@sjcrh/proteinpaint-types 2.174.1 → 2.176.0

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Files changed (23) hide show
  1. package/dist/{chunk-JKELINOM.js → chunk-CJKG67B2.js} +81 -21
  2. package/dist/{chunk-KXAR65TO.js → chunk-CJVAIEUK.js} +2 -2
  3. package/dist/{chunk-OIQOK4UP.js → chunk-GZRRMIZZ.js} +2 -2
  4. package/dist/{chunk-JMWADQFZ.js → chunk-HJEEUTW3.js} +2 -2
  5. package/dist/{chunk-GDZUCVIB.js → chunk-RXJNXOZC.js} +2 -2
  6. package/dist/{chunk-LKRDK6V6.js → chunk-VZNEPZ73.js} +2 -16
  7. package/dist/index.js +6 -6
  8. package/dist/termdb.boxplot.js +1 -1
  9. package/dist/termdb.categories.js +1 -1
  10. package/dist/termdb.descrstats.js +1 -1
  11. package/dist/termdb.runChart.js +1 -1
  12. package/dist/termdb.sampleScatter.js +1 -1
  13. package/dist/termdb.violin.js +1 -1
  14. package/package.json +1 -1
  15. package/src/dataset.ts +10 -2
  16. package/src/index.ts +1 -0
  17. package/src/routes/termdb.boxplot.ts +0 -1
  18. package/src/routes/termdb.categories.ts +0 -5
  19. package/src/routes/termdb.chat.ts +27 -2
  20. package/src/routes/termdb.descrstats.ts +0 -1
  21. package/src/routes/termdb.runChart.ts +11 -9
  22. package/src/routes/termdb.sampleScatter.ts +3 -1
  23. package/src/routes/termdb.violin.ts +0 -1
package/dist/{chunk-JKELINOM.js → chunk-CJKG67B2.js} RENAMED
@@ -20,7 +20,11 @@ var runChartPayload = {
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  var validRunChartRequest = (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.term && null !== input3.term && "string" === typeof input3.term.id) && ("object" === typeof input3.term2 && null !== input3.term2 && "string" === typeof input3.term2.id) && ("median" === input3.aggregation || "mean" === input3.aggregation || "count" === input3.aggregation) && true && true;
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+ const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && ("object" === typeof input3.xtw && null !== input3.xtw && $io1(input3.xtw)) && ("object" === typeof input3.ytw && null !== input3.ytw && $io4(input3.ytw)) && "median" === input3.aggregation && true && true;
24
+ const $io1 = (input3) => "object" === typeof input3.term && null !== input3.term && "string" === typeof input3.term.id && (void 0 === input3.q || "object" === typeof input3.q && null !== input3.q && false === Array.isArray(input3.q) && $io3(input3.q)) && (void 0 === input3.$id || "string" === typeof input3.$id);
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+ const $io3 = (input3) => void 0 === input3.mode || "discrete" === input3.mode || "continuous" === input3.mode;
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+ const $io4 = (input3) => "object" === typeof input3.term && null !== input3.term && "string" === typeof input3.term.id && (void 0 === input3.q || "object" === typeof input3.q && null !== input3.q && false === Array.isArray(input3.q) && $io6(input3.q)) && (void 0 === input3.$id || "string" === typeof input3.$id);
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+ const $io6 = (input3) => void 0 === input3.mode || "string" === typeof input3.mode;
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  return "object" === typeof input2 && null !== input2 && $io0(input2);
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  };
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  if (false === __is(input)) {
@@ -34,37 +38,89 @@ var validRunChartRequest = (input) => {
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  path: _path2 + ".dslabel",
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  expected: "string",
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  value: input3.dslabel
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- }), ("object" === typeof input3.term && null !== input3.term || $report(_exceptionable2, {
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- path: _path2 + ".term",
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+ }), ("object" === typeof input3.xtw && null !== input3.xtw || $report(_exceptionable2, {
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+ path: _path2 + ".xtw",
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  expected: "__type",
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- value: input3.term
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- })) && $vo1(input3.term, _path2 + ".term", _exceptionable2) || $report(_exceptionable2, {
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- path: _path2 + ".term",
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+ value: input3.xtw
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+ })) && $vo1(input3.xtw, _path2 + ".xtw", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".xtw",
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  expected: "__type",
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- value: input3.term
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- }), ("object" === typeof input3.term2 && null !== input3.term2 || $report(_exceptionable2, {
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- path: _path2 + ".term2",
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- expected: "__type.o1",
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- value: input3.term2
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- })) && $vo2(input3.term2, _path2 + ".term2", _exceptionable2) || $report(_exceptionable2, {
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- path: _path2 + ".term2",
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- expected: "__type.o1",
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- value: input3.term2
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- }), "median" === input3.aggregation || "mean" === input3.aggregation || "count" === input3.aggregation || $report(_exceptionable2, {
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+ value: input3.xtw
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+ }), ("object" === typeof input3.ytw && null !== input3.ytw || $report(_exceptionable2, {
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+ path: _path2 + ".ytw",
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+ expected: "__type.o3",
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+ value: input3.ytw
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+ })) && $vo4(input3.ytw, _path2 + ".ytw", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".ytw",
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+ expected: "__type.o3",
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+ value: input3.ytw
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+ }), "median" === input3.aggregation || $report(_exceptionable2, {
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  path: _path2 + ".aggregation",
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- expected: '("count" | "mean" | "median")',
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+ expected: '"median"',
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  value: input3.aggregation
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  }), true, true].every((flag) => flag);
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- const $vo1 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.id || $report(_exceptionable2, {
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+ const $vo1 = (input3, _path2, _exceptionable2 = true) => [("object" === typeof input3.term && null !== input3.term || $report(_exceptionable2, {
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+ path: _path2 + ".term",
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+ expected: "__type.o1",
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+ value: input3.term
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+ })) && $vo2(input3.term, _path2 + ".term", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".term",
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+ expected: "__type.o1",
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+ value: input3.term
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+ }), void 0 === input3.q || ("object" === typeof input3.q && null !== input3.q && false === Array.isArray(input3.q) || $report(_exceptionable2, {
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+ path: _path2 + ".q",
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+ expected: "(__type.o2 | undefined)",
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+ value: input3.q
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+ })) && $vo3(input3.q, _path2 + ".q", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".q",
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+ expected: "(__type.o2 | undefined)",
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+ value: input3.q
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+ }), void 0 === input3.$id || "string" === typeof input3.$id || $report(_exceptionable2, {
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+ path: _path2 + ".$id",
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+ expected: "(string | undefined)",
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+ value: input3.$id
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+ })].every((flag) => flag);
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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
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  })].every((flag) => flag);
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- const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.id || $report(_exceptionable2, {
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+ const $vo3 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.mode || "discrete" === input3.mode || "continuous" === input3.mode || $report(_exceptionable2, {
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+ path: _path2 + ".mode",
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+ expected: '("continuous" | "discrete" | undefined)',
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+ value: input3.mode
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+ })].every((flag) => flag);
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+ const $vo4 = (input3, _path2, _exceptionable2 = true) => [("object" === typeof input3.term && null !== input3.term || $report(_exceptionable2, {
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+ path: _path2 + ".term",
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+ expected: "__type.o4",
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+ value: input3.term
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+ })) && $vo5(input3.term, _path2 + ".term", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".term",
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+ expected: "__type.o4",
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+ value: input3.term
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+ }), void 0 === input3.q || ("object" === typeof input3.q && null !== input3.q && false === Array.isArray(input3.q) || $report(_exceptionable2, {
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+ path: _path2 + ".q",
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+ expected: "(__type.o5 | undefined)",
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+ value: input3.q
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+ })) && $vo6(input3.q, _path2 + ".q", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".q",
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+ expected: "(__type.o5 | undefined)",
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+ value: input3.q
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+ }), void 0 === input3.$id || "string" === typeof input3.$id || $report(_exceptionable2, {
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+ path: _path2 + ".$id",
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+ expected: "(string | undefined)",
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+ value: input3.$id
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+ })].every((flag) => flag);
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+ const $vo5 = (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
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  })].every((flag) => flag);
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+ const $vo6 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.mode || "string" === typeof input3.mode || $report(_exceptionable2, {
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+ path: _path2 + ".mode",
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+ expected: "(string | undefined)",
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+ value: input3.mode
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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: "RunChartRequest",
@@ -87,7 +143,7 @@ var validRunChartResponse = (input) => {
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  const errors = [];
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  const __is = (input2) => {
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  const $io0 = (input3) => ("ok" === input3.status || "error" === input3.status) && (Array.isArray(input3.series) && input3.series.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)));
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- const $io1 = (input3) => "number" === typeof input3.median && (Array.isArray(input3.points) && input3.points.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)));
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+ const $io1 = (input3) => (void 0 === input3.seriesId || "string" === typeof input3.seriesId) && "number" === typeof input3.median && (Array.isArray(input3.points) && input3.points.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)));
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  const $io2 = (input3) => "number" === typeof input3.x && "string" === typeof input3.xName && "number" === typeof input3.y && "number" === typeof input3.sampleCount;
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  return "object" === typeof input2 && null !== input2 && $io0(input2);
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  };
@@ -115,7 +171,11 @@ var validRunChartResponse = (input) => {
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  expected: "Array<__type>",
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  value: input3.series
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  })].every((flag) => flag);
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- const $vo1 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.median || $report(_exceptionable2, {
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+ const $vo1 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.seriesId || "string" === typeof input3.seriesId || $report(_exceptionable2, {
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+ path: _path2 + ".seriesId",
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+ expected: "(string | undefined)",
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+ value: input3.seriesId
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+ }), "number" === typeof input3.median || $report(_exceptionable2, {
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  path: _path2 + ".median",
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  expected: "number",
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  value: input3.median
package/dist/{chunk-KXAR65TO.js → chunk-CJVAIEUK.js} RENAMED
@@ -73,7 +73,7 @@ var validBoxPlotRequest = (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) => "object" === typeof input3.tw && null !== input3.tw && $iu6(input3.tw) && "string" === typeof input3.genome && "string" === typeof input3.dslabel && "boolean" === typeof input3.isLogScale && "boolean" === typeof input3.orderByMedian && (void 0 === input3.removeOutliers || "boolean" === typeof input3.removeOutliers) && (void 0 === input3.showAssocTests || "boolean" === typeof input3.showAssocTests) && (void 0 === input3.overlayTw || "object" === typeof input3.overlayTw && null !== input3.overlayTw && $iu6(input3.overlayTw)) && (void 0 === input3.divideTw || "object" === typeof input3.divideTw && null !== input3.divideTw && $iu6(input3.divideTw)) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io6(input3.filter)) && true && true;
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+ const $io0 = (input3) => "object" === typeof input3.tw && null !== input3.tw && $iu6(input3.tw) && "string" === typeof input3.genome && "string" === typeof input3.dslabel && "boolean" === typeof input3.isLogScale && "boolean" === typeof input3.orderByMedian && (void 0 === input3.removeOutliers || "boolean" === typeof input3.removeOutliers) && (void 0 === input3.showAssocTests || "boolean" === typeof input3.showAssocTests) && (void 0 === input3.overlayTw || "object" === typeof input3.overlayTw && null !== input3.overlayTw && $iu6(input3.overlayTw)) && (void 0 === input3.divideTw || "object" === typeof input3.divideTw && null !== input3.divideTw && $iu6(input3.divideTw)) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io6(input3.filter)) && true;
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  const $io1 = (input3) => (void 0 === input3.id || "string" === typeof input3.id) && (void 0 === input3.$id || "string" === typeof input3.$id) && (void 0 === input3.isAtomic || true === input3.isAtomic) && true && (void 0 === input3.settings || "object" === typeof input3.settings && null !== input3.settings && false === Array.isArray(input3.settings) && $io2(input3.settings)) && true && (void 0 === input3.minNumSamples || "number" === typeof input3.minNumSamples) && true && ("object" === typeof input3.term && null !== input3.term && $iu7(input3.term)) && ("object" === typeof input3.q && null !== input3.q && $io47(input3.q)) && "QualTWValues" === input3.type;
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  const $io2 = (input3) => Object.keys(input3).every((key) => {
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  const value = input3[key];
@@ -396,7 +396,7 @@ var validBoxPlotRequest = (input) => {
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  path: _path2 + ".filter",
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  expected: "(Filter | undefined)",
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  value: input3.filter
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- }), true, true].every((flag) => flag);
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+ }), true].every((flag) => flag);
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  const $vo1 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.id || "string" === typeof input3.id || $report(_exceptionable2, {
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  path: _path2 + ".id",
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  expected: "(string | undefined)",
package/dist/{chunk-OIQOK4UP.js → chunk-GZRRMIZZ.js} RENAMED
@@ -58,7 +58,7 @@ var validDescrStatsRequest = (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) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "string" === typeof input3.embedder && ("object" === typeof input3.tw && null !== input3.tw && $iu6(input3.tw)) && (void 0 === input3.logScale || "boolean" === typeof input3.logScale) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io6(input3.filter)) && true && true;
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+ const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "string" === typeof input3.embedder && ("object" === typeof input3.tw && null !== input3.tw && $iu6(input3.tw)) && (void 0 === input3.logScale || "boolean" === typeof input3.logScale) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io6(input3.filter)) && true;
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  const $io1 = (input3) => (void 0 === input3.id || "string" === typeof input3.id) && (void 0 === input3.$id || "string" === typeof input3.$id) && (void 0 === input3.isAtomic || true === input3.isAtomic) && true && (void 0 === input3.settings || "object" === typeof input3.settings && null !== input3.settings && false === Array.isArray(input3.settings) && $io2(input3.settings)) && true && (void 0 === input3.minNumSamples || "number" === typeof input3.minNumSamples) && true && ("object" === typeof input3.term && null !== input3.term && $iu7(input3.term)) && ("object" === typeof input3.q && null !== input3.q && $io47(input3.q)) && "QualTWValues" === input3.type;
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  const $io2 = (input3) => Object.keys(input3).every((key) => {
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  const value = input3[key];
@@ -357,7 +357,7 @@ var validDescrStatsRequest = (input) => {
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  path: _path2 + ".filter",
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  expected: "(Filter | undefined)",
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  value: input3.filter
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- }), true, true].every((flag) => flag);
360
+ }), true].every((flag) => flag);
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  const $vo1 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.id || "string" === typeof input3.id || $report(_exceptionable2, {
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  path: _path2 + ".id",
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  expected: "(string | undefined)",
package/dist/{chunk-JMWADQFZ.js → chunk-HJEEUTW3.js} RENAMED
@@ -59,7 +59,7 @@ var validViolinRequest = (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.axisHeight && (Array.isArray(input3.currentGeneNames) && input3.currentGeneNames.every((elem) => "string" === typeof elem)) && "string" === typeof input3.datasymbol && "number" === typeof input3.devicePixelRatio && true && true && "string" === typeof input3.dslabel && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io1(input3.filter)) && true && "string" === typeof input3.genome && "boolean" === typeof input3.isKDE && ("horizontal" === input3.orientation || "vertical" === input3.orientation) && "number" === typeof input3.radius && "number" === typeof input3.rightMargin && true && "number" === typeof input3.strokeWidth && "number" === typeof input3.svgw && "number" === typeof input3.ticks && true && "string" === typeof input3.unit && true;
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+ const $io0 = (input3) => "number" === typeof input3.axisHeight && (Array.isArray(input3.currentGeneNames) && input3.currentGeneNames.every((elem) => "string" === typeof elem)) && "string" === typeof input3.datasymbol && "number" === typeof input3.devicePixelRatio && true && true && "string" === typeof input3.dslabel && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io1(input3.filter)) && true && "string" === typeof input3.genome && "boolean" === typeof input3.isKDE && ("horizontal" === input3.orientation || "vertical" === input3.orientation) && "number" === typeof input3.radius && "number" === typeof input3.rightMargin && true && "number" === typeof input3.strokeWidth && "number" === typeof input3.svgw && "number" === typeof input3.ticks && true && "string" === typeof input3.unit;
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  const $io1 = (input3) => "tvslst" === input3.type && "boolean" === typeof input3["in"] && "string" === typeof input3.join && (void 0 === input3.tag || "string" === typeof input3.tag) && (Array.isArray(input3.lst) && input3.lst.every((elem) => "object" === typeof elem && null !== elem && $iu0(elem)));
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  const $io2 = (input3) => "tvs" === input3.type && ("object" === typeof input3.tvs && null !== input3.tvs && $iu4(input3.tvs));
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  const $io3 = (input3) => (void 0 === input3.join || "string" === typeof input3.join) && (void 0 === input3.isnot || "boolean" === typeof input3.isnot) && ("object" === typeof input3.term && null !== input3.term && $io4(input3.term)) && (void 0 === input3.groupset_label || "string" === typeof input3.groupset_label) && (Array.isArray(input3.values) && input3.values.every((elem) => "object" === typeof elem && null !== elem && false === Array.isArray(elem) && $io6(elem)));
@@ -298,7 +298,7 @@ var validViolinRequest = (input) => {
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  path: _path2 + ".unit",
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  expected: "string",
300
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  value: input3.unit
301
- }), true].every((flag) => flag);
301
+ })].every((flag) => flag);
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  const $vo1 = (input3, _path2, _exceptionable2 = true) => ["tvslst" === input3.type || $report(_exceptionable2, {
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  path: _path2 + ".type",
304
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  expected: '"tvslst"',
package/dist/{chunk-GDZUCVIB.js → chunk-RXJNXOZC.js} RENAMED
@@ -20,7 +20,7 @@ var termdbSampleScatterPayload = {
20
20
  var validTermdbSampleScatterRequest = (input) => {
21
21
  const errors = [];
22
22
  const __is = (input2) => {
23
- const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && true && true && true && true && (void 0 === input3.coordTWs || Array.isArray(input3.coordTWs)) && (void 0 === input3.plotName || "string" === typeof input3.plotName) && true && true && (void 0 === input3.chartType || "string" === typeof input3.chartType) && true;
23
+ const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && true && true && true && true && (void 0 === input3.coordTWs || Array.isArray(input3.coordTWs)) && (void 0 === input3.plotName || "string" === typeof input3.plotName) && true && true && (void 0 === input3.chartType || "string" === typeof input3.chartType) && true && true && true;
24
24
  return "object" === typeof input2 && null !== input2 && $io0(input2);
25
25
  };
26
26
  if (false === __is(input)) {
@@ -46,7 +46,7 @@ var validTermdbSampleScatterRequest = (input) => {
46
46
  path: _path2 + ".chartType",
47
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  expected: "(string | undefined)",
48
48
  value: input3.chartType
49
- }), true].every((flag) => flag);
49
+ }), true, true, true].every((flag) => flag);
50
50
  return ("object" === typeof input2 && null !== input2 || $report(true, {
51
51
  path: _path + "",
52
52
  expected: "TermdbSampleScatterRequest",
package/dist/{chunk-LKRDK6V6.js → chunk-VZNEPZ73.js} RENAMED
@@ -58,7 +58,7 @@ var validCategoriesRequest = (input) => {
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  const errors = [];
59
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  const __is = (input2) => {
60
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  const $join = import_typia.createValidate.join;
61
- const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "string" === typeof input3.embedder && ("object" === typeof input3.tw && null !== input3.tw && $iu6(input3.tw)) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io6(input3.filter)) && true && (void 0 === input3.currentGeneNames || Array.isArray(input3.currentGeneNames) && input3.currentGeneNames.every((elem) => "string" === typeof elem)) && true && (void 0 === input3.__protected__ || "object" === typeof input3.__protected__ && null !== input3.__protected__ && false === Array.isArray(input3.__protected__) && $io82(input3.__protected__));
61
+ const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "string" === typeof input3.embedder && ("object" === typeof input3.tw && null !== input3.tw && $iu6(input3.tw)) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io6(input3.filter)) && true && (void 0 === input3.currentGeneNames || Array.isArray(input3.currentGeneNames) && input3.currentGeneNames.every((elem) => "string" === typeof elem)) && true;
62
62
  const $io1 = (input3) => (void 0 === input3.id || "string" === typeof input3.id) && (void 0 === input3.$id || "string" === typeof input3.$id) && (void 0 === input3.isAtomic || true === input3.isAtomic) && true && (void 0 === input3.settings || "object" === typeof input3.settings && null !== input3.settings && false === Array.isArray(input3.settings) && $io2(input3.settings)) && true && (void 0 === input3.minNumSamples || "number" === typeof input3.minNumSamples) && true && ("object" === typeof input3.term && null !== input3.term && $iu7(input3.term)) && ("object" === typeof input3.q && null !== input3.q && $io47(input3.q)) && "QualTWValues" === input3.type;
63
63
  const $io2 = (input3) => Object.keys(input3).every((key) => {
64
64
  const value = input3[key];
@@ -177,7 +177,6 @@ var validCategoriesRequest = (input) => {
177
177
  const $io79 = (input3) => "string" === typeof input3.k && ("string" === typeof input3.v || "number" === typeof input3.v);
178
178
  const $io80 = (input3) => (void 0 === input3.id || "string" === typeof input3.id) && (void 0 === input3.$id || "string" === typeof input3.$id) && (void 0 === input3.isAtomic || true === input3.isAtomic) && true && (void 0 === input3.settings || "object" === typeof input3.settings && null !== input3.settings && false === Array.isArray(input3.settings) && $io2(input3.settings)) && true && (void 0 === input3.minNumSamples || "number" === typeof input3.minNumSamples) && true && "TermCollectionTWValues" === input3.type && ("object" === typeof input3.term && null !== input3.term && $io42(input3.term)) && ("object" === typeof input3.q && null !== input3.q && $io81(input3.q));
179
179
  const $io81 = (input3) => (void 0 === input3.hiddenValues || "object" === typeof input3.hiddenValues && null !== input3.hiddenValues && false === Array.isArray(input3.hiddenValues) && $io15(input3.hiddenValues)) && (void 0 === input3.isAtomic || true === input3.isAtomic) && (void 0 === input3.name || "string" === typeof input3.name) && (void 0 === input3.reuseId || "string" === typeof input3.reuseId) && "continuous" === input3.mode && "values" === input3.type && (Array.isArray(input3.lst) && input3.lst.every((elem) => "string" === typeof elem)) && (void 0 === input3.numerators || Array.isArray(input3.numerators) && input3.numerators.every((elem) => "string" === typeof elem));
180
- const $io82 = (input3) => (void 0 === input3.sessionId || "string" === typeof input3.sessionId) && true && true;
181
180
  const $iu0 = (input3) => (() => {
182
181
  if ("tvslst" === input3.type)
183
182
  return $io6(input3);
@@ -366,15 +365,7 @@ var validCategoriesRequest = (input) => {
366
365
  path: _path2 + ".currentGeneNames",
367
366
  expected: "(Array<string> | undefined)",
368
367
  value: input3.currentGeneNames
369
- }), true, void 0 === input3.__protected__ || ("object" === typeof input3.__protected__ && null !== input3.__protected__ && false === Array.isArray(input3.__protected__) || $report(_exceptionable2, {
370
- path: _path2 + ".__protected__",
371
- expected: "(__type.o11 | undefined)",
372
- value: input3.__protected__
373
- })) && $vo82(input3.__protected__, _path2 + ".__protected__", _exceptionable2) || $report(_exceptionable2, {
374
- path: _path2 + ".__protected__",
375
- expected: "(__type.o11 | undefined)",
376
- value: input3.__protected__
377
- })].every((flag) => flag);
368
+ }), true].every((flag) => flag);
378
369
  const $vo1 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.id || "string" === typeof input3.id || $report(_exceptionable2, {
379
370
  path: _path2 + ".id",
380
371
  expected: "(string | undefined)",
@@ -4322,11 +4313,6 @@ var validCategoriesRequest = (input) => {
4322
4313
  expected: "(Array<string> | undefined)",
4323
4314
  value: input3.numerators
4324
4315
  })].every((flag) => flag);
4325
- const $vo82 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.sessionId || "string" === typeof input3.sessionId || $report(_exceptionable2, {
4326
- path: _path2 + ".sessionId",
4327
- expected: "(string | undefined)",
4328
- value: input3.sessionId
4329
- }), true, true].every((flag) => flag);
4330
4316
  const $vu0 = (input3, _path2, _exceptionable2 = true) => (() => {
4331
4317
  if ("tvslst" === input3.type)
4332
4318
  return $vo6(input3, _path2, _exceptionable2);
package/dist/index.js CHANGED
@@ -22,7 +22,7 @@ import {
22
22
  validViolinRequest,
23
23
  validViolinResponse,
24
24
  violinPayload
25
- } from "./chunk-JMWADQFZ.js";
25
+ } from "./chunk-HJEEUTW3.js";
26
26
  import {
27
27
  tilePayload,
28
28
  validTileRequest,
@@ -42,7 +42,7 @@ import {
42
42
  runChartPayload,
43
43
  validRunChartRequest,
44
44
  validRunChartResponse
45
- } from "./chunk-JKELINOM.js";
45
+ } from "./chunk-CJKG67B2.js";
46
46
  import {
47
47
  termdbSampleImagesPayload,
48
48
  validTermdbSampleImagesRequest,
@@ -52,7 +52,7 @@ import {
52
52
  termdbSampleScatterPayload,
53
53
  validTermdbSampleScatterRequest,
54
54
  validTermdbSampleScatterResponse
55
- } from "./chunk-GDZUCVIB.js";
55
+ } from "./chunk-RXJNXOZC.js";
56
56
  import {
57
57
  termdbSingleSampleMutationPayload,
58
58
  validTermdbSingleSampleMutationRequest,
@@ -87,7 +87,7 @@ import {
87
87
  descrStatsPayload,
88
88
  validDescrStatsRequest,
89
89
  validDescrStatsResponse
90
- } from "./chunk-OIQOK4UP.js";
90
+ } from "./chunk-GZRRMIZZ.js";
91
91
  import {
92
92
  FilterTermValuesPayload,
93
93
  validFilterTermValuesRequest,
@@ -137,12 +137,12 @@ import {
137
137
  boxplotPayload,
138
138
  validBoxPlotRequest,
139
139
  validBoxPlotResponse
140
- } from "./chunk-KXAR65TO.js";
140
+ } from "./chunk-CJVAIEUK.js";
141
141
  import {
142
142
  termdbCategoriesPayload,
143
143
  validCategoriesRequest,
144
144
  validCategoriesResponse
145
- } from "./chunk-LKRDK6V6.js";
145
+ } from "./chunk-VZNEPZ73.js";
146
146
  import {
147
147
  ChatPayload,
148
148
  validChatRequest,
package/dist/termdb.boxplot.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  boxplotPayload,
3
3
  validBoxPlotRequest,
4
4
  validBoxPlotResponse
5
- } from "./chunk-KXAR65TO.js";
5
+ } from "./chunk-CJVAIEUK.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  boxplotPayload,
package/dist/termdb.categories.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termdbCategoriesPayload,
3
3
  validCategoriesRequest,
4
4
  validCategoriesResponse
5
- } from "./chunk-LKRDK6V6.js";
5
+ } from "./chunk-VZNEPZ73.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termdbCategoriesPayload,
package/dist/termdb.descrstats.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  descrStatsPayload,
3
3
  validDescrStatsRequest,
4
4
  validDescrStatsResponse
5
- } from "./chunk-OIQOK4UP.js";
5
+ } from "./chunk-GZRRMIZZ.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  descrStatsPayload,
package/dist/termdb.runChart.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  runChartPayload,
3
3
  validRunChartRequest,
4
4
  validRunChartResponse
5
- } from "./chunk-JKELINOM.js";
5
+ } from "./chunk-CJKG67B2.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  runChartPayload,
package/dist/termdb.sampleScatter.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termdbSampleScatterPayload,
3
3
  validTermdbSampleScatterRequest,
4
4
  validTermdbSampleScatterResponse
5
- } from "./chunk-GDZUCVIB.js";
5
+ } from "./chunk-RXJNXOZC.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termdbSampleScatterPayload,
package/dist/termdb.violin.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  validViolinRequest,
3
3
  validViolinResponse,
4
4
  violinPayload
5
- } from "./chunk-JMWADQFZ.js";
5
+ } from "./chunk-HJEEUTW3.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  validViolinRequest,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@sjcrh/proteinpaint-types",
3
- "version": "2.174.1",
3
+ "version": "2.176.0",
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
@@ -1124,8 +1124,6 @@ type DataDownloadCatch = {
1124
1124
  jwt: { [index: string]: string }
1125
1125
  }
1126
1126
 
1127
- //Plots
1128
-
1129
1127
  type ScatterPlotsEntry = {
1130
1128
  name: string
1131
1129
  dimension: number
@@ -1154,8 +1152,18 @@ this is limited to only one term and doesn't allow switching between multiple te
1154
1152
  }
1155
1153
 
1156
1154
  type Scatterplots = {
1155
+ /**
1156
+ if defined:
1157
+ ds-supplied getter, arg is clientAuthResult, returns list of plot available for this request based on auth
1158
+ here plots[] array is still needed! so on loading a plot the server can find the matching plot by requested name
1159
+ if not defined:
1160
+ entire plots[] is always send to client
1161
+ */
1162
+ get?: (clientAuthResult: any) => ScatterPlotsEntry[]
1163
+ /** hardcoded plots */
1157
1164
  plots: ScatterPlotsEntry[]
1158
1165
  }
1166
+
1159
1167
  /** this plot compares correlation of one feature against a bunch of variables across samples
1160
1168
  */
1161
1169
  type CorrelationVolcano = {
package/src/index.ts CHANGED
@@ -34,6 +34,7 @@ export * from './routes/img.ts'
34
34
  export * from './routes/isoformlst.ts'
35
35
  export * from './routes/ntseq.ts'
36
36
  export * from './routes/pdomain.ts'
37
+ export * from './routes/routeApi.ts'
37
38
  export * from './routes/samplewsimages.ts'
38
39
  export * from './routes/saveWSIAnnotation.ts'
39
40
  export * from './routes/snp.ts'
package/src/routes/termdb.boxplot.ts CHANGED
@@ -23,7 +23,6 @@ export type BoxPlotRequest = {
23
23
  divideTw?: TermWrapper
24
24
  filter?: Filter
25
25
  filter0?: any
26
- __protected__: any
27
26
  }
28
27
 
29
28
  export type BoxPlotResponse = {
package/src/routes/termdb.categories.ts CHANGED
@@ -14,11 +14,6 @@ export type CategoriesRequest = {
14
14
  currentGeneNames?: string[]
15
15
  /** optional property added by mds3 tk, to limit to cases mutated in this region */
16
16
  rglst?: any
17
- __protected__?: {
18
- sessionId?: string
19
- clientAuthResults?: any
20
- ignoredTermIds?: any
21
- }
22
17
  }
23
18
 
24
19
  interface Entries {
package/src/routes/termdb.chat.ts CHANGED
@@ -18,11 +18,12 @@ type HtmlResponse = {
18
18
  }
19
19
  export type PlotResponse = {
20
20
  type: 'plot'
21
- /** plot state. Currently only supports summary chart, will add other chart types later */
22
21
  plot: object
23
22
  /** Specifies what action to take e.g. Summary plot or no action. Will add more chart types later */
24
23
  }
25
24
 
25
+ export type LlmConfig = { provider: 'SJ' | 'ollama'; api: string; modelName: string }
26
+
26
27
  export type ChatResponse = HtmlResponse | PlotResponse
27
28
 
28
29
  export const ChatPayload: RoutePayload = {
@@ -42,6 +43,8 @@ export type SummaryType = {
42
43
  term2?: string
43
44
  /** Optional simple filter terms */
44
45
  simpleFilter: FilterTerm[]
46
+ /** Optional explicit child type requested by the user. If omitted, the logic of the data types picks the child type. */
47
+ childType?: 'violin' | 'boxplot' | 'sampleScatter' | 'barchart'
45
48
  }
46
49
 
47
50
  export type FilterTerm =
@@ -101,7 +104,7 @@ export type plot_type = {
101
104
  /** When type == plot, show the corresponding plot in the plot field */
102
105
  type: 'plot'
103
106
  /** The type of plot to be displayed on the UI. */
104
- plot: 'summary' | 'dge' | 'none' | 'survival'
107
+ plot: 'summary' | 'dge' | 'none' | 'survival' | 'matrix' | 'sampleScatter'
105
108
  }
106
109
 
107
110
  export type DEType = {
@@ -112,3 +115,25 @@ export type DEType = {
112
115
  /** Method used for carrying out differential gene expression analysis */
113
116
  method?: 'edgeR' | 'limma' | 'wilcoxon'
114
117
  }
118
+
119
+ export type MatrixType = {
120
+ /** Names of dictionary terms to include as rows in the matrix (e.g. "Diagnosis", "Gender", "Race") */
121
+ terms?: string[]
122
+ /** Names of genes to include as gene variant rows in the matrix (e.g. "TP53", "KRAS", "NRAS") */
123
+ geneNames?: string[]
124
+ /** Optional simple filter terms to restrict the sample set */
125
+ simpleFilter?: FilterTerm[]
126
+ }
127
+
128
+ export type SampleScatterType = {
129
+ /** Name of the pre-built plot (e.g. "Transcriptome t-SNE", "Transcriptome UMAP") */
130
+ plotName: string
131
+ /** Term or gene name to overlay as color, or null to remove color overlay */
132
+ colorTW?: string | null
133
+ /** Term or gene name to overlay as shape, or null to remove shape overlay */
134
+ shapeTW?: string | null
135
+ /** Term or gene name to overlay as Z-divide, or null to remove divide overlay */
136
+ term0?: string | null
137
+ /** Optional simple filter terms */
138
+ simpleFilter?: FilterTerm[]
139
+ }
package/src/routes/termdb.descrstats.ts CHANGED
@@ -16,7 +16,6 @@ export type DescrStatsRequest = {
16
16
  filter?: Filter
17
17
  /** optional gdc filter */
18
18
  filter0?: any
19
- __protected__?: any //reuse definition from termdb.matrix.ts!!!
20
19
  }
21
20
 
22
21
  export type DescrStats = {
package/src/routes/termdb.runChart.ts CHANGED
@@ -3,15 +3,15 @@ import type { RoutePayload } from './routeApi.ts'
3
3
  export type RunChartRequest = {
4
4
  genome: string
5
5
  dslabel: string
6
- /** date term for x axis */
7
- term: {
8
- id: string
9
- }
10
- /** timeline/duration term for y axis */
11
- term2: {
12
- id: string
13
- }
14
- aggregation: 'mean' | 'median' | 'count'
6
+ /**
7
+ * term wrapper for x axis: { term, q }.
8
+ * runChart2: q.mode='continuous' → 1 series.
9
+ * runChart2Period: q.mode='discrete' (with bins) → multiple series by period.
10
+ */
11
+ xtw: { term: { id: string }; q?: { mode?: 'continuous' | 'discrete' }; $id?: string }
12
+ /** term wrapper for y axis: { term, q } */
13
+ ytw: { term: { id: string }; q?: { mode?: string }; $id?: string }
14
+ aggregation: 'median'
15
15
  filter?: any
16
16
  __protected__?: any // auth token for accessing protected data
17
17
  }
@@ -20,6 +20,8 @@ export type RunChartResponse = {
20
20
  status: 'ok' | 'error'
21
21
  /** each series is one curve, with a median. a runchart may show 1 or multiple curves */
22
22
  series: {
23
+ /** period/series identifier */
24
+ seriesId?: string
23
25
  /** calculated Y median value for this curve */
24
26
  median: number
25
27
  points: Point[]
package/src/routes/termdb.sampleScatter.ts CHANGED
@@ -14,7 +14,9 @@ export type TermdbSampleScatterRequest = {
14
14
  filter?: any
15
15
  filter0?: any
16
16
  chartType?: string
17
- __protected__?: any // auth token for accessing protected data
17
+ singleCellPlot?: any
18
+ colorColumn?: any
19
+ excludeOutliers?: any
18
20
  }
19
21
 
20
22
  export type ScatterSample = {
package/src/routes/termdb.violin.ts CHANGED
@@ -49,7 +49,6 @@ export type ViolinRequest = {
49
49
  tw: any
50
50
  /** A string representing a unit of measurement (e.g., 'log' for log scale) */
51
51
  unit: string
52
- __protected__: any
53
52
  }
54
53
 
55
54
  /** ?? TODO: Needs description */