@sjcrh/proteinpaint-shared 2.83.0 → 2.85.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.83.0",
+  "version": "2.85.0",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/common.js

@@ -1293,5 +1293,7 @@ export const colorScaleMap = {
 	blueBlackYellow: {
 		domain: [0, 0.17, 0.33, 0.5, 0.67, 0.83, 1],
 		range: ['#0000FF', '#0000CC', '#000099', '#202020', '#999900', '#CCCC00', '#FFFF00']
-	}
+	},
+	// when hierCluster z-score transformation is not performed, should use two-color scale
+	whiteRed: { domain: [0, 1], range: ['white', 'red'] }
 }

package/src/helpers.js

@@ -1,15 +1,25 @@
 /*
 this is a helper file with a collection of functions to be used in backend and client side code. Here is a list.
 
-1. isNumeric(n) - checks whether given argument n is Numeric
-2. convertUnits - converts a value from a unit to another unit
+1. isNumeric(n)
+2. strictNumeric(n) 
+2. convertUnits
 3. TODO - move computepercentile, roundValue, etc here?
 */
 
+// checks whether given argument n is Numeric, with option to cast from string
 export function isNumeric(n) {
-	return Number.isFinite(n) || !isNaN(parseFloat(n))
+	const v = typeof n != 'string' || n === '' ? n : Number(n)
+	const f = parseFloat(n)
+	return !isNaN(f) && Number.isFinite(v) && v === f
 }
 
+// like isNumeric but does not cast from string
+export function isStrictNumeric(n) {
+	return typeof n === 'number' && Number.isFinite(n)
+}
+
+// converts a value from a unit to another unit
 export function convertUnits(v, fromUnit, toUnit, scaleFactor, compact) {
 	// do floor() on toUnit
 	// do ceil() on fromUnit, in case v is decimal (from violin range selection) and to keep showing integer fromUnit

package/src/termdb.bins.js

@@ -1,6 +1,6 @@
 import { format } from 'd3-format'
 import { getColors } from './common.js'
-import { isNumeric, convertUnits } from './helpers.js'
+import { isStrictNumeric, convertUnits } from './helpers.js'
 
 export default function validate_bins(binconfig) {
 	// Number.isFinite('1') returns false, which is desired
@@ -35,14 +35,14 @@ export default function validate_bins(binconfig) {
 				if (!('stop' in bin)) {
 					throw `a custom first bin must define a bin.stop value`
 				}
-				if (!isNumeric(bin.stop)) {
+				if (!isStrictNumeric(bin.stop)) {
 					throw `a custom first bin.stop value should be numeric`
 				}
 			} else if (bin == last_bin) {
 				if (!('start' in bin)) {
 					throw `a custom last bin must define a bin.start value`
 				}
-				if (!isNumeric(bin.start)) {
+				if (!isStrictNumeric(bin.start)) {
 					throw `a custom last bin.start must be numeric`
 				}
 				if ('stopunbounded' in bin && !bin.stopunbounded) {
@@ -53,8 +53,8 @@ export default function validate_bins(binconfig) {
 					throw 'a custom last bin must not set a bin.stop value'
 				}
 			} else {
-				if (!isNumeric(bin.start)) throw 'bin.start must be numeric for a non-first bin'
-				if (!isNumeric(bin.stop)) throw 'bin.stop must be numeric for a non-last bin'
+				if (!isStrictNumeric(bin.start)) throw 'bin.start must be numeric for a non-first bin'
+				if (!isStrictNumeric(bin.stop)) throw 'bin.stop must be numeric for a non-last bin'
 			}
 		}
 	} else if (bc.type == 'regular-bin') {
@@ -156,19 +156,19 @@ summaryfxn (percentiles)=> return {min, max, pX, pY, ...}
 			? maxCeil // in order to include the max value in the last bin
 			: bc.last_bin.stop_percentile
 			? summary['p' + bc.last_bin.stop_percentile]
-			: isNumeric(bc.last_bin.stop) && bc.last_bin.stop <= summary.max
+			: isNumeric(bc.last_bin.stop) && bc.last_bin.stop <= summary.max // '0.0088' < 0.0088
 			? bc.last_bin.stop
 			: maxCeil // in order to include the max value in the last bin
-		last_start = isNumeric(bc.last_bin.start_percentile)
+		last_start = isStrictNumeric(bc.last_bin.start_percentile)
 			? summary['p' + bc.last_bin.start_percentile]
-			: isNumeric(bc.last_bin.start)
+			: isStrictNumeric(bc.last_bin.start)
 			? bc.last_bin.start
 			: undefined
 		last_stop = bc.last_bin.stopunbounded
 			? null
 			: bc.last_bin.stop_percentile
 			? summary['p' + bc.last_bin.stop_percentile]
-			: isNumeric(bc.last_bin.stop)
+			: isStrictNumeric(bc.last_bin.stop)
 			? bc.last_bin.stop
 			: null
 	} else if (bc.lst) {
@@ -181,9 +181,9 @@ summaryfxn (percentiles)=> return {min, max, pX, pY, ...}
 		last_stop = maxCeil
 	}
 
-	const numericMax = isNumeric(max)
-	const numericLastStart = isNumeric(last_start)
-	const numericLastStop = isNumeric(last_stop)
+	const numericMax = isStrictNumeric(max)
+	const numericLastStart = isStrictNumeric(last_start)
+	const numericLastStop = isStrictNumeric(last_stop)
 
 	if (!numericMax && !numericLastStart) return [] //throw 'unable to compute the last bin start or stop'
 
@@ -191,16 +191,16 @@ summaryfxn (percentiles)=> return {min, max, pX, pY, ...}
 	let currBin = {
 		startunbounded: bc.first_bin.startunbounded,
 		start: bc.first_bin.startunbounded ? undefined : min,
-		stop: isNumeric(bc.first_bin.stop_percentile)
+		stop: isStrictNumeric(bc.first_bin.stop_percentile)
 			? +summary['p' + bc.first_bin.stop_percentile]
-			: isNumeric(bc.first_bin.stop)
+			: isStrictNumeric(bc.first_bin.stop)
 			? +bc.first_bin.stop
 			: min + bc.bin_size,
 		startinclusive: bc.startinclusive,
 		stopinclusive: bc.stopinclusive
 	}
 
-	if (!isNumeric(currBin.stop)) throw 'the computed first_bin.stop is non-numeric' + currBin.stop
+	if (!isStrictNumeric(currBin.stop)) throw 'the computed first_bin.stop is non-numeric' + currBin.stop
 	const maxNumBins = 100 // harcoded limit for now to not stress sqlite
 
 	while ((numericMax && currBin.stop <= max) || (currBin.startunbounded && !bins.length) || currBin.stopunbounded) {
@@ -372,10 +372,10 @@ export function get_bin_range_equation(bin, binconfig) {
 export function target_percentiles(binconfig) {
 	const percentiles = []
 	const f = binconfig.first_bin
-	if (f && isNumeric(f.start_percentile)) percentiles.push(f.start_percentile)
-	if (f && isNumeric(f.stop_percentile)) percentiles.push(f.stop_percentile)
+	if (f && isStrictNumeric(f.start_percentile)) percentiles.push(f.start_percentile)
+	if (f && isStrictNumeric(f.stop_percentile)) percentiles.push(f.stop_percentile)
 	const l = binconfig.last_bin
-	if (l && isNumeric(l.start_percentile)) percentiles.push(l.start_percentile)
-	if (l && isNumeric(l.stop_percentile)) percentiles.push(l.stop_percentile)
+	if (l && isStrictNumeric(l.start_percentile)) percentiles.push(l.start_percentile)
+	if (l && isStrictNumeric(l.stop_percentile)) percentiles.push(l.stop_percentile)
 	return percentiles
 }

package/src/urljson.js

@@ -1,3 +1,4 @@
+import { isNumeric } from "./helpers.js";
 const reserved = ["false", "true", "null", "undefined"];
 const delimiters = ['"', "{", "["];
 function encode(rawObject) {
@@ -23,9 +24,6 @@ function decode(query) {
   }
   return query;
 }
-function isNumeric(d) {
-  return !isNaN(parseFloat(d)) && isFinite(d) && d !== "";
-}
 export {
   decode,
   encode