@sjcrh/proteinpaint-types 2.189.0 → 2.190.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +8 -20
- package/dist/index.js +422 -553
- package/dist/index.js.map +7 -0
- package/package.json +13 -25
- package/dist/aiProjectAdmin.js +0 -11
- package/dist/aiProjectSelectedWSImages.js +0 -11
- package/dist/aiProjectTrainModel.js +0 -11
- package/dist/alphaGenome.js +0 -11
- package/dist/alphaGenomeTypes.js +0 -11
- package/dist/brainImaging.js +0 -11
- package/dist/brainImagingSamples.js +0 -11
- package/dist/burden.js +0 -11
- package/dist/chunk-2744ACBX.js +0 -126
- package/dist/chunk-2BCLGYAG.js +0 -96
- package/dist/chunk-2C4X5B6N.js +0 -62
- package/dist/chunk-2VJRTZE2.js +0 -287
- package/dist/chunk-2X36CBQF.js +0 -158
- package/dist/chunk-46YIGVUP.js +0 -908
- package/dist/chunk-4EAGOSMN.js +0 -128
- package/dist/chunk-5H2LJKPX.js +0 -104
- package/dist/chunk-5L4VF3ZL.js +0 -266
- package/dist/chunk-5N7V62ZL.js +0 -231
- package/dist/chunk-62XTWOVJ.js +0 -273
- package/dist/chunk-6GKG55BT.js +0 -232
- package/dist/chunk-7MUISZHS.js +0 -61
- package/dist/chunk-7OA6G77M.js +0 -113
- package/dist/chunk-BCBSHTHS.js +0 -75
- package/dist/chunk-CQXBQY2H.js +0 -161
- package/dist/chunk-CWACV4MW.js +0 -305
- package/dist/chunk-D7AKQKDG.js +0 -238
- package/dist/chunk-DDKGTDDB.js +0 -6739
- package/dist/chunk-DI4Q26E7.js +0 -16
- package/dist/chunk-EIJT53QB.js +0 -240
- package/dist/chunk-EOKM345J.js +0 -222
- package/dist/chunk-FK7OCBPT.js +0 -341
- package/dist/chunk-FMC4G5BP.js +0 -62
- package/dist/chunk-GCJESMM2.js +0 -354
- package/dist/chunk-GTS2G4R4.js +0 -62
- package/dist/chunk-HD3J5BKM.js +0 -409
- package/dist/chunk-HQV2A7JV.js +0 -62
- package/dist/chunk-IS74WYQF.js +0 -207
- package/dist/chunk-JEQGBUK2.js +0 -5993
- package/dist/chunk-K4FSDTDW.js +0 -109
- package/dist/chunk-KCMPDEH7.js +0 -62
- package/dist/chunk-KXYFG2HO.js +0 -307
- package/dist/chunk-LC6KLHCJ.js +0 -8903
- package/dist/chunk-LQYSPLDQ.js +0 -3613
- package/dist/chunk-LRVF7U64.js +0 -62
- package/dist/chunk-MHDQO7R5.js +0 -195
- package/dist/chunk-MKYLCBTP.js +0 -5475
- package/dist/chunk-MNT3GF7M.js +0 -3628
- package/dist/chunk-MVB7LQS5.js +0 -3986
- package/dist/chunk-P25WDNMD.js +0 -171
- package/dist/chunk-P3WBZJFF.js +0 -158
- package/dist/chunk-PTE2I7DF.js +0 -91
- package/dist/chunk-Q3HGHP3J.js +0 -174
- package/dist/chunk-RPX4TVMD.js +0 -14
- package/dist/chunk-RXJNXOZC.js +0 -326
- package/dist/chunk-SDZIGJY3.js +0 -5931
- package/dist/chunk-SLXGWQZ4.js +0 -458
- package/dist/chunk-SZZXZZKO.js +0 -3991
- package/dist/chunk-TD4YLTHL.js +0 -158
- package/dist/chunk-TEXOICIS.js +0 -11810
- package/dist/chunk-THQOFV2K.js +0 -205
- package/dist/chunk-TLZ5ROOU.js +0 -347
- package/dist/chunk-TQQWSHFM.js +0 -5980
- package/dist/chunk-U3BTVE5T.js +0 -111
- package/dist/chunk-UBOVHONH.js +0 -62
- package/dist/chunk-UDTEGP3G.js +0 -365
- package/dist/chunk-UYJA4UM7.js +0 -97
- package/dist/chunk-V3JDD3ZG.js +0 -3671
- package/dist/chunk-VUKRI3TG.js +0 -164
- package/dist/chunk-W3F3CLYP.js +0 -61
- package/dist/chunk-X4JBWMXY.js +0 -130
- package/dist/chunk-X5E72ZXA.js +0 -5979
- package/dist/chunk-YNHC5SXO.js +0 -1780
- package/dist/chunk-YPEFUAJW.js +0 -62
- package/dist/chunk-YSTMGNYR.js +0 -113
- package/dist/chunk-Z3IYM5OK.js +0 -296
- package/dist/chunk-ZCV62ELK.js +0 -96
- package/dist/chunk-ZIOJDN75.js +0 -197
- package/dist/chunk-ZMDZYG5B.js +0 -4224
- package/dist/clearwsisession.js +0 -78
- package/dist/clearwsisessions.js +0 -13
- package/dist/correlationVolcano.js +0 -11
- package/dist/dataset.js +0 -11
- package/dist/deleteWSITileSelection.js +0 -11
- package/dist/dsdata.js +0 -11
- package/dist/dzimages.js +0 -11
- package/dist/gdc.grin2.js +0 -17
- package/dist/gdc.maf.js +0 -11
- package/dist/gdc.mafBuild.js +0 -11
- package/dist/genelookup.js +0 -11
- package/dist/genesetEnrichment.js +0 -11
- package/dist/genesetOverrepresentation.js +0 -11
- package/dist/grin2.js +0 -11
- package/dist/healthcheck.js +0 -11
- package/dist/hicdata.js +0 -11
- package/dist/hicgenome.js +0 -11
- package/dist/hicstat.js +0 -11
- package/dist/img.js +0 -11
- package/dist/isoformlst.js +0 -11
- package/dist/ntseq.js +0 -11
- package/dist/pdomain.js +0 -11
- package/dist/samplewsimages.js +0 -13
- package/dist/saveWSIAnnotation.js +0 -11
- package/dist/snp.js +0 -11
- package/dist/termdb.DE.js +0 -11
- package/dist/termdb.categories.js +0 -11
- package/dist/termdb.chat.js +0 -3631
- package/dist/termdb.chat2.js +0 -15
- package/dist/termdb.cluster.js +0 -11
- package/dist/termdb.cohort.summary.js +0 -11
- package/dist/termdb.cohorts.js +0 -11
- package/dist/termdb.dapVolcano.js +0 -11
- package/dist/termdb.descrstats.js +0 -11
- package/dist/termdb.diffMeth.js +0 -11
- package/dist/termdb.dmr.js +0 -11
- package/dist/termdb.filterTermValues.js +0 -11
- package/dist/termdb.isoformAvailability.js +0 -11
- package/dist/termdb.numericcategories.js +0 -11
- package/dist/termdb.percentile.js +0 -11
- package/dist/termdb.profileFormScores.js +0 -11
- package/dist/termdb.profileForms2Scores.js +0 -11
- package/dist/termdb.profileScores.js +0 -11
- package/dist/termdb.proteome.js +0 -11
- package/dist/termdb.rootterm.js +0 -11
- package/dist/termdb.runChart.js +0 -13
- package/dist/termdb.sampleImages.js +0 -11
- package/dist/termdb.sampleScatter.js +0 -11
- package/dist/termdb.singleSampleMutation.js +0 -11
- package/dist/termdb.singlecellDEgenes.js +0 -11
- package/dist/termdb.singlecellData.js +0 -11
- package/dist/termdb.singlecellSamples.js +0 -11
- package/dist/termdb.termchildren.js +0 -11
- package/dist/termdb.termsbyids.js +0 -11
- package/dist/termdb.topMutatedGenes.js +0 -11
- package/dist/termdb.topTermsByType.js +0 -11
- package/dist/termdb.topVariablyExpressedGenes.js +0 -11
- package/dist/termdb.violinBox.js +0 -17
- package/dist/tileserver.js +0 -11
- package/dist/wsimages.js +0 -11
- package/dist/wsisamples.js +0 -11
- package/src/Mclass.ts +0 -8
- package/src/dataset.ts +0 -2188
- package/src/docs.json +0 -16417
- package/src/fileOrUrl.ts +0 -15
- package/src/filter.ts +0 -110
- package/src/genome.ts +0 -129
- package/src/index.ts +0 -94
- package/src/routes/aiProjectAdmin.ts +0 -37
- package/src/routes/aiProjectSelectedWSImages.ts +0 -47
- package/src/routes/aiProjectTrainModel.ts +0 -20
- package/src/routes/alphaGenome.ts +0 -27
- package/src/routes/alphaGenomeTypes.ts +0 -21
- package/src/routes/brainImaging.ts +0 -47
- package/src/routes/brainImagingSamples.ts +0 -25
- package/src/routes/burden.ts +0 -113
- package/src/routes/clearwsisessions.ts +0 -19
- package/src/routes/correlationVolcano.ts +0 -51
- package/src/routes/dataset.ts +0 -14
- package/src/routes/deleteWSITileSelection.ts +0 -25
- package/src/routes/dsdata.ts +0 -14
- package/src/routes/dzimages.ts +0 -25
- package/src/routes/errorResponse.ts +0 -6
- package/src/routes/filter.gdc.ts +0 -15
- package/src/routes/gdc.grin2.ts +0 -246
- package/src/routes/gdc.maf.ts +0 -52
- package/src/routes/gdc.mafBuild.ts +0 -20
- package/src/routes/genelookup.ts +0 -22
- package/src/routes/genesetEnrichment.ts +0 -116
- package/src/routes/genesetOverrepresentation.ts +0 -48
- package/src/routes/grin2.ts +0 -173
- package/src/routes/healthcheck.ts +0 -80
- package/src/routes/hicdata.ts +0 -48
- package/src/routes/hicgenome.ts +0 -50
- package/src/routes/hicstat.ts +0 -57
- package/src/routes/img.ts +0 -23
- package/src/routes/isoformlst.ts +0 -14
- package/src/routes/ntseq.ts +0 -14
- package/src/routes/pdomain.ts +0 -14
- package/src/routes/routeApi.ts +0 -47
- package/src/routes/samplewsimages.ts +0 -44
- package/src/routes/saveWSIAnnotation.ts +0 -25
- package/src/routes/snp.ts +0 -13
- package/src/routes/termdb.DE.ts +0 -226
- package/src/routes/termdb.categories.ts +0 -74
- package/src/routes/termdb.chat2.ts +0 -190
- package/src/routes/termdb.cluster.ts +0 -134
- package/src/routes/termdb.cohort.summary.ts +0 -14
- package/src/routes/termdb.cohorts.ts +0 -14
- package/src/routes/termdb.dapVolcano.ts +0 -35
- package/src/routes/termdb.descrstats.ts +0 -75
- package/src/routes/termdb.diffMeth.ts +0 -63
- package/src/routes/termdb.dmr.ts +0 -121
- package/src/routes/termdb.filterTermValues.ts +0 -23
- package/src/routes/termdb.isoformAvailability.ts +0 -22
- package/src/routes/termdb.numericcategories.ts +0 -32
- package/src/routes/termdb.percentile.ts +0 -67
- package/src/routes/termdb.profileFormScores.ts +0 -26
- package/src/routes/termdb.profileForms2Scores.ts +0 -25
- package/src/routes/termdb.profileScores.ts +0 -27
- package/src/routes/termdb.proteome.ts +0 -13
- package/src/routes/termdb.rootterm.ts +0 -49
- package/src/routes/termdb.runChart.ts +0 -66
- package/src/routes/termdb.sampleImages.ts +0 -26
- package/src/routes/termdb.sampleScatter.ts +0 -60
- package/src/routes/termdb.singleSampleMutation.ts +0 -51
- package/src/routes/termdb.singlecellDEgenes.ts +0 -50
- package/src/routes/termdb.singlecellData.ts +0 -75
- package/src/routes/termdb.singlecellSamples.ts +0 -50
- package/src/routes/termdb.termchildren.ts +0 -49
- package/src/routes/termdb.termsbyids.ts +0 -26
- package/src/routes/termdb.topMutatedGenes.ts +0 -51
- package/src/routes/termdb.topTermsByType.ts +0 -32
- package/src/routes/termdb.topVariablyExpressedGenes.ts +0 -54
- package/src/routes/termdb.violinBox.ts +0 -230
- package/src/routes/tileserver.ts +0 -14
- package/src/routes/wsimages.ts +0 -34
- package/src/routes/wsisamples.ts +0 -25
- package/src/termdb.matrix.ts +0 -57
- package/src/terms/categorical.ts +0 -18
- package/src/terms/condition.ts +0 -73
- package/src/terms/date.ts +0 -20
- package/src/terms/dnaMethylation.ts +0 -28
- package/src/terms/geneExpression.ts +0 -38
- package/src/terms/geneVariant.ts +0 -132
- package/src/terms/isoformExpression.ts +0 -36
- package/src/terms/metaboliteIntensity.ts +0 -30
- package/src/terms/numeric.ts +0 -278
- package/src/terms/proteomeAbundance.ts +0 -38
- package/src/terms/q.ts +0 -105
- package/src/terms/qualitative.ts +0 -73
- package/src/terms/samplelst.ts +0 -34
- package/src/terms/singleCellCellType.ts +0 -18
- package/src/terms/singleCellGeneExpression.ts +0 -32
- package/src/terms/snp.ts +0 -24
- package/src/terms/snps.ts +0 -111
- package/src/terms/ssGSEA.ts +0 -26
- package/src/terms/term.ts +0 -60
- package/src/terms/termCollection.ts +0 -139
- package/src/terms/tw.ts +0 -64
- package/src/termsetting.ts +0 -201
- package/src/test/numeric.type.spec.ts +0 -275
- package/src/vocab.ts +0 -37
package/dist/index.js
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1
|
+
// src/routes/aiProjectSelectedWSImages.ts
|
|
2
|
+
var FlagStatus = {
|
|
3
|
+
Normal: 0,
|
|
4
|
+
Skipped: 1,
|
|
5
|
+
Flagged: 2,
|
|
6
|
+
Deleted: 3
|
|
7
|
+
};
|
|
8
|
+
var FeaturePrefixes = {
|
|
9
|
+
Star: "annotation-star-",
|
|
10
|
+
Square: "annotation-square-",
|
|
11
|
+
Border: "annotation-border-",
|
|
12
|
+
PredBorder: "prediction-border-"
|
|
13
|
+
};
|
|
14
|
+
var SelectionPrefixes = {
|
|
15
|
+
TileSelection: "ts_",
|
|
16
|
+
Prediction: "pred_",
|
|
17
|
+
Annotation: "anno_"
|
|
18
|
+
};
|
|
19
|
+
var FlagStatusMessages = {
|
|
20
|
+
[FlagStatus.Normal]: "",
|
|
21
|
+
[FlagStatus.Skipped]: "(Skipped)",
|
|
22
|
+
[FlagStatus.Flagged]: "(Flagged)"
|
|
23
|
+
// Didn't add Deleted to FlagStatusMessages because deleted annotations dont exist
|
|
24
|
+
// and deleted predictons are filtered out in proteinpaint/server/routes/aiProjectSelectedWSImages.ts around line 119
|
|
25
|
+
};
|
|
26
|
+
function createSelectionID(prefix, coordinates) {
|
|
27
|
+
return prefix + JSON.stringify(coordinates);
|
|
28
|
+
}
|
|
29
|
+
function checkSelectionType(tileSelection, suspectedPrefix) {
|
|
30
|
+
return tileSelection.id.startsWith(suspectedPrefix);
|
|
31
|
+
}
|
|
32
|
+
function createFeatureID(featurePrefix, coords) {
|
|
33
|
+
return featurePrefix + JSON.stringify(coords);
|
|
34
|
+
}
|
|
35
|
+
|
|
36
|
+
// src/routes/hicgenome.ts
|
|
37
|
+
var hicGenomePayloadExample = {
|
|
38
|
+
examples: [
|
|
39
|
+
{
|
|
40
|
+
request: {
|
|
41
|
+
body: {
|
|
42
|
+
embedder: "localhost",
|
|
43
|
+
url: "https://proteinpaint.stjude.org/ppdemo/hg19/hic/hic_demo.hic",
|
|
44
|
+
matrixType: "observed",
|
|
45
|
+
nmeth: "NONE",
|
|
46
|
+
pos1: "3",
|
|
47
|
+
pos2: "2",
|
|
48
|
+
resolution: 1e6
|
|
49
|
+
}
|
|
50
|
+
// satisfies HicGenomeRequest // TODO: fix the type or example
|
|
51
|
+
},
|
|
52
|
+
response: {
|
|
53
|
+
header: { status: 200 }
|
|
54
|
+
}
|
|
55
|
+
}
|
|
56
|
+
]
|
|
57
|
+
};
|
|
58
|
+
|
|
59
|
+
// src/routes/samplewsimages.ts
|
|
60
|
+
var WSImage = class {
|
|
61
|
+
constructor(filename) {
|
|
62
|
+
this.filename = filename;
|
|
63
|
+
}
|
|
64
|
+
};
|
|
65
|
+
|
|
66
|
+
// src/routes/termdb.categories.ts
|
|
67
|
+
var termdbCategoriesPayloadExamples = {
|
|
68
|
+
request: {
|
|
69
|
+
typeId: "CategoriesRequest"
|
|
70
|
+
},
|
|
71
|
+
response: {
|
|
72
|
+
typeId: "CategoriesResponse"
|
|
73
|
+
},
|
|
74
|
+
examples: [
|
|
75
|
+
{
|
|
76
|
+
request: {
|
|
77
|
+
body: {
|
|
78
|
+
genome: "hg38-test",
|
|
79
|
+
dslabel: "TermdbTest",
|
|
80
|
+
embedder: "localhost",
|
|
81
|
+
tw: { id: "diaggrp" },
|
|
82
|
+
filter: {
|
|
83
|
+
type: "tvslst",
|
|
84
|
+
in: true,
|
|
85
|
+
join: "",
|
|
86
|
+
lst: [
|
|
87
|
+
{
|
|
88
|
+
//tag: 'cohortFilter',
|
|
89
|
+
type: "tvs",
|
|
90
|
+
tvs: {
|
|
91
|
+
term: {
|
|
92
|
+
name: "Cohort",
|
|
93
|
+
type: "categorical",
|
|
94
|
+
values: { ABC: { label: "ABC" }, XYZ: { label: "XYZ" } },
|
|
95
|
+
id: "subcohort",
|
|
96
|
+
isleaf: false,
|
|
97
|
+
groupsetting: { disabled: true }
|
|
98
|
+
},
|
|
99
|
+
values: [{ key: "ABC", label: "ABC" }]
|
|
100
|
+
}
|
|
101
|
+
}
|
|
102
|
+
]
|
|
103
|
+
}
|
|
104
|
+
}
|
|
105
|
+
// satisfies CategoriesRequest // TODO: use the type definition
|
|
106
|
+
},
|
|
107
|
+
response: {
|
|
108
|
+
header: { status: 200 }
|
|
109
|
+
}
|
|
110
|
+
}
|
|
111
|
+
]
|
|
112
|
+
};
|
|
113
|
+
|
|
114
|
+
// src/routes/termdb.chat.ts
|
|
115
|
+
var createAmbiguousPoints = () => [];
|
|
116
|
+
|
|
117
|
+
// src/routes/termdb.descrstats.ts
|
|
118
|
+
var descrStatsPayloadExamples = {
|
|
119
|
+
request: {
|
|
120
|
+
typeId: "DescrStatsRequest"
|
|
121
|
+
},
|
|
122
|
+
response: {
|
|
123
|
+
typeId: "DescrStatsResponse"
|
|
124
|
+
},
|
|
125
|
+
examples: [
|
|
126
|
+
{
|
|
127
|
+
request: {
|
|
128
|
+
body: {
|
|
129
|
+
genome: "hg38-test",
|
|
130
|
+
dslabel: "TermdbTest",
|
|
131
|
+
embedder: "localhost",
|
|
132
|
+
tw: { term: { id: "hrtavg" }, q: { mode: "continuous" } },
|
|
133
|
+
filter: {
|
|
134
|
+
type: "tvslst",
|
|
135
|
+
in: true,
|
|
136
|
+
join: "",
|
|
137
|
+
lst: [
|
|
138
|
+
{
|
|
139
|
+
tag: "cohortFilter",
|
|
140
|
+
type: "tvs",
|
|
141
|
+
tvs: {
|
|
142
|
+
term: {
|
|
143
|
+
name: "Cohort",
|
|
144
|
+
type: "categorical",
|
|
145
|
+
values: { ABC: { label: "ABC" }, XYZ: { label: "XYZ" } },
|
|
146
|
+
id: "subcohort",
|
|
147
|
+
isleaf: false,
|
|
148
|
+
groupsetting: { disabled: true }
|
|
149
|
+
},
|
|
150
|
+
values: [{ key: "ABC", label: "ABC" }]
|
|
151
|
+
}
|
|
152
|
+
}
|
|
153
|
+
]
|
|
154
|
+
}
|
|
155
|
+
}
|
|
156
|
+
// satisfies DescrStatsRequest // TODO: enable type check
|
|
157
|
+
},
|
|
158
|
+
response: {
|
|
159
|
+
header: { status: 200 }
|
|
160
|
+
}
|
|
161
|
+
}
|
|
162
|
+
]
|
|
163
|
+
};
|
|
164
|
+
|
|
165
|
+
// src/routes/termdb.percentile.ts
|
|
166
|
+
var percentilePayloadExamples = {
|
|
167
|
+
request: {
|
|
168
|
+
typeId: "PercentileRequest"
|
|
169
|
+
},
|
|
170
|
+
response: {
|
|
171
|
+
typeId: "PercentileResponse"
|
|
172
|
+
},
|
|
173
|
+
examples: [
|
|
174
|
+
{
|
|
175
|
+
request: {
|
|
176
|
+
body: {
|
|
177
|
+
genome: "hg38-test",
|
|
178
|
+
dslabel: "TermdbTest",
|
|
179
|
+
embedder: "localhost",
|
|
180
|
+
getpercentile: [50],
|
|
181
|
+
term: { id: "agedx" },
|
|
182
|
+
filter: {
|
|
183
|
+
type: "tvslst",
|
|
184
|
+
in: true,
|
|
185
|
+
join: "",
|
|
186
|
+
lst: [
|
|
187
|
+
{
|
|
188
|
+
tag: "cohortFilter",
|
|
189
|
+
type: "tvs",
|
|
190
|
+
tvs: {
|
|
191
|
+
term: {
|
|
192
|
+
name: "Cohort",
|
|
193
|
+
type: "categorical",
|
|
194
|
+
values: { ABC: { label: "ABC" }, XYZ: { label: "XYZ" } },
|
|
195
|
+
id: "subcohort",
|
|
196
|
+
isleaf: false,
|
|
197
|
+
groupsetting: { disabled: true }
|
|
198
|
+
},
|
|
199
|
+
values: [{ key: "ABC", label: "ABC" }]
|
|
200
|
+
}
|
|
201
|
+
}
|
|
202
|
+
]
|
|
203
|
+
}
|
|
204
|
+
}
|
|
205
|
+
// satisfies PercentileRequest // TODO: enable type check
|
|
206
|
+
},
|
|
207
|
+
response: {
|
|
208
|
+
header: { status: 200 }
|
|
209
|
+
}
|
|
210
|
+
}
|
|
211
|
+
]
|
|
212
|
+
};
|
|
213
|
+
|
|
214
|
+
// src/routes/termdb.runChart.ts
|
|
215
|
+
function isRunChartSuccess(r) {
|
|
216
|
+
return "status" in r && r.status === "ok";
|
|
217
|
+
}
|
|
218
|
+
|
|
219
|
+
// src/routes/termdb.rootterm.ts
|
|
220
|
+
var rootTermPayloadExamples = {
|
|
221
|
+
request: {
|
|
222
|
+
typeId: "RootTermRequest"
|
|
223
|
+
},
|
|
224
|
+
response: {
|
|
225
|
+
typeId: "RootTermResponse"
|
|
226
|
+
},
|
|
227
|
+
examples: [
|
|
228
|
+
{
|
|
229
|
+
request: {
|
|
230
|
+
body: {
|
|
231
|
+
genome: "hg38-test",
|
|
232
|
+
dslabel: "TermdbTest",
|
|
233
|
+
embedder: "localhost",
|
|
234
|
+
default_rootterm: 1,
|
|
235
|
+
cohortValues: "ABC"
|
|
236
|
+
}
|
|
237
|
+
// satisfies RootTermRequest // TODO: enable type check
|
|
238
|
+
},
|
|
239
|
+
response: {
|
|
240
|
+
header: { status: 200 }
|
|
241
|
+
}
|
|
242
|
+
}
|
|
243
|
+
]
|
|
244
|
+
};
|
|
245
|
+
|
|
246
|
+
// src/routes/termdb.termchildren.ts
|
|
247
|
+
var termChildrenPayloadExamples = {
|
|
248
|
+
request: {
|
|
249
|
+
typeId: "TermChildrenRequest"
|
|
250
|
+
},
|
|
251
|
+
response: {
|
|
252
|
+
typeId: "TermChildrenResponse"
|
|
253
|
+
},
|
|
254
|
+
examples: [
|
|
255
|
+
{
|
|
256
|
+
request: {
|
|
257
|
+
body: {
|
|
258
|
+
genome: "hg38-test",
|
|
259
|
+
dslabel: "TermdbTest",
|
|
260
|
+
embedder: "localhost",
|
|
261
|
+
get_children: 1,
|
|
262
|
+
cohortValues: "ABC",
|
|
263
|
+
tid: "GO:0000001"
|
|
264
|
+
}
|
|
265
|
+
// TODO: enable type check
|
|
266
|
+
},
|
|
267
|
+
response: {
|
|
268
|
+
header: { status: 200 }
|
|
269
|
+
}
|
|
270
|
+
}
|
|
271
|
+
]
|
|
272
|
+
};
|
|
273
|
+
|
|
274
|
+
// src/routes/termdb.violinBox.ts
|
|
275
|
+
function isErrorResponse(response) {
|
|
276
|
+
return "error" in response && "status" in response;
|
|
277
|
+
}
|
|
278
|
+
function isBoxPlotResponse(response) {
|
|
279
|
+
return !isErrorResponse(response) && "charts" in response && "descrStats" in response;
|
|
280
|
+
}
|
|
281
|
+
function isViolinResponse(response) {
|
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282
|
+
return !isErrorResponse(response) && "min" in response && "max" in response;
|
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283
|
+
}
|
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284
|
+
var violinBoxPayload = {
|
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285
|
+
request: {
|
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286
|
+
typeId: "ViolinBoxRequest"
|
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287
|
+
},
|
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288
|
+
response: {
|
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289
|
+
typeId: "ViolinBoxResponse"
|
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290
|
+
},
|
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291
|
+
examples: [
|
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292
|
+
{
|
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293
|
+
request: {
|
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294
|
+
body: {
|
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295
|
+
plotType: "violin",
|
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296
|
+
genome: "hg38-test",
|
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297
|
+
dslabel: "TermdbTest",
|
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298
|
+
tw: {
|
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299
|
+
term: { id: "aaclassic_5", type: "float" },
|
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300
|
+
q: { mode: "continuous" }
|
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301
|
+
},
|
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302
|
+
devicePixelRatio: 2,
|
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303
|
+
svgw: 200,
|
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304
|
+
orientation: "horizontal",
|
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305
|
+
datasymbol: "rug",
|
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306
|
+
radius: 5,
|
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307
|
+
isLogScale: false
|
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308
|
+
}
|
|
309
|
+
// satisfies ViolinBoxRequest // TODO: enable type check
|
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310
|
+
},
|
|
311
|
+
response: {
|
|
312
|
+
header: { status: 200 }
|
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313
|
+
}
|
|
314
|
+
},
|
|
315
|
+
{
|
|
316
|
+
request: {
|
|
317
|
+
body: {
|
|
318
|
+
plotType: "box",
|
|
319
|
+
genome: "hg38-test",
|
|
320
|
+
dslabel: "TermdbTest",
|
|
321
|
+
tw: {
|
|
322
|
+
term: { id: "agedx", type: "float" },
|
|
323
|
+
q: { mode: "continuous" }
|
|
324
|
+
},
|
|
325
|
+
overlayTw: {
|
|
326
|
+
term: { id: "sex", type: "categorical" }
|
|
327
|
+
},
|
|
328
|
+
orderByMedian: true
|
|
329
|
+
}
|
|
330
|
+
// satisfies ViolinBoxRequest // TODO: enable type check
|
|
331
|
+
},
|
|
332
|
+
response: {
|
|
333
|
+
header: { status: 200 }
|
|
334
|
+
}
|
|
335
|
+
}
|
|
336
|
+
]
|
|
337
|
+
};
|
|
338
|
+
|
|
339
|
+
// src/terms/constants.ts
|
|
340
|
+
var CATEGORICAL = "categorical";
|
|
341
|
+
var CONDITION = "condition";
|
|
342
|
+
var DATE = "date";
|
|
343
|
+
var DNA_METHYLATION = "dnaMethylation";
|
|
344
|
+
var FLOAT = "float";
|
|
345
|
+
var GENE_VARIANT = "geneVariant";
|
|
346
|
+
var GENE_EXPRESSION = "geneExpression";
|
|
347
|
+
var ISOFORM_EXPRESSION = "isoformExpression";
|
|
348
|
+
var INTEGER = "integer";
|
|
349
|
+
var METABOLITE_INTENSITY = "metaboliteIntensity";
|
|
350
|
+
var MULTIVALUE = "multivalue";
|
|
351
|
+
var SAMPLELST = "samplelst";
|
|
352
|
+
var SINGLECELL_CELLTYPE = "singleCellCellType";
|
|
353
|
+
var SINGLECELL_GENE_EXPRESSION = "singleCellGeneExpression";
|
|
354
|
+
var SNP = "snp";
|
|
355
|
+
var SNP_LIST = "snplst";
|
|
356
|
+
var SNP_LOCUS = "snplocus";
|
|
357
|
+
var SSGSEA = "ssGSEA";
|
|
358
|
+
var SURVIVAL = "survival";
|
|
359
|
+
var TERM_COLLECTION = "termCollection";
|
|
360
|
+
var PROTEOME_ABUNDANCE = "proteomeAbundance";
|
|
361
|
+
var PROTEOME_DAP = "proteomeDAP";
|
|
362
|
+
var TermTypes = {
|
|
363
|
+
GENE_VARIANT,
|
|
364
|
+
GENE_EXPRESSION,
|
|
365
|
+
ISOFORM_EXPRESSION,
|
|
366
|
+
SSGSEA,
|
|
367
|
+
DNA_METHYLATION,
|
|
368
|
+
CATEGORICAL,
|
|
369
|
+
INTEGER,
|
|
370
|
+
FLOAT,
|
|
371
|
+
SNP,
|
|
372
|
+
SNP_LIST,
|
|
373
|
+
SNP_LOCUS,
|
|
374
|
+
CONDITION,
|
|
375
|
+
SURVIVAL,
|
|
376
|
+
SAMPLELST,
|
|
377
|
+
METABOLITE_INTENSITY,
|
|
378
|
+
PROTEOME_ABUNDANCE,
|
|
379
|
+
SINGLECELL_CELLTYPE,
|
|
380
|
+
SINGLECELL_GENE_EXPRESSION,
|
|
381
|
+
MULTIVALUE,
|
|
382
|
+
DATE,
|
|
383
|
+
TERM_COLLECTION
|
|
384
|
+
};
|
|
350
385
|
export {
|
|
351
|
-
|
|
352
|
-
|
|
353
|
-
|
|
354
|
-
|
|
355
|
-
|
|
356
|
-
|
|
357
|
-
|
|
358
|
-
|
|
359
|
-
|
|
360
|
-
|
|
386
|
+
CATEGORICAL,
|
|
387
|
+
CONDITION,
|
|
388
|
+
DATE,
|
|
389
|
+
DNA_METHYLATION,
|
|
390
|
+
FLOAT,
|
|
391
|
+
FeaturePrefixes,
|
|
392
|
+
FlagStatus,
|
|
393
|
+
FlagStatusMessages,
|
|
394
|
+
GENE_EXPRESSION,
|
|
395
|
+
GENE_VARIANT,
|
|
396
|
+
INTEGER,
|
|
397
|
+
ISOFORM_EXPRESSION,
|
|
398
|
+
METABOLITE_INTENSITY,
|
|
399
|
+
MULTIVALUE,
|
|
400
|
+
PROTEOME_ABUNDANCE,
|
|
401
|
+
PROTEOME_DAP,
|
|
402
|
+
SAMPLELST,
|
|
403
|
+
SINGLECELL_CELLTYPE,
|
|
404
|
+
SINGLECELL_GENE_EXPRESSION,
|
|
405
|
+
SNP,
|
|
406
|
+
SNP_LIST,
|
|
407
|
+
SNP_LOCUS,
|
|
408
|
+
SSGSEA,
|
|
409
|
+
SURVIVAL,
|
|
410
|
+
SelectionPrefixes,
|
|
411
|
+
TERM_COLLECTION,
|
|
412
|
+
TermTypes,
|
|
361
413
|
WSImage,
|
|
362
|
-
|
|
363
|
-
aiProjectSelectedWSImagesResponsePayload,
|
|
364
|
-
aiProjectTrainModelPayload,
|
|
365
|
-
alphaGenomePayload,
|
|
366
|
-
alphaGenomeTypesPayload,
|
|
367
|
-
brainImagingPayload,
|
|
368
|
-
brainImagingSamplesPayload,
|
|
369
|
-
burdenPayload,
|
|
370
|
-
clearWSImagesSessionsPayload,
|
|
414
|
+
checkSelectionType,
|
|
371
415
|
createAmbiguousPoints,
|
|
372
|
-
|
|
373
|
-
|
|
374
|
-
|
|
375
|
-
|
|
376
|
-
diffExpPayload,
|
|
377
|
-
diffMethPayload,
|
|
378
|
-
dsDataPayload,
|
|
379
|
-
dzImagesPayload,
|
|
380
|
-
gdcGRIN2listPayload,
|
|
381
|
-
gdcMafPayload,
|
|
382
|
-
geneLookupPayload,
|
|
383
|
-
genesetEnrichmentPayload,
|
|
384
|
-
genesetOverrepresentationPayload,
|
|
385
|
-
healthcheckPayload,
|
|
386
|
-
hicGenomePayload,
|
|
387
|
-
hicdataPayload,
|
|
388
|
-
hicstatPayload,
|
|
389
|
-
imgPayload,
|
|
416
|
+
createFeatureID,
|
|
417
|
+
createSelectionID,
|
|
418
|
+
descrStatsPayloadExamples,
|
|
419
|
+
hicGenomePayloadExample,
|
|
390
420
|
isBoxPlotResponse,
|
|
391
421
|
isErrorResponse,
|
|
392
422
|
isRunChartSuccess,
|
|
393
423
|
isViolinResponse,
|
|
394
|
-
|
|
395
|
-
|
|
396
|
-
|
|
397
|
-
|
|
398
|
-
|
|
399
|
-
rootTermPayload,
|
|
400
|
-
runChartPayload,
|
|
401
|
-
runGRIN2Payload,
|
|
402
|
-
sampleWSImagesPayload,
|
|
403
|
-
saveWSIAnnotationPayload,
|
|
404
|
-
snpPayload,
|
|
405
|
-
termChildrenPayload,
|
|
406
|
-
termdbCategoriesPayload,
|
|
407
|
-
termdbClusterPayload,
|
|
408
|
-
termdbCohortSummaryPayload,
|
|
409
|
-
termdbCohortsPayload,
|
|
410
|
-
termdbProteomePayload,
|
|
411
|
-
termdbSampleImagesPayload,
|
|
412
|
-
termdbSampleScatterPayload,
|
|
413
|
-
termdbSingleCellDEgenesPayload,
|
|
414
|
-
termdbSingleCellDataPayload,
|
|
415
|
-
termdbSingleCellSamplesPayload,
|
|
416
|
-
termdbSingleSampleMutationPayload,
|
|
417
|
-
termdbTopTermsByTypePayload,
|
|
418
|
-
termdbTopVariablyExpressedGenesPayload,
|
|
419
|
-
termsByIdsPayload,
|
|
420
|
-
tilePayload,
|
|
421
|
-
topMutatedGenePayload,
|
|
422
|
-
validAIProjectAdminRequest,
|
|
423
|
-
validAIProjectAdminResponse,
|
|
424
|
-
validAIProjectTrainModelRequest,
|
|
425
|
-
validAIProjectTrainModelResponse,
|
|
426
|
-
validAiProjectSelectedWSImagesRequest,
|
|
427
|
-
validAiProjectSelectedWSImagesResponse,
|
|
428
|
-
validBrainImagingRequest,
|
|
429
|
-
validBrainImagingResponse,
|
|
430
|
-
validBrainImagingSamplesRequest,
|
|
431
|
-
validBrainImagingSamplesResponse,
|
|
432
|
-
validBurdenRequest,
|
|
433
|
-
validBurdenResponse,
|
|
434
|
-
validCategoriesRequest,
|
|
435
|
-
validCategoriesResponse,
|
|
436
|
-
validChatRequest,
|
|
437
|
-
validChatResponse,
|
|
438
|
-
validClearWSImagesSessionsRequest,
|
|
439
|
-
validClearWSImagesSessionsResponse,
|
|
440
|
-
validCorrelationVolcanoRequest,
|
|
441
|
-
validCorrelationVolcanoResponse,
|
|
442
|
-
validDERequest,
|
|
443
|
-
validDEResponse,
|
|
444
|
-
validDZImagesRequest,
|
|
445
|
-
validDZImagesResponse,
|
|
446
|
-
validDapVolcanoRequest,
|
|
447
|
-
validDapVolcanoResponse,
|
|
448
|
-
validDatasetRequest,
|
|
449
|
-
validDatasetResponse,
|
|
450
|
-
validDeleteWSITileSelectionRequest,
|
|
451
|
-
validDeleteWSITileSelectionResponse,
|
|
452
|
-
validDescrStatsRequest,
|
|
453
|
-
validDescrStatsResponse,
|
|
454
|
-
validDiffMethRequest,
|
|
455
|
-
validDiffMethResponse,
|
|
456
|
-
validDsDataRequest,
|
|
457
|
-
validDsDataResponse,
|
|
458
|
-
validFilterTermValuesRequest,
|
|
459
|
-
validFilterTermValuesResponse,
|
|
460
|
-
validGRIN2Request,
|
|
461
|
-
validGRIN2Response,
|
|
462
|
-
validGdcGRIN2listRequest,
|
|
463
|
-
validGdcGRIN2listResponse,
|
|
464
|
-
validGdcMafBuildRequest,
|
|
465
|
-
validGdcMafBuildResponse,
|
|
466
|
-
validGdcMafRequest,
|
|
467
|
-
validGdcMafResponse,
|
|
468
|
-
validGeneLookupRequest,
|
|
469
|
-
validGeneLookupResponse,
|
|
470
|
-
validGenesetEnrichmentRequest,
|
|
471
|
-
validGenesetEnrichmentResponse,
|
|
472
|
-
validGenesetOverrepresentationRequest,
|
|
473
|
-
validGenesetOverrepresentationResponse,
|
|
474
|
-
validHealthCheckRequest,
|
|
475
|
-
validHealthCheckResponse,
|
|
476
|
-
validHicGenomeRequest,
|
|
477
|
-
validHicGenomeResponse,
|
|
478
|
-
validHicdataRequest,
|
|
479
|
-
validHicdataResponse,
|
|
480
|
-
validHicstatRequest,
|
|
481
|
-
validHicstatResponse,
|
|
482
|
-
validIsoformLstRequest,
|
|
483
|
-
validIsoformLstResponse,
|
|
484
|
-
validNtseqRequest,
|
|
485
|
-
validNtseqResponse,
|
|
486
|
-
validNumericCategoriesRequest,
|
|
487
|
-
validNumericCategoriesResponse,
|
|
488
|
-
validPdomainRequest,
|
|
489
|
-
validPdomainResponse,
|
|
490
|
-
validPercentileRequest,
|
|
491
|
-
validPercentileResponse,
|
|
492
|
-
validProfileFormScoresRequest,
|
|
493
|
-
validProfileFormScoresResponse,
|
|
494
|
-
validProfileForms2ScoresRequest,
|
|
495
|
-
validProfileForms2ScoresResponse,
|
|
496
|
-
validProfileScoresRequest,
|
|
497
|
-
validProfileScoresResponse,
|
|
498
|
-
validRootTermRequest,
|
|
499
|
-
validRootTermResponse,
|
|
500
|
-
validRunChartRequest,
|
|
501
|
-
validRunChartResponse,
|
|
502
|
-
validRunGRIN2Request,
|
|
503
|
-
validRunGRIN2Response,
|
|
504
|
-
validSampleWSImagesRequest,
|
|
505
|
-
validSampleWSImagesResponse,
|
|
506
|
-
validSaveWSIAnnotationRequest,
|
|
507
|
-
validSaveWSIAnnotationResponse,
|
|
508
|
-
validSnpRequest,
|
|
509
|
-
validSnpResponse,
|
|
510
|
-
validTermChildrenRequest,
|
|
511
|
-
validTermChildrenResponse,
|
|
512
|
-
validTermdbClusterRequest,
|
|
513
|
-
validTermdbClusterResponse,
|
|
514
|
-
validTermdbCohortSummaryRequest,
|
|
515
|
-
validTermdbCohortSummaryResponse,
|
|
516
|
-
validTermdbCohortsRequest,
|
|
517
|
-
validTermdbCohortsResponse,
|
|
518
|
-
validTermdbDmrRequest,
|
|
519
|
-
validTermdbDmrResponse,
|
|
520
|
-
validTermdbIsoformAvailabilityRequest,
|
|
521
|
-
validTermdbIsoformAvailabilityResponse,
|
|
522
|
-
validTermdbProteomeRequest,
|
|
523
|
-
validTermdbProteomeResponse,
|
|
524
|
-
validTermdbSampleImagesRequest,
|
|
525
|
-
validTermdbSampleImagesResponse,
|
|
526
|
-
validTermdbSampleScatterRequest,
|
|
527
|
-
validTermdbSampleScatterResponse,
|
|
528
|
-
validTermdbSingleCellDEgenesRequest,
|
|
529
|
-
validTermdbSingleCellDEgenesResponse,
|
|
530
|
-
validTermdbSingleCellDataRequest,
|
|
531
|
-
validTermdbSingleCellDataResponse,
|
|
532
|
-
validTermdbSingleCellSamplesRequest,
|
|
533
|
-
validTermdbSingleCellSamplesResponse,
|
|
534
|
-
validTermdbSingleSampleMutationRequest,
|
|
535
|
-
validTermdbSingleSampleMutationResponse,
|
|
536
|
-
validTermdbTopTermsByTypeRequest,
|
|
537
|
-
validTermdbTopTermsByTypeResponse,
|
|
538
|
-
validTermdbTopVariablyExpressedGenesRequest,
|
|
539
|
-
validTermdbTopVariablyExpressedGenesResponse,
|
|
540
|
-
validTermsByIdsRequest,
|
|
541
|
-
validTermsByIdsResponse,
|
|
542
|
-
validTileRequest,
|
|
543
|
-
validTileResponse,
|
|
544
|
-
validViolinBoxRequest,
|
|
545
|
-
validViolinBoxResponse,
|
|
546
|
-
validWSISamplesRequest,
|
|
547
|
-
validWSISamplesResponse,
|
|
548
|
-
validWSImagesRequest,
|
|
549
|
-
validWSImagesResponse,
|
|
550
|
-
validalphaGenomeRequest,
|
|
551
|
-
validalphaGenomeResponse,
|
|
552
|
-
validalphaGenomeTypesRequest,
|
|
553
|
-
validalphaGenomeTypesResponse,
|
|
554
|
-
validimgRequest,
|
|
555
|
-
validimgResponse,
|
|
556
|
-
validtopMutatedGeneRequest,
|
|
557
|
-
validtopMutatedGeneResponse,
|
|
558
|
-
violinBoxPayload,
|
|
559
|
-
wsImagesPayload,
|
|
560
|
-
wsiSamplesPayload
|
|
424
|
+
percentilePayloadExamples,
|
|
425
|
+
rootTermPayloadExamples,
|
|
426
|
+
termChildrenPayloadExamples,
|
|
427
|
+
termdbCategoriesPayloadExamples,
|
|
428
|
+
violinBoxPayload
|
|
561
429
|
};
|
|
430
|
+
//# sourceMappingURL=index.js.map
|