@sjcrh/proteinpaint-types 2.151.1-0 → 2.152.1-0

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-75GS5ZG5.js";
+} from "./chunk-LXW2FSLR.js";
 import "./chunk-YNHC5SXO.js";
 export {
   CorrelationVolcanoPayload,

package/dist/gdc.grin2.js

@@ -5,7 +5,7 @@ import {
   validGdcGRIN2listResponse,
   validRunGRIN2Request,
   validRunGRIN2Response
-} from "./chunk-2WSENLMK.js";
+} from "./chunk-46YIGVUP.js";
 import "./chunk-YNHC5SXO.js";
 export {
   gdcGRIN2listPayload,

package/dist/gdc.maf.js

@@ -2,7 +2,7 @@ import {
   gdcMafPayload,
   validGdcMafRequest,
   validGdcMafResponse
-} from "./chunk-MIOIOFBZ.js";
+} from "./chunk-TD4YLTHL.js";
 import "./chunk-YNHC5SXO.js";
 export {
   gdcMafPayload,

package/dist/index.js

@@ -7,17 +7,17 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-KQNLROUN.js";
+} from "./chunk-GZKTMVAU.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-OZ3CVAFP.js";
+} from "./chunk-EBPGV76U.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-MMFL6N5M.js";
+} from "./chunk-OLXOQLZH.js";
 import {
   tilePayload,
   validTileRequest,
@@ -72,7 +72,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-WL7ZVGZS.js";
+} from "./chunk-C27KCAQH.js";
 import {
   termdbCohortsPayload,
   validTermdbCohortsRequest,
@@ -82,7 +82,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-4SJC57Y6.js";
+} from "./chunk-ZXPLL3NT.js";
 import {
   FilterTermValuesPayload,
   validFilterTermValuesRequest,
@@ -92,12 +92,12 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-4MLQS6N7.js";
+} from "./chunk-OLWNM7QP.js";
 import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-TTUU5XQC.js";
+} from "./chunk-5F24QFE7.js";
 import {
   ProfileFormScoresPayload,
   validProfileFormScoresRequest,
@@ -132,22 +132,22 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-3SKFYOKV.js";
+} from "./chunk-JT4DSNJ3.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-RA7IEGS4.js";
+} from "./chunk-MCL6EDOS.js";
 import {
   ChatPayload,
   validChatRequest,
   validChatResponse
-} from "./chunk-DBSRGRXR.js";
+} from "./chunk-OAETETAO.js";
 import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-5MGSKBUU.js";
+} from "./chunk-CC32XCET.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -192,7 +192,7 @@ import {
   gdcMafPayload,
   validGdcMafRequest,
   validGdcMafResponse
-} from "./chunk-MIOIOFBZ.js";
+} from "./chunk-TD4YLTHL.js";
 import {
   GdcMafPayload,
   validGdcMafBuildRequest,
@@ -239,7 +239,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-75GS5ZG5.js";
+} from "./chunk-LXW2FSLR.js";
 import {
   datasetPayload,
   validDatasetRequest,
@@ -267,7 +267,7 @@ import {
   validGdcGRIN2listResponse,
   validRunGRIN2Request,
   validRunGRIN2Response
-} from "./chunk-2WSENLMK.js";
+} from "./chunk-46YIGVUP.js";
 import {
   aiProjectAdminPayload,
   validAIProjectAdminRequest,
@@ -297,7 +297,7 @@ import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-KSVIBMFQ.js";
+} from "./chunk-5OMJAZK4.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-3SKFYOKV.js";
+} from "./chunk-JT4DSNJ3.js";
 import "./chunk-YNHC5SXO.js";
 export {
   boxplotPayload,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-RA7IEGS4.js";
+} from "./chunk-MCL6EDOS.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.chat.js

@@ -2,7 +2,7 @@ import {
   ChatPayload,
   validChatRequest,
   validChatResponse
-} from "./chunk-DBSRGRXR.js";
+} from "./chunk-OAETETAO.js";
 import "./chunk-YNHC5SXO.js";
 export {
   ChatPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-5MGSKBUU.js";
+} from "./chunk-CC32XCET.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-4SJC57Y6.js";
+} from "./chunk-ZXPLL3NT.js";
 import "./chunk-YNHC5SXO.js";
 export {
   descrStatsPayload,

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-4MLQS6N7.js";
+} from "./chunk-OLWNM7QP.js";
 import "./chunk-YNHC5SXO.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-TTUU5XQC.js";
+} from "./chunk-5F24QFE7.js";
 import "./chunk-YNHC5SXO.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-WL7ZVGZS.js";
+} from "./chunk-C27KCAQH.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-KQNLROUN.js";
+} from "./chunk-GZKTMVAU.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-OZ3CVAFP.js";
+} from "./chunk-EBPGV76U.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-MMFL6N5M.js";
+} from "./chunk-OLXOQLZH.js";
 import "./chunk-YNHC5SXO.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.151.1-0",
+  "version": "2.152.1-0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -15,11 +15,6 @@ type KeyVal = {
 	v?: string
 }
 
-type KeyLabel = {
-	key: string
-	label: string
-}
-
 /** a set of categories about a vcf INFO field */
 export type InfoFieldCategories = {
 	/** category key from an INFO field of a vcf file */
@@ -1062,7 +1057,7 @@ export type WSImages = {
 	/**  ds supplied */
 	getAnnotationClasses?: (projectId: string) => Promise<WSIClass[] | undefined>
 	/**  ds supplied */
-	retrainModel?: (projectId: string) => Promise<void>
+	retrainModel?: (projectId: string, wsimages: string[]) => Promise<void>
 }
 
 export type WSIClass = { id: number; key_shortcut: string; label: string; color: string }
@@ -1172,24 +1167,6 @@ type UiLabels = {
 	[propName: string]: string | { label: string; [otherAttr: string]: string }
 }
 
-type SurvPlotsEntry = {
-	name: string
-	serialtimekey: string
-	iscensoredkey: string
-	timelabel: string
-}
-
-type SurvPlots = {
-	[index: string]: SurvPlotsEntry
-}
-
-type sampleGroupAttrLstEntry = { key: string }
-
-type SurvivalPlot = {
-	plots: SurvPlots
-	samplegroupattrlst: sampleGroupAttrLstEntry[]
-}
-
 type TieBreakerFilterValuesEntry = {
 	dt: number
 }
@@ -1778,257 +1755,6 @@ type Title = {
 	text: string
 	link?: string
 }
-/*** types supporting MdsCohort type ***/
-type SampleAttribute = {
-	attributes: Attributes
-}
-
-type HierarchiesLstEntry = {
-	name: string
-	levels: KeyLabelFull[]
-}
-
-type Hierarchies = {
-	lst: HierarchiesLstEntry[]
-}
-
-type SetSamples = {
-	file: string
-	valuename: string
-	skipzero: boolean
-}
-
-type SetSignatures = {
-	[index: number]: { name: string; color: string }
-}
-
-type MutSigSets = {
-	[index: string]: {
-		name: string
-		samples: SetSamples
-		signatures: SetSignatures
-	}
-}
-
-type MutationSignature = {
-	sets: MutSigSets
-}
-
-type MdsCohort = {
-	//Does not apply to Mds3 or genomes!
-	files: FileObj[]
-	samplenamekey: string
-	tohash: (item: any, ds: any) => void //Fix later
-	sampleAttribute?: SampleAttribute
-	hierarchies?: Hierarchies
-	survivalplot?: SurvivalPlot
-	mutation_signature?: MutationSignature
-	//scatterplot - skipping b/c codes to the old scatterplot, not mass
-}
-
-/*** types supporting MdsQueries type ***/
-type BaseTrack = {
-	name?: string
-	istrack?: boolean
-	type?: string
-	file?: string
-	hideforthemoment?: number
-	viewrangeupperlimit?: number
-}
-
-type LegendVOrigin = {
-	key: string
-	somatic: string
-	germline: string
-}
-
-type GroupSampleByAttr = {
-	attrlst: KeyLabelFull[]
-	sortgroupby?: {
-		key: string
-		order: string[]
-	}
-	attrnamespacer?: string
-}
-
-type Svcnv = BaseTrack & {
-	valueCutoff: number
-	bplengthUpperLimit: number
-	segmeanValueCutoff?: number
-	no_loh?: number
-	lohLengthUpperLimit?: number
-	hideLOHwithCNVoverlap?: boolean
-	vcf_querykey?: string
-	expressionrank_querykey?: string
-	multihidelabel_vcf: boolean
-	multihidelabel_fusion?: boolean
-	multihidelabel_sv: boolean
-	legend_vorigin?: LegendVOrigin
-	groupsamplebyattr?: GroupSampleByAttr
-}
-
-type KeyLabelFull = {
-	/* Used in: 
-                queries.genefpkm.boxplotbysamplegroup.attributes
-                cohort.hierarchies.lst[i].levels
-*/
-	k: string
-	label: string
-	full?: string
-}
-
-type ASE = {
-	qvalue: number
-	meandelta_monoallelic: number
-	asemarkernumber_biallelic: number
-	color_noinfo: string
-	color_notsure: string
-	color_biallelic: string
-	color_monoallelic: string
-}
-
-type GeneFpkmOutlier = {
-	pvalue: number
-	color: string
-}
-
-type BoxPlotAdditionalsEntry = {
-	label: string
-	attributes: KeyVal[]
-}
-
-type BoxPlotBySampleGroup = {
-	attributes: KeyLabelFull[]
-	additionals?: BoxPlotAdditionalsEntry[]
-}
-
-type Fpkm = BaseTrack & {
-	datatype: string
-	itemcolor: string
-}
-
-type GeneFpkm = Fpkm & {
-	isgenenumeric: boolean
-	boxplotbysamplegroup?: BoxPlotBySampleGroup
-	ase?: ASE
-	outlier?: GeneFpkmOutlier
-}
-
-type CutoffValueLstEntry = {
-	/** '<' or '>' to add to the label */
-	side: string
-	value: number
-	label: string
-}
-
-type ValuePerSample = KeyLabel & {
-	cutoffValueLst: CutoffValueLstEntry[]
-}
-
-type InfoFilterCatEntry = {
-	label: string
-	color: string
-	valuePerSample?: ValuePerSample
-}
-
-type InfoFilterCat = {
-	[index: string]: InfoFilterCatEntry
-}
-
-type InfoFilterLstEntry = KeyLabel & {
-	categories: InfoFilterCat
-	hiddenCategories: { Unannotated: number }
-}
-
-type InfoFilter = {
-	lst: InfoFilterLstEntry[]
-}
-
-type ReadCountBoxPlotPerCohort = {
-	groups: KeyLabel[]
-}
-
-type SingleJunctionSummary = {
-	readcountboxplotpercohort: ReadCountBoxPlotPerCohort
-}
-
-type Junction = BaseTrack & {
-	readcountCutoff: number
-	infoFilter: InfoFilter
-	singlejunctionsummary: SingleJunctionSummary
-}
-
-type MdsSnvindel = BaseTrack & {
-	tracks: BaseTrack[]
-	singlesamples?: {
-		tablefile: string
-	}
-}
-
-type SomaticCnv = BaseTrack & {
-	valueLabel: string
-	valueCutoff: number
-	bplengthUpperLimit: number
-}
-
-type Vcf = BaseTrack & {
-	tracks: BaseTrack[]
-}
-
-type MdsQueries = {
-	svcnv?: Svcnv
-	genefpkm?: GeneFpkm
-	junction?: Junction
-	snvindel?: MdsSnvindel
-	somaticcnv?: SomaticCnv
-	vcf?: Vcf
-	fpkm?: Fpkm
-}
-
-type AttrValues = {
-	[index: string]: {
-		name?: string
-		label?: string
-		color?: string
-	}
-}
-
-type AttributesEntry = {
-	label: string
-	values?: AttrValues
-	hidden?: number
-	filter?: number
-	appendto_link?: string
-	isfloat?: number | boolean
-	isinteger?: number | boolean
-	clientnoshow?: number
-	showintrack?: boolean
-}
-
-type Attributes = {
-	[index: string]: AttributesEntry
-}
-
-type MutationAttribute = {
-	attributes: Attributes
-}
-
-type MutationTypesEntry = {
-	db_col: string
-	label?: string
-	default: number
-	sizecutoff?: string
-	log2cutoff?: number
-}
-
-type Gene2MutCount = {
-	dbfile: string
-	mutationTypes: MutationTypesEntry[]
-}
-
-type LocusAttribute = {
-	attributes: Attributes
-}
 
 type ViewMode = {
 	byAttribute?: string
@@ -2043,17 +1769,18 @@ type BaseMds = {
 }
 
 export type Mds = BaseMds & {
+	// replaced by mds3!!!
 	isMds: boolean
 	about?: KeyVal[]
 	sampleAssayTrack?: FileObj
 	singlesamplemutationjson?: FileObj
-	cohort?: MdsCohort
-	queries?: MdsQueries
-	mutationAttribute?: MutationAttribute
+	cohort?: any
+	queries?: any
+	mutationAttribute?: any
 	dbFile?: string
 	version?: { label: string; link: string }
-	gene2mutcount?: Gene2MutCount
-	locusAttribute?: LocusAttribute
+	gene2mutcount?: any
+	locusAttribute?: any
 	alleleAttribute?: {
 		attributes: {
 			[attrName: string]: {

package/src/routes/gdc.grin2.ts

@@ -20,8 +20,8 @@ export type GdcGRIN2File = {
 	file_format?: 'MAF'
 }
 
-enum ExperimentalStrategy {
-	wxs = 'WXS'
+type ExperimentalStrategy = {
+	wxs: 'WXS'
 }
 
 /**

package/src/routes/gdc.maf.ts

@@ -20,9 +20,9 @@ export type GdcMafFile = {
 	project_id: string
 }
 
-enum ExperimentalStrategy {
-	targeted = 'Targeted Sequencing',
-	wxs = 'WXS'
+export type ExperimentalStrategy = {
+	targeted: 'Targeted Sequencing'
+	wxs: 'WXS'
 }
 
 export type GdcMafRequest = {

package/src/terms/numeric.ts

@@ -108,14 +108,27 @@ export type RegularNumericBinConfig = MinBaseQ & {
 	// if last_bin?.start is set, then a fixed last bin is used; otherwise it's not fixed and computed from data
 	last_bin?: StopUnboundedBin | FullyBoundedBin
 	label_offset?: number
+	startinclusive?: boolean
+	stopinclusive?: boolean
+	/** a d3-format value to format the bin boundary values.
+	 * Defaults to none, in which case the computed bin start and stop values
+	 * (float numbers in javascript) will be used as-is for labels.
+	 * Or, when using the browser UI to edit the numeric bin, the number of decimals
+	 * in the bin_size will be used as the number of fixed decimals;
+	 * for example, bin_size = 0.25 and bin_size = 0.250 will imply a ‘.2f’ and ‘.3f’ d3-format value, respectively.
+	 * Note that the generated bin labels may use integer values in some cases for less clutter, such as when bins.size = 1.
+	 *  */
+	rounding?: string
 }
 
+export type CustomNumericBinConfigLst = [NumericBin, ...NumericBin[]]
+
 export type CustomNumericBinConfig = MinBaseQ & {
 	type: 'custom-bin'
 	mode?: 'discrete' | 'binary'
 	// since ts will allow NumericBin[] to be empty,
 	// use this workaround to define a non-empty array
-	lst: [NumericBin, ...NumericBin[]]
+	lst: CustomNumericBinConfigLst
 	preferredBins?: 'median'
 }
 
@@ -142,6 +155,8 @@ export type BinaryNumericQ = MinBaseQ & {
 	type: 'custom-bin'
 	// tuple type with 2 members
 	lst: [StartUnboundedBin | FullyBoundedBin, StopUnboundedBin | FullyBoundedBin]
+	cutoffType?: 'normal' | 'percentile'
+	cutoffPercentile?: number
 }
 
 export type ContinuousNumericQ = MinBaseQ & {
@@ -154,6 +169,7 @@ export type ContinuousNumericQ = MinBaseQ & {
 	// making type optional here makes NumericQ operations/conditions
 	// work consistently within the TermWrapper union type
 	type?: undefined
+	scale?: number
 }
 
 export type SplineNumericQ = MinBaseQ & {

package/src/terms/term.ts

@@ -39,6 +39,11 @@ export type BaseTerm = {
 	/** Do not build .values{} when building termdb. Used for 
 	making categorical term with empty .values{} in TermdbTest */
 	skipValuesBuild?: boolean
+	valueConversion?: {
+		fromUnit: string
+		toUnit: string
+		scaleFactor: string
+	}
 }
 
 // NumericTerm includes integer, float, date, geneExpression, metaboliteIntensity, and other non-dict terms