conceptql 0.6.0 → 0.7.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (126) hide show
  1. checksums.yaml +4 -4
  2. data/CHANGELOG.md +176 -0
  3. data/README.md +4 -2
  4. data/assets/diagram/diagram.css +331 -0
  5. data/assets/diagram/fonts/OFL.txt +93 -0
  6. data/assets/diagram/fonts/Roboto-400.ttf +0 -0
  7. data/assets/diagram/fonts/Roboto-700.ttf +0 -0
  8. data/assets/diagram/fonts/Roboto-Italic-400.ttf +0 -0
  9. data/assets/diagram/fonts/Roboto-Italic-Latin.woff2 +0 -0
  10. data/assets/diagram/fonts/Roboto-Normal-Latin.woff2 +0 -0
  11. data/assets/diagram/operators.svg +224 -0
  12. data/config/vocabularies.csv +85 -85
  13. data/docs/spec/README.md +2624 -0
  14. data/docs/spec/examples/after-operator.json +562 -0
  15. data/docs/spec/examples/any-overlap-operator.json +106 -0
  16. data/docs/spec/examples/before-operator.json +437 -0
  17. data/docs/spec/examples/co-reported-operator.json +168 -0
  18. data/docs/spec/examples/contains-operator.json +97 -0
  19. data/docs/spec/examples/date-range-operator.json +275 -0
  20. data/docs/spec/examples/death-operator.json +103 -0
  21. data/docs/spec/examples/during-operator.json +178 -0
  22. data/docs/spec/examples/episode-operator.json +80 -0
  23. data/docs/spec/examples/equal-operator.json +79 -0
  24. data/docs/spec/examples/ethnicity-operator.json +86 -0
  25. data/docs/spec/examples/except-operator.json +536 -0
  26. data/docs/spec/examples/filter-operator.json +218 -0
  27. data/docs/spec/examples/first-operator.json +148 -0
  28. data/docs/spec/examples/gender-operator.json +257 -0
  29. data/docs/spec/examples/hospice-operator.json +40 -0
  30. data/docs/spec/examples/hospitalization-operator.json +131 -0
  31. data/docs/spec/examples/information-periods-operator.json +131 -0
  32. data/docs/spec/examples/last-operator.json +148 -0
  33. data/docs/spec/examples/match-operator.json +186 -0
  34. data/docs/spec/examples/nth-occurrence-operator.json +300 -0
  35. data/docs/spec/examples/numeric-filter-operator.json +77 -0
  36. data/docs/spec/examples/one-in-two-out-operator.json +158 -0
  37. data/docs/spec/examples/person-filter-operator.json +919 -0
  38. data/docs/spec/examples/person-operator.json +274 -0
  39. data/docs/spec/examples/place-of-service-filter-operator.json +57 -0
  40. data/docs/spec/examples/provenance-operator.json +148 -0
  41. data/docs/spec/examples/provider-filter-operator.json +77 -0
  42. data/docs/spec/examples/race-operator.json +131 -0
  43. data/docs/spec/examples/recall-operator.json +289 -0
  44. data/docs/spec/examples/snf-operator.json +40 -0
  45. data/docs/spec/examples/time-window-operator.json +736 -0
  46. data/docs/spec/examples/trim-date-end-operator.json +201 -0
  47. data/docs/spec/examples/trim-date-start-operator.json +201 -0
  48. data/docs/spec/examples/union-operator.json +547 -0
  49. data/docs/spec/examples/vocabulary-operator.json +232 -0
  50. data/lib/conceptql/behaviors/metadatable.rb +68 -2
  51. data/lib/conceptql/behaviors/provenanceable.rb +4 -1
  52. data/lib/conceptql/behaviors/utilizable.rb +3 -0
  53. data/lib/conceptql/code_case_mismatch_error.rb +50 -0
  54. data/lib/conceptql/data_model/gdm.rb +23 -2
  55. data/lib/conceptql/diagram_renderer/app.rb +59 -0
  56. data/lib/conceptql/diagram_renderer/configuration.rb +87 -0
  57. data/lib/conceptql/diagram_renderer/diagram_data.rb +80 -0
  58. data/lib/conceptql/diagram_renderer/drawing.rb +255 -0
  59. data/lib/conceptql/diagram_renderer/geometry.rb +380 -0
  60. data/lib/conceptql/diagram_renderer/input_error.rb +11 -0
  61. data/lib/conceptql/diagram_renderer/js_format.rb +112 -0
  62. data/lib/conceptql/diagram_renderer/resvg.rb +120 -0
  63. data/lib/conceptql/diagram_renderer/sprite.rb +73 -0
  64. data/lib/conceptql/diagram_renderer/static.rb +70 -0
  65. data/lib/conceptql/diagram_renderer/svg.rb +73 -0
  66. data/lib/conceptql/diagram_renderer/tree_layout.rb +287 -0
  67. data/lib/conceptql/diagram_renderer.rb +82 -0
  68. data/lib/conceptql/lexicon/lexicon_strategy.rb +16 -0
  69. data/lib/conceptql/lexicon.rb +63 -11
  70. data/lib/conceptql/nodifier.rb +5 -3
  71. data/lib/conceptql/operators/after.rb +15 -1
  72. data/lib/conceptql/operators/any_overlap.rb +6 -1
  73. data/lib/conceptql/operators/before.rb +11 -1
  74. data/lib/conceptql/operators/binary_operator_operator.rb +12 -2
  75. data/lib/conceptql/operators/co_reported.rb +9 -4
  76. data/lib/conceptql/operators/contains.rb +6 -1
  77. data/lib/conceptql/operators/count.rb +2 -0
  78. data/lib/conceptql/operators/date_range.rb +15 -3
  79. data/lib/conceptql/operators/death.rb +5 -1
  80. data/lib/conceptql/operators/dedup.rb +2 -0
  81. data/lib/conceptql/operators/during.rb +6 -1
  82. data/lib/conceptql/operators/episode.rb +13 -2
  83. data/lib/conceptql/operators/equal.rb +11 -1
  84. data/lib/conceptql/operators/ethnicity.rb +19 -7
  85. data/lib/conceptql/operators/except.rb +10 -1
  86. data/lib/conceptql/operators/filter.rb +6 -1
  87. data/lib/conceptql/operators/first.rb +19 -9
  88. data/lib/conceptql/operators/from.rb +3 -0
  89. data/lib/conceptql/operators/gender.rb +10 -2
  90. data/lib/conceptql/operators/hospice.rb +7 -1
  91. data/lib/conceptql/operators/hospitalization.rb +6 -1
  92. data/lib/conceptql/operators/information_periods.rb +26 -7
  93. data/lib/conceptql/operators/invalid.rb +4 -0
  94. data/lib/conceptql/operators/last.rb +19 -9
  95. data/lib/conceptql/operators/match.rb +6 -1
  96. data/lib/conceptql/operators/multiple_vocabularies.rb +17 -3
  97. data/lib/conceptql/operators/numeric.rb +4 -0
  98. data/lib/conceptql/operators/numeric_filter.rb +13 -3
  99. data/lib/conceptql/operators/occurrence.rb +33 -12
  100. data/lib/conceptql/operators/one_in_two_out.rb +22 -5
  101. data/lib/conceptql/operators/operator.rb +8 -4
  102. data/lib/conceptql/operators/person.rb +5 -1
  103. data/lib/conceptql/operators/person_filter.rb +14 -1
  104. data/lib/conceptql/operators/place_of_service_filter.rb +14 -3
  105. data/lib/conceptql/operators/provenance.rb +17 -8
  106. data/lib/conceptql/operators/provider_filter.rb +18 -6
  107. data/lib/conceptql/operators/race.rb +14 -9
  108. data/lib/conceptql/operators/read.rb +11 -1
  109. data/lib/conceptql/operators/recall.rb +34 -2
  110. data/lib/conceptql/operators/snf.rb +7 -1
  111. data/lib/conceptql/operators/sum.rb +4 -0
  112. data/lib/conceptql/operators/temporal_operator.rb +4 -2
  113. data/lib/conceptql/operators/time_window.rb +27 -4
  114. data/lib/conceptql/operators/trim_date.rb +6 -14
  115. data/lib/conceptql/operators/trim_date_end.rb +9 -3
  116. data/lib/conceptql/operators/trim_date_start.rb +9 -3
  117. data/lib/conceptql/operators/union.rb +13 -1
  118. data/lib/conceptql/operators/vocabulary.rb +80 -6
  119. data/lib/conceptql/paths.rb +9 -1
  120. data/lib/conceptql/version.rb +1 -1
  121. data/lib/conceptql/vocabularies/drg_systems.rb +3 -2
  122. data/lib/conceptql/vocabularies/entry.rb +14 -11
  123. data/lib/conceptql/vocabularies/vocabulary_class_factory.rb +2 -1
  124. data/lib/conceptql.rb +3 -0
  125. metadata +75 -2
  126. data/doc/spec.md +0 -2091
data/docs/spec/examples/filter-operator.json ADDED
@@ -0,0 +1,218 @@
1
+ {
2
+ "spec_id": "filter-operator",
3
+ "examples": [
4
+ {
5
+ "title": "MIs that are a patient's first diagnosis of MI or diabetes",
6
+ "statement": [
7
+ "filter",
8
+ {
9
+ "left": ["icd9", "412"],
10
+ "right": ["first", ["union", ["icd9", "412"], ["icd9", "250.01"]]]
11
+ }
12
+ ],
13
+ "help": true,
14
+ "columns": [
15
+ "person_id",
16
+ "criterion_id",
17
+ "criterion_table",
18
+ "criterion_domain",
19
+ "start_date",
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+ "end_date",
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+ "source_value"
22
+ ],
23
+ "rows": [
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+ [
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+ 11,
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+ 82614,
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+ "observations",
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+ "condition_occurrence",
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+ "2008-10-29",
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+ "2008-10-29",
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+ "412"
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+ ],
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+ [
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+ 17,
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+ 27269,
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+ "observations",
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+ "condition_occurrence",
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+ "2008-08-25",
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+ "2008-08-25",
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+ "412"
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+ ],
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+ [
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+ 38,
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+ 40556,
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+ "observations",
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+ "condition_occurrence",
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+ "2010-02-12",
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+ "2010-02-12",
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+ "412"
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+ ],
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+ [
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+ 54,
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+ 74606,
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+ "observations",
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+ "condition_occurrence",
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+ "2008-06-05",
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+ "2008-06-05",
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+ "412"
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+ ],
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+ [
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+ 60,
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+ 986,
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+ "observations",
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+ "condition_occurrence",
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+ "2009-07-19",
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+ "2009-07-22",
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+ "412"
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+ ],
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+ [
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+ 66,
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+ 16171,
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+ "observations",
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+ "condition_occurrence",
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+ "2009-07-25",
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+ "2009-07-25",
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+ "412"
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+ ],
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+ [
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+ 73,
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+ 52843,
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+ "observations",
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+ "condition_occurrence",
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+ "2008-11-16",
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+ "2008-11-16",
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+ "412"
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+ ],
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+ [
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+ 81,
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+ 1405,
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+ "observations",
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+ "condition_occurrence",
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+ "2009-01-28",
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+ "2009-01-30",
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+ "412"
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+ ],
96
+ [
97
+ 88,
98
+ 1572,
99
+ "observations",
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+ "condition_occurrence",
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+ "2009-01-03",
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+ "2009-01-09",
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+ "412"
104
+ ],
105
+ [
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+ 90,
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+ 33940,
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+ "observations",
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+ "condition_occurrence",
110
+ "2010-05-26",
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+ "2010-05-26",
112
+ "412"
113
+ ]
114
+ ],
115
+ "tree": {
116
+ "format": "conceptql-diagram/v1",
117
+ "statements": [
118
+ {
119
+ "name": "filter",
120
+ "base": "filter",
121
+ "humanName": "Filter",
122
+ "outputTypes": ["condition_occurrence"],
123
+ "parameters": {},
124
+ "values": [],
125
+ "children": [
126
+ {
127
+ "name": "icd9",
128
+ "base": "selection",
129
+ "humanName": "ICD-9 CM",
130
+ "vocabularyId": "ICD9CM",
131
+ "outputTypes": ["condition_occurrence"],
132
+ "parameters": {},
133
+ "values": ["412"],
134
+ "children": [],
135
+ "counts": {
136
+ "condition_occurrence": {
137
+ "rows": 48,
138
+ "n": 37
139
+ }
140
+ }
141
+ },
142
+ {
143
+ "name": "first",
144
+ "base": "temporal",
145
+ "humanName": "First",
146
+ "outputTypes": ["condition_occurrence"],
147
+ "parameters": {},
148
+ "values": [],
149
+ "children": [
150
+ {
151
+ "name": "union",
152
+ "base": "set",
153
+ "humanName": "Union",
154
+ "outputTypes": ["condition_occurrence"],
155
+ "parameters": {},
156
+ "values": [],
157
+ "children": [
158
+ {
159
+ "name": "icd9",
160
+ "base": "selection",
161
+ "humanName": "ICD-9 CM",
162
+ "vocabularyId": "ICD9CM",
163
+ "outputTypes": ["condition_occurrence"],
164
+ "parameters": {},
165
+ "values": ["412"],
166
+ "children": [],
167
+ "counts": {
168
+ "condition_occurrence": {
169
+ "rows": 48,
170
+ "n": 37
171
+ }
172
+ }
173
+ },
174
+ {
175
+ "name": "icd9",
176
+ "base": "selection",
177
+ "humanName": "ICD-9 CM",
178
+ "vocabularyId": "ICD9CM",
179
+ "outputTypes": ["condition_occurrence"],
180
+ "parameters": {},
181
+ "values": ["250.01"],
182
+ "children": [],
183
+ "counts": {
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+ "condition_occurrence": {
185
+ "rows": 82,
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+ "n": 45
187
+ }
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+ }
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+ }
190
+ ],
191
+ "counts": {
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+ "condition_occurrence": {
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+ "rows": 130,
194
+ "n": 68
195
+ }
196
+ }
197
+ }
198
+ ],
199
+ "counts": {
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+ "condition_occurrence": {
201
+ "rows": 68,
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+ "n": 68
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+ }
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+ }
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+ }
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+ ],
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+ "counts": {
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+ "condition_occurrence": {
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+ "rows": 32,
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+ "n": 32
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+ }
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+ }
213
+ }
214
+ ]
215
+ }
216
+ }
217
+ ]
218
+ }
data/docs/spec/examples/first-operator.json ADDED
@@ -0,0 +1,148 @@
1
+ {
2
+ "spec_id": "first-operator",
3
+ "examples": [
4
+ {
5
+ "title": "For each patient, select the Condition that represents the first occurrence of an MI",
6
+ "statement": ["first", ["icd9", "412"]],
7
+ "help": true,
8
+ "columns": [
9
+ "person_id",
10
+ "criterion_id",
11
+ "criterion_table",
12
+ "criterion_domain",
13
+ "start_date",
14
+ "end_date",
15
+ "source_value"
16
+ ],
17
+ "rows": [
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+ [
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+ 11,
20
+ 82614,
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+ "observations",
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+ "condition_occurrence",
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+ "2008-10-29",
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+ "2008-10-29",
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+ "412"
26
+ ],
27
+ [
28
+ 17,
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+ 27269,
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+ "observations",
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+ "condition_occurrence",
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+ "2008-08-25",
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+ "2008-08-25",
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+ "412"
35
+ ],
36
+ [
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+ 38,
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+ 40556,
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+ "observations",
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+ "condition_occurrence",
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+ "2010-02-12",
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+ "2010-02-12",
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+ "412"
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+ ],
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+ [
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+ 54,
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+ 74606,
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+ "observations",
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+ "condition_occurrence",
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+ "2008-06-05",
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+ "2008-06-05",
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+ "412"
53
+ ],
54
+ [
55
+ 60,
56
+ 986,
57
+ "observations",
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+ "condition_occurrence",
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+ "2009-07-19",
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+ "2009-07-22",
61
+ "412"
62
+ ],
63
+ [
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+ 66,
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+ 16171,
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+ "observations",
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+ "condition_occurrence",
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+ "2009-07-25",
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+ "2009-07-25",
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+ "412"
71
+ ],
72
+ [
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+ 73,
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+ 52843,
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+ "observations",
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+ "condition_occurrence",
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+ "2008-11-16",
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+ "2008-11-16",
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+ "412"
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+ ],
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+ [
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+ 77,
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+ 58165,
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+ "observations",
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+ "condition_occurrence",
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+ "2010-10-06",
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+ "2010-10-06",
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+ "412"
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+ ],
90
+ [
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+ 81,
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+ 1405,
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+ "observations",
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+ "condition_occurrence",
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+ "2009-01-28",
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+ "2009-01-30",
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+ "412"
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+ ],
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+ [
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+ 88,
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+ 1572,
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+ "observations",
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+ "condition_occurrence",
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+ "2009-01-03",
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+ "2009-01-09",
106
+ "412"
107
+ ]
108
+ ],
109
+ "tree": {
110
+ "format": "conceptql-diagram/v1",
111
+ "statements": [
112
+ {
113
+ "name": "first",
114
+ "base": "temporal",
115
+ "humanName": "First",
116
+ "outputTypes": ["condition_occurrence"],
117
+ "parameters": {},
118
+ "values": [],
119
+ "children": [
120
+ {
121
+ "name": "icd9",
122
+ "base": "selection",
123
+ "humanName": "ICD-9 CM",
124
+ "vocabularyId": "ICD9CM",
125
+ "outputTypes": ["condition_occurrence"],
126
+ "parameters": {},
127
+ "values": ["412"],
128
+ "children": [],
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+ "counts": {
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+ "condition_occurrence": {
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+ "rows": 48,
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+ "n": 37
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+ }
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+ }
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+ }
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+ ],
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+ "counts": {
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+ "rows": 37,
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+ "n": 37
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+ }
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+ }
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+ }
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+ ]
145
+ }
146
+ }
147
+ ]
148
+ }
data/docs/spec/examples/gender-operator.json ADDED
@@ -0,0 +1,257 @@
1
+ {
2
+ "spec_id": "gender-operator",
3
+ "examples": [
4
+ {
5
+ "title": "All female patients",
6
+ "statement": ["gender", "Female"],
7
+ "help": true,
8
+ "columns": [
9
+ "person_id",
10
+ "criterion_id",
11
+ "criterion_table",
12
+ "criterion_domain",
13
+ "start_date",
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+ "end_date",
15
+ "source_value"
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+ ],
17
+ "rows": [
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+ [
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+ 3,
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+ 3,
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+ "patients",
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+ "person",
23
+ "1936-09-01",
24
+ "1936-09-01",
25
+ "0001FDD721E223DC"
26
+ ],
27
+ [
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+ 9,
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+ 9,
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+ "patients",
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+ "person",
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+ "1976-09-01",
33
+ "1976-09-01",
34
+ "000345A39D4157C9"
35
+ ],
36
+ [
37
+ 10,
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+ 10,
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+ "patients",
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+ "person",
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+ "1938-10-01",
42
+ "1938-10-01",
43
+ "00036A21B65B0206"
44
+ ],
45
+ [
46
+ 11,
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+ 11,
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+ "patients",
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+ "person",
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+ "1934-02-01",
51
+ "1934-02-01",
52
+ "000489E7EAAD463F"
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+ ],
54
+ [
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+ 13,
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+ 13,
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+ "patients",
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+ "person",
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+ "1936-07-01",
60
+ "1936-07-01",
61
+ "0004F0ABD505251D"
62
+ ],
63
+ [
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+ 15,
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+ 15,
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+ "patients",
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+ "person",
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+ "1936-03-01",
69
+ "1936-03-01",
70
+ "00070B63745BE497"
71
+ ],
72
+ [
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+ 17,
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+ 17,
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+ "patients",
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+ "person",
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+ "1919-09-01",
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+ "1919-09-01",
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+ "0007F12A492FD25D"
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+ ],
81
+ [
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+ 18,
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+ 18,
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+ "patients",
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+ "person",
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+ "1919-10-01",
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+ "1919-10-01",
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+ "000A005BA0BED3EA"
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+ ],
90
+ [
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+ 19,
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+ 19,
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+ "patients",
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+ "person",
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+ "1942-07-01",
96
+ "1942-07-01",
97
+ "000B4662348C35B4"
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+ ],
99
+ [
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+ 26,
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+ 26,
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+ "patients",
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+ "person",
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+ "1939-12-01",
105
+ "1939-12-01",
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+ "0010D6F80D245D62"
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+ ]
108
+ ],
109
+ "tree": {
110
+ "format": "conceptql-diagram/v1",
111
+ "statements": [
112
+ {
113
+ "name": "gender",
114
+ "base": "selection",
115
+ "humanName": "Gender",
116
+ "outputTypes": ["person"],
117
+ "parameters": {},
118
+ "values": ["Female"],
119
+ "children": [],
120
+ "counts": {
121
+ "person": {
122
+ "rows": 125,
123
+ "n": 125
124
+ }
125
+ }
126
+ }
127
+ ]
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data/docs/spec/examples/hospice-operator.json ADDED
@@ -0,0 +1,40 @@
1
+ {
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+ "spec_id": "hospice-operator",
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