@sjcrh/proteinpaint-types 2.109.1-0 → 2.110.0

package/dist/index.js

@@ -2,233 +2,233 @@ import {
   termChildrenPayload,
   validTermChildrenRequest,
   validTermChildrenResponse
-} from "./chunk-5RZYB4M4.js";
+} from "./chunk-HKGWC7OO.js";
 import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-PFG6MDVS.js";
+} from "./chunk-TXZQ56TX.js";
 import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-WSXS2FSQ.js";
+} from "./chunk-4CCAF4O5.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-MUMDRXDY.js";
+} from "./chunk-A72XYNKT.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-JGY7OWQH.js";
+} from "./chunk-ZFUF4XMD.js";
 import {
   tilePayload,
   validTileRequest,
   validTileResponse
-} from "./chunk-6EFB6ZMB.js";
+} from "./chunk-KFVYRW7D.js";
 import {
   validWSImagesRequest,
   validWSImagesResponse,
   wsImagesPayload
-} from "./chunk-W3KUIWKN.js";
+} from "./chunk-HR6GSKDC.js";
 import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-OK6BVEFI.js";
+} from "./chunk-ES6BRZ4L.js";
 import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-MD7FPJ6R.js";
+} from "./chunk-GHAIGRB7.js";
 import {
   rootTermPayload,
   validRootTermRequest,
   validRootTermResponse
-} from "./chunk-GU7LIGHN.js";
+} from "./chunk-AASWRJMS.js";
 import {
   termdbSampleImagesPayload,
   validTermdbSampleImagesRequest,
   validTermdbSampleImagesResponse
-} from "./chunk-37ZPCVP5.js";
+} from "./chunk-X2CX5K24.js";
 import {
   termdbSingleSampleMutationPayload,
   validTermdbSingleSampleMutationRequest,
   validTermdbSingleSampleMutationResponse
-} from "./chunk-QDIIM52V.js";
+} from "./chunk-VZMNH6SN.js";
 import {
   termdbSingleCellDEgenesPayload,
   validTermdbSingleCellDEgenesRequest,
   validTermdbSingleCellDEgenesResponse
-} from "./chunk-XGAOGA3F.js";
+} from "./chunk-XEQWKMZN.js";
 import {
   termdbSingleCellDataPayload,
   validTermdbSingleCellDataRequest,
   validTermdbSingleCellDataResponse
-} from "./chunk-FDTUTGQG.js";
+} from "./chunk-ZAMCS7PC.js";
 import {
   termdbSingleCellSamplesPayload,
   validTermdbSingleCellSamplesRequest,
   validTermdbSingleCellSamplesResponse
-} from "./chunk-FZ6QOTGM.js";
+} from "./chunk-GRI3224V.js";
 import {
   snpPayload,
   validSnpRequest,
   validSnpResponse
-} from "./chunk-XJCQEOPB.js";
+} from "./chunk-J4QAF4EU.js";
 import {
   diffExpPayload,
   validDERequest,
   validDEResponse
-} from "./chunk-2HMIFPRH.js";
+} from "./chunk-QNDN265J.js";
 import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-A7N3MZBR.js";
+} from "./chunk-2WZPM25H.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-KADNDGDN.js";
+} from "./chunk-7Z3AE4AY.js";
 import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-C7NNY32H.js";
+} from "./chunk-NPVDG36X.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
   validTermdbCohortSummaryResponse
-} from "./chunk-7PMGKVWQ.js";
+} from "./chunk-QX3MRSSK.js";
 import {
   termdbCohortsPayload,
   validTermdbCohortsRequest,
   validTermdbCohortsResponse
-} from "./chunk-EWRK4PKZ.js";
+} from "./chunk-EH7VAE5S.js";
 import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-QVDCLRUP.js";
+} from "./chunk-KHPBBU43.js";
 import {
   hicGenomePayload,
   validHicGenomeRequest,
   validHicGenomeResponse
-} from "./chunk-W3QYIXXF.js";
+} from "./chunk-I2KWGMNM.js";
 import {
   hicstatPayload,
   validHicstatRequest,
   validHicstatResponse
-} from "./chunk-QX7QLUKY.js";
+} from "./chunk-FXCCZCTN.js";
 import {
   imgPayload,
   validimgRequest,
   validimgResponse
-} from "./chunk-NBLSSFQV.js";
+} from "./chunk-KVUJPR42.js";
 import {
   isoformlstPayload,
   validIsoformLstRequest,
   validIsoformLstResponse
-} from "./chunk-UIU3IQH4.js";
+} from "./chunk-B43GFRT4.js";
 import {
   ntseqPayload,
   validNtseqRequest,
   validNtseqResponse
-} from "./chunk-5GG2FNAY.js";
+} from "./chunk-HIPWQ6AW.js";
 import {
   pdomainPayload,
   validPdomainRequest,
   validPdomainResponse
-} from "./chunk-OMHEDUNA.js";
+} from "./chunk-L5DFYFWX.js";
 import {
   sampleWSImagesPayload,
   validSampleWSImagesRequest,
   validSampleWSImagesResponse
-} from "./chunk-75VJBEAQ.js";
+} from "./chunk-W4JULXYD.js";
 import {
   gdcMafPayload,
   validGdcMafRequest,
   validGdcMafResponse
-} from "./chunk-OTFT3JZB.js";
+} from "./chunk-K4RV3N2T.js";
 import {
   GdcMafPayload,
   validGdcMafBuildRequest,
   validGdcMafBuildResponse
-} from "./chunk-DIDZMC3G.js";
+} from "./chunk-F5XGJIUS.js";
 import {
   gdcTopMutatedGenePayload,
   validGdcTopMutatedGeneRequest,
   validGdcTopMutatedGeneResponse
-} from "./chunk-7Z3IHB43.js";
+} from "./chunk-Q5F2XI6A.js";
 import {
   geneLookupPayload,
   validGeneLookupRequest,
   validGeneLookupResponse
-} from "./chunk-XQQ5G6N6.js";
+} from "./chunk-HNETXFC7.js";
 import {
   genesetEnrichmentPayload,
   validGenesetEnrichmentRequest,
   validGenesetEnrichmentResponse
-} from "./chunk-ERA5PPKH.js";
+} from "./chunk-XZAH6P4D.js";
 import {
   genesetOverrepresentationPayload,
   validGenesetOverrepresentationRequest,
   validGenesetOverrepresentationResponse
-} from "./chunk-K2KQTFQI.js";
+} from "./chunk-VMSVBNM6.js";
 import {
   healthcheckPayload,
   validHealthCheckRequest,
   validHealthCheckResponse
-} from "./chunk-B3D26X6X.js";
+} from "./chunk-KRYTJ2SL.js";
 import {
   hicdataPayload,
   validHicdataRequest,
   validHicdataResponse
-} from "./chunk-5JWTIWVB.js";
+} from "./chunk-VKBTOKI2.js";
 import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-XPPUNYBL.js";
+} from "./chunk-GGKNEHME.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,
   validBrainImagingSamplesResponse
-} from "./chunk-OY3EKV7F.js";
+} from "./chunk-IVU6STSJ.js";
 import {
   burdenPayload,
   validBurdenRequest,
   validBurdenResponse
-} from "./chunk-GHD26RNJ.js";
+} from "./chunk-ZVTZJRGS.js";
 import {
   clearWSImagesSessionsPayload,
   validClearWSImagesSessionsRequest,
   validClearWSImagesSessionsResponse
-} from "./chunk-GT3NJM3E.js";
+} from "./chunk-QNBBWHEY.js";
 import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-2R2EFRAW.js";
+} from "./chunk-FMW25T52.js";
 import {
   datasetPayload,
   validDatasetRequest,
   validDatasetResponse
-} from "./chunk-MUJUKENL.js";
+} from "./chunk-5S3UWYSK.js";
 import {
   dsDataPayload,
   validDsDataRequest,
   validDsDataResponse
-} from "./chunk-N45Z3JCY.js";
+} from "./chunk-4GCROGGK.js";
 import {
   dzImagesPayload,
   validDZImagesRequest,
   validDZImagesResponse
-} from "./chunk-SDOWCOGK.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-XT2IWGYK.js";
+import "./chunk-CNSSF43V.js";
 export {
   CorrelationVolcanoPayload,
   GdcMafPayload,

package/dist/isoformlst.js

@@ -2,8 +2,8 @@ import {
   isoformlstPayload,
   validIsoformLstRequest,
   validIsoformLstResponse
-} from "./chunk-UIU3IQH4.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-B43GFRT4.js";
+import "./chunk-CNSSF43V.js";
 export {
   isoformlstPayload,
   validIsoformLstRequest,

package/dist/ntseq.js

@@ -2,8 +2,8 @@ import {
   ntseqPayload,
   validNtseqRequest,
   validNtseqResponse
-} from "./chunk-5GG2FNAY.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-HIPWQ6AW.js";
+import "./chunk-CNSSF43V.js";
 export {
   ntseqPayload,
   validNtseqRequest,

package/dist/pdomain.js

@@ -2,8 +2,8 @@ import {
   pdomainPayload,
   validPdomainRequest,
   validPdomainResponse
-} from "./chunk-OMHEDUNA.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-L5DFYFWX.js";
+import "./chunk-CNSSF43V.js";
 export {
   pdomainPayload,
   validPdomainRequest,

package/dist/samplewsimages.js

@@ -2,8 +2,8 @@ import {
   sampleWSImagesPayload,
   validSampleWSImagesRequest,
   validSampleWSImagesResponse
-} from "./chunk-75VJBEAQ.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-W4JULXYD.js";
+import "./chunk-CNSSF43V.js";
 export {
   sampleWSImagesPayload,
   validSampleWSImagesRequest,

package/dist/snp.js

@@ -2,8 +2,8 @@ import {
   snpPayload,
   validSnpRequest,
   validSnpResponse
-} from "./chunk-XJCQEOPB.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-J4QAF4EU.js";
+import "./chunk-CNSSF43V.js";
 export {
   snpPayload,
   validSnpRequest,

package/dist/termdb.DE.js

@@ -2,8 +2,8 @@ import {
   diffExpPayload,
   validDERequest,
   validDEResponse
-} from "./chunk-2HMIFPRH.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-QNDN265J.js";
+import "./chunk-CNSSF43V.js";
 export {
   diffExpPayload,
   validDERequest,

package/dist/termdb.boxplot.js

@@ -2,8 +2,8 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-A7N3MZBR.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-2WZPM25H.js";
+import "./chunk-CNSSF43V.js";
 export {
   boxplotPayload,
   validBoxPlotRequest,

package/dist/termdb.categories.js

@@ -2,8 +2,8 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-KADNDGDN.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-7Z3AE4AY.js";
+import "./chunk-CNSSF43V.js";
 export {
   termdbCategoriesPayload,
   validCategoriesRequest,

package/dist/termdb.cluster.js

@@ -2,8 +2,8 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-C7NNY32H.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-NPVDG36X.js";
+import "./chunk-CNSSF43V.js";
 export {
   termdbClusterPayload,
   validTermdbClusterRequest,

package/dist/termdb.cohort.summary.js

@@ -2,8 +2,8 @@ import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
   validTermdbCohortSummaryResponse
-} from "./chunk-7PMGKVWQ.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-QX3MRSSK.js";
+import "./chunk-CNSSF43V.js";
 export {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,

package/dist/termdb.cohorts.js

@@ -2,8 +2,8 @@ import {
   termdbCohortsPayload,
   validTermdbCohortsRequest,
   validTermdbCohortsResponse
-} from "./chunk-EWRK4PKZ.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-EH7VAE5S.js";
+import "./chunk-CNSSF43V.js";
 export {
   termdbCohortsPayload,
   validTermdbCohortsRequest,

package/dist/termdb.descrstats.js

@@ -2,8 +2,8 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-QVDCLRUP.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-KHPBBU43.js";
+import "./chunk-CNSSF43V.js";
 export {
   descrStatsPayload,
   validDescrStatsRequest,

package/dist/termdb.numericcategories.js

@@ -2,8 +2,8 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-OK6BVEFI.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-ES6BRZ4L.js";
+import "./chunk-CNSSF43V.js";
 export {
   numericCategoriesPayload,
   validNumericCategoriesRequest,

package/dist/termdb.percentile.js

@@ -2,8 +2,8 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-MD7FPJ6R.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-GHAIGRB7.js";
+import "./chunk-CNSSF43V.js";
 export {
   percentilePayload,
   validPercentileRequest,

package/dist/termdb.rootterm.js

@@ -2,8 +2,8 @@ import {
   rootTermPayload,
   validRootTermRequest,
   validRootTermResponse
-} from "./chunk-GU7LIGHN.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-AASWRJMS.js";
+import "./chunk-CNSSF43V.js";
 export {
   rootTermPayload,
   validRootTermRequest,

package/dist/termdb.sampleImages.js

@@ -2,8 +2,8 @@ import {
   termdbSampleImagesPayload,
   validTermdbSampleImagesRequest,
   validTermdbSampleImagesResponse
-} from "./chunk-37ZPCVP5.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-X2CX5K24.js";
+import "./chunk-CNSSF43V.js";
 export {
   termdbSampleImagesPayload,
   validTermdbSampleImagesRequest,

package/dist/termdb.singleSampleMutation.js

@@ -2,8 +2,8 @@ import {
   termdbSingleSampleMutationPayload,
   validTermdbSingleSampleMutationRequest,
   validTermdbSingleSampleMutationResponse
-} from "./chunk-QDIIM52V.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-VZMNH6SN.js";
+import "./chunk-CNSSF43V.js";
 export {
   termdbSingleSampleMutationPayload,
   validTermdbSingleSampleMutationRequest,

package/dist/termdb.singlecellDEgenes.js

@@ -2,8 +2,8 @@ import {
   termdbSingleCellDEgenesPayload,
   validTermdbSingleCellDEgenesRequest,
   validTermdbSingleCellDEgenesResponse
-} from "./chunk-XGAOGA3F.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-XEQWKMZN.js";
+import "./chunk-CNSSF43V.js";
 export {
   termdbSingleCellDEgenesPayload,
   validTermdbSingleCellDEgenesRequest,

package/dist/termdb.singlecellData.js

@@ -2,8 +2,8 @@ import {
   termdbSingleCellDataPayload,
   validTermdbSingleCellDataRequest,
   validTermdbSingleCellDataResponse
-} from "./chunk-FDTUTGQG.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-ZAMCS7PC.js";
+import "./chunk-CNSSF43V.js";
 export {
   termdbSingleCellDataPayload,
   validTermdbSingleCellDataRequest,

package/dist/termdb.singlecellSamples.js

@@ -2,8 +2,8 @@ import {
   termdbSingleCellSamplesPayload,
   validTermdbSingleCellSamplesRequest,
   validTermdbSingleCellSamplesResponse
-} from "./chunk-FZ6QOTGM.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-GRI3224V.js";
+import "./chunk-CNSSF43V.js";
 export {
   termdbSingleCellSamplesPayload,
   validTermdbSingleCellSamplesRequest,

package/dist/termdb.termchildren.js

@@ -2,8 +2,8 @@ import {
   termChildrenPayload,
   validTermChildrenRequest,
   validTermChildrenResponse
-} from "./chunk-5RZYB4M4.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-HKGWC7OO.js";
+import "./chunk-CNSSF43V.js";
 export {
   termChildrenPayload,
   validTermChildrenRequest,

package/dist/termdb.termsbyids.js

@@ -2,8 +2,8 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-PFG6MDVS.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-TXZQ56TX.js";
+import "./chunk-CNSSF43V.js";
 export {
   termsByIdsPayload,
   validTermsByIdsRequest,

package/dist/termdb.topTermsByType.js

@@ -2,8 +2,8 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-WSXS2FSQ.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-4CCAF4O5.js";
+import "./chunk-CNSSF43V.js";
 export {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,8 +2,8 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-MUMDRXDY.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-A72XYNKT.js";
+import "./chunk-CNSSF43V.js";
 export {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,

package/dist/termdb.violin.js

@@ -2,8 +2,8 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-JGY7OWQH.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-ZFUF4XMD.js";
+import "./chunk-CNSSF43V.js";
 export {
   validViolinRequest,
   validViolinResponse,

package/dist/tileserver.js

@@ -2,8 +2,8 @@ import {
   tilePayload,
   validTileRequest,
   validTileResponse
-} from "./chunk-6EFB6ZMB.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-KFVYRW7D.js";
+import "./chunk-CNSSF43V.js";
 export {
   tilePayload,
   validTileRequest,

package/dist/wsimages.js

@@ -2,8 +2,8 @@ import {
   validWSImagesRequest,
   validWSImagesResponse,
   wsImagesPayload
-} from "./chunk-W3KUIWKN.js";
-import "./chunk-Z6B6IQIY.js";
+} from "./chunk-HR6GSKDC.js";
+import "./chunk-CNSSF43V.js";
 export {
   validWSImagesRequest,
   validWSImagesResponse,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.109.1-0",
+  "version": "2.110.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -556,21 +556,23 @@ export type MetaboliteIntensityQuery = MetaboliteIntensityQueryNative
 
 /** the geneExpression query */
 export type GeneExpressionQueryGdc = {
-	src: 'gdcapi' | string
+	src: 'gdcapi'
 	geneExpression2bins?: { [index: string]: any }
 }
 
 export type GeneExpressionQueryNative = {
-	src: 'native' | string
+	src: 'native'
+	/** bgzip-compressed, tabix-index file.
+	first line must be "#chr \t start \t stop \t gene \t sample1 \t ..." */
 	file: string
 	/** dynamically added during server launch, list of sample integer IDs from file */
 	samples?: number[]
+	/** dynamically added flag during launch */
 	nochr?: boolean
+	/** dynamically added getter */
 	get?: (param: any) => void
 	/** This dictionary is used to store/cache the default bins calculated for a geneExpression term when initialized in the fillTermWrapper */
 	geneExpression2bins?: { [index: string]: any }
-	/** Type of data format HDF5 or bed */
-	storage_type?: 'HDF5' | 'bed'
 }
 
 export type GeneExpressionQuery = GeneExpressionQueryGdc | GeneExpressionQueryNative

package/src/routes/termdb.DE.ts

@@ -59,6 +59,10 @@ export type DEResponse = {
 	sample_size2: number
 	/** Method of DE used wilcoxon/edgeR */
 	method: string
+	/** Image name from edgeR describing the quality of the fitting from QL pipeline, this is only generated for edgeR not for wilcoxon method  */
+	ql_image?: string
+	/** Image name from edgeR showing the MDS plot of samples from both groups, this is only generated for edgeR not for wilcoxon method */
+	mds_image?: string
 }
 
 export const diffExpPayload: RoutePayload = {