@sjcrh/proteinpaint-types 2.131.0 → 2.132.0

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Files changed (6) hide show
  1. package/dist/{chunk-5VCMJ7QL.js → chunk-45AF7AQH.js} +118 -74
  2. package/dist/gdc.grin2.js +1 -1
  3. package/dist/index.js +1 -1
  4. package/package.json +1 -1
  5. package/src/dataset.ts +7 -0
  6. package/src/routes/gdc.grin2.ts +41 -32
package/dist/{chunk-5VCMJ7QL.js → chunk-45AF7AQH.js} RENAMED
@@ -28,8 +28,9 @@ var runGRIN2Payload = {
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  var validGdcGRIN2listRequest = (input) => {
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  const errors = [];
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  const __is = (input2) => {
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- const $io0 = (input3) => (void 0 === input3.mafOptions || "object" === typeof input3.mafOptions && null !== input3.mafOptions && $io1(input3.mafOptions)) && true && true;
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+ const $io0 = (input3) => (void 0 === input3.mafOptions || "object" === typeof input3.mafOptions && null !== input3.mafOptions && $io1(input3.mafOptions)) && (void 0 === input3.cnvOptions || "object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) && $io2(input3.cnvOptions)) && true;
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  const $io1 = (input3) => "WXS" === input3.experimentalStrategy;
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+ const $io2 = (input3) => void 0 === input3.dataType || "string" === typeof input3.dataType;
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  return "object" === typeof input2 && null !== input2 && false === Array.isArray(input2) && $io0(input2);
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  };
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  if (false === __is(input)) {
@@ -43,12 +44,25 @@ var validGdcGRIN2listRequest = (input) => {
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  path: _path2 + ".mafOptions",
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  expected: "(__type | undefined)",
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  value: input3.mafOptions
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- }), true, true].every((flag) => flag);
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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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+ }), true].every((flag) => flag);
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  const $vo1 = (input3, _path2, _exceptionable2 = true) => ["WXS" === input3.experimentalStrategy || $report(_exceptionable2, {
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  path: _path2 + ".experimentalStrategy",
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  expected: '"WXS"',
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  value: input3.experimentalStrategy
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  })].every((flag) => flag);
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+ const $vo2 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.dataType || "string" === typeof input3.dataType || $report(_exceptionable2, {
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+ path: _path2 + ".dataType",
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+ expected: "(string | undefined)",
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+ value: input3.dataType
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+ })].every((flag) => flag);
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  return ("object" === typeof input2 && null !== input2 && false === Array.isArray(input2) || $report(true, {
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  path: _path + "",
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  expected: "GdcGRIN2listRequest",
@@ -70,21 +84,38 @@ var validGdcGRIN2listRequest = (input) => {
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  var validGdcGRIN2listResponse = (input) => {
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  const errors = [];
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  const __is = (input2) => {
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- const $io0 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)) && "number" === typeof input3.filesTotal && "number" === typeof input3.maxTotalSizeCompressed && (void 0 === input3.fileCounts || "object" === typeof input3.fileCounts && null !== input3.fileCounts && $io2(input3.fileCounts)) && (void 0 === input3.appliedFilters || "object" === typeof input3.appliedFilters && null !== input3.appliedFilters && false === Array.isArray(input3.appliedFilters) && $io3(input3.appliedFilters)) && (void 0 === input3.deduplicationStats || "object" === typeof input3.deduplicationStats && null !== input3.deduplicationStats && $io4(input3.deduplicationStats)) && (void 0 === input3.mafFiles || "object" === typeof input3.mafFiles && null !== input3.mafFiles && $io7(input3.mafFiles)) && (void 0 === input3.cnvFiles || "object" === typeof input3.cnvFiles && null !== input3.cnvFiles && $io8(input3.cnvFiles));
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- const $io1 = (input3) => "string" === typeof input3.id && "string" === typeof input3.case_submitter_id && "string" === typeof input3.case_uuid && "number" === typeof input3.file_size && (Array.isArray(input3.sample_types) && input3.sample_types.every((elem) => "string" === typeof elem)) && "string" === typeof input3.project_id && (void 0 === input3.file_format || "MAF" === input3.file_format);
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- const $io2 = (input3) => "number" === typeof input3.maf;
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- const $io3 = (input3) => void 0 === input3.experimentalStrategy || "WXS" === input3.experimentalStrategy;
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- const $io4 = (input3) => "number" === typeof input3.originalFileCount && "number" === typeof input3.deduplicatedFileCount && "number" === typeof input3.duplicatesRemoved && (void 0 === input3.caseDetails || Array.isArray(input3.caseDetails) && input3.caseDetails.every((elem) => "object" === typeof elem && null !== elem && $io5(elem))) && (Array.isArray(input3.filteredFiles) && input3.filteredFiles.every((elem) => "object" === typeof elem && null !== elem && $io6(elem)));
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- const $io5 = (input3) => "string" === typeof input3.caseName && "number" === typeof input3.fileCount && "number" === typeof input3.keptFileSize;
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- const $io6 = (input3) => "string" === typeof input3.fileId && "number" === typeof input3.fileSize && "string" === typeof input3.reason;
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- const $io7 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io1(elem));
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- const $io8 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io1(elem));
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- return "object" === typeof input2 && null !== input2 && $io0(input2);
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+ const $io0 = (input3) => (void 0 === input3.mafFiles || "object" === typeof input3.mafFiles && null !== input3.mafFiles && $io1(input3.mafFiles)) && (void 0 === input3.cnvFiles || "object" === typeof input3.cnvFiles && null !== input3.cnvFiles && $io8(input3.cnvFiles));
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+ const $io1 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && "number" === typeof input3.filesTotal && "number" === typeof input3.maxTotalSizeCompressed && (void 0 === input3.fileCounts || "object" === typeof input3.fileCounts && null !== input3.fileCounts && $io3(input3.fileCounts)) && (void 0 === input3.appliedFilters || "object" === typeof input3.appliedFilters && null !== input3.appliedFilters && false === Array.isArray(input3.appliedFilters) && $io4(input3.appliedFilters)) && (void 0 === input3.deduplicationStats || "object" === typeof input3.deduplicationStats && null !== input3.deduplicationStats && $io5(input3.deduplicationStats));
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+ const $io2 = (input3) => "string" === typeof input3.id && "string" === typeof input3.case_submitter_id && "string" === typeof input3.case_uuid && "number" === typeof input3.file_size && (Array.isArray(input3.sample_types) && input3.sample_types.every((elem) => "string" === typeof elem)) && "string" === typeof input3.project_id && (void 0 === input3.file_format || "MAF" === input3.file_format);
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+ const $io3 = (input3) => "number" === typeof input3.maf;
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+ const $io4 = (input3) => void 0 === input3.experimentalStrategy || "WXS" === input3.experimentalStrategy;
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+ const $io5 = (input3) => "number" === typeof input3.originalFileCount && "number" === typeof input3.deduplicatedFileCount && "number" === typeof input3.duplicatesRemoved && (void 0 === input3.caseDetails || Array.isArray(input3.caseDetails) && input3.caseDetails.every((elem) => "object" === typeof elem && null !== elem && $io6(elem))) && (Array.isArray(input3.filteredFiles) && input3.filteredFiles.every((elem) => "object" === typeof elem && null !== elem && $io7(elem)));
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+ const $io6 = (input3) => "string" === typeof input3.caseName && "number" === typeof input3.fileCount && "number" === typeof input3.keptFileSize;
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+ const $io7 = (input3) => "string" === typeof input3.fileId && "number" === typeof input3.fileSize && "string" === typeof input3.reason;
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+ const $io8 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && "number" === typeof input3.maxTotalSizeCompressed;
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+ return "object" === typeof input2 && null !== input2 && false === Array.isArray(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.files) || $report(_exceptionable2, {
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+ const $vo0 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.mafFiles || ("object" === typeof input3.mafFiles && null !== input3.mafFiles || $report(_exceptionable2, {
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+ path: _path2 + ".mafFiles",
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+ expected: "(__type | undefined)",
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+ value: input3.mafFiles
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+ })) && $vo1(input3.mafFiles, _path2 + ".mafFiles", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".mafFiles",
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+ expected: "(__type | undefined)",
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+ value: input3.mafFiles
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+ }), void 0 === input3.cnvFiles || ("object" === typeof input3.cnvFiles && null !== input3.cnvFiles || $report(_exceptionable2, {
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+ path: _path2 + ".cnvFiles",
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+ expected: "(__type.o6 | undefined)",
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+ value: input3.cnvFiles
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+ })) && $vo8(input3.cnvFiles, _path2 + ".cnvFiles", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".cnvFiles",
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+ expected: "(__type.o6 | undefined)",
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+ value: input3.cnvFiles
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+ })].every((flag) => flag);
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+ const $vo1 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
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  path: _path2 + ".files",
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  expected: "Array<GdcGRIN2File>",
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  value: input3.files
@@ -92,7 +123,7 @@ var validGdcGRIN2listResponse = (input) => {
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  path: _path2 + ".files[" + _index1 + "]",
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  expected: "GdcGRIN2File",
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  value: elem
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- })) && $vo1(elem, _path2 + ".files[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
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+ })) && $vo2(elem, _path2 + ".files[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
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  path: _path2 + ".files[" + _index1 + "]",
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  expected: "GdcGRIN2File",
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  value: elem
@@ -110,46 +141,30 @@ var validGdcGRIN2listResponse = (input) => {
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  value: input3.maxTotalSizeCompressed
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  }), void 0 === input3.fileCounts || ("object" === typeof input3.fileCounts && null !== input3.fileCounts || $report(_exceptionable2, {
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  path: _path2 + ".fileCounts",
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- expected: "(__type | undefined)",
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+ expected: "(__type.o1 | undefined)",
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  value: input3.fileCounts
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- })) && $vo2(input3.fileCounts, _path2 + ".fileCounts", _exceptionable2) || $report(_exceptionable2, {
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+ })) && $vo3(input3.fileCounts, _path2 + ".fileCounts", _exceptionable2) || $report(_exceptionable2, {
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  path: _path2 + ".fileCounts",
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- expected: "(__type | undefined)",
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+ expected: "(__type.o1 | undefined)",
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  value: input3.fileCounts
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  }), void 0 === input3.appliedFilters || ("object" === typeof input3.appliedFilters && null !== input3.appliedFilters && false === Array.isArray(input3.appliedFilters) || $report(_exceptionable2, {
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  path: _path2 + ".appliedFilters",
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- expected: "(__type.o1 | undefined)",
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+ expected: "(__type.o2 | undefined)",
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  value: input3.appliedFilters
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- })) && $vo3(input3.appliedFilters, _path2 + ".appliedFilters", _exceptionable2) || $report(_exceptionable2, {
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+ })) && $vo4(input3.appliedFilters, _path2 + ".appliedFilters", _exceptionable2) || $report(_exceptionable2, {
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  path: _path2 + ".appliedFilters",
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- expected: "(__type.o1 | undefined)",
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+ expected: "(__type.o2 | undefined)",
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  value: input3.appliedFilters
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  }), void 0 === input3.deduplicationStats || ("object" === typeof input3.deduplicationStats && null !== input3.deduplicationStats || $report(_exceptionable2, {
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  path: _path2 + ".deduplicationStats",
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- expected: "(__type.o2 | undefined)",
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+ expected: "(__type.o3 | undefined)",
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  value: input3.deduplicationStats
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- })) && $vo4(input3.deduplicationStats, _path2 + ".deduplicationStats", _exceptionable2) || $report(_exceptionable2, {
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+ })) && $vo5(input3.deduplicationStats, _path2 + ".deduplicationStats", _exceptionable2) || $report(_exceptionable2, {
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  path: _path2 + ".deduplicationStats",
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- expected: "(__type.o2 | undefined)",
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+ expected: "(__type.o3 | undefined)",
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  value: input3.deduplicationStats
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- }), void 0 === input3.mafFiles || ("object" === typeof input3.mafFiles && null !== input3.mafFiles || $report(_exceptionable2, {
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- path: _path2 + ".mafFiles",
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- expected: "(__type.o5 | undefined)",
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- value: input3.mafFiles
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- })) && $vo7(input3.mafFiles, _path2 + ".mafFiles", _exceptionable2) || $report(_exceptionable2, {
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- path: _path2 + ".mafFiles",
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- expected: "(__type.o5 | undefined)",
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- value: input3.mafFiles
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- }), void 0 === input3.cnvFiles || ("object" === typeof input3.cnvFiles && null !== input3.cnvFiles || $report(_exceptionable2, {
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- path: _path2 + ".cnvFiles",
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- expected: "(__type.o6 | undefined)",
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- value: input3.cnvFiles
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- })) && $vo8(input3.cnvFiles, _path2 + ".cnvFiles", _exceptionable2) || $report(_exceptionable2, {
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- path: _path2 + ".cnvFiles",
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- expected: "(__type.o6 | undefined)",
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- value: input3.cnvFiles
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  })].every((flag) => flag);
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- const $vo1 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.id || $report(_exceptionable2, {
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+ const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.id || $report(_exceptionable2, {
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  path: _path2 + ".id",
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  expected: "string",
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  value: input3.id
@@ -186,17 +201,17 @@ var validGdcGRIN2listResponse = (input) => {
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  expected: '("MAF" | undefined)',
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  value: input3.file_format
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  })].every((flag) => flag);
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- const $vo2 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.maf || $report(_exceptionable2, {
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+ const $vo3 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.maf || $report(_exceptionable2, {
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  path: _path2 + ".maf",
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  expected: "number",
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  value: input3.maf
193
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  })].every((flag) => flag);
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- const $vo3 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.experimentalStrategy || "WXS" === input3.experimentalStrategy || $report(_exceptionable2, {
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+ const $vo4 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.experimentalStrategy || "WXS" === input3.experimentalStrategy || $report(_exceptionable2, {
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  path: _path2 + ".experimentalStrategy",
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  expected: '("WXS" | undefined)',
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  value: input3.experimentalStrategy
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  })].every((flag) => flag);
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- const $vo4 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.originalFileCount || $report(_exceptionable2, {
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+ const $vo5 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.originalFileCount || $report(_exceptionable2, {
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  path: _path2 + ".originalFileCount",
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  expected: "number",
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  value: input3.originalFileCount
@@ -214,11 +229,11 @@ var validGdcGRIN2listResponse = (input) => {
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  value: input3.caseDetails
215
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  })) && input3.caseDetails.map((elem, _index3) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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  path: _path2 + ".caseDetails[" + _index3 + "]",
217
- expected: "__type.o3",
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+ expected: "__type.o4",
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  value: elem
219
- })) && $vo5(elem, _path2 + ".caseDetails[" + _index3 + "]", _exceptionable2) || $report(_exceptionable2, {
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+ })) && $vo6(elem, _path2 + ".caseDetails[" + _index3 + "]", _exceptionable2) || $report(_exceptionable2, {
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  path: _path2 + ".caseDetails[" + _index3 + "]",
221
- expected: "__type.o3",
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+ expected: "__type.o4",
222
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  value: elem
223
238
  })).every((flag) => flag) || $report(_exceptionable2, {
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  path: _path2 + ".caseDetails",
@@ -230,18 +245,18 @@ var validGdcGRIN2listResponse = (input) => {
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  value: input3.filteredFiles
231
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  })) && input3.filteredFiles.map((elem, _index4) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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  path: _path2 + ".filteredFiles[" + _index4 + "]",
233
- expected: "__type.o4",
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+ expected: "__type.o5",
234
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  value: elem
235
- })) && $vo6(elem, _path2 + ".filteredFiles[" + _index4 + "]", _exceptionable2) || $report(_exceptionable2, {
250
+ })) && $vo7(elem, _path2 + ".filteredFiles[" + _index4 + "]", _exceptionable2) || $report(_exceptionable2, {
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  path: _path2 + ".filteredFiles[" + _index4 + "]",
237
- expected: "__type.o4",
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+ expected: "__type.o5",
238
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  value: elem
239
254
  })).every((flag) => flag) || $report(_exceptionable2, {
240
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  path: _path2 + ".filteredFiles",
241
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  expected: "Array<__type>.o1",
242
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  value: input3.filteredFiles
243
258
  })].every((flag) => flag);
244
- const $vo5 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.caseName || $report(_exceptionable2, {
259
+ const $vo6 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.caseName || $report(_exceptionable2, {
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  path: _path2 + ".caseName",
246
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  expected: "string",
247
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  value: input3.caseName
@@ -254,7 +269,7 @@ var validGdcGRIN2listResponse = (input) => {
254
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  expected: "number",
255
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  value: input3.keptFileSize
256
271
  })].every((flag) => flag);
257
- const $vo6 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.fileId || $report(_exceptionable2, {
272
+ const $vo7 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.fileId || $report(_exceptionable2, {
258
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  path: _path2 + ".fileId",
259
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  expected: "string",
260
275
  value: input3.fileId
@@ -267,7 +282,7 @@ var validGdcGRIN2listResponse = (input) => {
267
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  expected: "string",
268
283
  value: input3.reason
269
284
  })].every((flag) => flag);
270
- const $vo7 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
285
+ const $vo8 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
271
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  path: _path2 + ".files",
272
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  expected: "Array<GdcGRIN2File>",
273
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  value: input3.files
@@ -275,7 +290,7 @@ var validGdcGRIN2listResponse = (input) => {
275
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  path: _path2 + ".files[" + _index5 + "]",
276
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  expected: "GdcGRIN2File",
277
292
  value: elem
278
- })) && $vo1(elem, _path2 + ".files[" + _index5 + "]", _exceptionable2) || $report(_exceptionable2, {
293
+ })) && $vo2(elem, _path2 + ".files[" + _index5 + "]", _exceptionable2) || $report(_exceptionable2, {
279
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  path: _path2 + ".files[" + _index5 + "]",
280
295
  expected: "GdcGRIN2File",
281
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  value: elem
@@ -283,25 +298,12 @@ var validGdcGRIN2listResponse = (input) => {
283
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  path: _path2 + ".files",
284
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  expected: "Array<GdcGRIN2File>",
285
300
  value: input3.files
301
+ }), "number" === typeof input3.maxTotalSizeCompressed || $report(_exceptionable2, {
302
+ path: _path2 + ".maxTotalSizeCompressed",
303
+ expected: "number",
304
+ value: input3.maxTotalSizeCompressed
286
305
  })].every((flag) => flag);
287
- const $vo8 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
288
- path: _path2 + ".files",
289
- expected: "Array<GdcGRIN2File>",
290
- value: input3.files
291
- })) && input3.files.map((elem, _index6) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
292
- path: _path2 + ".files[" + _index6 + "]",
293
- expected: "GdcGRIN2File",
294
- value: elem
295
- })) && $vo1(elem, _path2 + ".files[" + _index6 + "]", _exceptionable2) || $report(_exceptionable2, {
296
- path: _path2 + ".files[" + _index6 + "]",
297
- expected: "GdcGRIN2File",
298
- value: elem
299
- })).every((flag) => flag) || $report(_exceptionable2, {
300
- path: _path2 + ".files",
301
- expected: "Array<GdcGRIN2File>",
302
- value: input3.files
303
- })].every((flag) => flag);
304
- return ("object" === typeof input2 && null !== input2 || $report(true, {
306
+ return ("object" === typeof input2 && null !== input2 && false === Array.isArray(input2) || $report(true, {
305
307
  path: _path + "",
306
308
  expected: "GdcGRIN2listResponse",
307
309
  value: input2
@@ -323,7 +325,7 @@ var validRunGRIN2Request = (input) => {
323
325
  const errors = [];
324
326
  const __is = (input2) => {
325
327
  const $join = import_typia.createValidate.join;
326
- const $io0 = (input3) => "object" === typeof input3.caseFiles && null !== input3.caseFiles && false === Array.isArray(input3.caseFiles) && $io1(input3.caseFiles) && (void 0 === input3.mafOptions || "object" === typeof input3.mafOptions && null !== input3.mafOptions && false === Array.isArray(input3.mafOptions) && $io3(input3.mafOptions));
328
+ const $io0 = (input3) => "object" === typeof input3.caseFiles && null !== input3.caseFiles && false === Array.isArray(input3.caseFiles) && $io1(input3.caseFiles) && (void 0 === input3.mafOptions || "object" === typeof input3.mafOptions && null !== input3.mafOptions && false === Array.isArray(input3.mafOptions) && $io3(input3.mafOptions)) && (void 0 === input3.cnvOptions || "object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) && $io4(input3.cnvOptions));
327
329
  const $io1 = (input3) => Object.keys(input3).every((key) => {
328
330
  const value = input3[key];
329
331
  if (void 0 === value)
@@ -332,8 +334,9 @@ var validRunGRIN2Request = (input) => {
332
334
  return "object" === typeof value && null !== value && false === Array.isArray(value) && $io2(value);
333
335
  return true;
334
336
  });
335
- const $io2 = (input3) => void 0 === input3.maf || "string" === typeof input3.maf;
336
- const $io3 = (input3) => (void 0 === input3.minTotalDepth || "number" === typeof input3.minTotalDepth) && (void 0 === input3.minAltAlleleCount || "number" === typeof input3.minAltAlleleCount);
337
+ const $io2 = (input3) => (void 0 === input3.maf || "string" === typeof input3.maf) && (void 0 === input3.cnv || "string" === typeof input3.cnv);
338
+ const $io3 = (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);
339
+ const $io4 = (input3) => (void 0 === input3.lossThreshold || "number" === typeof input3.lossThreshold) && (void 0 === input3.gainThreshold || "number" === typeof input3.gainThreshold) && (void 0 === input3.segLength || "number" === typeof input3.segLength);
337
340
  return "object" === typeof input2 && null !== input2 && $io0(input2);
338
341
  };
339
342
  if (false === __is(input)) {
@@ -356,6 +359,14 @@ var validRunGRIN2Request = (input) => {
356
359
  path: _path2 + ".mafOptions",
357
360
  expected: "(__type.o2 | undefined)",
358
361
  value: input3.mafOptions
362
+ }), void 0 === input3.cnvOptions || ("object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) || $report(_exceptionable2, {
363
+ path: _path2 + ".cnvOptions",
364
+ expected: "(__type.o3 | undefined)",
365
+ value: input3.cnvOptions
366
+ })) && $vo4(input3.cnvOptions, _path2 + ".cnvOptions", _exceptionable2) || $report(_exceptionable2, {
367
+ path: _path2 + ".cnvOptions",
368
+ expected: "(__type.o3 | undefined)",
369
+ value: input3.cnvOptions
359
370
  })].every((flag) => flag);
360
371
  const $vo1 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
361
372
  const value = input3[key];
@@ -377,6 +388,10 @@ var validRunGRIN2Request = (input) => {
377
388
  path: _path2 + ".maf",
378
389
  expected: "(string | undefined)",
379
390
  value: input3.maf
391
+ }), void 0 === input3.cnv || "string" === typeof input3.cnv || $report(_exceptionable2, {
392
+ path: _path2 + ".cnv",
393
+ expected: "(string | undefined)",
394
+ value: input3.cnv
380
395
  })].every((flag) => flag);
381
396
  const $vo3 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.minTotalDepth || "number" === typeof input3.minTotalDepth || $report(_exceptionable2, {
382
397
  path: _path2 + ".minTotalDepth",
@@ -386,6 +401,35 @@ var validRunGRIN2Request = (input) => {
386
401
  path: _path2 + ".minAltAlleleCount",
387
402
  expected: "(number | undefined)",
388
403
  value: input3.minAltAlleleCount
404
+ }), void 0 === input3.consequences || (Array.isArray(input3.consequences) || $report(_exceptionable2, {
405
+ path: _path2 + ".consequences",
406
+ expected: "(Array<string> | undefined)",
407
+ value: input3.consequences
408
+ })) && input3.consequences.map((elem, _index1) => "string" === typeof elem || $report(_exceptionable2, {
409
+ path: _path2 + ".consequences[" + _index1 + "]",
410
+ expected: "string",
411
+ value: elem
412
+ })).every((flag) => flag) || $report(_exceptionable2, {
413
+ path: _path2 + ".consequences",
414
+ expected: "(Array<string> | undefined)",
415
+ value: input3.consequences
416
+ }), void 0 === input3.hyperMutator || "number" === typeof input3.hyperMutator || $report(_exceptionable2, {
417
+ path: _path2 + ".hyperMutator",
418
+ expected: "(number | undefined)",
419
+ value: input3.hyperMutator
420
+ })].every((flag) => flag);
421
+ const $vo4 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.lossThreshold || "number" === typeof input3.lossThreshold || $report(_exceptionable2, {
422
+ path: _path2 + ".lossThreshold",
423
+ expected: "(number | undefined)",
424
+ value: input3.lossThreshold
425
+ }), void 0 === input3.gainThreshold || "number" === typeof input3.gainThreshold || $report(_exceptionable2, {
426
+ path: _path2 + ".gainThreshold",
427
+ expected: "(number | undefined)",
428
+ value: input3.gainThreshold
429
+ }), void 0 === input3.segLength || "number" === typeof input3.segLength || $report(_exceptionable2, {
430
+ path: _path2 + ".segLength",
431
+ expected: "(number | undefined)",
432
+ value: input3.segLength
389
433
  })].every((flag) => flag);
390
434
  return ("object" === typeof input2 && null !== input2 || $report(true, {
391
435
  path: _path + "",
package/dist/gdc.grin2.js CHANGED
@@ -5,7 +5,7 @@ import {
5
5
  validGdcGRIN2listResponse,
6
6
  validRunGRIN2Request,
7
7
  validRunGRIN2Response
8
- } from "./chunk-5VCMJ7QL.js";
8
+ } from "./chunk-45AF7AQH.js";
9
9
  import "./chunk-CNSSF43V.js";
10
10
  export {
11
11
  gdcGRIN2listPayload,
package/dist/index.js CHANGED
@@ -175,7 +175,7 @@ import {
175
175
  validGdcGRIN2listResponse,
176
176
  validRunGRIN2Request,
177
177
  validRunGRIN2Response
178
- } from "./chunk-5VCMJ7QL.js";
178
+ } from "./chunk-45AF7AQH.js";
179
179
  import {
180
180
  gdcMafPayload,
181
181
  validGdcMafRequest,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@sjcrh/proteinpaint-types",
3
- "version": "2.131.0",
3
+ "version": "2.132.0",
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
@@ -1508,6 +1508,13 @@ type DtAssayAvailability = DtAssayAvailabilityGetter | DtAssayAvailabilityTerm
1508
1508
 
1509
1509
  /** using ds-supplied getter */
1510
1510
  type DtAssayAvailabilityGetter = {
1511
+ /** define q
1512
+ returns:
1513
+ {
1514
+ yesSamples: Set() of sample ids
1515
+ noSamples: Set() of sample ids
1516
+ }
1517
+ */
1511
1518
  get: (q: any) => any
1512
1519
  }
1513
1520
  /** using dictionary term */
package/src/routes/gdc.grin2.ts CHANGED
@@ -37,8 +37,11 @@ export type GdcGRIN2listRequest = {
37
37
  experimentalStrategy: ExperimentalStrategy
38
38
  }
39
39
 
40
- /** Options for CNV file retrieval. Presence indicates CNV files should be returned (for future use) */
41
- cnvOptions?: any
40
+ /** Options for CNV file retrieval. Presence indicates CNV files should be returned */
41
+ cnvOptions?: {
42
+ /** Data type for CNV analysis */
43
+ dataType?: string
44
+ }
42
45
 
43
46
  /** Options for fusion file retrieval. Presence indicates fusion files should be returned (for future use) */
44
47
  fusionOptions?: any
@@ -48,39 +51,38 @@ export type GdcGRIN2listRequest = {
48
51
  * Response for GRIN2 file listing
49
52
  */
50
53
  export type GdcGRIN2listResponse = {
51
- /** List of file objects passing filter and to be displayed on client */
52
- files: GdcGRIN2File[]
53
- /** Total number of files found by API (in case bigger than files.length) */
54
- filesTotal: number
55
- /** Maximum total size of files allowed, for indicating on UI while selecting files */
56
- maxTotalSizeCompressed: number
57
- /** File counts by type */
58
- fileCounts?: {
59
- maf: number
60
- }
61
- /** Applied filters (for UI reference) */
62
- appliedFilters?: {
63
- experimentalStrategy?: ExperimentalStrategy
64
- }
65
- /** Deduplication stats */
66
- deduplicationStats?: {
67
- originalFileCount: number
68
- deduplicatedFileCount: number
69
- duplicatesRemoved: number
70
- caseDetails?: Array<{ caseName: string; fileCount: number; keptFileSize: number }>
71
- filteredFiles: Array<{ fileId: string; fileSize: number; reason: string }>
72
- }
73
54
  /** all maf-related results when mafOptions is supplied */
74
55
  mafFiles?: {
75
56
  // TODO suggest to move above maf-related results under mafFiles{}
76
57
  /** list of maf files returned to client */
77
58
  files: GdcGRIN2File[]
59
+ /** Total number of files found by API (in case bigger than files.length) */
60
+ filesTotal: number
61
+ /** Maximum total size of files allowed, for indicating on UI while selecting files */
62
+ maxTotalSizeCompressed: number
63
+ /** File counts by type */
64
+ fileCounts?: {
65
+ maf: number
66
+ }
67
+ /** Applied filters (for UI reference) */
68
+ appliedFilters?: {
69
+ experimentalStrategy?: ExperimentalStrategy
70
+ }
71
+ /** Deduplication stats */
72
+ deduplicationStats?: {
73
+ originalFileCount: number
74
+ deduplicatedFileCount: number
75
+ duplicatesRemoved: number
76
+ caseDetails?: Array<{ caseName: string; fileCount: number; keptFileSize: number }>
77
+ filteredFiles: Array<{ fileId: string; fileSize: number; reason: string }>
78
+ }
78
79
  }
79
80
  /** all cnv-related results when cnvOptions is supplied */
80
81
  cnvFiles?: {
81
82
  /** list of cnv files returned to client */
82
83
  files: GdcGRIN2File[]
83
- /** to add additional stats on cnv file listing */
84
+ /** Maximum total size of files allowed, for indicating on UI while selecting files */
85
+ maxTotalSizeCompressed: number
84
86
  }
85
87
  }
86
88
 
@@ -93,6 +95,7 @@ export type RunGRIN2Request = {
93
95
  caseFiles: {
94
96
  [caseId: string]: {
95
97
  maf?: string
98
+ cnv?: string
96
99
  }
97
100
  }
98
101
  /** Options for filtering MAF file content */
@@ -101,14 +104,20 @@ export type RunGRIN2Request = {
101
104
  minTotalDepth?: number // Default: 10
102
105
  /** Minimum alternate allele count of returned MAF files */
103
106
  minAltAlleleCount?: number // Default: 2
107
+ /** String array of consequence types */
108
+ consequences?: string[]
109
+ /** Maximum mutation count cutoff for highly mutated scenarios */
110
+ hyperMutator?: number
111
+ }
112
+ /** Options for filtering CNV file content*/
113
+ cnvOptions?: {
114
+ /** Threshold for copy number loss detection */
115
+ lossThreshold?: number // Default: -0.4
116
+ /** Threshold for copy number gain detection */
117
+ gainThreshold?: number // Default: 0.3
118
+ /** Maximum segment length to include (0 = no filter) */
119
+ segLength?: number // Default: 0
104
120
  }
105
- /** Options for CNV file retrieval (will be added later)
106
- cnvOptions?: {
107
- * lossThreshold?: number // Default: -0.5
108
- * gainThreshold?: number // Default: 0.5
109
- * segLength?: number // Default: 2000000
110
- *}
111
- */
112
121
  }
113
122
 
114
123
  /** Error entry from failed file downloads */