conceptql 0.2.0 → 0.3.0

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Files changed (1192) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +2 -0
  3. data/CHANGELOG.md +32 -104
  4. data/Gemfile +2 -0
  5. data/README.md +43 -21
  6. data/Rakefile +34 -0
  7. data/conceptql.gemspec +3 -4
  8. data/config/provenance.yml +454 -0
  9. data/doc/converter.rb +33 -0
  10. data/doc/metadata.md +89 -0
  11. data/doc/spec.md +1775 -861
  12. data/doc/spec.md.cql +1930 -0
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  77. data/doc/spec/ff7d5b5573d09bd7c4cdd3aeda124d18bf82ec46673a62881b399a75d69f3f53.png +0 -0
  78. data/lib/conceptql.rb +21 -1
  79. data/lib/conceptql/annotate_grapher.rb +127 -0
  80. data/lib/conceptql/behaviors/drugish.rb +12 -0
  81. data/lib/conceptql/behaviors/labish.rb +13 -0
  82. data/lib/conceptql/behaviors/metadatable.rb +156 -71
  83. data/lib/conceptql/behaviors/provenanceable.rb +30 -0
  84. data/lib/conceptql/cli.rb +81 -37
  85. data/lib/conceptql/database.rb +42 -0
  86. data/lib/conceptql/date_adjuster.rb +22 -4
  87. data/lib/conceptql/fake_annotater.rb +129 -0
  88. data/lib/conceptql/knitter.rb +221 -0
  89. data/lib/conceptql/nodifier.rb +34 -23
  90. data/lib/conceptql/operators/after.rb +20 -3
  91. data/lib/conceptql/operators/any_overlap.rb +3 -1
  92. data/lib/conceptql/operators/before.rb +19 -3
  93. data/lib/conceptql/operators/binary_operator_operator.rb +24 -20
  94. data/lib/conceptql/operators/casting_operator.rb +39 -31
  95. data/lib/conceptql/operators/co_reported.rb +42 -0
  96. data/lib/conceptql/operators/complement.rb +21 -16
  97. data/lib/conceptql/operators/concurrent_within.rb +57 -0
  98. data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator.rb +34 -0
  99. data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator_union.rb +28 -0
  100. data/lib/conceptql/operators/condition_type.rb +12 -4
  101. data/lib/conceptql/operators/contains.rb +6 -2
  102. data/lib/conceptql/operators/count.rb +10 -2
  103. data/lib/conceptql/operators/cpt.rb +5 -2
  104. data/lib/conceptql/operators/cpt_or_hcpcs.rb +27 -0
  105. data/lib/conceptql/operators/date_range.rb +20 -8
  106. data/lib/conceptql/operators/death.rb +4 -2
  107. data/lib/conceptql/operators/drg.rb +42 -0
  108. data/lib/conceptql/operators/drug_type_concept.rb +11 -2
  109. data/lib/conceptql/operators/during.rb +4 -2
  110. data/lib/conceptql/operators/equal.rb +4 -1
  111. data/lib/conceptql/operators/except.rb +16 -4
  112. data/lib/conceptql/operators/filter.rb +6 -3
  113. data/lib/conceptql/operators/first.rb +3 -1
  114. data/lib/conceptql/operators/from.rb +32 -5
  115. data/lib/conceptql/operators/from_seer_visits.rb +11 -5
  116. data/lib/conceptql/operators/gender.rb +9 -2
  117. data/lib/conceptql/operators/hcpcs.rb +5 -2
  118. data/lib/conceptql/operators/icd10.rb +6 -15
  119. data/lib/conceptql/operators/icd10_pcs.rb +28 -0
  120. data/lib/conceptql/operators/icd9.rb +6 -15
  121. data/lib/conceptql/operators/icd9_procedure.rb +5 -2
  122. data/lib/conceptql/operators/intersect.rb +15 -10
  123. data/lib/conceptql/operators/invalid.rb +36 -0
  124. data/lib/conceptql/operators/last.rb +3 -1
  125. data/lib/conceptql/operators/loinc.rb +5 -2
  126. data/lib/conceptql/operators/medcode.rb +5 -16
  127. data/lib/conceptql/operators/medcode_procedure.rb +3 -2
  128. data/lib/conceptql/operators/ndc.rb +5 -2
  129. data/lib/conceptql/operators/numeric.rb +30 -11
  130. data/lib/conceptql/operators/observation_by_enttype.rb +5 -2
  131. data/lib/conceptql/operators/observation_period.rb +6 -4
  132. data/lib/conceptql/operators/occurrence.rb +47 -11
  133. data/lib/conceptql/operators/one_in_two_out.rb +96 -33
  134. data/lib/conceptql/operators/operator.rb +628 -95
  135. data/lib/conceptql/operators/overlapped_by.rb +8 -5
  136. data/lib/conceptql/operators/overlaps.rb +7 -5
  137. data/lib/conceptql/operators/pass_thru.rb +12 -2
  138. data/lib/conceptql/operators/person.rb +7 -5
  139. data/lib/conceptql/operators/person_filter.rb +5 -1
  140. data/lib/conceptql/operators/place_of_service_code.rb +12 -5
  141. data/lib/conceptql/operators/place_of_service_filter.rb +47 -0
  142. data/lib/conceptql/operators/procedure_occurrence.rb +4 -2
  143. data/lib/conceptql/operators/prodcode.rb +5 -2
  144. data/lib/conceptql/operators/provenance.rb +66 -0
  145. data/lib/conceptql/operators/provider_filter.rb +36 -0
  146. data/lib/conceptql/operators/race.rb +11 -4
  147. data/lib/conceptql/operators/read.rb +149 -0
  148. data/lib/conceptql/operators/recall.rb +42 -7
  149. data/lib/conceptql/operators/revenue_code.rb +40 -0
  150. data/lib/conceptql/operators/rxnorm.rb +5 -1
  151. data/lib/conceptql/operators/snomed.rb +3 -2
  152. data/lib/conceptql/operators/source_vocabulary_operator.rb +44 -14
  153. data/lib/conceptql/operators/standard_vocabulary_operator.rb +36 -15
  154. data/lib/conceptql/operators/started_by.rb +2 -1
  155. data/lib/conceptql/operators/sum.rb +7 -1
  156. data/lib/conceptql/operators/temporal_operator.rb +75 -9
  157. data/lib/conceptql/operators/time_window.rb +13 -23
  158. data/lib/conceptql/operators/to_seer_visits.rb +6 -1
  159. data/lib/conceptql/operators/trim_date_end.rb +20 -12
  160. data/lib/conceptql/operators/trim_date_start.rb +22 -12
  161. data/lib/conceptql/operators/union.rb +39 -2
  162. data/lib/conceptql/operators/visit_occurrence.rb +5 -3
  163. data/lib/conceptql/operators/vocabulary_operator.rb +45 -0
  164. data/lib/conceptql/query.rb +68 -22
  165. data/lib/conceptql/query_modifiers/drug_query_modifier.rb +45 -0
  166. data/lib/conceptql/query_modifiers/pos_query_modifier.rb +31 -0
  167. data/lib/conceptql/query_modifiers/query_modifier.rb +16 -0
  168. data/lib/conceptql/scope.rb +169 -31
  169. data/lib/conceptql/sql_formatter.rb +22 -0
  170. data/lib/conceptql/version.rb +1 -1
  171. data/test/all.rb +3 -0
  172. data/test/all_operations_test.rb +45 -0
  173. data/test/code_list_test.rb +23 -0
  174. data/test/data/omopv4/care_site.csv +0 -0
  175. data/test/data/omopv4/cohort.csv +0 -0
  176. data/test/data/omopv4/condition_era.csv +0 -0
  177. data/test/data/omopv4/condition_occurrence.csv +34044 -0
  178. data/test/data/omopv4/death.csv +1 -0
  179. data/test/data/omopv4/drug_cost.csv +0 -0
  180. data/test/data/omopv4/drug_era.csv +0 -0
  181. data/test/data/omopv4/drug_exposure.csv +2 -0
  182. data/test/data/omopv4/location.csv +0 -0
  183. data/test/data/omopv4/observation.csv +2 -0
  184. data/test/data/omopv4/observation_period.csv +1 -0
  185. data/test/data/omopv4/organization.csv +0 -0
  186. data/test/data/omopv4/payer_plan_period.csv +0 -0
  187. data/test/data/omopv4/person.csv +250 -0
  188. data/test/data/omopv4/procedure_cost.csv +0 -0
  189. data/test/data/omopv4/procedure_occurrence.csv +35099 -0
  190. data/test/data/omopv4/provider.csv +0 -0
  191. data/test/data/omopv4/visit_occurrence.csv +14931 -0
  192. data/test/data/omopv4_plus/care_site.csv +0 -0
  193. data/test/data/omopv4_plus/cohort.csv +0 -0
  194. data/test/data/omopv4_plus/concept.csv +352 -0
  195. data/test/data/omopv4_plus/condition_era.csv +0 -0
  196. data/test/data/omopv4_plus/condition_occurrence.csv +46673 -0
  197. data/test/data/omopv4_plus/death.csv +9 -0
  198. data/test/data/omopv4_plus/drug_cost.csv +13921 -0
  199. data/test/data/omopv4_plus/drug_era.csv +0 -0
  200. data/test/data/omopv4_plus/drug_exposure.csv +13921 -0
  201. data/test/data/omopv4_plus/headers/care_site.csv +1 -0
  202. data/test/data/omopv4_plus/headers/cohort.csv +1 -0
  203. data/test/data/omopv4_plus/headers/concept.csv +1 -0
  204. data/test/data/omopv4_plus/headers/condition_era.csv +1 -0
  205. data/test/data/omopv4_plus/headers/condition_occurrence.csv +1 -0
  206. data/test/data/omopv4_plus/headers/death.csv +1 -0
  207. data/test/data/omopv4_plus/headers/drug_cost.csv +1 -0
  208. data/test/data/omopv4_plus/headers/drug_era.csv +1 -0
  209. data/test/data/omopv4_plus/headers/drug_exposure.csv +1 -0
  210. data/test/data/omopv4_plus/headers/location.csv +1 -0
  211. data/test/data/omopv4_plus/headers/observation.csv +1 -0
  212. data/test/data/omopv4_plus/headers/observation_period.csv +1 -0
  213. data/test/data/omopv4_plus/headers/organization.csv +1 -0
  214. data/test/data/omopv4_plus/headers/payer_plan_period.csv +1 -0
  215. data/test/data/omopv4_plus/headers/person.csv +1 -0
  216. data/test/data/omopv4_plus/headers/procedure_cost.csv +1 -0
  217. data/test/data/omopv4_plus/headers/procedure_occurrence.csv +1 -0
  218. data/test/data/omopv4_plus/headers/provider.csv +1 -0
  219. data/test/data/omopv4_plus/headers/source_to_concept_map.csv +1 -0
  220. data/test/data/omopv4_plus/headers/visit_occurrence.csv +1 -0
  221. data/test/data/omopv4_plus/headers/vocabulary.csv +1 -0
  222. data/test/data/omopv4_plus/location.csv +0 -0
  223. data/test/data/omopv4_plus/observation.csv +0 -0
  224. data/test/data/omopv4_plus/observation_period.csv +147 -0
  225. data/test/data/omopv4_plus/organization.csv +736 -0
  226. data/test/data/omopv4_plus/payer_plan_period.csv +808 -0
  227. data/test/data/omopv4_plus/person.csv +250 -0
  228. data/test/data/omopv4_plus/procedure_cost.csv +20123 -0
  229. data/test/data/omopv4_plus/procedure_occurrence.csv +27273 -0
  230. data/test/data/omopv4_plus/provider.csv +10193 -0
  231. data/test/data/omopv4_plus/source_to_concept_map.csv +285 -0
  232. data/test/data/omopv4_plus/visit_occurrence.csv +45125 -0
  233. data/test/data/omopv4_plus/vocabulary.csv +60 -0
  234. data/test/db.rb +15 -0
  235. data/test/db_setup.rb +408 -0
  236. data/test/db_teardown.rb +33 -0
  237. data/test/fake_annotater_test.rb +31 -0
  238. data/test/helper.rb +129 -0
  239. data/test/knitter/conceptql.md.cql +39 -0
  240. data/test/knitter/conceptql.md.expect +43 -0
  241. data/test/knitter/empty.md.cql +0 -0
  242. data/test/knitter/except.md.cql +13 -0
  243. data/test/knitter/except.md.expect +14 -0
  244. data/test/knitter/fake.md.cql +10 -0
  245. data/test/knitter/fake.md.expect +13 -0
  246. data/test/knitter/many.md.cql +7 -0
  247. data/test/knitter/many.md.expect +14 -0
  248. data/test/knitter/no_conceptql.md.cql +36 -0
  249. data/test/knitter/title.md.cql +12 -0
  250. data/test/knitter/title.md.expect +15 -0
  251. data/test/knitter/union.md.cql +11 -0
  252. data/test/knitter/union.md.expect +14 -0
  253. data/test/knitter_test.rb +69 -0
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  1165. data/spec/conceptql/operators/medcode_spec.rb +0 -34
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  1169. data/spec/conceptql/operators/overlaps_spec.rb +0 -21
  1170. data/spec/conceptql/operators/person_filter_spec.rb +0 -15
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  1173. data/spec/conceptql/operators/procedure_occurrence_spec.rb +0 -10
  1174. data/spec/conceptql/operators/prodcode_spec.rb +0 -35
  1175. data/spec/conceptql/operators/query_double.rb +0 -20
  1176. data/spec/conceptql/operators/query_double_spec.rb +0 -7
  1177. data/spec/conceptql/operators/race_spec.rb +0 -21
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  1179. data/spec/conceptql/operators/snomed_spec.rb +0 -29
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  1182. data/spec/conceptql/operators/started_by_spec.rb +0 -22
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  1191. data/spec/doubles/stream_for_temporal_double.rb +0 -6
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