conceptql 0.3.0 → 0.4.1

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.
Files changed (1208) hide show
  1. checksums.yaml +5 -5
  2. data/CHANGELOG.md +228 -27
  3. data/LICENSE +21 -0
  4. data/README.md +28 -98
  5. data/bin/conceptql +2 -1
  6. data/bin/conceptql_utils +6 -0
  7. data/config/multiple_vocabularies.csv +4 -0
  8. data/config/provenance.yml +471 -436
  9. data/config/race.yml +50 -0
  10. data/config/vocabularies.csv +87 -0
  11. data/lib/conceptql/behaviors/code_lister.rb +23 -0
  12. data/lib/conceptql/behaviors/drugish.rb +13 -8
  13. data/lib/conceptql/behaviors/labish.rb +15 -9
  14. data/lib/conceptql/behaviors/metadatable.rb +102 -34
  15. data/lib/conceptql/behaviors/provenanceable.rb +15 -19
  16. data/lib/conceptql/behaviors/single_event.rb +11 -0
  17. data/lib/conceptql/behaviors/timeless.rb +11 -0
  18. data/lib/conceptql/behaviors/utilizable.rb +206 -0
  19. data/lib/conceptql/behaviors/windowable.rb +27 -0
  20. data/lib/conceptql/cli.rb +99 -134
  21. data/lib/conceptql/columnizer.rb +75 -0
  22. data/lib/conceptql/data_model/base.rb +462 -0
  23. data/lib/conceptql/data_model/gdm.rb +155 -0
  24. data/lib/conceptql/data_model/gdm_wide.rb +42 -0
  25. data/lib/conceptql/data_model/omopv4_plus.rb +12 -0
  26. data/lib/conceptql/data_model.rb +30 -0
  27. data/lib/conceptql/database.rb +195 -23
  28. data/lib/conceptql/date_adjuster.rb +57 -27
  29. data/lib/conceptql/diagram.rb +243 -0
  30. data/lib/conceptql/lexicon/lexicon_gdm.rb +47 -0
  31. data/lib/conceptql/lexicon/lexicon_no_db.rb +49 -0
  32. data/lib/conceptql/lexicon/lexicon_ohdsi.rb +63 -0
  33. data/lib/conceptql/lexicon/lexicon_strategy.rb +116 -0
  34. data/lib/conceptql/lexicon.rb +111 -0
  35. data/lib/conceptql/nodifier.rb +45 -15
  36. data/lib/conceptql/operators/after.rb +24 -21
  37. data/lib/conceptql/operators/any_overlap.rb +6 -6
  38. data/lib/conceptql/operators/before.rb +24 -16
  39. data/lib/conceptql/operators/binary_operator_operator.rb +52 -13
  40. data/lib/conceptql/operators/casting_operator.rb +24 -17
  41. data/lib/conceptql/operators/co_reported.rb +78 -9
  42. data/lib/conceptql/operators/concurrent_within.rb +29 -17
  43. data/lib/conceptql/operators/contains.rb +9 -9
  44. data/lib/conceptql/operators/count.rb +9 -9
  45. data/lib/conceptql/operators/date_range.rb +40 -18
  46. data/lib/conceptql/operators/death.rb +10 -2
  47. data/lib/conceptql/operators/dedup.rb +31 -0
  48. data/lib/conceptql/operators/during.rb +5 -12
  49. data/lib/conceptql/operators/episode.rb +146 -0
  50. data/lib/conceptql/operators/equal.rb +6 -3
  51. data/lib/conceptql/operators/ethnicity.rb +49 -0
  52. data/lib/conceptql/operators/except.rb +15 -20
  53. data/lib/conceptql/operators/filter.rb +20 -8
  54. data/lib/conceptql/operators/first.rb +14 -3
  55. data/lib/conceptql/operators/from.rb +33 -12
  56. data/lib/conceptql/operators/gender.rb +27 -11
  57. data/lib/conceptql/operators/hospice.rb +19 -0
  58. data/lib/conceptql/operators/hospitalization.rb +19 -0
  59. data/lib/conceptql/operators/information_periods.rb +36 -0
  60. data/lib/conceptql/operators/invalid.rb +4 -5
  61. data/lib/conceptql/operators/last.rb +14 -3
  62. data/lib/conceptql/operators/match.rb +91 -0
  63. data/lib/conceptql/operators/multiple_vocabularies.rb +172 -0
  64. data/lib/conceptql/operators/numeric.rb +52 -29
  65. data/lib/conceptql/operators/numeric_filter.rb +68 -0
  66. data/lib/conceptql/operators/occurrence.rb +133 -48
  67. data/lib/conceptql/operators/one_in_two_out.rb +198 -62
  68. data/lib/conceptql/operators/operator.rb +321 -408
  69. data/lib/conceptql/operators/pass_thru.rb +9 -5
  70. data/lib/conceptql/operators/person.rb +12 -2
  71. data/lib/conceptql/operators/person_filter.rb +5 -3
  72. data/lib/conceptql/operators/place_of_service_filter.rb +11 -15
  73. data/lib/conceptql/operators/provenance.rb +25 -36
  74. data/lib/conceptql/operators/provider_filter.rb +40 -14
  75. data/lib/conceptql/operators/race.rb +48 -7
  76. data/lib/conceptql/operators/read.rb +77 -58
  77. data/lib/conceptql/operators/recall.rb +20 -20
  78. data/lib/conceptql/operators/snf.rb +19 -0
  79. data/lib/conceptql/operators/sum.rb +23 -12
  80. data/lib/conceptql/operators/temporal_operator.rb +80 -54
  81. data/lib/conceptql/operators/time_window.rb +13 -15
  82. data/lib/conceptql/operators/trim_date.rb +71 -0
  83. data/lib/conceptql/operators/trim_date_end.rb +20 -40
  84. data/lib/conceptql/operators/trim_date_start.rb +20 -43
  85. data/lib/conceptql/operators/union.rb +59 -35
  86. data/lib/conceptql/operators/vocabulary.rb +151 -0
  87. data/lib/conceptql/paths.rb +41 -0
  88. data/lib/conceptql/query.rb +168 -46
  89. data/lib/conceptql/query_modifiers/gdm/admission_date_query_modifier.rb +46 -0
  90. data/lib/conceptql/query_modifiers/gdm/drug_query_modifier.rb +54 -0
  91. data/lib/conceptql/query_modifiers/gdm/lab_query_modifier.rb +57 -0
  92. data/lib/conceptql/query_modifiers/gdm/pos_query_modifier.rb +46 -0
  93. data/lib/conceptql/query_modifiers/gdm/provenance_query_modifier.rb +45 -0
  94. data/lib/conceptql/query_modifiers/gdm/provider_query_modifier.rb +53 -0
  95. data/lib/conceptql/query_modifiers/gdm_wide/admission_date_query_modifier.rb +42 -0
  96. data/lib/conceptql/query_modifiers/gdm_wide/drug_query_modifier.rb +52 -0
  97. data/lib/conceptql/query_modifiers/gdm_wide/lab_query_modifier.rb +55 -0
  98. data/lib/conceptql/query_modifiers/gdm_wide/pos_query_modifier.rb +37 -0
  99. data/lib/conceptql/query_modifiers/gdm_wide/provenance_query_modifier.rb +38 -0
  100. data/lib/conceptql/query_modifiers/omopv4_plus/admission_date_query_modifier.rb +45 -0
  101. data/lib/conceptql/query_modifiers/omopv4_plus/drug_query_modifier.rb +80 -0
  102. data/lib/conceptql/query_modifiers/omopv4_plus/pos_query_modifier.rb +47 -0
  103. data/lib/conceptql/query_modifiers/omopv4_plus/provenance_query_modifier.rb +45 -0
  104. data/lib/conceptql/query_modifiers/omopv4_plus/provider_query_modifier.rb +26 -0
  105. data/lib/conceptql/query_modifiers/query_modifier.rb +6 -2
  106. data/lib/conceptql/rdbms/duckdb.rb +21 -0
  107. data/lib/conceptql/rdbms/generic.rb +116 -0
  108. data/lib/conceptql/rdbms/postgres.rb +47 -0
  109. data/lib/conceptql/rdbms/spark.rb +18 -0
  110. data/lib/conceptql/rdbms.rb +22 -0
  111. data/lib/conceptql/scope.rb +353 -41
  112. data/lib/conceptql/utils.rb +70 -0
  113. data/lib/conceptql/utils_cli.rb +17 -0
  114. data/lib/conceptql/version.rb +3 -1
  115. data/lib/conceptql/visitors/metadata_extractor.rb +54 -0
  116. data/lib/conceptql/vocabularies/behaviors/costish.rb +24 -0
  117. data/lib/conceptql/vocabularies/behaviors/gdmish.rb +19 -0
  118. data/lib/conceptql/vocabularies/behaviors/omopish.rb +32 -0
  119. data/lib/conceptql/vocabularies/dynamic_vocabularies.rb +63 -0
  120. data/lib/conceptql/vocabularies/entry.rb +138 -0
  121. data/lib/conceptql/vocabularies/vocabulary_class_factory.rb +85 -0
  122. data/lib/conceptql/window/base.rb +26 -0
  123. data/lib/conceptql/window/date_range.rb +25 -0
  124. data/lib/conceptql/window/table.rb +116 -0
  125. data/lib/conceptql/window.rb +72 -0
  126. data/lib/conceptql.rb +53 -10
  127. data/lib/sequel/extensions/pg_ctas_explain.rb +22 -0
  128. data/lib/sequel/extensions/pg_vacuum_table.rb +23 -0
  129. data/schemas/gdm.yml +882 -0
  130. data/schemas/gdm_wide.yml +757 -0
  131. data/schemas/ohdsi_vocabs.yml +143 -0
  132. data/schemas/omopv4_plus.yml +729 -0
  133. data/schemas/omopv4_plus_more_ignorables.tsv +13 -0
  134. metadata +271 -2065
  135. data/.gitignore +0 -25
  136. data/Gemfile +0 -6
  137. data/Guardfile +0 -56
  138. data/LICENSE.txt +0 -22
  139. data/Rakefile +0 -35
  140. data/conceptql.gemspec +0 -31
  141. data/doc/ConceptQL Specification (alpha).pdf +0 -0
  142. data/doc/converter.rb +0 -33
  143. data/doc/diagram_0.png +0 -0
  144. data/doc/implementation_notes.md +0 -39
  145. data/doc/metadata.md +0 -89
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  211. data/doc/spec.md +0 -2258
  212. data/doc/spec.md.cql +0 -1930
  213. data/lib/conceptql/annotate_grapher.rb +0 -127
  214. data/lib/conceptql/fake_annotater.rb +0 -129
  215. data/lib/conceptql/knitter.rb +0 -221
  216. data/lib/conceptql/logger.rb +0 -10
  217. data/lib/conceptql/operators/complement.rb +0 -43
  218. data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator.rb +0 -34
  219. data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator_union.rb +0 -28
  220. data/lib/conceptql/operators/condition_type.rb +0 -79
  221. data/lib/conceptql/operators/cpt.rb +0 -28
  222. data/lib/conceptql/operators/cpt_or_hcpcs.rb +0 -27
  223. data/lib/conceptql/operators/drg.rb +0 -42
  224. data/lib/conceptql/operators/drug_type_concept.rb +0 -30
  225. data/lib/conceptql/operators/from_seer_visits.rb +0 -29
  226. data/lib/conceptql/operators/hcpcs.rb +0 -28
  227. data/lib/conceptql/operators/icd10.rb +0 -19
  228. data/lib/conceptql/operators/icd10_pcs.rb +0 -28
  229. data/lib/conceptql/operators/icd9.rb +0 -19
  230. data/lib/conceptql/operators/icd9_procedure.rb +0 -28
  231. data/lib/conceptql/operators/intersect.rb +0 -39
  232. data/lib/conceptql/operators/loinc.rb +0 -28
  233. data/lib/conceptql/operators/medcode.rb +0 -17
  234. data/lib/conceptql/operators/medcode_procedure.rb +0 -28
  235. data/lib/conceptql/operators/ndc.rb +0 -32
  236. data/lib/conceptql/operators/observation_by_enttype.rb +0 -32
  237. data/lib/conceptql/operators/observation_period.rb +0 -32
  238. data/lib/conceptql/operators/overlapped_by.rb +0 -26
  239. data/lib/conceptql/operators/overlaps.rb +0 -21
  240. data/lib/conceptql/operators/place_of_service_code.rb +0 -31
  241. data/lib/conceptql/operators/procedure_occurrence.rb +0 -27
  242. data/lib/conceptql/operators/prodcode.rb +0 -32
  243. data/lib/conceptql/operators/revenue_code.rb +0 -40
  244. data/lib/conceptql/operators/rxnorm.rb +0 -28
  245. data/lib/conceptql/operators/snomed.rb +0 -25
  246. data/lib/conceptql/operators/source_vocabulary_operator.rb +0 -88
  247. data/lib/conceptql/operators/standard_vocabulary_operator.rb +0 -66
  248. data/lib/conceptql/operators/started_by.rb +0 -23
  249. data/lib/conceptql/operators/to_seer_visits.rb +0 -29
  250. data/lib/conceptql/operators/visit_occurrence.rb +0 -32
  251. data/lib/conceptql/operators/vocabulary_operator.rb +0 -45
  252. data/lib/conceptql/query_modifiers/drug_query_modifier.rb +0 -45
  253. data/lib/conceptql/query_modifiers/pos_query_modifier.rb +0 -31
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  772. data/test/results/omopv4_plus/from_seer_visits/crit_4 +0 -2
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  818. data/test/results/omopv4_plus/one_in_two_out/count_1 +0 -3
  819. data/test/results/omopv4_plus/one_in_two_out/count_same_as_1 +0 -3
  820. data/test/results/omopv4_plus/one_in_two_out/crit_hcpcs +0 -2
  821. data/test/results/omopv4_plus/one_in_two_out/crit_icd9 +0 -19
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30
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31
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data/test/statements/except/crit_412_cpt DELETED
@@ -1,13 +0,0 @@
1
- [
2
- "except",
3
- {
4
- "left": [
5
- "icd9",
6
- "412"
7
- ],
8
- "right": [
9
- "cpt",
10
- "99214"
11
- ]
12
- }
13
- ]
data/test/statements/except/crit_412_inpatient DELETED
@@ -1,13 +0,0 @@
1
- [
2
- "except",
3
- {
4
- "left": [
5
- "icd9",
6
- "412"
7
- ],
8
- "right": [
9
- "condition_type",
10
- "inpatient_header"
11
- ]
12
- }
13
- ]
data/test/statements/filter/crit_1 DELETED
@@ -1,15 +0,0 @@
1
- [
2
- "filter",
3
- {
4
- "left": [
5
- "icd9",
6
- "411",
7
- "412"
8
- ],
9
- "right": [
10
- "icd9",
11
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12
- "413"
13
- ]
14
- }
15
- ]
data/test/statements/first/anno_argument DELETED
@@ -1,4 +0,0 @@
1
- [
2
- "first",
3
- 1
4
- ]