@sjcrh/proteinpaint-types 2.135.2-0 → 2.136.0

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Files changed (6) hide show
  1. package/dist/{chunk-ZAMCS7PC.js → chunk-K5POIB3P.js} +71 -43
  2. package/dist/index.js +1 -1
  3. package/dist/termdb.singlecellData.js +1 -1
  4. package/package.json +1 -1
  5. package/src/dataset.ts +12 -10
  6. package/src/routes/termdb.singlecellData.ts +10 -8
package/dist/{chunk-ZAMCS7PC.js → chunk-K5POIB3P.js} RENAMED
@@ -21,13 +21,31 @@ var termdbSingleCellDataPayload = {
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  var validTermdbSingleCellDataRequest = (input) => {
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  const errors = [];
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  const __is = (input2) => {
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- const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && ("object" === typeof input3.sample && null !== input3.sample && $io1(input3.sample)) && (Array.isArray(input3.plots) && input3.plots.every((elem) => "string" === typeof elem)) && (void 0 === input3.gene || "string" === typeof input3.gene);
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+ const $join = import_typia.createValidate.join;
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+ const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && ("object" === typeof input3.sample && null !== input3.sample && $io1(input3.sample)) && (Array.isArray(input3.plots) && input3.plots.every((elem) => "string" === typeof elem)) && (void 0 === input3.gene || "string" === typeof input3.gene) && (void 0 === input3.colorBy || "object" === typeof input3.colorBy && null !== input3.colorBy && false === Array.isArray(input3.colorBy) && $io2(input3.colorBy)) && (void 0 === input3.colorMap || "object" === typeof input3.colorMap && null !== input3.colorMap && false === Array.isArray(input3.colorMap) && $io3(input3.colorMap));
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  const $io1 = (input3) => (void 0 === input3.eID || "string" === typeof input3.eID) && "string" === typeof input3.sID;
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+ const $io2 = (input3) => Object.keys(input3).every((key) => {
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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 "string" === typeof value;
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+ return true;
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+ });
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+ const $io3 = (input3) => Object.keys(input3).every((key) => {
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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 "string" === typeof value;
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+ return true;
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+ });
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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 $join = import_typia.createValidate.join;
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  const $vo0 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.genome || $report(_exceptionable2, {
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  path: _path2 + ".genome",
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  expected: "string",
@@ -60,6 +78,22 @@ var validTermdbSingleCellDataRequest = (input) => {
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  path: _path2 + ".gene",
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  expected: "(string | undefined)",
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  value: input3.gene
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+ }), void 0 === input3.colorBy || ("object" === typeof input3.colorBy && null !== input3.colorBy && false === Array.isArray(input3.colorBy) || $report(_exceptionable2, {
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+ path: _path2 + ".colorBy",
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+ expected: "(__type.o1 | undefined)",
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+ value: input3.colorBy
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+ })) && $vo2(input3.colorBy, _path2 + ".colorBy", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".colorBy",
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+ expected: "(__type.o1 | undefined)",
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+ value: input3.colorBy
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+ }), void 0 === input3.colorMap || ("object" === typeof input3.colorMap && null !== input3.colorMap && false === Array.isArray(input3.colorMap) || $report(_exceptionable2, {
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+ path: _path2 + ".colorMap",
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+ expected: "(__type.o2 | undefined)",
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+ value: input3.colorMap
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+ })) && $vo3(input3.colorMap, _path2 + ".colorMap", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".colorMap",
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+ expected: "(__type.o2 | undefined)",
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+ value: input3.colorMap
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  })].every((flag) => flag);
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  const $vo1 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.eID || "string" === typeof input3.eID || $report(_exceptionable2, {
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  path: _path2 + ".eID",
@@ -70,6 +104,30 @@ var validTermdbSingleCellDataRequest = (input) => {
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  expected: "string",
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  value: input3.sID
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  })].every((flag) => flag);
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+ const $vo2 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
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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 "string" === typeof value || $report(_exceptionable2, {
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+ path: _path2 + $join(key),
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+ expected: "string",
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+ value
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+ });
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+ return true;
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+ }).every((flag) => flag)].every((flag) => flag);
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+ const $vo3 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
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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 "string" === typeof value || $report(_exceptionable2, {
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+ path: _path2 + $join(key),
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+ expected: "string",
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+ value
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+ });
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+ return true;
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+ }).every((flag) => flag)].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: "TermdbSingleCellDataRequest",
@@ -91,20 +149,11 @@ var validTermdbSingleCellDataRequest = (input) => {
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  var validTermdbSingleCellDataResponse = (input) => {
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  const errors = [];
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  const __is = (input2) => {
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- const $join = import_typia.createValidate.join;
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  const $io0 = (input3) => "number" === typeof input3.status && "string" === typeof input3.error;
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  const $io1 = (input3) => "boolean" === typeof input3.nodata;
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  const $io2 = (input3) => Array.isArray(input3.plots) && input3.plots.every((elem) => "object" === typeof elem && null !== elem && $io3(elem));
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- const $io3 = (input3) => "string" === typeof input3.name && (void 0 === input3.expCells || Array.isArray(input3.expCells) && input3.expCells.every((elem) => "object" === typeof elem && null !== elem && $io4(elem))) && (void 0 === input3.noExpCells || Array.isArray(input3.noExpCells) && input3.noExpCells.every((elem) => "object" === typeof elem && null !== elem && $io4(elem))) && "string" === typeof input3.colorBy && (Array.isArray(input3.colorColumns) && input3.colorColumns.every((elem) => "string" === typeof elem)) && (void 0 === input3.colorMap || "object" === typeof input3.colorMap && null !== input3.colorMap && false === Array.isArray(input3.colorMap) && $io5(input3.colorMap));
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+ const $io3 = (input3) => "string" === typeof input3.name && (Array.isArray(input3.expCells) && input3.expCells.every((elem) => "object" === typeof elem && null !== elem && $io4(elem))) && (Array.isArray(input3.noExpCells) && input3.noExpCells.every((elem) => "object" === typeof elem && null !== elem && $io4(elem))) && (Array.isArray(input3.colorColumns) && input3.colorColumns.every((elem) => "string" === typeof elem)) && "string" === typeof input3.colorBy && true;
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  const $io4 = (input3) => "string" === typeof input3.cellId && "number" === typeof input3.x && "number" === typeof input3.y && (void 0 === input3.z || "number" === typeof input3.z) && "string" === typeof input3.category && (void 0 === input3.geneExp || "number" === typeof input3.geneExp);
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- const $io5 = (input3) => Object.keys(input3).every((key) => {
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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 "string" === typeof value;
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- return true;
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- });
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  const $iu0 = (input3) => (() => {
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  if (void 0 !== input3.status)
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  return $io0(input3);
@@ -119,7 +168,6 @@ var validTermdbSingleCellDataResponse = (input) => {
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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 $join = import_typia.createValidate.join;
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  const $vo0 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.status || $report(_exceptionable2, {
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  path: _path2 + ".status",
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  expected: "number",
@@ -155,9 +203,9 @@ var validTermdbSingleCellDataResponse = (input) => {
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  path: _path2 + ".name",
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  expected: "string",
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  value: input3.name
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- }), void 0 === input3.expCells || (Array.isArray(input3.expCells) || $report(_exceptionable2, {
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+ }), (Array.isArray(input3.expCells) || $report(_exceptionable2, {
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  path: _path2 + ".expCells",
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- expected: "(Array<Cell> | undefined)",
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+ expected: "Array<Cell>",
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  value: input3.expCells
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  })) && input3.expCells.map((elem, _index2) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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  path: _path2 + ".expCells[" + _index2 + "]",
@@ -169,11 +217,11 @@ var validTermdbSingleCellDataResponse = (input) => {
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  value: elem
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  })).every((flag) => flag) || $report(_exceptionable2, {
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  path: _path2 + ".expCells",
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- expected: "(Array<Cell> | undefined)",
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+ expected: "Array<Cell>",
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  value: input3.expCells
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- }), void 0 === input3.noExpCells || (Array.isArray(input3.noExpCells) || $report(_exceptionable2, {
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+ }), (Array.isArray(input3.noExpCells) || $report(_exceptionable2, {
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  path: _path2 + ".noExpCells",
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- expected: "(Array<Cell> | undefined)",
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+ expected: "Array<Cell>",
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  value: input3.noExpCells
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  })) && input3.noExpCells.map((elem, _index3) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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  path: _path2 + ".noExpCells[" + _index3 + "]",
@@ -185,12 +233,8 @@ var validTermdbSingleCellDataResponse = (input) => {
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  value: elem
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  })).every((flag) => flag) || $report(_exceptionable2, {
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  path: _path2 + ".noExpCells",
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- expected: "(Array<Cell> | undefined)",
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+ expected: "Array<Cell>",
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  value: input3.noExpCells
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- }), "string" === typeof input3.colorBy || $report(_exceptionable2, {
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- path: _path2 + ".colorBy",
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- expected: "string",
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- value: input3.colorBy
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  }), (Array.isArray(input3.colorColumns) || $report(_exceptionable2, {
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  path: _path2 + ".colorColumns",
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  expected: "Array<string>",
@@ -203,15 +247,11 @@ var validTermdbSingleCellDataResponse = (input) => {
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  path: _path2 + ".colorColumns",
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  expected: "Array<string>",
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  value: input3.colorColumns
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- }), void 0 === input3.colorMap || ("object" === typeof input3.colorMap && null !== input3.colorMap && false === Array.isArray(input3.colorMap) || $report(_exceptionable2, {
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- path: _path2 + ".colorMap",
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- expected: "(__type | undefined)",
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- value: input3.colorMap
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- })) && $vo5(input3.colorMap, _path2 + ".colorMap", _exceptionable2) || $report(_exceptionable2, {
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- path: _path2 + ".colorMap",
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- expected: "(__type | undefined)",
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- value: input3.colorMap
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- })].every((flag) => flag);
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+ }), "string" === typeof input3.colorBy || $report(_exceptionable2, {
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+ path: _path2 + ".colorBy",
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+ expected: "string",
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+ value: input3.colorBy
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+ }), true].every((flag) => flag);
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  const $vo4 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.cellId || $report(_exceptionable2, {
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  path: _path2 + ".cellId",
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  expected: "string",
@@ -237,18 +277,6 @@ var validTermdbSingleCellDataResponse = (input) => {
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  expected: "(number | undefined)",
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  value: input3.geneExp
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  })].every((flag) => flag);
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- const $vo5 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
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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 "string" === typeof value || $report(_exceptionable2, {
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- path: _path2 + $join(key),
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- expected: "string",
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- value
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- });
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- return true;
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- }).every((flag) => flag)].every((flag) => flag);
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  const $vu0 = (input3, _path2, _exceptionable2 = true) => (() => {
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  if (void 0 !== input3.status)
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  return $vo0(input3, _path2, _exceptionable2);
package/dist/index.js CHANGED
@@ -47,7 +47,7 @@ import {
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  termdbSingleCellDataPayload,
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  validTermdbSingleCellDataRequest,
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  validTermdbSingleCellDataResponse
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- } from "./chunk-ZAMCS7PC.js";
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+ } from "./chunk-K5POIB3P.js";
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  import {
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  termdbSingleCellSamplesPayload,
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  validTermdbSingleCellSamplesRequest,
package/dist/termdb.singlecellData.js CHANGED
@@ -2,7 +2,7 @@ import {
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  termdbSingleCellDataPayload,
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  validTermdbSingleCellDataRequest,
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  validTermdbSingleCellDataResponse
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- } from "./chunk-ZAMCS7PC.js";
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+ } from "./chunk-K5POIB3P.js";
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  import "./chunk-CNSSF43V.js";
7
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  export {
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  termdbSingleCellDataPayload,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
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  {
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  "name": "@sjcrh/proteinpaint-types",
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- "version": "2.135.2-0",
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+ "version": "2.136.0",
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  "type": "module",
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  "description": "Shared type definitions between ProteinPaint server and client code",
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  "main": "src/index.ts",
package/src/dataset.ts CHANGED
@@ -766,24 +766,26 @@ type ColorColumn = {
766
766
 
767
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  /** defines a tsne type of plot for cells from one sample */
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  type SingleCellPlot = {
769
- /** type of the plot, e.g. tsne or umap, also display as plot name on ui */
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+ /** value is display as plot name on ui and also used as identifier for a plot, must be unique */
770
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  name: string
771
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  /** folder in which per-sample files are stored.
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- each file is a tabular text file with all cells (rows) from that sample.
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- all files must have same set of columns
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- file columns include cell types and x/y coords, as described by other parameters
775
- */
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+ each file is a tabular text file with all cells (rows) from that sample.
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+ all files must have same set of columns:
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+ - 1st column is cell barcode
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+ - x/y coordinate column number is defined in coordsColumns{x,y} below
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+ - additional columns for cell annotations, corresponds to colorColumns
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+ */
776
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  folder: string
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+ /** 0-based column number for x/y coordinate for this plot */
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+ coordsColumns: { x: number; y: number }
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  /** optional suffix to locate the file for a sample, via ${folder}/${sampleName}${fileSuffix}
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- assumes that file name always start with sample name.
779
- if not introduce filePrefix
780
- */
782
+ assumes that file name always start with sample name.
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+ if not introduce filePrefix
784
+ */
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  fileSuffix?: string
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786
  /** list of columns in tabular text file that define cell categories and can be used to color the cells in the plot. must have categorical values
783
787
  */
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  colorColumns: ColorColumn[]
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- /** 0-based column number for x/y coordinate for this plot */
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- coordsColumns: { x: number; y: number }
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789
  /** if true the plot is shown by default. otherwise hidden */
788
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  selected?: boolean
789
791
  }
package/src/routes/termdb.singlecellData.ts CHANGED
@@ -20,13 +20,12 @@ export type Plot = {
20
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  /** name of the plot */
21
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  name: string
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  /** List of cells with gene expression */
23
- expCells?: Cell[]
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+ expCells: Cell[]
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  /** List of cells with no gene expression, if no gene provided all cells will be here */
25
- noExpCells?: Cell[]
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- /** Column name to color by, e.g Cell type, CNV, Fusion */
27
- colorBy: string
25
+ noExpCells: Cell[]
28
26
  colorColumns: string[]
29
- colorMap?: { [key: string]: string }
27
+ colorBy: string
28
+ colorMap: any
30
29
  }
31
30
 
32
31
  export type TermdbSingleCellDataRequest = {
@@ -41,14 +40,17 @@ export type TermdbSingleCellDataRequest = {
41
40
  plots: string[]
42
41
  /** Gene name to retrieve expression data for all cells of the given sample, and to overlay on maps */
43
42
  gene?: string
43
+ /** in each plot, what Column name to color by
44
+ key: plot.name, value: column name
45
+ if missing, use default setting of the plot
46
+ */
47
+ colorBy?: { [key: string]: string }
48
+ colorMap?: { [key: string]: string }
44
49
  }
45
50
 
46
51
  export type HasdataResponse = {
47
52
  /** List of plots from singlecell experiment of this sample */
48
53
  plots: Plot[]
49
-
50
- /** Terms used to annotate cells */
51
- //terms: Term[]
52
54
  }
53
55
 
54
56
  export type NodataResponse = {