@sjcrh/proteinpaint-types 2.149.0 → 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.
- package/dist/alphaGenome.js +11 -0
- package/dist/alphaGenomeTypes.js +11 -0
- package/dist/chunk-4EAGOSMN.js +128 -0
- package/dist/chunk-5H2LJKPX.js +104 -0
- package/dist/{chunk-Z7KZU2H5.js → chunk-HI2IT25E.js} +56 -22
- package/dist/{chunk-FIQM2YN4.js → chunk-LJFPSUAL.js} +6 -2
- package/dist/grin2.js +1 -1
- package/dist/index.js +75 -59
- package/dist/termdb.DE.js +1 -1
- package/package.json +1 -1
- package/src/dataset.ts +23 -37
- package/src/routes/alphaGenome.ts +27 -0
- package/src/routes/alphaGenomeTypes.ts +21 -0
- package/src/routes/grin2.ts +23 -2
- package/src/routes/termdb.DE.ts +2 -0
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@@ -0,0 +1,11 @@
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import {
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alphaGenomeTypesPayload,
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validalphaGenomeTypesRequest,
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validalphaGenomeTypesResponse
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} from "./chunk-5H2LJKPX.js";
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import "./chunk-YNHC5SXO.js";
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export {
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alphaGenomeTypesPayload,
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validalphaGenomeTypesRequest,
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validalphaGenomeTypesResponse
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};
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@@ -0,0 +1,128 @@
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import {
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__toESM,
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require_lib
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} from "./chunk-YNHC5SXO.js";
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// dist/alphaGenome.ts
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var import_typia = __toESM(require_lib(), 1);
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// src/routes/alphaGenome.ts
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var alphaGenomePayload = {
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request: {
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typeId: "alphaGenomeRequest"
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},
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response: {
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typeId: "alphaGenomeResponse"
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}
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};
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// dist/alphaGenome.ts
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var validalphaGenomeRequest = (input) => {
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const errors = [];
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const __is = (input2) => {
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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;
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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) => [void 0 === input3.genome || "string" === typeof input3.genome || $report(_exceptionable2, {
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path: _path2 + ".genome",
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expected: "(string | undefined)",
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value: input3.genome
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}), void 0 === input3.dslabel || "string" === typeof input3.dslabel || $report(_exceptionable2, {
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path: _path2 + ".dslabel",
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expected: "(string | undefined)",
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value: input3.dslabel
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}), "string" === typeof input3.chromosome || $report(_exceptionable2, {
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path: _path2 + ".chromosome",
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expected: "string",
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value: input3.chromosome
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}), "number" === typeof input3.position || $report(_exceptionable2, {
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path: _path2 + ".position",
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expected: "number",
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value: input3.position
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}), "string" === typeof input3.reference || $report(_exceptionable2, {
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path: _path2 + ".reference",
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expected: "string",
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value: input3.reference
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}), "string" === typeof input3.alternate || $report(_exceptionable2, {
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path: _path2 + ".alternate",
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expected: "string",
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value: input3.alternate
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}), (Array.isArray(input3.ontologyTerms) || $report(_exceptionable2, {
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path: _path2 + ".ontologyTerms",
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expected: "Array<string>",
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value: input3.ontologyTerms
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})) && input3.ontologyTerms.map((elem, _index1) => "string" === typeof elem || $report(_exceptionable2, {
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path: _path2 + ".ontologyTerms[" + _index1 + "]",
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expected: "string",
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value: elem
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})).every((flag) => flag) || $report(_exceptionable2, {
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path: _path2 + ".ontologyTerms",
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expected: "Array<string>",
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value: input3.ontologyTerms
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}), void 0 === input3.outputType || "number" === typeof input3.outputType || $report(_exceptionable2, {
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path: _path2 + ".outputType",
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expected: "(number | undefined)",
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value: input3.outputType
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}), "number" === typeof input3.interval || $report(_exceptionable2, {
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path: _path2 + ".interval",
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expected: "number",
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value: input3.interval
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})].every((flag) => flag);
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return ("object" === typeof input2 && null !== input2 || $report(true, {
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path: _path + "",
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expected: "alphaGenomeRequest",
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value: input2
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})) && $vo0(input2, _path + "", true) || $report(true, {
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path: _path + "",
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expected: "alphaGenomeRequest",
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value: input2
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});
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})(input, "$input", true);
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}
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const success = 0 === errors.length;
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return {
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success,
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errors,
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data: success ? input : void 0
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};
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};
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var validalphaGenomeResponse = (input) => {
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const errors = [];
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const __is = (input2) => {
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return "object" === typeof input2 && null !== input2 && "string" === typeof input2.plotImage;
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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.plotImage || $report(_exceptionable2, {
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path: _path2 + ".plotImage",
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expected: "string",
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value: input3.plotImage
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})].every((flag) => flag);
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return ("object" === typeof input2 && null !== input2 || $report(true, {
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path: _path + "",
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expected: "alphaGenomeResponse",
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value: input2
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})) && $vo0(input2, _path + "", true) || $report(true, {
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path: _path + "",
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expected: "alphaGenomeResponse",
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value: input2
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});
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})(input, "$input", true);
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}
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const success = 0 === errors.length;
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return {
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success,
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errors,
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data: success ? input : void 0
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};
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};
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export {
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alphaGenomePayload,
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validalphaGenomeRequest,
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validalphaGenomeResponse
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};
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@@ -0,0 +1,104 @@
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import {
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__toESM,
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require_lib
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} from "./chunk-YNHC5SXO.js";
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// dist/alphaGenomeTypes.ts
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var import_typia = __toESM(require_lib(), 1);
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// src/routes/alphaGenomeTypes.ts
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var alphaGenomeTypesPayload = {
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request: {
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typeId: "alphaGenomeTypesRequest"
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},
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response: {
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typeId: "alphaGenomeTypesResponse"
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}
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};
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// dist/alphaGenomeTypes.ts
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var validalphaGenomeTypesRequest = (input) => {
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const errors = [];
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const __is = (input2) => {
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return "object" === typeof input2 && null !== input2 && "string" === typeof input2.dslabel;
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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.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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})].every((flag) => flag);
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return ("object" === typeof input2 && null !== input2 || $report(true, {
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path: _path + "",
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expected: "alphaGenomeTypesRequest",
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value: input2
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})) && $vo0(input2, _path + "", true) || $report(true, {
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path: _path + "",
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expected: "alphaGenomeTypesRequest",
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value: input2
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});
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})(input, "$input", true);
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}
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const success = 0 === errors.length;
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return {
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success,
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errors,
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data: success ? input : void 0
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};
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};
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var validalphaGenomeTypesResponse = (input) => {
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const errors = [];
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const __is = (input2) => {
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const $io0 = (input3) => Array.isArray(input3.ontologyTerms) && Array.isArray(input3.outputTypes) && (Array.isArray(input3.intervals) && input3.intervals.every((elem) => "number" === typeof elem));
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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) => [Array.isArray(input3.ontologyTerms) || $report(_exceptionable2, {
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path: _path2 + ".ontologyTerms",
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expected: "Array<any>",
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value: input3.ontologyTerms
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}), Array.isArray(input3.outputTypes) || $report(_exceptionable2, {
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path: _path2 + ".outputTypes",
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expected: "Array<any>",
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value: input3.outputTypes
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}), (Array.isArray(input3.intervals) || $report(_exceptionable2, {
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path: _path2 + ".intervals",
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expected: "Array<number>",
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value: input3.intervals
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})) && input3.intervals.map((elem, _index1) => "number" === typeof elem || $report(_exceptionable2, {
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path: _path2 + ".intervals[" + _index1 + "]",
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expected: "number",
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value: elem
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})).every((flag) => flag) || $report(_exceptionable2, {
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path: _path2 + ".intervals",
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expected: "Array<number>",
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value: input3.intervals
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})].every((flag) => flag);
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return ("object" === typeof input2 && null !== input2 || $report(true, {
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path: _path + "",
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expected: "alphaGenomeTypesResponse",
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value: input2
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})) && $vo0(input2, _path + "", true) || $report(true, {
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path: _path + "",
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expected: "alphaGenomeTypesResponse",
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value: input2
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});
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})(input, "$input", true);
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}
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const success = 0 === errors.length;
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return {
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success,
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errors,
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data: success ? input : void 0
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};
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};
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export {
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alphaGenomeTypesPayload,
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validalphaGenomeTypesRequest,
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validalphaGenomeTypesResponse
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};
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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 $
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const $
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const $
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const $
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const $
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const value = input3[key];
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if (void 0 === value)
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return true;
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if (RegExp(/(.*)/).test(key))
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return true;
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return true;
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});
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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);
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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) && (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
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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.hyperMutator || "number" === typeof input3.hyperMutator) && (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
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const $io3 = (input3) => (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
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const $io4 = (input3) => (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
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value: input3.svOptions
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}), void 0 === input3.maxGenesToShow || "number" === typeof input3.maxGenesToShow || $report(_exceptionable2, {
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value: input3.hyperMutator
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}), void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize || $report(_exceptionable2, {
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}), void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize || $report(_exceptionable2, {
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}), void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize || $report(_exceptionable2, {
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value: input3.fivePrimeFlankSize
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}), void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize || $report(_exceptionable2, {
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})].every((flag) => flag);
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})].every((flag) => flag);
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const $vo4 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize || $report(_exceptionable2, {
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}), void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize || $report(_exceptionable2, {
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}).every((flag) => flag)].every((flag) => flag);
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|
|
@@ -159,7 +189,7 @@ var validGRIN2Response = (input) => {
|
|
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|
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|
|
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|
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|
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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));
|
|
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|
+
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);
|
|
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|
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",
|
|
@@ -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 && "number" === typeof input3.cpm_cutoff && ("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)) {
|
|
@@ -56,7 +56,11 @@ var validDERequest = (input) => {
|
|
|
56
56
|
path: _path2 + ".method",
|
|
57
57
|
expected: "(string | undefined)",
|
|
58
58
|
value: input3.method
|
|
59
|
-
}), true, true
|
|
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);
|
|
60
64
|
return ("object" === typeof input2 && null !== input2 || $report(true, {
|
|
61
65
|
path: _path + "",
|
|
62
66
|
expected: "DERequest",
|
package/dist/grin2.js
CHANGED
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,
|
|
@@ -23,6 +33,16 @@ import {
|
|
|
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
|
-
|
|
58
|
-
|
|
59
|
-
|
|
60
|
-
} from "./chunk-
|
|
77
|
+
termdbCohortsPayload,
|
|
78
|
+
validTermdbCohortsRequest,
|
|
79
|
+
validTermdbCohortsResponse
|
|
80
|
+
} from "./chunk-FMC4G5BP.js";
|
|
61
81
|
import {
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
|
|
65
|
-
} from "./chunk-
|
|
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
|
-
|
|
98
|
-
|
|
99
|
-
|
|
100
|
-
} from "./chunk-
|
|
117
|
+
saveWSIAnnotationPayload,
|
|
118
|
+
validSaveWSIAnnotationRequest,
|
|
119
|
+
validSaveWSIAnnotationResponse
|
|
120
|
+
} from "./chunk-KVE2NBC6.js";
|
|
101
121
|
import {
|
|
102
|
-
|
|
103
|
-
|
|
104
|
-
|
|
105
|
-
} from "./chunk-
|
|
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-
|
|
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
|
-
|
|
138
|
-
|
|
139
|
-
|
|
140
|
-
} from "./chunk-
|
|
157
|
+
hicGenomePayload,
|
|
158
|
+
validHicGenomeRequest,
|
|
159
|
+
validHicGenomeResponse
|
|
160
|
+
} from "./chunk-62XTWOVJ.js";
|
|
141
161
|
import {
|
|
142
|
-
|
|
143
|
-
|
|
144
|
-
|
|
145
|
-
} from "./chunk-
|
|
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
|
-
|
|
173
|
-
|
|
174
|
-
|
|
175
|
-
} from "./chunk-
|
|
192
|
+
gdcMafPayload,
|
|
193
|
+
validGdcMafRequest,
|
|
194
|
+
validGdcMafResponse
|
|
195
|
+
} from "./chunk-MIOIOFBZ.js";
|
|
176
196
|
import {
|
|
177
|
-
|
|
178
|
-
|
|
179
|
-
|
|
180
|
-
} from "./chunk-
|
|
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-
|
|
220
|
+
} from "./chunk-HI2IT25E.js";
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healthcheckPayload,
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validHealthCheckRequest,
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validHicdataResponse
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validClearWSImagesSessionsRequest,
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validClearWSImagesSessionsResponse
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} from "./chunk-BCBSHTHS.js";
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validHicstatResponse
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clearWSImagesSessionsPayload
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} from "./chunk-RPX4TVMD.js";
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import {
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CorrelationVolcanoPayload,
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@@ -251,16 +268,6 @@ import {
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validRunGRIN2Request,
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validRunGRIN2Response
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gdcMafPayload,
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validGdcMafRequest,
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validGdcMafResponse
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GdcMafPayload,
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validGdcMafBuildRequest,
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validGdcMafBuildResponse
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} from "./chunk-2BCLGYAG.js";
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import {
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aiProjectAdminPayload,
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validAIProjectAdminRequest,
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@@ -276,6 +283,16 @@ import {
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validAIProjectTrainModelRequest,
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validAIProjectTrainModelResponse
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import {
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alphaGenomePayload,
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validalphaGenomeRequest,
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validalphaGenomeResponse
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+
} from "./chunk-4EAGOSMN.js";
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import {
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alphaGenomeTypesPayload,
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validalphaGenomeTypesRequest,
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validalphaGenomeTypesResponse
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+
} from "./chunk-5H2LJKPX.js";
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import {
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brainImagingPayload,
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validBrainImagingRequest,
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@@ -291,13 +308,6 @@ import {
|
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validBurdenRequest,
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validBurdenResponse
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|
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|
-
import {
|
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|
-
validClearWSImagesSessionsRequest,
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validClearWSImagesSessionsResponse
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-
} from "./chunk-BCBSHTHS.js";
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|
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import {
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|
-
clearWSImagesSessionsPayload
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|
-
} from "./chunk-RPX4TVMD.js";
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|
import "./chunk-YNHC5SXO.js";
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|
export {
|
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ChatPayload,
|
|
@@ -310,6 +320,8 @@ export {
|
|
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|
aiProjectAdminPayload,
|
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311
321
|
aiProjectSelectedWSImagesResponsePayload,
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|
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322
|
aiProjectTrainModelPayload,
|
|
323
|
+
alphaGenomePayload,
|
|
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|
+
alphaGenomeTypesPayload,
|
|
313
325
|
boxplotPayload,
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|
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
package/package.json
CHANGED
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
|
-
|
|
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
|
|
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
|
-
|
|
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,
|
|
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 */
|
|
@@ -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
|
+
}
|
|
@@ -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
|
-
/**
|
|
62
|
-
|
|
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