conceptql 0.2.0 → 0.4.0

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Files changed (242) hide show
  1. checksums.yaml +5 -5
  2. data/CHANGELOG.md +226 -117
  3. data/LICENSE +21 -0
  4. data/README.md +35 -83
  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 +489 -0
  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 +17 -0
  13. data/lib/conceptql/behaviors/labish.rb +19 -0
  14. data/lib/conceptql/behaviors/metadatable.rb +226 -73
  15. data/lib/conceptql/behaviors/provenanceable.rb +26 -0
  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 +117 -108
  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 +214 -0
  28. data/lib/conceptql/date_adjuster.rb +66 -18
  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 +65 -24
  36. data/lib/conceptql/operators/after.rb +34 -14
  37. data/lib/conceptql/operators/any_overlap.rb +8 -6
  38. data/lib/conceptql/operators/before.rb +34 -10
  39. data/lib/conceptql/operators/binary_operator_operator.rb +66 -23
  40. data/lib/conceptql/operators/casting_operator.rb +51 -36
  41. data/lib/conceptql/operators/co_reported.rb +111 -0
  42. data/lib/conceptql/operators/concurrent_within.rb +69 -0
  43. data/lib/conceptql/operators/contains.rb +12 -8
  44. data/lib/conceptql/operators/count.rb +17 -9
  45. data/lib/conceptql/operators/date_range.rb +48 -14
  46. data/lib/conceptql/operators/death.rb +14 -4
  47. data/lib/conceptql/operators/dedup.rb +31 -0
  48. data/lib/conceptql/operators/during.rb +7 -12
  49. data/lib/conceptql/operators/episode.rb +146 -0
  50. data/lib/conceptql/operators/equal.rb +9 -3
  51. data/lib/conceptql/operators/ethnicity.rb +49 -0
  52. data/lib/conceptql/operators/except.rb +19 -12
  53. data/lib/conceptql/operators/filter.rb +23 -8
  54. data/lib/conceptql/operators/first.rb +16 -3
  55. data/lib/conceptql/operators/from.rb +52 -4
  56. data/lib/conceptql/operators/gender.rb +34 -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 +35 -0
  61. data/lib/conceptql/operators/last.rb +16 -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 +65 -23
  65. data/lib/conceptql/operators/numeric_filter.rb +68 -0
  66. data/lib/conceptql/operators/occurrence.rb +153 -32
  67. data/lib/conceptql/operators/one_in_two_out.rb +237 -38
  68. data/lib/conceptql/operators/operator.rb +624 -178
  69. data/lib/conceptql/operators/pass_thru.rb +17 -3
  70. data/lib/conceptql/operators/person.rb +18 -6
  71. data/lib/conceptql/operators/person_filter.rb +9 -3
  72. data/lib/conceptql/operators/place_of_service_filter.rb +43 -0
  73. data/lib/conceptql/operators/provenance.rb +55 -0
  74. data/lib/conceptql/operators/provider_filter.rb +62 -0
  75. data/lib/conceptql/operators/race.rb +55 -7
  76. data/lib/conceptql/operators/read.rb +168 -0
  77. data/lib/conceptql/operators/recall.rb +49 -14
  78. data/lib/conceptql/operators/snf.rb +19 -0
  79. data/lib/conceptql/operators/sum.rb +29 -12
  80. data/lib/conceptql/operators/temporal_operator.rb +108 -16
  81. data/lib/conceptql/operators/time_window.rb +20 -32
  82. data/lib/conceptql/operators/trim_date.rb +71 -0
  83. data/lib/conceptql/operators/trim_date_end.rb +28 -40
  84. data/lib/conceptql/operators/trim_date_start.rb +28 -41
  85. data/lib/conceptql/operators/union.rb +67 -6
  86. data/lib/conceptql/operators/vocabulary.rb +151 -0
  87. data/lib/conceptql/paths.rb +41 -0
  88. data/lib/conceptql/query.rb +191 -26
  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 +20 -0
  106. data/lib/conceptql/rdbms/duckdb.rb +25 -0
  107. data/lib/conceptql/rdbms/generic.rb +120 -0
  108. data/lib/conceptql/rdbms/postgres.rb +51 -0
  109. data/lib/conceptql/rdbms/spark.rb +22 -0
  110. data/lib/conceptql/rdbms.rb +22 -0
  111. data/lib/conceptql/scope.rb +481 -31
  112. data/lib/conceptql/sql_formatters/formatter.rb +25 -0
  113. data/lib/conceptql/sql_formatters.rb +22 -0
  114. data/lib/conceptql/utils.rb +113 -0
  115. data/lib/conceptql/utils_cli.rb +17 -0
  116. data/lib/conceptql/version.rb +3 -1
  117. data/lib/conceptql/visitors/metadata_extractor.rb +54 -0
  118. data/lib/conceptql/vocabularies/behaviors/costish.rb +24 -0
  119. data/lib/conceptql/vocabularies/behaviors/gdmish.rb +19 -0
  120. data/lib/conceptql/vocabularies/behaviors/omopish.rb +32 -0
  121. data/lib/conceptql/vocabularies/dynamic_vocabularies.rb +63 -0
  122. data/lib/conceptql/vocabularies/entry.rb +138 -0
  123. data/lib/conceptql/vocabularies/vocabulary_class_factory.rb +85 -0
  124. data/lib/conceptql/window/base.rb +26 -0
  125. data/lib/conceptql/window/date_range.rb +25 -0
  126. data/lib/conceptql/window/table.rb +116 -0
  127. data/lib/conceptql/window.rb +72 -0
  128. data/lib/conceptql.rb +65 -2
  129. data/lib/sequel/extensions/pg_ctas_explain.rb +22 -0
  130. data/lib/sequel/extensions/pg_vacuum_table.rb +23 -0
  131. data/schemas/gdm.yml +882 -0
  132. data/schemas/gdm_wide.yml +757 -0
  133. data/schemas/ohdsi_vocabs.yml +143 -0
  134. data/schemas/omopv4_plus.yml +729 -0
  135. data/schemas/omopv4_plus_more_ignorables.tsv +13 -0
  136. metadata +267 -207
  137. data/.gitignore +0 -23
  138. data/Gemfile +0 -4
  139. data/Guardfile +0 -56
  140. data/LICENSE.txt +0 -22
  141. data/Rakefile +0 -1
  142. data/conceptql.gemspec +0 -32
  143. data/doc/ConceptQL Specification (alpha).pdf +0 -0
  144. data/doc/diagram_0.png +0 -0
  145. data/doc/implementation_notes.md +0 -39
  146. data/doc/spec.md +0 -1344
  147. data/lib/conceptql/behaviors/debuggable.rb +0 -70
  148. data/lib/conceptql/behaviors/dottable.rb +0 -103
  149. data/lib/conceptql/behaviors/preppable.rb +0 -20
  150. data/lib/conceptql/converter.rb +0 -65
  151. data/lib/conceptql/debugger.rb +0 -48
  152. data/lib/conceptql/fake_grapher.rb +0 -20
  153. data/lib/conceptql/graph.rb +0 -52
  154. data/lib/conceptql/graph_nodifier.rb +0 -203
  155. data/lib/conceptql/logger.rb +0 -10
  156. data/lib/conceptql/operators/complement.rb +0 -38
  157. data/lib/conceptql/operators/concept.rb +0 -70
  158. data/lib/conceptql/operators/condition_type.rb +0 -71
  159. data/lib/conceptql/operators/cpt.rb +0 -25
  160. data/lib/conceptql/operators/drug_type_concept.rb +0 -21
  161. data/lib/conceptql/operators/from_seer_visits.rb +0 -23
  162. data/lib/conceptql/operators/hcpcs.rb +0 -25
  163. data/lib/conceptql/operators/icd10.rb +0 -28
  164. data/lib/conceptql/operators/icd9.rb +0 -28
  165. data/lib/conceptql/operators/icd9_procedure.rb +0 -25
  166. data/lib/conceptql/operators/intersect.rb +0 -34
  167. data/lib/conceptql/operators/loinc.rb +0 -25
  168. data/lib/conceptql/operators/medcode.rb +0 -28
  169. data/lib/conceptql/operators/medcode_procedure.rb +0 -27
  170. data/lib/conceptql/operators/ndc.rb +0 -29
  171. data/lib/conceptql/operators/observation_by_enttype.rb +0 -29
  172. data/lib/conceptql/operators/observation_period.rb +0 -30
  173. data/lib/conceptql/operators/overlapped_by.rb +0 -23
  174. data/lib/conceptql/operators/overlaps.rb +0 -19
  175. data/lib/conceptql/operators/place_of_service_code.rb +0 -24
  176. data/lib/conceptql/operators/procedure_occurrence.rb +0 -25
  177. data/lib/conceptql/operators/prodcode.rb +0 -29
  178. data/lib/conceptql/operators/rxnorm.rb +0 -24
  179. data/lib/conceptql/operators/snomed.rb +0 -24
  180. data/lib/conceptql/operators/snomed_condition.rb +0 -26
  181. data/lib/conceptql/operators/source_vocabulary_operator.rb +0 -58
  182. data/lib/conceptql/operators/standard_vocabulary_operator.rb +0 -45
  183. data/lib/conceptql/operators/started_by.rb +0 -22
  184. data/lib/conceptql/operators/to_seer_visits.rb +0 -24
  185. data/lib/conceptql/operators/visit.rb +0 -15
  186. data/lib/conceptql/operators/visit_occurrence.rb +0 -30
  187. data/lib/conceptql/tree.rb +0 -53
  188. data/lib/conceptql/utils/temp_table.rb +0 -72
  189. data/spec/conceptql/behaviors/dottable_spec.rb +0 -99
  190. data/spec/conceptql/converter_spec.rb +0 -51
  191. data/spec/conceptql/date_adjuster_spec.rb +0 -68
  192. data/spec/conceptql/operators/after_spec.rb +0 -16
  193. data/spec/conceptql/operators/before_spec.rb +0 -16
  194. data/spec/conceptql/operators/casting_operator_spec.rb +0 -68
  195. data/spec/conceptql/operators/complement_spec.rb +0 -15
  196. data/spec/conceptql/operators/concept_spec.rb +0 -40
  197. data/spec/conceptql/operators/condition_type_spec.rb +0 -128
  198. data/spec/conceptql/operators/contains_spec.rb +0 -19
  199. data/spec/conceptql/operators/cpt_spec.rb +0 -29
  200. data/spec/conceptql/operators/date_range_spec.rb +0 -33
  201. data/spec/conceptql/operators/death_spec.rb +0 -10
  202. data/spec/conceptql/operators/during_spec.rb +0 -30
  203. data/spec/conceptql/operators/except_spec.rb +0 -15
  204. data/spec/conceptql/operators/first_spec.rb +0 -35
  205. data/spec/conceptql/operators/from_spec.rb +0 -13
  206. data/spec/conceptql/operators/gender_spec.rb +0 -27
  207. data/spec/conceptql/operators/hcpcs_spec.rb +0 -29
  208. data/spec/conceptql/operators/icd10_spec.rb +0 -34
  209. data/spec/conceptql/operators/icd9_procedure_spec.rb +0 -29
  210. data/spec/conceptql/operators/icd9_spec.rb +0 -34
  211. data/spec/conceptql/operators/intersect_spec.rb +0 -28
  212. data/spec/conceptql/operators/last_spec.rb +0 -36
  213. data/spec/conceptql/operators/loinc_spec.rb +0 -29
  214. data/spec/conceptql/operators/medcode_procedure_spec.rb +0 -34
  215. data/spec/conceptql/operators/medcode_spec.rb +0 -34
  216. data/spec/conceptql/operators/observation_period_spec.rb +0 -10
  217. data/spec/conceptql/operators/occurrence_spec.rb +0 -87
  218. data/spec/conceptql/operators/overlapped_by_spec.rb +0 -32
  219. data/spec/conceptql/operators/overlaps_spec.rb +0 -21
  220. data/spec/conceptql/operators/person_filter_spec.rb +0 -15
  221. data/spec/conceptql/operators/person_spec.rb +0 -10
  222. data/spec/conceptql/operators/place_of_service_code_spec.rb +0 -24
  223. data/spec/conceptql/operators/procedure_occurrence_spec.rb +0 -10
  224. data/spec/conceptql/operators/prodcode_spec.rb +0 -35
  225. data/spec/conceptql/operators/query_double.rb +0 -20
  226. data/spec/conceptql/operators/query_double_spec.rb +0 -7
  227. data/spec/conceptql/operators/race_spec.rb +0 -21
  228. data/spec/conceptql/operators/rxnorm_spec.rb +0 -29
  229. data/spec/conceptql/operators/snomed_spec.rb +0 -29
  230. data/spec/conceptql/operators/source_vocabulary_operator_spec.rb +0 -35
  231. data/spec/conceptql/operators/standard_vocabulary_operator_spec.rb +0 -35
  232. data/spec/conceptql/operators/started_by_spec.rb +0 -22
  233. data/spec/conceptql/operators/temporal_operator_spec.rb +0 -51
  234. data/spec/conceptql/operators/time_window_spec.rb +0 -77
  235. data/spec/conceptql/operators/union_spec.rb +0 -21
  236. data/spec/conceptql/operators/visit_occurrence_spec.rb +0 -10
  237. data/spec/conceptql/query_spec.rb +0 -22
  238. data/spec/conceptql/tree_spec.rb +0 -50
  239. data/spec/doubles/stream_for_casting_double.rb +0 -9
  240. data/spec/doubles/stream_for_occurrence_double.rb +0 -25
  241. data/spec/doubles/stream_for_temporal_double.rb +0 -6
  242. data/spec/spec_helper.rb +0 -102
data/schemas/ohdsi_vocabs.yml ADDED
@@ -0,0 +1,143 @@
1
+ ---
2
+ :concept:
3
+ :columns:
4
+ :concept_id:
5
+ :type: :integer
6
+ :concept_name:
7
+ :type: :string
8
+ :domain_id:
9
+ :type: :string
10
+ :vocabulary_id:
11
+ :type: :string
12
+ :concept_class_id:
13
+ :type: :string
14
+ :standard_concept:
15
+ :type: :string
16
+ :concept_code:
17
+ :type: :string
18
+ :valid_start_date:
19
+ :type: :date
20
+ :valid_end_date:
21
+ :type: :date
22
+ :invalid_reason:
23
+ :type: :string
24
+ :concept_ancestor:
25
+ :columns:
26
+ :ancestor_concept_id:
27
+ :type: :integer
28
+ :descendant_concept_id:
29
+ :type: :integer
30
+ :min_levels_of_separation:
31
+ :type: :integer
32
+ :max_levels_of_separation:
33
+ :type: :integer
34
+ :concept_class:
35
+ :columns:
36
+ :concept_class_id:
37
+ :type: :string
38
+ :concept_class_name:
39
+ :type: :string
40
+ :concept_class_concept_id:
41
+ :type: :integer
42
+ :concept_relationship:
43
+ :columns:
44
+ :concept_id_1:
45
+ :type: :integer
46
+ :concept_id_2:
47
+ :type: :integer
48
+ :relationship_id:
49
+ :type: :string
50
+ :valid_start_date:
51
+ :type: :date
52
+ :valid_end_date:
53
+ :type: :date
54
+ :invalid_reason:
55
+ :type: :string
56
+ :concept_synonym:
57
+ :columns:
58
+ :concept_id:
59
+ :type: :integer
60
+ :concept_synonym_name:
61
+ :type: :string
62
+ :language_concept_id:
63
+ :type: :integer
64
+ :domain:
65
+ :columns:
66
+ :domain_id:
67
+ :type: :string
68
+ :domain_name:
69
+ :type: :string
70
+ :domain_concept_id:
71
+ :type: :integer
72
+ :drug_strength:
73
+ :columns:
74
+ :drug_concept_id:
75
+ :type: :integer
76
+ :ingredient_concept_id:
77
+ :type: :integer
78
+ :amount_value:
79
+ :type: :decimal
80
+ :amount_unit_concept_id:
81
+ :type: :integer
82
+ :numerator_value:
83
+ :type: :decimal
84
+ :numerator_unit_concept_id:
85
+ :type: :integer
86
+ :denominator_value:
87
+ :type: :decimal
88
+ :denominator_unit_concept_id:
89
+ :type: :integer
90
+ :box_size:
91
+ :type: :integer
92
+ :valid_start_date:
93
+ :type: :date
94
+ :valid_end_date:
95
+ :type: :date
96
+ :invalid_reason:
97
+ :type: :string
98
+ :relationship:
99
+ :columns:
100
+ :relationship_id:
101
+ :type: :string
102
+ :relationship_name:
103
+ :type: :string
104
+ :is_hierarchical:
105
+ :type: :string
106
+ :defines_ancestry:
107
+ :type: :string
108
+ :reverse_relationship_id:
109
+ :type: :string
110
+ :relationship_concept_id:
111
+ :type: :integer
112
+ :source_to_concept_map:
113
+ :columns:
114
+ :source_code:
115
+ :type: :string
116
+ :source_concept_id:
117
+ :type: :integer
118
+ :source_vocabulary_id:
119
+ :type: :string
120
+ :source_code_description:
121
+ :type: :string
122
+ :target_concept_id:
123
+ :type: :integer
124
+ :target_vocabulary_id:
125
+ :type: :string
126
+ :valid_start_date:
127
+ :type: :date
128
+ :valid_end_date:
129
+ :type: :date
130
+ :invalid_reason:
131
+ :type: :string
132
+ :vocabulary:
133
+ :columns:
134
+ :vocabulary_id:
135
+ :type: :string
136
+ :vocabulary_name:
137
+ :type: :string
138
+ :vocabulary_reference:
139
+ :type: :string
140
+ :vocabulary_version:
141
+ :type: :string
142
+ :vocabulary_concept_id:
143
+ :type: :integer