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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  1146. data/spec/conceptql/operators/concept_spec.rb +0 -40
  1147. data/spec/conceptql/operators/condition_type_spec.rb +0 -128
  1148. data/spec/conceptql/operators/contains_spec.rb +0 -19
  1149. data/spec/conceptql/operators/cpt_spec.rb +0 -29
  1150. data/spec/conceptql/operators/date_range_spec.rb +0 -33
  1151. data/spec/conceptql/operators/death_spec.rb +0 -10
  1152. data/spec/conceptql/operators/during_spec.rb +0 -30
  1153. data/spec/conceptql/operators/except_spec.rb +0 -15
  1154. data/spec/conceptql/operators/first_spec.rb +0 -35
  1155. data/spec/conceptql/operators/from_spec.rb +0 -13
  1156. data/spec/conceptql/operators/gender_spec.rb +0 -27
  1157. data/spec/conceptql/operators/hcpcs_spec.rb +0 -29
  1158. data/spec/conceptql/operators/icd10_spec.rb +0 -34
  1159. data/spec/conceptql/operators/icd9_procedure_spec.rb +0 -29
  1160. data/spec/conceptql/operators/icd9_spec.rb +0 -34
  1161. data/spec/conceptql/operators/intersect_spec.rb +0 -28
  1162. data/spec/conceptql/operators/last_spec.rb +0 -36
  1163. data/spec/conceptql/operators/loinc_spec.rb +0 -29
  1164. data/spec/conceptql/operators/medcode_procedure_spec.rb +0 -34
  1165. data/spec/conceptql/operators/medcode_spec.rb +0 -34
  1166. data/spec/conceptql/operators/observation_period_spec.rb +0 -10
  1167. data/spec/conceptql/operators/occurrence_spec.rb +0 -87
  1168. data/spec/conceptql/operators/overlapped_by_spec.rb +0 -32
  1169. data/spec/conceptql/operators/overlaps_spec.rb +0 -21
  1170. data/spec/conceptql/operators/person_filter_spec.rb +0 -15
  1171. data/spec/conceptql/operators/person_spec.rb +0 -10
  1172. data/spec/conceptql/operators/place_of_service_code_spec.rb +0 -24
  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
  1178. data/spec/conceptql/operators/rxnorm_spec.rb +0 -29
  1179. data/spec/conceptql/operators/snomed_spec.rb +0 -29
  1180. data/spec/conceptql/operators/source_vocabulary_operator_spec.rb +0 -35
  1181. data/spec/conceptql/operators/standard_vocabulary_operator_spec.rb +0 -35
  1182. data/spec/conceptql/operators/started_by_spec.rb +0 -22
  1183. data/spec/conceptql/operators/temporal_operator_spec.rb +0 -51
  1184. data/spec/conceptql/operators/time_window_spec.rb +0 -77
  1185. data/spec/conceptql/operators/union_spec.rb +0 -21
  1186. data/spec/conceptql/operators/visit_occurrence_spec.rb +0 -10
  1187. data/spec/conceptql/query_spec.rb +0 -22
  1188. data/spec/conceptql/tree_spec.rb +0 -50
  1189. data/spec/doubles/stream_for_casting_double.rb +0 -9
  1190. data/spec/doubles/stream_for_occurrence_double.rb +0 -25
  1191. data/spec/doubles/stream_for_temporal_double.rb +0 -6
  1192. data/spec/spec_helper.rb +0 -102
data/test/statements/union/count_4 ADDED
@@ -0,0 +1,18 @@
1
+ [
2
+ "union",
3
+ [
4
+ "union",
5
+ [
6
+ "icd9",
7
+ "412"
8
+ ],
9
+ [
10
+ "icd10",
11
+ "Z56.1"
12
+ ]
13
+ ],
14
+ [
15
+ "icd9",
16
+ "401.9"
17
+ ]
18
+ ]
data/test/statements/union/count_5 ADDED
@@ -0,0 +1,18 @@
1
+ [
2
+ "union",
3
+ [
4
+ "union",
5
+ [
6
+ "icd9",
7
+ "412"
8
+ ],
9
+ [
10
+ "icd9",
11
+ "401.9"
12
+ ]
13
+ ],
14
+ [
15
+ "place_of_service_code",
16
+ "21"
17
+ ]
18
+ ]
data/test/statements/union/scanno_1 ADDED
@@ -0,0 +1,3 @@
1
+ [
2
+ "union"
3
+ ]
data/test/statements/union/scanno_2 ADDED
@@ -0,0 +1,18 @@
1
+ [
2
+ "union",
3
+ [
4
+ "icd9",
5
+ "412",
6
+ "XYS",
7
+ {
8
+ "id": 1
9
+ }
10
+ ],
11
+ [
12
+ "icd9",
13
+ "401.9",
14
+ {
15
+ "id": 2
16
+ }
17
+ ]
18
+ ]
data/test/statements/visit_occurrence/anno_1 ADDED
@@ -0,0 +1,11 @@
1
+ [
2
+ "visit_occurrence",
3
+ [
4
+ "icd9",
5
+ "412"
6
+ ],
7
+ [
8
+ "icd9",
9
+ "412"
10
+ ]
11
+ ]
data/test/statements/visit_occurrence/anno_2 ADDED
@@ -0,0 +1,8 @@
1
+ [
2
+ "visit_occurrence",
3
+ 21,
4
+ [
5
+ "icd9",
6
+ "412"
7
+ ]
8
+ ]
data/test/statements/visit_occurrence/crit_1 ADDED
@@ -0,0 +1,7 @@
1
+ [
2
+ "visit_occurrence",
3
+ [
4
+ "icd9",
5
+ "412"
6
+ ]
7
+ ]
data/test/statements/visit_occurrence/crit_2 ADDED
@@ -0,0 +1,7 @@
1
+ [
2
+ "visit_occurrence",
3
+ [
4
+ "gender",
5
+ "Male"
6
+ ]
7
+ ]
data/test/statements/visit_occurrence/crit_3 ADDED
@@ -0,0 +1,3 @@
1
+ [
2
+ "visit_occurrence"
3
+ ]
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: conceptql
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.2.0
4
+ version: 0.3.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Ryan Duryea
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2015-12-11 00:00:00.000000000 Z
11
+ date: 2016-11-09 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: facets
@@ -30,14 +30,14 @@ dependencies:
30
30
  requirements:
31
31
  - - "~>"
32
32
  - !ruby/object:Gem::Version
33
- version: '0.0'
33
+ version: '0.1'
34
34
  type: :runtime
35
35
  prerelease: false
36
36
  version_requirements: !ruby/object:Gem::Requirement
37
37
  requirements:
38
38
  - - "~>"
39
39
  - !ruby/object:Gem::Version
40
- version: '0.0'
40
+ version: '0.1'
41
41
  - !ruby/object:Gem::Dependency
42
42
  name: thor
43
43
  requirement: !ruby/object:Gem::Requirement
@@ -52,20 +52,6 @@ dependencies:
52
52
  - - "~>"
53
53
  - !ruby/object:Gem::Version
54
54
  version: '0.19'
55
- - !ruby/object:Gem::Dependency
56
- name: pg
57
- requirement: !ruby/object:Gem::Requirement
58
- requirements:
59
- - - "~>"
60
- - !ruby/object:Gem::Version
61
- version: '0.17'
62
- type: :runtime
63
- prerelease: false
64
- version_requirements: !ruby/object:Gem::Requirement
65
- requirements:
66
- - - "~>"
67
- - !ruby/object:Gem::Version
68
- version: '0.17'
69
55
  - !ruby/object:Gem::Dependency
70
56
  name: ruby-graphviz
71
57
  requirement: !ruby/object:Gem::Requirement
@@ -123,47 +109,47 @@ dependencies:
123
109
  - !ruby/object:Gem::Version
124
110
  version: '10.3'
125
111
  - !ruby/object:Gem::Dependency
126
- name: rspec
112
+ name: minitest
127
113
  requirement: !ruby/object:Gem::Requirement
128
114
  requirements:
129
115
  - - "~>"
130
116
  - !ruby/object:Gem::Version
131
- version: '3.2'
117
+ version: '5.0'
132
118
  type: :development
133
119
  prerelease: false
134
120
  version_requirements: !ruby/object:Gem::Requirement
135
121
  requirements:
136
122
  - - "~>"
137
123
  - !ruby/object:Gem::Version
138
- version: '3.2'
124
+ version: '5.0'
139
125
  - !ruby/object:Gem::Dependency
140
- name: guard-rspec
126
+ name: byebug
141
127
  requirement: !ruby/object:Gem::Requirement
142
128
  requirements:
143
129
  - - "~>"
144
130
  - !ruby/object:Gem::Version
145
- version: '4.5'
131
+ version: '4.0'
146
132
  type: :development
147
133
  prerelease: false
148
134
  version_requirements: !ruby/object:Gem::Requirement
149
135
  requirements:
150
136
  - - "~>"
151
137
  - !ruby/object:Gem::Version
152
- version: '4.5'
138
+ version: '4.0'
153
139
  - !ruby/object:Gem::Dependency
154
- name: byebug
140
+ name: simplecov
155
141
  requirement: !ruby/object:Gem::Requirement
156
142
  requirements:
157
143
  - - "~>"
158
144
  - !ruby/object:Gem::Version
159
- version: '4.0'
145
+ version: '0.11'
160
146
  type: :development
161
147
  prerelease: false
162
148
  version_requirements: !ruby/object:Gem::Requirement
163
149
  requirements:
164
150
  - - "~>"
165
151
  - !ruby/object:Gem::Version
166
- version: '4.0'
152
+ version: '0.11'
167
153
  description: ConceptQL is a query language for specifying queries to be run OMOP CDMv4
168
154
  structured data
169
155
  email:
@@ -182,22 +168,90 @@ files:
182
168
  - Rakefile
183
169
  - bin/conceptql
184
170
  - conceptql.gemspec
171
+ - config/provenance.yml
185
172
  - doc/ConceptQL Specification (alpha).pdf
173
+ - doc/converter.rb
186
174
  - doc/diagram_0.png
187
175
  - doc/implementation_notes.md
176
+ - doc/metadata.md
188
177
  - doc/spec.md
178
+ - doc/spec.md.cql
179
+ - doc/spec/02f44ad35d266ddd0a4df1691d26bf4a297b30604fc3f44b0391d6d852d23a9f.png
180
+ - doc/spec/0360fc0c2b7a88fd82ffc4d13387b76766649d5d42aa8f9349bbf60a81ac6119.png
181
+ - doc/spec/04491942fcbd741982514f9eb12aeecf3d54b5b69a2b50c8331f7700169d5521.png
182
+ - doc/spec/05f9b844571ffceeed2def3025fb60c68552817b8b73d3c8a76939dbc08b7c65.png
183
+ - doc/spec/067241a3579767a802d4f8e20fd35b60adbe377c9a6512ef135f164a5accfb27.png
184
+ - doc/spec/1102fa717b1c2df67af5220bf3ae219afafd79be7bba0c117e301983385ada52.png
185
+ - doc/spec/11f57941951bad5a75f9a16f38a31a3c6bf3046a475aac6e398e780892fab4ad.png
186
+ - doc/spec/15268bc45993d3f57ccf915877f91e48bdee684f24faa614249915833cac4af9.png
187
+ - doc/spec/253845fe6162621af407ebd110296ff4f6d8a3f23ec75dfb4ea8cda30be71262.png
188
+ - doc/spec/26fd52b5ac55438dd9f81b4a3f3913f1058c9f225c8a5e129007c1e9413d5881.png
189
+ - doc/spec/2b57886a9cba66bb696e4b399c51ad0dc95cd64b952709fafc819a79d573f09e.png
190
+ - doc/spec/307a8b5a7edd6e42f8be16523a4c939faf1a0533385c861d7004b6af8addd7d1.png
191
+ - doc/spec/328467a6a419c7c05e299b8097e5e000686068ded8dc6d5f2e2de6f51976c315.png
192
+ - doc/spec/39d6a8eb71cae51b1d6937c97134e51f04fd47c54535ff0915fe6a8b4f197fb2.png
193
+ - doc/spec/3f46dee4d775d1a29d52b68af6552f8ea3abd8303094e749714fc77bd7958155.png
194
+ - doc/spec/44ec6743d5d77d15b8a487c2058bf3e455d34adc91c46ea05767f6e0e471a75e.png
195
+ - doc/spec/462153be527b28dc2cb5259c0aec62e1f529e8b60dc6e9c23fd1e06e8be933c9.png
196
+ - doc/spec/4a3b47ed1c54f96ebdae693d41c36c51884c4546ef799a4108085708fb7b964e.png
197
+ - doc/spec/514f263e976d07c0d9e0a86c79bcbdcddc7d444d7b72135294ad78758effd28f.png
198
+ - doc/spec/58113a57a37431a402d2547369eba3a481bf1dbbfd82dc384406a5c91f6df01f.png
199
+ - doc/spec/5d331d74c460d75814b2d3138a9b7d90b5ddb2dcd85e1f5f260d183745fc3a1e.png
200
+ - doc/spec/5d6ff62038b75d6f240d65f35d1520a131c221f47d3801554c8c2be5d528ebb0.png
201
+ - doc/spec/62323426e381ec21c967971a67e1f4a6d89dae92154bd937284e00b67f67fdd3.png
202
+ - doc/spec/6705af65d728c0d5c50d6c4d46253017a91eb459dbb1f40f92449f05d5562f4a.png
203
+ - doc/spec/68fac940a32c7e40caacf8e560c61da552d57633d015ba98f2e98ec040a00c5b.png
204
+ - doc/spec/6a34c0ef589c9c976fe41f3e67e799e198499f5b9c3ebfd240fb91f73e893573.png
205
+ - doc/spec/6b48534236697d1ccfa1f5403764782f9d228f9eb706789cfa80203882b7b13a.png
206
+ - doc/spec/7aa76b4d29874719466c2cbafc9936e9f12e504bf31e1a09d26ca3fffa8ba1a6.png
207
+ - doc/spec/7b9db2986ab9ada45cfb9451ef87ff1a2d99c908083334b7ccdceb8a92387fa9.png
208
+ - doc/spec/8101d9b89d9ba8070d585432707b43a8acdb4c2a3e9d37c3f7114b5e3ea9e800.png
209
+ - doc/spec/886bf85249a704668a55c5161bceaac10be4a41a94b91606f49851dfa017526c.png
210
+ - doc/spec/8ed478d8c81a58a202d0c51348fca246df206fc24a0567b163d4e0bdab56ca46.png
211
+ - doc/spec/9139440329dcb815df89bc70182c3827868402a74ff64d0253706dcaff723dca.png
212
+ - doc/spec/99392f56dfb0e5be3f45a12a7f1ba846d094e430f526dfeaa30b606837cd34c0.png
213
+ - doc/spec/a4450e8c0fe0e2fde92fe9bd61952f907b1976c1aa3ba963b809bed079d42b09.png
214
+ - doc/spec/a4bc7382a1154ea9856544fd48418f3dd9ce474ca94b8859fc323749c6cc1f55.png
215
+ - doc/spec/a79274742cf6fac6f6c9f4a0eb651aeb452f9c43b537c8e6ccaefecd05b7105c.png
216
+ - doc/spec/a9b4528726adec2a90f3f00139d8d0492f13c51f03c2f9ed6a5134b1b26b44a9.png
217
+ - doc/spec/af5ae3787e80bf0771f18f1a04fe4c5d9291e1e0f963ac408a7bc198d2f1ee28.png
218
+ - doc/spec/ba572c4f4dbade65be55f141df16cf7b3e7d09e0aec4e4e5debc4f2075277371.png
219
+ - doc/spec/ba90ef705f7be91c53c5eb4a81a439fa0f7c48532214bd3db3cc5c069160543e.png
220
+ - doc/spec/c1d0402862221d85aceedc7d76b3f82149b612cbd972f14d0ca9011e1e2c455c.png
221
+ - doc/spec/c2157d8a6b73abe4f22ba5042159f32502c74bf6d762be28d2df6831586822c7.png
222
+ - doc/spec/c5329a7f4937096a57b2e01efb9d542f84a4e2329a1e9381d08c630583ccad37.png
223
+ - doc/spec/c82077b9455d0f9abc2c45ee1a298e38b99c9ce9cd685f65d87b376d7718d7ad.png
224
+ - doc/spec/c93dd18894a245a5647f99e1867d3779e4cd34c9c8f8860600ff0c837a5ffa53.png
225
+ - doc/spec/cc960a268d51ccf2ebde657d36848f780213834844900018bce3d111843f7b0f.png
226
+ - doc/spec/d39452b58257c95a7cba07afed4877417b0c227f3690e2bff22c9eca89eac845.png
227
+ - doc/spec/d64993258ffbef9406d9ab9136de7af530626b3a69e9eeb75835e11f11dabf62.png
228
+ - doc/spec/da450cdd0c94a1301bd98560339a45caa8041e09974352a56ecfb144e9a5e4d4.png
229
+ - doc/spec/dbc66b3ae6bd7123d77dd04b64f8a24498d048725a55c5340b15f5ae0a1ff307.png
230
+ - doc/spec/de589af36fa854e006a1563c93e644e2210f2a5616babb779f7f38aadb6c1ed7.png
231
+ - doc/spec/defbd0b853d895802663f507761ad297d82e167f516c6082686a2a19b76012c5.png
232
+ - doc/spec/e1cb0863b21e14256d61a54200316791f6547c78ba2f0156c110f4500f9bbd49.png
233
+ - doc/spec/e8630103287f7c9d28eff40b3b1826e24846e776b877f7b8554257acbe621e1c.png
234
+ - doc/spec/e9b384fa7dec5f1a06479c4b289e06b1e60e4f23f7630aff6d03c52595f500f8.png
235
+ - doc/spec/ea935ac31f3b57ff373646780a1fba34a38c9e086dc771eb7fc16c65a7e20cfc.png
236
+ - doc/spec/eb8f5511f7d88bd0f8ba73420fc10f7c78405db7f4373d778a827058707f888e.png
237
+ - doc/spec/ebacbd092e3d1a3c7b745a381e51e8ff9d63a21db23a16940193e18e57bc866f.png
238
+ - doc/spec/ed039f82867241393b1a6a7153d3690461103934c72c1f3eaa3d99a12bb40885.png
239
+ - doc/spec/ee283d6a4b69cf10da2df703be3a16830be9cd8cd4f68c5f7afdf558ea28fa76.png
240
+ - doc/spec/f0c734b099841a754ae0366afb00e992ad4814479b65e4a7de23c6e3dd85c09a.png
241
+ - doc/spec/f6b4fc31703cfb6327bbbd4614af8bb72da6d39fa3d53ada63a70157f2fad80e.png
242
+ - doc/spec/f766f2e3aa13420e3ba0f823ac7956b311ed7c6c20be26b72324fadd87f36712.png
243
+ - doc/spec/ff7d5b5573d09bd7c4cdd3aeda124d18bf82ec46673a62881b399a75d69f3f53.png
189
244
  - lib/conceptql.rb
190
- - lib/conceptql/behaviors/debuggable.rb
191
- - lib/conceptql/behaviors/dottable.rb
245
+ - lib/conceptql/annotate_grapher.rb
246
+ - lib/conceptql/behaviors/drugish.rb
247
+ - lib/conceptql/behaviors/labish.rb
192
248
  - lib/conceptql/behaviors/metadatable.rb
193
- - lib/conceptql/behaviors/preppable.rb
249
+ - lib/conceptql/behaviors/provenanceable.rb
194
250
  - lib/conceptql/cli.rb
195
- - lib/conceptql/converter.rb
251
+ - lib/conceptql/database.rb
196
252
  - lib/conceptql/date_adjuster.rb
197
- - lib/conceptql/debugger.rb
198
- - lib/conceptql/fake_grapher.rb
199
- - lib/conceptql/graph.rb
200
- - lib/conceptql/graph_nodifier.rb
253
+ - lib/conceptql/fake_annotater.rb
254
+ - lib/conceptql/knitter.rb
201
255
  - lib/conceptql/logger.rb
202
256
  - lib/conceptql/nodifier.rb
203
257
  - lib/conceptql/operators/after.rb
@@ -205,14 +259,19 @@ files:
205
259
  - lib/conceptql/operators/before.rb
206
260
  - lib/conceptql/operators/binary_operator_operator.rb
207
261
  - lib/conceptql/operators/casting_operator.rb
262
+ - lib/conceptql/operators/co_reported.rb
208
263
  - lib/conceptql/operators/complement.rb
209
- - lib/conceptql/operators/concept.rb
264
+ - lib/conceptql/operators/concurrent_within.rb
265
+ - lib/conceptql/operators/condition_occurrence_source_vocabulary_operator.rb
266
+ - lib/conceptql/operators/condition_occurrence_source_vocabulary_operator_union.rb
210
267
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+ - lib/conceptql/query_modifiers/drug_query_modifier.rb
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+ - lib/conceptql/query_modifiers/pos_query_modifier.rb
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+ - lib/conceptql/query_modifiers/query_modifier.rb
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- - spec/conceptql/behaviors/dottable_spec.rb
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- - spec/conceptql/operators/hcpcs_spec.rb
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- - spec/conceptql/operators/icd9_procedure_spec.rb
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- - spec/conceptql/operators/intersect_spec.rb
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- - spec/conceptql/operators/medcode_procedure_spec.rb
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- - spec/conceptql/operators/query_double.rb
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- - spec/conceptql/operators/query_double_spec.rb
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- - spec/conceptql/operators/race_spec.rb
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- - spec/conceptql/operators/rxnorm_spec.rb
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- - spec/conceptql/operators/snomed_spec.rb
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- - spec/conceptql/operators/source_vocabulary_operator_spec.rb
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- - spec/conceptql/operators/standard_vocabulary_operator_spec.rb
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- - spec/conceptql/operators/started_by_spec.rb
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- - spec/conceptql/operators/temporal_operator_spec.rb
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- - spec/conceptql/operators/time_window_spec.rb
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- - spec/conceptql/operators/visit_occurrence_spec.rb
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- - spec/doubles/stream_for_occurrence_double.rb
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- - spec/spec_helper.rb
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+ - test/all.rb
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+ - test/all_operations_test.rb
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+ - test/code_list_test.rb
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+ - test/data/omopv4/care_site.csv
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+ - test/data/omopv4/cohort.csv
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+ - test/data/omopv4_plus/concept.csv
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+ - test/data/omopv4_plus/drug_exposure.csv
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+ - test/data/omopv4_plus/headers/care_site.csv
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+ - test/data/omopv4_plus/headers/concept.csv
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+ - test/data/omopv4_plus/headers/death.csv
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+ - test/data/omopv4_plus/headers/organization.csv
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+ - test/data/omopv4_plus/headers/source_to_concept_map.csv
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+ - test/data/omopv4_plus/headers/vocabulary.csv
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+ - test/data/omopv4_plus/observation.csv
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+ - test/data/omopv4_plus/observation_period.csv
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+ - test/data/omopv4_plus/organization.csv
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+ - test/data/omopv4_plus/payer_plan_period.csv
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+ - test/data/omopv4_plus/procedure_cost.csv
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+ - test/data/omopv4_plus/procedure_occurrence.csv
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+ - test/data/omopv4_plus/provider.csv
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+ - test/data/omopv4_plus/source_to_concept_map.csv
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+ - test/data/omopv4_plus/visit_occurrence.csv
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+ - test/data/omopv4_plus/vocabulary.csv
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+ - test/db.rb
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+ - test/db_setup.rb
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+ - test/db_teardown.rb
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+ - test/fake_annotater_test.rb
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+ - test/helper.rb
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+ - test/knitter/conceptql.md.cql
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+ - test/knitter/conceptql.md.expect
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+ - test/knitter/many.md.cql
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+ - test/knitter/title.md.cql
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+ - test/knitter/title.md.expect
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+ - test/knitter/union.md.cql
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+ - test/knitter/union.md.expect
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+ - test/knitter_test.rb
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+ - test/query_test.rb
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+ - test/results/omopv4/after/anno_1
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+ - test/results/omopv4/after/crit_occurrences
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+ - test/results/omopv4/any_overlap/crit_basic1
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+ - test/results/omopv4/any_overlap/crit_basic2
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+ - test/results/omopv4/any_overlap/crit_occurrences1
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+ - test/results/omopv4/any_overlap/crit_occurrences2
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+ - test/results/omopv4/any_overlap/crit_within
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+ - test/results/omopv4/before/crit_at_least
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+ - test/results/omopv4/co_reported/anno_1
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+ - test/results/omopv4/complement/anno_duplicate_params
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+ - test/results/omopv4/complement/count_3way_intersect
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+ - test/results/omopv4/complement/count_3way_union
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+ - test/results/omopv4/complement/count_intersect
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+ - test/results/omopv4/complement/count_union_and_intersect
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+ - test/results/omopv4/complement/crit_3way_union
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+ - test/results/omopv4/complement/crit_icd9_selector
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+ - test/statements/union/count_1
1281
+ - test/statements/union/count_2
1282
+ - test/statements/union/count_3
1283
+ - test/statements/union/count_4
1284
+ - test/statements/union/count_5
1285
+ - test/statements/union/scanno_1
1286
+ - test/statements/union/scanno_2
1287
+ - test/statements/visit_occurrence/anno_1
1288
+ - test/statements/visit_occurrence/anno_2
1289
+ - test/statements/visit_occurrence/crit_1
1290
+ - test/statements/visit_occurrence/crit_2
1291
+ - test/statements/visit_occurrence/crit_3
325
1292
  homepage: https://github.com/outcomesinsights/conceptql
326
1293
  licenses:
327
1294
  - MIT
@@ -342,63 +1309,962 @@ required_rubygems_version: !ruby/object:Gem::Requirement
342
1309
  version: '0'
343
1310
  requirements: []
344
1311
  rubyforge_project:
345
- rubygems_version: 2.4.5.1
1312
+ rubygems_version: 2.4.8
346
1313
  signing_key:
347
1314
  specification_version: 4
348
1315
  summary: Generate OMOP CDMv4-compatible queries from a ConceptQL file
349
1316
  test_files:
350
- - spec/conceptql/behaviors/dottable_spec.rb
351
- - spec/conceptql/converter_spec.rb
352
- - spec/conceptql/date_adjuster_spec.rb
353
- - spec/conceptql/operators/after_spec.rb
354
- - spec/conceptql/operators/before_spec.rb
355
- - spec/conceptql/operators/casting_operator_spec.rb
356
- - spec/conceptql/operators/complement_spec.rb
357
- - spec/conceptql/operators/concept_spec.rb
358
- - spec/conceptql/operators/condition_type_spec.rb
359
- - spec/conceptql/operators/contains_spec.rb
360
- - spec/conceptql/operators/cpt_spec.rb
361
- - spec/conceptql/operators/date_range_spec.rb
362
- - spec/conceptql/operators/death_spec.rb
363
- - spec/conceptql/operators/during_spec.rb
364
- - spec/conceptql/operators/except_spec.rb
365
- - spec/conceptql/operators/first_spec.rb
366
- - spec/conceptql/operators/from_spec.rb
367
- - spec/conceptql/operators/gender_spec.rb
368
- - spec/conceptql/operators/hcpcs_spec.rb
369
- - spec/conceptql/operators/icd10_spec.rb
370
- - spec/conceptql/operators/icd9_procedure_spec.rb
371
- - spec/conceptql/operators/icd9_spec.rb
372
- - spec/conceptql/operators/intersect_spec.rb
373
- - spec/conceptql/operators/last_spec.rb
374
- - spec/conceptql/operators/loinc_spec.rb
375
- - spec/conceptql/operators/medcode_procedure_spec.rb
376
- - spec/conceptql/operators/medcode_spec.rb
377
- - spec/conceptql/operators/observation_period_spec.rb
378
- - spec/conceptql/operators/occurrence_spec.rb
379
- - spec/conceptql/operators/overlapped_by_spec.rb
380
- - spec/conceptql/operators/overlaps_spec.rb
381
- - spec/conceptql/operators/person_filter_spec.rb
382
- - spec/conceptql/operators/person_spec.rb
383
- - spec/conceptql/operators/place_of_service_code_spec.rb
384
- - spec/conceptql/operators/procedure_occurrence_spec.rb
385
- - spec/conceptql/operators/prodcode_spec.rb
386
- - spec/conceptql/operators/query_double.rb
387
- - spec/conceptql/operators/query_double_spec.rb
388
- - spec/conceptql/operators/race_spec.rb
389
- - spec/conceptql/operators/rxnorm_spec.rb
390
- - spec/conceptql/operators/snomed_spec.rb
391
- - spec/conceptql/operators/source_vocabulary_operator_spec.rb
392
- - spec/conceptql/operators/standard_vocabulary_operator_spec.rb
393
- - spec/conceptql/operators/started_by_spec.rb
394
- - spec/conceptql/operators/temporal_operator_spec.rb
395
- - spec/conceptql/operators/time_window_spec.rb
396
- - spec/conceptql/operators/union_spec.rb
397
- - spec/conceptql/operators/visit_occurrence_spec.rb
398
- - spec/conceptql/query_spec.rb
399
- - spec/conceptql/tree_spec.rb
400
- - spec/doubles/stream_for_casting_double.rb
401
- - spec/doubles/stream_for_occurrence_double.rb
402
- - spec/doubles/stream_for_temporal_double.rb
403
- - spec/spec_helper.rb
404
- has_rdoc:
1317
+ - test/all.rb
1318
+ - test/all_operations_test.rb
1319
+ - test/code_list_test.rb
1320
+ - test/data/omopv4/care_site.csv
1321
+ - test/data/omopv4/cohort.csv
1322
+ - test/data/omopv4/condition_era.csv
1323
+ - test/data/omopv4/condition_occurrence.csv
1324
+ - test/data/omopv4/death.csv
1325
+ - test/data/omopv4/drug_cost.csv
1326
+ - test/data/omopv4/drug_era.csv
1327
+ - test/data/omopv4/drug_exposure.csv
1328
+ - test/data/omopv4/location.csv
1329
+ - test/data/omopv4/observation.csv
1330
+ - test/data/omopv4/observation_period.csv
1331
+ - test/data/omopv4/organization.csv
1332
+ - test/data/omopv4/payer_plan_period.csv
1333
+ - test/data/omopv4/person.csv
1334
+ - test/data/omopv4/procedure_cost.csv
1335
+ - test/data/omopv4/procedure_occurrence.csv
1336
+ - test/data/omopv4/provider.csv
1337
+ - test/data/omopv4/visit_occurrence.csv
1338
+ - test/data/omopv4_plus/care_site.csv
1339
+ - test/data/omopv4_plus/cohort.csv
1340
+ - test/data/omopv4_plus/concept.csv
1341
+ - test/data/omopv4_plus/condition_era.csv
1342
+ - test/data/omopv4_plus/condition_occurrence.csv
1343
+ - test/data/omopv4_plus/death.csv
1344
+ - test/data/omopv4_plus/drug_cost.csv
1345
+ - test/data/omopv4_plus/drug_era.csv
1346
+ - test/data/omopv4_plus/drug_exposure.csv
1347
+ - test/data/omopv4_plus/headers/care_site.csv
1348
+ - test/data/omopv4_plus/headers/cohort.csv
1349
+ - test/data/omopv4_plus/headers/concept.csv
1350
+ - test/data/omopv4_plus/headers/condition_era.csv
1351
+ - test/data/omopv4_plus/headers/condition_occurrence.csv
1352
+ - test/data/omopv4_plus/headers/death.csv
1353
+ - test/data/omopv4_plus/headers/drug_cost.csv
1354
+ - test/data/omopv4_plus/headers/drug_era.csv
1355
+ - test/data/omopv4_plus/headers/drug_exposure.csv
1356
+ - test/data/omopv4_plus/headers/location.csv
1357
+ - test/data/omopv4_plus/headers/observation.csv
1358
+ - test/data/omopv4_plus/headers/observation_period.csv
1359
+ - test/data/omopv4_plus/headers/organization.csv
1360
+ - test/data/omopv4_plus/headers/payer_plan_period.csv
1361
+ - test/data/omopv4_plus/headers/person.csv
1362
+ - test/data/omopv4_plus/headers/procedure_cost.csv
1363
+ - test/data/omopv4_plus/headers/procedure_occurrence.csv
1364
+ - test/data/omopv4_plus/headers/provider.csv
1365
+ - test/data/omopv4_plus/headers/source_to_concept_map.csv
1366
+ - test/data/omopv4_plus/headers/visit_occurrence.csv
1367
+ - test/data/omopv4_plus/headers/vocabulary.csv
1368
+ - test/data/omopv4_plus/location.csv
1369
+ - test/data/omopv4_plus/observation.csv
1370
+ - test/data/omopv4_plus/observation_period.csv
1371
+ - test/data/omopv4_plus/organization.csv
1372
+ - test/data/omopv4_plus/payer_plan_period.csv
1373
+ - test/data/omopv4_plus/person.csv
1374
+ - test/data/omopv4_plus/procedure_cost.csv
1375
+ - test/data/omopv4_plus/procedure_occurrence.csv
1376
+ - test/data/omopv4_plus/provider.csv
1377
+ - test/data/omopv4_plus/source_to_concept_map.csv
1378
+ - test/data/omopv4_plus/visit_occurrence.csv
1379
+ - test/data/omopv4_plus/vocabulary.csv
1380
+ - test/db.rb
1381
+ - test/db_setup.rb
1382
+ - test/db_teardown.rb
1383
+ - test/fake_annotater_test.rb
1384
+ - test/helper.rb
1385
+ - test/knitter/conceptql.md.cql
1386
+ - test/knitter/conceptql.md.expect
1387
+ - test/knitter/empty.md.cql
1388
+ - test/knitter/except.md.cql
1389
+ - test/knitter/except.md.expect
1390
+ - test/knitter/fake.md.cql
1391
+ - test/knitter/fake.md.expect
1392
+ - test/knitter/many.md.cql
1393
+ - test/knitter/many.md.expect
1394
+ - test/knitter/no_conceptql.md.cql
1395
+ - test/knitter/title.md.cql
1396
+ - test/knitter/title.md.expect
1397
+ - test/knitter/union.md.cql
1398
+ - test/knitter/union.md.expect
1399
+ - test/knitter_test.rb
1400
+ - test/query_test.rb
1401
+ - test/results/omopv4/after/anno_1
1402
+ - test/results/omopv4/after/anno_2
1403
+ - test/results/omopv4/after/anno_3
1404
+ - test/results/omopv4/after/anno_4
1405
+ - test/results/omopv4/after/anno_5
1406
+ - test/results/omopv4/after/anno_6
1407
+ - test/results/omopv4/after/crit_at_least
1408
+ - test/results/omopv4/after/crit_basic
1409
+ - test/results/omopv4/after/crit_occurrences
1410
+ - test/results/omopv4/after/crit_within
1411
+ - test/results/omopv4/any_overlap/crit_basic1
1412
+ - test/results/omopv4/any_overlap/crit_basic2
1413
+ - test/results/omopv4/any_overlap/crit_occurrences1
1414
+ - test/results/omopv4/any_overlap/crit_occurrences2
1415
+ - test/results/omopv4/any_overlap/crit_within
1416
+ - test/results/omopv4/before/crit_at_least
1417
+ - test/results/omopv4/before/crit_basic1
1418
+ - test/results/omopv4/before/crit_basic2
1419
+ - test/results/omopv4/before/crit_occurrences
1420
+ - test/results/omopv4/before/crit_within
1421
+ - test/results/omopv4/co_reported/anno_1
1422
+ - test/results/omopv4/co_reported/anno_2
1423
+ - test/results/omopv4/complement/anno_duplicate_params
1424
+ - test/results/omopv4/complement/anno_invalid_params
1425
+ - test/results/omopv4/complement/anno_no_params
1426
+ - test/results/omopv4/complement/count_3way_intersect
1427
+ - test/results/omopv4/complement/count_3way_union
1428
+ - test/results/omopv4/complement/count_intersect
1429
+ - test/results/omopv4/complement/count_union
1430
+ - test/results/omopv4/complement/count_union_and_intersect
1431
+ - test/results/omopv4/complement/crit_3way_intersect
1432
+ - test/results/omopv4/complement/crit_3way_union
1433
+ - test/results/omopv4/complement/crit_basic1
1434
+ - test/results/omopv4/complement/crit_icd9_selector
1435
+ - test/results/omopv4/complement/crit_intersect
1436
+ - test/results/omopv4/complement/crit_union
1437
+ - test/results/omopv4/complement/crit_union_and_intersect
1438
+ - test/results/omopv4/complex/anno_1
1439
+ - test/results/omopv4/complex/crit_1
1440
+ - test/results/omopv4/complex/crit_2
1441
+ - test/results/omopv4/complex/crit_3
1442
+ - test/results/omopv4/complex/crit_4
1443
+ - test/results/omopv4/complex/crit_5
1444
+ - test/results/omopv4/complex/crit_6
1445
+ - test/results/omopv4/complex/crit_7
1446
+ - test/results/omopv4/complex/crit_out_of_order_ctes
1447
+ - test/results/omopv4/complex/scanno_1
1448
+ - test/results/omopv4/concurrent_within/crit_icd9
1449
+ - test/results/omopv4/concurrent_within/crit_icd9_and_place_of_service
1450
+ - test/results/omopv4/concurrent_within/crit_negative_start
1451
+ - test/results/omopv4/condition_type/anno_icd9
1452
+ - test/results/omopv4/condition_type/count_condition_era
1453
+ - test/results/omopv4/condition_type/count_condition_era_30_day_window
1454
+ - test/results/omopv4/condition_type/count_ehr_problem_list
1455
+ - test/results/omopv4/condition_type/count_era_0
1456
+ - test/results/omopv4/condition_type/count_inpatient
1457
+ - test/results/omopv4/condition_type/count_inpatient_detail
1458
+ - test/results/omopv4/condition_type/count_inpatient_header
1459
+ - test/results/omopv4/condition_type/count_inpatient_header_2
1460
+ - test/results/omopv4/condition_type/count_inpatient_header_3
1461
+ - test/results/omopv4/condition_type/count_inpatient_header_4
1462
+ - test/results/omopv4/condition_type/count_inpatient_header_5
1463
+ - test/results/omopv4/condition_type/count_inpatient_outpatient_detail
1464
+ - test/results/omopv4/condition_type/count_inpatient_primary
1465
+ - test/results/omopv4/condition_type/count_inpatient_primary_or_first
1466
+ - test/results/omopv4/condition_type/count_outpatient
1467
+ - test/results/omopv4/condition_type/count_outpatient_detail
1468
+ - test/results/omopv4/condition_type/count_outpatient_header
1469
+ - test/results/omopv4/condition_type/count_outpatient_primary
1470
+ - test/results/omopv4/condition_type/count_primary
1471
+ - test/results/omopv4/condition_type/crit_condition_era
1472
+ - test/results/omopv4/condition_type/crit_condition_era_30_day_window
1473
+ - test/results/omopv4/condition_type/crit_ehr_problem_list
1474
+ - test/results/omopv4/condition_type/crit_era_0
1475
+ - test/results/omopv4/condition_type/crit_inpatient
1476
+ - test/results/omopv4/condition_type/crit_inpatient_detail
1477
+ - test/results/omopv4/condition_type/crit_inpatient_header
1478
+ - test/results/omopv4/condition_type/crit_inpatient_header_2
1479
+ - test/results/omopv4/condition_type/crit_inpatient_header_3
1480
+ - test/results/omopv4/condition_type/crit_inpatient_header_4
1481
+ - test/results/omopv4/condition_type/crit_inpatient_header_5
1482
+ - test/results/omopv4/condition_type/crit_inpatient_primary
1483
+ - test/results/omopv4/condition_type/crit_inpatient_primary_or_first
1484
+ - test/results/omopv4/condition_type/crit_outpatient
1485
+ - test/results/omopv4/condition_type/crit_outpatient_detail
1486
+ - test/results/omopv4/condition_type/crit_outpatient_header
1487
+ - test/results/omopv4/condition_type/crit_outpatient_primary
1488
+ - test/results/omopv4/condition_type/crit_primary
1489
+ - test/results/omopv4/contains/crit_1
1490
+ - test/results/omopv4/contains/crit_2
1491
+ - test/results/omopv4/contains/crit_3
1492
+ - test/results/omopv4/count/anno_multiple_upstreams
1493
+ - test/results/omopv4/count/anno_no_upstream1
1494
+ - test/results/omopv4/count/anno_no_upstream2
1495
+ - test/results/omopv4/count/crit_icd9_ndc
1496
+ - test/results/omopv4/count/crit_ndc
1497
+ - test/results/omopv4/count/crit_person
1498
+ - test/results/omopv4/cpt/anno_icd9_upstream
1499
+ - test/results/omopv4/cpt/anno_invalid_code
1500
+ - test/results/omopv4/cpt/count_1
1501
+ - test/results/omopv4/cpt/crit_1
1502
+ - test/results/omopv4/cpt/crit_2
1503
+ - test/results/omopv4/cpt/scanno_1
1504
+ - test/results/omopv4/cpt_or_hcpcs/anno_bad_format
1505
+ - test/results/omopv4/cpt_or_hcpcs/count_1
1506
+ - test/results/omopv4/cpt_or_hcpcs/crit_1
1507
+ - test/results/omopv4/cpt_or_hcpcs/crit_2
1508
+ - test/results/omopv4/date_range/anno_1
1509
+ - test/results/omopv4/date_range/anno_extra_argument
1510
+ - test/results/omopv4/date_range/anno_invalid_argument
1511
+ - test/results/omopv4/date_range/anno_missing_argument1
1512
+ - test/results/omopv4/date_range/anno_missing_argument2
1513
+ - test/results/omopv4/date_range/anno_no_upstreams
1514
+ - test/results/omopv4/date_range/count_1
1515
+ - test/results/omopv4/date_range/count_2
1516
+ - test/results/omopv4/date_range/crit_1
1517
+ - test/results/omopv4/date_range/crit_2
1518
+ - test/results/omopv4/death/anno_multiple_upstreams
1519
+ - test/results/omopv4/death/anno_no_upstreams
1520
+ - test/results/omopv4/death/crit_basic
1521
+ - test/results/omopv4/death/crit_person
1522
+ - test/results/omopv4/drug_type_concept/anno_has_upstreams
1523
+ - test/results/omopv4/drug_type_concept/anno_no_arguments
1524
+ - test/results/omopv4/drug_type_concept/crit_basic1
1525
+ - test/results/omopv4/drug_type_concept/crit_basic2
1526
+ - test/results/omopv4/during/crit_1
1527
+ - test/results/omopv4/during/crit_2
1528
+ - test/results/omopv4/equal/crit_1
1529
+ - test/results/omopv4/equal/crit_2
1530
+ - test/results/omopv4/except/anno_1
1531
+ - test/results/omopv4/except/anno_2
1532
+ - test/results/omopv4/except/count_complex
1533
+ - test/results/omopv4/except/crit_412_cpt
1534
+ - test/results/omopv4/except/crit_412_inpatient
1535
+ - test/results/omopv4/except/crit_complex
1536
+ - test/results/omopv4/filter/crit_1
1537
+ - test/results/omopv4/first/anno_argument
1538
+ - test/results/omopv4/first/anno_no_upstream
1539
+ - test/results/omopv4/first/crit_cpt
1540
+ - test/results/omopv4/first/crit_icd9
1541
+ - test/results/omopv4/first/crit_union
1542
+ - test/results/omopv4/from/anno_has_upstreams
1543
+ - test/results/omopv4/from/anno_multiple_arguments
1544
+ - test/results/omopv4/from/count_condition_occurrence
1545
+ - test/results/omopv4/from/count_observation_period
1546
+ - test/results/omopv4/from/count_person
1547
+ - test/results/omopv4/from_seer_visits/anno_multiple_upstreams
1548
+ - test/results/omopv4/from_seer_visits/anno_no_upstream
1549
+ - test/results/omopv4/from_seer_visits/crit_1
1550
+ - test/results/omopv4/from_seer_visits/crit_2
1551
+ - test/results/omopv4/from_seer_visits/crit_3
1552
+ - test/results/omopv4/from_seer_visits/crit_4
1553
+ - test/results/omopv4/gender/anno_has_upstreams
1554
+ - test/results/omopv4/gender/crit_male
1555
+ - test/results/omopv4/hcpcs/anno_bad_format
1556
+ - test/results/omopv4/hcpcs/crit_A0382
1557
+ - test/results/omopv4/icd10/anno_bad_format
1558
+ - test/results/omopv4/icd10/anno_has_upstreams
1559
+ - test/results/omopv4/icd10/crit_1
1560
+ - test/results/omopv4/icd10pcs/anno_bad_format
1561
+ - test/results/omopv4/icd10pcs/anno_has_upstreams
1562
+ - test/results/omopv4/icd10pcs/crit_1
1563
+ - test/results/omopv4/icd9/anno_empty_label
1564
+ - test/results/omopv4/icd9/anno_invalid_code
1565
+ - test/results/omopv4/icd9/crit_1
1566
+ - test/results/omopv4/icd9_procedure/crit_1
1567
+ - test/results/omopv4/intersect/anno_412_inpatient
1568
+ - test/results/omopv4/intersect/anno_has_arguments
1569
+ - test/results/omopv4/intersect/anno_no_upstream
1570
+ - test/results/omopv4/intersect/crit_412_inpatient
1571
+ - test/results/omopv4/intersect/crit_412_male
1572
+ - test/results/omopv4/intersect/crit_complex
1573
+ - test/results/omopv4/invalid/anno_bad_op
1574
+ - test/results/omopv4/invalid/scanno_1
1575
+ - test/results/omopv4/last/crit_icd9
1576
+ - test/results/omopv4/loinc/crit_basic
1577
+ - test/results/omopv4/ndc/crit_basic
1578
+ - test/results/omopv4/numeric/anno_multiple_upstreams
1579
+ - test/results/omopv4/numeric/num_values_1
1580
+ - test/results/omopv4/numeric/num_values_2
1581
+ - test/results/omopv4/numeric/num_values_3
1582
+ - test/results/omopv4/observation_period/anno_has_arguments
1583
+ - test/results/omopv4/observation_period/anno_multiple_upstreams
1584
+ - test/results/omopv4/observation_period/count_all_periods
1585
+ - test/results/omopv4/observation_period/crit_female
1586
+ - test/results/omopv4/observation_period/crit_icd9
1587
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1897
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1898
+ - test/results/omopv4_plus/person_filter/count_1
1899
+ - test/results/omopv4_plus/person_filter/crit_1
1900
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1901
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1902
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1903
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1904
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1905
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1906
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1907
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1908
+ - test/results/omopv4_plus/procedure_occurrence/anno_multiple_upstreams
1909
+ - test/results/omopv4_plus/procedure_occurrence/count_gender
1910
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1911
+ - test/results/omopv4_plus/procedure_occurrence/count_started_by
1912
+ - test/results/omopv4_plus/provenance/anno_1
1913
+ - test/results/omopv4_plus/provenance/anno_bad_keyword
1914
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1915
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1916
+ - test/results/omopv4_plus/provider_filter/anno_1
1917
+ - test/results/omopv4_plus/race/anno_1
1918
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1919
+ - test/results/omopv4_plus/race/crit_1
1920
+ - test/results/omopv4_plus/read/anno_1
1921
+ - test/results/omopv4_plus/read/crit_1
1922
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1923
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1924
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1925
+ - test/results/omopv4_plus/recall/anno_4
1926
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1927
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1928
+ - test/results/omopv4_plus/recall/crit_1
1929
+ - test/results/omopv4_plus/recall/crit_2
1930
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1931
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1932
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1933
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1934
+ - test/results/omopv4_plus/revenue_code/crit_1
1935
+ - test/results/omopv4_plus/revenue_code/crit_basic
1936
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1937
+ - test/results/omopv4_plus/revenue_code/domains_drg100
1938
+ - test/results/omopv4_plus/rxnorm/crit_1
1939
+ - test/results/omopv4_plus/snomed/crit_1
1940
+ - test/results/omopv4_plus/started_by/crit_1
1941
+ - test/results/omopv4_plus/started_by/crit_2
1942
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1943
+ - test/results/omopv4_plus/sum/anno_1
1944
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1945
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1946
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1947
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1948
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1949
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1950
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1951
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1952
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1953
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1954
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1955
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1956
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1957
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1958
+ - test/results/omopv4_plus/trim_date_end/crit_2
1959
+ - test/results/omopv4_plus/trim_date_end/crit_3
1960
+ - test/results/omopv4_plus/trim_date_end/crit_at_least
1961
+ - test/results/omopv4_plus/trim_date_end/crit_occurrences_1
1962
+ - test/results/omopv4_plus/trim_date_end/crit_occurrences_2
1963
+ - test/results/omopv4_plus/trim_date_end/crit_within
1964
+ - test/results/omopv4_plus/trim_date_start/crit_1
1965
+ - test/results/omopv4_plus/trim_date_start/crit_2
1966
+ - test/results/omopv4_plus/trim_date_start/crit_3
1967
+ - test/results/omopv4_plus/trim_date_start/crit_at_least
1968
+ - test/results/omopv4_plus/trim_date_start/crit_occurrences_1
1969
+ - test/results/omopv4_plus/trim_date_start/crit_occurrences_2
1970
+ - test/results/omopv4_plus/trim_date_start/crit_within
1971
+ - test/results/omopv4_plus/union/anno_1
1972
+ - test/results/omopv4_plus/union/anno_2
1973
+ - test/results/omopv4_plus/union/anno_3
1974
+ - test/results/omopv4_plus/union/anno_4
1975
+ - test/results/omopv4_plus/union/anno_5
1976
+ - test/results/omopv4_plus/union/anno_6
1977
+ - test/results/omopv4_plus/union/count_1
1978
+ - test/results/omopv4_plus/union/count_2
1979
+ - test/results/omopv4_plus/union/count_3
1980
+ - test/results/omopv4_plus/union/count_4
1981
+ - test/results/omopv4_plus/union/count_5
1982
+ - test/results/omopv4_plus/union/optcc_1
1983
+ - test/results/omopv4_plus/union/optcc_2
1984
+ - test/results/omopv4_plus/union/optcc_3
1985
+ - test/results/omopv4_plus/union/optcc_4
1986
+ - test/results/omopv4_plus/union/optcc_5
1987
+ - test/results/omopv4_plus/union/optcc_6
1988
+ - test/results/omopv4_plus/union/scanno_1
1989
+ - test/results/omopv4_plus/union/scanno_2
1990
+ - test/results/omopv4_plus/visit_occurrence/anno_1
1991
+ - test/results/omopv4_plus/visit_occurrence/anno_2
1992
+ - test/results/omopv4_plus/visit_occurrence/crit_1
1993
+ - test/results/omopv4_plus/visit_occurrence/crit_2
1994
+ - test/results/omopv4_plus/visit_occurrence/crit_3
1995
+ - test/statements/after/anno_1
1996
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1997
+ - test/statements/after/anno_3
1998
+ - test/statements/after/anno_4
1999
+ - test/statements/after/anno_5
2000
+ - test/statements/after/anno_6
2001
+ - test/statements/after/crit_at_least
2002
+ - test/statements/after/crit_basic
2003
+ - test/statements/after/crit_occurrences
2004
+ - test/statements/after/crit_within
2005
+ - test/statements/any_overlap/crit_basic1
2006
+ - test/statements/any_overlap/crit_basic2
2007
+ - test/statements/any_overlap/crit_occurrences1
2008
+ - test/statements/any_overlap/crit_occurrences2
2009
+ - test/statements/any_overlap/crit_within
2010
+ - test/statements/before/crit_at_least
2011
+ - test/statements/before/crit_basic1
2012
+ - test/statements/before/crit_basic2
2013
+ - test/statements/before/crit_occurrences
2014
+ - test/statements/before/crit_within
2015
+ - test/statements/co_reported/anno_1
2016
+ - test/statements/co_reported/anno_2
2017
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2018
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2019
+ - test/statements/complement/anno_invalid_params
2020
+ - test/statements/complement/anno_no_params
2021
+ - test/statements/complement/count_3way_intersect
2022
+ - test/statements/complement/count_3way_union
2023
+ - test/statements/complement/count_intersect
2024
+ - test/statements/complement/count_union
2025
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2026
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2027
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2028
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2029
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2030
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2031
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2032
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2033
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2034
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2035
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2036
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2037
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2038
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2039
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2040
+ - test/statements/concurrent_within/crit_negative_start
2041
+ - test/statements/condition_type/anno_icd9
2042
+ - test/statements/condition_type/count_condition_era
2043
+ - test/statements/condition_type/count_condition_era_30_day_window
2044
+ - test/statements/condition_type/count_ehr_problem_list
2045
+ - test/statements/condition_type/count_era_0
2046
+ - test/statements/condition_type/count_inpatient
2047
+ - test/statements/condition_type/count_inpatient_detail
2048
+ - test/statements/condition_type/count_inpatient_header
2049
+ - test/statements/condition_type/count_inpatient_header_2
2050
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2051
+ - test/statements/condition_type/count_inpatient_header_4
2052
+ - test/statements/condition_type/count_inpatient_header_5
2053
+ - test/statements/condition_type/count_inpatient_outpatient_detail
2054
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2055
+ - test/statements/condition_type/count_inpatient_primary_or_first
2056
+ - test/statements/condition_type/count_outpatient
2057
+ - test/statements/condition_type/count_outpatient_detail
2058
+ - test/statements/condition_type/count_outpatient_header
2059
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2060
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2061
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2062
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2063
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2064
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2065
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2066
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2067
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2068
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2069
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2070
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2071
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2072
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2073
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2074
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2075
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2076
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2077
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2078
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2079
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2080
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2081
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2082
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2083
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2084
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2085
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2086
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2087
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2088
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2089
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2090
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2091
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2092
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2093
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2094
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2095
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2096
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2097
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2098
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2099
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2100
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2101
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2102
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2103
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2104
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2105
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2106
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2107
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2108
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2109
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2110
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2111
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2112
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2113
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2114
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2115
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2116
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2117
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2118
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2119
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2120
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2121
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2122
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2123
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2124
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2125
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2126
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2127
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2128
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2129
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2130
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2131
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2132
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2133
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2134
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2135
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2136
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2137
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2138
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2139
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2140
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2141
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2142
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2143
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2144
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2145
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2146
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2147
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2148
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2149
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2150
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2151
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2152
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2153
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2154
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2155
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2156
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2157
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2158
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2159
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2160
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2161
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2162
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2163
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2164
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2165
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2166
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2167
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2168
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2169
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2170
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2171
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2172
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2173
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2174
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2175
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2176
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2177
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2178
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2179
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2180
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2181
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2182
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2183
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2184
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2185
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2186
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2187
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2188
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2189
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2190
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2191
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2192
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2193
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2194
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2195
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2196
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2197
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2198
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2199
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2200
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2201
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2202
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2203
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2204
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2205
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2206
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2207
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2208
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2209
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2210
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2211
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2212
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2213
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2214
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2215
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2216
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2217
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2218
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2219
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2220
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2221
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2222
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2223
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2224
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2225
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2226
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2227
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2228
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2229
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2230
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2231
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2232
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2233
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2234
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2235
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2236
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2237
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2238
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2239
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2240
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2241
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2242
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2243
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2244
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2245
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2246
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2247
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2248
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2249
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2250
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2251
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2252
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2253
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2254
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2255
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2256
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2257
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2258
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2259
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2260
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2261
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2262
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2263
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2264
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2265
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2266
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2267
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2268
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2269
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2270
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