@sjcrh/proteinpaint-types 2.174.1 → 2.175.0

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Files changed (6) hide show
  1. package/dist/{chunk-JKELINOM.js → chunk-CJKG67B2.js} +81 -21
  2. package/dist/index.js +1 -1
  3. package/dist/termdb.runChart.js +1 -1
  4. package/package.json +1 -1
  5. package/src/routes/termdb.chat.ts +14 -2
  6. package/src/routes/termdb.runChart.ts +11 -9
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;
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+ 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/index.js CHANGED
@@ -42,7 +42,7 @@ import {
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  runChartPayload,
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  validRunChartRequest,
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  validRunChartResponse
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- } from "./chunk-JKELINOM.js";
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+ } from "./chunk-CJKG67B2.js";
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  import {
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  termdbSampleImagesPayload,
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  validTermdbSampleImagesRequest,
package/dist/termdb.runChart.js CHANGED
@@ -2,7 +2,7 @@ import {
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  runChartPayload,
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  validRunChartRequest,
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  validRunChartResponse
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- } from "./chunk-JKELINOM.js";
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+ } from "./chunk-CJKG67B2.js";
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  import "./chunk-YNHC5SXO.js";
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  export {
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  runChartPayload,
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@sjcrh/proteinpaint-types",
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- "version": "2.174.1",
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+ "version": "2.175.0",
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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/routes/termdb.chat.ts CHANGED
@@ -18,11 +18,12 @@ type HtmlResponse = {
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  }
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  export type PlotResponse = {
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  type: 'plot'
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- /** plot state. Currently only supports summary chart, will add other chart types later */
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  plot: object
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  /** Specifies what action to take e.g. Summary plot or no action. Will add more chart types later */
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  }
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+ export type LlmConfig = { provider: 'SJ' | 'ollama'; api: string; modelName: string }
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+
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  export type ChatResponse = HtmlResponse | PlotResponse
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  export const ChatPayload: RoutePayload = {
@@ -42,6 +43,8 @@ export type SummaryType = {
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  term2?: string
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  /** Optional simple filter terms */
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  simpleFilter: FilterTerm[]
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+ /** Optional explicit child type requested by the user. If omitted, the logic of the data types picks the child type. */
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+ childType?: 'violin' | 'boxplot' | 'sampleScatter' | 'barchart'
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  }
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  export type FilterTerm =
@@ -101,7 +104,7 @@ export type plot_type = {
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  /** When type == plot, show the corresponding plot in the plot field */
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  type: 'plot'
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  /** The type of plot to be displayed on the UI. */
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- plot: 'summary' | 'dge' | 'none' | 'survival'
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+ plot: 'summary' | 'dge' | 'none' | 'survival' | 'matrix'
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  }
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  export type DEType = {
@@ -112,3 +115,12 @@ export type DEType = {
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  /** Method used for carrying out differential gene expression analysis */
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  method?: 'edgeR' | 'limma' | 'wilcoxon'
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  }
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+
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+ export type MatrixType = {
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+ /** Names of dictionary terms to include as rows in the matrix (e.g. "Diagnosis", "Gender", "Race") */
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+ terms?: string[]
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+ /** Names of genes to include as gene variant rows in the matrix (e.g. "TP53", "KRAS", "NRAS") */
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+ geneNames?: string[]
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+ /** Optional simple filter terms to restrict the sample set */
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+ simpleFilter?: FilterTerm[]
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+ }
package/src/routes/termdb.runChart.ts CHANGED
@@ -3,15 +3,15 @@ import type { RoutePayload } from './routeApi.ts'
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  export type RunChartRequest = {
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  genome: string
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  dslabel: string
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- /** date term for x axis */
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- term: {
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- id: string
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- }
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- /** timeline/duration term for y axis */
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- term2: {
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- id: string
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- }
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- aggregation: 'mean' | 'median' | 'count'
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+ /**
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+ * term wrapper for x axis: { term, q }.
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+ * runChart2: q.mode='continuous' → 1 series.
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+ * runChart2Period: q.mode='discrete' (with bins) → multiple series by period.
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+ */
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+ xtw: { term: { id: string }; q?: { mode?: 'continuous' | 'discrete' }; $id?: string }
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+ /** term wrapper for y axis: { term, q } */
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+ ytw: { term: { id: string }; q?: { mode?: string }; $id?: string }
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+ aggregation: 'median'
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  filter?: any
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  __protected__?: any // auth token for accessing protected data
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  }
@@ -20,6 +20,8 @@ export type RunChartResponse = {
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  status: 'ok' | 'error'
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  /** each series is one curve, with a median. a runchart may show 1 or multiple curves */
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  series: {
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+ /** period/series identifier */
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+ seriesId?: string
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  /** calculated Y median value for this curve */
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  median: number
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  points: Point[]