@sjcrh/proteinpaint-types 2.78.0-0 → 2.79.4

package/LICENSE

@@ -0,0 +1,42 @@
+Copyright ©St. Jude Children’s Research Hospital 2023
+
+ 
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+
+of the ProteinPaint web browser and associated documentation files (the "Software"), to utilize
+
+the Software for academic use without restriction, including without limitation the rights
+
+to use, copy, modify, merge, publish, distribute and sublicense
+
+copies of the Software for academic use, and to permit persons to whom the Software is
+
+furnished to do so, subject to the following conditions:
+
+ 
+
+The above copyright notice and this permission notice shall be included in all
+
+copies or substantial portions of the Software.
+
+ 
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+
+SOFTWARE.
+
+ 
+
+Anyone interested in commercial use of the Software should contact the
+St. Jude Office of Technology Licensing at technology.licensing@stjude.org.

package/README.md

@@ -0,0 +1,17 @@
+# @sjcrh/proteinpaint-types
+
+## Background
+
+This workspace was separated from the deprecated `server/shared/types` dir.
+The type definitions here are meant to used by the tsc compiler, and will not
+be included in runtime bundles.
+
+Put type definitions that are used in client and server code in this workspace.
+Do NOT put here type definitions that are specific to one workspace,
+those should be saved in the applicable workspace.
+
+## Test
+
+```sh
+npm test
+```

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.78.0-0",
+  "version": "2.79.4",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",
@@ -15,7 +15,8 @@
     "#shared": "@sjcrh/proteinpaint-shared"
   },
   "scripts": {
-    "prepare": "ts-patch install"
+    "prepare": "ts-patch install",
+    "test": "tsc"
   },
   "devDependencies": {
     "ts-node": "^10.9.2",

package/src/dataset.ts

@@ -69,8 +69,10 @@ type bcfMafFile = {
 type SnvindelByRange = {
 	/** if true, served from gdc. no other parameters TODO change to src='gdc/native' */
 	gdcapi?: boolean
-	/**local file can have following different setup
-	 * one single bcf file */
+
+	//local ds can have following different setup
+
+	/** one single bcf file */
 	bcffile?: string
 	/** one bcf file per chr */
 	chr2bcffile?: Chr2bcffile
@@ -78,6 +80,8 @@ type SnvindelByRange = {
 	bcfMafFile?: bcfMafFile
 	/** allow to apply special configurations to certain INFO fields of the bcf file */
 	infoFields?: InfoFieldEntry[]
+	/** if true, bcf or chr2bcf uses string sample name in header. to be used during this migrating so the code can deal with old files with integer sample ids and new ones; TODO once all datasets are migrated, delete the flag */
+	tempflag_sampleNameInVcfHeader?: boolean
 }
 
 type SvfusionByRange = {
@@ -482,7 +486,7 @@ export type SingleCellDEgeneGdc = {
 
 type GDCSingleCellPlot = {
 	name: string
-	colorColumn: ColorColumn
+	colorColumns: ColorColumn[]
 	coordsColumns: { x: number; y: number }
 }
 
@@ -510,10 +514,9 @@ type SingleCellPlot = {
 	if not introduce filePrefix
 	*/
 	fileSuffix?: string
-	/** specify which column to color the cells in the plot. must have categorical values
-	TODO define a set of color columns and specify a default one, and let ui to switch from
-	*/
-	colorColumn: ColorColumn
+	/** list of columns in tabular text file that define cell categories and can be used to color the cells in the plot. must have categorical values
+	 */
+	colorColumns: ColorColumn[]
 	/** 0-based column number for x/y coordinate for this plot */
 	coordsColumns: { x: number; y: number }
 }
@@ -1003,6 +1006,7 @@ type Termdb = {
 		html: string
 	}
 	hasSampleAncestry?: boolean
+	sampleTypes?: SampleType[]
 
 	tracks?: {
 		/** allow color or shape changes in the lollipop */
@@ -1010,6 +1014,12 @@ type Termdb = {
 	}
 }
 
+type SampleType = {
+	name: string
+	plural_name: string
+	parent_id: string
+}
+
 type ChartConfigByType = {
 	[index: string]: ChartConfig
 }

package/src/index.ts

@@ -1,4 +1,4 @@
-// please list in alphanumeric order
+// please list in alphanumeric order, include file extension
 export * from './genome.ts'
 export * from './dataset.ts'
 export * from './termsetting.ts'

package/src/routes/burden.ts

@@ -57,11 +57,13 @@ export type BurdenRequest = {
 	chest: number
 }
 
+// tentative code for migrating api code from `server/routes` code
 export type BurdenResponse = {
 	status: string
 	keys: string[]
 	rows: number[][]
 }
 
+// tentative code to generate runtime "type" checkers
 export const validBurdenRequest = createValidate<BurdenRequest>()
 export const validBurdenResponse = createValidate<BurdenResponse>()

package/src/routes/termdb.singlecellData.ts

@@ -1,4 +1,4 @@
-import type { ErrorResponse } from './errorResponse.ts'
+import { ErrorResponse } from './errorResponse.ts'
 
 export type Cell = {
 	/** Cell id or barcode */
@@ -22,6 +22,7 @@ export type Plot = {
 	cells: Cell[]
 	/** Column name to color by, e.g Cell type, CNV, Fusion */
 	colorBy: string
+	colorColumns: string[]
 	colorMap?: { [key: string]: string }
 }
 
@@ -39,7 +40,7 @@ export type TermdbSinglecellDataRequest = {
 	gene?: string
 }
 
-type HasdataResponse = {
+export type HasdataResponse = {
 	/** List of plots from singlecell experiment of this sample */
 	plots: Plot[]