rxome-generator 0.1.0
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.
- package/LICENSE +21 -0
- package/README.md +484 -0
- package/demos/demo_data_full.json +149 -0
- package/demos/demo_data_full_compressed.json +76 -0
- package/demos/demo_from_gui.json +64 -0
- package/demos/rxome.decrypt.json +1 -0
- package/demos/rxome.encrypt.json +1 -0
- package/demos/testmessage_cipher +19 -0
- package/index.js +3 -0
- package/lib/phenopackets.json +1948 -0
- package/lib/rxome-api-demo.js +56 -0
- package/lib/rxome-api.js +119 -0
- package/lib/rxome-api.test.js +22 -0
- package/lib/rxome-generator.js +349 -0
- package/lib/rxome-generator.test.js +379 -0
- package/package.json +50 -0
- package/rxcode +401 -0
- package/rxcode.test.js +104 -0
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+
},
|
|
368
|
+
"pathologicalStage": {
|
|
369
|
+
"type": "OntologyClass",
|
|
370
|
+
"id": 14
|
|
371
|
+
},
|
|
372
|
+
"pathologicalTnmFinding": {
|
|
373
|
+
"rule": "repeated",
|
|
374
|
+
"type": "OntologyClass",
|
|
375
|
+
"id": 15
|
|
376
|
+
},
|
|
377
|
+
"diagnosticMarkers": {
|
|
378
|
+
"rule": "repeated",
|
|
379
|
+
"type": "OntologyClass",
|
|
380
|
+
"id": 16
|
|
381
|
+
},
|
|
382
|
+
"procedure": {
|
|
383
|
+
"type": "Procedure",
|
|
384
|
+
"id": 17
|
|
385
|
+
},
|
|
386
|
+
"files": {
|
|
387
|
+
"rule": "repeated",
|
|
388
|
+
"type": "File",
|
|
389
|
+
"id": 18
|
|
390
|
+
},
|
|
391
|
+
"materialSample": {
|
|
392
|
+
"type": "OntologyClass",
|
|
393
|
+
"id": 19
|
|
394
|
+
},
|
|
395
|
+
"sampleProcessing": {
|
|
396
|
+
"type": "OntologyClass",
|
|
397
|
+
"id": 20
|
|
398
|
+
},
|
|
399
|
+
"sampleStorage": {
|
|
400
|
+
"type": "OntologyClass",
|
|
401
|
+
"id": 21
|
|
402
|
+
}
|
|
403
|
+
}
|
|
404
|
+
},
|
|
405
|
+
"Measurement": {
|
|
406
|
+
"oneofs": {
|
|
407
|
+
"measurementValue": {
|
|
408
|
+
"oneof": [
|
|
409
|
+
"value",
|
|
410
|
+
"complexValue"
|
|
411
|
+
]
|
|
412
|
+
}
|
|
413
|
+
},
|
|
414
|
+
"fields": {
|
|
415
|
+
"description": {
|
|
416
|
+
"type": "string",
|
|
417
|
+
"id": 1
|
|
418
|
+
},
|
|
419
|
+
"assay": {
|
|
420
|
+
"type": "OntologyClass",
|
|
421
|
+
"id": 2
|
|
422
|
+
},
|
|
423
|
+
"value": {
|
|
424
|
+
"type": "Value",
|
|
425
|
+
"id": 3
|
|
426
|
+
},
|
|
427
|
+
"complexValue": {
|
|
428
|
+
"type": "ComplexValue",
|
|
429
|
+
"id": 4
|
|
430
|
+
},
|
|
431
|
+
"timeObserved": {
|
|
432
|
+
"type": "TimeElement",
|
|
433
|
+
"id": 5
|
|
434
|
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},
|
|
435
|
+
"procedure": {
|
|
436
|
+
"type": "Procedure",
|
|
437
|
+
"id": 6
|
|
438
|
+
}
|
|
439
|
+
}
|
|
440
|
+
},
|
|
441
|
+
"Value": {
|
|
442
|
+
"oneofs": {
|
|
443
|
+
"value": {
|
|
444
|
+
"oneof": [
|
|
445
|
+
"quantity",
|
|
446
|
+
"ontologyClass"
|
|
447
|
+
]
|
|
448
|
+
}
|
|
449
|
+
},
|
|
450
|
+
"fields": {
|
|
451
|
+
"quantity": {
|
|
452
|
+
"type": "Quantity",
|
|
453
|
+
"id": 1
|
|
454
|
+
},
|
|
455
|
+
"ontologyClass": {
|
|
456
|
+
"type": "OntologyClass",
|
|
457
|
+
"id": 2
|
|
458
|
+
}
|
|
459
|
+
}
|
|
460
|
+
},
|
|
461
|
+
"ComplexValue": {
|
|
462
|
+
"fields": {
|
|
463
|
+
"typedQuantities": {
|
|
464
|
+
"rule": "repeated",
|
|
465
|
+
"type": "TypedQuantity",
|
|
466
|
+
"id": 1
|
|
467
|
+
}
|
|
468
|
+
}
|
|
469
|
+
},
|
|
470
|
+
"Quantity": {
|
|
471
|
+
"fields": {
|
|
472
|
+
"unit": {
|
|
473
|
+
"type": "OntologyClass",
|
|
474
|
+
"id": 1
|
|
475
|
+
},
|
|
476
|
+
"value": {
|
|
477
|
+
"type": "double",
|
|
478
|
+
"id": 2
|
|
479
|
+
},
|
|
480
|
+
"referenceRange": {
|
|
481
|
+
"type": "ReferenceRange",
|
|
482
|
+
"id": 3
|
|
483
|
+
}
|
|
484
|
+
}
|
|
485
|
+
},
|
|
486
|
+
"TypedQuantity": {
|
|
487
|
+
"fields": {
|
|
488
|
+
"type": {
|
|
489
|
+
"type": "OntologyClass",
|
|
490
|
+
"id": 1
|
|
491
|
+
},
|
|
492
|
+
"quantity": {
|
|
493
|
+
"type": "Quantity",
|
|
494
|
+
"id": 2
|
|
495
|
+
}
|
|
496
|
+
}
|
|
497
|
+
},
|
|
498
|
+
"ReferenceRange": {
|
|
499
|
+
"fields": {
|
|
500
|
+
"unit": {
|
|
501
|
+
"type": "OntologyClass",
|
|
502
|
+
"id": 1
|
|
503
|
+
},
|
|
504
|
+
"low": {
|
|
505
|
+
"type": "double",
|
|
506
|
+
"id": 2
|
|
507
|
+
},
|
|
508
|
+
"high": {
|
|
509
|
+
"type": "double",
|
|
510
|
+
"id": 3
|
|
511
|
+
}
|
|
512
|
+
}
|
|
513
|
+
},
|
|
514
|
+
"PhenotypicFeature": {
|
|
515
|
+
"fields": {
|
|
516
|
+
"description": {
|
|
517
|
+
"type": "string",
|
|
518
|
+
"id": 1
|
|
519
|
+
},
|
|
520
|
+
"type": {
|
|
521
|
+
"type": "OntologyClass",
|
|
522
|
+
"id": 2
|
|
523
|
+
},
|
|
524
|
+
"excluded": {
|
|
525
|
+
"type": "bool",
|
|
526
|
+
"id": 3
|
|
527
|
+
},
|
|
528
|
+
"severity": {
|
|
529
|
+
"type": "OntologyClass",
|
|
530
|
+
"id": 4
|
|
531
|
+
},
|
|
532
|
+
"modifiers": {
|
|
533
|
+
"rule": "repeated",
|
|
534
|
+
"type": "OntologyClass",
|
|
535
|
+
"id": 5
|
|
536
|
+
},
|
|
537
|
+
"onset": {
|
|
538
|
+
"type": "TimeElement",
|
|
539
|
+
"id": 6
|
|
540
|
+
},
|
|
541
|
+
"resolution": {
|
|
542
|
+
"type": "TimeElement",
|
|
543
|
+
"id": 7
|
|
544
|
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},
|
|
545
|
+
"evidence": {
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|
546
|
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"rule": "repeated",
|
|
547
|
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"type": "Evidence",
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|
548
|
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"id": 8
|
|
549
|
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}
|
|
550
|
+
}
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|
551
|
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},
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|
552
|
+
"Disease": {
|
|
553
|
+
"fields": {
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|
554
|
+
"term": {
|
|
555
|
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"type": "OntologyClass",
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556
|
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"id": 1
|
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557
|
+
},
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|
558
|
+
"excluded": {
|
|
559
|
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"type": "bool",
|
|
560
|
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"id": 2
|
|
561
|
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},
|
|
562
|
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"onset": {
|
|
563
|
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"type": "TimeElement",
|
|
564
|
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"id": 3
|
|
565
|
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},
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|
566
|
+
"resolution": {
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|
567
|
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"type": "TimeElement",
|
|
568
|
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"id": 4
|
|
569
|
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},
|
|
570
|
+
"diseaseStage": {
|
|
571
|
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"rule": "repeated",
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|
572
|
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"type": "OntologyClass",
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|
573
|
+
"id": 5
|
|
574
|
+
},
|
|
575
|
+
"clinicalTnmFinding": {
|
|
576
|
+
"rule": "repeated",
|
|
577
|
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"type": "OntologyClass",
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|
578
|
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"id": 6
|
|
579
|
+
},
|
|
580
|
+
"primarySite": {
|
|
581
|
+
"type": "OntologyClass",
|
|
582
|
+
"id": 7
|
|
583
|
+
},
|
|
584
|
+
"laterality": {
|
|
585
|
+
"type": "OntologyClass",
|
|
586
|
+
"id": 8
|
|
587
|
+
}
|
|
588
|
+
}
|
|
589
|
+
},
|
|
590
|
+
"Interpretation": {
|
|
591
|
+
"fields": {
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|
592
|
+
"id": {
|
|
593
|
+
"type": "string",
|
|
594
|
+
"id": 1
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|
595
|
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},
|
|
596
|
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"progressStatus": {
|
|
597
|
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"type": "ProgressStatus",
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|
598
|
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"id": 2
|
|
599
|
+
},
|
|
600
|
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"diagnosis": {
|
|
601
|
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"type": "Diagnosis",
|
|
602
|
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"id": 3
|
|
603
|
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},
|
|
604
|
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"summary": {
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|
605
|
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"type": "string",
|
|
606
|
+
"id": 4
|
|
607
|
+
}
|
|
608
|
+
},
|
|
609
|
+
"nested": {
|
|
610
|
+
"ProgressStatus": {
|
|
611
|
+
"values": {
|
|
612
|
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"UNKNOWN_PROGRESS": 0,
|
|
613
|
+
"IN_PROGRESS": 1,
|
|
614
|
+
"COMPLETED": 2,
|
|
615
|
+
"SOLVED": 3,
|
|
616
|
+
"UNSOLVED": 4
|
|
617
|
+
}
|
|
618
|
+
}
|
|
619
|
+
}
|
|
620
|
+
},
|
|
621
|
+
"Diagnosis": {
|
|
622
|
+
"fields": {
|
|
623
|
+
"disease": {
|
|
624
|
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"type": "OntologyClass",
|
|
625
|
+
"id": 1
|
|
626
|
+
},
|
|
627
|
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"genomicInterpretations": {
|
|
628
|
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"rule": "repeated",
|
|
629
|
+
"type": "GenomicInterpretation",
|
|
630
|
+
"id": 2
|
|
631
|
+
}
|
|
632
|
+
}
|
|
633
|
+
},
|
|
634
|
+
"GenomicInterpretation": {
|
|
635
|
+
"oneofs": {
|
|
636
|
+
"call": {
|
|
637
|
+
"oneof": [
|
|
638
|
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"gene",
|
|
639
|
+
"variantInterpretation"
|
|
640
|
+
]
|
|
641
|
+
}
|
|
642
|
+
},
|
|
643
|
+
"fields": {
|
|
644
|
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"subjectOrBiosampleId": {
|
|
645
|
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"type": "string",
|
|
646
|
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"id": 1
|
|
647
|
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},
|
|
648
|
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"interpretationStatus": {
|
|
649
|
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"type": "InterpretationStatus",
|
|
650
|
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"id": 2
|
|
651
|
+
},
|
|
652
|
+
"gene": {
|
|
653
|
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"type": "org.ga4gh.vrsatile.v1.GeneDescriptor",
|
|
654
|
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"id": 3
|
|
655
|
+
},
|
|
656
|
+
"variantInterpretation": {
|
|
657
|
+
"type": "VariantInterpretation",
|
|
658
|
+
"id": 4
|
|
659
|
+
}
|
|
660
|
+
},
|
|
661
|
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"nested": {
|
|
662
|
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"InterpretationStatus": {
|
|
663
|
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"values": {
|
|
664
|
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"UNKNOWN_STATUS": 0,
|
|
665
|
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"REJECTED": 1,
|
|
666
|
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"CANDIDATE": 2,
|
|
667
|
+
"CONTRIBUTORY": 3,
|
|
668
|
+
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|
|
669
|
+
}
|
|
670
|
+
}
|
|
671
|
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}
|
|
672
|
+
},
|
|
673
|
+
"AcmgPathogenicityClassification": {
|
|
674
|
+
"values": {
|
|
675
|
+
"NOT_PROVIDED": 0,
|
|
676
|
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"BENIGN": 1,
|
|
677
|
+
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|
|
678
|
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"UNCERTAIN_SIGNIFICANCE": 3,
|
|
679
|
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"LIKELY_PATHOGENIC": 4,
|
|
680
|
+
"PATHOGENIC": 5
|
|
681
|
+
}
|
|
682
|
+
},
|
|
683
|
+
"TherapeuticActionability": {
|
|
684
|
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"values": {
|
|
685
|
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"UNKNOWN_ACTIONABILITY": 0,
|
|
686
|
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"NOT_ACTIONABLE": 1,
|
|
687
|
+
"ACTIONABLE": 2
|
|
688
|
+
}
|
|
689
|
+
},
|
|
690
|
+
"VariantInterpretation": {
|
|
691
|
+
"fields": {
|
|
692
|
+
"acmgPathogenicityClassification": {
|
|
693
|
+
"type": "AcmgPathogenicityClassification",
|
|
694
|
+
"id": 1
|
|
695
|
+
},
|
|
696
|
+
"therapeuticActionability": {
|
|
697
|
+
"type": "TherapeuticActionability",
|
|
698
|
+
"id": 2
|
|
699
|
+
},
|
|
700
|
+
"variationDescriptor": {
|
|
701
|
+
"type": "org.ga4gh.vrsatile.v1.VariationDescriptor",
|
|
702
|
+
"id": 3
|
|
703
|
+
}
|
|
704
|
+
}
|
|
705
|
+
},
|
|
706
|
+
"Individual": {
|
|
707
|
+
"fields": {
|
|
708
|
+
"id": {
|
|
709
|
+
"type": "string",
|
|
710
|
+
"id": 1
|
|
711
|
+
},
|
|
712
|
+
"alternateIds": {
|
|
713
|
+
"rule": "repeated",
|
|
714
|
+
"type": "string",
|
|
715
|
+
"id": 2
|
|
716
|
+
},
|
|
717
|
+
"dateOfBirth": {
|
|
718
|
+
"type": "string",
|
|
719
|
+
"id": 3
|
|
720
|
+
},
|
|
721
|
+
"timeAtLastEncounter": {
|
|
722
|
+
"type": "TimeElement",
|
|
723
|
+
"id": 4
|
|
724
|
+
},
|
|
725
|
+
"vitalStatus": {
|
|
726
|
+
"type": "VitalStatus",
|
|
727
|
+
"id": 5
|
|
728
|
+
},
|
|
729
|
+
"sex": {
|
|
730
|
+
"type": "Sex",
|
|
731
|
+
"id": 6
|
|
732
|
+
},
|
|
733
|
+
"karyotypicSex": {
|
|
734
|
+
"type": "KaryotypicSex",
|
|
735
|
+
"id": 7
|
|
736
|
+
},
|
|
737
|
+
"gender": {
|
|
738
|
+
"type": "OntologyClass",
|
|
739
|
+
"id": 8
|
|
740
|
+
},
|
|
741
|
+
"taxonomy": {
|
|
742
|
+
"type": "OntologyClass",
|
|
743
|
+
"id": 9
|
|
744
|
+
}
|
|
745
|
+
}
|
|
746
|
+
},
|
|
747
|
+
"VitalStatus": {
|
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"type": "uint64",
|
|
1870
|
+
"id": 1
|
|
1871
|
+
},
|
|
1872
|
+
"comparator": {
|
|
1873
|
+
"type": "string",
|
|
1874
|
+
"id": 2
|
|
1875
|
+
}
|
|
1876
|
+
}
|
|
1877
|
+
},
|
|
1878
|
+
"DefiniteRange": {
|
|
1879
|
+
"fields": {
|
|
1880
|
+
"min": {
|
|
1881
|
+
"type": "uint64",
|
|
1882
|
+
"id": 1
|
|
1883
|
+
},
|
|
1884
|
+
"max": {
|
|
1885
|
+
"type": "uint64",
|
|
1886
|
+
"id": 2
|
|
1887
|
+
}
|
|
1888
|
+
}
|
|
1889
|
+
},
|
|
1890
|
+
"SequenceState": {
|
|
1891
|
+
"fields": {
|
|
1892
|
+
"sequence": {
|
|
1893
|
+
"type": "string",
|
|
1894
|
+
"id": 1
|
|
1895
|
+
}
|
|
1896
|
+
}
|
|
1897
|
+
},
|
|
1898
|
+
"SimpleInterval": {
|
|
1899
|
+
"fields": {
|
|
1900
|
+
"start": {
|
|
1901
|
+
"type": "uint64",
|
|
1902
|
+
"id": 1
|
|
1903
|
+
},
|
|
1904
|
+
"end": {
|
|
1905
|
+
"type": "uint64",
|
|
1906
|
+
"id": 2
|
|
1907
|
+
}
|
|
1908
|
+
}
|
|
1909
|
+
}
|
|
1910
|
+
}
|
|
1911
|
+
}
|
|
1912
|
+
}
|
|
1913
|
+
}
|
|
1914
|
+
}
|
|
1915
|
+
}
|
|
1916
|
+
}
|
|
1917
|
+
},
|
|
1918
|
+
"google": {
|
|
1919
|
+
"nested": {
|
|
1920
|
+
"protobuf": {
|
|
1921
|
+
"options": {
|
|
1922
|
+
"csharp_namespace": "Google.Protobuf.WellKnownTypes",
|
|
1923
|
+
"cc_enable_arenas": true,
|
|
1924
|
+
"go_package": "google.golang.org/protobuf/types/known/timestamppb",
|
|
1925
|
+
"java_package": "com.google.protobuf",
|
|
1926
|
+
"java_outer_classname": "TimestampProto",
|
|
1927
|
+
"java_multiple_files": true,
|
|
1928
|
+
"objc_class_prefix": "GPB"
|
|
1929
|
+
},
|
|
1930
|
+
"nested": {
|
|
1931
|
+
"Timestamp": {
|
|
1932
|
+
"fields": {
|
|
1933
|
+
"seconds": {
|
|
1934
|
+
"type": "int64",
|
|
1935
|
+
"id": 1
|
|
1936
|
+
},
|
|
1937
|
+
"nanos": {
|
|
1938
|
+
"type": "int32",
|
|
1939
|
+
"id": 2
|
|
1940
|
+
}
|
|
1941
|
+
}
|
|
1942
|
+
}
|
|
1943
|
+
}
|
|
1944
|
+
}
|
|
1945
|
+
}
|
|
1946
|
+
}
|
|
1947
|
+
}
|
|
1948
|
+
}
|