@sjcrh/proteinpaint-types 2.153.1-2 → 2.157.0

package/dist/{chunk-EYKGJDKU.js → chunk-4LOGWDCZ.js}

@@ -69,12 +69,12 @@ var validTermdbSingleCellDEgenesResponse = (input) => {
   const errors = [];
   const __is = (input2) => {
     const $io0 = (input3) => "number" === typeof input3.status && "string" === typeof input3.error;
-    const $io1 = (input3) => Array.isArray(input3.genes) && input3.genes.every((elem) => "object" === typeof elem && null !== elem && $io2(elem));
-    const $io2 = (input3) => "string" === typeof input3.name && "number" === typeof input3.p_val_adj && "number" === typeof input3.avg_log2FC;
+    const $io1 = (input3) => Array.isArray(input3.data) && input3.data.every((elem) => "object" === typeof elem && null !== elem && $io2(elem));
+    const $io2 = (input3) => "string" === typeof input3.gene_name && "number" === typeof input3.adjusted_p_value && "number" === typeof input3.original_p_value && "number" === typeof input3.fold_change;
     const $iu0 = (input3) => (() => {
       if (void 0 !== input3.status)
         return $io0(input3);
-      if (void 0 !== input3.genes)
+      if (void 0 !== input3.data)
         return $io1(input3);
       return false;
     })();
@@ -92,40 +92,44 @@ var validTermdbSingleCellDEgenesResponse = (input) => {
         expected: "string",
         value: input3.error
       })].every((flag) => flag);
-      const $vo1 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.genes) || $report(_exceptionable2, {
-        path: _path2 + ".genes",
+      const $vo1 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.data) || $report(_exceptionable2, {
+        path: _path2 + ".data",
         expected: "Array<__type>",
-        value: input3.genes
-      })) && input3.genes.map((elem, _index1) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
-        path: _path2 + ".genes[" + _index1 + "]",
+        value: input3.data
+      })) && input3.data.map((elem, _index1) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
+        path: _path2 + ".data[" + _index1 + "]",
         expected: "__type",
         value: elem
-      })) && $vo2(elem, _path2 + ".genes[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
-        path: _path2 + ".genes[" + _index1 + "]",
+      })) && $vo2(elem, _path2 + ".data[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".data[" + _index1 + "]",
         expected: "__type",
         value: elem
       })).every((flag) => flag) || $report(_exceptionable2, {
-        path: _path2 + ".genes",
+        path: _path2 + ".data",
         expected: "Array<__type>",
-        value: input3.genes
+        value: input3.data
       })].every((flag) => flag);
-      const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.name || $report(_exceptionable2, {
-        path: _path2 + ".name",
+      const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.gene_name || $report(_exceptionable2, {
+        path: _path2 + ".gene_name",
         expected: "string",
-        value: input3.name
-      }), "number" === typeof input3.p_val_adj || $report(_exceptionable2, {
-        path: _path2 + ".p_val_adj",
+        value: input3.gene_name
+      }), "number" === typeof input3.adjusted_p_value || $report(_exceptionable2, {
+        path: _path2 + ".adjusted_p_value",
         expected: "number",
-        value: input3.p_val_adj
-      }), "number" === typeof input3.avg_log2FC || $report(_exceptionable2, {
-        path: _path2 + ".avg_log2FC",
+        value: input3.adjusted_p_value
+      }), "number" === typeof input3.original_p_value || $report(_exceptionable2, {
+        path: _path2 + ".original_p_value",
         expected: "number",
-        value: input3.avg_log2FC
+        value: input3.original_p_value
+      }), "number" === typeof input3.fold_change || $report(_exceptionable2, {
+        path: _path2 + ".fold_change",
+        expected: "number",
+        value: input3.fold_change
       })].every((flag) => flag);
       const $vu0 = (input3, _path2, _exceptionable2 = true) => (() => {
         if (void 0 !== input3.status)
           return $vo0(input3, _path2, _exceptionable2);
-        if (void 0 !== input3.genes)
+        if (void 0 !== input3.data)
           return $vo1(input3, _path2, _exceptionable2);
         return $report(_exceptionable2, {
           path: _path2,

package/dist/{chunk-4LZHDYI3.js → chunk-WCF7WIJY.js}

@@ -190,8 +190,8 @@ var validGRIN2Response = (input) => {
   const __is = (input2) => {
     const $join = import_typia.createValidate.join;
     const $io0 = (input3) => ("error" === input3.status || "success" === input3.status) && (void 0 === input3.error || "string" === typeof input3.error) && (void 0 === input3.pngImg || "string" === typeof input3.pngImg) && (void 0 === input3.plotData || "object" === typeof input3.plotData && null !== input3.plotData && $io1(input3.plotData)) && true && (void 0 === input3.topGeneTable || "object" === typeof input3.topGeneTable && null !== input3.topGeneTable && $io5(input3.topGeneTable)) && (void 0 === input3.totalGenes || "number" === typeof input3.totalGenes) && (void 0 === input3.showingTop || "number" === typeof input3.showingTop) && (void 0 === input3.timing || "object" === typeof input3.timing && null !== input3.timing && $io8(input3.timing)) && (void 0 === input3.processingSummary || "object" === typeof input3.processingSummary && null !== input3.processingSummary && false === Array.isArray(input3.processingSummary) && $io9(input3.processingSummary)) && (void 0 === input3.cacheFileName || "string" === typeof input3.cacheFileName);
-    const $io1 = (input3) => Array.isArray(input3.points) && input3.points.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && ("object" === typeof input3.chrom_data && null !== input3.chrom_data && false === Array.isArray(input3.chrom_data) && $io3(input3.chrom_data)) && "boolean" === typeof input3.y_axis_scaled && "number" === typeof input3.scale_factor && "number" === typeof input3.total_genome_length && "number" === typeof input3.plot_width && "number" === typeof input3.plot_height && "number" === typeof input3.device_pixel_ratio && "number" === typeof input3.dpi;
-    const $io2 = (input3) => "number" === typeof input3.x && "number" === typeof input3.y && "number" === typeof input3.svg_x && "number" === typeof input3.svg_y && "string" === typeof input3.color && "string" === typeof input3.type && "string" === typeof input3.gene && "string" === typeof input3.chrom && "number" === typeof input3.pos && "number" === typeof input3.q_value;
+    const $io1 = (input3) => Array.isArray(input3.points) && input3.points.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && ("object" === typeof input3.chrom_data && null !== input3.chrom_data && false === Array.isArray(input3.chrom_data) && $io3(input3.chrom_data)) && "number" === typeof input3.total_genome_length;
+    const $io2 = (input3) => "number" === typeof input3.x && "number" === typeof input3.y && "string" === typeof input3.color && "string" === typeof input3.type && "string" === typeof input3.gene && "string" === typeof input3.chrom && "number" === typeof input3.start && "number" === typeof input3.end && "number" === typeof input3.pos && "number" === typeof input3.nsubj;
     const $io3 = (input3) => Object.keys(input3).every((key) => {
       const value = input3[key];
       if (void 0 === value)
@@ -302,34 +302,10 @@ var validGRIN2Response = (input) => {
         path: _path2 + ".chrom_data",
         expected: "Record<string, __type>",
         value: input3.chrom_data
-      }), "boolean" === typeof input3.y_axis_scaled || $report(_exceptionable2, {
-        path: _path2 + ".y_axis_scaled",
-        expected: "boolean",
-        value: input3.y_axis_scaled
-      }), "number" === typeof input3.scale_factor || $report(_exceptionable2, {
-        path: _path2 + ".scale_factor",
-        expected: "number",
-        value: input3.scale_factor
       }), "number" === typeof input3.total_genome_length || $report(_exceptionable2, {
         path: _path2 + ".total_genome_length",
         expected: "number",
         value: input3.total_genome_length
-      }), "number" === typeof input3.plot_width || $report(_exceptionable2, {
-        path: _path2 + ".plot_width",
-        expected: "number",
-        value: input3.plot_width
-      }), "number" === typeof input3.plot_height || $report(_exceptionable2, {
-        path: _path2 + ".plot_height",
-        expected: "number",
-        value: input3.plot_height
-      }), "number" === typeof input3.device_pixel_ratio || $report(_exceptionable2, {
-        path: _path2 + ".device_pixel_ratio",
-        expected: "number",
-        value: input3.device_pixel_ratio
-      }), "number" === typeof input3.dpi || $report(_exceptionable2, {
-        path: _path2 + ".dpi",
-        expected: "number",
-        value: input3.dpi
       })].every((flag) => flag);
       const $vo2 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.x || $report(_exceptionable2, {
         path: _path2 + ".x",
@@ -339,14 +315,6 @@ var validGRIN2Response = (input) => {
         path: _path2 + ".y",
         expected: "number",
         value: input3.y
-      }), "number" === typeof input3.svg_x || $report(_exceptionable2, {
-        path: _path2 + ".svg_x",
-        expected: "number",
-        value: input3.svg_x
-      }), "number" === typeof input3.svg_y || $report(_exceptionable2, {
-        path: _path2 + ".svg_y",
-        expected: "number",
-        value: input3.svg_y
       }), "string" === typeof input3.color || $report(_exceptionable2, {
         path: _path2 + ".color",
         expected: "string",
@@ -363,14 +331,22 @@ var validGRIN2Response = (input) => {
         path: _path2 + ".chrom",
         expected: "string",
         value: input3.chrom
+      }), "number" === typeof input3.start || $report(_exceptionable2, {
+        path: _path2 + ".start",
+        expected: "number",
+        value: input3.start
+      }), "number" === typeof input3.end || $report(_exceptionable2, {
+        path: _path2 + ".end",
+        expected: "number",
+        value: input3.end
       }), "number" === typeof input3.pos || $report(_exceptionable2, {
         path: _path2 + ".pos",
         expected: "number",
         value: input3.pos
-      }), "number" === typeof input3.q_value || $report(_exceptionable2, {
-        path: _path2 + ".q_value",
+      }), "number" === typeof input3.nsubj || $report(_exceptionable2, {
+        path: _path2 + ".nsubj",
         expected: "number",
-        value: input3.q_value
+        value: input3.nsubj
       })].every((flag) => flag);
       const $vo3 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
         const value = input3[key];

package/dist/grin2.js

@@ -2,7 +2,7 @@ import {
   GRIN2Payload,
   validGRIN2Request,
   validGRIN2Response
-} from "./chunk-4LZHDYI3.js";
+} from "./chunk-WCF7WIJY.js";
 import "./chunk-YNHC5SXO.js";
 export {
   GRIN2Payload,

package/dist/index.js

@@ -52,7 +52,7 @@ import {
   termdbSingleCellDEgenesPayload,
   validTermdbSingleCellDEgenesRequest,
   validTermdbSingleCellDEgenesResponse
-} from "./chunk-EYKGJDKU.js";
+} from "./chunk-4LOGWDCZ.js";
 import {
   termdbSingleCellDataPayload,
   validTermdbSingleCellDataRequest,
@@ -217,7 +217,7 @@ import {
   GRIN2Payload,
   validGRIN2Request,
   validGRIN2Response
-} from "./chunk-4LZHDYI3.js";
+} from "./chunk-WCF7WIJY.js";
 import {
   healthcheckPayload,
   validHealthCheckRequest,

package/dist/termdb.singlecellDEgenes.js

@@ -2,7 +2,7 @@ import {
   termdbSingleCellDEgenesPayload,
   validTermdbSingleCellDEgenesRequest,
   validTermdbSingleCellDEgenesResponse
-} from "./chunk-EYKGJDKU.js";
+} from "./chunk-4LOGWDCZ.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbSingleCellDEgenesPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.153.1-2",
+  "version": "2.157.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/routes/grin2.ts

@@ -82,21 +82,22 @@ export type GRIN2Request = {
 	maxGenesToShow?: number // Default: 500
 }
 
-/** Simple Interface to store the complex plot data from the python Manhattan plot */
+/** Simple Interface to store the complex plot data from the rust Manhattan plot */
 interface grin2PlotData {
 	points: Array<{
-		x: number
-		y: number
-		svg_x: number
-		svg_y: number
-		color: string
-		type: string
-		gene: string
-		chrom: string
-		pos: number
-		q_value: number
+		x: number // X-axis position (base pair/genomic position in the pixel space)
+		y: number // Y-axis position (-log10(q-value) in the pixel space)
+		color: string // Point color (hexadecimal string representing a color for mutation type)
+		type: string // Mutation type (e.g., 'mutation', 'loss', 'gain', 'fusion', 'sv')
+		gene: string // Gene symbol
+		chrom: string // Chromosome in the form of <chrX>
+		start: number // Starting position of this chromosome in base pairs/genomic coordinates. Used in hover table
+		end: number // Ending position of this chromosome in base pairs/genomic coordinates
+		pos: number // Mid-point of this chromosome in base pairs/genomic coordinates
+		nsubj: number // Number of subjects with this mutation. Used for hover table subject count
 	}>
 	chrom_data: Record<
+		// Data for chromosome labels and positioning on the x-axis
 		string,
 		{
 			start: number
@@ -104,13 +105,7 @@ interface grin2PlotData {
 			center: number
 		}
 	>
-	y_axis_scaled: boolean
-	scale_factor: number
-	total_genome_length: number
-	plot_width: number
-	plot_height: number
-	device_pixel_ratio: number
-	dpi: number
+	total_genome_length: number // Gives us the full length of the genome so we can easily append x buffer space when building d3 x-axis
 }
 
 /**

package/src/routes/termdb.singlecellDEgenes.ts

@@ -18,14 +18,16 @@ export type TermdbSingleCellDEgenesRequest = {
 
 export type HasDataResponse = {
 	/** list of significant DE genes for the given category in the sample */
-	genes: {
+	data: {
 		/** gene name */
-		name: string
+		gene_name: string
 		/** adjusted p-value */
-		p_val_adj: number
-		/** log foldchange */
-		avg_log2FC: number
-	}[]
+		adjusted_p_value: number
+		/** original p-value */
+		original_p_value: number
+		/** log2 fold change */
+		fold_change: number
+	}[] // TODO: May replace with DataEntry from termdb.DE.ts in the future
 }
 
 export type TermdbSingleCellDEgenesResponse = ErrorResponse | HasDataResponse