@sjcrh/proteinpaint-types 2.152.0 → 2.153.1-2

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 (12) hide show
  1. package/dist/{chunk-2WSENLMK.js → chunk-46YIGVUP.js} +44 -24
  2. package/dist/{chunk-HI2IT25E.js → chunk-4LZHDYI3.js} +60 -1
  3. package/dist/{chunk-MIOIOFBZ.js → chunk-TD4YLTHL.js} +17 -3
  4. package/dist/gdc.grin2.js +1 -1
  5. package/dist/gdc.maf.js +1 -1
  6. package/dist/grin2.js +1 -1
  7. package/dist/index.js +3 -3
  8. package/package.json +7 -2
  9. package/src/dataset.ts +7 -280
  10. package/src/routes/gdc.grin2.ts +2 -2
  11. package/src/routes/gdc.maf.ts +3 -3
  12. package/src/routes/grin2.ts +11 -0
package/dist/{chunk-2WSENLMK.js → chunk-46YIGVUP.js} RENAMED
@@ -28,9 +28,10 @@ var runGRIN2Payload = {
28
28
  var validGdcGRIN2listRequest = (input) => {
29
29
  const errors = [];
30
30
  const __is = (input2) => {
31
- const $io0 = (input3) => (void 0 === input3.mafOptions || "object" === typeof input3.mafOptions && null !== input3.mafOptions && $io1(input3.mafOptions)) && (void 0 === input3.cnvOptions || "object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) && $io2(input3.cnvOptions)) && true;
32
- const $io1 = (input3) => "WXS" === input3.experimentalStrategy;
33
- const $io2 = (input3) => void 0 === input3.dataType || "string" === typeof input3.dataType;
31
+ const $io0 = (input3) => (void 0 === input3.mafOptions || "object" === typeof input3.mafOptions && null !== input3.mafOptions && $io1(input3.mafOptions)) && (void 0 === input3.cnvOptions || "object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) && $io3(input3.cnvOptions)) && true;
32
+ const $io1 = (input3) => "object" === typeof input3.experimentalStrategy && null !== input3.experimentalStrategy && $io2(input3.experimentalStrategy);
33
+ const $io2 = (input3) => "WXS" === input3.wxs;
34
+ const $io3 = (input3) => void 0 === input3.dataType || "string" === typeof input3.dataType;
34
35
  return "object" === typeof input2 && null !== input2 && false === Array.isArray(input2) && $io0(input2);
35
36
  };
36
37
  if (false === __is(input)) {
@@ -48,17 +49,26 @@ var validGdcGRIN2listRequest = (input) => {
48
49
  path: _path2 + ".cnvOptions",
49
50
  expected: "(__type.o1 | undefined)",
50
51
  value: input3.cnvOptions
51
- })) && $vo2(input3.cnvOptions, _path2 + ".cnvOptions", _exceptionable2) || $report(_exceptionable2, {
52
+ })) && $vo3(input3.cnvOptions, _path2 + ".cnvOptions", _exceptionable2) || $report(_exceptionable2, {
52
53
  path: _path2 + ".cnvOptions",
53
54
  expected: "(__type.o1 | undefined)",
54
55
  value: input3.cnvOptions
55
56
  }), true].every((flag) => flag);
56
- const $vo1 = (input3, _path2, _exceptionable2 = true) => ["WXS" === input3.experimentalStrategy || $report(_exceptionable2, {
57
+ const $vo1 = (input3, _path2, _exceptionable2 = true) => [("object" === typeof input3.experimentalStrategy && null !== input3.experimentalStrategy || $report(_exceptionable2, {
57
58
  path: _path2 + ".experimentalStrategy",
58
- expected: '"WXS"',
59
+ expected: "ExperimentalStrategy",
60
+ value: input3.experimentalStrategy
61
+ })) && $vo2(input3.experimentalStrategy, _path2 + ".experimentalStrategy", _exceptionable2) || $report(_exceptionable2, {
62
+ path: _path2 + ".experimentalStrategy",
63
+ expected: "ExperimentalStrategy",
59
64
  value: input3.experimentalStrategy
60
65
  })].every((flag) => flag);
61
- const $vo2 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.dataType || "string" === typeof input3.dataType || $report(_exceptionable2, {
66
+ const $vo2 = (input3, _path2, _exceptionable2 = true) => ["WXS" === input3.wxs || $report(_exceptionable2, {
67
+ path: _path2 + ".wxs",
68
+ expected: '"WXS"',
69
+ value: input3.wxs
70
+ })].every((flag) => flag);
71
+ const $vo3 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.dataType || "string" === typeof input3.dataType || $report(_exceptionable2, {
62
72
  path: _path2 + ".dataType",
63
73
  expected: "(string | undefined)",
64
74
  value: input3.dataType
@@ -84,15 +94,16 @@ var validGdcGRIN2listRequest = (input) => {
84
94
  var validGdcGRIN2listResponse = (input) => {
85
95
  const errors = [];
86
96
  const __is = (input2) => {
87
- const $io0 = (input3) => (void 0 === input3.mafFiles || "object" === typeof input3.mafFiles && null !== input3.mafFiles && $io1(input3.mafFiles)) && (void 0 === input3.cnvFiles || "object" === typeof input3.cnvFiles && null !== input3.cnvFiles && $io8(input3.cnvFiles));
88
- const $io1 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && "number" === typeof input3.filesTotal && "number" === typeof input3.maxTotalSizeCompressed && (void 0 === input3.fileCounts || "object" === typeof input3.fileCounts && null !== input3.fileCounts && $io3(input3.fileCounts)) && (void 0 === input3.appliedFilters || "object" === typeof input3.appliedFilters && null !== input3.appliedFilters && false === Array.isArray(input3.appliedFilters) && $io4(input3.appliedFilters)) && (void 0 === input3.deduplicationStats || "object" === typeof input3.deduplicationStats && null !== input3.deduplicationStats && $io5(input3.deduplicationStats));
97
+ const $io0 = (input3) => (void 0 === input3.mafFiles || "object" === typeof input3.mafFiles && null !== input3.mafFiles && $io1(input3.mafFiles)) && (void 0 === input3.cnvFiles || "object" === typeof input3.cnvFiles && null !== input3.cnvFiles && $io9(input3.cnvFiles));
98
+ const $io1 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && "number" === typeof input3.filesTotal && "number" === typeof input3.maxTotalSizeCompressed && (void 0 === input3.fileCounts || "object" === typeof input3.fileCounts && null !== input3.fileCounts && $io3(input3.fileCounts)) && (void 0 === input3.appliedFilters || "object" === typeof input3.appliedFilters && null !== input3.appliedFilters && false === Array.isArray(input3.appliedFilters) && $io4(input3.appliedFilters)) && (void 0 === input3.deduplicationStats || "object" === typeof input3.deduplicationStats && null !== input3.deduplicationStats && $io6(input3.deduplicationStats));
89
99
  const $io2 = (input3) => "string" === typeof input3.id && "string" === typeof input3.case_submitter_id && "string" === typeof input3.case_uuid && "number" === typeof input3.file_size && (Array.isArray(input3.sample_types) && input3.sample_types.every((elem) => "string" === typeof elem)) && "string" === typeof input3.project_id && (void 0 === input3.file_format || "MAF" === input3.file_format);
90
100
  const $io3 = (input3) => "number" === typeof input3.maf;
91
- const $io4 = (input3) => void 0 === input3.experimentalStrategy || "WXS" === input3.experimentalStrategy;
92
- const $io5 = (input3) => "number" === typeof input3.originalFileCount && "number" === typeof input3.deduplicatedFileCount && "number" === typeof input3.duplicatesRemoved && (void 0 === input3.caseDetails || Array.isArray(input3.caseDetails) && input3.caseDetails.every((elem) => "object" === typeof elem && null !== elem && $io6(elem))) && (Array.isArray(input3.filteredFiles) && input3.filteredFiles.every((elem) => "object" === typeof elem && null !== elem && $io7(elem)));
93
- const $io6 = (input3) => "string" === typeof input3.caseName && "number" === typeof input3.fileCount && "number" === typeof input3.keptFileSize;
94
- const $io7 = (input3) => "string" === typeof input3.fileId && "number" === typeof input3.fileSize && "string" === typeof input3.reason;
95
- const $io8 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && "number" === typeof input3.maxTotalSizeCompressed;
101
+ const $io4 = (input3) => void 0 === input3.experimentalStrategy || "object" === typeof input3.experimentalStrategy && null !== input3.experimentalStrategy && $io5(input3.experimentalStrategy);
102
+ const $io5 = (input3) => "WXS" === input3.wxs;
103
+ const $io6 = (input3) => "number" === typeof input3.originalFileCount && "number" === typeof input3.deduplicatedFileCount && "number" === typeof input3.duplicatesRemoved && (void 0 === input3.caseDetails || Array.isArray(input3.caseDetails) && input3.caseDetails.every((elem) => "object" === typeof elem && null !== elem && $io7(elem))) && (Array.isArray(input3.filteredFiles) && input3.filteredFiles.every((elem) => "object" === typeof elem && null !== elem && $io8(elem)));
104
+ const $io7 = (input3) => "string" === typeof input3.caseName && "number" === typeof input3.fileCount && "number" === typeof input3.keptFileSize;
105
+ const $io8 = (input3) => "string" === typeof input3.fileId && "number" === typeof input3.fileSize && "string" === typeof input3.reason;
106
+ const $io9 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && "number" === typeof input3.maxTotalSizeCompressed;
96
107
  return "object" === typeof input2 && null !== input2 && false === Array.isArray(input2) && $io0(input2);
97
108
  };
98
109
  if (false === __is(input)) {
@@ -110,7 +121,7 @@ var validGdcGRIN2listResponse = (input) => {
110
121
  path: _path2 + ".cnvFiles",
111
122
  expected: "(__type.o6 | undefined)",
112
123
  value: input3.cnvFiles
113
- })) && $vo8(input3.cnvFiles, _path2 + ".cnvFiles", _exceptionable2) || $report(_exceptionable2, {
124
+ })) && $vo9(input3.cnvFiles, _path2 + ".cnvFiles", _exceptionable2) || $report(_exceptionable2, {
114
125
  path: _path2 + ".cnvFiles",
115
126
  expected: "(__type.o6 | undefined)",
116
127
  value: input3.cnvFiles
@@ -159,7 +170,7 @@ var validGdcGRIN2listResponse = (input) => {
159
170
  path: _path2 + ".deduplicationStats",
160
171
  expected: "(__type.o3 | undefined)",
161
172
  value: input3.deduplicationStats
162
- })) && $vo5(input3.deduplicationStats, _path2 + ".deduplicationStats", _exceptionable2) || $report(_exceptionable2, {
173
+ })) && $vo6(input3.deduplicationStats, _path2 + ".deduplicationStats", _exceptionable2) || $report(_exceptionable2, {
163
174
  path: _path2 + ".deduplicationStats",
164
175
  expected: "(__type.o3 | undefined)",
165
176
  value: input3.deduplicationStats
@@ -206,12 +217,21 @@ var validGdcGRIN2listResponse = (input) => {
206
217
  expected: "number",
207
218
  value: input3.maf
208
219
  })].every((flag) => flag);
209
- const $vo4 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.experimentalStrategy || "WXS" === input3.experimentalStrategy || $report(_exceptionable2, {
220
+ const $vo4 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.experimentalStrategy || ("object" === typeof input3.experimentalStrategy && null !== input3.experimentalStrategy || $report(_exceptionable2, {
210
221
  path: _path2 + ".experimentalStrategy",
211
- expected: '("WXS" | undefined)',
222
+ expected: "(ExperimentalStrategy | undefined)",
212
223
  value: input3.experimentalStrategy
224
+ })) && $vo5(input3.experimentalStrategy, _path2 + ".experimentalStrategy", _exceptionable2) || $report(_exceptionable2, {
225
+ path: _path2 + ".experimentalStrategy",
226
+ expected: "(ExperimentalStrategy | undefined)",
227
+ value: input3.experimentalStrategy
228
+ })].every((flag) => flag);
229
+ const $vo5 = (input3, _path2, _exceptionable2 = true) => ["WXS" === input3.wxs || $report(_exceptionable2, {
230
+ path: _path2 + ".wxs",
231
+ expected: '"WXS"',
232
+ value: input3.wxs
213
233
  })].every((flag) => flag);
214
- const $vo5 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.originalFileCount || $report(_exceptionable2, {
234
+ const $vo6 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.originalFileCount || $report(_exceptionable2, {
215
235
  path: _path2 + ".originalFileCount",
216
236
  expected: "number",
217
237
  value: input3.originalFileCount
@@ -231,7 +251,7 @@ var validGdcGRIN2listResponse = (input) => {
231
251
  path: _path2 + ".caseDetails[" + _index3 + "]",
232
252
  expected: "__type.o4",
233
253
  value: elem
234
- })) && $vo6(elem, _path2 + ".caseDetails[" + _index3 + "]", _exceptionable2) || $report(_exceptionable2, {
254
+ })) && $vo7(elem, _path2 + ".caseDetails[" + _index3 + "]", _exceptionable2) || $report(_exceptionable2, {
235
255
  path: _path2 + ".caseDetails[" + _index3 + "]",
236
256
  expected: "__type.o4",
237
257
  value: elem
@@ -247,7 +267,7 @@ var validGdcGRIN2listResponse = (input) => {
247
267
  path: _path2 + ".filteredFiles[" + _index4 + "]",
248
268
  expected: "__type.o5",
249
269
  value: elem
250
- })) && $vo7(elem, _path2 + ".filteredFiles[" + _index4 + "]", _exceptionable2) || $report(_exceptionable2, {
270
+ })) && $vo8(elem, _path2 + ".filteredFiles[" + _index4 + "]", _exceptionable2) || $report(_exceptionable2, {
251
271
  path: _path2 + ".filteredFiles[" + _index4 + "]",
252
272
  expected: "__type.o5",
253
273
  value: elem
@@ -256,7 +276,7 @@ var validGdcGRIN2listResponse = (input) => {
256
276
  expected: "Array<__type>.o1",
257
277
  value: input3.filteredFiles
258
278
  })].every((flag) => flag);
259
- const $vo6 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.caseName || $report(_exceptionable2, {
279
+ const $vo7 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.caseName || $report(_exceptionable2, {
260
280
  path: _path2 + ".caseName",
261
281
  expected: "string",
262
282
  value: input3.caseName
@@ -269,7 +289,7 @@ var validGdcGRIN2listResponse = (input) => {
269
289
  expected: "number",
270
290
  value: input3.keptFileSize
271
291
  })].every((flag) => flag);
272
- const $vo7 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.fileId || $report(_exceptionable2, {
292
+ const $vo8 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.fileId || $report(_exceptionable2, {
273
293
  path: _path2 + ".fileId",
274
294
  expected: "string",
275
295
  value: input3.fileId
@@ -282,7 +302,7 @@ var validGdcGRIN2listResponse = (input) => {
282
302
  expected: "string",
283
303
  value: input3.reason
284
304
  })].every((flag) => flag);
285
- const $vo8 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
305
+ const $vo9 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
286
306
  path: _path2 + ".files",
287
307
  expected: "Array<GdcGRIN2File>",
288
308
  value: input3.files
package/dist/{chunk-HI2IT25E.js → chunk-4LZHDYI3.js} RENAMED
@@ -204,8 +204,17 @@ var validGRIN2Response = (input) => {
204
204
  const $io6 = (input3) => "string" === typeof input3.label && "boolean" === typeof input3.sortable;
205
205
  const $io7 = (input3) => "string" === typeof input3.value || "number" === typeof input3.value;
206
206
  const $io8 = (input3) => "number" === typeof input3.processingTime && "number" === typeof input3.grin2Time && "number" === typeof input3.totalTime;
207
- const $io9 = (input3) => (void 0 === input3.totalSamples || "number" === typeof input3.totalSamples) && (void 0 === input3.processedSamples || "number" === typeof input3.processedSamples) && (void 0 === input3.failedSamples || "number" === typeof input3.failedSamples) && (void 0 === input3.failedFiles || Array.isArray(input3.failedFiles) && input3.failedFiles.every((elem) => "object" === typeof elem && null !== elem && $io10(elem))) && (void 0 === input3.totalLesions || "number" === typeof input3.totalLesions) && (void 0 === input3.processedLesions || "number" === typeof input3.processedLesions) && (void 0 === input3.unprocessedSamples || "number" === typeof input3.unprocessedSamples);
207
+ const $io9 = (input3) => (void 0 === input3.totalSamples || "number" === typeof input3.totalSamples) && (void 0 === input3.processedSamples || "number" === typeof input3.processedSamples) && (void 0 === input3.failedSamples || "number" === typeof input3.failedSamples) && (void 0 === input3.failedFiles || Array.isArray(input3.failedFiles) && input3.failedFiles.every((elem) => "object" === typeof elem && null !== elem && $io10(elem))) && (void 0 === input3.totalLesions || "number" === typeof input3.totalLesions) && (void 0 === input3.processedLesions || "number" === typeof input3.processedLesions) && (void 0 === input3.unprocessedSamples || "number" === typeof input3.unprocessedSamples) && (void 0 === input3.lesionCounts || "object" === typeof input3.lesionCounts && null !== input3.lesionCounts && false === Array.isArray(input3.lesionCounts) && $io11(input3.lesionCounts));
208
208
  const $io10 = (input3) => "string" === typeof input3.sampleName && "string" === typeof input3.filePath && "string" === typeof input3.error;
209
+ const $io11 = (input3) => (void 0 === input3.total || "number" === typeof input3.total) && (void 0 === input3.byType || "object" === typeof input3.byType && null !== input3.byType && false === Array.isArray(input3.byType) && $io12(input3.byType));
210
+ const $io12 = (input3) => Object.keys(input3).every((key) => {
211
+ const value = input3[key];
212
+ if (void 0 === value)
213
+ return true;
214
+ if (RegExp(/(.*)/).test(key))
215
+ return "object" === typeof value && null !== value && ("number" === typeof value.count && "boolean" === typeof value.capped && "number" === typeof value.samples);
216
+ return true;
217
+ });
209
218
  return "object" === typeof input2 && null !== input2 && $io0(input2);
210
219
  };
211
220
  if (false === __is(input)) {
@@ -500,6 +509,14 @@ var validGRIN2Response = (input) => {
500
509
  path: _path2 + ".unprocessedSamples",
501
510
  expected: "(number | undefined)",
502
511
  value: input3.unprocessedSamples
512
+ }), void 0 === input3.lesionCounts || ("object" === typeof input3.lesionCounts && null !== input3.lesionCounts && false === Array.isArray(input3.lesionCounts) || $report(_exceptionable2, {
513
+ path: _path2 + ".lesionCounts",
514
+ expected: "(__type.o8 | undefined)",
515
+ value: input3.lesionCounts
516
+ })) && $vo11(input3.lesionCounts, _path2 + ".lesionCounts", _exceptionable2) || $report(_exceptionable2, {
517
+ path: _path2 + ".lesionCounts",
518
+ expected: "(__type.o8 | undefined)",
519
+ value: input3.lesionCounts
503
520
  })].every((flag) => flag);
504
521
  const $vo10 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.sampleName || $report(_exceptionable2, {
505
522
  path: _path2 + ".sampleName",
@@ -514,6 +531,48 @@ var validGRIN2Response = (input) => {
514
531
  expected: "string",
515
532
  value: input3.error
516
533
  })].every((flag) => flag);
534
+ const $vo11 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.total || "number" === typeof input3.total || $report(_exceptionable2, {
535
+ path: _path2 + ".total",
536
+ expected: "(number | undefined)",
537
+ value: input3.total
538
+ }), void 0 === input3.byType || ("object" === typeof input3.byType && null !== input3.byType && false === Array.isArray(input3.byType) || $report(_exceptionable2, {
539
+ path: _path2 + ".byType",
540
+ expected: "(Record<string, __type>.o1 | undefined)",
541
+ value: input3.byType
542
+ })) && $vo12(input3.byType, _path2 + ".byType", _exceptionable2) || $report(_exceptionable2, {
543
+ path: _path2 + ".byType",
544
+ expected: "(Record<string, __type>.o1 | undefined)",
545
+ value: input3.byType
546
+ })].every((flag) => flag);
547
+ const $vo12 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
548
+ const value = input3[key];
549
+ if (void 0 === value)
550
+ return true;
551
+ if (RegExp(/(.*)/).test(key))
552
+ return ("object" === typeof value && null !== value || $report(_exceptionable2, {
553
+ path: _path2 + $join(key),
554
+ expected: "__type.o9",
555
+ value
556
+ })) && $vo13(value, _path2 + $join(key), _exceptionable2) || $report(_exceptionable2, {
557
+ path: _path2 + $join(key),
558
+ expected: "__type.o9",
559
+ value
560
+ });
561
+ return true;
562
+ }).every((flag) => flag)].every((flag) => flag);
563
+ const $vo13 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.count || $report(_exceptionable2, {
564
+ path: _path2 + ".count",
565
+ expected: "number",
566
+ value: input3.count
567
+ }), "boolean" === typeof input3.capped || $report(_exceptionable2, {
568
+ path: _path2 + ".capped",
569
+ expected: "boolean",
570
+ value: input3.capped
571
+ }), "number" === typeof input3.samples || $report(_exceptionable2, {
572
+ path: _path2 + ".samples",
573
+ expected: "number",
574
+ value: input3.samples
575
+ })].every((flag) => flag);
517
576
  return ("object" === typeof input2 && null !== input2 || $report(true, {
518
577
  path: _path + "",
519
578
  expected: "GRIN2Response",
package/dist/{chunk-MIOIOFBZ.js → chunk-TD4YLTHL.js} RENAMED
@@ -21,17 +21,31 @@ var gdcMafPayload = {
21
21
  var validGdcMafRequest = (input) => {
22
22
  const errors = [];
23
23
  const __is = (input2) => {
24
- const $io0 = (input3) => ("Targeted Sequencing" === input3.experimentalStrategy || "WXS" === input3.experimentalStrategy) && true;
24
+ const $io0 = (input3) => "object" === typeof input3.experimentalStrategy && null !== input3.experimentalStrategy && $io1(input3.experimentalStrategy) && true;
25
+ const $io1 = (input3) => "Targeted Sequencing" === input3.targeted && "WXS" === input3.wxs;
25
26
  return "object" === typeof input2 && null !== input2 && $io0(input2);
26
27
  };
27
28
  if (false === __is(input)) {
28
29
  const $report = import_typia.createValidate.report(errors);
29
30
  ((input2, _path, _exceptionable = true) => {
30
- const $vo0 = (input3, _path2, _exceptionable2 = true) => ["Targeted Sequencing" === input3.experimentalStrategy || "WXS" === input3.experimentalStrategy || $report(_exceptionable2, {
31
+ const $vo0 = (input3, _path2, _exceptionable2 = true) => [("object" === typeof input3.experimentalStrategy && null !== input3.experimentalStrategy || $report(_exceptionable2, {
31
32
  path: _path2 + ".experimentalStrategy",
32
- expected: '("Targeted Sequencing" | "WXS")',
33
+ expected: "ExperimentalStrategy",
34
+ value: input3.experimentalStrategy
35
+ })) && $vo1(input3.experimentalStrategy, _path2 + ".experimentalStrategy", _exceptionable2) || $report(_exceptionable2, {
36
+ path: _path2 + ".experimentalStrategy",
37
+ expected: "ExperimentalStrategy",
33
38
  value: input3.experimentalStrategy
34
39
  }), true].every((flag) => flag);
40
+ const $vo1 = (input3, _path2, _exceptionable2 = true) => ["Targeted Sequencing" === input3.targeted || $report(_exceptionable2, {
41
+ path: _path2 + ".targeted",
42
+ expected: '"Targeted Sequencing"',
43
+ value: input3.targeted
44
+ }), "WXS" === input3.wxs || $report(_exceptionable2, {
45
+ path: _path2 + ".wxs",
46
+ expected: '"WXS"',
47
+ value: input3.wxs
48
+ })].every((flag) => flag);
35
49
  return ("object" === typeof input2 && null !== input2 || $report(true, {
36
50
  path: _path + "",
37
51
  expected: "GdcMafRequest",
package/dist/gdc.grin2.js CHANGED
@@ -5,7 +5,7 @@ import {
5
5
  validGdcGRIN2listResponse,
6
6
  validRunGRIN2Request,
7
7
  validRunGRIN2Response
8
- } from "./chunk-2WSENLMK.js";
8
+ } from "./chunk-46YIGVUP.js";
9
9
  import "./chunk-YNHC5SXO.js";
10
10
  export {
11
11
  gdcGRIN2listPayload,
package/dist/gdc.maf.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  gdcMafPayload,
3
3
  validGdcMafRequest,
4
4
  validGdcMafResponse
5
- } from "./chunk-MIOIOFBZ.js";
5
+ } from "./chunk-TD4YLTHL.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  gdcMafPayload,
package/dist/grin2.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  GRIN2Payload,
3
3
  validGRIN2Request,
4
4
  validGRIN2Response
5
- } from "./chunk-HI2IT25E.js";
5
+ } from "./chunk-4LZHDYI3.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  GRIN2Payload,
package/dist/index.js CHANGED
@@ -192,7 +192,7 @@ import {
192
192
  gdcMafPayload,
193
193
  validGdcMafRequest,
194
194
  validGdcMafResponse
195
- } from "./chunk-MIOIOFBZ.js";
195
+ } from "./chunk-TD4YLTHL.js";
196
196
  import {
197
197
  GdcMafPayload,
198
198
  validGdcMafBuildRequest,
@@ -217,7 +217,7 @@ import {
217
217
  GRIN2Payload,
218
218
  validGRIN2Request,
219
219
  validGRIN2Response
220
- } from "./chunk-HI2IT25E.js";
220
+ } from "./chunk-4LZHDYI3.js";
221
221
  import {
222
222
  healthcheckPayload,
223
223
  validHealthCheckRequest,
@@ -267,7 +267,7 @@ import {
267
267
  validGdcGRIN2listResponse,
268
268
  validRunGRIN2Request,
269
269
  validRunGRIN2Response
270
- } from "./chunk-2WSENLMK.js";
270
+ } from "./chunk-46YIGVUP.js";
271
271
  import {
272
272
  aiProjectAdminPayload,
273
273
  validAIProjectAdminRequest,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@sjcrh/proteinpaint-types",
3
- "version": "2.152.0",
3
+ "version": "2.153.1-2",
4
4
  "type": "module",
5
5
  "description": "Shared type definitions between ProteinPaint server and client code",
6
6
  "main": "src/index.ts",
@@ -36,5 +36,10 @@
36
36
  "files": [
37
37
  "dist/*.js",
38
38
  "src"
39
- ]
39
+ ],
40
+ "repository": {
41
+ "type": "git",
42
+ "url": "https://github.com/stjude/proteinpaint",
43
+ "directory": "server"
44
+ }
40
45
  }
package/src/dataset.ts CHANGED
@@ -15,11 +15,6 @@ type KeyVal = {
15
15
  v?: string
16
16
  }
17
17
 
18
- type KeyLabel = {
19
- key: string
20
- label: string
21
- }
22
-
23
18
  /** a set of categories about a vcf INFO field */
24
19
  export type InfoFieldCategories = {
25
20
  /** category key from an INFO field of a vcf file */
@@ -1062,7 +1057,7 @@ export type WSImages = {
1062
1057
  /** ds supplied */
1063
1058
  getAnnotationClasses?: (projectId: string) => Promise<WSIClass[] | undefined>
1064
1059
  /** ds supplied */
1065
- retrainModel?: (projectId: string) => Promise<void>
1060
+ retrainModel?: (projectId: string, wsimages: string[]) => Promise<void>
1066
1061
  }
1067
1062
 
1068
1063
  export type WSIClass = { id: number; key_shortcut: string; label: string; color: string }
@@ -1172,24 +1167,6 @@ type UiLabels = {
1172
1167
  [propName: string]: string | { label: string; [otherAttr: string]: string }
1173
1168
  }
1174
1169
 
1175
- type SurvPlotsEntry = {
1176
- name: string
1177
- serialtimekey: string
1178
- iscensoredkey: string
1179
- timelabel: string
1180
- }
1181
-
1182
- type SurvPlots = {
1183
- [index: string]: SurvPlotsEntry
1184
- }
1185
-
1186
- type sampleGroupAttrLstEntry = { key: string }
1187
-
1188
- type SurvivalPlot = {
1189
- plots: SurvPlots
1190
- samplegroupattrlst: sampleGroupAttrLstEntry[]
1191
- }
1192
-
1193
1170
  type TieBreakerFilterValuesEntry = {
1194
1171
  dt: number
1195
1172
  }
@@ -1778,257 +1755,6 @@ type Title = {
1778
1755
  text: string
1779
1756
  link?: string
1780
1757
  }
1781
- /*** types supporting MdsCohort type ***/
1782
- type SampleAttribute = {
1783
- attributes: Attributes
1784
- }
1785
-
1786
- type HierarchiesLstEntry = {
1787
- name: string
1788
- levels: KeyLabelFull[]
1789
- }
1790
-
1791
- type Hierarchies = {
1792
- lst: HierarchiesLstEntry[]
1793
- }
1794
-
1795
- type SetSamples = {
1796
- file: string
1797
- valuename: string
1798
- skipzero: boolean
1799
- }
1800
-
1801
- type SetSignatures = {
1802
- [index: number]: { name: string; color: string }
1803
- }
1804
-
1805
- type MutSigSets = {
1806
- [index: string]: {
1807
- name: string
1808
- samples: SetSamples
1809
- signatures: SetSignatures
1810
- }
1811
- }
1812
-
1813
- type MutationSignature = {
1814
- sets: MutSigSets
1815
- }
1816
-
1817
- type MdsCohort = {
1818
- //Does not apply to Mds3 or genomes!
1819
- files: FileObj[]
1820
- samplenamekey: string
1821
- tohash: (item: any, ds: any) => void //Fix later
1822
- sampleAttribute?: SampleAttribute
1823
- hierarchies?: Hierarchies
1824
- survivalplot?: SurvivalPlot
1825
- mutation_signature?: MutationSignature
1826
- //scatterplot - skipping b/c codes to the old scatterplot, not mass
1827
- }
1828
-
1829
- /*** types supporting MdsQueries type ***/
1830
- type BaseTrack = {
1831
- name?: string
1832
- istrack?: boolean
1833
- type?: string
1834
- file?: string
1835
- hideforthemoment?: number
1836
- viewrangeupperlimit?: number
1837
- }
1838
-
1839
- type LegendVOrigin = {
1840
- key: string
1841
- somatic: string
1842
- germline: string
1843
- }
1844
-
1845
- type GroupSampleByAttr = {
1846
- attrlst: KeyLabelFull[]
1847
- sortgroupby?: {
1848
- key: string
1849
- order: string[]
1850
- }
1851
- attrnamespacer?: string
1852
- }
1853
-
1854
- type Svcnv = BaseTrack & {
1855
- valueCutoff: number
1856
- bplengthUpperLimit: number
1857
- segmeanValueCutoff?: number
1858
- no_loh?: number
1859
- lohLengthUpperLimit?: number
1860
- hideLOHwithCNVoverlap?: boolean
1861
- vcf_querykey?: string
1862
- expressionrank_querykey?: string
1863
- multihidelabel_vcf: boolean
1864
- multihidelabel_fusion?: boolean
1865
- multihidelabel_sv: boolean
1866
- legend_vorigin?: LegendVOrigin
1867
- groupsamplebyattr?: GroupSampleByAttr
1868
- }
1869
-
1870
- type KeyLabelFull = {
1871
- /* Used in:
1872
- queries.genefpkm.boxplotbysamplegroup.attributes
1873
- cohort.hierarchies.lst[i].levels
1874
- */
1875
- k: string
1876
- label: string
1877
- full?: string
1878
- }
1879
-
1880
- type ASE = {
1881
- qvalue: number
1882
- meandelta_monoallelic: number
1883
- asemarkernumber_biallelic: number
1884
- color_noinfo: string
1885
- color_notsure: string
1886
- color_biallelic: string
1887
- color_monoallelic: string
1888
- }
1889
-
1890
- type GeneFpkmOutlier = {
1891
- pvalue: number
1892
- color: string
1893
- }
1894
-
1895
- type BoxPlotAdditionalsEntry = {
1896
- label: string
1897
- attributes: KeyVal[]
1898
- }
1899
-
1900
- type BoxPlotBySampleGroup = {
1901
- attributes: KeyLabelFull[]
1902
- additionals?: BoxPlotAdditionalsEntry[]
1903
- }
1904
-
1905
- type Fpkm = BaseTrack & {
1906
- datatype: string
1907
- itemcolor: string
1908
- }
1909
-
1910
- type GeneFpkm = Fpkm & {
1911
- isgenenumeric: boolean
1912
- boxplotbysamplegroup?: BoxPlotBySampleGroup
1913
- ase?: ASE
1914
- outlier?: GeneFpkmOutlier
1915
- }
1916
-
1917
- type CutoffValueLstEntry = {
1918
- /** '<' or '>' to add to the label */
1919
- side: string
1920
- value: number
1921
- label: string
1922
- }
1923
-
1924
- type ValuePerSample = KeyLabel & {
1925
- cutoffValueLst: CutoffValueLstEntry[]
1926
- }
1927
-
1928
- type InfoFilterCatEntry = {
1929
- label: string
1930
- color: string
1931
- valuePerSample?: ValuePerSample
1932
- }
1933
-
1934
- type InfoFilterCat = {
1935
- [index: string]: InfoFilterCatEntry
1936
- }
1937
-
1938
- type InfoFilterLstEntry = KeyLabel & {
1939
- categories: InfoFilterCat
1940
- hiddenCategories: { Unannotated: number }
1941
- }
1942
-
1943
- type InfoFilter = {
1944
- lst: InfoFilterLstEntry[]
1945
- }
1946
-
1947
- type ReadCountBoxPlotPerCohort = {
1948
- groups: KeyLabel[]
1949
- }
1950
-
1951
- type SingleJunctionSummary = {
1952
- readcountboxplotpercohort: ReadCountBoxPlotPerCohort
1953
- }
1954
-
1955
- type Junction = BaseTrack & {
1956
- readcountCutoff: number
1957
- infoFilter: InfoFilter
1958
- singlejunctionsummary: SingleJunctionSummary
1959
- }
1960
-
1961
- type MdsSnvindel = BaseTrack & {
1962
- tracks: BaseTrack[]
1963
- singlesamples?: {
1964
- tablefile: string
1965
- }
1966
- }
1967
-
1968
- type SomaticCnv = BaseTrack & {
1969
- valueLabel: string
1970
- valueCutoff: number
1971
- bplengthUpperLimit: number
1972
- }
1973
-
1974
- type Vcf = BaseTrack & {
1975
- tracks: BaseTrack[]
1976
- }
1977
-
1978
- type MdsQueries = {
1979
- svcnv?: Svcnv
1980
- genefpkm?: GeneFpkm
1981
- junction?: Junction
1982
- snvindel?: MdsSnvindel
1983
- somaticcnv?: SomaticCnv
1984
- vcf?: Vcf
1985
- fpkm?: Fpkm
1986
- }
1987
-
1988
- type AttrValues = {
1989
- [index: string]: {
1990
- name?: string
1991
- label?: string
1992
- color?: string
1993
- }
1994
- }
1995
-
1996
- type AttributesEntry = {
1997
- label: string
1998
- values?: AttrValues
1999
- hidden?: number
2000
- filter?: number
2001
- appendto_link?: string
2002
- isfloat?: number | boolean
2003
- isinteger?: number | boolean
2004
- clientnoshow?: number
2005
- showintrack?: boolean
2006
- }
2007
-
2008
- type Attributes = {
2009
- [index: string]: AttributesEntry
2010
- }
2011
-
2012
- type MutationAttribute = {
2013
- attributes: Attributes
2014
- }
2015
-
2016
- type MutationTypesEntry = {
2017
- db_col: string
2018
- label?: string
2019
- default: number
2020
- sizecutoff?: string
2021
- log2cutoff?: number
2022
- }
2023
-
2024
- type Gene2MutCount = {
2025
- dbfile: string
2026
- mutationTypes: MutationTypesEntry[]
2027
- }
2028
-
2029
- type LocusAttribute = {
2030
- attributes: Attributes
2031
- }
2032
1758
 
2033
1759
  type ViewMode = {
2034
1760
  byAttribute?: string
@@ -2043,17 +1769,18 @@ type BaseMds = {
2043
1769
  }
2044
1770
 
2045
1771
  export type Mds = BaseMds & {
1772
+ // replaced by mds3!!!
2046
1773
  isMds: boolean
2047
1774
  about?: KeyVal[]
2048
1775
  sampleAssayTrack?: FileObj
2049
1776
  singlesamplemutationjson?: FileObj
2050
- cohort?: MdsCohort
2051
- queries?: MdsQueries
2052
- mutationAttribute?: MutationAttribute
1777
+ cohort?: any
1778
+ queries?: any
1779
+ mutationAttribute?: any
2053
1780
  dbFile?: string
2054
1781
  version?: { label: string; link: string }
2055
- gene2mutcount?: Gene2MutCount
2056
- locusAttribute?: LocusAttribute
1782
+ gene2mutcount?: any
1783
+ locusAttribute?: any
2057
1784
  alleleAttribute?: {
2058
1785
  attributes: {
2059
1786
  [attrName: string]: {
package/src/routes/gdc.grin2.ts CHANGED
@@ -20,8 +20,8 @@ export type GdcGRIN2File = {
20
20
  file_format?: 'MAF'
21
21
  }
22
22
 
23
- enum ExperimentalStrategy {
24
- wxs = 'WXS'
23
+ type ExperimentalStrategy = {
24
+ wxs: 'WXS'
25
25
  }
26
26
 
27
27
  /**
package/src/routes/gdc.maf.ts CHANGED
@@ -20,9 +20,9 @@ export type GdcMafFile = {
20
20
  project_id: string
21
21
  }
22
22
 
23
- enum ExperimentalStrategy {
24
- targeted = 'Targeted Sequencing',
25
- wxs = 'WXS'
23
+ export type ExperimentalStrategy = {
24
+ targeted: 'Targeted Sequencing'
25
+ wxs: 'WXS'
26
26
  }
27
27
 
28
28
  export type GdcMafRequest = {
package/src/routes/grin2.ts CHANGED
@@ -166,6 +166,17 @@ export type GRIN2Response = {
166
166
  totalLesions?: number
167
167
  processedLesions?: number
168
168
  unprocessedSamples?: number
169
+ lesionCounts?: {
170
+ total?: number
171
+ byType?: Record<
172
+ string, // Our key is the GRIN2 lesion type
173
+ {
174
+ count: number
175
+ capped: boolean
176
+ samples: number
177
+ }
178
+ >
179
+ }
169
180
  }
170
181
  /** Cache file name for storing GRIN2 results */
171
182
  cacheFileName?: string