@sjcrh/proteinpaint-shared 2.98.0 → 2.99.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.98.0",
+  "version": "2.99.1",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",
@@ -9,7 +9,7 @@
     "./*": "./src/*"
   },
   "scripts": {
-    "build": "esbuild src/*.ts --platform=node --outdir=src/ --format=esm",
+    "build": "esbuild src/*.ts --platform=node --outdir=src/ --format=esm && prettier --no-semi --use-tabs --write src/urljson.js src/joinUrl.js src/doc.js",
     "prepack": "npm run build",
     "test": "ls src/test/*.spec* | xargs node"
   },

package/src/common.js

@@ -307,7 +307,7 @@ mclass[mclasscnvloss] = {
 export const mclasscnvAmp = 'CNV_amplification'
 mclass[mclasscnvAmp] = {
 	label: 'Copy number amplification',
-	color: '#900000',
+	color: '#ff0000',
 	dt: dtcnv,
 	desc: 'Copy number amplification',
 	key: mclasscnvAmp
@@ -316,7 +316,7 @@ mclass[mclasscnvAmp] = {
 export const mclasscnvHomozygousDel = 'CNV_homozygous_deletion'
 mclass[mclasscnvHomozygousDel] = {
 	label: 'Copy number homozygous deletion',
-	color: '#00457C',
+	color: '#0000ff',
 	dt: dtcnv,
 	desc: 'Copy number homozygous deletion',
 	key: mclasscnvHomozygousDel

package/src/doc.js

@@ -1,10 +1,6 @@
-const test = {};
+const test = {}
 function doc(opts) {
-  if (opts.type in test)
-    throw `test['${opts.type}'] already exists`;
-  test[opts.type] = opts.test;
+	if (opts.type in test) throw `test['${opts.type}'] already exists`
+	test[opts.type] = opts.test
 }
-export {
-  doc,
-  test
-};
+export { doc, test }

package/src/joinUrl.js

@@ -0,0 +1,7 @@
+function joinUrl(p1, p2) {
+	if (typeof p1 != 'string' || typeof p2 != 'string') throw `both arguments must be string type`
+	if (!p1 || !p2) throw 'blank string not allowed'
+	if (p1.indexOf('?') != -1) throw 'search string not allowed'
+	return (p1.endsWith('/') ? p1 : p1 + '/') + (p2.startsWith('/') ? p2.substring(1) : p2)
+}
+export { joinUrl }

package/src/termdb.usecase.js

@@ -181,6 +181,18 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 			}
 		// no specific rule for filter. pass and use default rules
 
+		case 'correlationVolcano':
+			if (usecase.detail == 'numeric') {
+				if (isNumericTerm(term)) {
+					uses.add('plot')
+				}
+				if (hasNumericChild(child_types)) uses.add('branch')
+			} else {
+				if (graphableTypes.has(term.type)) uses.add('plot')
+				if (!term.isleaf) uses.add('branch')
+			}
+			return uses
+
 		default:
 			if (graphableTypes.has(term.type)) uses.add('plot')
 			if (!term.isleaf) uses.add('branch')

package/src/terms.js

@@ -184,3 +184,25 @@ export function getParentType(types, ds) {
 	}
 	return null //no parent found
 }
+
+//Returns human readable type (nice label) for the given type
+export function getReadableType(type) {
+	const typeMap = {
+		categorical: 'Categorical',
+		condition: 'Condition',
+		float: 'Numeric',
+		integer: 'Numeric',
+		geneExpression: 'Gene Expression',
+		geneVariant: 'Gene Variant',
+		metaboliteIntensity: 'Metabolite Intensity',
+		multiValue: 'Multi Value',
+		samplelst: 'Sample List',
+		singleCellGeneExpression: 'Single Cell, Gene Expression',
+		singleCellCellType: 'Single Cell, Cell Type',
+		snplocus: 'SNP Locus',
+		snp: 'SNP',
+		snplst: 'SNP List'
+	}
+
+	return typeMap[type] || 'Unknown type [shared/utils/src/terms.js getReadableType()]'
+}

package/src/urljson.js

@@ -1,30 +1,32 @@
-import { isNumeric } from "./helpers.js";
-const reserved = ["false", "true", "null", "undefined"];
-const delimiters = ['"', "{", "["];
+import { isNumeric } from './helpers.js'
+const reserved = ['false', 'true', 'null', 'undefined']
+const delimiters = ['"', '{', '[']
 function encode(rawObject) {
-  const params = [];
-  for (const [key, value] of Object.entries(rawObject)) {
-    if (typeof value == "string" && !isNumeric(value) && !reserved.includes(value) && !delimiters.includes(value[0])) {
-      params.push(`${key}=${encodeURIComponent(value)}`);
-    } else if (value !== void 0) {
-      params.push(`${key}=${encodeURIComponent(JSON.stringify(value))}`);
-    }
-  }
-  return params.join("&");
+	const params = []
+	for (const [key, value] of Object.entries(rawObject)) {
+		if (typeof value == 'string' && !isNumeric(value) && !reserved.includes(value) && !delimiters.includes(value[0])) {
+			params.push(`${key}=${encodeURIComponent(value)}`)
+		} else if (value !== void 0) {
+			params.push(`${key}=${encodeURIComponent(JSON.stringify(value))}`)
+		}
+	}
+	return params.join('&')
 }
 function decode(query) {
-  const encoding = query.encoding;
-  for (const [key, value] of Object.entries(query)) {
-    if (encoding == "json" || value == "null" || // not new, always been
-    value == "true" || // NEED TO FIND-REPLACE CODE THAT USES value == 'true'
-    value == "false" || // NEED TO FIND-REPLACE CODE THAT USES value == 'false'
-    isNumeric(value) || // NEED TO check
-    value.startsWith('"') && value.endsWith('"') || value.startsWith("{") && value.endsWith("}") || value.startsWith("[") && value.endsWith("]"))
-      query[key] = JSON.parse(value);
-  }
-  return query;
+	const encoding = query.encoding
+	for (const [key, value] of Object.entries(query)) {
+		if (
+			encoding == 'json' ||
+			value == 'null' || // not new, always been
+			value == 'true' || // NEED TO FIND-REPLACE CODE THAT USES value == 'true'
+			value == 'false' || // NEED TO FIND-REPLACE CODE THAT USES value == 'false'
+			isNumeric(value) || // NEED TO check
+			(value.startsWith('"') && value.endsWith('"')) ||
+			(value.startsWith('{') && value.endsWith('}')) ||
+			(value.startsWith('[') && value.endsWith(']'))
+		)
+			query[key] = JSON.parse(value)
+	}
+	return query
 }
-export {
-  decode,
-  encode
-};
+export { decode, encode }