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/nth-occurrence-operator.json ADDED
@@ -0,0 +1,300 @@
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+ {
2
+ "spec_id": "nth-occurrence-operator",
3
+ "examples": [
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+ {
5
+ "title": "For each patient, select the Condition that represents the second occurrence of an MI",
6
+ "statement": ["occurrence", 2, ["icd9", "412"]],
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+ "help": true,
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+ "columns": [
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+ "person_id",
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+ "criterion_id",
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+ "criterion_table",
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+ "criterion_domain",
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+ "start_date",
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+ "end_date",
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+ "source_value"
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+ ],
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+ "rows": [
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+ [
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+ 17,
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+ "observations",
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+ "2009-04-30",
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+ "412"
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+ ],
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+ [
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+ "condition_occurrence",
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+ "412"
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+ ],
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+ [
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+ 152,
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+ "observations",
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+ "condition_occurrence",
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+ "2010-11-22",
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+ "2010-11-22",
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+ "412"
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+ ],
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+ [
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+ 177,
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+ "condition_occurrence",
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+ "2009-06-13",
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+ "2009-06-16",
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+ "412"
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+ ],
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+ [
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+ 187,
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+ "observations",
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+ "condition_occurrence",
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+ "2010-12-26",
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+ "2010-12-26",
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+ "412"
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+ ],
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+ [
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+ 212,
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+ 34052,
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+ "observations",
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+ "condition_occurrence",
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+ "2009-10-07",
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+ "412"
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+ ],
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+ [
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+ 213,
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+ ],
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+ [
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+ "412"
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+ ],
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+ [
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+ 220,
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+ "observations",
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+ "condition_occurrence",
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+ "2009-10-31",
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+ "2009-10-31",
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+ "412"
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+ ],
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+ [
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+ 223,
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+ "observations",
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+ "condition_occurrence",
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+ "2008-10-31",
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+ "2008-10-31",
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+ "412"
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+ ]
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+ ],
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+ "tree": {
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+ "format": "conceptql-diagram/v1",
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+ "statements": [
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+ {
113
+ "name": "occurrence",
114
+ "base": "temporal",
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+ "humanName": "Nth Occurrence",
116
+ "outputTypes": ["condition_occurrence"],
117
+ "parameters": {},
118
+ "values": [2],
119
+ "children": [
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+ {
121
+ "name": "icd9",
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+ "base": "selection",
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+ "humanName": "ICD-9 CM",
124
+ "vocabularyId": "ICD9CM",
125
+ "outputTypes": ["condition_occurrence"],
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+ "parameters": {},
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+ "values": ["412"],
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+ "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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+ "condition_occurrence": {
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+ "rows": 11,
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+ "n": 11
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+ }
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+ }
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+ }
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+ ]
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+ }
146
+ },
147
+ {
148
+ "title": "For each patient, the first record on the second day with any of these diagnoses",
149
+ "statement": [
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+ "occurrence",
151
+ 2,
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+ ["icd9", "410.00", "410.01", "250.00", "250.01"],
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+ {
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+ "group_by_date": true
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+ }
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+ ],
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+ "help": true,
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+ "columns": [
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+ "person_id",
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+ "criterion_id",
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+ "criterion_table",
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+ "criterion_domain",
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+ "start_date",
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+ "end_date",
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+ "source_value"
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+ ],
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+ "rows": [
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+ ],
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+ "tree": {
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+ "format": "conceptql-diagram/v1",
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+ "statements": [
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+ {
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+ "name": "occurrence",
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+ "base": "temporal",
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+ "humanName": "Nth Occurrence",
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+ "outputTypes": ["condition_occurrence"],
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+ "parameters": {
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+ "group_by_date": true
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+ },
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+ "values": [2],
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+ "children": [
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+ {
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+ "name": "icd9",
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+ "base": "selection",
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+ "humanName": "ICD-9 CM",
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+ "vocabularyId": "ICD9CM",
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+ "outputTypes": ["condition_occurrence"],
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+ "parameters": {},
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+ "values": ["410.00", "410.01", "250.00", "250.01"],
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+ "children": [],
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+ "n": 163
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+ }
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+ }
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+ ],
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+ "counts": {
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+ "n": 134
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+ }
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+ }
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+ }
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+ ]
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+ }
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+ }
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+ ]
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+ }
data/docs/spec/examples/numeric-filter-operator.json ADDED
@@ -0,0 +1,77 @@
1
+ {
2
+ "spec_id": "numeric-filter-operator",
3
+ "examples": [
4
+ {
5
+ "title": "Hemoglobin A1c results (LOINC 4548-4) with a value from 5 to 7",
6
+ "statement": [
7
+ "numeric_filter",
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+ ["loinc", "4548-4"],
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+ {
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+ "greater_than_or_equal_to": 5,
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+ "less_than_or_equal_to": 7
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+ }
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+ ],
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+ "help": true,
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+ "columns": [
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+ "person_id",
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+ "criterion_id",
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+ "criterion_table",
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+ "criterion_domain",
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+ "start_date",
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+ "end_date",
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+ "source_value"
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+ ],
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+ "rows": [
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+ "4548-4"
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+ ]
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+ ],
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+ "tree": {
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+ "format": "conceptql-diagram/v1",
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+ "statements": [
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+ {
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+ "name": "numeric_filter",
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+ "base": "temporal",
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+ "humanName": "Numeric Filter",
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+ "outputTypes": ["observation"],
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+ "parameters": {
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+ "greater_than_or_equal_to": 5,
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+ "less_than_or_equal_to": 7
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+ },
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+ "values": [],
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+ "children": [
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+ {
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+ "name": "loinc",
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+ "base": "selection",
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+ "humanName": "Logical Observation Identifiers Names and Codes (Regenstrief Institute)",
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+ "vocabularyId": "LOINC",
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+ "outputTypes": ["observation"],
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+ "parameters": {},
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+ "values": ["4548-4"],
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+ "children": [],
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+ "n": 1
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+ }
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+ }
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+ }
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+ ]
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+ }
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+ }
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+ ]
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+ }
data/docs/spec/examples/one-in-two-out-operator.json ADDED
@@ -0,0 +1,158 @@
1
+ {
2
+ "spec_id": "one-in-two-out-operator",
3
+ "examples": [
4
+ {
5
+ "title": "First diabetes diagnosis, either found once in an inpatient record, or twice in outpatient records at least 30 days apart",
6
+ "statement": [
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+ "one_in_two_out",
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+ ["icd9", "250.00"],
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+ {
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+ "outpatient_minimum_gap": "30d",
11
+ "outpatient_event_to_return": "Initial Event"
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+ }
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+ ],
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+ "help": true,
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+ "columns": [
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+ "person_id",
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+ "criterion_id",
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+ "rows": [
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