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/person-operator.json ADDED
@@ -0,0 +1,274 @@
1
+ {
2
+ "spec_id": "person-operator",
3
+ "examples": [
4
+ {
5
+ "title": "All patients",
6
+ "statement": ["person"],
7
+ "help": true,
8
+ "columns": [
9
+ "person_id",
10
+ "criterion_id",
11
+ "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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+ 1,
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+ 1,
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+ "patients",
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+ "person",
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+ "1923-05-01",
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+ "1923-05-01",
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+ "00013D2EFD8E45D1"
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+ ],
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+ [
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+ 2,
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+ 2,
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+ "patients",
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+ "person",
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+ "1943-01-01",
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+ "1943-01-01",
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+ "00016F745862898F"
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+ ],
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+ [
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+ 3,
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+ 3,
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+ "patients",
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+ "person",
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+ "1936-09-01",
42
+ "1936-09-01",
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+ "0001FDD721E223DC"
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+ ],
45
+ [
46
+ 4,
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+ 4,
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+ "patients",
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+ "person",
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+ "1941-06-01",
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+ "1941-06-01",
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+ "00021CA6FF03E670"
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+ ],
54
+ [
55
+ 5,
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+ 5,
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+ "patients",
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+ "person",
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+ "1936-08-01",
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+ "1936-08-01",
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+ "00024B3D2352D2D0"
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+ ],
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+ [
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+ 6,
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+ 6,
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+ "patients",
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+ "person",
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+ "1943-10-01",
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+ "1943-10-01",
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+ "0002DAE1C81CC70D"
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+ ],
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+ [
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+ 7,
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+ 7,
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+ "patients",
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+ "person",
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+ "1922-07-01",
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+ "1922-07-01",
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+ "0002F28CE057345B"
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+ ],
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+ [
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+ 8,
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+ 8,
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+ "patients",
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+ "person",
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+ "1935-09-01",
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+ "1935-09-01",
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+ "000308435E3E5B76"
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+ ],
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+ [
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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",
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+ "1976-09-01",
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+ "000345A39D4157C9"
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+ ],
99
+ [
100
+ 10,
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+ 10,
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+ "patients",
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+ "person",
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+ "1938-10-01",
105
+ "1938-10-01",
106
+ "00036A21B65B0206"
107
+ ]
108
+ ],
109
+ "tree": {
110
+ "format": "conceptql-diagram/v1",
111
+ "statements": [
112
+ {
113
+ "name": "person",
114
+ "base": "cast",
115
+ "humanName": "Person",
116
+ "outputTypes": ["person"],
117
+ "parameters": {},
118
+ "values": [],
119
+ "children": [],
120
+ "counts": {
121
+ "person": {
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+ "rows": 249,
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+ "n": 249
124
+ }
125
+ }
126
+ }
127
+ ]
128
+ }
129
+ },
130
+ {
131
+ "title": "The patients with an old myocardial infarction (ICD-9-CM 412)",
132
+ "statement": ["person", ["icd9cm", "412"]],
133
+ "help": true,
134
+ "columns": [
135
+ "person_id",
136
+ "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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+ 11,
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+ 11,
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+ "patients",
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+ "person",
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+ "1934-02-01",
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+ "1934-02-01",
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+ "000489E7EAAD463F"
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+ ],
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+ [
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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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+ ],
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+ [
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+ 38,
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+ 38,
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+ "patients",
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+ "person",
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+ "1922-12-01",
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+ "1922-12-01",
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+ "001731EB127233DA"
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+ ],
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+ [
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+ 54,
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+ 54,
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+ "patients",
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+ "person",
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+ "1931-02-01",
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+ "1931-02-01",
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+ "001CAFF084B21E14"
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+ ],
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+ [
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+ 60,
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+ 60,
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+ "patients",
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+ "person",
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+ "1925-07-01",
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+ "1925-07-01",
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+ "001EA2F4DB30F105"
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+ ],
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+ [
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+ 66,
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+ 66,
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+ "patients",
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+ "person",
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+ "1920-04-01",
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+ "1920-04-01",
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+ "0021B3C854C968C8"
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+ ],
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+ [
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+ 73,
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+ 73,
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+ "patients",
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+ "person",
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+ "1925-09-01",
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+ "1925-09-01",
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+ "00237322613CFC3C"
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+ ],
207
+ [
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+ 77,
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+ 77,
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+ "patients",
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+ "person",
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+ "1929-03-01",
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+ "1929-03-01",
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+ "00244B6D9AB50F9B"
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+ ],
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+ [
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+ 81,
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+ 81,
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+ "patients",
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+ "person",
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+ "1940-06-01",
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+ "1940-06-01",
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+ "0024E5A7B7272E75"
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+ ],
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+ [
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+ 88,
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+ 88,
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+ "patients",
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+ "person",
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+ "1922-05-01",
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+ "1922-05-01",
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+ "00291F39917544B1"
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+ ]
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+ ],
235
+ "tree": {
236
+ "format": "conceptql-diagram/v1",
237
+ "statements": [
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+ {
239
+ "name": "person",
240
+ "base": "cast",
241
+ "humanName": "Person",
242
+ "outputTypes": ["person"],
243
+ "parameters": {},
244
+ "values": [],
245
+ "children": [
246
+ {
247
+ "name": "icd9cm",
248
+ "base": "selection",
249
+ "humanName": "ICD-9 CM",
250
+ "vocabularyId": "ICD9CM",
251
+ "outputTypes": ["condition_occurrence"],
252
+ "parameters": {},
253
+ "values": ["412"],
254
+ "children": [],
255
+ "counts": {
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+ "condition_occurrence": {
257
+ "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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+ "person": {
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+ "rows": 37,
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+ "n": 37
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+ }
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+ }
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+ }
270
+ ]
271
+ }
272
+ }
273
+ ]
274
+ }
data/docs/spec/examples/place-of-service-filter-operator.json ADDED
@@ -0,0 +1,57 @@
1
+ {
2
+ "spec_id": "place-of-service-filter-operator",
3
+ "examples": [
4
+ {
5
+ "title": "Diabetes diagnoses (ICD-9 250.00) with the place of service outpatient hospital (22)",
6
+ "statement": ["place_of_service_filter", 22, ["icd9", "250.00"]],
7
+ "help": false,
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": [],
18
+ "tree": {
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+ "format": "conceptql-diagram/v1",
20
+ "statements": [
21
+ {
22
+ "name": "place_of_service_filter",
23
+ "base": "temporal",
24
+ "humanName": "Place Of Service Filter",
25
+ "outputTypes": ["condition_occurrence"],
26
+ "parameters": {},
27
+ "values": [22],
28
+ "children": [
29
+ {
30
+ "name": "icd9",
31
+ "base": "selection",
32
+ "humanName": "ICD-9 CM",
33
+ "vocabularyId": "ICD9CM",
34
+ "outputTypes": ["condition_occurrence"],
35
+ "parameters": {},
36
+ "values": ["250.00"],
37
+ "children": [],
38
+ "counts": {
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+ "condition_occurrence": {
40
+ "rows": 1036,
41
+ "n": 162
42
+ }
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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": 0,
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+ "n": 0
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+ }
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+ }
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+ }
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+ ]
54
+ }
55
+ }
56
+ ]
57
+ }
data/docs/spec/examples/provenance-operator.json ADDED
@@ -0,0 +1,148 @@
1
+ {
2
+ "spec_id": "provenance-operator",
3
+ "examples": [
4
+ {
5
+ "title": "Diabetes diagnoses (ICD-9 250.00) from inpatient files",
6
+ "statement": ["provenance", "inpatient", ["icd9", "250.00"]],
7
+ "help": true,
8
+ "columns": [
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+ "person_id",
10
+ "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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+ 929,
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+ "observations",
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+ "condition_occurrence",
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+ "2010-05-22",
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+ "2010-06-12",
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+ "25000"
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+ ],
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+ [
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+ 21,
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+ 1024,
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+ "observations",
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+ "condition_occurrence",
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+ "2008-10-15",
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+ "2008-10-21",
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+ "25000"
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+ ],
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+ [
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+ 28,
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+ 1446,
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+ "observations",
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+ "condition_occurrence",
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+ "2008-04-21",
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+ "2008-04-26",
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+ "25000"
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+ ],
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+ [
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+ 32,
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+ "observations",
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+ "condition_occurrence",
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+ "2010-08-30",
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+ "2010-09-07",
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+ "25000"
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+ ],
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+ [
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+ 37,
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+ 310,
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+ "observations",
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+ "condition_occurrence",
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+ "2009-01-19",
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+ "2009-01-20",
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+ "25000"
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+ ],
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+ [
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+ 60,
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+ 983,
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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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+ "25000"
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+ ],
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+ [
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+ 66,
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+ 1146,
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+ "observations",
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+ "condition_occurrence",
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+ "2008-12-08",
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+ "2008-12-13",
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+ "25000"
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+ ],
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+ [
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+ 66,
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+ 1507,
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+ "observations",
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+ "condition_occurrence",
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+ "2009-12-29",
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+ "2009-12-31",
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+ "25000"
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+ ],
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+ [
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+ 68,
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+ 19,
93
+ "observations",
94
+ "condition_occurrence",
95
+ "2008-04-19",
96
+ "2008-04-23",
97
+ "25000"
98
+ ],
99
+ [
100
+ 68,
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+ 1596,
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+ "observations",
103
+ "condition_occurrence",
104
+ "2008-11-10",
105
+ "2008-11-11",
106
+ "25000"
107
+ ]
108
+ ],
109
+ "tree": {
110
+ "format": "conceptql-diagram/v1",
111
+ "statements": [
112
+ {
113
+ "name": "provenance",
114
+ "base": "temporal",
115
+ "humanName": "Provenance",
116
+ "outputTypes": ["condition_occurrence"],
117
+ "parameters": {},
118
+ "values": ["inpatient"],
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": ["250.00"],
128
+ "children": [],
129
+ "counts": {
130
+ "condition_occurrence": {
131
+ "rows": 1036,
132
+ "n": 162
133
+ }
134
+ }
135
+ }
136
+ ],
137
+ "counts": {
138
+ "condition_occurrence": {
139
+ "rows": 35,
140
+ "n": 29
141
+ }
142
+ }
143
+ }
144
+ ]
145
+ }
146
+ }
147
+ ]
148
+ }
data/docs/spec/examples/provider-filter-operator.json ADDED
@@ -0,0 +1,77 @@
1
+ {
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