@sjcrh/proteinpaint-types 2.136.0 → 2.137.0

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Files changed (7) hide show
  1. package/dist/chunk-Z2VOERJ2.js +339 -0
  2. package/dist/grin2.js +11 -0
  3. package/dist/index.js +25 -17
  4. package/package.json +1 -1
  5. package/src/dataset.ts +35 -1
  6. package/src/index.ts +1 -0
  7. package/src/routes/grin2.ts +119 -0
package/dist/chunk-Z2VOERJ2.js ADDED
@@ -0,0 +1,339 @@
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+ import {
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+ __toESM,
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+ require_lib
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+ } from "./chunk-CNSSF43V.js";
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+
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+ // dist/grin2.ts
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+ var import_typia = __toESM(require_lib(), 1);
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+
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+ // src/routes/grin2.ts
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+ var GRIN2Payload = {
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+ request: {
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+ typeId: "GRIN2Request"
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+ },
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+ response: {
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+ typeId: "GRIN2Response"
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+ }
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+ };
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+
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+ // dist/grin2.ts
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+ var validGRIN2Request = (input) => {
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+ const errors = [];
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+ const __is = (input2) => {
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+ const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && 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));
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+ 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);
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+ 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.minSegLength || "number" === typeof input3.minSegLength) && (void 0 === input3.hyperMutator || "number" === typeof input3.hyperMutator);
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+ const $io3 = (input3) => (void 0 === input3.fusionTypes || Array.isArray(input3.fusionTypes) && input3.fusionTypes.every((elem) => "gene-gene" === elem || "gene-intergenic" === elem || "readthrough" === elem)) && (void 0 === input3.minConfidence || "number" === typeof input3.minConfidence);
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+ return "object" === typeof input2 && null !== input2 && $io0(input2);
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+ };
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+ if (false === __is(input)) {
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+ const $report = import_typia.createValidate.report(errors);
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+ ((input2, _path, _exceptionable = true) => {
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+ const $vo0 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.genome || $report(_exceptionable2, {
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+ path: _path2 + ".genome",
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+ expected: "string",
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+ value: input3.genome
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+ }), "string" === typeof input3.dslabel || $report(_exceptionable2, {
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+ path: _path2 + ".dslabel",
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+ expected: "string",
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+ value: input3.dslabel
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+ }), true, void 0 === input3.snvindelOptions || ("object" === typeof input3.snvindelOptions && null !== input3.snvindelOptions && false === Array.isArray(input3.snvindelOptions) || $report(_exceptionable2, {
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+ path: _path2 + ".snvindelOptions",
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+ expected: "(__type | undefined)",
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+ value: input3.snvindelOptions
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+ })) && $vo1(input3.snvindelOptions, _path2 + ".snvindelOptions", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".snvindelOptions",
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+ expected: "(__type | undefined)",
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+ value: input3.snvindelOptions
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+ }), void 0 === input3.cnvOptions || ("object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) || $report(_exceptionable2, {
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+ path: _path2 + ".cnvOptions",
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+ expected: "(__type.o1 | undefined)",
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+ value: input3.cnvOptions
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+ })) && $vo2(input3.cnvOptions, _path2 + ".cnvOptions", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".cnvOptions",
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+ expected: "(__type.o1 | undefined)",
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+ value: input3.cnvOptions
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+ }), void 0 === input3.fusionOptions || ("object" === typeof input3.fusionOptions && null !== input3.fusionOptions && false === Array.isArray(input3.fusionOptions) || $report(_exceptionable2, {
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+ path: _path2 + ".fusionOptions",
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+ expected: "(__type.o2 | undefined)",
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+ value: input3.fusionOptions
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+ })) && $vo3(input3.fusionOptions, _path2 + ".fusionOptions", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".fusionOptions",
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+ expected: "(__type.o2 | undefined)",
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+ value: input3.fusionOptions
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+ })].every((flag) => flag);
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+ const $vo1 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.minTotalDepth || "number" === typeof input3.minTotalDepth || $report(_exceptionable2, {
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+ path: _path2 + ".minTotalDepth",
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+ expected: "(number | undefined)",
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+ value: input3.minTotalDepth
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+ }), void 0 === input3.minAltAlleleCount || "number" === typeof input3.minAltAlleleCount || $report(_exceptionable2, {
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+ path: _path2 + ".minAltAlleleCount",
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+ expected: "(number | undefined)",
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+ value: input3.minAltAlleleCount
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+ }), void 0 === input3.consequences || (Array.isArray(input3.consequences) || $report(_exceptionable2, {
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+ path: _path2 + ".consequences",
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+ expected: "(Array<string> | undefined)",
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+ value: input3.consequences
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+ })) && input3.consequences.map((elem, _index1) => "string" === typeof elem || $report(_exceptionable2, {
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+ path: _path2 + ".consequences[" + _index1 + "]",
79
+ expected: "string",
80
+ value: elem
81
+ })).every((flag) => flag) || $report(_exceptionable2, {
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+ path: _path2 + ".consequences",
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+ expected: "(Array<string> | undefined)",
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+ value: input3.consequences
85
+ }), void 0 === input3.hyperMutator || "number" === typeof input3.hyperMutator || $report(_exceptionable2, {
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+ path: _path2 + ".hyperMutator",
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+ expected: "(number | undefined)",
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+ value: input3.hyperMutator
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+ })].every((flag) => flag);
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+ const $vo2 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.lossThreshold || "number" === typeof input3.lossThreshold || $report(_exceptionable2, {
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+ path: _path2 + ".lossThreshold",
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+ expected: "(number | undefined)",
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+ value: input3.lossThreshold
94
+ }), void 0 === input3.gainThreshold || "number" === typeof input3.gainThreshold || $report(_exceptionable2, {
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+ path: _path2 + ".gainThreshold",
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+ expected: "(number | undefined)",
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+ value: input3.gainThreshold
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+ }), void 0 === input3.maxSegLength || "number" === typeof input3.maxSegLength || $report(_exceptionable2, {
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+ path: _path2 + ".maxSegLength",
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+ expected: "(number | undefined)",
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+ value: input3.maxSegLength
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+ }), void 0 === input3.minSegLength || "number" === typeof input3.minSegLength || $report(_exceptionable2, {
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+ path: _path2 + ".minSegLength",
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+ expected: "(number | undefined)",
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+ value: input3.minSegLength
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+ }), void 0 === input3.hyperMutator || "number" === typeof input3.hyperMutator || $report(_exceptionable2, {
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+ path: _path2 + ".hyperMutator",
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+ expected: "(number | undefined)",
109
+ value: input3.hyperMutator
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+ })].every((flag) => flag);
111
+ const $vo3 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.fusionTypes || (Array.isArray(input3.fusionTypes) || $report(_exceptionable2, {
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+ path: _path2 + ".fusionTypes",
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+ expected: '(Array<"gene-gene" | "gene-intergenic" | "readthrough"> | undefined)',
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+ value: input3.fusionTypes
115
+ })) && input3.fusionTypes.map((elem, _index2) => "gene-gene" === elem || "gene-intergenic" === elem || "readthrough" === elem || $report(_exceptionable2, {
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+ path: _path2 + ".fusionTypes[" + _index2 + "]",
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+ expected: '("gene-gene" | "gene-intergenic" | "readthrough")',
118
+ value: elem
119
+ })).every((flag) => flag) || $report(_exceptionable2, {
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+ path: _path2 + ".fusionTypes",
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+ expected: '(Array<"gene-gene" | "gene-intergenic" | "readthrough"> | undefined)',
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+ value: input3.fusionTypes
123
+ }), void 0 === input3.minConfidence || "number" === typeof input3.minConfidence || $report(_exceptionable2, {
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+ path: _path2 + ".minConfidence",
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+ expected: "(number | undefined)",
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+ value: input3.minConfidence
127
+ })].every((flag) => flag);
128
+ return ("object" === typeof input2 && null !== input2 || $report(true, {
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+ path: _path + "",
130
+ expected: "GRIN2Request",
131
+ value: input2
132
+ })) && $vo0(input2, _path + "", true) || $report(true, {
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+ path: _path + "",
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+ expected: "GRIN2Request",
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+ value: input2
136
+ });
137
+ })(input, "$input", true);
138
+ }
139
+ const success = 0 === errors.length;
140
+ return {
141
+ success,
142
+ errors,
143
+ data: success ? input : void 0
144
+ };
145
+ };
146
+ var validGRIN2Response = (input) => {
147
+ const errors = [];
148
+ const __is = (input2) => {
149
+ const $io0 = (input3) => ("success" === input3.status || "error" === input3.status) && (void 0 === input3.error || "string" === typeof input3.error) && (void 0 === input3.pngImg || "string" === typeof input3.pngImg) && true && (void 0 === input3.topGeneTable || "object" === typeof input3.topGeneTable && null !== input3.topGeneTable && $io1(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 && $io4(input3.timing)) && (void 0 === input3.processingSummary || "object" === typeof input3.processingSummary && null !== input3.processingSummary && $io5(input3.processingSummary));
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+ const $io1 = (input3) => Array.isArray(input3.columns) && input3.columns.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && (Array.isArray(input3.rows) && input3.rows.every((elem) => Array.isArray(elem) && elem.every((elem2) => "object" === typeof elem2 && null !== elem2 && $io3(elem2))));
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+ const $io2 = (input3) => "string" === typeof input3.label && "boolean" === typeof input3.sortable;
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+ const $io3 = (input3) => "string" === typeof input3.value || "number" === typeof input3.value;
153
+ const $io4 = (input3) => "number" === typeof input3.processingTime && "number" === typeof input3.grin2Time && "number" === typeof input3.totalTime;
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+ const $io5 = (input3) => "number" === typeof input3.totalSamples && "number" === typeof input3.successfulSamples && "number" === typeof input3.failedSamples && (Array.isArray(input3.failedFiles) && input3.failedFiles.every((elem) => "object" === typeof elem && null !== elem && $io6(elem)));
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+ const $io6 = (input3) => "string" === typeof input3.sampleName && "string" === typeof input3.filePath && "string" === typeof input3.error;
156
+ return "object" === typeof input2 && null !== input2 && $io0(input2);
157
+ };
158
+ if (false === __is(input)) {
159
+ const $report = import_typia.createValidate.report(errors);
160
+ ((input2, _path, _exceptionable = true) => {
161
+ const $vo0 = (input3, _path2, _exceptionable2 = true) => ["success" === input3.status || "error" === input3.status || $report(_exceptionable2, {
162
+ path: _path2 + ".status",
163
+ expected: '("error" | "success")',
164
+ value: input3.status
165
+ }), void 0 === input3.error || "string" === typeof input3.error || $report(_exceptionable2, {
166
+ path: _path2 + ".error",
167
+ expected: "(string | undefined)",
168
+ value: input3.error
169
+ }), void 0 === input3.pngImg || "string" === typeof input3.pngImg || $report(_exceptionable2, {
170
+ path: _path2 + ".pngImg",
171
+ expected: "(string | undefined)",
172
+ value: input3.pngImg
173
+ }), true, void 0 === input3.topGeneTable || ("object" === typeof input3.topGeneTable && null !== input3.topGeneTable || $report(_exceptionable2, {
174
+ path: _path2 + ".topGeneTable",
175
+ expected: "(__type | undefined)",
176
+ value: input3.topGeneTable
177
+ })) && $vo1(input3.topGeneTable, _path2 + ".topGeneTable", _exceptionable2) || $report(_exceptionable2, {
178
+ path: _path2 + ".topGeneTable",
179
+ expected: "(__type | undefined)",
180
+ value: input3.topGeneTable
181
+ }), void 0 === input3.totalGenes || "number" === typeof input3.totalGenes || $report(_exceptionable2, {
182
+ path: _path2 + ".totalGenes",
183
+ expected: "(number | undefined)",
184
+ value: input3.totalGenes
185
+ }), void 0 === input3.showingTop || "number" === typeof input3.showingTop || $report(_exceptionable2, {
186
+ path: _path2 + ".showingTop",
187
+ expected: "(number | undefined)",
188
+ value: input3.showingTop
189
+ }), void 0 === input3.timing || ("object" === typeof input3.timing && null !== input3.timing || $report(_exceptionable2, {
190
+ path: _path2 + ".timing",
191
+ expected: "(__type.o3 | undefined)",
192
+ value: input3.timing
193
+ })) && $vo4(input3.timing, _path2 + ".timing", _exceptionable2) || $report(_exceptionable2, {
194
+ path: _path2 + ".timing",
195
+ expected: "(__type.o3 | undefined)",
196
+ value: input3.timing
197
+ }), void 0 === input3.processingSummary || ("object" === typeof input3.processingSummary && null !== input3.processingSummary || $report(_exceptionable2, {
198
+ path: _path2 + ".processingSummary",
199
+ expected: "(__type.o4 | undefined)",
200
+ value: input3.processingSummary
201
+ })) && $vo5(input3.processingSummary, _path2 + ".processingSummary", _exceptionable2) || $report(_exceptionable2, {
202
+ path: _path2 + ".processingSummary",
203
+ expected: "(__type.o4 | undefined)",
204
+ value: input3.processingSummary
205
+ })].every((flag) => flag);
206
+ const $vo1 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.columns) || $report(_exceptionable2, {
207
+ path: _path2 + ".columns",
208
+ expected: "Array<__type>",
209
+ value: input3.columns
210
+ })) && input3.columns.map((elem, _index1) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
211
+ path: _path2 + ".columns[" + _index1 + "]",
212
+ expected: "__type.o1",
213
+ value: elem
214
+ })) && $vo2(elem, _path2 + ".columns[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
215
+ path: _path2 + ".columns[" + _index1 + "]",
216
+ expected: "__type.o1",
217
+ value: elem
218
+ })).every((flag) => flag) || $report(_exceptionable2, {
219
+ path: _path2 + ".columns",
220
+ expected: "Array<__type>",
221
+ value: input3.columns
222
+ }), (Array.isArray(input3.rows) || $report(_exceptionable2, {
223
+ path: _path2 + ".rows",
224
+ expected: "Array<Array<__type>>",
225
+ value: input3.rows
226
+ })) && input3.rows.map((elem, _index2) => (Array.isArray(elem) || $report(_exceptionable2, {
227
+ path: _path2 + ".rows[" + _index2 + "]",
228
+ expected: "Array<__type>.o1",
229
+ value: elem
230
+ })) && elem.map((elem2, _index3) => ("object" === typeof elem2 && null !== elem2 || $report(_exceptionable2, {
231
+ path: _path2 + ".rows[" + _index2 + "][" + _index3 + "]",
232
+ expected: "__type.o2",
233
+ value: elem2
234
+ })) && $vo3(elem2, _path2 + ".rows[" + _index2 + "][" + _index3 + "]", _exceptionable2) || $report(_exceptionable2, {
235
+ path: _path2 + ".rows[" + _index2 + "][" + _index3 + "]",
236
+ expected: "__type.o2",
237
+ value: elem2
238
+ })).every((flag) => flag) || $report(_exceptionable2, {
239
+ path: _path2 + ".rows[" + _index2 + "]",
240
+ expected: "Array<__type>.o1",
241
+ value: elem
242
+ })).every((flag) => flag) || $report(_exceptionable2, {
243
+ path: _path2 + ".rows",
244
+ expected: "Array<Array<__type>>",
245
+ value: input3.rows
246
+ })].every((flag) => flag);
247
+ const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.label || $report(_exceptionable2, {
248
+ path: _path2 + ".label",
249
+ expected: "string",
250
+ value: input3.label
251
+ }), "boolean" === typeof input3.sortable || $report(_exceptionable2, {
252
+ path: _path2 + ".sortable",
253
+ expected: "boolean",
254
+ value: input3.sortable
255
+ })].every((flag) => flag);
256
+ const $vo3 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.value || "number" === typeof input3.value || $report(_exceptionable2, {
257
+ path: _path2 + ".value",
258
+ expected: "(number | string)",
259
+ value: input3.value
260
+ })].every((flag) => flag);
261
+ const $vo4 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.processingTime || $report(_exceptionable2, {
262
+ path: _path2 + ".processingTime",
263
+ expected: "number",
264
+ value: input3.processingTime
265
+ }), "number" === typeof input3.grin2Time || $report(_exceptionable2, {
266
+ path: _path2 + ".grin2Time",
267
+ expected: "number",
268
+ value: input3.grin2Time
269
+ }), "number" === typeof input3.totalTime || $report(_exceptionable2, {
270
+ path: _path2 + ".totalTime",
271
+ expected: "number",
272
+ value: input3.totalTime
273
+ })].every((flag) => flag);
274
+ const $vo5 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.totalSamples || $report(_exceptionable2, {
275
+ path: _path2 + ".totalSamples",
276
+ expected: "number",
277
+ value: input3.totalSamples
278
+ }), "number" === typeof input3.successfulSamples || $report(_exceptionable2, {
279
+ path: _path2 + ".successfulSamples",
280
+ expected: "number",
281
+ value: input3.successfulSamples
282
+ }), "number" === typeof input3.failedSamples || $report(_exceptionable2, {
283
+ path: _path2 + ".failedSamples",
284
+ expected: "number",
285
+ value: input3.failedSamples
286
+ }), (Array.isArray(input3.failedFiles) || $report(_exceptionable2, {
287
+ path: _path2 + ".failedFiles",
288
+ expected: "Array<__type>.o2",
289
+ value: input3.failedFiles
290
+ })) && input3.failedFiles.map((elem, _index4) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
291
+ path: _path2 + ".failedFiles[" + _index4 + "]",
292
+ expected: "__type.o5",
293
+ value: elem
294
+ })) && $vo6(elem, _path2 + ".failedFiles[" + _index4 + "]", _exceptionable2) || $report(_exceptionable2, {
295
+ path: _path2 + ".failedFiles[" + _index4 + "]",
296
+ expected: "__type.o5",
297
+ value: elem
298
+ })).every((flag) => flag) || $report(_exceptionable2, {
299
+ path: _path2 + ".failedFiles",
300
+ expected: "Array<__type>.o2",
301
+ value: input3.failedFiles
302
+ })].every((flag) => flag);
303
+ const $vo6 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.sampleName || $report(_exceptionable2, {
304
+ path: _path2 + ".sampleName",
305
+ expected: "string",
306
+ value: input3.sampleName
307
+ }), "string" === typeof input3.filePath || $report(_exceptionable2, {
308
+ path: _path2 + ".filePath",
309
+ expected: "string",
310
+ value: input3.filePath
311
+ }), "string" === typeof input3.error || $report(_exceptionable2, {
312
+ path: _path2 + ".error",
313
+ expected: "string",
314
+ value: input3.error
315
+ })].every((flag) => flag);
316
+ return ("object" === typeof input2 && null !== input2 || $report(true, {
317
+ path: _path + "",
318
+ expected: "GRIN2Response",
319
+ value: input2
320
+ })) && $vo0(input2, _path + "", true) || $report(true, {
321
+ path: _path + "",
322
+ expected: "GRIN2Response",
323
+ value: input2
324
+ });
325
+ })(input, "$input", true);
326
+ }
327
+ const success = 0 === errors.length;
328
+ return {
329
+ success,
330
+ errors,
331
+ data: success ? input : void 0
332
+ };
333
+ };
334
+
335
+ export {
336
+ GRIN2Payload,
337
+ validGRIN2Request,
338
+ validGRIN2Response
339
+ };
package/dist/grin2.js ADDED
@@ -0,0 +1,11 @@
1
+ import {
2
+ GRIN2Payload,
3
+ validGRIN2Request,
4
+ validGRIN2Response
5
+ } from "./chunk-Z2VOERJ2.js";
6
+ import "./chunk-CNSSF43V.js";
7
+ export {
8
+ GRIN2Payload,
9
+ validGRIN2Request,
10
+ validGRIN2Response
11
+ };
package/dist/index.js CHANGED
@@ -1,3 +1,8 @@
1
+ import {
2
+ topMutatedGenePayload,
3
+ validtopMutatedGeneRequest,
4
+ validtopMutatedGeneResponse
5
+ } from "./chunk-YGX6BZZY.js";
1
6
  import {
2
7
  termdbTopTermsByTypePayload,
3
8
  validTermdbTopTermsByTypeRequest,
@@ -28,6 +33,11 @@ import {
28
33
  validWSISamplesResponse,
29
34
  wsiSamplesPayload
30
35
  } from "./chunk-W6NLM363.js";
36
+ import {
37
+ rootTermPayload,
38
+ validRootTermRequest,
39
+ validRootTermResponse
40
+ } from "./chunk-AASWRJMS.js";
31
41
  import {
32
42
  termdbSampleImagesPayload,
33
43
  validTermdbSampleImagesRequest,
@@ -64,10 +74,10 @@ import {
64
74
  validTermsByIdsResponse
65
75
  } from "./chunk-HLGKC33X.js";
66
76
  import {
67
- topMutatedGenePayload,
68
- validtopMutatedGeneRequest,
69
- validtopMutatedGeneResponse
70
- } from "./chunk-YGX6BZZY.js";
77
+ boxplotPayload,
78
+ validBoxPlotRequest,
79
+ validBoxPlotResponse
80
+ } from "./chunk-VMZC4IN7.js";
71
81
  import {
72
82
  termdbCategoriesPayload,
73
83
  validCategoriesRequest,
@@ -104,10 +114,10 @@ import {
104
114
  validPercentileResponse
105
115
  } from "./chunk-GVBBTRW4.js";
106
116
  import {
107
- rootTermPayload,
108
- validRootTermRequest,
109
- validRootTermResponse
110
- } from "./chunk-AASWRJMS.js";
117
+ ntseqPayload,
118
+ validNtseqRequest,
119
+ validNtseqResponse
120
+ } from "./chunk-HIPWQ6AW.js";
111
121
  import {
112
122
  pdomainPayload,
113
123
  validPdomainRequest,
@@ -144,10 +154,10 @@ import {
144
154
  validDEResponse
145
155
  } from "./chunk-3C26VWPU.js";
146
156
  import {
147
- boxplotPayload,
148
- validBoxPlotRequest,
149
- validBoxPlotResponse
150
- } from "./chunk-VMZC4IN7.js";
157
+ GRIN2Payload,
158
+ validGRIN2Request,
159
+ validGRIN2Response
160
+ } from "./chunk-Z2VOERJ2.js";
151
161
  import {
152
162
  healthcheckPayload,
153
163
  validHealthCheckRequest,
@@ -178,11 +188,6 @@ import {
178
188
  validIsoformLstRequest,
179
189
  validIsoformLstResponse
180
190
  } from "./chunk-B43GFRT4.js";
181
- import {
182
- ntseqPayload,
183
- validNtseqRequest,
184
- validNtseqResponse
185
- } from "./chunk-HIPWQ6AW.js";
186
191
  import {
187
192
  dzImagesPayload,
188
193
  validDZImagesRequest,
@@ -267,6 +272,7 @@ import "./chunk-CNSSF43V.js";
267
272
  export {
268
273
  CorrelationVolcanoPayload,
269
274
  FilterTermValuesPayload,
275
+ GRIN2Payload,
270
276
  GdcMafPayload,
271
277
  ProfileFormScoresPayload,
272
278
  ProfileScoresPayload,
@@ -341,6 +347,8 @@ export {
341
347
  validDsDataResponse,
342
348
  validFilterTermValuesRequest,
343
349
  validFilterTermValuesResponse,
350
+ validGRIN2Request,
351
+ validGRIN2Response,
344
352
  validGdcGRIN2listRequest,
345
353
  validGdcGRIN2listResponse,
346
354
  validGdcMafBuildRequest,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@sjcrh/proteinpaint-types",
3
- "version": "2.136.0",
3
+ "version": "2.137.0",
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
@@ -371,11 +371,45 @@ type SvFusion = {
371
371
  }
372
372
 
373
373
  type SingleSampleMutationQuery = {
374
+ /** for native ds, each file should contain a stringified json array with elements below
375
+ for non-native ds, the getter should return an json array with same structure:
376
+
377
+ cnv example entry:
378
+ {
379
+ "chromosome": "chr1",
380
+ "start": 123456,
381
+ "end": 123789,
382
+ "type": "cnv",
383
+ "log2Ratio": null
384
+ }
385
+
386
+ snvindel example entry:
387
+ {
388
+ "chromosome": "chr1",
389
+ "start": 123456,
390
+ "end": 123789,
391
+ "type": "snvindel"
392
+ }
393
+ TODO specify property names for read depth; needed for grin2 filtering
394
+
395
+ fusion example entry:
396
+ {
397
+ "chromosome": "chr1",
398
+ "start": 123456,
399
+ "end": 123789,
400
+ "type": "fusion",
401
+ "fusionType": null,
402
+ "confidence": null
403
+ }
404
+ */
374
405
  src: 'native' | 'gdcapi' | string
375
406
  /** which property of client mutation object to retrieve sample identifier for
376
407
  * querying single sample data with */
377
408
  sample_id_key: string
378
- /** only required for src=native */
409
+ /** only required for src=native
410
+ folder contains a set of files, one file per sample, file named by sample name
411
+ each file contains a stringified json array of mutation/cnv/sv entries (aka mlst)
412
+ */
379
413
  folder?: string
380
414
  /** disco plot will be launched when singleSampleMutation is enabled. supply customization options here */
381
415
  discoPlot?: {
package/src/index.ts CHANGED
@@ -18,6 +18,7 @@ export * from './routes/filter.gdc.ts'
18
18
  export * from './routes/gdc.maf.ts'
19
19
  export * from './routes/gdc.mafBuild.ts'
20
20
  export * from './routes/gdc.grin2.ts'
21
+ export * from './routes/grin2.ts'
21
22
  export * from './routes/termdb.topMutatedGenes.ts'
22
23
  export * from './routes/genelookup.ts'
23
24
  export * from './routes/genesetEnrichment.ts'
package/src/routes/grin2.ts ADDED
@@ -0,0 +1,119 @@
1
+ /** General GRIN2 route
2
+ * This route handles the GRIN2 analysis for any non-GDC data.
3
+ * It processes the incoming data structure via PP's existing filter infrastructure
4
+ * and returns the same structured results as GDC-GRIN2.
5
+ * Specifically it will return a sortable table of top mutated genes and
6
+ * a static PNG manhattan-like plot of the -log10(q-value).
7
+ * We allow the user to customize the snvindel, CNV, and fusion filtering options.
8
+ */
9
+
10
+ import type { RoutePayload } from './routeApi.js'
11
+
12
+ /** GRIN2 request */
13
+ export type GRIN2Request = {
14
+ /** Genome build identifier (e.g., 'hg38', 'hg19') */
15
+ genome: string
16
+
17
+ /** Dataset label within the genome */
18
+ dslabel: string
19
+
20
+ /** Filter from existing PP infrastructure */
21
+ filter: any // Filter object passed to get_samples(filter, ds)
22
+
23
+ /** Options for filtering SNV/indel file content */
24
+ snvindelOptions?: {
25
+ /** Minimum total depth of returned SNV/indel files */
26
+ minTotalDepth?: number // Default: 10
27
+ /** Minimum alternate allele count of returned SNV/indel files */
28
+ minAltAlleleCount?: number // Default: 2
29
+ /** String array of consequence types to include */
30
+ consequences?: string[]
31
+ /** Maximum mutation count cutoff for highly mutated scenarios */
32
+ hyperMutator?: number // Default: 1000
33
+ }
34
+
35
+ /** Options for filtering CNV file content */
36
+ cnvOptions?: {
37
+ /** Threshold for copy number loss detection */
38
+ lossThreshold?: number // Default: -0.4
39
+ /** Threshold for copy number gain detection */
40
+ gainThreshold?: number // Default: 0.3
41
+ /** Maximum segment length to include (0 = no filter) */
42
+ maxSegLength?: number // Default: 0
43
+ /** Minimum segment length to include (0 = no filter) */
44
+ minSegLength?: number // Default: 0
45
+ /** Hypermutator max cut off for CNVs per case */
46
+ hyperMutator?: number // Default: 500
47
+ }
48
+
49
+ /** Options for filtering fusion file content */
50
+ fusionOptions?: {
51
+ /** Filter by fusion type */
52
+ fusionTypes?: ('gene-gene' | 'gene-intergenic' | 'readthrough')[]
53
+ /** Minimum confidence score (0-1) */
54
+ minConfidence?: number // Default: 0.7
55
+ }
56
+ }
57
+
58
+ /**
59
+ * Response for GRIN2 analysis run
60
+ */
61
+ export type GRIN2Response = {
62
+ /** Status of the analysis */
63
+ status: 'success' | 'error'
64
+ /** Error message if status is 'error' */
65
+ error?: string
66
+ /** Base64-encoded PNG Manhattan plot image */
67
+ pngImg?: string
68
+ /** Download status/info */
69
+ download?: any
70
+ /** Sortable table of top genes identified by GRIN2 */
71
+ topGeneTable?: {
72
+ /** Column definitions with labels and sort capabilities */
73
+ columns: Array<{
74
+ label: string
75
+ sortable: boolean
76
+ }>
77
+ /** Data rows with gene information and statistics */
78
+ rows: Array<
79
+ Array<{
80
+ value: string | number
81
+ }>
82
+ >
83
+ }
84
+ /** Summary statistics */
85
+ totalGenes?: number
86
+ showingTop?: number
87
+ /** Timing info for the analysis */
88
+ timing?: {
89
+ /** Time taken to run data processing */
90
+ processingTime: number
91
+ /** Time taken to run GRIN2 processing */
92
+ grin2Time: number
93
+ /** Total time taken for the entire run */
94
+ totalTime: number
95
+ }
96
+ /** Detailed processing summary */
97
+ processingSummary?: {
98
+ totalSamples: number
99
+ successfulSamples: number
100
+ failedSamples: number
101
+ failedFiles: Array<{
102
+ sampleName: string
103
+ filePath: string
104
+ error: string
105
+ }>
106
+ }
107
+ }
108
+
109
+ /**
110
+ * Route payload definitions for type checking
111
+ */
112
+ export const GRIN2Payload: RoutePayload = {
113
+ request: {
114
+ typeId: 'GRIN2Request'
115
+ },
116
+ response: {
117
+ typeId: 'GRIN2Response'
118
+ }
119
+ }