql/behaviors/metadatable.rb +102 -34
- data/lib/conceptql/behaviors/provenanceable.rb +15 -19
- data/lib/conceptql/behaviors/single_event.rb +11 -0
- data/lib/conceptql/behaviors/timeless.rb +11 -0
- data/lib/conceptql/behaviors/utilizable.rb +206 -0
- data/lib/conceptql/behaviors/windowable.rb +27 -0
- data/lib/conceptql/cli.rb +99 -134
- data/lib/conceptql/columnizer.rb +75 -0
- data/lib/conceptql/data_model/base.rb +462 -0
- data/lib/conceptql/data_model/gdm.rb +155 -0
- data/lib/conceptql/data_model/gdm_wide.rb +42 -0
- data/lib/conceptql/data_model/omopv4_plus.rb +12 -0
- data/lib/conceptql/data_model.rb +30 -0
- data/lib/conceptql/database.rb +195 -23
- data/lib/conceptql/date_adjuster.rb +57 -27
- data/lib/conceptql/diagram.rb +243 -0
- data/lib/conceptql/lexicon/lexicon_gdm.rb +47 -0
- data/lib/conceptql/lexicon/lexicon_no_db.rb +49 -0
- data/lib/conceptql/lexicon/lexicon_ohdsi.rb +63 -0
- data/lib/conceptql/lexicon/lexicon_strategy.rb +116 -0
- data/lib/conceptql/lexicon.rb +111 -0
- data/lib/conceptql/nodifier.rb +45 -15
- data/lib/conceptql/operators/after.rb +24 -21
- data/lib/conceptql/operators/any_overlap.rb +6 -6
- data/lib/conceptql/operators/before.rb +24 -16
- data/lib/conceptql/operators/binary_operator_operator.rb +52 -13
- data/lib/conceptql/operators/casting_operator.rb +24 -17
- data/lib/conceptql/operators/co_reported.rb +78 -9
- data/lib/conceptql/operators/concurrent_within.rb +29 -17
- data/lib/conceptql/operators/contains.rb +9 -9
- data/lib/conceptql/operators/count.rb +9 -9
- data/lib/conceptql/operators/date_range.rb +40 -18
- data/lib/conceptql/operators/death.rb +10 -2
- data/lib/conceptql/operators/dedup.rb +31 -0
- data/lib/conceptql/operators/during.rb +5 -12
- data/lib/conceptql/operators/episode.rb +146 -0
- data/lib/conceptql/operators/equal.rb +6 -3
- data/lib/conceptql/operators/ethnicity.rb +49 -0
- data/lib/conceptql/operators/except.rb +15 -20
- data/lib/conceptql/operators/filter.rb +20 -8
- data/lib/conceptql/operators/first.rb +14 -3
- data/lib/conceptql/operators/from.rb +33 -12
- data/lib/conceptql/operators/gender.rb +27 -11
- data/lib/conceptql/operators/hospice.rb +19 -0
- data/lib/conceptql/operators/hospitalization.rb +19 -0
- data/lib/conceptql/operators/information_periods.rb +36 -0
- data/lib/conceptql/operators/invalid.rb +4 -5
- data/lib/conceptql/operators/last.rb +14 -3
- data/lib/conceptql/operators/match.rb +91 -0
- data/lib/conceptql/operators/multiple_vocabularies.rb +172 -0
- data/lib/conceptql/operators/numeric.rb +52 -29
- data/lib/conceptql/operators/numeric_filter.rb +68 -0
- data/lib/conceptql/operators/occurrence.rb +133 -48
- data/lib/conceptql/operators/one_in_two_out.rb +198 -62
- data/lib/conceptql/operators/operator.rb +321 -408
- data/lib/conceptql/operators/pass_thru.rb +9 -5
- data/lib/conceptql/operators/person.rb +12 -2
- data/lib/conceptql/operators/person_filter.rb +5 -3
- data/lib/conceptql/operators/place_of_service_filter.rb +11 -15
- data/lib/conceptql/operators/provenance.rb +25 -36
- data/lib/conceptql/operators/provider_filter.rb +40 -14
- data/lib/conceptql/operators/race.rb +48 -7
- data/lib/conceptql/operators/read.rb +77 -58
- data/lib/conceptql/operators/recall.rb +20 -20
- data/lib/conceptql/operators/snf.rb +19 -0
- data/lib/conceptql/operators/sum.rb +23 -12
- data/lib/conceptql/operators/temporal_operator.rb +80 -54
- data/lib/conceptql/operators/time_window.rb +13 -15
- data/lib/conceptql/operators/trim_date.rb +71 -0
- data/lib/conceptql/operators/trim_date_end.rb +20 -40
- data/lib/conceptql/operators/trim_date_start.rb +20 -43
- data/lib/conceptql/operators/union.rb +59 -35
- data/lib/conceptql/operators/vocabulary.rb +151 -0
- data/lib/conceptql/paths.rb +41 -0
- data/lib/conceptql/query.rb +165 -46
- data/lib/conceptql/query_modifiers/gdm/admission_date_query_modifier.rb +46 -0
- data/lib/conceptql/query_modifiers/gdm/drug_query_modifier.rb +54 -0
- data/lib/conceptql/query_modifiers/gdm/lab_query_modifier.rb +57 -0
- data/lib/conceptql/query_modifiers/gdm/pos_query_modifier.rb +46 -0
- data/lib/conceptql/query_modifiers/gdm/provenance_query_modifier.rb +45 -0
- data/lib/conceptql/query_modifiers/gdm/provider_query_modifier.rb +53 -0
- data/lib/conceptql/query_modifiers/gdm_wide/admission_date_query_modifier.rb +42 -0
- data/lib/conceptql/query_modifiers/gdm_wide/drug_query_modifier.rb +52 -0
- data/lib/conceptql/query_modifiers/gdm_wide/lab_query_modifier.rb +55 -0
- data/lib/conceptql/query_modifiers/gdm_wide/pos_query_modifier.rb +37 -0
- data/lib/conceptql/query_modifiers/gdm_wide/provenance_query_modifier.rb +38 -0
- data/lib/conceptql/query_modifiers/omopv4_plus/admission_date_query_modifier.rb +45 -0
- data/lib/conceptql/query_modifiers/omopv4_plus/drug_query_modifier.rb +80 -0
- data/lib/conceptql/query_modifiers/omopv4_plus/pos_query_modifier.rb +47 -0
- data/lib/conceptql/query_modifiers/omopv4_plus/provenance_query_modifier.rb +45 -0
- data/lib/conceptql/query_modifiers/omopv4_plus/provider_query_modifier.rb +26 -0
- data/lib/conceptql/query_modifiers/query_modifier.rb +6 -2
- data/lib/conceptql/rdbms/duckdb.rb +25 -0
- data/lib/conceptql/rdbms/generic.rb +120 -0
- data/lib/conceptql/rdbms/postgres.rb +51 -0
- data/lib/conceptql/rdbms/spark.rb +22 -0
- data/lib/conceptql/rdbms.rb +22 -0
- data/lib/conceptql/scope.rb +353 -41
- data/lib/conceptql/sql_formatters/formatter.rb +25 -0
- data/lib/conceptql/sql_formatters.rb +22 -0
- data/lib/conceptql/utils.rb +113 -0
- data/lib/conceptql/utils_cli.rb +17 -0
- data/lib/conceptql/version.rb +3 -1
- data/lib/conceptql/visitors/metadata_extractor.rb +54 -0
- data/lib/conceptql/vocabularies/behaviors/costish.rb +24 -0
- data/lib/conceptql/vocabularies/behaviors/gdmish.rb +19 -0
- data/lib/conceptql/vocabularies/behaviors/omopish.rb +32 -0
- data/lib/conceptql/vocabularies/dynamic_vocabularies.rb +63 -0
- data/lib/conceptql/vocabularies/entry.rb +138 -0
- data/lib/conceptql/vocabularies/vocabulary_class_factory.rb +85 -0
- data/lib/conceptql/window/base.rb +26 -0
- data/lib/conceptql/window/date_range.rb +25 -0
- data/lib/conceptql/window/table.rb +116 -0
- data/lib/conceptql/window.rb +72 -0
- data/lib/conceptql.rb +53 -10
- data/lib/sequel/extensions/pg_ctas_explain.rb +22 -0
- data/lib/sequel/extensions/pg_vacuum_table.rb +23 -0
- data/schemas/gdm.yml +882 -0
- data/schemas/gdm_wide.yml +757 -0
- data/schemas/ohdsi_vocabs.yml +143 -0
- data/schemas/omopv4_plus.yml +729 -0
- data/schemas/omopv4_plus_more_ignorables.tsv +13 -0
- metadata +262 -2068
- data/.gitignore +0 -25
- data/Gemfile +0 -6
- data/Guardfile +0 -56
- data/LICENSE.txt +0 -22
- data/Rakefile +0 -35
- data/conceptql.gemspec +0 -31
- data/doc/ConceptQL Specification (alpha).pdf +0 -0
- data/doc/converter.rb +0 -33
- data/doc/diagram_0.png +0 -0
- data/doc/implementation_notes.md +0 -39
- data/doc/metadata.md +0 -89
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- data/doc/spec.md +0 -2258
- data/doc/spec.md.cql +0 -1930
- data/lib/conceptql/annotate_grapher.rb +0 -127
- data/lib/conceptql/fake_annotater.rb +0 -129
- data/lib/conceptql/knitter.rb +0 -221
- data/lib/conceptql/logger.rb +0 -10
- data/lib/conceptql/operators/complement.rb +0 -43
- data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator.rb +0 -34
- data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator_union.rb +0 -28
- data/lib/conceptql/operators/condition_type.rb +0 -79
- data/lib/conceptql/operators/cpt.rb +0 -28
- data/lib/conceptql/operators/cpt_or_hcpcs.rb +0 -27
- data/lib/conceptql/operators/drg.rb +0 -42
- data/lib/conceptql/operators/drug_type_concept.rb +0 -30
- data/lib/conceptql/operators/from_seer_visits.rb +0 -29
- data/lib/conceptql/operators/hcpcs.rb +0 -28
- data/lib/conceptql/operators/icd10.rb +0 -19
- data/lib/conceptql/operators/icd10_pcs.rb +0 -28
- data/lib/conceptql/operators/icd9.rb +0 -19
- data/lib/conceptql/operators/icd9_procedure.rb +0 -28
- data/lib/conceptql/operators/intersect.rb +0 -39
- data/lib/conceptql/operators/loinc.rb +0 -28
- data/lib/conceptql/operators/medcode.rb +0 -17
- data/lib/conceptql/operators/medcode_procedure.rb +0 -28
- data/lib/conceptql/operators/ndc.rb +0 -32
- data/lib/conceptql/operators/observation_by_enttype.rb +0 -32
- data/lib/conceptql/operators/observation_period.rb +0 -32
- data/lib/conceptql/operators/overlapped_by.rb +0 -26
- data/lib/conceptql/operators/overlaps.rb +0 -21
- data/lib/conceptql/operators/place_of_service_code.rb +0 -31
- data/lib/conceptql/operators/procedure_occurrence.rb +0 -27
- data/lib/conceptql/operators/prodcode.rb +0 -32
- data/lib/conceptql/operators/revenue_code.rb +0 -40
- data/lib/conceptql/operators/rxnorm.rb +0 -28
- data/lib/conceptql/operators/snomed.rb +0 -25
- data/lib/conceptql/operators/source_vocabulary_operator.rb +0 -88
- data/lib/conceptql/operators/standard_vocabulary_operator.rb +0 -66
- data/lib/conceptql/operators/started_by.rb +0 -23
- data/lib/conceptql/operators/to_seer_visits.rb +0 -29
- data/lib/conceptql/operators/visit_occurrence.rb +0 -32
- data/lib/conceptql/operators/vocabulary_operator.rb +0 -45
- data/lib/conceptql/query_modifiers/drug_query_modifier.rb +0 -45
- data/lib/conceptql/query_modifiers/pos_query_modifier.rb +0 -31
- data/lib/conceptql/sql_formatter.rb +0 -22
- data/test/all.rb +0 -3
- data/test/all_operations_test.rb +0 -45
- data/test/code_list_test.rb +0 -23
- 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 +0 -34044
- data/test/data/omopv4/death.csv +0 -1
- 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 +0 -2
- data/test/data/omopv4/location.csv +0 -0
- data/test/data/omopv4/observation.csv +0 -2
- data/test/data/omopv4/observation_period.csv +0 -1
- data/test/data/omopv4/organization.csv +0 -0
- data/test/data/omopv4/payer_plan_period.csv +0 -0
- data/test/data/omopv4/person.csv +0 -250
- data/test/data/omopv4/procedure_cost.csv +0 -0
- data/test/data/omopv4/procedure_occurrence.csv +0 -35099
- data/test/data/omopv4/provider.csv +0 -0
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{"person":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,17,18,19,20,21,23,25,26,27,28,29,30,31,32,33,34,36,37,38,39,40,41,42,43,45,47,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,115,116,117,119,120,121,123,124,125,127,128,129,130,131,132,133,134,135,136,138,139,140,142,143,144,145,146,147,148,149,150,152,153,154,155,156,157,158,160,161,163,164,165,168,169,171,172,173,174,175,176,177,178,179,180,181,182,183,184,186,187,188,189,190,191,192,193,194,195,197,198,200,201,202,203,204,205,206,207,208,209,211,212,214,215,217,218,219,220,222,224,226,227,229,230,231,232,233,234,235,236,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,257,258,259,260,262,263,264,265,266,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,287,288,289]}
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{"person":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,17,18,19,20,21,23,25,26,27,28,29,30,31,32,33,34,36,37,38,39,40,41,42,43,45,47,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,115,116,117,119,120,121,123,124,125,127,128,129,130,131,132,133,134,135,136,138,139,140,142,143,144,145,146,147,148,149,150,152,153,154,155,156,157,158,160,161,163,164,165,168,169,171,172,173,174,175,176,177,178,179,180,181,182,183,184,186,187,188,189,190,191,192,193,194,195,197,198,200,201,202,203,204,205,206,207,208,209,211,212,214,215,217,218,219,220,222,224,226,227,229,230,231,232,233,234,235,236,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,257,258,259,260,262,263,264,265,266,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,287,288,289]}
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