@sjcrh/proteinpaint-types 2.136.0 → 2.137.1-0

package/src/dataset.ts

@@ -371,11 +371,45 @@ type SvFusion = {
 }
 
 type SingleSampleMutationQuery = {
+	/** for native ds, each file should contain a stringified json array with elements below
+	for non-native ds, the getter should return an json array with same structure:
+
+	cnv example entry:
+	             {
+	               "chromosome": "chr1",
+	               "start": 123456,
+	               "end": 123789,
+	               "type": "cnv",
+	               "log2Ratio": null
+	             }
+
+	snvindel example entry:
+	             {
+	               "chromosome": "chr1",
+	               "start": 123456,
+	               "end": 123789,
+	               "type": "snvindel"
+	             }
+		TODO specify property names for read depth; needed for grin2 filtering
+
+	fusion example entry:
+			     {
+	               "chromosome": "chr1",
+	               "start": 123456,
+	               "end": 123789,
+	               "type": "fusion",
+				   "fusionType": null,
+	               "confidence": null
+	             }
+	*/
 	src: 'native' | 'gdcapi' | string
 	/** which property of client mutation object to retrieve sample identifier for
 	 * querying single sample data with */
 	sample_id_key: string
-	/** only required for src=native */
+	/** only required for src=native
+	folder contains a set of files, one file per sample, file named by sample name
+	each file contains a stringified json array of mutation/cnv/sv entries (aka mlst)
+	*/
 	folder?: string
 	/** disco plot will be launched when singleSampleMutation is enabled. supply customization options here */
 	discoPlot?: {

package/src/filter.ts

@@ -57,6 +57,9 @@ type GeneVariantTvs = BaseTvs & {
 	values: { key: string; label: string; value: string }[]
 	/** boolean for including not tested classes (excluded by default) */
 	includeNotTested?: boolean
+	/** boolean for excluding gene name from pill name (included by default)
+	 * used by geneVariant edit ui to exclude unnecessary gene name */
+	excludeGeneName?: boolean
 }
 
 /*** types supporting Filter type ***/

package/src/index.ts

@@ -18,6 +18,7 @@ export * from './routes/filter.gdc.ts'
 export * from './routes/gdc.maf.ts'
 export * from './routes/gdc.mafBuild.ts'
 export * from './routes/gdc.grin2.ts'
+export * from './routes/grin2.ts'
 export * from './routes/termdb.topMutatedGenes.ts'
 export * from './routes/genelookup.ts'
 export * from './routes/genesetEnrichment.ts'

package/src/routes/grin2.ts

@@ -0,0 +1,119 @@
+/** General GRIN2 route
+ * This route handles the GRIN2 analysis for any non-GDC data.
+ * It processes the incoming data structure via PP's existing filter infrastructure
+ * and returns the same structured results as GDC-GRIN2.
+ * Specifically it will return a sortable table of top mutated genes and
+ * a static PNG manhattan-like plot of the -log10(q-value).
+ * We allow the user to customize the snvindel, CNV, and fusion filtering options.
+ */
+
+import type { RoutePayload } from './routeApi.js'
+
+/** GRIN2 request */
+export type GRIN2Request = {
+	/** Genome build identifier (e.g., 'hg38', 'hg19') */
+	genome: string
+
+	/** Dataset label within the genome */
+	dslabel: string
+
+	/** Filter from existing PP infrastructure */
+	filter: any // Filter object passed to get_samples(filter, ds)
+
+	/** Options for filtering SNV/indel file content */
+	snvindelOptions?: {
+		/** Minimum total depth of returned SNV/indel files */
+		minTotalDepth?: number // Default: 10
+		/** Minimum alternate allele count of returned SNV/indel files */
+		minAltAlleleCount?: number // Default: 2
+		/** String array of consequence types to include */
+		consequences?: string[]
+		/** Maximum mutation count cutoff for highly mutated scenarios */
+		hyperMutator?: number // Default: 1000
+	}
+
+	/** Options for filtering CNV file content */
+	cnvOptions?: {
+		/** Threshold for copy number loss detection */
+		lossThreshold?: number // Default: -0.4
+		/** Threshold for copy number gain detection */
+		gainThreshold?: number // Default: 0.3
+		/** Maximum segment length to include (0 = no filter) */
+		maxSegLength?: number // Default: 0
+		/** Minimum segment length to include (0 = no filter) */
+		minSegLength?: number // Default: 0
+		/** Hypermutator max cut off for CNVs per case */
+		hyperMutator?: number // Default: 500
+	}
+
+	/** Options for filtering fusion file content */
+	fusionOptions?: {
+		/** Filter by fusion type */
+		fusionTypes?: ('gene-gene' | 'gene-intergenic' | 'readthrough')[]
+		/** Minimum confidence score (0-1) */
+		minConfidence?: number // Default: 0.7
+	}
+}
+
+/**
+ * Response for GRIN2 analysis run
+ */
+export type GRIN2Response = {
+	/** Status of the analysis */
+	status: 'success' | 'error'
+	/** Error message if status is 'error' */
+	error?: string
+	/** Base64-encoded PNG Manhattan plot image */
+	pngImg?: string
+	/** Download status/info */
+	download?: any
+	/** Sortable table of top genes identified by GRIN2 */
+	topGeneTable?: {
+		/** Column definitions with labels and sort capabilities */
+		columns: Array<{
+			label: string
+			sortable: boolean
+		}>
+		/** Data rows with gene information and statistics */
+		rows: Array<
+			Array<{
+				value: string | number
+			}>
+		>
+	}
+	/** Summary statistics */
+	totalGenes?: number
+	showingTop?: number
+	/** Timing info for the analysis */
+	timing?: {
+		/** Time taken to run data processing */
+		processingTime: number
+		/** Time taken to run GRIN2 processing */
+		grin2Time: number
+		/** Total time taken for the entire run */
+		totalTime: number
+	}
+	/** Detailed processing summary */
+	processingSummary?: {
+		totalSamples: number
+		successfulSamples: number
+		failedSamples: number
+		failedFiles: Array<{
+			sampleName: string
+			filePath: string
+			error: string
+		}>
+	}
+}
+
+/**
+ * Route payload definitions for type checking
+ */
+export const GRIN2Payload: RoutePayload = {
+	request: {
+		typeId: 'GRIN2Request'
+	},
+	response: {
+		typeId: 'GRIN2Response'
+	}
+}

package/src/terms/term.ts

@@ -123,7 +123,7 @@ export type FilterGroup = {
 	name: string
 	type: 'filter'
 	filter: Filter
-	uncomputable: boolean
+	color: string
 }
 
 export type GroupEntry = ValuesGroup | FilterGroup