@sjcrh/proteinpaint-types 2.185.0 → 2.186.0

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Files changed (41) hide show
  1. package/dist/brainImaging.js +1 -1
  2. package/dist/{chunk-NO3ZZD3L.js → chunk-46DTJOK5.js} +6 -2
  3. package/dist/{chunk-2NINVZOB.js → chunk-AYTV7V46.js} +13 -5
  4. package/dist/{chunk-QMEKJW2A.js → chunk-DPJUULKQ.js} +6 -2
  5. package/dist/{chunk-TUM3OZ7K.js → chunk-DVMD6CBJ.js} +6 -2
  6. package/dist/{chunk-UGGNWTJZ.js → chunk-EBSBUEOG.js} +21 -1
  7. package/dist/{chunk-UWK6LBTQ.js → chunk-F2QRI6B2.js} +6 -2
  8. package/dist/{chunk-CWJZUUEF.js → chunk-FEMYT7FL.js} +21 -1
  9. package/dist/{chunk-TI565XIR.js → chunk-HG2TK6UO.js} +6 -2
  10. package/dist/{chunk-ONNT3XV7.js → chunk-I3QGRA7O.js} +7 -3
  11. package/dist/{chunk-WNUWRPXG.js → chunk-IIWTMQJZ.js} +6 -2
  12. package/dist/{chunk-Y6FNAG22.js → chunk-MMNSJ72P.js} +6 -2
  13. package/dist/{chunk-LOFBLGRE.js → chunk-NKV3NWPF.js} +6 -2
  14. package/dist/{chunk-NLANDPY7.js → chunk-OCH5BJCV.js} +21 -1
  15. package/dist/{chunk-INIT6CVR.js → chunk-RY4Y5ESC.js} +6 -2
  16. package/dist/{chunk-JMVDRHBL.js → chunk-SGMHY5K7.js} +15 -7
  17. package/dist/{chunk-LDLZU2QY.js → chunk-VWLYQ33F.js} +6 -2
  18. package/dist/{chunk-734AZGID.js → chunk-W2Z4RFLX.js} +6 -2
  19. package/dist/correlationVolcano.js +1 -1
  20. package/dist/grin2.js +1 -1
  21. package/dist/index.js +17 -17
  22. package/dist/termdb.DE.js +1 -1
  23. package/dist/termdb.categories.js +1 -1
  24. package/dist/termdb.chat.js +6 -2
  25. package/dist/termdb.chat2.js +1 -1
  26. package/dist/termdb.cluster.js +1 -1
  27. package/dist/termdb.descrstats.js +1 -1
  28. package/dist/termdb.diffMeth.js +1 -1
  29. package/dist/termdb.dmr.js +1 -1
  30. package/dist/termdb.numericcategories.js +1 -1
  31. package/dist/termdb.percentile.js +1 -1
  32. package/dist/termdb.singlecellDEgenes.js +1 -1
  33. package/dist/termdb.termsbyids.js +1 -1
  34. package/dist/termdb.topTermsByType.js +1 -1
  35. package/dist/termdb.topVariablyExpressedGenes.js +1 -1
  36. package/dist/termdb.violinBox.js +1 -1
  37. package/package.json +1 -1
  38. package/src/dataset.ts +15 -3
  39. package/src/routes/termdb.DE.ts +13 -3
  40. package/src/routes/termdb.cluster.ts +1 -1
  41. package/src/terms/proteomeAbundance.ts +2 -1
package/dist/{chunk-734AZGID.js → chunk-W2Z4RFLX.js} RENAMED
@@ -65,7 +65,7 @@ var validGRIN2Request = (input) => {
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  const $io25 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "isoformExpression" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && (void 0 === input3.kind || "isoform" === input3.kind) && "string" === typeof input3.isoform && (void 0 === input3.gene || "string" === typeof input3.gene) && (void 0 === input3.chr || "string" === typeof input3.chr) && (void 0 === input3.start || "number" === typeof input3.start) && (void 0 === input3.stop || "number" === typeof input3.stop);
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  const $io26 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "isoformExpression" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && (void 0 === input3.kind || "coord" === input3.kind) && (void 0 === input3.isoform || "string" === typeof input3.isoform) && (void 0 === input3.gene || "string" === typeof input3.gene) && "string" === typeof input3.chr && "number" === typeof input3.start && "number" === typeof input3.stop;
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  const $io27 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "metaboliteIntensity" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.metabolite && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
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- const $io28 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "proteomeAbundance" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.protein && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && ("object" === typeof input3.proteomeDetails && null !== input3.proteomeDetails && ("string" === typeof input3.proteomeDetails.assay && "string" === typeof input3.proteomeDetails.cohort));
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+ const $io28 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "proteomeAbundance" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.protein && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && ("object" === typeof input3.proteomeDetails && null !== input3.proteomeDetails && ("string" === typeof input3.proteomeDetails.organism && "string" === typeof input3.proteomeDetails.assay && "string" === typeof input3.proteomeDetails.cohort));
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  const $io30 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "date" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
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  const $io31 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "ssGSEA" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.genes || Array.isArray(input3.genes) && input3.genes.every((elem) => "string" === typeof elem)) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
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  const $io32 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "dnaMethylation" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.chr && "number" === typeof input3.start && "number" === typeof input3.stop && ("gene" === input3.genomicFeatureType || "promoter" === input3.genomicFeatureType || "region" === input3.genomicFeatureType || "enhancer" === input3.genomicFeatureType) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
@@ -1756,7 +1756,11 @@ var validGRIN2Request = (input) => {
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  expected: "ProteomeDetails",
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  value: input3.proteomeDetails
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  })].every((flag) => flag);
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- const $vo29 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.assay || $report(_exceptionable2, {
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+ const $vo29 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.organism || $report(_exceptionable2, {
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+ path: _path2 + ".organism",
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+ expected: "string",
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+ value: input3.organism
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+ }), "string" === typeof input3.assay || $report(_exceptionable2, {
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  path: _path2 + ".assay",
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  expected: "string",
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  value: input3.assay
package/dist/correlationVolcano.js CHANGED
@@ -2,7 +2,7 @@ import {
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  CorrelationVolcanoPayload,
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  validCorrelationVolcanoRequest,
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  validCorrelationVolcanoResponse
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- } from "./chunk-LOFBLGRE.js";
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+ } from "./chunk-NKV3NWPF.js";
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  import "./chunk-YNHC5SXO.js";
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  export {
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  CorrelationVolcanoPayload,
package/dist/grin2.js CHANGED
@@ -2,7 +2,7 @@ import {
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  GRIN2Payload,
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  validGRIN2Request,
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  validGRIN2Response
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- } from "./chunk-734AZGID.js";
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+ } from "./chunk-W2Z4RFLX.js";
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  import "./chunk-YNHC5SXO.js";
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  export {
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  GRIN2Payload,
package/dist/index.js CHANGED
@@ -2,7 +2,7 @@ import {
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  validViolinBoxRequest,
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  validViolinBoxResponse,
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  violinBoxPayload
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- } from "./chunk-WNUWRPXG.js";
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+ } from "./chunk-IIWTMQJZ.js";
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  import {
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  tilePayload,
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  validTileRequest,
@@ -22,7 +22,7 @@ import {
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  termdbSingleCellDEgenesPayload,
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  validTermdbSingleCellDEgenesRequest,
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  validTermdbSingleCellDEgenesResponse
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- } from "./chunk-NLANDPY7.js";
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+ } from "./chunk-OCH5BJCV.js";
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  import {
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  termdbSingleCellDataPayload,
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  validTermdbSingleCellDataRequest,
@@ -42,7 +42,7 @@ import {
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  termsByIdsPayload,
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  validTermsByIdsRequest,
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  validTermsByIdsResponse
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- } from "./chunk-UWK6LBTQ.js";
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+ } from "./chunk-F2QRI6B2.js";
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  import {
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  topMutatedGenePayload,
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  validtopMutatedGeneRequest,
@@ -52,12 +52,12 @@ import {
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  termdbTopTermsByTypePayload,
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  validTermdbTopTermsByTypeRequest,
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  validTermdbTopTermsByTypeResponse
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- } from "./chunk-2NINVZOB.js";
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+ } from "./chunk-AYTV7V46.js";
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  import {
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  termdbTopVariablyExpressedGenesPayload,
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  validTermdbTopVariablyExpressedGenesRequest,
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  validTermdbTopVariablyExpressedGenesResponse
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- } from "./chunk-QMEKJW2A.js";
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+ } from "./chunk-DPJUULKQ.js";
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  import {
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  ProfileFormScoresPayload,
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  validProfileFormScoresRequest,
@@ -107,17 +107,17 @@ import {
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  descrStatsPayload,
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  validDescrStatsRequest,
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  validDescrStatsResponse
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- } from "./chunk-Y6FNAG22.js";
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+ } from "./chunk-MMNSJ72P.js";
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  import {
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  diffMethPayload,
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  validDiffMethRequest,
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  validDiffMethResponse
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- } from "./chunk-CWJZUUEF.js";
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+ } from "./chunk-FEMYT7FL.js";
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  import {
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  TermdbDmrPayload,
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  validTermdbDmrRequest,
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  validTermdbDmrResponse
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- } from "./chunk-NO3ZZD3L.js";
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+ } from "./chunk-46DTJOK5.js";
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  import {
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  FilterTermValuesPayload,
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  validFilterTermValuesRequest,
@@ -132,12 +132,12 @@ import {
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  numericCategoriesPayload,
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  validNumericCategoriesRequest,
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  validNumericCategoriesResponse
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- } from "./chunk-LDLZU2QY.js";
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+ } from "./chunk-VWLYQ33F.js";
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  import {
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  percentilePayload,
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  validPercentileRequest,
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  validPercentileResponse
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- } from "./chunk-ONNT3XV7.js";
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+ } from "./chunk-I3QGRA7O.js";
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  import {
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  saveWSIAnnotationPayload,
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  validSaveWSIAnnotationRequest,
@@ -152,16 +152,16 @@ import {
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  diffExpPayload,
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  validDERequest,
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  validDEResponse
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- } from "./chunk-UGGNWTJZ.js";
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+ } from "./chunk-EBSBUEOG.js";
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  import {
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  termdbCategoriesPayload,
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  validCategoriesRequest,
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  validCategoriesResponse
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- } from "./chunk-INIT6CVR.js";
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+ } from "./chunk-RY4Y5ESC.js";
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  import {
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  validChatRequest,
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  validChatResponse
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- } from "./chunk-TUM3OZ7K.js";
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+ } from "./chunk-DVMD6CBJ.js";
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  import {
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  ChatPayload
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  } from "./chunk-FRXRNCDV.js";
@@ -169,7 +169,7 @@ import {
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  termdbClusterPayload,
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  validTermdbClusterRequest,
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  validTermdbClusterResponse
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- } from "./chunk-JMVDRHBL.js";
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+ } from "./chunk-SGMHY5K7.js";
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  import {
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  termdbCohortSummaryPayload,
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  validTermdbCohortSummaryRequest,
@@ -239,7 +239,7 @@ import {
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  GRIN2Payload,
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  validGRIN2Request,
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  validGRIN2Response
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- } from "./chunk-734AZGID.js";
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+ } from "./chunk-W2Z4RFLX.js";
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  import {
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  healthcheckPayload,
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  validHealthCheckRequest,
@@ -261,7 +261,7 @@ import {
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  CorrelationVolcanoPayload,
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  validCorrelationVolcanoRequest,
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  validCorrelationVolcanoResponse
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- } from "./chunk-LOFBLGRE.js";
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+ } from "./chunk-NKV3NWPF.js";
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  import {
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  datasetPayload,
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  validDatasetRequest,
@@ -319,7 +319,7 @@ import {
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  brainImagingPayload,
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  validBrainImagingRequest,
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  validBrainImagingResponse
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- } from "./chunk-TI565XIR.js";
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+ } from "./chunk-HG2TK6UO.js";
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  import {
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  brainImagingSamplesPayload,
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  validBrainImagingSamplesRequest,
package/dist/termdb.DE.js CHANGED
@@ -2,7 +2,7 @@ import {
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  diffExpPayload,
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  validDERequest,
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  validDEResponse
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- } from "./chunk-UGGNWTJZ.js";
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+ } from "./chunk-EBSBUEOG.js";
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  import "./chunk-YNHC5SXO.js";
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  export {
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  diffExpPayload,
package/dist/termdb.categories.js CHANGED
@@ -2,7 +2,7 @@ import {
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  termdbCategoriesPayload,
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  validCategoriesRequest,
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  validCategoriesResponse
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- } from "./chunk-INIT6CVR.js";
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+ } from "./chunk-RY4Y5ESC.js";
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  import "./chunk-YNHC5SXO.js";
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  export {
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  termdbCategoriesPayload,
package/dist/termdb.chat.js CHANGED
@@ -56,7 +56,7 @@ var validChatRequest = (input) => {
56
56
  const $io25 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "isoformExpression" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && (void 0 === input3.kind || "isoform" === input3.kind) && "string" === typeof input3.isoform && (void 0 === input3.gene || "string" === typeof input3.gene) && (void 0 === input3.chr || "string" === typeof input3.chr) && (void 0 === input3.start || "number" === typeof input3.start) && (void 0 === input3.stop || "number" === typeof input3.stop);
57
57
  const $io26 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "isoformExpression" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && (void 0 === input3.kind || "coord" === input3.kind) && (void 0 === input3.isoform || "string" === typeof input3.isoform) && (void 0 === input3.gene || "string" === typeof input3.gene) && "string" === typeof input3.chr && "number" === typeof input3.start && "number" === typeof input3.stop;
58
58
  const $io27 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "metaboliteIntensity" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.metabolite && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
59
- const $io28 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "proteomeAbundance" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.protein && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && ("object" === typeof input3.proteomeDetails && null !== input3.proteomeDetails && ("string" === typeof input3.proteomeDetails.assay && "string" === typeof input3.proteomeDetails.cohort));
59
+ const $io28 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "proteomeAbundance" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.protein && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && ("object" === typeof input3.proteomeDetails && null !== input3.proteomeDetails && ("string" === typeof input3.proteomeDetails.organism && "string" === typeof input3.proteomeDetails.assay && "string" === typeof input3.proteomeDetails.cohort));
60
60
  const $io30 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "date" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
61
61
  const $io31 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "ssGSEA" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.genes || Array.isArray(input3.genes) && input3.genes.every((elem) => "string" === typeof elem)) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
62
62
  const $io32 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "dnaMethylation" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.chr && "number" === typeof input3.start && "number" === typeof input3.stop && ("gene" === input3.genomicFeatureType || "promoter" === input3.genomicFeatureType || "region" === input3.genomicFeatureType || "enhancer" === input3.genomicFeatureType) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
@@ -1675,7 +1675,11 @@ var validChatRequest = (input) => {
1675
1675
  expected: "ProteomeDetails",
1676
1676
  value: input3.proteomeDetails
1677
1677
  })].every((flag) => flag);
1678
- const $vo29 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.assay || $report(_exceptionable2, {
1678
+ const $vo29 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.organism || $report(_exceptionable2, {
1679
+ path: _path2 + ".organism",
1680
+ expected: "string",
1681
+ value: input3.organism
1682
+ }), "string" === typeof input3.assay || $report(_exceptionable2, {
1679
1683
  path: _path2 + ".assay",
1680
1684
  expected: "string",
1681
1685
  value: input3.assay
package/dist/termdb.chat2.js CHANGED
@@ -1,7 +1,7 @@
1
1
  import {
2
2
  validChatRequest,
3
3
  validChatResponse
4
- } from "./chunk-TUM3OZ7K.js";
4
+ } from "./chunk-DVMD6CBJ.js";
5
5
  import {
6
6
  ChatPayload
7
7
  } from "./chunk-FRXRNCDV.js";
package/dist/termdb.cluster.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termdbClusterPayload,
3
3
  validTermdbClusterRequest,
4
4
  validTermdbClusterResponse
5
- } from "./chunk-JMVDRHBL.js";
5
+ } from "./chunk-SGMHY5K7.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termdbClusterPayload,
package/dist/termdb.descrstats.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  descrStatsPayload,
3
3
  validDescrStatsRequest,
4
4
  validDescrStatsResponse
5
- } from "./chunk-Y6FNAG22.js";
5
+ } from "./chunk-MMNSJ72P.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  descrStatsPayload,
package/dist/termdb.diffMeth.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  diffMethPayload,
3
3
  validDiffMethRequest,
4
4
  validDiffMethResponse
5
- } from "./chunk-CWJZUUEF.js";
5
+ } from "./chunk-FEMYT7FL.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  diffMethPayload,
package/dist/termdb.dmr.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  TermdbDmrPayload,
3
3
  validTermdbDmrRequest,
4
4
  validTermdbDmrResponse
5
- } from "./chunk-NO3ZZD3L.js";
5
+ } from "./chunk-46DTJOK5.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  TermdbDmrPayload,
package/dist/termdb.numericcategories.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  numericCategoriesPayload,
3
3
  validNumericCategoriesRequest,
4
4
  validNumericCategoriesResponse
5
- } from "./chunk-LDLZU2QY.js";
5
+ } from "./chunk-VWLYQ33F.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  numericCategoriesPayload,
package/dist/termdb.percentile.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  percentilePayload,
3
3
  validPercentileRequest,
4
4
  validPercentileResponse
5
- } from "./chunk-ONNT3XV7.js";
5
+ } from "./chunk-I3QGRA7O.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  percentilePayload,
package/dist/termdb.singlecellDEgenes.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termdbSingleCellDEgenesPayload,
3
3
  validTermdbSingleCellDEgenesRequest,
4
4
  validTermdbSingleCellDEgenesResponse
5
- } from "./chunk-NLANDPY7.js";
5
+ } from "./chunk-OCH5BJCV.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termdbSingleCellDEgenesPayload,
package/dist/termdb.termsbyids.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termsByIdsPayload,
3
3
  validTermsByIdsRequest,
4
4
  validTermsByIdsResponse
5
- } from "./chunk-UWK6LBTQ.js";
5
+ } from "./chunk-F2QRI6B2.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termsByIdsPayload,
package/dist/termdb.topTermsByType.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termdbTopTermsByTypePayload,
3
3
  validTermdbTopTermsByTypeRequest,
4
4
  validTermdbTopTermsByTypeResponse
5
- } from "./chunk-2NINVZOB.js";
5
+ } from "./chunk-AYTV7V46.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termdbTopTermsByTypePayload,
package/dist/termdb.topVariablyExpressedGenes.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  termdbTopVariablyExpressedGenesPayload,
3
3
  validTermdbTopVariablyExpressedGenesRequest,
4
4
  validTermdbTopVariablyExpressedGenesResponse
5
- } from "./chunk-QMEKJW2A.js";
5
+ } from "./chunk-DPJUULKQ.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  termdbTopVariablyExpressedGenesPayload,
package/dist/termdb.violinBox.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  validViolinBoxRequest,
3
3
  validViolinBoxResponse,
4
4
  violinBoxPayload
5
- } from "./chunk-WNUWRPXG.js";
5
+ } from "./chunk-IIWTMQJZ.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  validViolinBoxRequest,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@sjcrh/proteinpaint-types",
3
- "version": "2.185.0",
3
+ "version": "2.186.0",
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
@@ -734,9 +734,19 @@ type ProteomeAssayConfig = {
734
734
  export type ProteomeAbundanceQuery = {
735
735
  /** database file path */
736
736
  dbfile?: string
737
- overlayTerm?: BaseTerm
738
- /** document structure */
739
- assays: {
737
+ /** organism-keyed structure (new format) */
738
+ organisms?: {
739
+ [organism: string]: {
740
+ overlayTerm: BaseTerm
741
+ columnIdx: number
742
+ columnValue?: string
743
+ assays: {
744
+ [assayName: string]: ProteomeAssayConfig
745
+ }
746
+ }
747
+ }
748
+ /** flat assays structure (legacy format) */
749
+ assays?: {
740
750
  [assayName: string]: ProteomeAssayConfig
741
751
  }
742
752
  samples?: number[]
@@ -1377,6 +1387,8 @@ type MatrixSettings = {
1377
1387
  cnvUnit?: 'log2ratio' | 'segmedian'
1378
1388
  /** whether to show white cell border for SNVindel in oncoPrint mode */
1379
1389
  oncoPrintSNVindelCellBorder?: boolean
1390
+ /** use a geneset edit UI without or with initial radio inputs */
1391
+ genesetEditUiVersion?: '' | 'withTabs'
1380
1392
  }
1381
1393
 
1382
1394
  type NumericDictTermClusterSettings = {
package/src/routes/termdb.DE.ts CHANGED
@@ -94,13 +94,23 @@ export type VolcanoData<T extends DataEntry> = {
94
94
  /** Coordinate metadata returned by the `volcano` renderer, used by the client to overlay
95
95
  * interactive top-significant circles on top of the server-drawn PNG. */
96
96
  export type PlotExtent = {
97
- /** Data-space x domain used during rendering. */
97
+ /** Padded data-space x domain — used to position overlay dots so points near
98
+ * the real-data edges stay fully visible (mirror of manhattan's yPlot domain). */
98
99
  xMin: number
99
100
  xMax: number
100
- /** Data-space y domain used during rendering (on -log10 p-value scale). */
101
+ /** Padded data-space y domain (on -log10 p-value scale). */
101
102
  yMin: number
102
103
  yMax: number
103
- /** PNG canvas dimensions. */
104
+ /** Unpadded data-space x domain — used for the visible axis labels/ticks
105
+ * so the axis only spans the real data region. */
106
+ xMinUnpadded: number
107
+ xMaxUnpadded: number
108
+ /** Unpadded data-space y domain. */
109
+ yMinUnpadded: number
110
+ yMaxUnpadded: number
111
+ /** Dot radius in pixels (echoed back so overlay rings match the PNG). */
112
+ dotRadiusPx: number
113
+ /** PNG canvas dimensions (already include 2*dotRadiusPx of padding). */
104
114
  pixelWidth: number
105
115
  pixelHeight: number
106
116
  /** Inner drawing rect inside the PNG (after axis margins). Client overlay circles
package/src/routes/termdb.cluster.ts CHANGED
@@ -66,7 +66,7 @@ export type TermdbClusterRequestProteomeAbundance = TermdbClusterRequestBase & {
66
66
  terms: ProteomeAbundanceTW[]
67
67
  /** perform z-score transformation on values */
68
68
  zScoreTransformation?: string
69
- /** assay type and cohort for the selected proteome data */
69
+ /** organism, assay type and cohort for the selected proteome data */
70
70
  proteomeDetails: ProteomeDetails
71
71
  }
72
72
 
package/src/terms/proteomeAbundance.ts CHANGED
@@ -8,6 +8,7 @@ ProteomeTermSettingInstance
8
8
  */
9
9
 
10
10
  export type ProteomeDetails = {
11
+ organism: string
11
12
  assay: string
12
13
  cohort: string
13
14
  }
@@ -19,7 +20,7 @@ export type ProteomeAbundanceTerm = NumericBaseTerm & {
19
20
  protein: string
20
21
  bins?: PresetNumericBins
21
22
  unit?: string
22
- /** assay and cohort this term belongs to */
23
+ /** organism, assay and cohort this term belongs to */
23
24
  proteomeDetails: ProteomeDetails
24
25
  }
25
26