@sjcrh/proteinpaint-types 2.134.0 → 2.135.2-0

package/src/dataset.ts

@@ -1519,19 +1519,6 @@ type MutationSet = {
 }
 
 /** different methods to return samples with assay availability info */
-type DtAssayAvailability = DtAssayAvailabilityGetter | DtAssayAvailabilityTerm
-
-/** using ds-supplied getter */
-type DtAssayAvailabilityGetter = {
-	/** define q
-	returns:
-	{
-		yesSamples: Set() of sample ids
-		noSamples: Set() of sample ids
-	}
-	*/
-	get: (q: any) => any
-}
 /** using dictionary term */
 type DtAssayAvailabilityTerm = {
 	/** id of this assay term for this dt */
@@ -1542,21 +1529,32 @@ type DtAssayAvailabilityTerm = {
 	yes: { value: string[] }
 	/** categories meaning the sample doesn't have this assay */
 	no: { value: string[] }
+	/** dynamically generated cached sample lists on server launch, can also be ds-supplied.
+	each is a Set of sample integer id (non-gdc ds) or sample name (case uuid for gdc)
+	*/
+	yesSamples?: Set<string | number>
+	noSamples?: Set<string | number>
 }
 
 type DtAssayAvailabilityByOrigin = {
 	byOrigin: {
 		/** each key is an origin value or category */
-		[index: string]: DtAssayAvailability
+		[index: string]: DtAssayAvailabilityTerm
 	}
 }
 
+/** assay availability can be set up as below, during server init it will query by assay dictionary terms to populate yes/no samples for each dt
+or as in gdc, it is entirely setup ad-hoc
+*/
 type Mds3AssayAvailability = {
 	/** object of key-value pairs. keys are dt values */
 	byDt: {
 		/** each index is a dt value */
-		[index: number]: DtAssayAvailabilityByOrigin | DtAssayAvailability
+		[index: number]: DtAssayAvailabilityByOrigin | DtAssayAvailabilityTerm
 	}
+	/** if true, ds will use both filter and filter0 to filter samples (this is a temp quick fix)
+	 */
+	useFilter0?: true
 }
 
 // mds legacy; delete when all are migrated to mds3
@@ -2065,7 +2063,15 @@ export type Mds3 = BaseMds & {
 	the param contents will be assessed by ds specific getter
 	this is serverside only, not passed to termdbConfig
 	*/
-	mayGetGeneVariantDataParam?: { [key: string]: any }
+	mayGetGeneVariantDataParam?: {
+		[key: string]: any
+		/** this flag determines whether geneVariant data is filtered during post-processing
+		normally, geneVariant data is filtered during data query
+		but the filter structure used by gdc is not compatible with
+		geneVariant data filtering, so this flag is used to filter
+		data during post-processing */
+		postProcessDtFilter?: boolean
+	}
 	// !!! TODO: improve these type definitions below !!!
 	getHostHeaders?: (q?: any) => any
 	serverconfigFeatures?: any

package/src/filter.ts

@@ -55,6 +55,8 @@ export type ConditionTvs = BaseTvs & {
 type GeneVariantTvs = BaseTvs & {
 	term: DtTerm
 	values: { key: string; label: string; value: string }[]
+	/** boolean for including not tested classes (excluded by default) */
+	includeNotTested?: boolean
 }
 
 /*** types supporting Filter type ***/

package/src/routes/gdc.grin2.ts

@@ -133,15 +133,58 @@ export type RustErrorEntry = {
 
 /** Summary information from Rust processing */
 export type RustSummary = {
+	type: 'summary'
 	total_files: number
 	successful_files: number
 	failed_files: number
+	errors: RustErrorEntry[]
+	filtered_records: number
+	filtered_maf_records: number
+	filtered_cnv_records: number
+	included_maf_records: number
+	included_cnv_records: number
+
+	/** The complex nested structure of the per case object
+	 *  Records filtered by case, with MAF and CNV statistics
+	 */
+	filtered_records_by_case: Record<
+		string,
+		{
+			maf: {
+				matched_consequences: Record<string, any>
+				rejected_consequences: Record<string, any>
+				t_alt_count: number
+				t_depth: number
+				invalid_rows: number
+				excluded_by_min_depth: number
+				excluded_by_min_alt_count: number
+				excluded_by_consequence_type: number
+				total_processed: number
+				total_included: number
+				skipped_chromosomes: Record<string, number>
+			}
+			cnv: {
+				segment_mean: number
+				seg_length: number
+				invalid_rows: number
+				excluded_by_loss_threshold: number
+				excluded_by_gain_threshold: number
+				excluded_by_segment_length: number
+				total_processed: number
+				total_included: number
+				skipped_chromosomes: Record<string, number>
+			}
+		}
+	>
+
+	hyper_mutator_records: Record<string, string[]>
+	excluded_by_max_record: Record<string, string[]>
 }
 
 /** Structured output from Rust GRIN2 processing */
 export type RustGRIN2Result = {
-	/** Array of successful file data arrays */
-	successful_data: string[][]
+	/** String of successful file data */
+	successful_data: string
 	/** Array of failed file information */
 	failed_files: RustErrorEntry[]
 	/** Summary statistics */

package/src/routes/profileScores.ts

@@ -5,7 +5,7 @@ export type ProfileScoresRequest = {
 	filter?: any
 	isRadarFacility?: boolean
 	userSites?: string[]
-	site?: string
+	sites?: string[]
 	isAggregate?: boolean
 	facilityTW?: any
 }