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.
- checksums.yaml +4 -4
- data/CHANGELOG.md +176 -0
- data/README.md +4 -2
- data/assets/diagram/diagram.css +331 -0
- data/assets/diagram/fonts/OFL.txt +93 -0
- data/assets/diagram/fonts/Roboto-400.ttf +0 -0
- data/assets/diagram/fonts/Roboto-700.ttf +0 -0
- data/assets/diagram/fonts/Roboto-Italic-400.ttf +0 -0
- data/assets/diagram/fonts/Roboto-Italic-Latin.woff2 +0 -0
- data/assets/diagram/fonts/Roboto-Normal-Latin.woff2 +0 -0
- data/assets/diagram/operators.svg +224 -0
- data/config/vocabularies.csv +85 -85
- data/docs/spec/README.md +2624 -0
- data/docs/spec/examples/after-operator.json +562 -0
- data/docs/spec/examples/any-overlap-operator.json +106 -0
- data/docs/spec/examples/before-operator.json +437 -0
- data/docs/spec/examples/co-reported-operator.json +168 -0
- data/docs/spec/examples/contains-operator.json +97 -0
- data/docs/spec/examples/date-range-operator.json +275 -0
- data/docs/spec/examples/death-operator.json +103 -0
- data/docs/spec/examples/during-operator.json +178 -0
- data/docs/spec/examples/episode-operator.json +80 -0
- data/docs/spec/examples/equal-operator.json +79 -0
- data/docs/spec/examples/ethnicity-operator.json +86 -0
- data/docs/spec/examples/except-operator.json +536 -0
- data/docs/spec/examples/filter-operator.json +218 -0
- data/docs/spec/examples/first-operator.json +148 -0
- data/docs/spec/examples/gender-operator.json +257 -0
- data/docs/spec/examples/hospice-operator.json +40 -0
- data/docs/spec/examples/hospitalization-operator.json +131 -0
- data/docs/spec/examples/information-periods-operator.json +131 -0
- data/docs/spec/examples/last-operator.json +148 -0
- data/docs/spec/examples/match-operator.json +186 -0
- data/docs/spec/examples/nth-occurrence-operator.json +300 -0
- data/docs/spec/examples/numeric-filter-operator.json +77 -0
- data/docs/spec/examples/one-in-two-out-operator.json +158 -0
- data/docs/spec/examples/person-filter-operator.json +919 -0
- data/docs/spec/examples/person-operator.json +274 -0
- data/docs/spec/examples/place-of-service-filter-operator.json +57 -0
- data/docs/spec/examples/provenance-operator.json +148 -0
- data/docs/spec/examples/provider-filter-operator.json +77 -0
- data/docs/spec/examples/race-operator.json +131 -0
- data/docs/spec/examples/recall-operator.json +289 -0
- data/docs/spec/examples/snf-operator.json +40 -0
- data/docs/spec/examples/time-window-operator.json +736 -0
- data/docs/spec/examples/trim-date-end-operator.json +201 -0
- data/docs/spec/examples/trim-date-start-operator.json +201 -0
- data/docs/spec/examples/union-operator.json +547 -0
- data/docs/spec/examples/vocabulary-operator.json +232 -0
- data/lib/conceptql/behaviors/metadatable.rb +68 -2
- data/lib/conceptql/behaviors/provenanceable.rb +4 -1
- data/lib/conceptql/behaviors/utilizable.rb +3 -0
- data/lib/conceptql/code_case_mismatch_error.rb +50 -0
- data/lib/conceptql/data_model/gdm.rb +23 -2
- data/lib/conceptql/diagram_renderer/app.rb +59 -0
- data/lib/conceptql/diagram_renderer/configuration.rb +87 -0
- data/lib/conceptql/diagram_renderer/diagram_data.rb +80 -0
- data/lib/conceptql/diagram_renderer/drawing.rb +255 -0
- data/lib/conceptql/diagram_renderer/geometry.rb +380 -0
- data/lib/conceptql/diagram_renderer/input_error.rb +11 -0
- data/lib/conceptql/diagram_renderer/js_format.rb +112 -0
- data/lib/conceptql/diagram_renderer/resvg.rb +120 -0
- data/lib/conceptql/diagram_renderer/sprite.rb +73 -0
- data/lib/conceptql/diagram_renderer/static.rb +70 -0
- data/lib/conceptql/diagram_renderer/svg.rb +73 -0
- data/lib/conceptql/diagram_renderer/tree_layout.rb +287 -0
- data/lib/conceptql/diagram_renderer.rb +82 -0
- data/lib/conceptql/lexicon/lexicon_strategy.rb +16 -0
- data/lib/conceptql/lexicon.rb +63 -11
- data/lib/conceptql/nodifier.rb +5 -3
- data/lib/conceptql/operators/after.rb +15 -1
- data/lib/conceptql/operators/any_overlap.rb +6 -1
- data/lib/conceptql/operators/before.rb +11 -1
- data/lib/conceptql/operators/binary_operator_operator.rb +12 -2
- data/lib/conceptql/operators/co_reported.rb +9 -4
- data/lib/conceptql/operators/contains.rb +6 -1
- data/lib/conceptql/operators/count.rb +2 -0
- data/lib/conceptql/operators/date_range.rb +15 -3
- data/lib/conceptql/operators/death.rb +5 -1
- data/lib/conceptql/operators/dedup.rb +2 -0
- data/lib/conceptql/operators/during.rb +6 -1
- data/lib/conceptql/operators/episode.rb +13 -2
- data/lib/conceptql/operators/equal.rb +11 -1
- data/lib/conceptql/operators/ethnicity.rb +19 -7
- data/lib/conceptql/operators/except.rb +10 -1
- data/lib/conceptql/operators/filter.rb +6 -1
- data/lib/conceptql/operators/first.rb +19 -9
- data/lib/conceptql/operators/from.rb +3 -0
- data/lib/conceptql/operators/gender.rb +10 -2
- data/lib/conceptql/operators/hospice.rb +7 -1
- data/lib/conceptql/operators/hospitalization.rb +6 -1
- data/lib/conceptql/operators/information_periods.rb +26 -7
- data/lib/conceptql/operators/invalid.rb +4 -0
- data/lib/conceptql/operators/last.rb +19 -9
- data/lib/conceptql/operators/match.rb +6 -1
- data/lib/conceptql/operators/multiple_vocabularies.rb +17 -3
- data/lib/conceptql/operators/numeric.rb +4 -0
- data/lib/conceptql/operators/numeric_filter.rb +13 -3
- data/lib/conceptql/operators/occurrence.rb +33 -12
- data/lib/conceptql/operators/one_in_two_out.rb +22 -5
- data/lib/conceptql/operators/operator.rb +8 -4
- data/lib/conceptql/operators/person.rb +5 -1
- data/lib/conceptql/operators/person_filter.rb +14 -1
- data/lib/conceptql/operators/place_of_service_filter.rb +14 -3
- data/lib/conceptql/operators/provenance.rb +17 -8
- data/lib/conceptql/operators/provider_filter.rb +18 -6
- data/lib/conceptql/operators/race.rb +14 -9
- data/lib/conceptql/operators/read.rb +11 -1
- data/lib/conceptql/operators/recall.rb +34 -2
- data/lib/conceptql/operators/snf.rb +7 -1
- data/lib/conceptql/operators/sum.rb +4 -0
- data/lib/conceptql/operators/temporal_operator.rb +4 -2
- data/lib/conceptql/operators/time_window.rb +27 -4
- data/lib/conceptql/operators/trim_date.rb +6 -14
- data/lib/conceptql/operators/trim_date_end.rb +9 -3
- data/lib/conceptql/operators/trim_date_start.rb +9 -3
- data/lib/conceptql/operators/union.rb +13 -1
- data/lib/conceptql/operators/vocabulary.rb +80 -6
- data/lib/conceptql/paths.rb +9 -1
- data/lib/conceptql/version.rb +1 -1
- data/lib/conceptql/vocabularies/drg_systems.rb +3 -2
- data/lib/conceptql/vocabularies/entry.rb +14 -11
- data/lib/conceptql/vocabularies/vocabulary_class_factory.rb +2 -1
- data/lib/conceptql.rb +3 -0
- metadata +75 -2
- data/doc/spec.md +0 -2091
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+
"2008-11-16",
|
|
257
|
+
"2008-11-16",
|
|
258
|
+
"412"
|
|
259
|
+
],
|
|
260
|
+
[
|
|
261
|
+
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|
|
262
|
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|
|
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"observations",
|
|
264
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+
"condition_occurrence",
|
|
265
|
+
"2010-10-06",
|
|
266
|
+
"2010-10-06",
|
|
267
|
+
"412"
|
|
268
|
+
],
|
|
269
|
+
[
|
|
270
|
+
81,
|
|
271
|
+
1405,
|
|
272
|
+
"observations",
|
|
273
|
+
"condition_occurrence",
|
|
274
|
+
"2009-01-28",
|
|
275
|
+
"2009-01-30",
|
|
276
|
+
"412"
|
|
277
|
+
]
|
|
278
|
+
],
|
|
279
|
+
"tree": {
|
|
280
|
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"format": "conceptql-diagram/v1",
|
|
281
|
+
"statements": [
|
|
282
|
+
{
|
|
283
|
+
"name": "person_filter",
|
|
284
|
+
"base": "filter",
|
|
285
|
+
"humanName": "Person Filter",
|
|
286
|
+
"outputTypes": ["condition_occurrence"],
|
|
287
|
+
"parameters": {},
|
|
288
|
+
"values": [],
|
|
289
|
+
"children": [
|
|
290
|
+
{
|
|
291
|
+
"name": "icd9",
|
|
292
|
+
"base": "selection",
|
|
293
|
+
"humanName": "ICD-9 CM",
|
|
294
|
+
"vocabularyId": "ICD9CM",
|
|
295
|
+
"outputTypes": ["condition_occurrence"],
|
|
296
|
+
"parameters": {},
|
|
297
|
+
"values": ["412"],
|
|
298
|
+
"children": [],
|
|
299
|
+
"counts": {
|
|
300
|
+
"condition_occurrence": {
|
|
301
|
+
"rows": 48,
|
|
302
|
+
"n": 37
|
|
303
|
+
}
|
|
304
|
+
}
|
|
305
|
+
},
|
|
306
|
+
{
|
|
307
|
+
"name": "cpt",
|
|
308
|
+
"base": "selection",
|
|
309
|
+
"humanName": "CPT",
|
|
310
|
+
"vocabularyId": "CPT4",
|
|
311
|
+
"outputTypes": ["procedure_occurrence"],
|
|
312
|
+
"parameters": {},
|
|
313
|
+
"values": ["99214"],
|
|
314
|
+
"children": [],
|
|
315
|
+
"counts": {
|
|
316
|
+
"procedure_occurrence": {
|
|
317
|
+
"rows": 1073,
|
|
318
|
+
"n": 175
|
|
319
|
+
}
|
|
320
|
+
}
|
|
321
|
+
}
|
|
322
|
+
],
|
|
323
|
+
"counts": {
|
|
324
|
+
"condition_occurrence": {
|
|
325
|
+
"rows": 46,
|
|
326
|
+
"n": 36
|
|
327
|
+
}
|
|
328
|
+
}
|
|
329
|
+
}
|
|
330
|
+
]
|
|
331
|
+
}
|
|
332
|
+
},
|
|
333
|
+
{
|
|
334
|
+
"title": "The same result as the example above, with the office visits converted to patients first",
|
|
335
|
+
"statement": [
|
|
336
|
+
"person_filter",
|
|
337
|
+
{
|
|
338
|
+
"left": ["icd9", "412"],
|
|
339
|
+
"right": ["person", ["cpt", "99214"]]
|
|
340
|
+
}
|
|
341
|
+
],
|
|
342
|
+
"help": true,
|
|
343
|
+
"columns": [
|
|
344
|
+
"person_id",
|
|
345
|
+
"criterion_id",
|
|
346
|
+
"criterion_table",
|
|
347
|
+
"criterion_domain",
|
|
348
|
+
"start_date",
|
|
349
|
+
"end_date",
|
|
350
|
+
"source_value"
|
|
351
|
+
],
|
|
352
|
+
"rows": [
|
|
353
|
+
[
|
|
354
|
+
11,
|
|
355
|
+
82614,
|
|
356
|
+
"observations",
|
|
357
|
+
"condition_occurrence",
|
|
358
|
+
"2008-10-29",
|
|
359
|
+
"2008-10-29",
|
|
360
|
+
"412"
|
|
361
|
+
],
|
|
362
|
+
[
|
|
363
|
+
17,
|
|
364
|
+
27269,
|
|
365
|
+
"observations",
|
|
366
|
+
"condition_occurrence",
|
|
367
|
+
"2008-08-25",
|
|
368
|
+
"2008-08-25",
|
|
369
|
+
"412"
|
|
370
|
+
],
|
|
371
|
+
[
|
|
372
|
+
17,
|
|
373
|
+
46165,
|
|
374
|
+
"observations",
|
|
375
|
+
"condition_occurrence",
|
|
376
|
+
"2009-04-30",
|
|
377
|
+
"2009-04-30",
|
|
378
|
+
"412"
|
|
379
|
+
],
|
|
380
|
+
[
|
|
381
|
+
38,
|
|
382
|
+
40556,
|
|
383
|
+
"observations",
|
|
384
|
+
"condition_occurrence",
|
|
385
|
+
"2010-02-12",
|
|
386
|
+
"2010-02-12",
|
|
387
|
+
"412"
|
|
388
|
+
],
|
|
389
|
+
[
|
|
390
|
+
54,
|
|
391
|
+
74606,
|
|
392
|
+
"observations",
|
|
393
|
+
"condition_occurrence",
|
|
394
|
+
"2008-06-05",
|
|
395
|
+
"2008-06-05",
|
|
396
|
+
"412"
|
|
397
|
+
],
|
|
398
|
+
[
|
|
399
|
+
60,
|
|
400
|
+
986,
|
|
401
|
+
"observations",
|
|
402
|
+
"condition_occurrence",
|
|
403
|
+
"2009-07-19",
|
|
404
|
+
"2009-07-22",
|
|
405
|
+
"412"
|
|
406
|
+
],
|
|
407
|
+
[
|
|
408
|
+
66,
|
|
409
|
+
16171,
|
|
410
|
+
"observations",
|
|
411
|
+
"condition_occurrence",
|
|
412
|
+
"2009-07-25",
|
|
413
|
+
"2009-07-25",
|
|
414
|
+
"412"
|
|
415
|
+
],
|
|
416
|
+
[
|
|
417
|
+
73,
|
|
418
|
+
52843,
|
|
419
|
+
"observations",
|
|
420
|
+
"condition_occurrence",
|
|
421
|
+
"2008-11-16",
|
|
422
|
+
"2008-11-16",
|
|
423
|
+
"412"
|
|
424
|
+
],
|
|
425
|
+
[
|
|
426
|
+
77,
|
|
427
|
+
58165,
|
|
428
|
+
"observations",
|
|
429
|
+
"condition_occurrence",
|
|
430
|
+
"2010-10-06",
|
|
431
|
+
"2010-10-06",
|
|
432
|
+
"412"
|
|
433
|
+
],
|
|
434
|
+
[
|
|
435
|
+
81,
|
|
436
|
+
1405,
|
|
437
|
+
"observations",
|
|
438
|
+
"condition_occurrence",
|
|
439
|
+
"2009-01-28",
|
|
440
|
+
"2009-01-30",
|
|
441
|
+
"412"
|
|
442
|
+
]
|
|
443
|
+
],
|
|
444
|
+
"tree": {
|
|
445
|
+
"format": "conceptql-diagram/v1",
|
|
446
|
+
"statements": [
|
|
447
|
+
{
|
|
448
|
+
"name": "person_filter",
|
|
449
|
+
"base": "filter",
|
|
450
|
+
"humanName": "Person Filter",
|
|
451
|
+
"outputTypes": ["condition_occurrence"],
|
|
452
|
+
"parameters": {},
|
|
453
|
+
"values": [],
|
|
454
|
+
"children": [
|
|
455
|
+
{
|
|
456
|
+
"name": "icd9",
|
|
457
|
+
"base": "selection",
|
|
458
|
+
"humanName": "ICD-9 CM",
|
|
459
|
+
"vocabularyId": "ICD9CM",
|
|
460
|
+
"outputTypes": ["condition_occurrence"],
|
|
461
|
+
"parameters": {},
|
|
462
|
+
"values": ["412"],
|
|
463
|
+
"children": [],
|
|
464
|
+
"counts": {
|
|
465
|
+
"condition_occurrence": {
|
|
466
|
+
"rows": 48,
|
|
467
|
+
"n": 37
|
|
468
|
+
}
|
|
469
|
+
}
|
|
470
|
+
},
|
|
471
|
+
{
|
|
472
|
+
"name": "person",
|
|
473
|
+
"base": "cast",
|
|
474
|
+
"humanName": "Person",
|
|
475
|
+
"outputTypes": ["person"],
|
|
476
|
+
"parameters": {},
|
|
477
|
+
"values": [],
|
|
478
|
+
"children": [
|
|
479
|
+
{
|
|
480
|
+
"name": "cpt",
|
|
481
|
+
"base": "selection",
|
|
482
|
+
"humanName": "CPT",
|
|
483
|
+
"vocabularyId": "CPT4",
|
|
484
|
+
"outputTypes": ["procedure_occurrence"],
|
|
485
|
+
"parameters": {},
|
|
486
|
+
"values": ["99214"],
|
|
487
|
+
"children": [],
|
|
488
|
+
"counts": {
|
|
489
|
+
"procedure_occurrence": {
|
|
490
|
+
"rows": 1073,
|
|
491
|
+
"n": 175
|
|
492
|
+
}
|
|
493
|
+
}
|
|
494
|
+
}
|
|
495
|
+
],
|
|
496
|
+
"counts": {
|
|
497
|
+
"person": {
|
|
498
|
+
"rows": 175,
|
|
499
|
+
"n": 175
|
|
500
|
+
}
|
|
501
|
+
}
|
|
502
|
+
}
|
|
503
|
+
],
|
|
504
|
+
"counts": {
|
|
505
|
+
"condition_occurrence": {
|
|
506
|
+
"rows": 46,
|
|
507
|
+
"n": 36
|
|
508
|
+
}
|
|
509
|
+
}
|
|
510
|
+
}
|
|
511
|
+
]
|
|
512
|
+
}
|
|
513
|
+
},
|
|
514
|
+
{
|
|
515
|
+
"title": "All MI Conditions for people who are Male OR had an office visit at some point in the data",
|
|
516
|
+
"statement": [
|
|
517
|
+
"person_filter",
|
|
518
|
+
{
|
|
519
|
+
"left": ["icd9", "412"],
|
|
520
|
+
"right": ["union", ["cpt", "99214"], ["gender", "Male"]]
|
|
521
|
+
}
|
|
522
|
+
],
|
|
523
|
+
"help": true,
|
|
524
|
+
"columns": [
|
|
525
|
+
"person_id",
|
|
526
|
+
"criterion_id",
|
|
527
|
+
"criterion_table",
|
|
528
|
+
"criterion_domain",
|
|
529
|
+
"start_date",
|
|
530
|
+
"end_date",
|
|
531
|
+
"source_value"
|
|
532
|
+
],
|
|
533
|
+
"rows": [
|
|
534
|
+
[
|
|
535
|
+
11,
|
|
536
|
+
82614,
|
|
537
|
+
"observations",
|
|
538
|
+
"condition_occurrence",
|
|
539
|
+
"2008-10-29",
|
|
540
|
+
"2008-10-29",
|
|
541
|
+
"412"
|
|
542
|
+
],
|
|
543
|
+
[
|
|
544
|
+
17,
|
|
545
|
+
27269,
|
|
546
|
+
"observations",
|
|
547
|
+
"condition_occurrence",
|
|
548
|
+
"2008-08-25",
|
|
549
|
+
"2008-08-25",
|
|
550
|
+
"412"
|
|
551
|
+
],
|
|
552
|
+
[
|
|
553
|
+
17,
|
|
554
|
+
46165,
|
|
555
|
+
"observations",
|
|
556
|
+
"condition_occurrence",
|
|
557
|
+
"2009-04-30",
|
|
558
|
+
"2009-04-30",
|
|
559
|
+
"412"
|
|
560
|
+
],
|
|
561
|
+
[
|
|
562
|
+
38,
|
|
563
|
+
40556,
|
|
564
|
+
"observations",
|
|
565
|
+
"condition_occurrence",
|
|
566
|
+
"2010-02-12",
|
|
567
|
+
"2010-02-12",
|
|
568
|
+
"412"
|
|
569
|
+
],
|
|
570
|
+
[
|
|
571
|
+
54,
|
|
572
|
+
74606,
|
|
573
|
+
"observations",
|
|
574
|
+
"condition_occurrence",
|
|
575
|
+
"2008-06-05",
|
|
576
|
+
"2008-06-05",
|
|
577
|
+
"412"
|
|
578
|
+
],
|
|
579
|
+
[
|
|
580
|
+
60,
|
|
581
|
+
986,
|
|
582
|
+
"observations",
|
|
583
|
+
"condition_occurrence",
|
|
584
|
+
"2009-07-19",
|
|
585
|
+
"2009-07-22",
|
|
586
|
+
"412"
|
|
587
|
+
],
|
|
588
|
+
[
|
|
589
|
+
66,
|
|
590
|
+
16171,
|
|
591
|
+
"observations",
|
|
592
|
+
"condition_occurrence",
|
|
593
|
+
"2009-07-25",
|
|
594
|
+
"2009-07-25",
|
|
595
|
+
"412"
|
|
596
|
+
],
|
|
597
|
+
[
|
|
598
|
+
73,
|
|
599
|
+
52843,
|
|
600
|
+
"observations",
|
|
601
|
+
"condition_occurrence",
|
|
602
|
+
"2008-11-16",
|
|
603
|
+
"2008-11-16",
|
|
604
|
+
"412"
|
|
605
|
+
],
|
|
606
|
+
[
|
|
607
|
+
77,
|
|
608
|
+
58165,
|
|
609
|
+
"observations",
|
|
610
|
+
"condition_occurrence",
|
|
611
|
+
"2010-10-06",
|
|
612
|
+
"2010-10-06",
|
|
613
|
+
"412"
|
|
614
|
+
],
|
|
615
|
+
[
|
|
616
|
+
81,
|
|
617
|
+
1405,
|
|
618
|
+
"observations",
|
|
619
|
+
"condition_occurrence",
|
|
620
|
+
"2009-01-28",
|
|
621
|
+
"2009-01-30",
|
|
622
|
+
"412"
|
|
623
|
+
]
|
|
624
|
+
],
|
|
625
|
+
"tree": {
|
|
626
|
+
"format": "conceptql-diagram/v1",
|
|
627
|
+
"statements": [
|
|
628
|
+
{
|
|
629
|
+
"name": "person_filter",
|
|
630
|
+
"base": "filter",
|
|
631
|
+
"humanName": "Person Filter",
|
|
632
|
+
"outputTypes": ["condition_occurrence"],
|
|
633
|
+
"parameters": {},
|
|
634
|
+
"values": [],
|
|
635
|
+
"children": [
|
|
636
|
+
{
|
|
637
|
+
"name": "icd9",
|
|
638
|
+
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