@sjcrh/proteinpaint-types 2.148.1 → 2.150.0

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 (18) hide show
  1. package/dist/alphaGenome.js +11 -0
  2. package/dist/alphaGenomeTypes.js +11 -0
  3. package/dist/chunk-4EAGOSMN.js +128 -0
  4. package/dist/chunk-5H2LJKPX.js +104 -0
  5. package/dist/{chunk-Z7KZU2H5.js → chunk-HI2IT25E.js} +56 -22
  6. package/dist/{chunk-CP26DR4V.js → chunk-LJFPSUAL.js} +15 -3
  7. package/dist/{chunk-CT6IBFVP.js → chunk-VUKRI3TG.js} +13 -1
  8. package/dist/grin2.js +1 -1
  9. package/dist/index.js +76 -60
  10. package/dist/termdb.DE.js +1 -1
  11. package/dist/wsimages.js +1 -1
  12. package/package.json +1 -1
  13. package/src/dataset.ts +23 -37
  14. package/src/routes/alphaGenome.ts +27 -0
  15. package/src/routes/alphaGenomeTypes.ts +21 -0
  16. package/src/routes/grin2.ts +23 -2
  17. package/src/routes/termdb.DE.ts +6 -0
  18. package/src/routes/wsimages.ts +1 -0
package/dist/alphaGenome.js ADDED
@@ -0,0 +1,11 @@
1
+ import {
2
+ alphaGenomePayload,
3
+ validalphaGenomeRequest,
4
+ validalphaGenomeResponse
5
+ } from "./chunk-4EAGOSMN.js";
6
+ import "./chunk-YNHC5SXO.js";
7
+ export {
8
+ alphaGenomePayload,
9
+ validalphaGenomeRequest,
10
+ validalphaGenomeResponse
11
+ };
package/dist/alphaGenomeTypes.js ADDED
@@ -0,0 +1,11 @@
1
+ import {
2
+ alphaGenomeTypesPayload,
3
+ validalphaGenomeTypesRequest,
4
+ validalphaGenomeTypesResponse
5
+ } from "./chunk-5H2LJKPX.js";
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+ import "./chunk-YNHC5SXO.js";
7
+ export {
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+ alphaGenomeTypesPayload,
9
+ validalphaGenomeTypesRequest,
10
+ validalphaGenomeTypesResponse
11
+ };
package/dist/chunk-4EAGOSMN.js ADDED
@@ -0,0 +1,128 @@
1
+ import {
2
+ __toESM,
3
+ require_lib
4
+ } from "./chunk-YNHC5SXO.js";
5
+
6
+ // dist/alphaGenome.ts
7
+ var import_typia = __toESM(require_lib(), 1);
8
+
9
+ // src/routes/alphaGenome.ts
10
+ var alphaGenomePayload = {
11
+ request: {
12
+ typeId: "alphaGenomeRequest"
13
+ },
14
+ response: {
15
+ typeId: "alphaGenomeResponse"
16
+ }
17
+ };
18
+
19
+ // dist/alphaGenome.ts
20
+ var validalphaGenomeRequest = (input) => {
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+ const errors = [];
22
+ const __is = (input2) => {
23
+ const $io0 = (input3) => (void 0 === input3.genome || "string" === typeof input3.genome) && (void 0 === input3.dslabel || "string" === typeof input3.dslabel) && "string" === typeof input3.chromosome && "number" === typeof input3.position && "string" === typeof input3.reference && "string" === typeof input3.alternate && (Array.isArray(input3.ontologyTerms) && input3.ontologyTerms.every((elem) => "string" === typeof elem)) && (void 0 === input3.outputType || "number" === typeof input3.outputType) && "number" === typeof input3.interval;
24
+ return "object" === typeof input2 && null !== input2 && $io0(input2);
25
+ };
26
+ if (false === __is(input)) {
27
+ const $report = import_typia.createValidate.report(errors);
28
+ ((input2, _path, _exceptionable = true) => {
29
+ const $vo0 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.genome || "string" === typeof input3.genome || $report(_exceptionable2, {
30
+ path: _path2 + ".genome",
31
+ expected: "(string | undefined)",
32
+ value: input3.genome
33
+ }), void 0 === input3.dslabel || "string" === typeof input3.dslabel || $report(_exceptionable2, {
34
+ path: _path2 + ".dslabel",
35
+ expected: "(string | undefined)",
36
+ value: input3.dslabel
37
+ }), "string" === typeof input3.chromosome || $report(_exceptionable2, {
38
+ path: _path2 + ".chromosome",
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+ expected: "string",
40
+ value: input3.chromosome
41
+ }), "number" === typeof input3.position || $report(_exceptionable2, {
42
+ path: _path2 + ".position",
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+ expected: "number",
44
+ value: input3.position
45
+ }), "string" === typeof input3.reference || $report(_exceptionable2, {
46
+ path: _path2 + ".reference",
47
+ expected: "string",
48
+ value: input3.reference
49
+ }), "string" === typeof input3.alternate || $report(_exceptionable2, {
50
+ path: _path2 + ".alternate",
51
+ expected: "string",
52
+ value: input3.alternate
53
+ }), (Array.isArray(input3.ontologyTerms) || $report(_exceptionable2, {
54
+ path: _path2 + ".ontologyTerms",
55
+ expected: "Array<string>",
56
+ value: input3.ontologyTerms
57
+ })) && input3.ontologyTerms.map((elem, _index1) => "string" === typeof elem || $report(_exceptionable2, {
58
+ path: _path2 + ".ontologyTerms[" + _index1 + "]",
59
+ expected: "string",
60
+ value: elem
61
+ })).every((flag) => flag) || $report(_exceptionable2, {
62
+ path: _path2 + ".ontologyTerms",
63
+ expected: "Array<string>",
64
+ value: input3.ontologyTerms
65
+ }), void 0 === input3.outputType || "number" === typeof input3.outputType || $report(_exceptionable2, {
66
+ path: _path2 + ".outputType",
67
+ expected: "(number | undefined)",
68
+ value: input3.outputType
69
+ }), "number" === typeof input3.interval || $report(_exceptionable2, {
70
+ path: _path2 + ".interval",
71
+ expected: "number",
72
+ value: input3.interval
73
+ })].every((flag) => flag);
74
+ return ("object" === typeof input2 && null !== input2 || $report(true, {
75
+ path: _path + "",
76
+ expected: "alphaGenomeRequest",
77
+ value: input2
78
+ })) && $vo0(input2, _path + "", true) || $report(true, {
79
+ path: _path + "",
80
+ expected: "alphaGenomeRequest",
81
+ value: input2
82
+ });
83
+ })(input, "$input", true);
84
+ }
85
+ const success = 0 === errors.length;
86
+ return {
87
+ success,
88
+ errors,
89
+ data: success ? input : void 0
90
+ };
91
+ };
92
+ var validalphaGenomeResponse = (input) => {
93
+ const errors = [];
94
+ const __is = (input2) => {
95
+ return "object" === typeof input2 && null !== input2 && "string" === typeof input2.plotImage;
96
+ };
97
+ if (false === __is(input)) {
98
+ const $report = import_typia.createValidate.report(errors);
99
+ ((input2, _path, _exceptionable = true) => {
100
+ const $vo0 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.plotImage || $report(_exceptionable2, {
101
+ path: _path2 + ".plotImage",
102
+ expected: "string",
103
+ value: input3.plotImage
104
+ })].every((flag) => flag);
105
+ return ("object" === typeof input2 && null !== input2 || $report(true, {
106
+ path: _path + "",
107
+ expected: "alphaGenomeResponse",
108
+ value: input2
109
+ })) && $vo0(input2, _path + "", true) || $report(true, {
110
+ path: _path + "",
111
+ expected: "alphaGenomeResponse",
112
+ value: input2
113
+ });
114
+ })(input, "$input", true);
115
+ }
116
+ const success = 0 === errors.length;
117
+ return {
118
+ success,
119
+ errors,
120
+ data: success ? input : void 0
121
+ };
122
+ };
123
+
124
+ export {
125
+ alphaGenomePayload,
126
+ validalphaGenomeRequest,
127
+ validalphaGenomeResponse
128
+ };
package/dist/chunk-5H2LJKPX.js ADDED
@@ -0,0 +1,104 @@
1
+ import {
2
+ __toESM,
3
+ require_lib
4
+ } from "./chunk-YNHC5SXO.js";
5
+
6
+ // dist/alphaGenomeTypes.ts
7
+ var import_typia = __toESM(require_lib(), 1);
8
+
9
+ // src/routes/alphaGenomeTypes.ts
10
+ var alphaGenomeTypesPayload = {
11
+ request: {
12
+ typeId: "alphaGenomeTypesRequest"
13
+ },
14
+ response: {
15
+ typeId: "alphaGenomeTypesResponse"
16
+ }
17
+ };
18
+
19
+ // dist/alphaGenomeTypes.ts
20
+ var validalphaGenomeTypesRequest = (input) => {
21
+ const errors = [];
22
+ const __is = (input2) => {
23
+ return "object" === typeof input2 && null !== input2 && "string" === typeof input2.dslabel;
24
+ };
25
+ if (false === __is(input)) {
26
+ const $report = import_typia.createValidate.report(errors);
27
+ ((input2, _path, _exceptionable = true) => {
28
+ const $vo0 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.dslabel || $report(_exceptionable2, {
29
+ path: _path2 + ".dslabel",
30
+ expected: "string",
31
+ value: input3.dslabel
32
+ })].every((flag) => flag);
33
+ return ("object" === typeof input2 && null !== input2 || $report(true, {
34
+ path: _path + "",
35
+ expected: "alphaGenomeTypesRequest",
36
+ value: input2
37
+ })) && $vo0(input2, _path + "", true) || $report(true, {
38
+ path: _path + "",
39
+ expected: "alphaGenomeTypesRequest",
40
+ value: input2
41
+ });
42
+ })(input, "$input", true);
43
+ }
44
+ const success = 0 === errors.length;
45
+ return {
46
+ success,
47
+ errors,
48
+ data: success ? input : void 0
49
+ };
50
+ };
51
+ var validalphaGenomeTypesResponse = (input) => {
52
+ const errors = [];
53
+ const __is = (input2) => {
54
+ const $io0 = (input3) => Array.isArray(input3.ontologyTerms) && Array.isArray(input3.outputTypes) && (Array.isArray(input3.intervals) && input3.intervals.every((elem) => "number" === typeof elem));
55
+ return "object" === typeof input2 && null !== input2 && $io0(input2);
56
+ };
57
+ if (false === __is(input)) {
58
+ const $report = import_typia.createValidate.report(errors);
59
+ ((input2, _path, _exceptionable = true) => {
60
+ const $vo0 = (input3, _path2, _exceptionable2 = true) => [Array.isArray(input3.ontologyTerms) || $report(_exceptionable2, {
61
+ path: _path2 + ".ontologyTerms",
62
+ expected: "Array<any>",
63
+ value: input3.ontologyTerms
64
+ }), Array.isArray(input3.outputTypes) || $report(_exceptionable2, {
65
+ path: _path2 + ".outputTypes",
66
+ expected: "Array<any>",
67
+ value: input3.outputTypes
68
+ }), (Array.isArray(input3.intervals) || $report(_exceptionable2, {
69
+ path: _path2 + ".intervals",
70
+ expected: "Array<number>",
71
+ value: input3.intervals
72
+ })) && input3.intervals.map((elem, _index1) => "number" === typeof elem || $report(_exceptionable2, {
73
+ path: _path2 + ".intervals[" + _index1 + "]",
74
+ expected: "number",
75
+ value: elem
76
+ })).every((flag) => flag) || $report(_exceptionable2, {
77
+ path: _path2 + ".intervals",
78
+ expected: "Array<number>",
79
+ value: input3.intervals
80
+ })].every((flag) => flag);
81
+ return ("object" === typeof input2 && null !== input2 || $report(true, {
82
+ path: _path + "",
83
+ expected: "alphaGenomeTypesResponse",
84
+ value: input2
85
+ })) && $vo0(input2, _path + "", true) || $report(true, {
86
+ path: _path + "",
87
+ expected: "alphaGenomeTypesResponse",
88
+ value: input2
89
+ });
90
+ })(input, "$input", true);
91
+ }
92
+ const success = 0 === errors.length;
93
+ return {
94
+ success,
95
+ errors,
96
+ data: success ? input : void 0
97
+ };
98
+ };
99
+
100
+ export {
101
+ alphaGenomeTypesPayload,
102
+ validalphaGenomeTypesRequest,
103
+ validalphaGenomeTypesResponse
104
+ };
package/dist/{chunk-Z7KZU2H5.js → chunk-HI2IT25E.js} RENAMED
@@ -20,24 +20,16 @@ var GRIN2Payload = {
20
20
  var validGRIN2Request = (input) => {
21
21
  const errors = [];
22
22
  const __is = (input2) => {
23
- const $join = import_typia.createValidate.join;
24
- const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && (void 0 === input3.devicePixelRatio || "number" === typeof input3.devicePixelRatio) && (void 0 === input3.width || "number" === typeof input3.width) && (void 0 === input3.height || "number" === typeof input3.height) && (void 0 === input3.pngDotRadius || "number" === typeof input3.pngDotRadius) && true && (void 0 === input3.snvindelOptions || "object" === typeof input3.snvindelOptions && null !== input3.snvindelOptions && false === Array.isArray(input3.snvindelOptions) && $io1(input3.snvindelOptions)) && (void 0 === input3.cnvOptions || "object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) && $io2(input3.cnvOptions)) && (void 0 === input3.fusionOptions || "object" === typeof input3.fusionOptions && null !== input3.fusionOptions && false === Array.isArray(input3.fusionOptions) && $io3(input3.fusionOptions));
25
- const $io1 = (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);
26
- const $io2 = (input3) => (void 0 === input3.lossThreshold || "number" === typeof input3.lossThreshold) && (void 0 === input3.gainThreshold || "number" === typeof input3.gainThreshold) && (void 0 === input3.maxSegLength || "number" === typeof input3.maxSegLength) && (void 0 === input3.hyperMutator || "number" === typeof input3.hyperMutator);
27
- const $io3 = (input3) => Object.keys(input3).every((key) => {
28
- const value = input3[key];
29
- if (void 0 === value)
30
- return true;
31
- if (RegExp(/(.*)/).test(key))
32
- return true;
33
- return true;
34
- });
23
+ const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && (void 0 === input3.devicePixelRatio || "number" === typeof input3.devicePixelRatio) && (void 0 === input3.width || "number" === typeof input3.width) && (void 0 === input3.height || "number" === typeof input3.height) && (void 0 === input3.pngDotRadius || "number" === typeof input3.pngDotRadius) && true && (void 0 === input3.snvindelOptions || "object" === typeof input3.snvindelOptions && null !== input3.snvindelOptions && false === Array.isArray(input3.snvindelOptions) && $io1(input3.snvindelOptions)) && (void 0 === input3.cnvOptions || "object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) && $io2(input3.cnvOptions)) && (void 0 === input3.fusionOptions || "object" === typeof input3.fusionOptions && null !== input3.fusionOptions && false === Array.isArray(input3.fusionOptions) && $io3(input3.fusionOptions)) && (void 0 === input3.svOptions || "object" === typeof input3.svOptions && null !== input3.svOptions && false === Array.isArray(input3.svOptions) && $io4(input3.svOptions)) && (void 0 === input3.maxGenesToShow || "number" === typeof input3.maxGenesToShow);
24
+ const $io1 = (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) && (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
25
+ const $io2 = (input3) => (void 0 === input3.lossThreshold || "number" === typeof input3.lossThreshold) && (void 0 === input3.gainThreshold || "number" === typeof input3.gainThreshold) && (void 0 === input3.maxSegLength || "number" === typeof input3.maxSegLength) && (void 0 === input3.hyperMutator || "number" === typeof input3.hyperMutator) && (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
26
+ const $io3 = (input3) => (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
27
+ const $io4 = (input3) => (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
35
28
  return "object" === typeof input2 && null !== input2 && $io0(input2);
36
29
  };
37
30
  if (false === __is(input)) {
38
31
  const $report = import_typia.createValidate.report(errors);
39
32
  ((input2, _path, _exceptionable = true) => {
40
- const $join = import_typia.createValidate.join;
41
33
  const $vo0 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.genome || $report(_exceptionable2, {
42
34
  path: _path2 + ".genome",
43
35
  expected: "string",
@@ -86,6 +78,18 @@ var validGRIN2Request = (input) => {
86
78
  path: _path2 + ".fusionOptions",
87
79
  expected: "(__type.o2 | undefined)",
88
80
  value: input3.fusionOptions
81
+ }), void 0 === input3.svOptions || ("object" === typeof input3.svOptions && null !== input3.svOptions && false === Array.isArray(input3.svOptions) || $report(_exceptionable2, {
82
+ path: _path2 + ".svOptions",
83
+ expected: "(__type.o3 | undefined)",
84
+ value: input3.svOptions
85
+ })) && $vo4(input3.svOptions, _path2 + ".svOptions", _exceptionable2) || $report(_exceptionable2, {
86
+ path: _path2 + ".svOptions",
87
+ expected: "(__type.o3 | undefined)",
88
+ value: input3.svOptions
89
+ }), void 0 === input3.maxGenesToShow || "number" === typeof input3.maxGenesToShow || $report(_exceptionable2, {
90
+ path: _path2 + ".maxGenesToShow",
91
+ expected: "(number | undefined)",
92
+ value: input3.maxGenesToShow
89
93
  })].every((flag) => flag);
90
94
  const $vo1 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.minTotalDepth || "number" === typeof input3.minTotalDepth || $report(_exceptionable2, {
91
95
  path: _path2 + ".minTotalDepth",
@@ -111,6 +115,14 @@ var validGRIN2Request = (input) => {
111
115
  path: _path2 + ".hyperMutator",
112
116
  expected: "(number | undefined)",
113
117
  value: input3.hyperMutator
118
+ }), void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize || $report(_exceptionable2, {
119
+ path: _path2 + ".fivePrimeFlankSize",
120
+ expected: "(number | undefined)",
121
+ value: input3.fivePrimeFlankSize
122
+ }), void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize || $report(_exceptionable2, {
123
+ path: _path2 + ".threePrimeFlankSize",
124
+ expected: "(number | undefined)",
125
+ value: input3.threePrimeFlankSize
114
126
  })].every((flag) => flag);
115
127
  const $vo2 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.lossThreshold || "number" === typeof input3.lossThreshold || $report(_exceptionable2, {
116
128
  path: _path2 + ".lossThreshold",
@@ -128,15 +140,33 @@ var validGRIN2Request = (input) => {
128
140
  path: _path2 + ".hyperMutator",
129
141
  expected: "(number | undefined)",
130
142
  value: input3.hyperMutator
143
+ }), void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize || $report(_exceptionable2, {
144
+ path: _path2 + ".fivePrimeFlankSize",
145
+ expected: "(number | undefined)",
146
+ value: input3.fivePrimeFlankSize
147
+ }), void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize || $report(_exceptionable2, {
148
+ path: _path2 + ".threePrimeFlankSize",
149
+ expected: "(number | undefined)",
150
+ value: input3.threePrimeFlankSize
151
+ })].every((flag) => flag);
152
+ const $vo3 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize || $report(_exceptionable2, {
153
+ path: _path2 + ".fivePrimeFlankSize",
154
+ expected: "(number | undefined)",
155
+ value: input3.fivePrimeFlankSize
156
+ }), void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize || $report(_exceptionable2, {
157
+ path: _path2 + ".threePrimeFlankSize",
158
+ expected: "(number | undefined)",
159
+ value: input3.threePrimeFlankSize
160
+ })].every((flag) => flag);
161
+ const $vo4 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize || $report(_exceptionable2, {
162
+ path: _path2 + ".fivePrimeFlankSize",
163
+ expected: "(number | undefined)",
164
+ value: input3.fivePrimeFlankSize
165
+ }), void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize || $report(_exceptionable2, {
166
+ path: _path2 + ".threePrimeFlankSize",
167
+ expected: "(number | undefined)",
168
+ value: input3.threePrimeFlankSize
131
169
  })].every((flag) => flag);
132
- const $vo3 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
133
- const value = input3[key];
134
- if (void 0 === value)
135
- return true;
136
- if (RegExp(/(.*)/).test(key))
137
- return true;
138
- return true;
139
- }).every((flag) => flag)].every((flag) => flag);
140
170
  return ("object" === typeof input2 && null !== input2 || $report(true, {
141
171
  path: _path + "",
142
172
  expected: "GRIN2Request",
@@ -159,7 +189,7 @@ var validGRIN2Response = (input) => {
159
189
  const errors = [];
160
190
  const __is = (input2) => {
161
191
  const $join = import_typia.createValidate.join;
162
- const $io0 = (input3) => ("error" === input3.status || "success" === input3.status) && (void 0 === input3.error || "string" === typeof input3.error) && (void 0 === input3.pngImg || "string" === typeof input3.pngImg) && (void 0 === input3.plotData || "object" === typeof input3.plotData && null !== input3.plotData && $io1(input3.plotData)) && true && (void 0 === input3.topGeneTable || "object" === typeof input3.topGeneTable && null !== input3.topGeneTable && $io5(input3.topGeneTable)) && (void 0 === input3.totalGenes || "number" === typeof input3.totalGenes) && (void 0 === input3.showingTop || "number" === typeof input3.showingTop) && (void 0 === input3.timing || "object" === typeof input3.timing && null !== input3.timing && $io8(input3.timing)) && (void 0 === input3.processingSummary || "object" === typeof input3.processingSummary && null !== input3.processingSummary && false === Array.isArray(input3.processingSummary) && $io9(input3.processingSummary));
192
+ const $io0 = (input3) => ("error" === input3.status || "success" === input3.status) && (void 0 === input3.error || "string" === typeof input3.error) && (void 0 === input3.pngImg || "string" === typeof input3.pngImg) && (void 0 === input3.plotData || "object" === typeof input3.plotData && null !== input3.plotData && $io1(input3.plotData)) && true && (void 0 === input3.topGeneTable || "object" === typeof input3.topGeneTable && null !== input3.topGeneTable && $io5(input3.topGeneTable)) && (void 0 === input3.totalGenes || "number" === typeof input3.totalGenes) && (void 0 === input3.showingTop || "number" === typeof input3.showingTop) && (void 0 === input3.timing || "object" === typeof input3.timing && null !== input3.timing && $io8(input3.timing)) && (void 0 === input3.processingSummary || "object" === typeof input3.processingSummary && null !== input3.processingSummary && false === Array.isArray(input3.processingSummary) && $io9(input3.processingSummary)) && (void 0 === input3.cacheFileName || "string" === typeof input3.cacheFileName);
163
193
  const $io1 = (input3) => Array.isArray(input3.points) && input3.points.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && ("object" === typeof input3.chrom_data && null !== input3.chrom_data && false === Array.isArray(input3.chrom_data) && $io3(input3.chrom_data)) && "boolean" === typeof input3.y_axis_scaled && "number" === typeof input3.scale_factor && "number" === typeof input3.total_genome_length && "number" === typeof input3.plot_width && "number" === typeof input3.plot_height && "number" === typeof input3.device_pixel_ratio && "number" === typeof input3.dpi;
164
194
  const $io2 = (input3) => "number" === typeof input3.x && "number" === typeof input3.y && "number" === typeof input3.svg_x && "number" === typeof input3.svg_y && "string" === typeof input3.color && "string" === typeof input3.type && "string" === typeof input3.gene && "string" === typeof input3.chrom && "number" === typeof input3.pos && "number" === typeof input3.q_value;
165
195
  const $io3 = (input3) => Object.keys(input3).every((key) => {
@@ -234,6 +264,10 @@ var validGRIN2Response = (input) => {
234
264
  path: _path2 + ".processingSummary",
235
265
  expected: "(__type.o6 | undefined)",
236
266
  value: input3.processingSummary
267
+ }), void 0 === input3.cacheFileName || "string" === typeof input3.cacheFileName || $report(_exceptionable2, {
268
+ path: _path2 + ".cacheFileName",
269
+ expected: "(string | undefined)",
270
+ value: input3.cacheFileName
237
271
  })].every((flag) => flag);
238
272
  const $vo1 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.points) || $report(_exceptionable2, {
239
273
  path: _path2 + ".points",
package/dist/{chunk-CP26DR4V.js → chunk-LJFPSUAL.js} RENAMED
@@ -22,7 +22,7 @@ var diffExpPayload = {
22
22
  var validDERequest = (input) => {
23
23
  const errors = [];
24
24
  const __is = (input2) => {
25
- const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && true && "number" === typeof input3.min_count && "number" === typeof input3.min_total_count && ("text" === input3.storage_type || "HDF5" === input3.storage_type) && (void 0 === input3.method || "string" === typeof input3.method) && true && true;
25
+ const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && true && "number" === typeof input3.min_count && "number" === typeof input3.min_total_count && "number" === typeof input3.cpm_cutoff && ("text" === input3.storage_type || "HDF5" === input3.storage_type) && (void 0 === input3.method || "string" === typeof input3.method) && true && true && (void 0 === input3.preAnalysis || "boolean" === typeof input3.preAnalysis);
26
26
  return "object" === typeof input2 && null !== input2 && $io0(input2);
27
27
  };
28
28
  if (false === __is(input)) {
@@ -44,6 +44,10 @@ var validDERequest = (input) => {
44
44
  path: _path2 + ".min_total_count",
45
45
  expected: "number",
46
46
  value: input3.min_total_count
47
+ }), "number" === typeof input3.cpm_cutoff || $report(_exceptionable2, {
48
+ path: _path2 + ".cpm_cutoff",
49
+ expected: "number",
50
+ value: input3.cpm_cutoff
47
51
  }), "text" === input3.storage_type || "HDF5" === input3.storage_type || $report(_exceptionable2, {
48
52
  path: _path2 + ".storage_type",
49
53
  expected: '("HDF5" | "text")',
@@ -52,7 +56,11 @@ var validDERequest = (input) => {
52
56
  path: _path2 + ".method",
53
57
  expected: "(string | undefined)",
54
58
  value: input3.method
55
- }), true, true].every((flag) => flag);
59
+ }), true, true, void 0 === input3.preAnalysis || "boolean" === typeof input3.preAnalysis || $report(_exceptionable2, {
60
+ path: _path2 + ".preAnalysis",
61
+ expected: "(boolean | undefined)",
62
+ value: input3.preAnalysis
63
+ })].every((flag) => flag);
56
64
  return ("object" === typeof input2 && null !== input2 || $report(true, {
57
65
  path: _path + "",
58
66
  expected: "DERequest",
@@ -74,7 +82,7 @@ var validDERequest = (input) => {
74
82
  var validDEResponse = (input) => {
75
83
  const errors = [];
76
84
  const __is = (input2) => {
77
- const $io0 = (input3) => Array.isArray(input3.data) && input3.data.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)) && "number" === typeof input3.sample_size1 && "number" === typeof input3.sample_size2 && "string" === typeof input3.method && (void 0 === input3.images || Array.isArray(input3.images) && input3.images.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)));
85
+ const $io0 = (input3) => Array.isArray(input3.data) && input3.data.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)) && "number" === typeof input3.sample_size1 && "number" === typeof input3.sample_size2 && "string" === typeof input3.method && (void 0 === input3.images || Array.isArray(input3.images) && input3.images.every((elem) => "object" === typeof elem && null !== elem && $io2(elem))) && (void 0 === input3.bcv || "number" === typeof input3.bcv);
78
86
  const $io1 = (input3) => "number" === typeof input3.adjusted_p_value && "number" === typeof input3.original_p_value && "number" === typeof input3.fold_change && "string" === typeof input3.gene_id && "string" === typeof input3.gene_name;
79
87
  const $io2 = (input3) => "string" === typeof input3.src && "number" === typeof input3.size && "string" === typeof input3.key;
80
88
  return "object" === typeof input2 && null !== input2 && $io0(input2);
@@ -126,6 +134,10 @@ var validDEResponse = (input) => {
126
134
  path: _path2 + ".images",
127
135
  expected: "(Array<DEImage> | undefined)",
128
136
  value: input3.images
137
+ }), void 0 === input3.bcv || "number" === typeof input3.bcv || $report(_exceptionable2, {
138
+ path: _path2 + ".bcv",
139
+ expected: "(number | undefined)",
140
+ value: input3.bcv
129
141
  })].every((flag) => flag);
130
142
  const $vo1 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.adjusted_p_value || $report(_exceptionable2, {
131
143
  path: _path2 + ".adjusted_p_value",
package/dist/{chunk-CT6IBFVP.js → chunk-VUKRI3TG.js} RENAMED
@@ -69,7 +69,7 @@ var validWSImagesRequest = (input) => {
69
69
  var validWSImagesResponse = (input) => {
70
70
  const errors = [];
71
71
  const __is = (input2) => {
72
- const $io0 = (input3) => (void 0 === input3.wsiSessionId || "string" === typeof input3.wsiSessionId) && (void 0 === input3.overlays || Array.isArray(input3.overlays) && input3.overlays.every((elem) => "object" === typeof elem && null !== elem && $io1(elem))) && (Array.isArray(input3.slide_dimensions) && input3.slide_dimensions.every((elem) => "number" === typeof elem)) && "string" === typeof input3.status && (void 0 === input3.error || "string" === typeof input3.error);
72
+ const $io0 = (input3) => (void 0 === input3.wsiSessionId || "string" === typeof input3.wsiSessionId) && (void 0 === input3.overlays || Array.isArray(input3.overlays) && input3.overlays.every((elem) => "object" === typeof elem && null !== elem && $io1(elem))) && (Array.isArray(input3.slide_dimensions) && input3.slide_dimensions.every((elem) => "number" === typeof elem)) && (Array.isArray(input3.mpp) && input3.mpp.every((elem) => "number" === typeof elem)) && "string" === typeof input3.status && (void 0 === input3.error || "string" === typeof input3.error);
73
73
  const $io1 = (input3) => "string" === typeof input3.layerNumber && "string" === typeof input3.predictionOverlayType;
74
74
  return "object" === typeof input2 && null !== input2 && $io0(input2);
75
75
  };
@@ -108,6 +108,18 @@ var validWSImagesResponse = (input) => {
108
108
  path: _path2 + ".slide_dimensions",
109
109
  expected: "Array<number>",
110
110
  value: input3.slide_dimensions
111
+ }), (Array.isArray(input3.mpp) || $report(_exceptionable2, {
112
+ path: _path2 + ".mpp",
113
+ expected: "Array<number>",
114
+ value: input3.mpp
115
+ })) && input3.mpp.map((elem, _index3) => "number" === typeof elem || $report(_exceptionable2, {
116
+ path: _path2 + ".mpp[" + _index3 + "]",
117
+ expected: "number",
118
+ value: elem
119
+ })).every((flag) => flag) || $report(_exceptionable2, {
120
+ path: _path2 + ".mpp",
121
+ expected: "Array<number>",
122
+ value: input3.mpp
111
123
  }), "string" === typeof input3.status || $report(_exceptionable2, {
112
124
  path: _path2 + ".status",
113
125
  expected: "string",
package/dist/grin2.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  GRIN2Payload,
3
3
  validGRIN2Request,
4
4
  validGRIN2Response
5
- } from "./chunk-Z7KZU2H5.js";
5
+ } from "./chunk-HI2IT25E.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  GRIN2Payload,
package/dist/index.js CHANGED
@@ -1,3 +1,13 @@
1
+ import {
2
+ topMutatedGenePayload,
3
+ validtopMutatedGeneRequest,
4
+ validtopMutatedGeneResponse
5
+ } from "./chunk-EIJT53QB.js";
6
+ import {
7
+ termdbTopTermsByTypePayload,
8
+ validTermdbTopTermsByTypeRequest,
9
+ validTermdbTopTermsByTypeResponse
10
+ } from "./chunk-KQNLROUN.js";
1
11
  import {
2
12
  termdbTopVariablyExpressedGenesPayload,
3
13
  validTermdbTopVariablyExpressedGenesRequest,
@@ -17,12 +27,22 @@ import {
17
27
  validWSImagesRequest,
18
28
  validWSImagesResponse,
19
29
  wsImagesPayload
20
- } from "./chunk-CT6IBFVP.js";
30
+ } from "./chunk-VUKRI3TG.js";
21
31
  import {
22
32
  validWSISamplesRequest,
23
33
  validWSISamplesResponse,
24
34
  wsiSamplesPayload
25
35
  } from "./chunk-2744ACBX.js";
36
+ import {
37
+ termdbSampleImagesPayload,
38
+ validTermdbSampleImagesRequest,
39
+ validTermdbSampleImagesResponse
40
+ } from "./chunk-U3BTVE5T.js";
41
+ import {
42
+ termdbSampleScatterPayload,
43
+ validTermdbSampleScatterRequest,
44
+ validTermdbSampleScatterResponse
45
+ } from "./chunk-OSBVSZBB.js";
26
46
  import {
27
47
  termdbSingleSampleMutationPayload,
28
48
  validTermdbSingleSampleMutationRequest,
@@ -54,15 +74,15 @@ import {
54
74
  validTermsByIdsResponse
55
75
  } from "./chunk-WL7ZVGZS.js";
56
76
  import {
57
- topMutatedGenePayload,
58
- validtopMutatedGeneRequest,
59
- validtopMutatedGeneResponse
60
- } from "./chunk-EIJT53QB.js";
77
+ termdbCohortsPayload,
78
+ validTermdbCohortsRequest,
79
+ validTermdbCohortsResponse
80
+ } from "./chunk-FMC4G5BP.js";
61
81
  import {
62
- termdbTopTermsByTypePayload,
63
- validTermdbTopTermsByTypeRequest,
64
- validTermdbTopTermsByTypeResponse
65
- } from "./chunk-KQNLROUN.js";
82
+ descrStatsPayload,
83
+ validDescrStatsRequest,
84
+ validDescrStatsResponse
85
+ } from "./chunk-4SJC57Y6.js";
66
86
  import {
67
87
  FilterTermValuesPayload,
68
88
  validFilterTermValuesRequest,
@@ -94,20 +114,20 @@ import {
94
114
  validRootTermResponse
95
115
  } from "./chunk-Q3HGHP3J.js";
96
116
  import {
97
- termdbSampleImagesPayload,
98
- validTermdbSampleImagesRequest,
99
- validTermdbSampleImagesResponse
100
- } from "./chunk-U3BTVE5T.js";
117
+ saveWSIAnnotationPayload,
118
+ validSaveWSIAnnotationRequest,
119
+ validSaveWSIAnnotationResponse
120
+ } from "./chunk-KVE2NBC6.js";
101
121
  import {
102
- termdbSampleScatterPayload,
103
- validTermdbSampleScatterRequest,
104
- validTermdbSampleScatterResponse
105
- } from "./chunk-OSBVSZBB.js";
122
+ snpPayload,
123
+ validSnpRequest,
124
+ validSnpResponse
125
+ } from "./chunk-7MUISZHS.js";
106
126
  import {
107
127
  diffExpPayload,
108
128
  validDERequest,
109
129
  validDEResponse
110
- } from "./chunk-CP26DR4V.js";
130
+ } from "./chunk-LJFPSUAL.js";
111
131
  import {
112
132
  boxplotPayload,
113
133
  validBoxPlotRequest,
@@ -134,15 +154,15 @@ import {
134
154
  validTermdbCohortSummaryResponse
135
155
  } from "./chunk-LRVF7U64.js";
136
156
  import {
137
- termdbCohortsPayload,
138
- validTermdbCohortsRequest,
139
- validTermdbCohortsResponse
140
- } from "./chunk-FMC4G5BP.js";
157
+ hicGenomePayload,
158
+ validHicGenomeRequest,
159
+ validHicGenomeResponse
160
+ } from "./chunk-62XTWOVJ.js";
141
161
  import {
142
- descrStatsPayload,
143
- validDescrStatsRequest,
144
- validDescrStatsResponse
145
- } from "./chunk-4SJC57Y6.js";
162
+ hicstatPayload,
163
+ validHicstatRequest,
164
+ validHicstatResponse
165
+ } from "./chunk-6GKG55BT.js";
146
166
  import {
147
167
  imgPayload,
148
168
  validimgRequest,
@@ -169,15 +189,15 @@ import {
169
189
  validSampleWSImagesResponse
170
190
  } from "./chunk-ETMCI34A.js";
171
191
  import {
172
- saveWSIAnnotationPayload,
173
- validSaveWSIAnnotationRequest,
174
- validSaveWSIAnnotationResponse
175
- } from "./chunk-KVE2NBC6.js";
192
+ gdcMafPayload,
193
+ validGdcMafRequest,
194
+ validGdcMafResponse
195
+ } from "./chunk-MIOIOFBZ.js";
176
196
  import {
177
- snpPayload,
178
- validSnpRequest,
179
- validSnpResponse
180
- } from "./chunk-7MUISZHS.js";
197
+ GdcMafPayload,
198
+ validGdcMafBuildRequest,
199
+ validGdcMafBuildResponse
200
+ } from "./chunk-2BCLGYAG.js";
181
201
  import {
182
202
  geneLookupPayload,
183
203
  validGeneLookupRequest,
@@ -197,7 +217,7 @@ import {
197
217
  GRIN2Payload,
198
218
  validGRIN2Request,
199
219
  validGRIN2Response
200
- } from "./chunk-Z7KZU2H5.js";
220
+ } from "./chunk-HI2IT25E.js";
201
221
  import {
202
222
  healthcheckPayload,
203
223
  validHealthCheckRequest,
@@ -209,15 +229,12 @@ import {
209
229
  validHicdataResponse
210
230
  } from "./chunk-EOKM345J.js";
211
231
  import {
212
- hicGenomePayload,
213
- validHicGenomeRequest,
214
- validHicGenomeResponse
215
- } from "./chunk-62XTWOVJ.js";
232
+ validClearWSImagesSessionsRequest,
233
+ validClearWSImagesSessionsResponse
234
+ } from "./chunk-BCBSHTHS.js";
216
235
  import {
217
- hicstatPayload,
218
- validHicstatRequest,
219
- validHicstatResponse
220
- } from "./chunk-6GKG55BT.js";
236
+ clearWSImagesSessionsPayload
237
+ } from "./chunk-RPX4TVMD.js";
221
238
  import {
222
239
  CorrelationVolcanoPayload,
223
240
  validCorrelationVolcanoRequest,
@@ -251,16 +268,6 @@ import {
251
268
  validRunGRIN2Request,
252
269
  validRunGRIN2Response
253
270
  } from "./chunk-2WSENLMK.js";
254
- import {
255
- gdcMafPayload,
256
- validGdcMafRequest,
257
- validGdcMafResponse
258
- } from "./chunk-MIOIOFBZ.js";
259
- import {
260
- GdcMafPayload,
261
- validGdcMafBuildRequest,
262
- validGdcMafBuildResponse
263
- } from "./chunk-2BCLGYAG.js";
264
271
  import {
265
272
  aiProjectAdminPayload,
266
273
  validAIProjectAdminRequest,
@@ -276,6 +283,16 @@ import {
276
283
  validAIProjectTrainModelRequest,
277
284
  validAIProjectTrainModelResponse
278
285
  } from "./chunk-UYJA4UM7.js";
286
+ import {
287
+ alphaGenomePayload,
288
+ validalphaGenomeRequest,
289
+ validalphaGenomeResponse
290
+ } from "./chunk-4EAGOSMN.js";
291
+ import {
292
+ alphaGenomeTypesPayload,
293
+ validalphaGenomeTypesRequest,
294
+ validalphaGenomeTypesResponse
295
+ } from "./chunk-5H2LJKPX.js";
279
296
  import {
280
297
  brainImagingPayload,
281
298
  validBrainImagingRequest,
@@ -291,13 +308,6 @@ import {
291
308
  validBurdenRequest,
292
309
  validBurdenResponse
293
310
  } from "./chunk-D7AKQKDG.js";
294
- import {
295
- validClearWSImagesSessionsRequest,
296
- validClearWSImagesSessionsResponse
297
- } from "./chunk-BCBSHTHS.js";
298
- import {
299
- clearWSImagesSessionsPayload
300
- } from "./chunk-RPX4TVMD.js";
301
311
  import "./chunk-YNHC5SXO.js";
302
312
  export {
303
313
  ChatPayload,
@@ -310,6 +320,8 @@ export {
310
320
  aiProjectAdminPayload,
311
321
  aiProjectSelectedWSImagesResponsePayload,
312
322
  aiProjectTrainModelPayload,
323
+ alphaGenomePayload,
324
+ alphaGenomeTypesPayload,
313
325
  boxplotPayload,
314
326
  brainImagingPayload,
315
327
  brainImagingSamplesPayload,
@@ -473,6 +485,10 @@ export {
473
485
  validWSISamplesResponse,
474
486
  validWSImagesRequest,
475
487
  validWSImagesResponse,
488
+ validalphaGenomeRequest,
489
+ validalphaGenomeResponse,
490
+ validalphaGenomeTypesRequest,
491
+ validalphaGenomeTypesResponse,
476
492
  validimgRequest,
477
493
  validimgResponse,
478
494
  validtopMutatedGeneRequest,
package/dist/termdb.DE.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  diffExpPayload,
3
3
  validDERequest,
4
4
  validDEResponse
5
- } from "./chunk-CP26DR4V.js";
5
+ } from "./chunk-LJFPSUAL.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  diffExpPayload,
package/dist/wsimages.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  validWSImagesRequest,
3
3
  validWSImagesResponse,
4
4
  wsImagesPayload
5
- } from "./chunk-CT6IBFVP.js";
5
+ } from "./chunk-VUKRI3TG.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  validWSImagesRequest,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@sjcrh/proteinpaint-types",
3
- "version": "2.148.1",
3
+ "version": "2.150.0",
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
@@ -384,39 +384,14 @@ type SvFusion = {
384
384
  */
385
385
  file?: string
386
386
  }
387
+ /** list of dt values to indicate if this ds has sv, fusion, or both */
388
+ dtLst: number[]
387
389
  }
388
390
 
389
391
  type SingleSampleMutationQuery = {
390
392
  /** for native ds, each file should contain a stringified json array with elements below
391
- for non-native ds, the getter should return an json array with same structure:
392
-
393
- cnv example entry:
394
- {
395
- "chromosome": "chr1",
396
- "start": 123456,
397
- "end": 123789,
398
- "type": "cnv",
399
- "log2Ratio": null
400
- }
401
-
402
- snvindel example entry:
403
- {
404
- "chromosome": "chr1",
405
- "start": 123456,
406
- "end": 123789,
407
- "type": "snvindel"
408
- }
409
- TODO specify property names for read depth; needed for grin2 filtering
410
-
411
- fusion example entry:
412
- {
413
- "chromosome": "chr1",
414
- "start": 123456,
415
- "end": 123789,
416
- "type": "fusion",
417
- "fusionType": null,
418
- "confidence": null
419
- }
393
+ see file server/test/tp/files/hg38/TermdbTest/mutationpersample/3318 for example
394
+ for non-native ds, the getter should return an json array with same structure
420
395
  */
421
396
  src: 'native' | 'gdcapi' | string
422
397
  /** which property of client mutation object to retrieve sample identifier for
@@ -1011,6 +986,18 @@ type Mds3Queries = {
1011
986
  WSImages?: WSImages
1012
987
  images?: Images
1013
988
  chat?: any
989
+ alphaGenome?: {
990
+ ontologyTerm?: string // default ontology term for a dataset
991
+ default: {
992
+ gene: string
993
+ chromosome: string
994
+ position: number
995
+ reference: string
996
+ alternate: string
997
+ ontologyTerm: string
998
+ outputType: number
999
+ }
1000
+ }
1014
1001
  }
1015
1002
 
1016
1003
  /** chat app support
@@ -1054,7 +1041,7 @@ export type WSImages = {
1054
1041
  predictionColor?: Array<number>
1055
1042
  annotationsColor?: Array<number>
1056
1043
  tileSize?: number
1057
- uncertainty?: { color: string; label: string }[]
1044
+ uncertainty?: { color: string; label?: string }[]
1058
1045
 
1059
1046
  /** dynamically added on launch with built in logic */
1060
1047
  saveWSIAnnotation?: (annotation: SaveWSIAnnotationRequest) => Promise<void>
@@ -1182,12 +1169,7 @@ type CorrelationVolcano = {
1182
1169
  }
1183
1170
 
1184
1171
  type UiLabels = {
1185
- samples?: string
1186
- sample?: string
1187
- Samples?: string
1188
- Sample?: string
1189
- Mutations?: string
1190
- Mutation?: string
1172
+ [propName: string]: string | { label: string; [otherAttr: string]: string }
1191
1173
  }
1192
1174
 
1193
1175
  type SurvPlotsEntry = {
@@ -1230,8 +1212,10 @@ type SortPriorityEntry = {
1230
1212
  type SurvivalSettings = {
1231
1213
  /** The max time-to-event to be displayed in plot, hide all the samples with Time-to-Event longer than this maxTimeToEvent */
1232
1214
  maxTimeToEvent?: number
1233
- /** The time unit (months, years, etc) displayed in the x-axis of survival plot */
1215
+ /** The time unit (years, months, weeks, or days) displayed in the x-axis of survival plot */
1234
1216
  timeUnit?: string
1217
+ /** The number of raw survival data's time units that make up one year, e.g., 12 for months */
1218
+ numUnitInOneYear?: number
1235
1219
  /** the customized x-axis tick values of survival plot */
1236
1220
  xTickValues?: number[]
1237
1221
  }
@@ -1563,6 +1547,8 @@ keep this setting here for reason of:
1563
1547
  */
1564
1548
  hasSampleAncestry?: boolean
1565
1549
  sampleTypes?: SampleType[]
1550
+ /** ui labels used for plot controls and tooltips */
1551
+ uiLabels?: UiLabels
1566
1552
 
1567
1553
  tracks?: {
1568
1554
  /** allow color or shape changes in the lollipop */
package/src/routes/alphaGenome.ts ADDED
@@ -0,0 +1,27 @@
1
+ import type { RoutePayload } from './routeApi.ts'
2
+
3
+ export type alphaGenomeRequest = {
4
+ genome?: string
5
+ dslabel?: string
6
+ chromosome: string
7
+ position: number
8
+ reference: string
9
+ alternate: string
10
+ ontologyTerms: string[]
11
+ outputType?: number
12
+ interval: number
13
+ }
14
+
15
+ export type alphaGenomeResponse = {
16
+ /** the alpha genome plot */
17
+ plotImage: string
18
+ }
19
+
20
+ export const alphaGenomePayload: RoutePayload = {
21
+ request: {
22
+ typeId: 'alphaGenomeRequest'
23
+ },
24
+ response: {
25
+ typeId: 'alphaGenomeResponse'
26
+ }
27
+ }
package/src/routes/alphaGenomeTypes.ts ADDED
@@ -0,0 +1,21 @@
1
+ import type { RoutePayload } from './routeApi.ts'
2
+
3
+ export type alphaGenomeTypesRequest = {
4
+ dslabel: string
5
+ }
6
+ export type alphaGenomeTypesResponse = {
7
+ /** the alpha genome ontology terms supported by the dataset */
8
+ ontologyTerms: any[]
9
+ /** the alpha genome output types */
10
+ outputTypes: any[]
11
+ intervals: number[]
12
+ }
13
+
14
+ export const alphaGenomeTypesPayload: RoutePayload = {
15
+ request: {
16
+ typeId: 'alphaGenomeTypesRequest'
17
+ },
18
+ response: {
19
+ typeId: 'alphaGenomeTypesResponse'
20
+ }
21
+ }
package/src/routes/grin2.ts CHANGED
@@ -42,6 +42,10 @@ export type GRIN2Request = {
42
42
  consequences?: string[]
43
43
  /** Maximum mutation count cutoff for highly mutated scenarios */
44
44
  hyperMutator?: number // Default: 1000
45
+ /** Number of bases to include as 5' flank around the mutation position */
46
+ fivePrimeFlankSize?: number
47
+ /** Number of bases to include as 3' flank around the mutation position */
48
+ threePrimeFlankSize?: number
45
49
  }
46
50
 
47
51
  /** Options for filtering CNV file content */
@@ -54,13 +58,28 @@ export type GRIN2Request = {
54
58
  maxSegLength?: number // Default: 0
55
59
  /** Hypermutator max cut off for CNVs per case */
56
60
  hyperMutator?: number // Default: 500
61
+ /** Number of bases to include as 5' flank around the segment position */
62
+ fivePrimeFlankSize?: number
63
+ /** Number of bases to include as 3' flank around the segment position */
64
+ threePrimeFlankSize?: number
57
65
  }
58
66
 
59
67
  /** Options for filtering fusion file content */
60
68
  fusionOptions?: {
61
- /** Placeholder - fusion filtering options to be implemented */
62
- [key: string]: any
69
+ /** Number of bases to include as 5' flank around the fusion position */
70
+ fivePrimeFlankSize?: number
71
+ /** Number of bases to include as 3' flank around the fusion position */
72
+ threePrimeFlankSize?: number
63
73
  }
74
+
75
+ /** Options for filtering structural variant file content */
76
+ svOptions?: {
77
+ /** Number of bases to include as 5' flank around the sv position */
78
+ fivePrimeFlankSize?: number
79
+ /** Number of bases to include as 3' flank around the sv position */
80
+ threePrimeFlankSize?: number
81
+ }
82
+ maxGenesToShow?: number // Default: 500
64
83
  }
65
84
 
66
85
  /** Simple Interface to store the complex plot data from the python Manhattan plot */
@@ -148,6 +167,8 @@ export type GRIN2Response = {
148
167
  processedLesions?: number
149
168
  unprocessedSamples?: number
150
169
  }
170
+ /** Cache file name for storing GRIN2 results */
171
+ cacheFileName?: string
151
172
  }
152
173
 
153
174
  /**
package/src/routes/termdb.DE.ts CHANGED
@@ -11,6 +11,8 @@ export type DERequest = {
11
11
  min_count: number
12
12
  /** Minimum total read count required for each sample */
13
13
  min_total_count: number
14
+ /** Minimum normalized expression threshold to retain only genes with sufficient expression */
15
+ cpm_cutoff: number
14
16
  /** Storage_type for storing data. Will deprecate text files */
15
17
  storage_type: 'text' | 'HDF5'
16
18
  /** Method of DE used wilcoxon/edgeR */
@@ -19,6 +21,8 @@ export type DERequest = {
19
21
  tw?: any
20
22
  /** Term for confounding variable2 (if present) */
21
23
  tw2?: any
24
+ /** Option to return early with actual number of samples with expression values */
25
+ preAnalysis?: boolean
22
26
  }
23
27
 
24
28
  export type ExpressionInput = {
@@ -64,6 +68,8 @@ export type DEResponse = {
64
68
  /** QL: Image describing the quality of the fitting from QL pipeline, this is only generated for edgeR not for wilcoxon method */
65
69
  /** MDS: Image showing the MDS plot of samples from both groups, this is only generated for edgeR not for wilcoxon method */
66
70
  images?: DEImage[]
71
+ /** Biological coefficient of variation (BCV), this is only generated for edgeR*/
72
+ bcv?: number
67
73
  }
68
74
 
69
75
  export type DataEntry = {
package/src/routes/wsimages.ts CHANGED
@@ -13,6 +13,7 @@ export type WSImagesResponse = {
13
13
  wsiSessionId?: string
14
14
  overlays?: Array<PredictionOverlay>
15
15
  slide_dimensions: number[]
16
+ mpp: number[]
16
17
  status: string
17
18
  error?: string
18
19
  }