@sjcrh/proteinpaint-shared 2.169.0 → 2.170.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.169.0",
+  "version": "2.170.1",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/common.js

@@ -1323,9 +1323,7 @@ const dtTerms_temp = [
 		isleaf: true,
 		type: 'dtsnvindel',
 		dt: dtsnvindel,
-		values: Object.fromEntries(
-			mutationClasses.filter(key => key != 'Blank' && key != 'WT').map(key => [key, { label: mclass[key].label }])
-		)
+		values: {}
 	},
 	{
 		id: 'cnv',
@@ -1335,7 +1333,7 @@ const dtTerms_temp = [
 		isleaf: true,
 		type: 'dtcnv',
 		dt: dtcnv,
-		values: Object.fromEntries(CNVClasses.map(key => [key, { label: mclass[key].label }]))
+		values: {}
 	},
 	{
 		id: 'fusion',
@@ -1345,7 +1343,7 @@ const dtTerms_temp = [
 		isleaf: true,
 		type: 'dtfusion',
 		dt: dtfusionrna,
-		values: { [mclassfusionrna]: { label: mclass[mclassfusionrna].label } }
+		values: {}
 	},
 	{
 		id: 'sv',
@@ -1355,7 +1353,7 @@ const dtTerms_temp = [
 		isleaf: true,
 		type: 'dtsv',
 		dt: dtsv,
-		values: { [mclasssv]: { label: mclass[mclasssv].label } }
+		values: {}
 	}
 ]
 // add origin annotations to dt terms

package/src/fetch-helpers.js

@@ -15,8 +15,9 @@ import { encode } from './urljson.js'
 	init{headers?, body?}
 	- first two arguments are same as native fetch
 */
-export async function ezFetch(_url, init = {}) {
-	const url = mayAdjustRequest(_url, init)
+export async function ezFetch(_url, init = {}, opts = {}) {
+	const url = opts.autoMethod ? mayAdjustRequest(_url, init) : _url
+	if (typeof init.body === 'object') init.body = JSON.stringify(init.body)
 
 	return fetch(url, init).then(async r => {
 		const response = await processResponse(r)
@@ -73,6 +74,9 @@ export async function processResponse(r) {
 		if (ct.startsWith('multipart/form-data')) return processFormData(r)
 		else throw `cannot handle response content-type: '${ct}'`
 	}
+	if (ct == 'application/x-ndjson-nestedkey') {
+		return processNDJSON_nestedKey(r)
+	}
 	// call blob() as catch-all
 	// https://developer.mozilla.org/en-US/docs/Web/API/Response
 	return r.blob()
@@ -115,6 +119,44 @@ export async function processFormData(res) {
 	}
 }
 
+async function processNDJSON_nestedKey(r) {
+	// 1. Pipe through TextDecoder to convert bytes to text
+	const stream = r.body.pipeThrough(new TextDecoderStream())
+	const reader = stream.getReader()
+	let rootObj = {}
+
+	let buffer = ''
+
+	while (true) {
+		const { value, done } = await reader.read()
+		if (done) break
+
+		// 2. Add new chunk to buffer
+		buffer += value
+
+		// 3. Split by newline
+		let parts = buffer.split('\n')
+
+		// 4. Keep the last partial line in the buffer
+		buffer = parts.pop()
+
+		// 5. Process complete lines
+		for (const line of parts) {
+			if (line.trim()) {
+				const [keys, data] = JSON.parse(line) //; console.log(143, keys, data) // Process JSON data
+				if (!keys.length) rootObj = data
+				else {
+					const lastKey = keys.pop()
+					let target = rootObj
+					for (const k of keys) target = target[k]
+					target[lastKey] = data
+				}
+			}
+		}
+	}
+	return rootObj
+}
+
 // key: request object reference or conputed string dataName
 // value: fetch promise or response
 const dataCache = new Map()
@@ -145,6 +187,7 @@ const maxNumOfDataKeys = 360
 	  - if not provided, then a string cache data key will be computed from the request url, body, headers
 */
 export async function memFetch(url, init, opts = {}) {
+	if (typeof init.body === 'object') init.body = JSON.stringify(init.body)
 	const dataKey = opts.q || (await getDataName(url, init))
 	let result = dataCache.get(dataKey)
 
@@ -161,8 +204,13 @@ export async function memFetch(url, init, opts = {}) {
 				fetch(url, init).then(async r => {
 					const response = await processResponse(r)
 					if (!r.ok) {
-						console.log(response)
-						throw 'memFetch error ' + r.status
+						console.trace(response)
+						throw (
+							'memFetch error ' +
+							r.status +
+							': ' +
+							(typeof response == 'object' ? response.message || response.error : response)
+						)
 					}
 					// to-do: support opt.freeze to enforce deep freeze of data.json()
 					dataCache.set(dataKey, response)

package/src/index.js

@@ -9,6 +9,7 @@ export * from './filter.js'
 export * from './hash.js'
 export * from './helpers.js'
 export * from './joinUrl.js'
+export * from './manhattan.js'
 export * from './mds3tk.js'
 export * from './roundValue.js'
 export * from './termdb.bins.js'

package/src/manhattan.js

@@ -0,0 +1,3 @@
+// Contains shared constants for Manhattan plots
+// This constant defines the log cutoff for q-values in Manhattan plots before scaling the y-axis.
+export const MANHATTAN_LOG_QVALUE_CUTOFF = 40

package/src/termdb.usecase.js

@@ -20,7 +20,8 @@ export const graphableTypes = new Set([
 	TermTypes.METABOLITE_INTENSITY,
 	TermTypes.SINGLECELL_GENE_EXPRESSION,
 	TermTypes.SINGLECELL_CELLTYPE,
-	TermTypes.SNP
+	TermTypes.SNP,
+	TermTypes.TERM_COLLECTION
 ])
 
 /*