@sjcrh/proteinpaint-types 2.181.0 → 2.182.1

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Files changed (39) hide show
  1. package/dist/brainImaging.js +1 -1
  2. package/dist/{chunk-2QTCQFYE.js → chunk-2NINVZOB.js} +47 -11
  3. package/dist/{chunk-UBAJYDGK.js → chunk-734AZGID.js} +15 -3
  4. package/dist/{chunk-KNDCWQJD.js → chunk-INIT6CVR.js} +728 -580
  5. package/dist/{chunk-DDMUMMOL.js → chunk-LDLZU2QY.js} +15 -3
  6. package/dist/{chunk-URYAC364.js → chunk-LOFBLGRE.js} +311 -163
  7. package/dist/{chunk-UYKWZWCU.js → chunk-M7WMC7GC.js} +411 -199
  8. package/dist/{chunk-K6W2WEPW.js → chunk-NO3ZZD3L.js} +15 -3
  9. package/dist/{chunk-ZRTB7SRA.js → chunk-ONNT3XV7.js} +32 -8
  10. package/dist/{chunk-VUNM6QTX.js → chunk-QMEKJW2A.js} +15 -3
  11. package/dist/{chunk-J55IQXT7.js → chunk-TI565XIR.js} +470 -418
  12. package/dist/{chunk-ZKO7LMCC.js → chunk-TUM3OZ7K.js} +15 -3
  13. package/dist/{chunk-45VA4Y6L.js → chunk-UWK6LBTQ.js} +877 -778
  14. package/dist/chunk-W3F3CLYP.js +61 -0
  15. package/dist/{chunk-C5ECCXOT.js → chunk-WNUWRPXG.js} +733 -585
  16. package/dist/{chunk-3DA4MJ2U.js → chunk-Y6FNAG22.js} +372 -175
  17. package/dist/correlationVolcano.js +1 -1
  18. package/dist/grin2.js +1 -1
  19. package/dist/index.js +31 -23
  20. package/dist/termdb.categories.js +1 -1
  21. package/dist/termdb.chat.js +15 -3
  22. package/dist/termdb.chat2.js +1 -1
  23. package/dist/termdb.cluster.js +1 -1
  24. package/dist/termdb.descrstats.js +1 -1
  25. package/dist/termdb.dmr.js +1 -1
  26. package/dist/termdb.numericcategories.js +1 -1
  27. package/dist/termdb.percentile.js +1 -1
  28. package/dist/termdb.proteome.js +11 -0
  29. package/dist/termdb.termsbyids.js +1 -1
  30. package/dist/termdb.topTermsByType.js +1 -1
  31. package/dist/termdb.topVariablyExpressedGenes.js +1 -1
  32. package/dist/termdb.violinBox.js +1 -1
  33. package/package.json +1 -1
  34. package/src/dataset.ts +16 -4
  35. package/src/index.ts +1 -0
  36. package/src/routes/termdb.proteome.ts +13 -0
  37. package/src/terms/dnaMethylation.ts +12 -3
  38. package/src/terms/termCollection.ts +7 -1
  39. package/src/terms/tw.ts +1 -0
package/dist/correlationVolcano.js CHANGED
@@ -2,7 +2,7 @@ import {
2
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  CorrelationVolcanoPayload,
3
3
  validCorrelationVolcanoRequest,
4
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  validCorrelationVolcanoResponse
5
- } from "./chunk-URYAC364.js";
5
+ } from "./chunk-LOFBLGRE.js";
6
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  import "./chunk-YNHC5SXO.js";
7
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  export {
8
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  CorrelationVolcanoPayload,
package/dist/grin2.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  GRIN2Payload,
3
3
  validGRIN2Request,
4
4
  validGRIN2Response
5
- } from "./chunk-UBAJYDGK.js";
5
+ } from "./chunk-734AZGID.js";
6
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  import "./chunk-YNHC5SXO.js";
7
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  export {
8
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  GRIN2Payload,
package/dist/index.js CHANGED
@@ -1,3 +1,8 @@
1
+ import {
2
+ validViolinBoxRequest,
3
+ validViolinBoxResponse,
4
+ violinBoxPayload
5
+ } from "./chunk-WNUWRPXG.js";
1
6
  import {
2
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  tilePayload,
3
8
  validTileRequest,
@@ -13,6 +18,11 @@ import {
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  validWSISamplesResponse,
14
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  wsiSamplesPayload
15
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  } from "./chunk-2744ACBX.js";
21
+ import {
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+ termdbSingleCellDEgenesPayload,
23
+ validTermdbSingleCellDEgenesRequest,
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+ validTermdbSingleCellDEgenesResponse
25
+ } from "./chunk-3EVYVWI2.js";
16
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  import {
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  termdbSingleCellDataPayload,
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  validTermdbSingleCellDataRequest,
@@ -32,7 +42,7 @@ import {
32
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  termsByIdsPayload,
33
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  validTermsByIdsRequest,
34
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  validTermsByIdsResponse
35
- } from "./chunk-3DA4MJ2U.js";
45
+ } from "./chunk-UWK6LBTQ.js";
36
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  import {
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  topMutatedGenePayload,
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  validtopMutatedGeneRequest,
@@ -42,17 +52,12 @@ import {
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  termdbTopTermsByTypePayload,
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  validTermdbTopTermsByTypeRequest,
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  validTermdbTopTermsByTypeResponse
45
- } from "./chunk-2QTCQFYE.js";
55
+ } from "./chunk-2NINVZOB.js";
46
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  import {
47
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  termdbTopVariablyExpressedGenesPayload,
48
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  validTermdbTopVariablyExpressedGenesRequest,
49
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  validTermdbTopVariablyExpressedGenesResponse
50
- } from "./chunk-VUNM6QTX.js";
51
- import {
52
- validViolinBoxRequest,
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- validViolinBoxResponse,
54
- violinBoxPayload
55
- } from "./chunk-C5ECCXOT.js";
60
+ } from "./chunk-QMEKJW2A.js";
56
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  import {
57
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  ProfileFormScoresPayload,
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  validProfileFormScoresRequest,
@@ -63,6 +68,11 @@ import {
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  validProfileScoresRequest,
64
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  validProfileScoresResponse
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  } from "./chunk-MHDQO7R5.js";
71
+ import {
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+ termdbProteomePayload,
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+ validTermdbProteomeRequest,
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+ validTermdbProteomeResponse
75
+ } from "./chunk-W3F3CLYP.js";
66
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  import {
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  rootTermPayload,
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  validRootTermRequest,
@@ -88,11 +98,6 @@ import {
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  validTermdbSingleSampleMutationRequest,
89
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  validTermdbSingleSampleMutationResponse
90
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  } from "./chunk-5L4VF3ZL.js";
91
- import {
92
- termdbSingleCellDEgenesPayload,
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- validTermdbSingleCellDEgenesRequest,
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- validTermdbSingleCellDEgenesResponse
95
- } from "./chunk-3EVYVWI2.js";
96
101
  import {
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  termdbCohortsPayload,
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  validTermdbCohortsRequest,
@@ -102,7 +107,7 @@ import {
102
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  descrStatsPayload,
103
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  validDescrStatsRequest,
104
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  validDescrStatsResponse
105
- } from "./chunk-45VA4Y6L.js";
110
+ } from "./chunk-Y6FNAG22.js";
106
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  import {
107
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  diffMethPayload,
108
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  validDiffMethRequest,
@@ -112,7 +117,7 @@ import {
112
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  TermdbDmrPayload,
113
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  validTermdbDmrRequest,
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  validTermdbDmrResponse
115
- } from "./chunk-K6W2WEPW.js";
120
+ } from "./chunk-NO3ZZD3L.js";
116
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  import {
117
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  FilterTermValuesPayload,
118
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  validFilterTermValuesRequest,
@@ -127,12 +132,12 @@ import {
127
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  numericCategoriesPayload,
128
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  validNumericCategoriesRequest,
129
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  validNumericCategoriesResponse
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- } from "./chunk-DDMUMMOL.js";
135
+ } from "./chunk-LDLZU2QY.js";
131
136
  import {
132
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  percentilePayload,
133
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  validPercentileRequest,
134
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  validPercentileResponse
135
- } from "./chunk-ZRTB7SRA.js";
140
+ } from "./chunk-ONNT3XV7.js";
136
141
  import {
137
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  saveWSIAnnotationPayload,
138
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  validSaveWSIAnnotationRequest,
@@ -152,11 +157,11 @@ import {
152
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  termdbCategoriesPayload,
153
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  validCategoriesRequest,
154
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  validCategoriesResponse
155
- } from "./chunk-KNDCWQJD.js";
160
+ } from "./chunk-INIT6CVR.js";
156
161
  import {
157
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  validChatRequest,
158
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  validChatResponse
159
- } from "./chunk-ZKO7LMCC.js";
164
+ } from "./chunk-TUM3OZ7K.js";
160
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  import {
161
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  ChatPayload
162
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  } from "./chunk-FRXRNCDV.js";
@@ -164,7 +169,7 @@ import {
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  termdbClusterPayload,
165
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  validTermdbClusterRequest,
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  validTermdbClusterResponse
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- } from "./chunk-UYKWZWCU.js";
172
+ } from "./chunk-M7WMC7GC.js";
168
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  import {
169
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  termdbCohortSummaryPayload,
170
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  validTermdbCohortSummaryRequest,
@@ -234,7 +239,7 @@ import {
234
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  GRIN2Payload,
235
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  validGRIN2Request,
236
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  validGRIN2Response
237
- } from "./chunk-UBAJYDGK.js";
242
+ } from "./chunk-734AZGID.js";
238
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  import {
239
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  healthcheckPayload,
240
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  validHealthCheckRequest,
@@ -256,7 +261,7 @@ import {
256
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  CorrelationVolcanoPayload,
257
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  validCorrelationVolcanoRequest,
258
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  validCorrelationVolcanoResponse
259
- } from "./chunk-URYAC364.js";
264
+ } from "./chunk-LOFBLGRE.js";
260
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  import {
261
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  datasetPayload,
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  validDatasetRequest,
@@ -314,7 +319,7 @@ import {
314
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  brainImagingPayload,
315
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  validBrainImagingRequest,
316
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  validBrainImagingResponse
317
- } from "./chunk-J55IQXT7.js";
322
+ } from "./chunk-TI565XIR.js";
318
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  import {
319
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  brainImagingSamplesPayload,
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  validBrainImagingSamplesRequest,
@@ -378,6 +383,7 @@ export {
378
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  termdbClusterPayload,
379
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  termdbCohortSummaryPayload,
380
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  termdbCohortsPayload,
386
+ termdbProteomePayload,
381
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  termdbSampleImagesPayload,
382
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  termdbSampleScatterPayload,
383
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  termdbSingleCellDEgenesPayload,
@@ -485,6 +491,8 @@ export {
485
491
  validTermdbDmrResponse,
486
492
  validTermdbIsoformAvailabilityRequest,
487
493
  validTermdbIsoformAvailabilityResponse,
494
+ validTermdbProteomeRequest,
495
+ validTermdbProteomeResponse,
488
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  validTermdbSampleImagesRequest,
489
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  validTermdbSampleImagesResponse,
490
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  validTermdbSampleScatterRequest,
package/dist/termdb.categories.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termdbCategoriesPayload,
3
3
  validCategoriesRequest,
4
4
  validCategoriesResponse
5
- } from "./chunk-KNDCWQJD.js";
5
+ } from "./chunk-INIT6CVR.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termdbCategoriesPayload,
package/dist/termdb.chat.js CHANGED
@@ -59,7 +59,7 @@ var validChatRequest = (input) => {
59
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  const $io28 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "proteomeAbundance" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.protein && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && ("object" === typeof input3.proteomeDetails && null !== input3.proteomeDetails && ("string" === typeof input3.proteomeDetails.assay && "string" === typeof input3.proteomeDetails.cohort));
60
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  const $io30 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "date" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
61
61
  const $io31 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "ssGSEA" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.genes || Array.isArray(input3.genes) && input3.genes.every((elem) => "string" === typeof elem)) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
62
- const $io32 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "dnaMethylation" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.chr && "number" === typeof input3.start && "number" === typeof input3.stop && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
62
+ const $io32 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "dnaMethylation" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.chr && "number" === typeof input3.start && "number" === typeof input3.stop && ("gene" === input3.genomicFeatureType || "promoter" === input3.genomicFeatureType || "region" === input3.genomicFeatureType || "enhancer" === input3.genomicFeatureType) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
63
63
  const $io33 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "singleCellGeneExpression" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.gene && "string" === typeof input3.sample && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && (void 0 === input3.kind || "gene" === input3.kind) && (void 0 === input3.chr || "string" === typeof input3.chr) && (void 0 === input3.start || "number" === typeof input3.start) && (void 0 === input3.stop || "number" === typeof input3.stop);
64
64
  const $io34 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "singleCellGeneExpression" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.gene && "string" === typeof input3.sample && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && (void 0 === input3.kind || "coord" === input3.kind) && "string" === typeof input3.chr && "number" === typeof input3.start && "number" === typeof input3.stop;
65
65
  const $io35 = (input3) => "number" === typeof input3.value && (void 0 === input3.label || "string" === typeof input3.label) && (void 0 === input3.name || "string" === typeof input3.name);
@@ -85,7 +85,7 @@ var validChatRequest = (input) => {
85
85
  const $io46 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "geneVariant" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && "coord" === input3.kind && "string" === typeof input3.chr && "number" === typeof input3.start && "number" === typeof input3.stop && (Array.isArray(input3.genes) && input3.genes.every((elem) => "object" === typeof elem && null !== elem && $iu3(elem))) && (void 0 === input3.groupsetting || "object" === typeof input3.groupsetting && null !== input3.groupsetting && $io8(input3.groupsetting)) && (void 0 === input3.childTerms || Array.isArray(input3.childTerms) && input3.childTerms.every((elem) => "object" === typeof elem && null !== elem && $io42(elem)));
86
86
  const $io47 = (input3) => (void 0 === input3.key || "string" === typeof input3.key) && (void 0 === input3.label || "string" === typeof input3.label || "number" === typeof input3.label) && (void 0 === input3.value || "string" === typeof input3.value) && (void 0 === input3.dt || "number" === typeof input3.dt) && (void 0 === input3.mclasslst || Array.isArray(input3.mclasslst) && input3.mclasslst.every((elem) => "string" === typeof elem)) && (void 0 === input3.mclassExcludeLst || Array.isArray(input3.mclassExcludeLst) && input3.mclassExcludeLst.every((elem) => "string" === typeof elem)) && (void 0 === input3.origin || "string" === typeof input3.origin);
87
87
  const $io48 = (input3) => (void 0 === input3.join || "string" === typeof input3.join) && (void 0 === input3.isnot || "boolean" === typeof input3.isnot) && (void 0 === input3.bar_by_grade || "boolean" === typeof input3.bar_by_grade) && (void 0 === input3.bar_by_children || "boolean" === typeof input3.bar_by_children) && (void 0 === input3.value_by_max_grade || "boolean" === typeof input3.value_by_max_grade) && (void 0 === input3.value_by_most_recent || "boolean" === typeof input3.value_by_most_recent) && (void 0 === input3.value_by_computable_grade || "boolean" === typeof input3.value_by_computable_grade) && ("object" === typeof input3.term && null !== input3.term && $iu11(input3.term)) && "number" === typeof input3.ratio;
88
- const $io49 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "termCollection" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.termIds || Array.isArray(input3.termIds) && input3.termIds.every((elem) => "string" === typeof elem)) && (Array.isArray(input3.termlst) && input3.termlst.every((elem) => "object" === typeof elem && null !== elem && $io50(elem))) && (void 0 === input3.newTvs || "boolean" === typeof input3.newTvs) && ("object" === typeof input3.propsByTermId && null !== input3.propsByTermId && false === Array.isArray(input3.propsByTermId) && $io51(input3.propsByTermId)) && "numeric" === input3.memberType && (void 0 === input3.numerators || Array.isArray(input3.numerators) && input3.numerators.every((elem) => "string" === typeof elem)) && (void 0 === input3.valueTransform || "object" === typeof input3.valueTransform && null !== input3.valueTransform && false === Array.isArray(input3.valueTransform) && $io53(input3.valueTransform));
88
+ const $io49 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "termCollection" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.termIds || Array.isArray(input3.termIds) && input3.termIds.every((elem) => "string" === typeof elem)) && (Array.isArray(input3.termlst) && input3.termlst.every((elem) => "object" === typeof elem && null !== elem && $io50(elem))) && (void 0 === input3.newTvs || "boolean" === typeof input3.newTvs) && ("object" === typeof input3.propsByTermId && null !== input3.propsByTermId && false === Array.isArray(input3.propsByTermId) && $io51(input3.propsByTermId)) && (void 0 === input3.isCustom || "boolean" === typeof input3.isCustom) && "numeric" === input3.memberType && (void 0 === input3.numerators || Array.isArray(input3.numerators) && input3.numerators.every((elem) => "string" === typeof elem)) && (void 0 === input3.valueTransform || "object" === typeof input3.valueTransform && null !== input3.valueTransform && false === Array.isArray(input3.valueTransform) && $io53(input3.valueTransform));
89
89
  const $io50 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "string" === typeof input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion));
90
90
  const $io51 = (input3) => Object.keys(input3).every((key) => {
91
91
  const value = input3[key];
@@ -104,7 +104,7 @@ var validChatRequest = (input) => {
104
104
  return true;
105
105
  });
106
106
  const $io53 = (input3) => void 0 === input3.offset || "number" === typeof input3.offset;
107
- const $io54 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "termCollection" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.termIds || Array.isArray(input3.termIds) && input3.termIds.every((elem) => "string" === typeof elem)) && (Array.isArray(input3.termlst) && input3.termlst.every((elem) => "object" === typeof elem && null !== elem && $io50(elem))) && (void 0 === input3.newTvs || "boolean" === typeof input3.newTvs) && ("object" === typeof input3.propsByTermId && null !== input3.propsByTermId && false === Array.isArray(input3.propsByTermId) && $io51(input3.propsByTermId)) && "categorical" === input3.memberType && (Array.isArray(input3.categoryKeys) && input3.categoryKeys.every((elem) => "object" === typeof elem && null !== elem && $io55(elem)));
107
+ const $io54 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "termCollection" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.termIds || Array.isArray(input3.termIds) && input3.termIds.every((elem) => "string" === typeof elem)) && (Array.isArray(input3.termlst) && input3.termlst.every((elem) => "object" === typeof elem && null !== elem && $io50(elem))) && (void 0 === input3.newTvs || "boolean" === typeof input3.newTvs) && ("object" === typeof input3.propsByTermId && null !== input3.propsByTermId && false === Array.isArray(input3.propsByTermId) && $io51(input3.propsByTermId)) && (void 0 === input3.isCustom || "boolean" === typeof input3.isCustom) && "categorical" === input3.memberType && (Array.isArray(input3.categoryKeys) && input3.categoryKeys.every((elem) => "object" === typeof elem && null !== elem && $io55(elem)));
108
108
  const $io55 = (input3) => "string" === typeof input3.key && "boolean" === typeof input3.shown;
109
109
  const $iu0 = (input3) => (() => {
110
110
  if ("tvslst" === input3.type)
@@ -1954,6 +1954,10 @@ var validChatRequest = (input) => {
1954
1954
  path: _path2 + ".stop",
1955
1955
  expected: "number",
1956
1956
  value: input3.stop
1957
+ }), "gene" === input3.genomicFeatureType || "promoter" === input3.genomicFeatureType || "region" === input3.genomicFeatureType || "enhancer" === input3.genomicFeatureType || $report(_exceptionable2, {
1958
+ path: _path2 + ".genomicFeatureType",
1959
+ expected: '("enhancer" | "gene" | "promoter" | "region")',
1960
+ value: input3.genomicFeatureType
1957
1961
  }), void 0 === input3.bins || ("object" === typeof input3.bins && null !== input3.bins || $report(_exceptionable2, {
1958
1962
  path: _path2 + ".bins",
1959
1963
  expected: "(PresetNumericBins | undefined)",
@@ -3124,6 +3128,10 @@ var validChatRequest = (input) => {
3124
3128
  path: _path2 + ".propsByTermId",
3125
3129
  expected: "__type.o7",
3126
3130
  value: input3.propsByTermId
3131
+ }), void 0 === input3.isCustom || "boolean" === typeof input3.isCustom || $report(_exceptionable2, {
3132
+ path: _path2 + ".isCustom",
3133
+ expected: "(boolean | undefined)",
3134
+ value: input3.isCustom
3127
3135
  }), "numeric" === input3.memberType || $report(_exceptionable2, {
3128
3136
  path: _path2 + ".memberType",
3129
3137
  expected: '"numeric"',
@@ -3347,6 +3355,10 @@ var validChatRequest = (input) => {
3347
3355
  path: _path2 + ".propsByTermId",
3348
3356
  expected: "__type.o7",
3349
3357
  value: input3.propsByTermId
3358
+ }), void 0 === input3.isCustom || "boolean" === typeof input3.isCustom || $report(_exceptionable2, {
3359
+ path: _path2 + ".isCustom",
3360
+ expected: "(boolean | undefined)",
3361
+ value: input3.isCustom
3350
3362
  }), "categorical" === input3.memberType || $report(_exceptionable2, {
3351
3363
  path: _path2 + ".memberType",
3352
3364
  expected: '"categorical"',
package/dist/termdb.chat2.js CHANGED
@@ -1,7 +1,7 @@
1
1
  import {
2
2
  validChatRequest,
3
3
  validChatResponse
4
- } from "./chunk-ZKO7LMCC.js";
4
+ } from "./chunk-TUM3OZ7K.js";
5
5
  import {
6
6
  ChatPayload
7
7
  } from "./chunk-FRXRNCDV.js";
package/dist/termdb.cluster.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termdbClusterPayload,
3
3
  validTermdbClusterRequest,
4
4
  validTermdbClusterResponse
5
- } from "./chunk-UYKWZWCU.js";
5
+ } from "./chunk-M7WMC7GC.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termdbClusterPayload,
package/dist/termdb.descrstats.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  descrStatsPayload,
3
3
  validDescrStatsRequest,
4
4
  validDescrStatsResponse
5
- } from "./chunk-45VA4Y6L.js";
5
+ } from "./chunk-Y6FNAG22.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  descrStatsPayload,
package/dist/termdb.dmr.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  TermdbDmrPayload,
3
3
  validTermdbDmrRequest,
4
4
  validTermdbDmrResponse
5
- } from "./chunk-K6W2WEPW.js";
5
+ } from "./chunk-NO3ZZD3L.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  TermdbDmrPayload,
package/dist/termdb.numericcategories.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  numericCategoriesPayload,
3
3
  validNumericCategoriesRequest,
4
4
  validNumericCategoriesResponse
5
- } from "./chunk-DDMUMMOL.js";
5
+ } from "./chunk-LDLZU2QY.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  numericCategoriesPayload,
package/dist/termdb.percentile.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  percentilePayload,
3
3
  validPercentileRequest,
4
4
  validPercentileResponse
5
- } from "./chunk-ZRTB7SRA.js";
5
+ } from "./chunk-ONNT3XV7.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  percentilePayload,
package/dist/termdb.proteome.js ADDED
@@ -0,0 +1,11 @@
1
+ import {
2
+ termdbProteomePayload,
3
+ validTermdbProteomeRequest,
4
+ validTermdbProteomeResponse
5
+ } from "./chunk-W3F3CLYP.js";
6
+ import "./chunk-YNHC5SXO.js";
7
+ export {
8
+ termdbProteomePayload,
9
+ validTermdbProteomeRequest,
10
+ validTermdbProteomeResponse
11
+ };
package/dist/termdb.termsbyids.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termsByIdsPayload,
3
3
  validTermsByIdsRequest,
4
4
  validTermsByIdsResponse
5
- } from "./chunk-3DA4MJ2U.js";
5
+ } from "./chunk-UWK6LBTQ.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termsByIdsPayload,
package/dist/termdb.topTermsByType.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termdbTopTermsByTypePayload,
3
3
  validTermdbTopTermsByTypeRequest,
4
4
  validTermdbTopTermsByTypeResponse
5
- } from "./chunk-2QTCQFYE.js";
5
+ } from "./chunk-2NINVZOB.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termdbTopTermsByTypePayload,
package/dist/termdb.topVariablyExpressedGenes.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termdbTopVariablyExpressedGenesPayload,
3
3
  validTermdbTopVariablyExpressedGenesRequest,
4
4
  validTermdbTopVariablyExpressedGenesResponse
5
- } from "./chunk-VUNM6QTX.js";
5
+ } from "./chunk-QMEKJW2A.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termdbTopVariablyExpressedGenesPayload,
package/dist/termdb.violinBox.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  validViolinBoxRequest,
3
3
  validViolinBoxResponse,
4
4
  violinBoxPayload
5
- } from "./chunk-C5ECCXOT.js";
5
+ } from "./chunk-WNUWRPXG.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  validViolinBoxRequest,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@sjcrh/proteinpaint-types",
3
- "version": "2.181.0",
3
+ "version": "2.182.1",
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
@@ -711,12 +711,17 @@ export type MetaboliteIntensityQuery = MetaboliteIntensityQueryNative
711
711
  type CohortConfig = {
712
712
  file: string
713
713
  filter?: Tvs[]
714
+ ctlFilter?: Tvs[]
714
715
  overlayTerm?: BaseTerm
715
716
  }
716
717
  type AssayWithCohorts = {
717
718
  cohorts: {
718
719
  [cohortName: string]: CohortConfig
719
720
  }
721
+ /** optional PTM type for PTM assay type */
722
+ PTMType?: string
723
+ /** optional specific mclass override for PTM assay type */
724
+ mclassOverride?: Mclass
720
725
  }
721
726
  type AssayConfig = AssayWithCohorts
722
727
 
@@ -1445,6 +1450,12 @@ if missing, name is value of m[url.namekey], as used in url itself (e.g. snp rsi
1445
1450
  linkText?: string
1446
1451
  }
1447
1452
 
1453
+ export type GetSamplesOpts = {
1454
+ filter: any // pp filter
1455
+ filter0: any // mmrf filter
1456
+ ds: any
1457
+ }
1458
+
1448
1459
  /*** type of ds.cohort.termdb{} ***/
1449
1460
  export type Termdb = {
1450
1461
  /** Terms */
@@ -1477,7 +1488,7 @@ export type Termdb = {
1477
1488
  /** if true, backend is allowed to send sample names to client in charts */
1478
1489
  displaySampleIds?: (clientAuthResult: any) => boolean
1479
1490
  /** get samples that match supplied filter */
1480
- getSamples?: (filter: any, ds: any) => Promise<Set<any>>
1491
+ getSamples?: (opts: GetSamplesOpts) => Promise<Set<any>>
1481
1492
  converSampleIds?: boolean
1482
1493
  alwaysShowBranchTerms?: boolean
1483
1494
  minimumSampleAllowed4filter?: number
@@ -1660,14 +1671,15 @@ keep this setting here for reason of:
1660
1671
  type TermCollectionBase = {
1661
1672
  /** human readable name as well as unique identifier for this collection */
1662
1673
  name: string
1663
- /** array of dictionary term ids belonging to this collection */
1664
- termIds: string[]
1674
+ /** array of dictionary term ids belonging to this collection.
1675
+ * Optional for custom (non-dictionary) collections where termlst[] is the primary source. */
1676
+ termIds?: string[]
1665
1677
  /** full term objects corresponding to termIds[]; populated by server on dataset init,
1666
1678
  * sent to client so fill() can resolve member term names without extra requests */
1667
1679
  termlst?: BaseTerm[]
1668
1680
  /** array of branch term ids belonging to this collection,
1669
1681
  * may be used as state.tree.expandedTermIds[] option to termdb appInit() */
1670
- branchIds: string[]
1682
+ branchIds?: string[]
1671
1683
  propsByTermId: {
1672
1684
  [termId: string]: any
1673
1685
  }
package/src/index.ts CHANGED
@@ -50,6 +50,7 @@ export * from './routes/termdb.dmr.ts'
50
50
  export * from './routes/termdb.isoformAvailability.ts'
51
51
  export * from './routes/termdb.numericcategories.ts'
52
52
  export * from './routes/termdb.percentile.ts'
53
+ export * from './routes/termdb.proteome.ts'
53
54
  export * from './routes/termdb.runChart.ts'
54
55
  export * from './routes/termdb.rootterm.ts'
55
56
  export * from './routes/termdb.termchildren.ts'
package/src/routes/termdb.proteome.ts ADDED
@@ -0,0 +1,13 @@
1
+ import type { RoutePayload } from './routeApi.js'
2
+
3
+ export type TermdbProteomeRequest = any
4
+ export type TermdbProteomeResponse = any
5
+
6
+ export const termdbProteomePayload: RoutePayload = {
7
+ request: {
8
+ typeId: 'TermdbProteomeRequest'
9
+ },
10
+ response: {
11
+ typeId: 'TermdbProteomeResponse'
12
+ }
13
+ }
package/src/terms/dnaMethylation.ts CHANGED
@@ -3,16 +3,25 @@ import type { NumericBaseTerm, NumericQ, PresetNumericBins, NumTW, RawNumTW } fr
3
3
  export type DnaMethylationQ = NumericQ & { dt?: number }
4
4
 
5
5
  export type DnaMethylationTerm = NumericBaseTerm & {
6
- /** term.id: plan to be concatenated string value "chr:start-stop" */
7
- /** term.name: can be user-assigned */
8
6
  type: 'dnaMethylation'
7
+ /** concatenated string value "chr:start-stop" */
8
+ id?: string
9
9
  chr: string
10
10
  start: number
11
11
  stop: number
12
+ /** Type used to categorize the genomic feature */
13
+ genomicFeatureType: 'gene' | 'promoter' | 'region' | 'enhancer'
12
14
  bins?: PresetNumericBins
13
15
  }
14
16
 
15
- export type RawDnaMethylationTerm = DnaMethylationTerm & { name?: string }
17
+ export type RawDnaMethylationTerm = DnaMethylationTerm & {
18
+ /** Name of the genomic feature, e.g., gene name or promoter id/name, etc.
19
+ * Different than .name, which includes the genomic coordinates and unit,
20
+ * and is used for display purposes.*/
21
+ featureName?: string
22
+ name?: string
23
+ unit?: string
24
+ }
16
25
 
17
26
  export type DnaMethylationTW = NumTW & { term: DnaMethylationTerm }
18
27
 
package/src/terms/termCollection.ts CHANGED
@@ -10,7 +10,7 @@ type BaseTermCollection = BaseTerm & {
10
10
  type: 'termCollection'
11
11
  /** list of term.ids that are available in this collection. this is used in request payload and server side */
12
12
  termIds?: string[]
13
- /** list of term objs corresponding to termIds[].
13
+ /** list of term objs corresponding to termIds[].
14
14
  this is generated on server init, and sent to client, so client has easy access to show name of every term */
15
15
  termlst: BaseTerm[]
16
16
  /** TODO purpose */
@@ -20,6 +20,10 @@ type BaseTermCollection = BaseTerm & {
20
20
  [prop: string]: any
21
21
  }
22
22
  }
23
+ /** When true, member terms are non-dictionary terms (e.g. isoformExpression).
24
+ * getData() expands them into individual tws for existing handlers, then
25
+ * reconstitutes the grouped shape after data is returned. */
26
+ isCustom?: boolean
23
27
  }
24
28
 
25
29
  export type NumericTermCollection = BaseTermCollection & {
@@ -60,6 +64,7 @@ export type RawNumericTermCollection = {
60
64
  }
61
65
  }
62
66
  numerators?: string[]
67
+ isCustom?: boolean
63
68
  }
64
69
 
65
70
  /** Pre-fill shape for a categorical termCollection (memberType set by TermCollection.fill()) */
@@ -75,6 +80,7 @@ export type RawCategoricalTermCollection = {
75
80
  }
76
81
  }
77
82
  categoryKeys?: CategoryKey[]
83
+ isCustom?: boolean
78
84
  }
79
85
 
80
86
  export type RawTermCollection = RawNumericTermCollection | RawCategoricalTermCollection
package/src/terms/tw.ts CHANGED
@@ -19,6 +19,7 @@ export type BaseTW = {
19
19
  sortSamples?: any
20
20
  minNumSamples?: number
21
21
  valueFilter?: any
22
+ values?: { [key: string]: any }
22
23
  }
23
24
 
24
25
  export type TermWrapper = NumTW | GvTW | ConditionTW | SnpsTW | QualTW | TermCollectionTW