@sjcrh/proteinpaint-types 2.134.0 → 2.135.0
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/dist/{chunk-IJLAEEK7.js → chunk-FD6CMKNN.js} +13 -5
- package/dist/{chunk-TCSJGKT3.js → chunk-UMYBO3H4.js} +273 -8
- package/dist/gdc.grin2.js +1 -1
- package/dist/index.js +2 -2
- package/dist/profileScores.js +1 -1
- package/package.json +1 -1
- package/src/dataset.ts +13 -15
- package/src/routes/gdc.grin2.ts +42 -0
- package/src/routes/profileScores.ts +1 -1
|
@@ -20,7 +20,7 @@ var ProfileScoresPayload = {
|
|
|
20
20
|
var validProfileScoresRequest = (input) => {
|
|
21
21
|
const errors = [];
|
|
22
22
|
const __is = (input2) => {
|
|
23
|
-
const $io0 = (input3) => Array.isArray(input3.scoreTerms) && input3.scoreTerms.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)) && true && (void 0 === input3.isRadarFacility || "boolean" === typeof input3.isRadarFacility) && (void 0 === input3.userSites || Array.isArray(input3.userSites) && input3.userSites.every((elem) => "string" === typeof elem)) && (void 0 === input3.
|
|
23
|
+
const $io0 = (input3) => Array.isArray(input3.scoreTerms) && input3.scoreTerms.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)) && true && (void 0 === input3.isRadarFacility || "boolean" === typeof input3.isRadarFacility) && (void 0 === input3.userSites || Array.isArray(input3.userSites) && input3.userSites.every((elem) => "string" === typeof elem)) && (void 0 === input3.sites || Array.isArray(input3.sites) && input3.sites.every((elem) => "string" === typeof elem)) && (void 0 === input3.isAggregate || "boolean" === typeof input3.isAggregate) && true;
|
|
24
24
|
const $io1 = (input3) => true;
|
|
25
25
|
return "object" === typeof input2 && null !== input2 && $io0(input2);
|
|
26
26
|
};
|
|
@@ -59,10 +59,18 @@ var validProfileScoresRequest = (input) => {
|
|
|
59
59
|
path: _path2 + ".userSites",
|
|
60
60
|
expected: "(Array<string> | undefined)",
|
|
61
61
|
value: input3.userSites
|
|
62
|
-
}), void 0 === input3.
|
|
63
|
-
path: _path2 + ".
|
|
64
|
-
expected: "(string | undefined)",
|
|
65
|
-
value: input3.
|
|
62
|
+
}), void 0 === input3.sites || (Array.isArray(input3.sites) || $report(_exceptionable2, {
|
|
63
|
+
path: _path2 + ".sites",
|
|
64
|
+
expected: "(Array<string> | undefined)",
|
|
65
|
+
value: input3.sites
|
|
66
|
+
})) && input3.sites.map((elem, _index3) => "string" === typeof elem || $report(_exceptionable2, {
|
|
67
|
+
path: _path2 + ".sites[" + _index3 + "]",
|
|
68
|
+
expected: "string",
|
|
69
|
+
value: elem
|
|
70
|
+
})).every((flag) => flag) || $report(_exceptionable2, {
|
|
71
|
+
path: _path2 + ".sites",
|
|
72
|
+
expected: "(Array<string> | undefined)",
|
|
73
|
+
value: input3.sites
|
|
66
74
|
}), void 0 === input3.isAggregate || "boolean" === typeof input3.isAggregate || $report(_exceptionable2, {
|
|
67
75
|
path: _path2 + ".isAggregate",
|
|
68
76
|
expected: "(boolean | undefined)",
|
|
@@ -456,15 +456,53 @@ var validRunGRIN2Request = (input) => {
|
|
|
456
456
|
var validRunGRIN2Response = (input) => {
|
|
457
457
|
const errors = [];
|
|
458
458
|
const __is = (input2) => {
|
|
459
|
-
const $
|
|
460
|
-
const $
|
|
459
|
+
const $join = import_typia.createValidate.join;
|
|
460
|
+
const $io0 = (input3) => ("success" === input3.status || "error" === input3.status) && (void 0 === input3.error || "string" === typeof input3.error) && (void 0 === input3.pngImg || "string" === typeof input3.pngImg) && true && true && (void 0 === input3.rustResult || "object" === typeof input3.rustResult && null !== input3.rustResult && $io1(input3.rustResult)) && (void 0 === input3.timing || "object" === typeof input3.timing && null !== input3.timing && $io11(input3.timing));
|
|
461
|
+
const $io1 = (input3) => Array.isArray(input3.successful_data) && input3.successful_data.every((elem) => Array.isArray(elem) && elem.every((elem2) => "string" === typeof elem2)) && (Array.isArray(input3.failed_files) && input3.failed_files.every((elem) => "object" === typeof elem && null !== elem && $io2(elem))) && ("object" === typeof input3.summary && null !== input3.summary && $io3(input3.summary));
|
|
461
462
|
const $io2 = (input3) => "string" === typeof input3.case_id && "string" === typeof input3.data_type && "string" === typeof input3.error_type && "string" === typeof input3.error_details && "number" === typeof input3.attempts_made;
|
|
462
|
-
const $
|
|
463
|
+
const $io3 = (input3) => "summary" === input3.type && "number" === typeof input3.total_files && "number" === typeof input3.successful_files && "number" === typeof input3.failed_files && (Array.isArray(input3.errors) && input3.errors.every((elem) => "object" === typeof elem && null !== elem && $io2(elem))) && "number" === typeof input3.filtered_records && "number" === typeof input3.filtered_maf_records && "number" === typeof input3.filtered_cnv_records && "number" === typeof input3.included_maf_records && "number" === typeof input3.included_cnv_records && ("object" === typeof input3.filtered_records_by_case && null !== input3.filtered_records_by_case && false === Array.isArray(input3.filtered_records_by_case) && $io4(input3.filtered_records_by_case)) && ("object" === typeof input3.hyper_mutator_records && null !== input3.hyper_mutator_records && false === Array.isArray(input3.hyper_mutator_records) && $io10(input3.hyper_mutator_records));
|
|
464
|
+
const $io4 = (input3) => Object.keys(input3).every((key) => {
|
|
465
|
+
const value = input3[key];
|
|
466
|
+
if (void 0 === value)
|
|
467
|
+
return true;
|
|
468
|
+
if (RegExp(/(.*)/).test(key))
|
|
469
|
+
return "object" === typeof value && null !== value && $io5(value);
|
|
470
|
+
return true;
|
|
471
|
+
});
|
|
472
|
+
const $io5 = (input3) => "object" === typeof input3.maf && null !== input3.maf && $io6(input3.maf) && ("object" === typeof input3.cnv && null !== input3.cnv && $io9(input3.cnv));
|
|
473
|
+
const $io6 = (input3) => "object" === typeof input3.matched_consequences && null !== input3.matched_consequences && false === Array.isArray(input3.matched_consequences) && $io7(input3.matched_consequences) && ("object" === typeof input3.rejected_consequences && null !== input3.rejected_consequences && false === Array.isArray(input3.rejected_consequences) && $io7(input3.rejected_consequences)) && "number" === typeof input3.t_alt_count && "number" === typeof input3.t_depth && "number" === typeof input3.invalid_rows && "number" === typeof input3.excluded_by_min_depth && "number" === typeof input3.excluded_by_min_alt_count && "number" === typeof input3.excluded_by_consequence_type && "number" === typeof input3.total_processed && "number" === typeof input3.total_included && ("object" === typeof input3.skipped_chromosomes && null !== input3.skipped_chromosomes && false === Array.isArray(input3.skipped_chromosomes) && $io8(input3.skipped_chromosomes));
|
|
474
|
+
const $io7 = (input3) => Object.keys(input3).every((key) => {
|
|
475
|
+
const value = input3[key];
|
|
476
|
+
if (void 0 === value)
|
|
477
|
+
return true;
|
|
478
|
+
if (RegExp(/(.*)/).test(key))
|
|
479
|
+
return true;
|
|
480
|
+
return true;
|
|
481
|
+
});
|
|
482
|
+
const $io8 = (input3) => Object.keys(input3).every((key) => {
|
|
483
|
+
const value = input3[key];
|
|
484
|
+
if (void 0 === value)
|
|
485
|
+
return true;
|
|
486
|
+
if (RegExp(/(.*)/).test(key))
|
|
487
|
+
return "number" === typeof value;
|
|
488
|
+
return true;
|
|
489
|
+
});
|
|
490
|
+
const $io9 = (input3) => "number" === typeof input3.segment_mean && "number" === typeof input3.seg_length && "number" === typeof input3.invalid_rows && "number" === typeof input3.excluded_by_loss_threshold && "number" === typeof input3.excluded_by_gain_threshold && "number" === typeof input3.excluded_by_segment_length && "number" === typeof input3.total_processed && "number" === typeof input3.total_included && ("object" === typeof input3.skipped_chromosomes && null !== input3.skipped_chromosomes && false === Array.isArray(input3.skipped_chromosomes) && $io8(input3.skipped_chromosomes));
|
|
491
|
+
const $io10 = (input3) => Object.keys(input3).every((key) => {
|
|
492
|
+
const value = input3[key];
|
|
493
|
+
if (void 0 === value)
|
|
494
|
+
return true;
|
|
495
|
+
if (RegExp(/(.*)/).test(key))
|
|
496
|
+
return Array.isArray(value) && value.every((elem) => "string" === typeof elem);
|
|
497
|
+
return true;
|
|
498
|
+
});
|
|
499
|
+
const $io11 = (input3) => "number" === typeof input3.rustProcessingTime && "number" === typeof input3.grin2Time && "number" === typeof input3.totalTime;
|
|
463
500
|
return "object" === typeof input2 && null !== input2 && $io0(input2);
|
|
464
501
|
};
|
|
465
502
|
if (false === __is(input)) {
|
|
466
503
|
const $report = import_typia.createValidate.report(errors);
|
|
467
504
|
((input2, _path, _exceptionable = true) => {
|
|
505
|
+
const $join = import_typia.createValidate.join;
|
|
468
506
|
const $vo0 = (input3, _path2, _exceptionable2 = true) => ["success" === input3.status || "error" === input3.status || $report(_exceptionable2, {
|
|
469
507
|
path: _path2 + ".status",
|
|
470
508
|
expected: '("error" | "success")',
|
|
@@ -487,11 +525,11 @@ var validRunGRIN2Response = (input) => {
|
|
|
487
525
|
value: input3.rustResult
|
|
488
526
|
}), void 0 === input3.timing || ("object" === typeof input3.timing && null !== input3.timing || $report(_exceptionable2, {
|
|
489
527
|
path: _path2 + ".timing",
|
|
490
|
-
expected: "(__type | undefined)",
|
|
528
|
+
expected: "(__type.o3 | undefined)",
|
|
491
529
|
value: input3.timing
|
|
492
|
-
})) && $
|
|
530
|
+
})) && $vo11(input3.timing, _path2 + ".timing", _exceptionable2) || $report(_exceptionable2, {
|
|
493
531
|
path: _path2 + ".timing",
|
|
494
|
-
expected: "(__type | undefined)",
|
|
532
|
+
expected: "(__type.o3 | undefined)",
|
|
495
533
|
value: input3.timing
|
|
496
534
|
})].every((flag) => flag);
|
|
497
535
|
const $vo1 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.successful_data) || $report(_exceptionable2, {
|
|
@@ -560,7 +598,11 @@ var validRunGRIN2Response = (input) => {
|
|
|
560
598
|
expected: "number",
|
|
561
599
|
value: input3.attempts_made
|
|
562
600
|
})].every((flag) => flag);
|
|
563
|
-
const $vo3 = (input3, _path2, _exceptionable2 = true) => ["
|
|
601
|
+
const $vo3 = (input3, _path2, _exceptionable2 = true) => ["summary" === input3.type || $report(_exceptionable2, {
|
|
602
|
+
path: _path2 + ".type",
|
|
603
|
+
expected: '"summary"',
|
|
604
|
+
value: input3.type
|
|
605
|
+
}), "number" === typeof input3.total_files || $report(_exceptionable2, {
|
|
564
606
|
path: _path2 + ".total_files",
|
|
565
607
|
expected: "number",
|
|
566
608
|
value: input3.total_files
|
|
@@ -572,8 +614,231 @@ var validRunGRIN2Response = (input) => {
|
|
|
572
614
|
path: _path2 + ".failed_files",
|
|
573
615
|
expected: "number",
|
|
574
616
|
value: input3.failed_files
|
|
617
|
+
}), (Array.isArray(input3.errors) || $report(_exceptionable2, {
|
|
618
|
+
path: _path2 + ".errors",
|
|
619
|
+
expected: "Array<RustErrorEntry>",
|
|
620
|
+
value: input3.errors
|
|
621
|
+
})) && input3.errors.map((elem, _index4) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
|
|
622
|
+
path: _path2 + ".errors[" + _index4 + "]",
|
|
623
|
+
expected: "RustErrorEntry",
|
|
624
|
+
value: elem
|
|
625
|
+
})) && $vo2(elem, _path2 + ".errors[" + _index4 + "]", _exceptionable2) || $report(_exceptionable2, {
|
|
626
|
+
path: _path2 + ".errors[" + _index4 + "]",
|
|
627
|
+
expected: "RustErrorEntry",
|
|
628
|
+
value: elem
|
|
629
|
+
})).every((flag) => flag) || $report(_exceptionable2, {
|
|
630
|
+
path: _path2 + ".errors",
|
|
631
|
+
expected: "Array<RustErrorEntry>",
|
|
632
|
+
value: input3.errors
|
|
633
|
+
}), "number" === typeof input3.filtered_records || $report(_exceptionable2, {
|
|
634
|
+
path: _path2 + ".filtered_records",
|
|
635
|
+
expected: "number",
|
|
636
|
+
value: input3.filtered_records
|
|
637
|
+
}), "number" === typeof input3.filtered_maf_records || $report(_exceptionable2, {
|
|
638
|
+
path: _path2 + ".filtered_maf_records",
|
|
639
|
+
expected: "number",
|
|
640
|
+
value: input3.filtered_maf_records
|
|
641
|
+
}), "number" === typeof input3.filtered_cnv_records || $report(_exceptionable2, {
|
|
642
|
+
path: _path2 + ".filtered_cnv_records",
|
|
643
|
+
expected: "number",
|
|
644
|
+
value: input3.filtered_cnv_records
|
|
645
|
+
}), "number" === typeof input3.included_maf_records || $report(_exceptionable2, {
|
|
646
|
+
path: _path2 + ".included_maf_records",
|
|
647
|
+
expected: "number",
|
|
648
|
+
value: input3.included_maf_records
|
|
649
|
+
}), "number" === typeof input3.included_cnv_records || $report(_exceptionable2, {
|
|
650
|
+
path: _path2 + ".included_cnv_records",
|
|
651
|
+
expected: "number",
|
|
652
|
+
value: input3.included_cnv_records
|
|
653
|
+
}), ("object" === typeof input3.filtered_records_by_case && null !== input3.filtered_records_by_case && false === Array.isArray(input3.filtered_records_by_case) || $report(_exceptionable2, {
|
|
654
|
+
path: _path2 + ".filtered_records_by_case",
|
|
655
|
+
expected: "Record<string, __type>",
|
|
656
|
+
value: input3.filtered_records_by_case
|
|
657
|
+
})) && $vo4(input3.filtered_records_by_case, _path2 + ".filtered_records_by_case", _exceptionable2) || $report(_exceptionable2, {
|
|
658
|
+
path: _path2 + ".filtered_records_by_case",
|
|
659
|
+
expected: "Record<string, __type>",
|
|
660
|
+
value: input3.filtered_records_by_case
|
|
661
|
+
}), ("object" === typeof input3.hyper_mutator_records && null !== input3.hyper_mutator_records && false === Array.isArray(input3.hyper_mutator_records) || $report(_exceptionable2, {
|
|
662
|
+
path: _path2 + ".hyper_mutator_records",
|
|
663
|
+
expected: "Record<string, Array<string>>",
|
|
664
|
+
value: input3.hyper_mutator_records
|
|
665
|
+
})) && $vo10(input3.hyper_mutator_records, _path2 + ".hyper_mutator_records", _exceptionable2) || $report(_exceptionable2, {
|
|
666
|
+
path: _path2 + ".hyper_mutator_records",
|
|
667
|
+
expected: "Record<string, Array<string>>",
|
|
668
|
+
value: input3.hyper_mutator_records
|
|
669
|
+
})].every((flag) => flag);
|
|
670
|
+
const $vo4 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
|
|
671
|
+
const value = input3[key];
|
|
672
|
+
if (void 0 === value)
|
|
673
|
+
return true;
|
|
674
|
+
if (RegExp(/(.*)/).test(key))
|
|
675
|
+
return ("object" === typeof value && null !== value || $report(_exceptionable2, {
|
|
676
|
+
path: _path2 + $join(key),
|
|
677
|
+
expected: "__type",
|
|
678
|
+
value
|
|
679
|
+
})) && $vo5(value, _path2 + $join(key), _exceptionable2) || $report(_exceptionable2, {
|
|
680
|
+
path: _path2 + $join(key),
|
|
681
|
+
expected: "__type",
|
|
682
|
+
value
|
|
683
|
+
});
|
|
684
|
+
return true;
|
|
685
|
+
}).every((flag) => flag)].every((flag) => flag);
|
|
686
|
+
const $vo5 = (input3, _path2, _exceptionable2 = true) => [("object" === typeof input3.maf && null !== input3.maf || $report(_exceptionable2, {
|
|
687
|
+
path: _path2 + ".maf",
|
|
688
|
+
expected: "__type.o1",
|
|
689
|
+
value: input3.maf
|
|
690
|
+
})) && $vo6(input3.maf, _path2 + ".maf", _exceptionable2) || $report(_exceptionable2, {
|
|
691
|
+
path: _path2 + ".maf",
|
|
692
|
+
expected: "__type.o1",
|
|
693
|
+
value: input3.maf
|
|
694
|
+
}), ("object" === typeof input3.cnv && null !== input3.cnv || $report(_exceptionable2, {
|
|
695
|
+
path: _path2 + ".cnv",
|
|
696
|
+
expected: "__type.o2",
|
|
697
|
+
value: input3.cnv
|
|
698
|
+
})) && $vo9(input3.cnv, _path2 + ".cnv", _exceptionable2) || $report(_exceptionable2, {
|
|
699
|
+
path: _path2 + ".cnv",
|
|
700
|
+
expected: "__type.o2",
|
|
701
|
+
value: input3.cnv
|
|
702
|
+
})].every((flag) => flag);
|
|
703
|
+
const $vo6 = (input3, _path2, _exceptionable2 = true) => [("object" === typeof input3.matched_consequences && null !== input3.matched_consequences && false === Array.isArray(input3.matched_consequences) || $report(_exceptionable2, {
|
|
704
|
+
path: _path2 + ".matched_consequences",
|
|
705
|
+
expected: "Record<string, any>",
|
|
706
|
+
value: input3.matched_consequences
|
|
707
|
+
})) && $vo7(input3.matched_consequences, _path2 + ".matched_consequences", _exceptionable2) || $report(_exceptionable2, {
|
|
708
|
+
path: _path2 + ".matched_consequences",
|
|
709
|
+
expected: "Record<string, any>",
|
|
710
|
+
value: input3.matched_consequences
|
|
711
|
+
}), ("object" === typeof input3.rejected_consequences && null !== input3.rejected_consequences && false === Array.isArray(input3.rejected_consequences) || $report(_exceptionable2, {
|
|
712
|
+
path: _path2 + ".rejected_consequences",
|
|
713
|
+
expected: "Record<string, any>",
|
|
714
|
+
value: input3.rejected_consequences
|
|
715
|
+
})) && $vo7(input3.rejected_consequences, _path2 + ".rejected_consequences", _exceptionable2) || $report(_exceptionable2, {
|
|
716
|
+
path: _path2 + ".rejected_consequences",
|
|
717
|
+
expected: "Record<string, any>",
|
|
718
|
+
value: input3.rejected_consequences
|
|
719
|
+
}), "number" === typeof input3.t_alt_count || $report(_exceptionable2, {
|
|
720
|
+
path: _path2 + ".t_alt_count",
|
|
721
|
+
expected: "number",
|
|
722
|
+
value: input3.t_alt_count
|
|
723
|
+
}), "number" === typeof input3.t_depth || $report(_exceptionable2, {
|
|
724
|
+
path: _path2 + ".t_depth",
|
|
725
|
+
expected: "number",
|
|
726
|
+
value: input3.t_depth
|
|
727
|
+
}), "number" === typeof input3.invalid_rows || $report(_exceptionable2, {
|
|
728
|
+
path: _path2 + ".invalid_rows",
|
|
729
|
+
expected: "number",
|
|
730
|
+
value: input3.invalid_rows
|
|
731
|
+
}), "number" === typeof input3.excluded_by_min_depth || $report(_exceptionable2, {
|
|
732
|
+
path: _path2 + ".excluded_by_min_depth",
|
|
733
|
+
expected: "number",
|
|
734
|
+
value: input3.excluded_by_min_depth
|
|
735
|
+
}), "number" === typeof input3.excluded_by_min_alt_count || $report(_exceptionable2, {
|
|
736
|
+
path: _path2 + ".excluded_by_min_alt_count",
|
|
737
|
+
expected: "number",
|
|
738
|
+
value: input3.excluded_by_min_alt_count
|
|
739
|
+
}), "number" === typeof input3.excluded_by_consequence_type || $report(_exceptionable2, {
|
|
740
|
+
path: _path2 + ".excluded_by_consequence_type",
|
|
741
|
+
expected: "number",
|
|
742
|
+
value: input3.excluded_by_consequence_type
|
|
743
|
+
}), "number" === typeof input3.total_processed || $report(_exceptionable2, {
|
|
744
|
+
path: _path2 + ".total_processed",
|
|
745
|
+
expected: "number",
|
|
746
|
+
value: input3.total_processed
|
|
747
|
+
}), "number" === typeof input3.total_included || $report(_exceptionable2, {
|
|
748
|
+
path: _path2 + ".total_included",
|
|
749
|
+
expected: "number",
|
|
750
|
+
value: input3.total_included
|
|
751
|
+
}), ("object" === typeof input3.skipped_chromosomes && null !== input3.skipped_chromosomes && false === Array.isArray(input3.skipped_chromosomes) || $report(_exceptionable2, {
|
|
752
|
+
path: _path2 + ".skipped_chromosomes",
|
|
753
|
+
expected: "Record<string, number>",
|
|
754
|
+
value: input3.skipped_chromosomes
|
|
755
|
+
})) && $vo8(input3.skipped_chromosomes, _path2 + ".skipped_chromosomes", _exceptionable2) || $report(_exceptionable2, {
|
|
756
|
+
path: _path2 + ".skipped_chromosomes",
|
|
757
|
+
expected: "Record<string, number>",
|
|
758
|
+
value: input3.skipped_chromosomes
|
|
759
|
+
})].every((flag) => flag);
|
|
760
|
+
const $vo7 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
|
|
761
|
+
const value = input3[key];
|
|
762
|
+
if (void 0 === value)
|
|
763
|
+
return true;
|
|
764
|
+
if (RegExp(/(.*)/).test(key))
|
|
765
|
+
return true;
|
|
766
|
+
return true;
|
|
767
|
+
}).every((flag) => flag)].every((flag) => flag);
|
|
768
|
+
const $vo8 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
|
|
769
|
+
const value = input3[key];
|
|
770
|
+
if (void 0 === value)
|
|
771
|
+
return true;
|
|
772
|
+
if (RegExp(/(.*)/).test(key))
|
|
773
|
+
return "number" === typeof value || $report(_exceptionable2, {
|
|
774
|
+
path: _path2 + $join(key),
|
|
775
|
+
expected: "number",
|
|
776
|
+
value
|
|
777
|
+
});
|
|
778
|
+
return true;
|
|
779
|
+
}).every((flag) => flag)].every((flag) => flag);
|
|
780
|
+
const $vo9 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.segment_mean || $report(_exceptionable2, {
|
|
781
|
+
path: _path2 + ".segment_mean",
|
|
782
|
+
expected: "number",
|
|
783
|
+
value: input3.segment_mean
|
|
784
|
+
}), "number" === typeof input3.seg_length || $report(_exceptionable2, {
|
|
785
|
+
path: _path2 + ".seg_length",
|
|
786
|
+
expected: "number",
|
|
787
|
+
value: input3.seg_length
|
|
788
|
+
}), "number" === typeof input3.invalid_rows || $report(_exceptionable2, {
|
|
789
|
+
path: _path2 + ".invalid_rows",
|
|
790
|
+
expected: "number",
|
|
791
|
+
value: input3.invalid_rows
|
|
792
|
+
}), "number" === typeof input3.excluded_by_loss_threshold || $report(_exceptionable2, {
|
|
793
|
+
path: _path2 + ".excluded_by_loss_threshold",
|
|
794
|
+
expected: "number",
|
|
795
|
+
value: input3.excluded_by_loss_threshold
|
|
796
|
+
}), "number" === typeof input3.excluded_by_gain_threshold || $report(_exceptionable2, {
|
|
797
|
+
path: _path2 + ".excluded_by_gain_threshold",
|
|
798
|
+
expected: "number",
|
|
799
|
+
value: input3.excluded_by_gain_threshold
|
|
800
|
+
}), "number" === typeof input3.excluded_by_segment_length || $report(_exceptionable2, {
|
|
801
|
+
path: _path2 + ".excluded_by_segment_length",
|
|
802
|
+
expected: "number",
|
|
803
|
+
value: input3.excluded_by_segment_length
|
|
804
|
+
}), "number" === typeof input3.total_processed || $report(_exceptionable2, {
|
|
805
|
+
path: _path2 + ".total_processed",
|
|
806
|
+
expected: "number",
|
|
807
|
+
value: input3.total_processed
|
|
808
|
+
}), "number" === typeof input3.total_included || $report(_exceptionable2, {
|
|
809
|
+
path: _path2 + ".total_included",
|
|
810
|
+
expected: "number",
|
|
811
|
+
value: input3.total_included
|
|
812
|
+
}), ("object" === typeof input3.skipped_chromosomes && null !== input3.skipped_chromosomes && false === Array.isArray(input3.skipped_chromosomes) || $report(_exceptionable2, {
|
|
813
|
+
path: _path2 + ".skipped_chromosomes",
|
|
814
|
+
expected: "Record<string, number>",
|
|
815
|
+
value: input3.skipped_chromosomes
|
|
816
|
+
})) && $vo8(input3.skipped_chromosomes, _path2 + ".skipped_chromosomes", _exceptionable2) || $report(_exceptionable2, {
|
|
817
|
+
path: _path2 + ".skipped_chromosomes",
|
|
818
|
+
expected: "Record<string, number>",
|
|
819
|
+
value: input3.skipped_chromosomes
|
|
575
820
|
})].every((flag) => flag);
|
|
576
|
-
const $
|
|
821
|
+
const $vo10 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
|
|
822
|
+
const value = input3[key];
|
|
823
|
+
if (void 0 === value)
|
|
824
|
+
return true;
|
|
825
|
+
if (RegExp(/(.*)/).test(key))
|
|
826
|
+
return (Array.isArray(value) || $report(_exceptionable2, {
|
|
827
|
+
path: _path2 + $join(key),
|
|
828
|
+
expected: "Array<string>",
|
|
829
|
+
value
|
|
830
|
+
})) && value.map((elem, _index5) => "string" === typeof elem || $report(_exceptionable2, {
|
|
831
|
+
path: _path2 + $join(key) + "[" + _index5 + "]",
|
|
832
|
+
expected: "string",
|
|
833
|
+
value: elem
|
|
834
|
+
})).every((flag) => flag) || $report(_exceptionable2, {
|
|
835
|
+
path: _path2 + $join(key),
|
|
836
|
+
expected: "Array<string>",
|
|
837
|
+
value
|
|
838
|
+
});
|
|
839
|
+
return true;
|
|
840
|
+
}).every((flag) => flag)].every((flag) => flag);
|
|
841
|
+
const $vo11 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.rustProcessingTime || $report(_exceptionable2, {
|
|
577
842
|
path: _path2 + ".rustProcessingTime",
|
|
578
843
|
expected: "number",
|
|
579
844
|
value: input3.rustProcessingTime
|
package/dist/gdc.grin2.js
CHANGED
package/dist/index.js
CHANGED
|
@@ -122,7 +122,7 @@ import {
|
|
|
122
122
|
ProfileScoresPayload,
|
|
123
123
|
validProfileScoresRequest,
|
|
124
124
|
validProfileScoresResponse
|
|
125
|
-
} from "./chunk-
|
|
125
|
+
} from "./chunk-FD6CMKNN.js";
|
|
126
126
|
import {
|
|
127
127
|
sampleWsiAiApiPayload,
|
|
128
128
|
validSampleWSIAiApiRequest,
|
|
@@ -200,7 +200,7 @@ import {
|
|
|
200
200
|
validGdcGRIN2listResponse,
|
|
201
201
|
validRunGRIN2Request,
|
|
202
202
|
validRunGRIN2Response
|
|
203
|
-
} from "./chunk-
|
|
203
|
+
} from "./chunk-UMYBO3H4.js";
|
|
204
204
|
import {
|
|
205
205
|
gdcMafPayload,
|
|
206
206
|
validGdcMafRequest,
|
package/dist/profileScores.js
CHANGED
package/package.json
CHANGED
package/src/dataset.ts
CHANGED
|
@@ -1519,19 +1519,6 @@ type MutationSet = {
|
|
|
1519
1519
|
}
|
|
1520
1520
|
|
|
1521
1521
|
/** different methods to return samples with assay availability info */
|
|
1522
|
-
type DtAssayAvailability = DtAssayAvailabilityGetter | DtAssayAvailabilityTerm
|
|
1523
|
-
|
|
1524
|
-
/** using ds-supplied getter */
|
|
1525
|
-
type DtAssayAvailabilityGetter = {
|
|
1526
|
-
/** define q
|
|
1527
|
-
returns:
|
|
1528
|
-
{
|
|
1529
|
-
yesSamples: Set() of sample ids
|
|
1530
|
-
noSamples: Set() of sample ids
|
|
1531
|
-
}
|
|
1532
|
-
*/
|
|
1533
|
-
get: (q: any) => any
|
|
1534
|
-
}
|
|
1535
1522
|
/** using dictionary term */
|
|
1536
1523
|
type DtAssayAvailabilityTerm = {
|
|
1537
1524
|
/** id of this assay term for this dt */
|
|
@@ -1542,21 +1529,32 @@ type DtAssayAvailabilityTerm = {
|
|
|
1542
1529
|
yes: { value: string[] }
|
|
1543
1530
|
/** categories meaning the sample doesn't have this assay */
|
|
1544
1531
|
no: { value: string[] }
|
|
1532
|
+
/** dynamically generated cached sample lists on server launch, can also be ds-supplied.
|
|
1533
|
+
each is a Set of sample integer id (non-gdc ds) or sample name (case uuid for gdc)
|
|
1534
|
+
*/
|
|
1535
|
+
yesSamples?: Set<string | number>
|
|
1536
|
+
noSamples?: Set<string | number>
|
|
1545
1537
|
}
|
|
1546
1538
|
|
|
1547
1539
|
type DtAssayAvailabilityByOrigin = {
|
|
1548
1540
|
byOrigin: {
|
|
1549
1541
|
/** each key is an origin value or category */
|
|
1550
|
-
[index: string]:
|
|
1542
|
+
[index: string]: DtAssayAvailabilityTerm
|
|
1551
1543
|
}
|
|
1552
1544
|
}
|
|
1553
1545
|
|
|
1546
|
+
/** assay availability can be set up as below, during server init it will query by assay dictionary terms to populate yes/no samples for each dt
|
|
1547
|
+
or as in gdc, it is entirely setup ad-hoc
|
|
1548
|
+
*/
|
|
1554
1549
|
type Mds3AssayAvailability = {
|
|
1555
1550
|
/** object of key-value pairs. keys are dt values */
|
|
1556
1551
|
byDt: {
|
|
1557
1552
|
/** each index is a dt value */
|
|
1558
|
-
[index: number]: DtAssayAvailabilityByOrigin |
|
|
1553
|
+
[index: number]: DtAssayAvailabilityByOrigin | DtAssayAvailabilityTerm
|
|
1559
1554
|
}
|
|
1555
|
+
/** if true, ds will use both filter and filter0 to filter samples (this is a temp quick fix)
|
|
1556
|
+
*/
|
|
1557
|
+
useFilter0?: true
|
|
1560
1558
|
}
|
|
1561
1559
|
|
|
1562
1560
|
// mds legacy; delete when all are migrated to mds3
|
package/src/routes/gdc.grin2.ts
CHANGED
|
@@ -133,9 +133,51 @@ export type RustErrorEntry = {
|
|
|
133
133
|
|
|
134
134
|
/** Summary information from Rust processing */
|
|
135
135
|
export type RustSummary = {
|
|
136
|
+
type: 'summary'
|
|
136
137
|
total_files: number
|
|
137
138
|
successful_files: number
|
|
138
139
|
failed_files: number
|
|
140
|
+
errors: RustErrorEntry[]
|
|
141
|
+
filtered_records: number
|
|
142
|
+
filtered_maf_records: number
|
|
143
|
+
filtered_cnv_records: number
|
|
144
|
+
included_maf_records: number
|
|
145
|
+
included_cnv_records: number
|
|
146
|
+
|
|
147
|
+
/** The complex nested structure of the per case object
|
|
148
|
+
* Records filtered by case, with MAF and CNV statistics
|
|
149
|
+
*/
|
|
150
|
+
filtered_records_by_case: Record<
|
|
151
|
+
string,
|
|
152
|
+
{
|
|
153
|
+
maf: {
|
|
154
|
+
matched_consequences: Record<string, any>
|
|
155
|
+
rejected_consequences: Record<string, any>
|
|
156
|
+
t_alt_count: number
|
|
157
|
+
t_depth: number
|
|
158
|
+
invalid_rows: number
|
|
159
|
+
excluded_by_min_depth: number
|
|
160
|
+
excluded_by_min_alt_count: number
|
|
161
|
+
excluded_by_consequence_type: number
|
|
162
|
+
total_processed: number
|
|
163
|
+
total_included: number
|
|
164
|
+
skipped_chromosomes: Record<string, number>
|
|
165
|
+
}
|
|
166
|
+
cnv: {
|
|
167
|
+
segment_mean: number
|
|
168
|
+
seg_length: number
|
|
169
|
+
invalid_rows: number
|
|
170
|
+
excluded_by_loss_threshold: number
|
|
171
|
+
excluded_by_gain_threshold: number
|
|
172
|
+
excluded_by_segment_length: number
|
|
173
|
+
total_processed: number
|
|
174
|
+
total_included: number
|
|
175
|
+
skipped_chromosomes: Record<string, number>
|
|
176
|
+
}
|
|
177
|
+
}
|
|
178
|
+
>
|
|
179
|
+
|
|
180
|
+
hyper_mutator_records: Record<string, string[]>
|
|
139
181
|
}
|
|
140
182
|
|
|
141
183
|
/** Structured output from Rust GRIN2 processing */
|