@sjcrh/proteinpaint-client 2.190.2 → 2.191.2

package/dist/chunk-TVADJLMF.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/types/src/routes/aiProjectSelectedWSImages.ts", "../../shared/types/src/routes/hicgenome.ts", "../../shared/types/src/routes/samplewsimages.ts", "../../shared/types/src/routes/termdb.categories.ts", "../../shared/types/src/routes/termdb.chat.ts", "../../shared/types/src/routes/termdb.descrstats.ts", "../../shared/types/src/routes/termdb.percentile.ts", "../../shared/types/src/routes/termdb.runChart.ts", "../../shared/types/src/routes/termdb.rootterm.ts", "../../shared/types/src/routes/termdb.termchildren.ts", "../../shared/types/src/routes/termdb.violinBox.ts", "../../shared/types/src/terms/constants.ts", "../../shared/utils/src/terms.ts"],
+  "sourcesContent": ["import type { WSImage } from './samplewsimages.ts'\n\nexport const FlagStatus = {\n\tNormal: 0,\n\tSkipped: 1,\n\tFlagged: 2,\n\tDeleted: 3\n} as const\n\nexport type FlagStatusValues = (typeof FlagStatus)[keyof typeof FlagStatus]\n\nexport const FeaturePrefixes = {\n\tStar: 'annotation-star-',\n\tSquare: 'annotation-square-',\n\tBorder: 'annotation-border-',\n\tPredBorder: 'prediction-border-'\n} as const\n\nexport type FeaturePrefixValues = (typeof FeaturePrefixes)[keyof typeof FeaturePrefixes]\n\nexport const SelectionPrefixes = {\n\tTileSelection: 'ts_',\n\tPrediction: 'pred_',\n\tAnnotation: 'anno_'\n} as const\n\nexport type SelectionPrefixValues = (typeof SelectionPrefixes)[keyof typeof SelectionPrefixes]\n\nexport const FlagStatusMessages = {\n\t[FlagStatus.Normal]: '',\n\t[FlagStatus.Skipped]: '(Skipped)',\n\t[FlagStatus.Flagged]: '(Flagged)'\n\t// Didn't add Deleted to FlagStatusMessages because deleted annotations dont exist\n\t// and deleted predictons are filtered out in proteinpaint/server/routes/aiProjectSelectedWSImages.ts around line 119\n}\n\nexport type AiProjectSelectedWSImagesRequest = {\n\tgenome: string\n\tdslabel: string\n\tprojectId: number\n\twsimagesFilenames: Array<string>\n}\n\nexport type AiProjectSelectedWSImagesResponse = {\n\t// TODO create a type for WSImage with AI project specific fields\n\twsimages: WSImage[]\n}\n\nexport interface FlagPredictionInfo {\n\tflag: FlagStatusValues\n\ttimestamp: string\n}\n\n// TODO move to another class\nexport interface TileSelection {\n\tzoomCoordinates: [number, number]\n\tclass?: string\n\tflag: FlagStatusValues\n\tid: string\n\ttimestamp: string\n}\n\nexport interface Annotation extends TileSelection {\n\tclass: string\n}\n\nexport interface Prediction extends TileSelection {\n\tclass: string\n\tuncertainty: number\n}\n\nexport function createSelectionID(prefix: SelectionPrefixValues, coordinates: [number, number]): string {\n\treturn prefix + JSON.stringify(coordinates)\n}\n\nexport function checkSelectionType(tileSelection: TileSelection, suspectedPrefix: SelectionPrefixValues): boolean {\n\treturn tileSelection.id.startsWith(suspectedPrefix)\n}\n\nexport function createFeatureID(featurePrefix: FeaturePrefixValues, coords: [number, number]) {\n\treturn featurePrefix + JSON.stringify(coords)\n}\n\n// TODO: write payload examples to help with automated testing and documentation, for non-prod use only\n", "import type { BaseHicRequest, XYZCoord } from './hicdata.ts'\n\nexport type HicGenomeRequest = BaseHicRequest & {\n\t/** Entire chromosome list read from the file (see hicstate) */\n\tchrlst: string[]\n\t/** window location */\n\tembedder: string\n\t/** whether or not the file contains 'chr' for the chromosomes */\n\tnochr: boolean\n}\n\nexport type HicGenomeResponse = {\n\tdata: {\n\t\t/** First chromosome */\n\t\tlead: string\n\t\t/** Second chromosome */\n\t\tfollow: string\n\t\titems: XYZCoord[]\n\t}[]\n\t/** Error message to display on the client, if applicable */\n\terror?: string\n}\n\n// TODO: write payload examples to help with automated testing and documentation, for non-prod use only\n// The example below will not work in github CI where only termdb test\nexport const hicGenomePayloadExample = {\n\texamples: [\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tembedder: 'localhost',\n\t\t\t\t\turl: 'https://proteinpaint.stjude.org/ppdemo/hg19/hic/hic_demo.hic',\n\t\t\t\t\tmatrixType: 'observed',\n\t\t\t\t\tnmeth: 'NONE',\n\t\t\t\t\tpos1: '3',\n\t\t\t\t\tpos2: '2',\n\t\t\t\t\tresolution: 1000000\n\t\t\t\t} // satisfies HicGenomeRequest // TODO: fix the type or example\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t}\n\t]\n}\n", "import type { WSIClass } from '../dataset.ts'\nimport type { Annotation, Prediction } from './aiProjectSelectedWSImages.ts'\n\nexport type SampleWSImagesRequest = {\n\tgenome: string\n\tdslabel: string\n\tsample_id: string\n\twsimage: string\n}\n\nexport type SampleWSImagesResponse = {\n\tsampleWSImages: WSImage[]\n}\n\nexport class WSImage {\n\tid?: number\n\tfilename: string\n\tmetadata?: string\n\tpredictionLayers?: Array<string>\n\tannotations?: Array<Annotation>\n\tpredictions?: Array<Prediction>\n\tclasses?: Array<WSIClass>\n\t/** ds defined uncertainity labels and colors */\n\tuncertainty?: any\n\t/** Color to highlight active patches */\n\tactivePatchColor?: string\n\t/** Tile size in pixels needed for AI scripts */\n\ttileSize?: number\n\n\tconstructor(filename: string) {\n\t\tthis.filename = filename\n\t}\n}\n\n// TODO: write payload examples to help with automated testing and documentation, for non-prod use only\n", "import type { Filter } from '../filter.ts'\nimport type { TermWrapper } from '../terms/tw.ts'\n\nexport type CategoriesRequest = {\n\tgenome: string\n\tdslabel: string\n\tembedder: string\n\t/** termwrapper object */\n\ttw: TermWrapper\n\tfilter?: Filter\n\tfilter0?: any\n\t/** quick fix only for gdc */\n\tcurrentGeneNames?: string[]\n\t/** optional property added by mds3 tk, to limit to cases mutated in this region */\n\trglst?: any\n}\n\ninterface Entries {\n\tsamplecount: number\n\tkey: string\n\tlabel: string\n}\n\nexport type CategoriesResponse = {\n\tlst: Entries[]\n\torderedLabels?: []\n}\n\n// TODO: write more payload examples to help with automated testing and documentation, for non-prod use only\n\nexport const termdbCategoriesPayloadExamples = {\n\trequest: {\n\t\ttypeId: 'CategoriesRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'CategoriesResponse'\n\t},\n\texamples: [\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\tembedder: 'localhost',\n\t\t\t\t\ttw: { id: 'diaggrp' },\n\t\t\t\t\tfilter: {\n\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\tin: true,\n\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t//tag: 'cohortFilter',\n\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\tname: 'Cohort',\n\t\t\t\t\t\t\t\t\t\ttype: 'categorical',\n\t\t\t\t\t\t\t\t\t\tvalues: { ABC: { label: 'ABC' }, XYZ: { label: 'XYZ' } },\n\t\t\t\t\t\t\t\t\t\tid: 'subcohort',\n\t\t\t\t\t\t\t\t\t\tisleaf: false,\n\t\t\t\t\t\t\t\t\t\tgroupsetting: { disabled: true }\n\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\tvalues: [{ key: 'ABC', label: 'ABC' }]\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t}\n\t\t\t\t} // satisfies CategoriesRequest // TODO: use the type definition\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t}\n\t]\n}\n", "import type { TermTypes } from '../terms/constants.ts'\nimport type { Filter } from '../filter.ts'\n\n/** */\n// Helps track ambiguous points in the LLM reasoning process for debugging and improvement purposes.\n// Create a fresh array per request/pipeline run to avoid sharing mutable state across module consumers.\nexport const createAmbiguousPoints = (): string[] => []\n\nexport type ChatRequest = {\n\tgenome: string\n\tdslabel: string\n\tfilter?: Filter\n\t/** user prompt */\n\tprompt: string\n\t__protected__?: any\n}\n\nexport type TextResponse = {\n\ttype: 'text'\n\t/** Plain text message to display in the chat */\n\ttext: string\n}\nexport type HtmlResponse = {\n\ttype: 'html'\n\t/** Pre-approved HTML from the dataset JSON resources array */\n\thtml: string\n}\nexport type PlotResponse = {\n\ttype: 'plot'\n\tplot: object\n\tmsg?: string\n\t/** Specifies what action to take e.g. Summary plot or no action. Will add more chart types later */\n}\n\nexport type LlmConfig = {\n\tprovider: 'SJ' | 'ollama' | 'huggingface' | 'azure'\n\tEmbeddingProvider: 'SJ' | 'ollama' | 'huggingface'\n\tEmbeddingProviderApi: string\n\tapi: string\n\tapiToken?: string\n\tEmbeddingProviderApiToken?: string\n\tmodelName: string\n\tembeddingModelName: string\n\t/** Whether to load the embedding model locally (via transformers.js) or call a remote API. Defaults to 'api'. */\n\tembeddingModelAccess?: 'local' | 'api'\n\t/** Smaller model to use for LLM classification fallback. Defaults to modelName if not set. */\n\tclassifierModelName?: string\n\t/** Log verbose debug output (e.g. raw embedding arrays) to the terminal. Defaults to false. */\n\tverbose?: boolean\n}\n\nexport interface GeneDataTypeResult {\n\tgene: string\n\tdataType: string\n}\n\nexport interface GeneSetDataTypeResult {\n\tgeneSet: string\n\tdataType: typeof TermTypes.SSGSEA | typeof TermTypes.GENE_VARIANT | 'ambiguous' | typeof TermTypes.GENE_EXPRESSION\n}\n\nexport type ChatResponse = TextResponse | HtmlResponse | PlotResponse\n\nexport type SummaryType = {\n\t/** Name of 1st term */\n\tterm: string\n\t/** Name of 2nd term */\n\tterm2?: string\n\t/** Optional simple filter terms */\n\tsimpleFilter: FilterTerm[]\n\t/** Optional explicit child type requested by the user. If omitted, the logic of the data types picks the child type. */\n\tchildType?: 'violin' | 'boxplot' | 'sampleScatter' | 'barchart'\n}\n\nexport type FilterTerm =\n\t| CategoricalFilterTerm\n\t| NumericFilterTerm /** FilterTerm can either be numeric or categorical  */\n\nexport type CategoricalFilterTerm = {\n\t/** Name of categorical term */\n\tterm: string\n\t/** The category of the term */\n\tcategory: string\n\t/** join term to be used only when there is more than one filter term and should be placed from the 2nd filter term onwards describing how it connects to the previous term */\n\tjoin?: 'and' | 'or'\n}\n\nexport type NumericFilterTerm = {\n\t/** Name of numeric term */\n\tterm: string\n\t/** start position (or lower limit) of numeric term */\n\tstart?: number\n\t/** stop position (or upper limit) of numeric term */\n\tstop?: number\n\t/** join term to be used only when there is more than one filter term and should be placed from the 2nd filter term onwards describing how it connects to the previous term */\n\tjoin?: 'and' | 'or'\n}\n\nexport type DbRows = {\n\t/** Name of the term */\n\tname: string\n\t/** Description of the term in plain language */\n\tdescription: string\n\t/** The type of variable stored in the DB (e.g. categorical, float) */\n\tterm_type: string\n\t/** Array of {key,value} terms storing the possible categories for a categorical variable */\n\tvalues: DbValue[]\n}\n\nexport type DbValue = {\n\t/** Name of the key */\n\tkey: string\n\t/** Object of values corresponding to the key */\n\tvalue: any\n}\n\nexport type ClassificationType =\n\t| plot_type\n\t| resource_type\n\t| none_type /** Variable containing the type of action the UI needs to take */\n\nexport type plot_type = {\n\t/** When type == plot, show the corresponding plot in the plot field */\n\ttype: 'plot'\n\t/** The type of plot to be displayed on the UI.\n\t *  Standard categories are listed; datasets may define additional custom categories. */\n\tplot: 'summary' | 'dge' | 'survival' | 'matrix' | 'sampleScatter' | 'hierCluster' | 'genomeBrowser'\n}\n\nexport type resource_type = {\n\t/** When type == resource, invoke the resource agent to return a matching resource link */\n\ttype: 'resource'\n}\n\nexport type none_type = {\n\t/** When type == none, the query did not match any known category */\n\ttype: 'none'\n}\n\n/** Top-level classification returned by classifyQuery: plot or notplot (subtype determined separately by plot.ts) */\nexport type QueryClassification = { type: 'plot' } | { type: 'notplot' } | { type: 'binaryQuery' }\n\n/** Specific plot type returned by classifyPlotType in plot.ts */\nexport type PlotType = 'summary' | 'dge' | 'survival' | 'matrix' | 'prebuiltscatter' | 'hiercluster' | 'genomeBrowser'\n\nexport type DEType = {\n\t/** Name of group1 which is an array of filter terms */\n\tgroup1: FilterTerm[]\n\t/** Name of group2 which is an array of filter terms */\n\tgroup2: FilterTerm[]\n\t/** Method used for carrying out differential gene expression analysis */\n\tmethod?: 'edgeR' | 'limma' | 'wilcoxon'\n}\n\nexport type MatrixType = {\n\t/** Names of dictionary terms to include as rows in the matrix (e.g. \"Diagnosis\", \"Gender\", \"Race\") */\n\tterms?: string[]\n\t/** Names of genes to include as gene variant rows in the matrix (e.g. \"TP53\", \"KRAS\", \"NRAS\") */\n\tgeneNames?: string[]\n\t/** Names of gene sets containing ssGSEA enrichment scores */\n\tgenesetNames?: string[]\n\t/** Optional simple filter terms to restrict the sample set */\n\tsimpleFilter?: FilterTerm[]\n}\n\nexport type HierClusterType = {\n\t/** Names of genes to include in the hierarchical clustering (e.g. \"TP53\", \"KRAS\", \"BCR\") */\n\tgeneNames?: string[]\n\t/** Names of gene sets containing list of genes to be used for hierarchical clustering */\n\tgenesetNames?: string[]\n\t/** Optional simple filter terms to restrict the sample set */\n\tsimpleFilter?: FilterTerm[]\n}\n\nexport type SampleScatterType = {\n\t/** Name of the pre-built plot (e.g. \"Transcriptome t-SNE\", \"Transcriptome UMAP\") */\n\tplotName: string\n\t/** Term or gene name to overlay as color, or null to remove color overlay */\n\tcolorTW?: string | null\n\t/** Term or gene name to overlay as shape, or null to remove shape overlay */\n\tshapeTW?: string | null\n\t/** Term or gene name to overlay as Z-divide, or null to remove divide overlay */\n\tterm0?: string | null\n\t/** Optional simple filter terms */\n\tsimpleFilter?: FilterTerm[]\n}\n", "import type { Filter } from '../filter.ts'\nimport type { TermWrapper } from '../terms/tw.ts'\n\nexport type DescrStatsRequest = {\n\t/** genome label in the serverconfig.json */\n\tgenome: string\n\t/** dataset label for the given genome */\n\tdslabel: string\n\tembedder: string\n\t/** wrapper of a numeric term, q.mode can be any as getData() will always pull sample-level values for summarizing */\n\ttw: TermWrapper\n\t/** if true, the (violin) plot is in log scale and must exclude 0-values from the stat */\n\tlogScale?: boolean\n\t/** optional pp filter */\n\tfilter?: Filter\n\t/** optional gdc filter */\n\tfilter0?: any\n}\n\nexport type DescrStats = {\n\t[key: string]: {\n\t\tkey: string\n\t\tlabel: string\n\t\tvalue: number\n\t}\n}\n\nexport type DescrStatsResponse = DescrStats\n\n// TODO: write more payload examples to help with automated testing and documentation, for non-prod use only\n\nexport const descrStatsPayloadExamples = {\n\trequest: {\n\t\ttypeId: 'DescrStatsRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'DescrStatsResponse'\n\t},\n\texamples: [\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\tembedder: 'localhost',\n\t\t\t\t\ttw: { term: { id: 'hrtavg' }, q: { mode: 'continuous' } },\n\t\t\t\t\tfilter: {\n\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\tin: true,\n\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\ttag: 'cohortFilter',\n\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\tname: 'Cohort',\n\t\t\t\t\t\t\t\t\t\ttype: 'categorical',\n\t\t\t\t\t\t\t\t\t\tvalues: { ABC: { label: 'ABC' }, XYZ: { label: 'XYZ' } },\n\t\t\t\t\t\t\t\t\t\tid: 'subcohort',\n\t\t\t\t\t\t\t\t\t\tisleaf: false,\n\t\t\t\t\t\t\t\t\t\tgroupsetting: { disabled: true }\n\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\tvalues: [{ key: 'ABC', label: 'ABC' }]\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t}\n\t\t\t\t} // satisfies DescrStatsRequest // TODO: enable type check\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t}\n\t]\n}\n", "import type { Filter } from '../filter.ts'\nimport type { Term } from '../terms/term.ts'\n\nexport type PercentileRequest = {\n\t/** a user-defined genome label in the serverconfig.json, hg38, hg19, mm10, etc */\n\tgenome: string\n\t/** a user-defined dataset label in the serverconfig.json, such as ClinVar, SJLife, GDC, etc */\n\tdslabel: string\n\tembedder: string\n\tgetpercentile: number[]\n\t/** term id string */\n\tterm: Term\n\tfilter?: Filter\n\tfilter0?: any\n}\n\nexport type PercentileResponse = {\n\tvalues: number[]\n}\n\n// TODO: write more payload examples to help with automated testing and documentation, for non-prod use only\n\nexport const percentilePayloadExamples = {\n\trequest: {\n\t\ttypeId: 'PercentileRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'PercentileResponse'\n\t},\n\texamples: [\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\tembedder: 'localhost',\n\t\t\t\t\tgetpercentile: [50],\n\t\t\t\t\tterm: { id: 'agedx' },\n\t\t\t\t\tfilter: {\n\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\tin: true,\n\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\ttag: 'cohortFilter',\n\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\tname: 'Cohort',\n\t\t\t\t\t\t\t\t\t\ttype: 'categorical',\n\t\t\t\t\t\t\t\t\t\tvalues: { ABC: { label: 'ABC' }, XYZ: { label: 'XYZ' } },\n\t\t\t\t\t\t\t\t\t\tid: 'subcohort',\n\t\t\t\t\t\t\t\t\t\tisleaf: false,\n\t\t\t\t\t\t\t\t\t\tgroupsetting: { disabled: true }\n\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\tvalues: [{ key: 'ABC', label: 'ABC' }]\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t}\n\t\t\t\t} // satisfies PercentileRequest // TODO: enable type check\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t}\n\t]\n}\n", "export type RunChartRequest = {\n\tgenome: string\n\tdslabel: string\n\t/**\n\t * term wrapper for x axis: { term, q }.\n\t * runChart2: q.mode='continuous' \u2192 1 series.\n\t * runChart2Period: q.mode='discrete' (with bins) \u2192 multiple series by period.\n\t */\n\txtw: { term: { id: string }; q?: { mode?: 'continuous' | 'discrete' }; $id?: string }\n\t/** term wrapper for y axis: { term, q }. When omitted, chart renders as frequency (count per time bucket). */\n\tytw?: { term: { id: string }; q?: { mode?: string }; $id?: string }\n\taggregation?: 'median'\n\t/** When true (frequency mode only), series Y values are cumulative counts. */\n\tshowCumulativeFrequency?: boolean\n\tfilter?: any\n\t__protected__?: any // auth token for accessing protected data\n}\n\nexport type RunChartSeries = {\n\t/** period/series identifier */\n\tseriesId?: string\n\t/** calculated Y median value for this curve */\n\tmedian: number\n\tpoints: Point[]\n}\n\nexport type RunChartSuccessResponse = {\n\tstatus: 'ok'\n\t/** each series is one curve, with a median. a runchart may show 1 or multiple curves */\n\tseries: RunChartSeries[]\n}\n\nexport type RunChartErrorResponse = {\n\terror: string\n\t/** Always empty on error; present so response shape is consistent for clients/checkers. */\n\tseries: RunChartSeries[]\n}\n\n/** Discriminated union: server returns success shape on 200 or error shape with series: []. */\nexport type RunChartResponse = RunChartSuccessResponse | RunChartErrorResponse\n\nexport function isRunChartSuccess(r: RunChartResponse): r is RunChartSuccessResponse {\n\treturn 'status' in r && r.status === 'ok'\n}\n\ntype Point = {\n\t/** decimal year, e.g. 2024.21321321 */\n\tx: number\n\t/** text of human-readable x value, e.g. \"Jan 2024\" which may be by the months, depends on dataset customization */\n\txName: string\n\t/** timeline, e.g. number of days */\n\ty: number\n\t/** number of samples with this timeline at this time point */\n\tsampleCount: number\n}\n\n// TODO: write payload examples to help with automated testing and documentation, for non-prod use only\n", "export type RootTermRequest = {\n\t/** a user-defined genome label in the serverconfig.json, hg38, hg19, mm10, etc */\n\tgenome: string\n\t/** a user-defined dataset label in the serverconfig.json, such as ClinVar, SJLife, GDC, etc */\n\tdslabel: string\n\tembedder: string\n\tdefault_rootterm: number\n\tcohortValues: string\n\ttreeFilter: string\n}\n\ninterface Entries {\n\tname: string\n\tid: string\n\tisleaf: boolean\n\tincluded_types: string[]\n\tchild_types: string[]\n}\n\nexport type RootTermResponse = {\n\tlst: Entries[]\n}\n\nexport const rootTermPayloadExamples = {\n\trequest: {\n\t\ttypeId: 'RootTermRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'RootTermResponse'\n\t},\n\texamples: [\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\tembedder: 'localhost',\n\t\t\t\t\tdefault_rootterm: 1,\n\t\t\t\t\tcohortValues: 'ABC'\n\t\t\t\t} // satisfies RootTermRequest // TODO: enable type check\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t}\n\t]\n}\n", "export type TermChildrenRequest = {\n\t/** a user-defined genome label in the serverconfig.json, hg38, hg19, mm10, etc */\n\tgenome: string\n\t/** a user-defined dataset label in the serverconfig.json, such as ClinVar, SJLife, GDC, etc */\n\tdslabel: string\n\tembedder: string\n\tget_children: number\n\tcohortValues?: string\n\ttid: string\n}\n\ninterface Entries {\n\tname: string\n\tid: string\n\tisleaf: boolean\n\tincluded_types: string[]\n\tchild_types: string[]\n}\n\nexport type TermChildrenResponse = {\n\tlst: Entries[]\n}\n\nexport const termChildrenPayloadExamples = {\n\trequest: {\n\t\ttypeId: 'TermChildrenRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'TermChildrenResponse'\n\t},\n\texamples: [\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\tembedder: 'localhost',\n\t\t\t\t\tget_children: 1,\n\t\t\t\t\tcohortValues: 'ABC',\n\t\t\t\t\ttid: 'GO:0000001'\n\t\t\t\t} satisfies TermChildrenRequest // TODO: enable type check\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t}\n\t]\n}\n", "import type { TermWrapper } from '../terms/tw.ts'\nimport type { Filter } from '../filter.ts'\nimport type { ErrorResponse } from './errorResponse.ts'\nimport type { DescrStats } from './termdb.descrstats.ts'\n\n/** Common properties shared by both violin and box plots */\ntype CommonProps = {\n\t/** numeric tw to fetch numeric data. tw.q.mode must be continuous */\n\ttw: TermWrapper\n\tdslabel: string\n\tgenome: string\n\t/** overlay tw for multiple violins/boxplots */\n\toverlayTw?: TermWrapper\n\t/** tw to divide to multiple charts */\n\tdivideTw?: TermWrapper\n\t/** mass filter */\n\tfilter?: Filter\n\t/** read-only invisible filter */\n\tfilter0?: any\n\t/** TODO: Needs description FIXME delete */\n\tcurrentGeneNames?: string[]\n\t/** if true, use log scale; if false or undefined, use linear scale */\n\tisLogScale?: boolean\n}\n\n/** Request type for violin plots with required violin-specific parameters */\nexport type ViolinRequest = CommonProps & {\n\t/** Indicates the type of chart to render */\n\tplotType: 'violin'\n\t/** A number representing the dimension perpendicular to the violin spread */\n\taxisHeight?: number\n\t/** A string representing the type of symbol used on the plot */\n\tdatasymbol?: string\n\t/** A number representing the device's pixel ratio */\n\tdevicePixelRatio: number\n\t/** If true, uses KDE method to build plot */\n\tisKDE?: boolean\n\t/** A string with two possible values: 'horizontal' or 'vertical' */\n\torientation: string\n\t/** A number representing the radius of the data symbols */\n\tradius: number\n\t/** A number representing the right margin */\n\trightMargin?: number\n\t/** Term may be scaled from regression analysis */\n\tscale?: any\n\t/** A number representing the width of the stroke */\n\tstrokeWidth?: number\n\t/** A number representing the width of the SVG box */\n\tsvgw: number\n\t/** Number of bins to build the plot. Default is 20. */\n\tticks?: number\n}\n\n/** Request type for box plots with required box-specific parameters */\nexport type BoxRequest = CommonProps & {\n\t/** Indicates the type of chart to render */\n\tplotType: 'box'\n\t/** sort plots by median value */\n\torderByMedian?: boolean\n\t/** Remove outliers from the plot */\n\tremoveOutliers?: boolean\n\t/** If true, show association tests table */\n\tshowAssocTests?: boolean\n}\n\n/**Unified request type for violin and boxplot - union of ViolinRequest and BoxRequest */\nexport type ViolinBoxRequest = ViolinRequest | BoxRequest\n\nexport type ViolinBoxResponse = ViolinResponse | BoxPlotResponse | ErrorResponse\n\n/** Type guard to check if response is an ErrorResponse */\nexport function isErrorResponse(response: ViolinBoxResponse): response is ErrorResponse {\n\treturn 'error' in response && 'status' in response\n}\n\n/** Type guard to check if response is a BoxPlotResponse */\nexport function isBoxPlotResponse(response: ViolinBoxResponse): response is BoxPlotResponse {\n\treturn !isErrorResponse(response) && 'charts' in response && 'descrStats' in response\n}\n\n/** Type guard to check if response is a ViolinResponse */\nexport function isViolinResponse(response: ViolinBoxResponse): response is ViolinResponse {\n\treturn !isErrorResponse(response) && 'min' in response && 'max' in response\n}\n\n/** Violin response types */\ninterface BinsEntries {\n\tx0: number\n\tx1: number\n\tdensity: number\n}\n\ninterface ValuesEntries {\n\tid: string\n\tlabel: string\n\tvalue: number\n}\n\ninterface PValueEntries {\n\tvalue?: string\n\thtml?: string\n}\n\ntype ViolinDensity = {\n\tbins: BinsEntries[]\n\tdensityMax: number\n\tdensityMin: number\n}\n\nexport type ViolinPlotEntry = {\n\tcolor: string\n\tchartId: string\n\tdensity: ViolinDensity\n\tlabel: string\n\tplotValueCount: number\n\tseriesId: string\n\tsrc: string\n\tsummaryStats: ValuesEntries[]\n}\n\nexport type ViolinResponse = {\n\tbins: { [index: string]: any }\n\tcharts: {\n\t\t[index: string]: {\n\t\t\tchartId: string\n\t\t\tplots: ViolinPlotEntry[]\n\t\t\tpvalues?: PValueEntries[][]\n\t\t}\n\t}\n\tmin: number\n\tmax: number\n\tuncomputableValues: { [index: string]: number }[] | null\n\tdescrStats?: DescrStats\n}\n\n/** Boxplot response types */\nexport type BoxPlotData = {\n\tw1: number | undefined\n\tw2: number | undefined\n\tp05: number\n\tp25: number\n\tp50: number\n\tp75: number\n\tp95: number\n\tiqr: number\n\tout: { value: number }[]\n}\n\nexport type BoxPlotEntry = {\n\tboxplot: BoxPlotData & { label: string }\n\tcolor?: string\n\tdescrStats: DescrStats\n\tisHidden?: boolean\n\tkey: string\n\tseriesId?: string\n}\n\nexport type BoxPlotChartEntry = {\n\tchartId: string\n\tplots: BoxPlotEntry[]\n\tsampleCount: number\n\twilcoxon?: [{ value: string }, { value: string }, { html: string }][]\n}\n\nexport type BoxPlotResponse = {\n\tabsMin?: number\n\tabsMax?: number\n\tbins?: {\n\t\t[index: string]: any\n\t}\n\tcharts: {\n\t\t[chartId: string]: BoxPlotChartEntry\n\t}\n\tdescrStats: DescrStats\n\tuncomputableValues: { label: string; value: number }[] | null\n}\n\n// TODO: write more payload examples to help with automated testing and documentation, for non-prod use only\n\nexport const violinBoxPayload = {\n\trequest: {\n\t\ttypeId: 'ViolinBoxRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'ViolinBoxResponse'\n\t},\n\texamples: [\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tplotType: 'violin',\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\ttw: {\n\t\t\t\t\t\tterm: { id: 'aaclassic_5', type: 'float' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tdevicePixelRatio: 2,\n\t\t\t\t\tsvgw: 200,\n\t\t\t\t\torientation: 'horizontal',\n\t\t\t\t\tdatasymbol: 'rug',\n\t\t\t\t\tradius: 5,\n\t\t\t\t\tisLogScale: false\n\t\t\t\t} // satisfies ViolinBoxRequest // TODO: enable type check\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tplotType: 'box',\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\ttw: {\n\t\t\t\t\t\tterm: { id: 'agedx', type: 'float' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\toverlayTw: {\n\t\t\t\t\t\tterm: { id: 'sex', type: 'categorical' }\n\t\t\t\t\t},\n\t\t\t\t\torderByMedian: true\n\t\t\t\t} // satisfies ViolinBoxRequest // TODO: enable type check\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t}\n\t]\n}\n", "export const CATEGORICAL = 'categorical'\nexport const CONDITION = 'condition'\nexport const DATE = 'date'\nexport const DNA_METHYLATION = 'dnaMethylation'\nexport const FLOAT = 'float'\nexport const GENE_VARIANT = 'geneVariant'\nexport const GENE_EXPRESSION = 'geneExpression'\nexport const ISOFORM_EXPRESSION = 'isoformExpression'\nexport const INTEGER = 'integer'\nexport const METABOLITE_INTENSITY = 'metaboliteIntensity'\nexport const MULTIVALUE = 'multivalue'\nexport const SAMPLELST = 'samplelst'\nexport const SINGLECELL_CELLTYPE = 'singleCellCellType'\nexport const SINGLECELL_GENE_EXPRESSION = 'singleCellGeneExpression'\nexport const SNP = 'snp'\nexport const SNP_LIST = 'snplst'\nexport const SNP_LOCUS = 'snplocus'\nexport const SSGSEA = 'ssGSEA'\nexport const SURVIVAL = 'survival'\nexport const TERM_COLLECTION = 'termCollection'\nexport const PROTEOME_ABUNDANCE = 'proteomeAbundance'\nexport const PROTEOME_DAP = 'proteomeDAP'\n\n//Term types should be used gradually using these constants instead of hardcoding the values,\n// eg: type == CATEGORICAL instead of type == 'categorical'\nexport const TermTypes: { [key: string]: string } = {\n\tGENE_VARIANT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tCATEGORICAL,\n\tINTEGER,\n\tFLOAT,\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tCONDITION,\n\tSURVIVAL,\n\tSAMPLELST,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tMULTIVALUE,\n\tDATE,\n\tTERM_COLLECTION\n}\n", "import type { Term } from '#types'\nimport {\n\tdtgeneexpression,\n\tdtssgsea,\n\tdtdnamethylation,\n\tdtmetaboliteintensity,\n\tdtproteomeabundance,\n\tTermTypeGroups,\n\tdtTerms\n} from './common.js'\nimport {\n\tGENE_VARIANT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tCATEGORICAL,\n\tINTEGER,\n\tFLOAT,\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tCONDITION,\n\tSURVIVAL,\n\tSAMPLELST,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tMULTIVALUE,\n\tDATE,\n\tTERM_COLLECTION,\n\tTermTypes\n} from '#types'\n\n// legacy support - comsumers should import directly from #types (aka @sjcrh/proteinpaint-types)\nexport {\n\tGENE_VARIANT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tCATEGORICAL,\n\tINTEGER,\n\tFLOAT,\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tCONDITION,\n\tSURVIVAL,\n\tSAMPLELST,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tMULTIVALUE,\n\tDATE,\n\tTERM_COLLECTION,\n\tTermTypes\n} from '#types'\n\n// moved TermTypeGroups to `server/src/common.js`, so now has to re-export\nexport { TermTypeGroups } from './common.js'\n\n/*\nFor datasets with multiple types of samples the ROOT_SAMPLE_TYPE is used to represent the root sample type, for example, \nthe type patient, that has one or more samples associated to it. This should be the id used as sample_type, when generating the db to identify the root samples\nin sampleidmap or the terms annotating root samples in the terms table.\nThe samples associated to a patient have annotations that are specific to a timepoint, for example, the age of the patient,\nthe doses of the drugs the patient was taking at the time of the data collection, etc. These annotations are associated to a sample.\n*/\nexport const ROOT_SAMPLE_TYPE = 1\n\n//For datasets with one sample type the DEFAULT_SAMPLE_TYPE is used to represent the sample type\nexport const DEFAULT_SAMPLE_TYPE = 2\n\nexport const NumericModes = {\n\tcontinuous: 'continuous',\n\tdiscrete: 'discrete'\n}\n\nexport const dtTermTypes: Set<string> = new Set(dtTerms.map((t: any) => t.type))\nfor (const dtTermType of dtTermTypes) {\n\tTermTypes[dtTermType.toUpperCase()] = dtTermType\n}\n\nexport const NUMERIC_DICTIONARY_TERM = 'numericDictTerm'\n\nexport const TermTypes2Dt = {\n\t[GENE_EXPRESSION]: dtgeneexpression,\n\t[SSGSEA]: dtssgsea,\n\t[DNA_METHYLATION]: dtdnamethylation,\n\t[METABOLITE_INTENSITY]: dtmetaboliteintensity,\n\t[PROTEOME_ABUNDANCE]: dtproteomeabundance\n}\n\n// maps term type to group (as is shown as toggles in search ui)\nexport const typeGroup = {\n\t[CATEGORICAL]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[CONDITION]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[FLOAT]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[INTEGER]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[SAMPLELST]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[SURVIVAL]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[DATE]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[MULTIVALUE]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[GENE_VARIANT]: TermTypeGroups.MUTATION_CNV_FUSION,\n\t[SNP]: TermTypeGroups.SNP,\n\t[SNP_LIST]: TermTypeGroups.SNP_LIST,\n\t[SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,\n\t[GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,\n\t[ISOFORM_EXPRESSION]: TermTypeGroups.ISOFORM_EXPRESSION,\n\t[SSGSEA]: TermTypeGroups.SSGSEA,\n\t[DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,\n\t[METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,\n\t[PROTEOME_ABUNDANCE]: TermTypeGroups.PROTEOME_ABUNDANCE,\n\t[TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,\n\t[SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,\n\t[SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION\n}\n\nconst nonDictTypes = new Set([\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tGENE_VARIANT,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION\n])\n\nfor (const dtTermType of dtTermTypes) {\n\tnonDictTypes.add(TermTypes[dtTermType.toUpperCase()])\n}\n\nexport const numericTypes = new Set([\n\tINTEGER,\n\tFLOAT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tDATE\n])\n\n// dictionary numeric term types, exists in db tables, exclude non-dictionary term types\nexport const dictionaryNumericTypes = new Set([INTEGER, FLOAT, DATE])\n\nconst categoricalTypes = new Set([CATEGORICAL, SNP])\n\nconst singleCellTerms = new Set([SINGLECELL_CELLTYPE, SINGLECELL_GENE_EXPRESSION])\n\nexport function isSingleCellTerm(term: any) {\n\tif (!term) return false\n\treturn singleCellTerms.has(term.type)\n}\nexport function isNumericTerm(term: Term) {\n\tif (!term) return false\n\treturn numericTypes.has(term.type)\n}\nexport function isCategoricalTerm(term: Term) {\n\tif (!term) return false\n\treturn categoricalTypes.has(term.type)\n}\n\nexport function isDictionaryType(type: string) {\n\treturn !isNonDictionaryType(type)\n}\n\nexport function isNonDictionaryType(type: string) {\n\tif (!type) throw new Error('Type is not defined')\n\treturn nonDictTypes.has(type)\n}\n\nexport function isNumTermCollection(term: Term) {\n\tif (!term || !term.type) throw new Error('Term or term type is not defined')\n\t//Enable this check when memberType is added to term collection\n\t// return term.type === TERM_COLLECTION && term.memberType == 'numeric'\n\treturn term.type === TERM_COLLECTION\n}\n\nexport function equals(t1: any, t2: any) {\n\tif (!t1) throw new Error('First term is not defined ')\n\tif (!t2) throw new Error('Second term is not defined ')\n\tif (t1.type !== t2.type) return false //term types are different\n\tif (isDictionaryType(t1.type) && isDictionaryType(t2.type) && t1.type != SAMPLELST) return t1.id === t2.id\n\tswitch (t1.type) {\n\t\tcase GENE_EXPRESSION:\n\t\t\treturn t1.gene == t2.gene\n\t\tcase ISOFORM_EXPRESSION:\n\t\t\treturn t1.isoform == t2.isoform\n\t\tcase SSGSEA:\n\t\t\treturn t1.id == t2.id\n\t\tcase DNA_METHYLATION:\n\t\t\treturn t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop\n\t\tcase METABOLITE_INTENSITY:\n\t\tcase PROTEOME_ABUNDANCE:\n\t\t\treturn t1.name == t2.name\n\t\tcase GENE_VARIANT:\n\t\t\treturn t1.gene == t2.gene || (t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop)\n\n\t\t// TO DO: Add more cases\n\t\t// case SNP_LIST:\n\t\t// case SNP_LOCUS:\n\t\t// case SAMPLELST:\n\n\t\tdefault:\n\t\t\treturn false\n\t}\n}\n\nexport function getBin(lst: any[], value: number) {\n\tlet bin = lst.findIndex(\n\t\tb => (b.startunbounded && value < b.stop) || (b.startunbounded && b.stopinclusive && value == b.stop)\n\t)\n\tif (bin == -1)\n\t\tbin = lst.findIndex(\n\t\t\tb => (b.stopunbounded && value > b.start) || (b.stopunbounded && b.startinclusive && value == b.start)\n\t\t)\n\tif (bin == -1)\n\t\tbin = lst.findIndex(\n\t\t\tb =>\n\t\t\t\t(value > b.start && value < b.stop) ||\n\t\t\t\t(b.startinclusive && value == b.start) ||\n\t\t\t\t(b.stopinclusive && value == b.stop)\n\t\t)\n\treturn bin\n}\n//Terms may  have a sample type associated to them, in datasets with multiple types of samples.\n//For example the gender is associated to the patient while the age is associated to the type sample. This function is used\n//for example when calling getData or getFilter, to return either the parent or the child samples, depending on the use case.\nexport function getSampleType(term: any, ds: any) {\n\tif (!term) return null\n\t//non dict terms annotate only samples, eg: gene expression, metabolite intensity, gene variant.\n\t//Their sample type is the default sample type that may or may not have a parent type, depending on the dataset\n\tif (term.type && isNonDictionaryType(term.type)) return DEFAULT_SAMPLE_TYPE\n\t//dictionary terms may annotate different types of samples, eg: patient and sample or mouse and crop.\n\tif (term.id) return ds.cohort.termdb.term2SampleType.get(term.id)\n\tif (term.type == 'samplelst') {\n\t\tconst key = Object.keys(term.values)[0]\n\t\tconst sampleId = term.values[key].list[0]?.sampleId\n\t\tif (sampleId) return ds.sampleId2Type.get(Number(sampleId) || sampleId)\n\t\telse return DEFAULT_SAMPLE_TYPE\n\t}\n\t// samplelst or non dict terms\n\treturn DEFAULT_SAMPLE_TYPE //later own term needs to know what type annotates based on the samples\n}\n\nexport function getParentType(types: Set<string>, ds: any) {\n\tif (Object.keys(ds.cohort.termdb.sampleTypes).length == 0) return null //dataset only has one type of sample\n\tconst ids = Array.from(types)\n\tif (!ids || ids.length == 0) return null\n\tfor (const id of ids) {\n\t\tconst typeObj = ds.cohort.termdb.sampleTypes[id]\n\t\tif (!typeObj) continue\n\t\tif (typeObj.parent_id == null) return id //this is the root type\n\t\t//if my parent is in the list, then I am not the parent\n\t\tif (ids.includes(typeObj.parent_id)) continue\n\t\telse return typeObj.parent_id //my parent is not in the list, so I am the parent\n\t}\n\treturn null //no parent found\n}\n\n// whether the term annotates parent samples\nexport function isParentType(term: any, ds: any) {\n\tif (!ds.cohort.termdb.hasSampleAncestry) return false\n\tconst sampleType = getSampleType(term, ds)\n\tif (!sampleType) throw 'sample type is not defined'\n\tconst sampleTypeObj = ds.cohort.termdb.sampleTypes[sampleType]\n\tif (!sampleTypeObj) throw 'invalid sample type'\n\tif (Number.isInteger(sampleTypeObj.parent_id)) {\n\t\t// sample type has parent, so it is child sample type\n\t\treturn false\n\t} else {\n\t\t// sample type does not have parent, so it is parent sample type\n\t\treturn true\n\t}\n}\n\n//Returns human readable label for each term type; label is just for printing and not computing\nconst typeMap: { [key: string]: string } = {\n\tcategorical: 'Categorical',\n\tcondition: 'Condition',\n\tfloat: 'Numerical',\n\tinteger: 'Numerical',\n\tgeneExpression: 'Gene Expression',\n\tisoformExpression: 'Isoform Expression',\n\tssGSEA: 'Geneset Expression',\n\tdnaMethylation: 'DNA Methylation',\n\tgeneVariant: 'Gene Variant',\n\tmetaboliteIntensity: 'Metabolite Intensity',\n\tproteomeAbundance: 'Proteome Abundance',\n\tproteomeDAP: 'Proteome DAP',\n\tmultivalue: 'Multi Value',\n\tsingleCellGeneExpression: 'Single Cell, Gene Expression',\n\tsingleCellCellType: 'Single Cell, Cell Type',\n\tsnplocus: 'SNP Locus',\n\tsnp: 'SNP',\n\tsnplst: 'SNP List',\n\tnumericDictTerm: 'Numeric Dictionary Term',\n\ttermCollection: 'Term Collection'\n}\n\nexport function termType2label(type: string) {\n\treturn typeMap[type] || 'Unknown term type'\n}\n\nexport function getDateFromNumber(value: number) {\n\tconst year = Math.floor(value)\n\tconst january1st = new Date(year, 0, 1)\n\tconst totalDays = getDaysInYear(year)\n\tconst time = Math.round((value - year) * totalDays) * oneDayTime\n\tconst date = new Date(january1st.getTime() + time)\n\treturn date\n}\n/*\nValue is a decimal year.\nA decimal year is a way of expressing a date or time period as a year with a decimal part, where the decimal portion \nrepresents the fraction of the year that has elapsed. \nExample:\n2025.0 represents the beginning of the year 2025. \n2025.5 represents the middle of the year 2025. \n */\nconst oneDayTime = 24 * 60 * 60 * 1000\n\nexport function getDateStrFromNumber(value: number) {\n\tconst date = getDateFromNumber(value)\n\n\t//Omit day to  deidentify the patients\n\treturn date.toLocaleDateString('en-US', {\n\t\tyear: 'numeric',\n\t\tmonth: 'long'\n\t})\n}\n\n//The value returned is a decimal year\n//A decimal year is a way of expressing a date or time period as a year with a decimal part, where the decimal portion\n//represents the fraction of the year that has elapsed.\nexport function getNumberFromDateStr(str: string) {\n\tconst date = new Date(str)\n\treturn getNumberFromDate(date)\n}\n\nexport function getNumberFromDate(date: Date) {\n\tconst year = date.getFullYear()\n\tconst january1st: Date = new Date(year, 0, 1)\n\tconst diffDays = (date.getTime() - january1st.getTime()) / oneDayTime\n\tconst daysTotal = getDaysInYear(year)\n\tconst decimal = diffDays / daysTotal\n\treturn year + decimal\n}\n\nexport function getDaysInYear(year: number) {\n\tconst isLeap = new Date(year, 1, 29).getMonth() === 1\n\tconst days = isLeap ? 366 : 365\n\treturn days\n}\n"],
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+  "names": []
+}

package/dist/chunk-UCLROZRF.js

@@ -0,0 +1,142 @@
+import {
+  runproteinpaint
+} from "./chunk-YNBT4N6T.js";
+
+// test/front.helpers.js
+var serverData = /* @__PURE__ */ Object.create(null);
+function getRunPp(appname = "", defaultArgs = {}, _host = "http://localhost:3000") {
+  const host = window.testHost || _host;
+  const arg = {
+    host: window.testHost || _host,
+    noheader: 1,
+    nobox: true,
+    debug: 1,
+    norecover: true
+  };
+  if (appname == "mass" || appname == "termdb") {
+    defaultArgs.debounceInterval = 0;
+  }
+  if (appname) arg[appname] = defaultArgs;
+  else copyMerge(arg, defaultArgs);
+  const argStr = JSON.stringify(arg);
+  return function runpp(overrides = {}) {
+    const argCopy = JSON.parse(argStr);
+    if (appname) copyMerge(argCopy[appname], overrides);
+    else copyMerge(argCopy, overrides);
+    if (appname && defaultArgs.fetchOpts) {
+      argCopy[appname].fetchOpts = defaultArgs.fetchOpts;
+    }
+    return runproteinpaint(Object.assign(argCopy, { serverData }));
+  };
+}
+function copyMerge(base, ...args) {
+  const target = typeof base == "string" ? JSON.parse(base) : base;
+  for (const arg of args) {
+    if (arg) {
+      const source = typeof base == "string" ? JSON.parse(JSON.stringify(arg)) : arg;
+      for (const key in source) {
+        if (!target[key] || Array.isArray(target[key]) || typeof target[key] !== "object") target[key] = source[key];
+        else copyMerge(target[key], source[key]);
+      }
+    }
+  }
+  return target;
+}
+function rideInit(opts = {}) {
+  const self = new Ride(opts);
+  const rideApi = {
+    // ride on the default event bus
+    to(callback, sub = {}) {
+      self.addToThen(callback, Object.assign({}, opts, sub));
+      return rideApi;
+    },
+    use(triggerFxn, sub = {}) {
+      self.addUseThen(triggerFxn, Object.assign({}, opts, sub));
+      return rideApi;
+    },
+    change(sub = {}) {
+      Object.assign(opts, sub);
+      return rideApi;
+    },
+    // run callback without using bus, with or without timeout
+    run(callback, after = 0) {
+      self.addRunThen(callback, after, opts);
+      return rideApi;
+    },
+    // close the event bus
+    done(test) {
+      if (opts.bus) self.resolved.then(() => opts.bus.on(opts.eventType, null));
+      self.resolved.then(() => {
+        test.end();
+        if (!opts.preserve && test._ok && opts.arg.Inner.app && typeof opts.arg.Inner.app.destroy == "function") {
+          opts.arg.Inner.app.destroy();
+        }
+      }).catch(console.log);
+      return rideApi;
+    }
+  };
+  return Object.freeze(rideApi);
+}
+var Ride = class {
+  // mutable but private access props and methods
+  // when used inside rideInit()
+  constructor(opts) {
+    this.validateOpts(opts);
+    this.resolved = Promise.resolve();
+  }
+  validateOpts(opts) {
+    try {
+      if (opts.eventType && !opts.bus) {
+        if (!opts.arg) throw "must specify opts.bus or opts.arg for rideInit() argument";
+        opts.bus = opts.arg;
+      }
+      if (opts.bus) {
+        if (typeof opts.eventType !== "string") throw "invalid default.eventType";
+        opts.bus.on(opts.eventType, null);
+        return opts;
+      }
+    } catch (e) {
+      console.log(e);
+    }
+  }
+  addToThen(callback, opts) {
+    this.resolved = this.resolved.then(async (triggerFxn) => {
+      opts.bus.on(opts.eventType, null);
+      return new Promise(async (resolve, reject) => {
+        opts.bus.on(opts.eventType, async () => {
+          await sleep(opts.wait);
+          callback(opts.arg);
+          resolve();
+        });
+        if (triggerFxn) await triggerFxn();
+      });
+    });
+  }
+  // prepare a trigger function for use in the pattern
+  // rideInit().use(triggerFxn).to(...)
+  //
+  // .use() enables setting a different opts.arg to be used for triggerFxn
+  //
+  addUseThen(triggerFxn, opts) {
+    this.resolved = this.resolved.then(async (prevTriggerFxn) => {
+      if (typeof prevTriggerFxn == "function") await prevTriggerFxn();
+      await sleep(isNaN(opts.wait) ? 0 : opts.wait);
+      return () => triggerFxn(opts.arg);
+    });
+  }
+  addRunThen(callback, after, opts) {
+    this.resolved = this.resolved.then(async () => {
+      await sleep(typeof after == "number" ? after : 0);
+      callback(opts.arg);
+    });
+  }
+};
+function sleep(ms) {
+  return new Promise((resolve) => setTimeout(resolve, ms));
+}
+
+export {
+  getRunPp,
+  rideInit
+};
+//# sourceMappingURL=chunk-UCLROZRF.js.map

package/dist/chunk-VIHUKORE.js

@@ -0,0 +1,216 @@
+import {
+  make_radios
+} from "./chunk-L4TUTGTA.js";
+import {
+  initBinConfig
+} from "./chunk-6VKTEMFV.js";
+import {
+  format
+} from "./chunk-OAWQ6LOO.js";
+
+// termsetting/handlers/NumRegularBinEditor.ts
+var NumRegularBinEditor = class {
+  constructor(editHandler) {
+    this.dom = {};
+    this.editHandler = editHandler;
+    this.opts = editHandler.opts;
+    this.tw = editHandler.tw;
+    this.termsetting = editHandler.termsetting;
+  }
+  render(div) {
+    this.tw = this.editHandler.tw;
+    this.q = this.getDefaultQ();
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+    if (this.dom.binsTable) {
+      if (this.editHandler.dom.binsDiv?.node().contains(this.dom.binsTable.node())) return;
+      else {
+        this.dom.binsTable.remove();
+        delete this.dom.binsTable;
+      }
+    }
+    const binsTable = div.append("table");
+    this.dom.binsTable = binsTable;
+    this.renderBinSizeInput(binsTable.append("tr"));
+    this.renderFirstBinInput(binsTable.append("tr"));
+    this.renderLastBinInputs(binsTable.append("tr"));
+  }
+  getDefaultQ() {
+    if (this.tw.q.type == "regular-bin") return JSON.parse(JSON.stringify(this.tw.q));
+    const t = this.tw.term;
+    const defaultQ = this.termsetting.opts.use_bins_less && t.bins?.less || t.bins?.default;
+    if (defaultQ) return JSON.parse(JSON.stringify(defaultQ));
+    const binConfig = initBinConfig(this.editHandler.handler.density_data);
+    return typeof binConfig == "string" ? JSON.parse(binConfig) : binConfig;
+  }
+  renderBinSizeInput(tr) {
+    const handler = this.editHandler.handler;
+    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("Bin Size");
+    const { min, max } = handler.density_data;
+    const q = this.q;
+    const origBinSize = q.bin_size;
+    this.dom.bin_size_input = tr.append("td").append("input").attr("type", "number").attr("value", "rounding" in q ? format(q.rounding || ".0f")(q.bin_size) : q.bin_size).attr("data-testid", "sjpp-num-reg-bin-editor-size").style("margin-left", "15px").style("width", "100px").style("color", () => q.bin_size > Math.abs(max - min) ? "red" : "").on("change", (event) => {
+      const newValue = Number(event.target.value);
+      if (newValue <= 0) {
+        window.alert("Please enter non-negative bin size.");
+        event.target.value = origBinSize;
+        return;
+      }
+      if ((max - min) / newValue > 100) {
+        window.alert("Bin size too small. Try setting a bigger value.");
+        event.target.value = origBinSize;
+        return;
+      }
+      q.bin_size = newValue;
+      this.dom.bin_size_input.style("color", q.bin_size > max - min ? "red" : newValue != origBinSize ? "green" : "");
+      handler.density.setBinLines(this.getBoundaryOpts());
+    });
+  }
+  renderFirstBinInput(tr) {
+    const handler = this.editHandler.handler;
+    const q = this.q;
+    if (!q.first_bin) throw "missing q.first_bin";
+    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("First Bin Stop");
+    const { min, max } = handler.density_data;
+    const origValue = q.first_bin.stop;
+    this.dom.first_stop_input = tr.append("td").append("input").attr("type", "number").property("value", origValue).style("width", "100px").style("margin-left", "15px").on("change", (event) => {
+      const newValue = Number(event.target.value);
+      if (newValue < min || newValue > max) {
+        window.alert("First bin stop value out of bound.");
+        event.target.value = origValue;
+        return;
+      }
+      this.q.first_bin.stop = newValue;
+      handler.density.setBinLines(this.getBoundaryOpts());
+    });
+    tr.append("td").append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by left-most red line. Drag to change.");
+  }
+  renderLastBinInputs(tr) {
+    const handler = this.editHandler.handler;
+    const q = this.q;
+    const isAuto = !q.last_bin || !Number.isFinite(q.last_bin.start);
+    tr.append("td").style("padding-top", "4px").style("opacity", 0.5).style("vertical-align", "top").text("Last Bin Start");
+    const td1 = tr.append("td").style("padding-left", "15px").style("vertical-align", "top");
+    const radio_div = td1.append("div");
+    const radios = make_radios({
+      holder: radio_div,
+      options: [
+        { label: "Automatic", value: "auto", checked: isAuto },
+        { label: "Fixed", value: "fixed", checked: !isAuto }
+      ],
+      callback: (v) => {
+        if (v == "auto") {
+          delete q.last_bin;
+          edit_div.style("display", "none");
+          handler.density.setBinLines(this.getBoundaryOpts());
+          return;
+        }
+        edit_div.style("display", "inline-block");
+        if (this.dom.last_start_input.property("value") == "") {
+          this.dom.last_start_input.property("value", this.tw.q.last_bin?.start || handler.density_data.max);
+        }
+        this.setLastBinStart();
+      }
+    });
+    this.dom.fixed_radio = radios.inputs.filter((_, i) => i === 1);
+    const edit_div = tr.append("td").append("div").style("display", isAuto ? "none" : "inline-block");
+    this.dom.last_start_input = edit_div.append("input").attr("type", "number").property("value", q.last_bin?.start || "").style("width", "100px").on("change", () => this.setLastBinStart());
+    edit_div.append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by right-most red line. Drag to change.");
+  }
+  setLastBinStart() {
+    const q = this.q;
+    const { max } = this.editHandler.handler.density_data;
+    const strInput = this.dom.last_start_input.property("value");
+    if (strInput === "") return;
+    const inputValue = Number(strInput);
+    if (q.first_bin && inputValue <= q.first_bin.stop) {
+      window.alert("Last bin start cannot be smaller than first bin stop.");
+      this.dom.last_start_input.property("value", max);
+      return;
+    }
+    if (inputValue > max) {
+      window.alert("Last bin start value out of bound.");
+      this.dom.last_start_input.property("value", max);
+      return;
+    }
+    if (q.last_bin) q.last_bin.start = inputValue;
+    else
+      q.last_bin = {
+        start: inputValue,
+        stopunbounded: true,
+        stopinclusive: false
+      };
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+  getBoundaryOpts() {
+    const { min, max } = this.editHandler.handler.density_data;
+    const binLinesStop = this.q.last_bin?.start ?? max + Math.abs(this.q.first_bin.stop) - Math.min(min, 0);
+    const boundaryValues = [];
+    for (let i = this.q.first_bin.stop; i <= binLinesStop; i = i + this.q.bin_size) {
+      if (this.q.last_bin?.start === i) break;
+      if (i > binLinesStop) boundaryValues[boundaryValues.length - 1].isLastVisibleLine = true;
+      const isDraggable = i === this.q.first_bin.stop || i === this.q.bin_size - 1;
+      boundaryValues.push({ x: i, isDraggable, movesWithLineIndex: !isDraggable ? 0 : -1 });
+    }
+    if (this.q.last_bin) {
+      boundaryValues.push({
+        x: this.q.last_bin.start,
+        isDraggable: true,
+        isLastVisibleLine: true,
+        movesWithLineIndex: -1
+      });
+    }
+    return {
+      values: boundaryValues,
+      callback: (d, value) => {
+        if (d.index === 0) {
+          this.dom.first_stop_input.property("value", value);
+          this.q.first_bin.stop = value;
+        } else {
+          this.editHandler.handler.dom.last_start_input.property("value", value);
+          if (this.q.last_bin) this.q.last_bin.start = value;
+        }
+      }
+    };
+  }
+  getEditedQ(destroyDom = true) {
+    const bin_size = this.dom.bin_size_input.property("value");
+    const config = {
+      mode: "discrete",
+      type: "regular-bin",
+      startinclusive: this.editHandler.boundaryInclusion == "startinclusive",
+      stopinclusive: this.editHandler.boundaryInclusion == "stopinclusive",
+      bin_size: Number(bin_size),
+      first_bin: {
+        startunbounded: true,
+        stop: Number(this.dom.first_stop_input.property("value"))
+      },
+      rounding: bin_size.includes(".") && !bin_size.endsWith(".") ? `.${bin_size.split(".")[1].length}f` : ".0f"
+    };
+    if (this.dom.fixed_radio.property("checked")) {
+      config.last_bin = {
+        start: Number(this.dom.last_start_input.property("value")),
+        stopunbounded: true
+      };
+    }
+    if (destroyDom) {
+      for (const name of Object.keys(this.dom)) {
+        this.dom[name].remove();
+        delete this.dom[name];
+      }
+    }
+    return config;
+  }
+  undoEdits() {
+    this.q = this.getDefaultQ();
+    this.dom.binsTable.selectAll("*").remove();
+    this.renderBinSizeInput(this.dom.binsTable.append("tr"));
+    this.renderFirstBinInput(this.dom.binsTable.append("tr"));
+    this.renderLastBinInputs(this.dom.binsTable.append("tr"));
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+};
+
+export {
+  NumRegularBinEditor
+};
+//# sourceMappingURL=chunk-VIHUKORE.js.map

package/dist/chunk-VIHUKORE.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termsetting/handlers/NumRegularBinEditor.ts"],
+  "sourcesContent": ["import { format } from 'd3-format'\n//import { setDensityPlot } from './density'\nimport { make_radios } from '#dom'\nimport initBinConfig from '#shared/termdb.initbinconfig.js'\nimport type { NumRegularBin } from '#tw'\nimport type { NumDiscreteEditor } from './NumDiscreteEditor.ts'\nimport type { BoundaryOpts, BoundaryValue, DraggedLineData } from './NumericDensity.ts'\nimport type { TermSetting } from '../TermSetting.ts'\nimport type { RegularNumericBinConfig } from '#types'\n\n// This is a bin editor for NumDiscreteEditor\n// NumericHandler (handler) -> NumDiscreteEditor (editor) -> NumRegularBinEditor (bin editor)\nexport class NumRegularBinEditor {\n\ttw: NumRegularBin\n\tq!: RegularNumericBinConfig\n\teditHandler: NumDiscreteEditor\n\ttermsetting: TermSetting\n\topts: any\n\tdom: {\n\t\t[elemName: string]: any\n\t} = {}\n\n\tconstructor(editHandler) {\n\t\tthis.editHandler = editHandler\n\t\tthis.opts = editHandler.opts\n\t\tthis.tw = editHandler.tw\n\t\tthis.termsetting = editHandler.termsetting\n\t}\n\n\trender(div) {\n\t\tthis.tw = this.editHandler.tw as NumRegularBin\n\t\tthis.q = this.getDefaultQ()\n\t\tthis.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t\tif (this.dom.binsTable) {\n\t\t\tif (this.editHandler.dom.binsDiv?.node().contains(this.dom.binsTable.node())) return\n\t\t\telse {\n\t\t\t\tthis.dom.binsTable.remove()\n\t\t\t\tdelete this.dom.binsTable\n\t\t\t}\n\t\t}\n\t\tconst binsTable = div.append('table')\n\t\tthis.dom.binsTable = binsTable\n\t\tthis.renderBinSizeInput(binsTable.append('tr'))\n\t\tthis.renderFirstBinInput(binsTable.append('tr'))\n\t\tthis.renderLastBinInputs(binsTable.append('tr'))\n\t}\n\n\tgetDefaultQ(): RegularNumericBinConfig {\n\t\tif (this.tw.q.type == 'regular-bin') return JSON.parse(JSON.stringify(this.tw.q))\n\t\tconst t = this.tw.term\n\t\tconst defaultQ = (this.termsetting.opts.use_bins_less && t.bins?.less) || t.bins?.default\n\t\tif (defaultQ) return JSON.parse(JSON.stringify(defaultQ))\n\t\tconst binConfig = initBinConfig(this.editHandler.handler.density_data)\n\t\treturn typeof binConfig == 'string' ? JSON.parse(binConfig) : binConfig\n\t}\n\n\trenderBinSizeInput(tr: any) {\n\t\tconst handler = this.editHandler.handler\n\t\ttr.append('td').style('margin', '5px').style('opacity', 0.5).text('Bin Size')\n\n\t\tconst { min, max } = handler.density_data\n\t\tconst q = this.q\n\t\tconst origBinSize = q.bin_size\n\n\t\tthis.dom.bin_size_input = tr\n\t\t\t.append('td')\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr('value', 'rounding' in q ? format(q.rounding || '.0f')(q.bin_size) : q.bin_size)\n\t\t\t.attr('data-testid', 'sjpp-num-reg-bin-editor-size')\n\t\t\t.style('margin-left', '15px')\n\t\t\t.style('width', '100px')\n\t\t\t.style('color', () => (q.bin_size > Math.abs(max - min) ? 'red' : ''))\n\t\t\t.on('change', event => {\n\t\t\t\tconst newValue = Number(event.target.value)\n\t\t\t\t// must validate input value\n\t\t\t\tif (newValue <= 0) {\n\t\t\t\t\twindow.alert('Please enter non-negative bin size.')\n\t\t\t\t\t// must reset value in <input>, otherwise the wrong value will be recorded in self.q upon clicking Submit\n\t\t\t\t\tevent.target.value = origBinSize\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif ((max - min) / newValue > 100) {\n\t\t\t\t\t// avoid rendering too many svg lines and lock up browser\n\t\t\t\t\twindow.alert('Bin size too small. Try setting a bigger value.')\n\t\t\t\t\tevent.target.value = origBinSize\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tq.bin_size = newValue\n\t\t\t\tthis.dom.bin_size_input.style('color', q.bin_size > max - min ? 'red' : newValue != origBinSize ? 'green' : '')\n\t\t\t\thandler.density.setBinLines(this.getBoundaryOpts())\n\t\t\t})\n\t}\n\n\trenderFirstBinInput(tr: any) {\n\t\tconst handler = this.editHandler.handler\n\t\tconst q = this.q\n\t\tif (!q.first_bin) throw 'missing q.first_bin'\n\n\t\ttr.append('td').style('margin', '5px').style('opacity', 0.5).text('First Bin Stop')\n\n\t\tconst { min, max } = handler.density_data\n\t\tconst origValue = q.first_bin.stop\n\n\t\tthis.dom.first_stop_input = tr\n\t\t\t.append('td')\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.property('value', origValue)\n\t\t\t.style('width', '100px')\n\t\t\t.style('margin-left', '15px')\n\t\t\t.on('change', event => {\n\t\t\t\tconst newValue = Number(event.target.value)\n\t\t\t\tif (newValue < min || newValue > max) {\n\t\t\t\t\twindow.alert('First bin stop value out of bound.')\n\t\t\t\t\tevent.target.value = origValue\n\t\t\t\t\treturn\n\t\t\t\t}\n\n\t\t\t\t// first_bin should have already been set; adding the check just to skip the tsc error...\n\t\t\t\tthis.q.first_bin.stop = newValue\n\t\t\t\thandler.density.setBinLines(this.getBoundaryOpts())\n\t\t\t})\n\n\t\ttr.append('td')\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.6em')\n\t\t\t.style('opacity', 0.5)\n\t\t\t.style('display', handler.density.no_density_data ? 'none' : 'block')\n\t\t\t.text('Indicated by left-most red line. Drag to change.')\n\t}\n\n\trenderLastBinInputs(tr) {\n\t\tconst handler = this.editHandler.handler\n\t\tconst q = this.q\n\t\t// tell if last bin is automatic (not fixed)\n\t\tconst isAuto = !q.last_bin || !Number.isFinite(q.last_bin.start)\n\n\t\ttr.append('td')\n\t\t\t.style('padding-top', '4px')\n\t\t\t.style('opacity', 0.5)\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.text('Last Bin Start')\n\n\t\tconst td1 = tr.append('td').style('padding-left', '15px').style('vertical-align', 'top')\n\t\tconst radio_div = td1.append('div')\n\n\t\tconst radios = make_radios({\n\t\t\tholder: radio_div,\n\t\t\toptions: [\n\t\t\t\t{ label: 'Automatic', value: 'auto', checked: isAuto },\n\t\t\t\t{ label: 'Fixed', value: 'fixed', checked: !isAuto }\n\t\t\t],\n\t\t\tcallback: v => {\n\t\t\t\tif (v == 'auto') {\n\t\t\t\t\tdelete q.last_bin\n\t\t\t\t\t// if just deleting last_bin.start and keeps q.last_bin{}, density plot may set last_bin.bin='last' and will break bin validation\n\t\t\t\t\tedit_div.style('display', 'none')\n\t\t\t\t\thandler.density.setBinLines(this.getBoundaryOpts())\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\t// v is \"fixed\", to assign a number to self.q.last_bin.start\n\t\t\t\tedit_div.style('display', 'inline-block')\n\t\t\t\tif (this.dom.last_start_input.property('value') == '') {\n\t\t\t\t\t// blank input, fill max\n\t\t\t\t\tthis.dom.last_start_input.property('value', this.tw.q.last_bin?.start || handler.density_data.max)\n\t\t\t\t}\n\t\t\t\tthis.setLastBinStart()\n\t\t\t}\n\t\t})\n\n\t\tthis.dom.fixed_radio = radios.inputs.filter((_, i) => i === 1)\n\n\t\tconst edit_div = tr\n\t\t\t.append('td')\n\t\t\t.append('div')\n\t\t\t.style('display', isAuto ? 'none' : 'inline-block')\n\n\t\tthis.dom.last_start_input = edit_div\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.property('value', q.last_bin?.start || '')\n\t\t\t.style('width', '100px')\n\t\t\t.on('change', () => this.setLastBinStart())\n\n\t\tedit_div\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.6em')\n\t\t\t.style('opacity', 0.5)\n\t\t\t.style('display', handler.density.no_density_data ? 'none' : 'block')\n\t\t\t.text('Indicated by right-most red line. Drag to change.')\n\t}\n\n\tsetLastBinStart() {\n\t\tconst q = this.q\n\t\tconst { max } = this.editHandler.handler.density_data\n\t\t// only get value from <input>\n\t\tconst strInput = this.dom.last_start_input.property('value')\n\t\tif (strInput === '') return\n\t\tconst inputValue = Number(strInput)\n\n\t\t// TODO first_bin should be required\n\t\tif (q.first_bin && inputValue <= q.first_bin.stop) {\n\t\t\twindow.alert('Last bin start cannot be smaller than first bin stop.')\n\t\t\tthis.dom.last_start_input.property('value', max)\n\t\t\treturn\n\t\t}\n\t\tif (inputValue > max) {\n\t\t\twindow.alert('Last bin start value out of bound.')\n\t\t\tthis.dom.last_start_input.property('value', max)\n\t\t\treturn\n\t\t}\n\t\tif (q.last_bin) q.last_bin.start = inputValue\n\t\telse\n\t\t\tq.last_bin = {\n\t\t\t\tstart: inputValue,\n\t\t\t\tstopunbounded: true,\n\t\t\t\tstopinclusive: false\n\t\t\t}\n\n\t\tthis.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t}\n\n\tgetBoundaryOpts(): BoundaryOpts {\n\t\tconst { min, max } = this.editHandler.handler.density_data\n\t\tconst binLinesStop = this.q.last_bin?.start ?? max + Math.abs(this.q.first_bin.stop) - Math.min(min, 0)\n\t\tconst boundaryValues: BoundaryValue[] = []\n\t\tfor (let i = this.q.first_bin.stop; i <= binLinesStop; i = i + this.q.bin_size) {\n\t\t\tif (this.q.last_bin?.start === i) break\n\t\t\tif (i > binLinesStop) boundaryValues[boundaryValues.length - 1].isLastVisibleLine = true\n\t\t\tconst isDraggable = i === this.q.first_bin.stop || i === this.q.bin_size - 1\n\t\t\t// non-draggable lines should move with the first bin boundary line\n\t\t\tboundaryValues.push({ x: i, isDraggable, movesWithLineIndex: !isDraggable ? 0 : -1 })\n\t\t}\n\t\tif (this.q.last_bin) {\n\t\t\tboundaryValues.push({\n\t\t\t\tx: this.q.last_bin.start,\n\t\t\t\tisDraggable: true,\n\t\t\t\tisLastVisibleLine: true,\n\t\t\t\tmovesWithLineIndex: -1\n\t\t\t})\n\t\t}\n\n\t\treturn {\n\t\t\tvalues: boundaryValues,\n\t\t\tcallback: (d: DraggedLineData, value) => {\n\t\t\t\t//d.scaledX = Math.round(xscale(value))\n\t\t\t\tif (d.index === 0) {\n\t\t\t\t\tthis.dom.first_stop_input.property('value', value)\n\t\t\t\t\tthis.q.first_bin.stop = value as number\n\t\t\t\t} else {\n\t\t\t\t\tthis.editHandler.handler.dom.last_start_input.property('value', value)\n\t\t\t\t\t//if (!this.q.last_bin) this.q.last_bin = {}\n\t\t\t\t\tif (this.q.last_bin) this.q.last_bin.start = value\n\t\t\t\t\t//middleLines.style('display', (c: any) => (d.draggedX && c.scaledX >= d.draggedX ? 'none' : ''))\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tgetEditedQ(destroyDom = true): RegularNumericBinConfig {\n\t\tconst bin_size = this.dom.bin_size_input.property('value')\n\t\tconst config: RegularNumericBinConfig = {\n\t\t\tmode: 'discrete',\n\t\t\ttype: 'regular-bin',\n\t\t\tstartinclusive: this.editHandler.boundaryInclusion == 'startinclusive',\n\t\t\tstopinclusive: this.editHandler.boundaryInclusion == 'stopinclusive',\n\t\t\tbin_size: Number(bin_size),\n\t\t\tfirst_bin: {\n\t\t\t\tstartunbounded: true,\n\t\t\t\tstop: Number(this.dom.first_stop_input.property('value'))\n\t\t\t},\n\t\t\trounding: bin_size.includes('.') && !bin_size.endsWith('.') ? `.${bin_size.split('.')[1].length}f` : '.0f'\n\t\t}\n\n\t\tif (this.dom.fixed_radio.property('checked')) {\n\t\t\tconfig.last_bin = {\n\t\t\t\tstart: Number(this.dom.last_start_input.property('value')),\n\t\t\t\tstopunbounded: true\n\t\t\t}\n\t\t}\n\n\t\tif (destroyDom) {\n\t\t\tfor (const name of Object.keys(this.dom)) {\n\t\t\t\tthis.dom[name].remove()\n\t\t\t\tdelete this.dom[name]\n\t\t\t}\n\t\t}\n\n\t\treturn config\n\t}\n\n\tundoEdits() {\n\t\tthis.q = this.getDefaultQ()\n\t\tthis.dom.binsTable.selectAll('*').remove()\n\t\tthis.renderBinSizeInput(this.dom.binsTable.append('tr'))\n\t\tthis.renderFirstBinInput(this.dom.binsTable.append('tr'))\n\t\tthis.renderLastBinInputs(this.dom.binsTable.append('tr'))\n\t\tthis.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t}\n}\n"],
+  "mappings": 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+}