@sjcrh/proteinpaint-types 2.131.0 → 2.132.1-0

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.
Files changed (10) hide show
  1. package/dist/{chunk-5VCMJ7QL.js → chunk-7YC2GEEO.js} +141 -75
  2. package/dist/{chunk-3VVALC2P.js → chunk-QHN3YO6Q.js} +2 -2
  3. package/dist/gdc.grin2.js +1 -1
  4. package/dist/index.js +2 -2
  5. package/dist/termdb.categories.js +1 -1
  6. package/package.json +1 -1
  7. package/src/dataset.ts +31 -5
  8. package/src/routes/gdc.grin2.ts +51 -33
  9. package/src/routes/termdb.categories.ts +1 -0
  10. package/src/vocab.ts +1 -0
package/dist/{chunk-5VCMJ7QL.js → chunk-7YC2GEEO.js} RENAMED
@@ -28,8 +28,9 @@ 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)) && true && true;
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
32
  const $io1 = (input3) => "WXS" === input3.experimentalStrategy;
33
+ const $io2 = (input3) => void 0 === input3.dataType || "string" === typeof input3.dataType;
33
34
  return "object" === typeof input2 && null !== input2 && false === Array.isArray(input2) && $io0(input2);
34
35
  };
35
36
  if (false === __is(input)) {
@@ -43,12 +44,25 @@ var validGdcGRIN2listRequest = (input) => {
43
44
  path: _path2 + ".mafOptions",
44
45
  expected: "(__type | undefined)",
45
46
  value: input3.mafOptions
46
- }), true, true].every((flag) => flag);
47
+ }), void 0 === input3.cnvOptions || ("object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) || $report(_exceptionable2, {
48
+ path: _path2 + ".cnvOptions",
49
+ expected: "(__type.o1 | undefined)",
50
+ value: input3.cnvOptions
51
+ })) && $vo2(input3.cnvOptions, _path2 + ".cnvOptions", _exceptionable2) || $report(_exceptionable2, {
52
+ path: _path2 + ".cnvOptions",
53
+ expected: "(__type.o1 | undefined)",
54
+ value: input3.cnvOptions
55
+ }), true].every((flag) => flag);
47
56
  const $vo1 = (input3, _path2, _exceptionable2 = true) => ["WXS" === input3.experimentalStrategy || $report(_exceptionable2, {
48
57
  path: _path2 + ".experimentalStrategy",
49
58
  expected: '"WXS"',
50
59
  value: input3.experimentalStrategy
51
60
  })].every((flag) => flag);
61
+ const $vo2 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.dataType || "string" === typeof input3.dataType || $report(_exceptionable2, {
62
+ path: _path2 + ".dataType",
63
+ expected: "(string | undefined)",
64
+ value: input3.dataType
65
+ })].every((flag) => flag);
52
66
  return ("object" === typeof input2 && null !== input2 && false === Array.isArray(input2) || $report(true, {
53
67
  path: _path + "",
54
68
  expected: "GdcGRIN2listRequest",
@@ -70,21 +84,38 @@ var validGdcGRIN2listRequest = (input) => {
70
84
  var validGdcGRIN2listResponse = (input) => {
71
85
  const errors = [];
72
86
  const __is = (input2) => {
73
- const $io0 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)) && "number" === typeof input3.filesTotal && "number" === typeof input3.maxTotalSizeCompressed && (void 0 === input3.fileCounts || "object" === typeof input3.fileCounts && null !== input3.fileCounts && $io2(input3.fileCounts)) && (void 0 === input3.appliedFilters || "object" === typeof input3.appliedFilters && null !== input3.appliedFilters && false === Array.isArray(input3.appliedFilters) && $io3(input3.appliedFilters)) && (void 0 === input3.deduplicationStats || "object" === typeof input3.deduplicationStats && null !== input3.deduplicationStats && $io4(input3.deduplicationStats)) && (void 0 === input3.mafFiles || "object" === typeof input3.mafFiles && null !== input3.mafFiles && $io7(input3.mafFiles)) && (void 0 === input3.cnvFiles || "object" === typeof input3.cnvFiles && null !== input3.cnvFiles && $io8(input3.cnvFiles));
74
- const $io1 = (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);
75
- const $io2 = (input3) => "number" === typeof input3.maf;
76
- const $io3 = (input3) => void 0 === input3.experimentalStrategy || "WXS" === input3.experimentalStrategy;
77
- const $io4 = (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 && $io5(elem))) && (Array.isArray(input3.filteredFiles) && input3.filteredFiles.every((elem) => "object" === typeof elem && null !== elem && $io6(elem)));
78
- const $io5 = (input3) => "string" === typeof input3.caseName && "number" === typeof input3.fileCount && "number" === typeof input3.keptFileSize;
79
- const $io6 = (input3) => "string" === typeof input3.fileId && "number" === typeof input3.fileSize && "string" === typeof input3.reason;
80
- const $io7 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io1(elem));
81
- const $io8 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io1(elem));
82
- return "object" === typeof input2 && null !== input2 && $io0(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));
89
+ 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
+ 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;
96
+ return "object" === typeof input2 && null !== input2 && false === Array.isArray(input2) && $io0(input2);
83
97
  };
84
98
  if (false === __is(input)) {
85
99
  const $report = import_typia.createValidate.report(errors);
86
100
  ((input2, _path, _exceptionable = true) => {
87
- const $vo0 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
101
+ const $vo0 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.mafFiles || ("object" === typeof input3.mafFiles && null !== input3.mafFiles || $report(_exceptionable2, {
102
+ path: _path2 + ".mafFiles",
103
+ expected: "(__type | undefined)",
104
+ value: input3.mafFiles
105
+ })) && $vo1(input3.mafFiles, _path2 + ".mafFiles", _exceptionable2) || $report(_exceptionable2, {
106
+ path: _path2 + ".mafFiles",
107
+ expected: "(__type | undefined)",
108
+ value: input3.mafFiles
109
+ }), void 0 === input3.cnvFiles || ("object" === typeof input3.cnvFiles && null !== input3.cnvFiles || $report(_exceptionable2, {
110
+ path: _path2 + ".cnvFiles",
111
+ expected: "(__type.o6 | undefined)",
112
+ value: input3.cnvFiles
113
+ })) && $vo8(input3.cnvFiles, _path2 + ".cnvFiles", _exceptionable2) || $report(_exceptionable2, {
114
+ path: _path2 + ".cnvFiles",
115
+ expected: "(__type.o6 | undefined)",
116
+ value: input3.cnvFiles
117
+ })].every((flag) => flag);
118
+ const $vo1 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
88
119
  path: _path2 + ".files",
89
120
  expected: "Array<GdcGRIN2File>",
90
121
  value: input3.files
@@ -92,7 +123,7 @@ var validGdcGRIN2listResponse = (input) => {
92
123
  path: _path2 + ".files[" + _index1 + "]",
93
124
  expected: "GdcGRIN2File",
94
125
  value: elem
95
- })) && $vo1(elem, _path2 + ".files[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
126
+ })) && $vo2(elem, _path2 + ".files[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
96
127
  path: _path2 + ".files[" + _index1 + "]",
97
128
  expected: "GdcGRIN2File",
98
129
  value: elem
@@ -110,46 +141,30 @@ var validGdcGRIN2listResponse = (input) => {
110
141
  value: input3.maxTotalSizeCompressed
111
142
  }), void 0 === input3.fileCounts || ("object" === typeof input3.fileCounts && null !== input3.fileCounts || $report(_exceptionable2, {
112
143
  path: _path2 + ".fileCounts",
113
- expected: "(__type | undefined)",
144
+ expected: "(__type.o1 | undefined)",
114
145
  value: input3.fileCounts
115
- })) && $vo2(input3.fileCounts, _path2 + ".fileCounts", _exceptionable2) || $report(_exceptionable2, {
146
+ })) && $vo3(input3.fileCounts, _path2 + ".fileCounts", _exceptionable2) || $report(_exceptionable2, {
116
147
  path: _path2 + ".fileCounts",
117
- expected: "(__type | undefined)",
148
+ expected: "(__type.o1 | undefined)",
118
149
  value: input3.fileCounts
119
150
  }), void 0 === input3.appliedFilters || ("object" === typeof input3.appliedFilters && null !== input3.appliedFilters && false === Array.isArray(input3.appliedFilters) || $report(_exceptionable2, {
120
151
  path: _path2 + ".appliedFilters",
121
- expected: "(__type.o1 | undefined)",
152
+ expected: "(__type.o2 | undefined)",
122
153
  value: input3.appliedFilters
123
- })) && $vo3(input3.appliedFilters, _path2 + ".appliedFilters", _exceptionable2) || $report(_exceptionable2, {
154
+ })) && $vo4(input3.appliedFilters, _path2 + ".appliedFilters", _exceptionable2) || $report(_exceptionable2, {
124
155
  path: _path2 + ".appliedFilters",
125
- expected: "(__type.o1 | undefined)",
156
+ expected: "(__type.o2 | undefined)",
126
157
  value: input3.appliedFilters
127
158
  }), void 0 === input3.deduplicationStats || ("object" === typeof input3.deduplicationStats && null !== input3.deduplicationStats || $report(_exceptionable2, {
128
159
  path: _path2 + ".deduplicationStats",
129
- expected: "(__type.o2 | undefined)",
160
+ expected: "(__type.o3 | undefined)",
130
161
  value: input3.deduplicationStats
131
- })) && $vo4(input3.deduplicationStats, _path2 + ".deduplicationStats", _exceptionable2) || $report(_exceptionable2, {
162
+ })) && $vo5(input3.deduplicationStats, _path2 + ".deduplicationStats", _exceptionable2) || $report(_exceptionable2, {
132
163
  path: _path2 + ".deduplicationStats",
133
- expected: "(__type.o2 | undefined)",
164
+ expected: "(__type.o3 | undefined)",
134
165
  value: input3.deduplicationStats
135
- }), void 0 === input3.mafFiles || ("object" === typeof input3.mafFiles && null !== input3.mafFiles || $report(_exceptionable2, {
136
- path: _path2 + ".mafFiles",
137
- expected: "(__type.o5 | undefined)",
138
- value: input3.mafFiles
139
- })) && $vo7(input3.mafFiles, _path2 + ".mafFiles", _exceptionable2) || $report(_exceptionable2, {
140
- path: _path2 + ".mafFiles",
141
- expected: "(__type.o5 | undefined)",
142
- value: input3.mafFiles
143
- }), void 0 === input3.cnvFiles || ("object" === typeof input3.cnvFiles && null !== input3.cnvFiles || $report(_exceptionable2, {
144
- path: _path2 + ".cnvFiles",
145
- expected: "(__type.o6 | undefined)",
146
- value: input3.cnvFiles
147
- })) && $vo8(input3.cnvFiles, _path2 + ".cnvFiles", _exceptionable2) || $report(_exceptionable2, {
148
- path: _path2 + ".cnvFiles",
149
- expected: "(__type.o6 | undefined)",
150
- value: input3.cnvFiles
151
166
  })].every((flag) => flag);
152
- const $vo1 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.id || $report(_exceptionable2, {
167
+ const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.id || $report(_exceptionable2, {
153
168
  path: _path2 + ".id",
154
169
  expected: "string",
155
170
  value: input3.id
@@ -186,17 +201,17 @@ var validGdcGRIN2listResponse = (input) => {
186
201
  expected: '("MAF" | undefined)',
187
202
  value: input3.file_format
188
203
  })].every((flag) => flag);
189
- const $vo2 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.maf || $report(_exceptionable2, {
204
+ const $vo3 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.maf || $report(_exceptionable2, {
190
205
  path: _path2 + ".maf",
191
206
  expected: "number",
192
207
  value: input3.maf
193
208
  })].every((flag) => flag);
194
- const $vo3 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.experimentalStrategy || "WXS" === input3.experimentalStrategy || $report(_exceptionable2, {
209
+ const $vo4 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.experimentalStrategy || "WXS" === input3.experimentalStrategy || $report(_exceptionable2, {
195
210
  path: _path2 + ".experimentalStrategy",
196
211
  expected: '("WXS" | undefined)',
197
212
  value: input3.experimentalStrategy
198
213
  })].every((flag) => flag);
199
- const $vo4 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.originalFileCount || $report(_exceptionable2, {
214
+ const $vo5 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.originalFileCount || $report(_exceptionable2, {
200
215
  path: _path2 + ".originalFileCount",
201
216
  expected: "number",
202
217
  value: input3.originalFileCount
@@ -214,11 +229,11 @@ var validGdcGRIN2listResponse = (input) => {
214
229
  value: input3.caseDetails
215
230
  })) && input3.caseDetails.map((elem, _index3) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
216
231
  path: _path2 + ".caseDetails[" + _index3 + "]",
217
- expected: "__type.o3",
232
+ expected: "__type.o4",
218
233
  value: elem
219
- })) && $vo5(elem, _path2 + ".caseDetails[" + _index3 + "]", _exceptionable2) || $report(_exceptionable2, {
234
+ })) && $vo6(elem, _path2 + ".caseDetails[" + _index3 + "]", _exceptionable2) || $report(_exceptionable2, {
220
235
  path: _path2 + ".caseDetails[" + _index3 + "]",
221
- expected: "__type.o3",
236
+ expected: "__type.o4",
222
237
  value: elem
223
238
  })).every((flag) => flag) || $report(_exceptionable2, {
224
239
  path: _path2 + ".caseDetails",
@@ -230,18 +245,18 @@ var validGdcGRIN2listResponse = (input) => {
230
245
  value: input3.filteredFiles
231
246
  })) && input3.filteredFiles.map((elem, _index4) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
232
247
  path: _path2 + ".filteredFiles[" + _index4 + "]",
233
- expected: "__type.o4",
248
+ expected: "__type.o5",
234
249
  value: elem
235
- })) && $vo6(elem, _path2 + ".filteredFiles[" + _index4 + "]", _exceptionable2) || $report(_exceptionable2, {
250
+ })) && $vo7(elem, _path2 + ".filteredFiles[" + _index4 + "]", _exceptionable2) || $report(_exceptionable2, {
236
251
  path: _path2 + ".filteredFiles[" + _index4 + "]",
237
- expected: "__type.o4",
252
+ expected: "__type.o5",
238
253
  value: elem
239
254
  })).every((flag) => flag) || $report(_exceptionable2, {
240
255
  path: _path2 + ".filteredFiles",
241
256
  expected: "Array<__type>.o1",
242
257
  value: input3.filteredFiles
243
258
  })].every((flag) => flag);
244
- const $vo5 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.caseName || $report(_exceptionable2, {
259
+ const $vo6 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.caseName || $report(_exceptionable2, {
245
260
  path: _path2 + ".caseName",
246
261
  expected: "string",
247
262
  value: input3.caseName
@@ -254,7 +269,7 @@ var validGdcGRIN2listResponse = (input) => {
254
269
  expected: "number",
255
270
  value: input3.keptFileSize
256
271
  })].every((flag) => flag);
257
- const $vo6 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.fileId || $report(_exceptionable2, {
272
+ const $vo7 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.fileId || $report(_exceptionable2, {
258
273
  path: _path2 + ".fileId",
259
274
  expected: "string",
260
275
  value: input3.fileId
@@ -267,7 +282,7 @@ var validGdcGRIN2listResponse = (input) => {
267
282
  expected: "string",
268
283
  value: input3.reason
269
284
  })].every((flag) => flag);
270
- const $vo7 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
285
+ const $vo8 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
271
286
  path: _path2 + ".files",
272
287
  expected: "Array<GdcGRIN2File>",
273
288
  value: input3.files
@@ -275,7 +290,7 @@ var validGdcGRIN2listResponse = (input) => {
275
290
  path: _path2 + ".files[" + _index5 + "]",
276
291
  expected: "GdcGRIN2File",
277
292
  value: elem
278
- })) && $vo1(elem, _path2 + ".files[" + _index5 + "]", _exceptionable2) || $report(_exceptionable2, {
293
+ })) && $vo2(elem, _path2 + ".files[" + _index5 + "]", _exceptionable2) || $report(_exceptionable2, {
279
294
  path: _path2 + ".files[" + _index5 + "]",
280
295
  expected: "GdcGRIN2File",
281
296
  value: elem
@@ -283,25 +298,12 @@ var validGdcGRIN2listResponse = (input) => {
283
298
  path: _path2 + ".files",
284
299
  expected: "Array<GdcGRIN2File>",
285
300
  value: input3.files
301
+ }), "number" === typeof input3.maxTotalSizeCompressed || $report(_exceptionable2, {
302
+ path: _path2 + ".maxTotalSizeCompressed",
303
+ expected: "number",
304
+ value: input3.maxTotalSizeCompressed
286
305
  })].every((flag) => flag);
287
- const $vo8 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
288
- path: _path2 + ".files",
289
- expected: "Array<GdcGRIN2File>",
290
- value: input3.files
291
- })) && input3.files.map((elem, _index6) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
292
- path: _path2 + ".files[" + _index6 + "]",
293
- expected: "GdcGRIN2File",
294
- value: elem
295
- })) && $vo1(elem, _path2 + ".files[" + _index6 + "]", _exceptionable2) || $report(_exceptionable2, {
296
- path: _path2 + ".files[" + _index6 + "]",
297
- expected: "GdcGRIN2File",
298
- value: elem
299
- })).every((flag) => flag) || $report(_exceptionable2, {
300
- path: _path2 + ".files",
301
- expected: "Array<GdcGRIN2File>",
302
- value: input3.files
303
- })].every((flag) => flag);
304
- return ("object" === typeof input2 && null !== input2 || $report(true, {
306
+ return ("object" === typeof input2 && null !== input2 && false === Array.isArray(input2) || $report(true, {
305
307
  path: _path + "",
306
308
  expected: "GdcGRIN2listResponse",
307
309
  value: input2
@@ -323,7 +325,7 @@ var validRunGRIN2Request = (input) => {
323
325
  const errors = [];
324
326
  const __is = (input2) => {
325
327
  const $join = import_typia.createValidate.join;
326
- const $io0 = (input3) => "object" === typeof input3.caseFiles && null !== input3.caseFiles && false === Array.isArray(input3.caseFiles) && $io1(input3.caseFiles) && (void 0 === input3.mafOptions || "object" === typeof input3.mafOptions && null !== input3.mafOptions && false === Array.isArray(input3.mafOptions) && $io3(input3.mafOptions));
328
+ const $io0 = (input3) => "object" === typeof input3.caseFiles && null !== input3.caseFiles && false === Array.isArray(input3.caseFiles) && $io1(input3.caseFiles) && (void 0 === input3.mafOptions || "object" === typeof input3.mafOptions && null !== input3.mafOptions && false === Array.isArray(input3.mafOptions) && $io3(input3.mafOptions)) && (void 0 === input3.cnvOptions || "object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) && $io4(input3.cnvOptions));
327
329
  const $io1 = (input3) => Object.keys(input3).every((key) => {
328
330
  const value = input3[key];
329
331
  if (void 0 === value)
@@ -332,8 +334,9 @@ var validRunGRIN2Request = (input) => {
332
334
  return "object" === typeof value && null !== value && false === Array.isArray(value) && $io2(value);
333
335
  return true;
334
336
  });
335
- const $io2 = (input3) => void 0 === input3.maf || "string" === typeof input3.maf;
336
- const $io3 = (input3) => (void 0 === input3.minTotalDepth || "number" === typeof input3.minTotalDepth) && (void 0 === input3.minAltAlleleCount || "number" === typeof input3.minAltAlleleCount);
337
+ const $io2 = (input3) => (void 0 === input3.maf || "string" === typeof input3.maf) && (void 0 === input3.cnv || "string" === typeof input3.cnv);
338
+ const $io3 = (input3) => (void 0 === input3.minTotalDepth || "number" === typeof input3.minTotalDepth) && (void 0 === input3.minAltAlleleCount || "number" === typeof input3.minAltAlleleCount) && (void 0 === input3.consequences || Array.isArray(input3.consequences) && input3.consequences.every((elem) => "string" === typeof elem)) && (void 0 === input3.hyperMutator || "number" === typeof input3.hyperMutator);
339
+ const $io4 = (input3) => (void 0 === input3.lossThreshold || "number" === typeof input3.lossThreshold) && (void 0 === input3.gainThreshold || "number" === typeof input3.gainThreshold) && (void 0 === input3.segLength || "number" === typeof input3.segLength);
337
340
  return "object" === typeof input2 && null !== input2 && $io0(input2);
338
341
  };
339
342
  if (false === __is(input)) {
@@ -356,6 +359,14 @@ var validRunGRIN2Request = (input) => {
356
359
  path: _path2 + ".mafOptions",
357
360
  expected: "(__type.o2 | undefined)",
358
361
  value: input3.mafOptions
362
+ }), void 0 === input3.cnvOptions || ("object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) || $report(_exceptionable2, {
363
+ path: _path2 + ".cnvOptions",
364
+ expected: "(__type.o3 | undefined)",
365
+ value: input3.cnvOptions
366
+ })) && $vo4(input3.cnvOptions, _path2 + ".cnvOptions", _exceptionable2) || $report(_exceptionable2, {
367
+ path: _path2 + ".cnvOptions",
368
+ expected: "(__type.o3 | undefined)",
369
+ value: input3.cnvOptions
359
370
  })].every((flag) => flag);
360
371
  const $vo1 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
361
372
  const value = input3[key];
@@ -377,6 +388,10 @@ var validRunGRIN2Request = (input) => {
377
388
  path: _path2 + ".maf",
378
389
  expected: "(string | undefined)",
379
390
  value: input3.maf
391
+ }), void 0 === input3.cnv || "string" === typeof input3.cnv || $report(_exceptionable2, {
392
+ path: _path2 + ".cnv",
393
+ expected: "(string | undefined)",
394
+ value: input3.cnv
380
395
  })].every((flag) => flag);
381
396
  const $vo3 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.minTotalDepth || "number" === typeof input3.minTotalDepth || $report(_exceptionable2, {
382
397
  path: _path2 + ".minTotalDepth",
@@ -386,6 +401,35 @@ var validRunGRIN2Request = (input) => {
386
401
  path: _path2 + ".minAltAlleleCount",
387
402
  expected: "(number | undefined)",
388
403
  value: input3.minAltAlleleCount
404
+ }), void 0 === input3.consequences || (Array.isArray(input3.consequences) || $report(_exceptionable2, {
405
+ path: _path2 + ".consequences",
406
+ expected: "(Array<string> | undefined)",
407
+ value: input3.consequences
408
+ })) && input3.consequences.map((elem, _index1) => "string" === typeof elem || $report(_exceptionable2, {
409
+ path: _path2 + ".consequences[" + _index1 + "]",
410
+ expected: "string",
411
+ value: elem
412
+ })).every((flag) => flag) || $report(_exceptionable2, {
413
+ path: _path2 + ".consequences",
414
+ expected: "(Array<string> | undefined)",
415
+ value: input3.consequences
416
+ }), void 0 === input3.hyperMutator || "number" === typeof input3.hyperMutator || $report(_exceptionable2, {
417
+ path: _path2 + ".hyperMutator",
418
+ expected: "(number | undefined)",
419
+ value: input3.hyperMutator
420
+ })].every((flag) => flag);
421
+ const $vo4 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.lossThreshold || "number" === typeof input3.lossThreshold || $report(_exceptionable2, {
422
+ path: _path2 + ".lossThreshold",
423
+ expected: "(number | undefined)",
424
+ value: input3.lossThreshold
425
+ }), void 0 === input3.gainThreshold || "number" === typeof input3.gainThreshold || $report(_exceptionable2, {
426
+ path: _path2 + ".gainThreshold",
427
+ expected: "(number | undefined)",
428
+ value: input3.gainThreshold
429
+ }), void 0 === input3.segLength || "number" === typeof input3.segLength || $report(_exceptionable2, {
430
+ path: _path2 + ".segLength",
431
+ expected: "(number | undefined)",
432
+ value: input3.segLength
389
433
  })].every((flag) => flag);
390
434
  return ("object" === typeof input2 && null !== input2 || $report(true, {
391
435
  path: _path + "",
@@ -408,9 +452,10 @@ var validRunGRIN2Request = (input) => {
408
452
  var validRunGRIN2Response = (input) => {
409
453
  const errors = [];
410
454
  const __is = (input2) => {
411
- 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));
455
+ 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 && $io4(input3.timing));
412
456
  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 && ("number" === typeof input3.summary.total_files && "number" === typeof input3.summary.successful_files && "number" === typeof input3.summary.failed_files));
413
457
  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;
458
+ const $io4 = (input3) => "number" === typeof input3.rustProcessingTime && "number" === typeof input3.grin2Time && "number" === typeof input3.totalTime;
414
459
  return "object" === typeof input2 && null !== input2 && $io0(input2);
415
460
  };
416
461
  if (false === __is(input)) {
@@ -436,6 +481,14 @@ var validRunGRIN2Response = (input) => {
436
481
  path: _path2 + ".rustResult",
437
482
  expected: "(RustGRIN2Result | undefined)",
438
483
  value: input3.rustResult
484
+ }), void 0 === input3.timing || ("object" === typeof input3.timing && null !== input3.timing || $report(_exceptionable2, {
485
+ path: _path2 + ".timing",
486
+ expected: "(__type | undefined)",
487
+ value: input3.timing
488
+ })) && $vo4(input3.timing, _path2 + ".timing", _exceptionable2) || $report(_exceptionable2, {
489
+ path: _path2 + ".timing",
490
+ expected: "(__type | undefined)",
491
+ value: input3.timing
439
492
  })].every((flag) => flag);
440
493
  const $vo1 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.successful_data) || $report(_exceptionable2, {
441
494
  path: _path2 + ".successful_data",
@@ -516,6 +569,19 @@ var validRunGRIN2Response = (input) => {
516
569
  expected: "number",
517
570
  value: input3.failed_files
518
571
  })].every((flag) => flag);
572
+ const $vo4 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.rustProcessingTime || $report(_exceptionable2, {
573
+ path: _path2 + ".rustProcessingTime",
574
+ expected: "number",
575
+ value: input3.rustProcessingTime
576
+ }), "number" === typeof input3.grin2Time || $report(_exceptionable2, {
577
+ path: _path2 + ".grin2Time",
578
+ expected: "number",
579
+ value: input3.grin2Time
580
+ }), "number" === typeof input3.totalTime || $report(_exceptionable2, {
581
+ path: _path2 + ".totalTime",
582
+ expected: "number",
583
+ value: input3.totalTime
584
+ })].every((flag) => flag);
519
585
  return ("object" === typeof input2 && null !== input2 || $report(true, {
520
586
  path: _path + "",
521
587
  expected: "RunGRIN2Response",
package/dist/{chunk-3VVALC2P.js → chunk-QHN3YO6Q.js} RENAMED
@@ -58,7 +58,7 @@ var validCategoriesRequest = (input) => {
58
58
  const errors = [];
59
59
  const __is = (input2) => {
60
60
  const $join = import_typia.createValidate.join;
61
- const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "string" === typeof input3.embedder && ("object" === typeof input3.tw && null !== input3.tw && $iu5(input3.tw)) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io12(input3.filter)) && (void 0 === input3.currentGeneNames || Array.isArray(input3.currentGeneNames) && input3.currentGeneNames.every((elem) => "string" === typeof elem)) && true;
61
+ const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "string" === typeof input3.embedder && ("object" === typeof input3.tw && null !== input3.tw && $iu5(input3.tw)) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io12(input3.filter)) && true && (void 0 === input3.currentGeneNames || Array.isArray(input3.currentGeneNames) && input3.currentGeneNames.every((elem) => "string" === typeof elem)) && true;
62
62
  const $io1 = (input3) => (void 0 === input3.id || "string" === typeof input3.id) && (void 0 === input3.$id || "string" === typeof input3.$id) && (void 0 === input3.isAtomic || true === input3.isAtomic) && true && (void 0 === input3.settings || "object" === typeof input3.settings && null !== input3.settings && false === Array.isArray(input3.settings) && $io2(input3.settings)) && true && (void 0 === input3.minNumSamples || "number" === typeof input3.minNumSamples) && true && ("CatTWValues" === input3.type || "CatTWPredefinedGS" === input3.type || "CatTWCustomGS" === input3.type) && ("object" === typeof input3.q && null !== input3.q && false === Array.isArray(input3.q) && $iu6(input3.q)) && ("object" === typeof input3.term && null !== input3.term && $io15(input3.term));
63
63
  const $io2 = (input3) => Object.keys(input3).every((key) => {
64
64
  const value = input3[key];
@@ -356,7 +356,7 @@ var validCategoriesRequest = (input) => {
356
356
  path: _path2 + ".filter",
357
357
  expected: "(Filter | undefined)",
358
358
  value: input3.filter
359
- }), void 0 === input3.currentGeneNames || (Array.isArray(input3.currentGeneNames) || $report(_exceptionable2, {
359
+ }), true, void 0 === input3.currentGeneNames || (Array.isArray(input3.currentGeneNames) || $report(_exceptionable2, {
360
360
  path: _path2 + ".currentGeneNames",
361
361
  expected: "(Array<string> | undefined)",
362
362
  value: input3.currentGeneNames
package/dist/gdc.grin2.js CHANGED
@@ -5,7 +5,7 @@ import {
5
5
  validGdcGRIN2listResponse,
6
6
  validRunGRIN2Request,
7
7
  validRunGRIN2Response
8
- } from "./chunk-5VCMJ7QL.js";
8
+ } from "./chunk-7YC2GEEO.js";
9
9
  import "./chunk-CNSSF43V.js";
10
10
  export {
11
11
  gdcGRIN2listPayload,
package/dist/index.js CHANGED
@@ -112,7 +112,7 @@ import {
112
112
  termdbCategoriesPayload,
113
113
  validCategoriesRequest,
114
114
  validCategoriesResponse
115
- } from "./chunk-3VVALC2P.js";
115
+ } from "./chunk-QHN3YO6Q.js";
116
116
  import {
117
117
  termdbClusterPayload,
118
118
  validTermdbClusterRequest,
@@ -175,7 +175,7 @@ import {
175
175
  validGdcGRIN2listResponse,
176
176
  validRunGRIN2Request,
177
177
  validRunGRIN2Response
178
- } from "./chunk-5VCMJ7QL.js";
178
+ } from "./chunk-7YC2GEEO.js";
179
179
  import {
180
180
  gdcMafPayload,
181
181
  validGdcMafRequest,
package/dist/termdb.categories.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termdbCategoriesPayload,
3
3
  validCategoriesRequest,
4
4
  validCategoriesResponse
5
- } from "./chunk-3VVALC2P.js";
5
+ } from "./chunk-QHN3YO6Q.js";
6
6
  import "./chunk-CNSSF43V.js";
7
7
  export {
8
8
  termdbCategoriesPayload,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@sjcrh/proteinpaint-types",
3
- "version": "2.131.0",
3
+ "version": "2.132.1-0",
4
4
  "type": "module",
5
5
  "description": "Shared type definitions between ProteinPaint server and client code",
6
6
  "main": "src/index.ts",
package/src/dataset.ts CHANGED
@@ -910,6 +910,13 @@ type Mds3Queries = {
910
910
  snvindel?: SnvIndelQuery
911
911
  svfusion?: SvFusion
912
912
  cnv?: CnvSegmentQuery
913
+ /** gene-level cnv, only available on gdc; query by gene symbol, ds must define getter
914
+ */
915
+ geneCnv?: {
916
+ bygene: {
917
+ get: (q: any) => any
918
+ }
919
+ }
913
920
  trackLst?: TrackLst
914
921
  ld?: LdQuery
915
922
  defaultCoord?: string
@@ -928,11 +935,6 @@ type Mds3Queries = {
928
935
  file: string
929
936
  }
930
937
  singleCell?: SingleCellQuery
931
- geneCnv?: {
932
- bygene?: {
933
- gdcapi: true
934
- }
935
- }
936
938
  singleSampleGenomeQuantification?: SingleSampleGenomeQuantification
937
939
  singleSampleGbtk?: SingleSampleGbtk
938
940
  /** depreciated. replaced by WSImages */
@@ -1508,6 +1510,13 @@ type DtAssayAvailability = DtAssayAvailabilityGetter | DtAssayAvailabilityTerm
1508
1510
 
1509
1511
  /** using ds-supplied getter */
1510
1512
  type DtAssayAvailabilityGetter = {
1513
+ /** define q
1514
+ returns:
1515
+ {
1516
+ yesSamples: Set() of sample ids
1517
+ noSamples: Set() of sample ids
1518
+ }
1519
+ */
1511
1520
  get: (q: any) => any
1512
1521
  }
1513
1522
  /** using dictionary term */
@@ -2027,6 +2036,23 @@ export type Mds3 = BaseMds & {
2027
2036
  validate_filter0?: (f: any) => void
2028
2037
  ssm2canonicalisoform?: GdcApi
2029
2038
  variant2samples?: Variant2Samples
2039
+ /** disables switching to genomic mode for the protein view mds3 tk of this ds
2040
+ works by preventing block gmmode menu from showing "genomic" option
2041
+ is only passed via mds3 adhoc ds copy, but not termdbConfig
2042
+ for lack of a better place to put this attribute, as it's not appropriate to put in queries.snvindel{}
2043
+ as snvindel is optional so even a cnv-only ds can disable genomic mode
2044
+ */
2045
+ noGenomicMode4lollipopTk?: true
2046
+ /** if ds.queries{} exists, server launch adds this convenient getter to wrap multiple queries data types
2047
+ */
2048
+ mayGetGeneVariantData?: (f: any) => void
2049
+ /** optional key-value pairs to pass to genomic queries getter when called in mayGetGeneVariantData()
2050
+ - only used in mayGetGeneVariantData! not in mds3.load.js
2051
+ - for now only passed to snvindel.*.get and not yet other data types; add when needed
2052
+ the param contents will be assessed by ds specific getter
2053
+ this is serverside only, not passed to termdbConfig
2054
+ */
2055
+ mayGetGeneVariantDataParam?: { [key: string]: any }
2030
2056
  // !!! TODO: improve these type definitions below !!!
2031
2057
  getHostHeaders?: (q?: any) => any
2032
2058
  serverconfigFeatures?: any
package/src/routes/gdc.grin2.ts CHANGED
@@ -37,8 +37,11 @@ export type GdcGRIN2listRequest = {
37
37
  experimentalStrategy: ExperimentalStrategy
38
38
  }
39
39
 
40
- /** Options for CNV file retrieval. Presence indicates CNV files should be returned (for future use) */
41
- cnvOptions?: any
40
+ /** Options for CNV file retrieval. Presence indicates CNV files should be returned */
41
+ cnvOptions?: {
42
+ /** Data type for CNV analysis */
43
+ dataType?: string
44
+ }
42
45
 
43
46
  /** Options for fusion file retrieval. Presence indicates fusion files should be returned (for future use) */
44
47
  fusionOptions?: any
@@ -48,39 +51,38 @@ export type GdcGRIN2listRequest = {
48
51
  * Response for GRIN2 file listing
49
52
  */
50
53
  export type GdcGRIN2listResponse = {
51
- /** List of file objects passing filter and to be displayed on client */
52
- files: GdcGRIN2File[]
53
- /** Total number of files found by API (in case bigger than files.length) */
54
- filesTotal: number
55
- /** Maximum total size of files allowed, for indicating on UI while selecting files */
56
- maxTotalSizeCompressed: number
57
- /** File counts by type */
58
- fileCounts?: {
59
- maf: number
60
- }
61
- /** Applied filters (for UI reference) */
62
- appliedFilters?: {
63
- experimentalStrategy?: ExperimentalStrategy
64
- }
65
- /** Deduplication stats */
66
- deduplicationStats?: {
67
- originalFileCount: number
68
- deduplicatedFileCount: number
69
- duplicatesRemoved: number
70
- caseDetails?: Array<{ caseName: string; fileCount: number; keptFileSize: number }>
71
- filteredFiles: Array<{ fileId: string; fileSize: number; reason: string }>
72
- }
73
54
  /** all maf-related results when mafOptions is supplied */
74
55
  mafFiles?: {
75
56
  // TODO suggest to move above maf-related results under mafFiles{}
76
57
  /** list of maf files returned to client */
77
58
  files: GdcGRIN2File[]
59
+ /** Total number of files found by API (in case bigger than files.length) */
60
+ filesTotal: number
61
+ /** Maximum total size of files allowed, for indicating on UI while selecting files */
62
+ maxTotalSizeCompressed: number
63
+ /** File counts by type */
64
+ fileCounts?: {
65
+ maf: number
66
+ }
67
+ /** Applied filters (for UI reference) */
68
+ appliedFilters?: {
69
+ experimentalStrategy?: ExperimentalStrategy
70
+ }
71
+ /** Deduplication stats */
72
+ deduplicationStats?: {
73
+ originalFileCount: number
74
+ deduplicatedFileCount: number
75
+ duplicatesRemoved: number
76
+ caseDetails?: Array<{ caseName: string; fileCount: number; keptFileSize: number }>
77
+ filteredFiles: Array<{ fileId: string; fileSize: number; reason: string }>
78
+ }
78
79
  }
79
80
  /** all cnv-related results when cnvOptions is supplied */
80
81
  cnvFiles?: {
81
82
  /** list of cnv files returned to client */
82
83
  files: GdcGRIN2File[]
83
- /** to add additional stats on cnv file listing */
84
+ /** Maximum total size of files allowed, for indicating on UI while selecting files */
85
+ maxTotalSizeCompressed: number
84
86
  }
85
87
  }
86
88
 
@@ -93,6 +95,7 @@ export type RunGRIN2Request = {
93
95
  caseFiles: {
94
96
  [caseId: string]: {
95
97
  maf?: string
98
+ cnv?: string
96
99
  }
97
100
  }
98
101
  /** Options for filtering MAF file content */
@@ -101,14 +104,20 @@ export type RunGRIN2Request = {
101
104
  minTotalDepth?: number // Default: 10
102
105
  /** Minimum alternate allele count of returned MAF files */
103
106
  minAltAlleleCount?: number // Default: 2
107
+ /** String array of consequence types */
108
+ consequences?: string[]
109
+ /** Maximum mutation count cutoff for highly mutated scenarios */
110
+ hyperMutator?: number
111
+ }
112
+ /** Options for filtering CNV file content*/
113
+ cnvOptions?: {
114
+ /** Threshold for copy number loss detection */
115
+ lossThreshold?: number // Default: -0.4
116
+ /** Threshold for copy number gain detection */
117
+ gainThreshold?: number // Default: 0.3
118
+ /** Maximum segment length to include (0 = no filter) */
119
+ segLength?: number // Default: 0
104
120
  }
105
- /** Options for CNV file retrieval (will be added later)
106
- cnvOptions?: {
107
- * lossThreshold?: number // Default: -0.5
108
- * gainThreshold?: number // Default: 0.5
109
- * segLength?: number // Default: 2000000
110
- *}
111
- */
112
121
  }
113
122
 
114
123
  /** Error entry from failed file downloads */
@@ -151,8 +160,17 @@ export type RunGRIN2Response = {
151
160
  download?: any
152
161
  /** Table of top genes indentified by analysis */
153
162
  topGeneTable?: any
154
- /** Data from Rust for making the failed files div */
163
+ /** Data from Rust for making the analysis summary div */
155
164
  rustResult?: RustGRIN2Result
165
+ /** Timing info from nodejs */
166
+ timing?: {
167
+ /** Time taken to run Rust processing */
168
+ rustProcessingTime: number
169
+ /** Time taken to run GRIN2 processing */
170
+ grin2Time: number
171
+ /** Total time taken for the entire run */
172
+ totalTime: number
173
+ }
156
174
  }
157
175
  /**
158
176
  * Route payload definitions for type checking
package/src/routes/termdb.categories.ts CHANGED
@@ -9,6 +9,7 @@ export type CategoriesRequest = {
9
9
  /** termwrapper object */
10
10
  tw: TermWrapper
11
11
  filter?: Filter
12
+ filter0?: any
12
13
  /** quick fix only for gdc */
13
14
  currentGeneNames?: string[]
14
15
  /** optional property added by mds3 tk, to limit to cases mutated in this region */
package/src/vocab.ts CHANGED
@@ -13,6 +13,7 @@ VocabApi
13
13
 
14
14
  export type VocabApi = {
15
15
  termdbConfig: any
16
+ state?: any
16
17
  //Methods
17
18
  cacheTermQ: (term: Term, q: any) => any
18
19
  findTerm: (f: string, activeCohort: number, usecase: UseCase, x: string) => { lst: Term[] }