@sjcrh/proteinpaint-shared 2.180.0 → 2.180.1

package/src/filter.js

@@ -1,193 +1,221 @@
 function getFilteredSamples(sampleAnno, filter) {
-  setDatasetAnnotations(filter);
-  const samples = /* @__PURE__ */ new Set();
-  for (const anno of sampleAnno) {
-    if (samples.has(anno.sample)) continue;
-    const data = anno.s || anno.data;
-    if (data && sample_match_termvaluesetting(data, filter)) {
-      samples.add(anno.sample);
-    }
-  }
-  return samples;
+	setDatasetAnnotations(filter)
+	const samples = /* @__PURE__ */ new Set()
+	for (const anno of sampleAnno) {
+		if (samples.has(anno.sample)) continue
+		const data = anno.s || anno.data
+		if (data && sample_match_termvaluesetting(data, filter)) {
+			samples.add(anno.sample)
+		}
+	}
+	return samples
 }
-function sample_match_termvaluesetting(row, filter, _term = null, sample = null) {
-  const lst = filter.type == "tvslst" ? filter.lst : [filter];
-  let numberofmatchedterms = 0;
-  for (const item of lst) {
-    if ("type" in item && item.type == "tvslst") {
-      if (sample_match_termvaluesetting(row, item, _term, sample)) {
-        numberofmatchedterms++;
-      }
-    } else {
-      const itemCopy = JSON.parse(JSON.stringify(item));
-      const t = itemCopy.tvs;
-      if (_term && t.term) {
-        if (!(_term.name == t.term.name && _term.type == t.term.type)) {
-          numberofmatchedterms++;
-          continue;
-        }
-      }
-      let samplevalue;
-      if (_term && !t.term) {
-        if (t.term$type && t.term$type !== _term.type) {
-          numberofmatchedterms++;
-          continue;
-        }
-        t.term = _term;
-        samplevalue = typeof row === "object" && t.term.id in row ? row[t.term.id] : row;
-      } else if (sample && t.term.$id) {
-        samplevalue = sample[t.term.$id].value;
-      } else {
-        samplevalue = t.term.id in row ? row[t.term.id] : row;
-      }
-      setDatasetAnnotations(itemCopy);
-      let thistermmatch;
-      if (t.term.type == "categorical") {
-        if (samplevalue === void 0) continue;
-        thistermmatch = t.valueset.has(samplevalue);
-      } else if (t.term.type == "integer" || t.term.type == "float") {
-        if (samplevalue === void 0) continue;
-        for (const range of t.ranges) {
-          if ("value" in range) {
-            thistermmatch = samplevalue === range.value;
-            if (thistermmatch) break;
-          } else if (samplevalue == range.name) {
-            thistermmatch = true;
-            break;
-          } else {
-            if (t.term.values) {
-              const v = t.term.values[samplevalue.toString()];
-              if (v && v.uncomputable) {
-                continue;
-              }
-            }
-            let left, right;
-            if (range.startunbounded) {
-              left = true;
-            } else if ("start" in range) {
-              if (range.startinclusive) {
-                left = samplevalue >= range.start;
-              } else {
-                left = samplevalue > range.start;
-              }
-            }
-            if (range.stopunbounded) {
-              right = true;
-            } else if ("stop" in range) {
-              if (range.stopinclusive) {
-                right = samplevalue <= range.stop;
-              } else {
-                right = samplevalue < range.stop;
-              }
-            }
-            thistermmatch = left && right;
-          }
-          if (thistermmatch) break;
-        }
-      } else if (t.term.type == "condition") {
-        const key = getPrecomputedKey(t);
-        const anno = samplevalue && samplevalue[key];
-        if (anno) {
-          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
-        }
-      } else if (t.term.type == "geneVariant") {
-        const svalues = samplevalue.values || [samplevalue];
-        for (const sv of svalues) {
-          thistermmatch = t.values.find(
-            (v) => v.dt == sv.dt && (!v.origin || sv.origin == v.origin) && (!v.mclasslst || v.mclasslst.includes(sv.class))
-          ) && true;
-          if (thistermmatch) break;
-        }
-      } else {
-        throw "unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]";
-      }
-      if (t.isnot) {
-        thistermmatch = !thistermmatch;
-      }
-      if (thistermmatch) numberofmatchedterms++;
-    }
-    if (filter.join == "or") {
-      if (numberofmatchedterms && filter.in) return true;
-      if (!numberofmatchedterms && !filter.in) return true;
-    }
-  }
-  if (!("in" in filter)) filter.in = true;
-  return filter.in == (numberofmatchedterms == lst.length);
+function sample_match_termvaluesetting(
+	row,
+	filter,
+	_term = null,
+	sample = null
+) {
+	const lst = filter.type == "tvslst" ? filter.lst : [filter]
+	let numberofmatchedterms = 0
+	for (const item of lst) {
+		if ("type" in item && item.type == "tvslst") {
+			if (sample_match_termvaluesetting(row, item, _term, sample)) {
+				numberofmatchedterms++
+			}
+		} else {
+			const itemCopy = JSON.parse(JSON.stringify(item))
+			const t = itemCopy.tvs
+			if (_term && t.term) {
+				if (!(_term.name == t.term.name && _term.type == t.term.type)) {
+					numberofmatchedterms++
+					continue
+				}
+			}
+			let samplevalue
+			if (_term && !t.term) {
+				if (t.term$type && t.term$type !== _term.type) {
+					numberofmatchedterms++
+					continue
+				}
+				t.term = _term
+				samplevalue =
+					typeof row === "object" && t.term.id in row ? row[t.term.id] : row
+			} else if (sample && t.term.$id) {
+				samplevalue = sample[t.term.$id].value
+			} else {
+				samplevalue = t.term.id in row ? row[t.term.id] : row
+			}
+			setDatasetAnnotations(itemCopy)
+			let thistermmatch
+			if (t.term.type == "categorical") {
+				if (samplevalue === void 0) continue
+				thistermmatch = t.valueset.has(samplevalue)
+			} else if (t.term.type == "integer" || t.term.type == "float") {
+				if (samplevalue === void 0) continue
+				for (const range of t.ranges) {
+					if ("value" in range) {
+						thistermmatch = samplevalue === range.value
+						if (thistermmatch) break
+					} else if (samplevalue == range.name) {
+						thistermmatch = true
+						break
+					} else {
+						if (t.term.values) {
+							const v = t.term.values[samplevalue.toString()]
+							if (v && v.uncomputable) {
+								continue
+							}
+						}
+						let left, right
+						if (range.startunbounded) {
+							left = true
+						} else if ("start" in range) {
+							if (range.startinclusive) {
+								left = samplevalue >= range.start
+							} else {
+								left = samplevalue > range.start
+							}
+						}
+						if (range.stopunbounded) {
+							right = true
+						} else if ("stop" in range) {
+							if (range.stopinclusive) {
+								right = samplevalue <= range.stop
+							} else {
+								right = samplevalue < range.stop
+							}
+						}
+						thistermmatch = left && right
+					}
+					if (thistermmatch) break
+				}
+			} else if (t.term.type == "condition") {
+				const key = getPrecomputedKey(t)
+				const anno = samplevalue && samplevalue[key]
+				if (anno) {
+					thistermmatch = Array.isArray(anno)
+						? t.values.find((d) => anno.includes(d.key))
+						: t.values.find((d) => d.key == anno)
+				}
+			} else if (t.term.type == "geneVariant") {
+				const svalues = samplevalue.values || [samplevalue]
+				for (const sv of svalues) {
+					thistermmatch =
+						t.values.find(
+							(v) =>
+								v.dt == sv.dt &&
+								(!v.origin || sv.origin == v.origin) &&
+								(!v.mclasslst || v.mclasslst.includes(sv.class))
+						) && true
+					if (thistermmatch) break
+				}
+			} else {
+				throw "unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]"
+			}
+			if (t.isnot) {
+				thistermmatch = !thistermmatch
+			}
+			if (thistermmatch) numberofmatchedterms++
+		}
+		if (filter.join == "or") {
+			if (numberofmatchedterms && filter.in) return true
+			if (!numberofmatchedterms && !filter.in) return true
+		}
+	}
+	if (!("in" in filter)) filter.in = true
+	return filter.in == (numberofmatchedterms == lst.length)
 }
 function setDatasetAnnotations(item, ds = null) {
-  if (item.type == "tvslst") {
-    for (const subitem of item.lst) {
-      setDatasetAnnotations(subitem, ds);
-    }
-  } else {
-    if (ds && typeof ds.setAnnoByTermId == "function") {
-      ds.setAnnoByTermId(item.tvs.term.id);
-    }
-    if (item.tvs.term.type == "categorical") {
-      const tvsAny = item.tvs;
-      tvsAny.valueset = new Set(tvsAny.values.map((i) => i.key));
-    }
-  }
+	if (item.type == "tvslst") {
+		for (const subitem of item.lst) {
+			setDatasetAnnotations(subitem, ds)
+		}
+	} else {
+		if (ds && typeof ds.setAnnoByTermId == "function") {
+			ds.setAnnoByTermId(item.tvs.term.id)
+		}
+		if (item.tvs.term.type == "categorical") {
+			const tvsAny = item.tvs
+			tvsAny.valueset = new Set(tvsAny.values.map((i) => i.key))
+		}
+	}
 }
 function getPrecomputedKey(q) {
-  const precomputedKey = q.bar_by_children && q.value_by_max_grade ? "childrenAtMaxGrade" : q.bar_by_children && q.value_by_most_recent ? "childrenAtMostRecent" : q.bar_by_children && q.value_by_computable_grade ? "children" : q.bar_by_grade && q.value_by_max_grade ? "maxGrade" : q.bar_by_grade && q.value_by_most_recent ? "mostRecentGrades" : q.bar_by_grade && q.value_by_computable_grade ? "computableGrades" : "";
-  if (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`;
-  return precomputedKey;
+	const precomputedKey =
+		q.bar_by_children && q.value_by_max_grade
+			? "childrenAtMaxGrade"
+			: q.bar_by_children && q.value_by_most_recent
+			? "childrenAtMostRecent"
+			: q.bar_by_children && q.value_by_computable_grade
+			? "children"
+			: q.bar_by_grade && q.value_by_max_grade
+			? "maxGrade"
+			: q.bar_by_grade && q.value_by_most_recent
+			? "mostRecentGrades"
+			: q.bar_by_grade && q.value_by_computable_grade
+			? "computableGrades"
+			: ""
+	if (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`
+	return precomputedKey
 }
 function filterJoin(lst) {
-  if (!lst || lst.length == 0) return;
-  let f = JSON.parse(JSON.stringify(lst[0]));
-  if (lst.length == 1) return f;
-  if (f.lst.length < 2) {
-    if (f.join !== "") throw 'filter.join must be an empty string "" when filter.lst.length < 2';
-    f.join = "and";
-  } else if (f.join == "or") {
-    f = {
-      type: "tvslst",
-      join: "and",
-      in: true,
-      lst: [f]
-    };
-  } else if (f.join != "and") {
-    throw 'filter.join must be either "and" or "or" when .lst length > 1';
-  }
-  for (let i = 1; i < lst.length; i++) {
-    const f2 = JSON.parse(JSON.stringify(lst[i]));
-    if (f2.join == "or") f.lst.push(f2);
-    else f.lst.push(...f2.lst);
-  }
-  if (f.lst.length == 1 && f.lst[0].type == "tvs") {
-    f.join = "";
-  }
-  return f;
+	if (!lst || lst.length == 0) return
+	let f = JSON.parse(JSON.stringify(lst[0]))
+	if (lst.length == 1) return f
+	if (f.lst.length < 2) {
+		if (f.join !== "")
+			throw 'filter.join must be an empty string "" when filter.lst.length < 2'
+		f.join = "and"
+	} else if (f.join == "or") {
+		f = {
+			type: "tvslst",
+			join: "and",
+			in: true,
+			lst: [f],
+		}
+	} else if (f.join != "and") {
+		throw 'filter.join must be either "and" or "or" when .lst length > 1'
+	}
+	for (let i = 1; i < lst.length; i++) {
+		const f2 = JSON.parse(JSON.stringify(lst[i]))
+		if (f2.join == "or") f.lst.push(f2)
+		else f.lst.push(...f2.lst)
+	}
+	if (f.lst.length == 1 && f.lst[0].type == "tvs") {
+		f.join = ""
+	}
+	return f
 }
 function getWrappedTvslst(lst = [], join = "", $id = null) {
-  const filter = {
-    type: "tvslst",
-    in: true,
-    join,
-    lst
-  };
-  if ($id !== null) filter.$id = $id;
-  return filter;
+	const filter = {
+		type: "tvslst",
+		in: true,
+		join,
+		lst,
+	}
+	if ($id !== null) filter.$id = $id
+	return filter
 }
 function validateTermCollectionTvs(lst1, lst2) {
-  if (!Array.isArray(lst1)) throw new Error("numerator not array");
-  if (!Array.isArray(lst2)) throw new Error("denominator not array");
-  if (lst1.length == 0) throw new Error("numerator empty");
-  if (lst2.length == 0) throw new Error("denominator empty");
-  if (lst1.length > lst2.length) throw new Error("numerator longer than denominator");
-  for (const s of lst1) {
-    if (typeof s != "string") throw new Error("one of numerator not string");
-    if (!s) throw new Error("empty string in numerator");
-    if (!lst2.includes(s)) throw new Error("one of numerator not in denominator");
-  }
+	if (!Array.isArray(lst1)) throw new Error("numerator not array")
+	if (!Array.isArray(lst2)) throw new Error("denominator not array")
+	if (lst1.length == 0) throw new Error("numerator empty")
+	if (lst2.length == 0) throw new Error("denominator empty")
+	if (lst1.length > lst2.length)
+		throw new Error("numerator longer than denominator")
+	for (const s of lst1) {
+		if (typeof s != "string") throw new Error("one of numerator not string")
+		if (!s) throw new Error("empty string in numerator")
+		if (!lst2.includes(s))
+			throw new Error("one of numerator not in denominator")
+	}
 }
 export {
-  filterJoin,
-  getFilteredSamples,
-  getWrappedTvslst,
-  sample_match_termvaluesetting,
-  setDatasetAnnotations,
-  validateTermCollectionTvs
-};
+	filterJoin,
+	getFilteredSamples,
+	getWrappedTvslst,
+	sample_match_termvaluesetting,
+	setDatasetAnnotations,
+	validateTermCollectionTvs,
+}

package/src/hash.js

@@ -2,17 +2,20 @@ const encoder = new TextEncoder()
 
 export async function hash(message) {
 	const msgUint8 = encoder.encode(message) // encode as (utf-8) Uint8Array
-	const hashBuffer = await crypto.subtle.digest('SHA-1', msgUint8) // hash the message
+	const hashBuffer = await crypto.subtle.digest("SHA-1", msgUint8) // hash the message
 	const hashArray = Array.from(new Uint8Array(hashBuffer)) // convert buffer to byte array
-	const hashHex = hashArray.map(b => b.toString(16).padStart(2, '0')).join('') // convert bytes to hex string
-	return hexToBase64(hashHex).replace('=', '-') // shorten from 40 to 28 chars
+	const hashHex = hashArray.map((b) => b.toString(16).padStart(2, "0")).join("") // convert bytes to hex string
+	return hexToBase64(hashHex).replace("=", "-") // shorten from 40 to 28 chars
 }
 
 function hexToBase64(hexStr) {
 	return btoa(
 		[...hexStr].reduce(
-			(acc, _, i) => (acc += !((i - 1) & 1) ? String.fromCharCode(parseInt(hexStr.substring(i - 1, i + 1), 16)) : ''),
-			''
+			(acc, _, i) =>
+				(acc += !((i - 1) & 1)
+					? String.fromCharCode(parseInt(hexStr.substring(i - 1, i + 1), 16))
+					: ""),
+			""
 		)
 	)
 }

package/src/helpers.js

@@ -9,14 +9,14 @@ this is a helper file with a collection of functions to be used in backend and c
 
 // checks whether given argument n is Numeric, with option to cast from string
 export function isNumeric(n) {
-	const v = typeof n != 'string' || n === '' ? n : Number(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)
+	return typeof n === "number" && Number.isFinite(n)
 }
 
 // converts a value from a unit to another unit
@@ -26,24 +26,32 @@ export function convertUnits(v, fromUnit, toUnit, scaleFactor, compact) {
 	if (scaleFactor >= 1) {
 		const toUnitV = Math.floor(v * scaleFactor)
 		if (compact) return `${toUnitV}${toUnit.charAt(0)}`
-		return `${toUnitV} ${toUnitV > 1 ? toUnit + 's' : ''}`
+		return `${toUnitV} ${toUnitV > 1 ? toUnit + "s" : ""}`
 	}
 	const toUnitV = Math.floor(v * scaleFactor)
 	const fromUnitV = Math.ceil(v % (1 / scaleFactor))
 
 	if (fromUnitV == 0) {
 		if (compact) return `${toUnitV}${toUnit.charAt(0)}`
-		return `${toUnitV} ${toUnitV > 1 ? toUnit + 's' : ''}`
+		return `${toUnitV} ${toUnitV > 1 ? toUnit + "s" : ""}`
 	}
 
-	if (compact) return `${toUnitV}${toUnit.charAt(0)}${fromUnitV}${fromUnit.charAt(0)}`
-	return `${toUnitV} ${toUnitV > 1 ? toUnit + 's' : toUnit} ${fromUnitV} ${fromUnitV > 1 ? fromUnit + 's' : fromUnit}`
+	if (compact)
+		return `${toUnitV}${toUnit.charAt(0)}${fromUnitV}${fromUnit.charAt(0)}`
+	return `${toUnitV} ${toUnitV > 1 ? toUnit + "s" : toUnit} ${fromUnitV} ${
+		fromUnitV > 1 ? fromUnit + "s" : fromUnit
+	}`
 }
 
 export function deepEqual(x, y) {
 	if (x === y) {
 		return true
-	} else if (typeof x == 'object' && x != null && typeof y == 'object' && y != null) {
+	} else if (
+		typeof x == "object" &&
+		x != null &&
+		typeof y == "object" &&
+		y != null
+	) {
 		if (Object.keys(x).length != Object.keys(y).length) {
 			return false
 		}
@@ -63,13 +71,13 @@ export function deepFreeze(obj) {
 	Object.freeze(obj)
 	// not using for..in loop, in order to not descend into inherited props/methods
 	for (const value of Object.values(obj)) {
-		if (value !== null && typeof value == 'object') deepFreeze(value)
+		if (value !== null && typeof value == "object") deepFreeze(value)
 	}
 	return obj
 }
 
 export class CustomError extends Error {
-	level = '' // '' | 'warn'
+	level = "" // '' | 'warn'
 
 	constructor(message, opts = {}) {
 		super(message)

package/src/index.js

@@ -1,26 +1,26 @@
 // please list in alphanumeric order
-export * from './bulk.js'
-export * from './clustering.js'
-export * from './common.js'
-export * from './compute.percentile.js'
-export * from './fetch-helpers.js'
-export * from './fileSize.js'
-export * from './filter.js'
-export * from './hash.js'
-export * from './helpers.js'
-export * from './joinUrl.js'
-export * from './mds3tk.js'
-export * from './roundValue.js'
-export * from './termdb.bins.js'
-export * from './termdb.initbinconfig.js'
-export * from './termdb.usecase.js'
-export * from './terms.js'
-export * from './time.js'
-export * from './tree.js'
+export * from "./bulk.js"
+export * from "./clustering.js"
+export * from "./common.js"
+export * from "./compute.percentile.js"
+export * from "./fetch-helpers.js"
+export * from "./fileSize.js"
+export * from "./filter.js"
+export * from "./hash.js"
+export * from "./helpers.js"
+export * from "./joinUrl.js"
+export * from "./mds3tk.js"
+export * from "./roundValue.js"
+export * from "./termdb.bins.js"
+export * from "./termdb.initbinconfig.js"
+export * from "./termdb.usecase.js"
+export * from "./terms.js"
+export * from "./time.js"
+export * from "./tree.js"
 // do `npm run esm` to generate .js file from .ts file
-export * from './urljson.js'
-export * from './vcf.ann.js'
-export * from './vcf.csq.js'
-export * from './vcf.info.js'
-export * from './vcf.js'
-export * from './vcf.type.js'
+export * from "./urljson.js"
+export * from "./vcf.ann.js"
+export * from "./vcf.csq.js"
+export * from "./vcf.info.js"
+export * from "./vcf.js"
+export * from "./vcf.type.js"

package/src/mds3tk.js

@@ -1,4 +1,4 @@
-import { dtcnv, dtsnvindel, dtsv, dtfusionrna } from './common.js'
+import { dtcnv, dtsnvindel, dtsv, dtfusionrna } from "./common.js"
 
 // this script should contain mds3 track-related stuff shared between client and backend
 
@@ -15,7 +15,7 @@ svfusion: dt + chr + pos + strand + pairlstidx + mname
 
 the separator must avoid conflicting with characters from gene names, and can be changed based on needs
 */
-export const ssmIdFieldsSeparator = '__'
+export const ssmIdFieldsSeparator = "__"
 
 /*
 input: array of mixture of ssm, svfusion and cnv
@@ -59,7 +59,7 @@ export function guessSsmid(ssmid) {
 	if (l.length == 4) {
 		const [chr, tmp, ref, alt] = l
 		const pos = Number(tmp)
-		if (Number.isNaN(pos)) throw 'ssmid snvindel pos not integer'
+		if (Number.isNaN(pos)) throw "ssmid snvindel pos not integer"
 		return { dt: dtsnvindel, l: [chr, pos, ref, alt] }
 	}
 	if (l.length == 5) {
@@ -67,32 +67,34 @@ export function guessSsmid(ssmid) {
 		const [chr, _start, _stop, _class, _value] = l
 		const start = Number(_start),
 			stop = Number(_stop),
-			value = _value == '' ? null : Number(_value)
-		if (Number.isNaN(start) || Number.isNaN(stop)) throw 'ssmid cnv start/stop not integer'
+			value = _value == "" ? null : Number(_value)
+		if (Number.isNaN(start) || Number.isNaN(stop))
+			throw "ssmid cnv start/stop not integer"
 		return { dt: dtcnv, l: [chr, start, stop, _class, value] }
 	}
 	if (l.length == 6) {
-		if (l[3] == '+' || l[3] == '-') {
+		if (l[3] == "+" || l[3] == "-") {
 			// sv/fusion
 			const [_dt, chr, _pos, strand, _pi, _mname] = l
 
 			// mname is encoded in case it contains comma (and is same as ssmIdFieldsSeparator)
 			const mname = decodeURIComponent(_mname)
 			const dt = Number(_dt)
-			if (dt != dtsv && dt != dtfusionrna) throw 'ssmid dt not sv/fusion'
+			if (dt != dtsv && dt != dtfusionrna) throw "ssmid dt not sv/fusion"
 			const pos = Number(_pos)
-			if (Number.isNaN(pos)) throw 'ssmid svfusion position not integer'
+			if (Number.isNaN(pos)) throw "ssmid svfusion position not integer"
 			const pairlstIdx = Number(_pi)
-			if (Number.isNaN(pairlstIdx)) throw 'ssmid pairlstIdx not integer'
+			if (Number.isNaN(pairlstIdx)) throw "ssmid pairlstIdx not integer"
 			return { dt, l: [dt, chr, pos, strand, pairlstIdx, mname] }
 		}
 		// cnv with sample
 		const [chr, _start, _stop, _class, _value, sample] = l
 		const start = Number(_start),
 			stop = Number(_stop),
-			value = _value == '' ? null : Number(_value) // if cnv not using value, must avoid `Number('')=0`
-		if (Number.isNaN(start) || Number.isNaN(stop)) throw 'ssmid cnv start/stop not integer'
+			value = _value == "" ? null : Number(_value) // if cnv not using value, must avoid `Number('')=0`
+		if (Number.isNaN(start) || Number.isNaN(stop))
+			throw "ssmid cnv start/stop not integer"
 		return { dt: dtcnv, l: [chr, start, stop, _class, value, sample] }
 	}
-	throw 'unknown ssmid'
+	throw "unknown ssmid"
 }