@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

package/dist/chunk-YUMPQ3CJ.js

@@ -0,0 +1,203 @@
+import {
+  tkt
+} from "./chunk-7FEHI46K.js";
+import {
+  stratinput
+} from "./chunk-IQIXGTQV.js";
+import {
+  stratify_default
+} from "./chunk-TOU7EVFQ.js";
+
+// src/vcf.tkconvert.js
+function vcf2dstk(arg) {
+  const ds = {
+    id2vcf: {},
+    label: arg.name || "Unnamed VCF file"
+  };
+  let vcfobj;
+  if (arg.file) {
+    const id = Math.random().toString();
+    vcfobj = {
+      file: arg.file,
+      indexURL: arg.indexURL,
+      vcfid: id
+    };
+    ds.id2vcf[id] = vcfobj;
+  } else if (arg.url) {
+    const id = Math.random().toString();
+    vcfobj = {
+      url: arg.url,
+      indexURL: arg.indexURL,
+      vcfid: id
+    };
+    ds.id2vcf[id] = vcfobj;
+  } else {
+    return ["no .file or .url"];
+  }
+  vcfobj.headernotloaded = true;
+  if (arg.samplenamemap) {
+    vcfobj.samplenamemap = arg.samplenamemap;
+  }
+  if (arg.variant2img) {
+    if (!arg.variant2img.path) return [".path missing from .variant2img{}"];
+  }
+  const tk = {
+    type: tkt.ds,
+    // to be loaded by loadvcftk() as a custom track, rather than "/dsdata" for official ds
+    isvcf: true,
+    name: ds.label,
+    ds,
+    populationfrequencyfilter: arg.populationfrequencyfilter,
+    vcfinfofilter: arg.vcfinfofilter,
+    itemlabelname: arg.itemlabelname,
+    viewrangeupperlimit: arg.viewrangeupperlimit,
+    variant2img: arg.variant2img,
+    axisheight: arg.axisheight
+  };
+  if (arg.url4variant) {
+    const err = check_url4variant(arg.url4variant);
+    if (err) return [".url4variant error: " + err];
+    tk.url4variant = arg.url4variant;
+  }
+  if (arg.button4variant) {
+    const err = check_button4variant(arg.button4variant);
+    if (err) return [".button4variant error: " + err];
+    tk.button4variant = arg.button4variant;
+  }
+  if (arg.sampleannotation) {
+    const sn = arg.sampleannotation;
+    if (!sn.annotation) return [".annotation{} missing from .sampleannotation"];
+    if (sn.levels) {
+      if (!Array.isArray(sn.levels)) return [".sampleannotation.levels should be array"];
+      const lst = [];
+      for (const sample in sn.annotation) {
+        const o = { sample_name: sample };
+        for (const k in sn.annotation[sample]) {
+          o[k] = sn.annotation[sample][k];
+        }
+        lst.push(o);
+      }
+      const nodes = stratinput(lst, sn.levels);
+      sn.root = stratify_default()(nodes);
+      sn.root.sum((i) => i.value);
+    }
+    if (sn.variantsunburst) {
+      if (!sn.levels) return [".levels missing when .variantsunburst is on from .sampleannotation"];
+    }
+    tk.ds.cohort = sn;
+  }
+  if (arg.vcfcohorttrack) {
+    if (!arg.vcfcohorttrack.file && !arg.vcfcohorttrack.url) return ["no .file or .url provided from .vcfcohorttrack"];
+    tk.ds.vcfcohorttrack = arg.vcfcohorttrack;
+  }
+  if (arg.germline2dvafplot) {
+    if (!arg.germline2dvafplot.individualkey) return [".individualkey missing from germline2dvafplot"];
+    if (!arg.germline2dvafplot.sampletypekey) return [".sampletypekey missing from germline2dvafplot"];
+    if (!arg.germline2dvafplot.xsampletype) return [".xsampletype missing from germline2dvafplot"];
+    if (!arg.germline2dvafplot.yleftsampletype) return [".yleftsampletype missing from germline2dvafplot"];
+    if (arg.germline2dvafplot.yrightsampletype) {
+      if (arg.germline2dvafplot.yrightsampletype == arg.germline2dvafplot.yleftsampletype)
+        return [".yrightsampletype should not be same as yleftsampletype"];
+    }
+    tk.ds.germline2dvafplot = arg.germline2dvafplot;
+  }
+  if (arg.vaf2coverageplot) {
+    if (arg.vaf2coverageplot.categorykey) {
+      if (!arg.vaf2coverageplot.categories)
+        return [".categories missing when .categorykey is in use for .vaf2coverageplot"];
+    }
+    tk.ds.vaf2coverageplot = arg.vaf2coverageplot;
+  }
+  if (arg.genotype2boxplot) {
+    if (arg.genotype2boxplot.boxplotvaluekey) {
+    } else if (arg.genotype2boxplot.sampleannotationkey) {
+      if (!tk.ds.cohort) return ["sampleannotation missing when using genotype2boxplot.sampleannotationkey"];
+      if (!tk.ds.cohort.annotation)
+        return ["sampleannotation.annotation missing when using genotype2boxplot.sampleannotationkey"];
+      let found = false;
+      for (const k in tk.ds.cohort.annotation) {
+        if (arg.genotype2boxplot.sampleannotationkey in tk.ds.cohort.annotation[k]) {
+          found = true;
+          break;
+        }
+      }
+      if (!found) return [arg.genotype2boxplot.sampleannotationkey + " not found in any sample annotation"];
+    } else {
+      return ["incomplete instruction for genotype2boxplot"];
+    }
+    tk.ds.genotype2boxplot = arg.genotype2boxplot;
+  }
+  if (arg.discardsymbolicallele) {
+    tk.ds.discardsymbolicallele = true;
+  }
+  if (arg.samplebynumericvalue) {
+    if (!arg.samplebynumericvalue.attrkey) return ["attrkey missing from samplebynumericvalue"];
+    if (!tk.ds.cohort) return ["sampleannotation missing when using samplebynumericvalue"];
+    if (!tk.ds.cohort.annotation) return ["sampleannotation.annotation missing when using samplebynumericvalue"];
+    let found = false;
+    for (const k in tk.ds.cohort.annotation) {
+      if (Number.isFinite(tk.ds.cohort.annotation[k][arg.samplebynumericvalue.attrkey])) {
+        found = true;
+        break;
+      }
+    }
+    if (!found) return ["samplebynumericvalue.attrkey not found in any sample annotation"];
+    tk.ds.samplebynumericvalue = arg.samplebynumericvalue;
+  }
+  {
+    const g = arg.genotypebynumericvalue;
+    if (g) {
+      if (!g.refref) return [tk.name + ": refref missing from genotypebynumericvalue"];
+      if (!g.refalt) return [tk.name + ": refalt missing from genotypebynumericvalue"];
+      if (!g.altalt) return [tk.name + ": altalt missing from genotypebynumericvalue"];
+      if (!g.refref.infokey) return [tk.name + ": refref.infokey missing from genotypebynumericvalue"];
+      if (!g.refalt.infokey) return [tk.name + ": refalt.infokey missing from genotypebynumericvalue"];
+      if (!g.altalt.infokey) return [tk.name + ": altalt.infokey missing from genotypebynumericvalue"];
+      if (g.refref.genotypeCountInfokey || g.refalt.genotypeCountInfokey || g.altalt.genotypeCountInfokey) {
+        if (!g.refref.genotypeCountInfokey)
+          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.refref{}"];
+        if (!g.refalt.genotypeCountInfokey)
+          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.refalt{}"];
+        if (!g.altalt.genotypeCountInfokey)
+          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.altalt{}"];
+      }
+      tk.ds.genotypebynumericvalue = g;
+    }
+  }
+  if (arg.pointdown) {
+    tk.aboveprotein = false;
+  }
+  if (arg.dstk_novcferror) {
+    tk.dstk_novcferror = true;
+  }
+  return [null, tk];
+}
+function check_url4variant(lst) {
+  if (!Array.isArray(lst)) return "value is not an array";
+  for (const item of lst) {
+    if (!item.makeurl) {
+      return ".makeurl missing";
+    }
+    if (typeof item.makeurl != "function") {
+      return ".makeurl must be a function";
+    }
+  }
+  return false;
+}
+function check_button4variant(lst) {
+  if (!Array.isArray(lst)) return "value is not an array";
+  for (const item of lst) {
+    if (!item.makebutton) {
+      return ".makebutton missing";
+    }
+    if (typeof item.makebutton != "function") {
+      return ".makebutton must be a function";
+    }
+  }
+  return false;
+}
+
+export {
+  vcf2dstk
+};
+//# sourceMappingURL=chunk-YUMPQ3CJ.js.map

package/dist/chunk-ZIBWLDQI.js

@@ -0,0 +1,230 @@
+import {
+  StoreBase,
+  getAppInit,
+  getStoreInit
+} from "./chunk-MVTCBVSX.js";
+
+// test/test.helpers.js
+function sleep(ms) {
+  return new Promise((resolve) => setTimeout(resolve, ms));
+}
+async function detectLst(_opts = {}) {
+  const defaults = {
+    target: _opts.target || _opts.elem,
+    selector: _opts.selector,
+    maxTime: 12e3,
+    // default is increased from 5 to 12 specifically for gdc live tests with high latency
+    observe: {
+      childList: true,
+      subtree: true,
+      attributes: true,
+      characterData: true
+    }
+  };
+  if (!_opts.matcher) {
+    defaults.count = 1;
+    defaults.matchAs = "=";
+  }
+  const opts = Object.assign(defaults, _opts);
+  if (!opts.target) throw `missing opts.target (alias for opts.elem)`;
+  if (!opts.trigger && opts.count > 0) await sleep(0);
+  const start = Date.now();
+  return new Promise((resolve, reject) => {
+    if (!opts.matcher && opts.selector) {
+      const elems = opts.target.querySelectorAll(opts.selector);
+      const matched = matchedCount(elems.length, opts);
+      if (matched) {
+        resolve([...elems]);
+        return;
+      }
+    }
+    const callback = (mutations) => {
+      const elems = opts.selector ? [...opts.target.querySelectorAll(opts.selector)] : [opts.target];
+      const mutated = mutations.filter((m) => elems.includes(m.target));
+      if (!mutated.length && opts.count !== 0) return;
+      const matched = opts.matcher ? opts.matcher(mutated, observer) : matchedCount(elems.length, opts);
+      const expired = Date.now() - start > opts.maxTime;
+      if (matched || expired) {
+        observer.disconnect();
+        if (t) clearTimeout(t);
+        if (matched) resolve(Array.isArray(matched) ? matched : elems);
+        else reject(`test exceeded maxTime=${opts.maxTime}`);
+      }
+    };
+    const observer = new MutationObserver(callback);
+    observer.observe(opts.target, opts.observe);
+    let t;
+    if (opts.maxTime) {
+      t = setTimeout(() => {
+        if (opts.count === 0) {
+        } else reject(`the elem '${opts.target}' did not render within ${opts.maxTime} milliseconds`);
+      }, opts.maxTime);
+    }
+    if (opts.trigger) opts.trigger();
+  });
+}
+function matchedCount(actual, opts) {
+  const expected = opts.count;
+  switch (opts.matchAs) {
+    case "=":
+      return actual === expected;
+    case "<":
+      return actual < expected;
+    case "<=":
+      return actual <= expected;
+    case ">":
+      return actual > expected;
+    case ">=":
+      return actual >= expected;
+    default:
+      throw `unknown matchAs='${opts.matchAs}'`;
+  }
+}
+async function detectAttr(opts) {
+  if (!opts.observe) opts.observe = {};
+  opts.observe.attributes = true;
+  const lst = await detectLst(opts);
+  return lst;
+}
+async function detectChildAttr(opts) {
+  if (!opts.observe) opts.observe = {};
+  opts.observe.subtree = true;
+  opts.observe.attributes = true;
+  if (opts.attr) {
+    if (opts.matcher) console.warn(`will not use opts.attr since an opts.matcher is already available`);
+    else {
+      if (!("count" in opts)) opts.count = 1;
+      opts.matcher = (mutations) => {
+        const matched = mutations.filter((m) => {
+          for (const key in opts.attr) {
+            if (typeof opts.attr[key] === "function") {
+              const value2 = m.target.getAttribute(key);
+              if (!opts.attr[key](value2)) return false;
+            } else if (value != opts.attr[key]) {
+              return false;
+            }
+          }
+          return true;
+        });
+        if (matched.length === opts.count) return matched.map((d) => d.target);
+      };
+    }
+  }
+  const lst = await detectLst(opts);
+  return lst;
+}
+async function detectStyle(opts) {
+  if (!opts.observe) opts.observe = {};
+  opts.observe.attributes = true;
+  opts.observe.attributeFilter = ["style"];
+  const lst = await detectLst(opts);
+  return lst;
+}
+async function detectChildStyle(opts) {
+  if (!opts.observe) opts.observe = {};
+  opts.observe.subtree = true;
+  opts.observe.attributes = true;
+  opts.observe.attributeFilter = ["style"];
+  if (opts.style) {
+    if (opts.matcher) console.warn(`will not use opts.style since an opts.matcher is already available`);
+    else {
+      if (!("count" in opts)) opts.count = 1;
+      opts.matcher = (mutations) => {
+        const matched = mutations.filter((m) => {
+          for (const key in opts.style) {
+            const value2 = m.target.style[key];
+            if (typeof opts.style[key] == "function") {
+              if (!opts.style[key](value2)) return false;
+            } else if (value2 != opts.style[key]) return false;
+          }
+          return true;
+        });
+        if (matched.length === opts.count) return matched.map((d) => d.target);
+      };
+    }
+  }
+  const lst = await detectLst(opts);
+  return lst;
+}
+async function detectGt(opts) {
+  opts.matchAs = ">";
+  const lst = await detectLst(opts);
+  return lst;
+}
+async function detectGte(opts) {
+  opts.matchAs = ">=";
+  const lst = await detectLst(opts);
+  return lst;
+}
+async function detectOne(opts) {
+  opts.count = 1;
+  const lst = await detectLst(opts);
+  return lst[0];
+}
+async function whenVisible(elem, opts = {}) {
+  const intervalWait = 25;
+  const totalWait = opts.wait || 5e3;
+  const numRepeats = totalWait / intervalWait;
+  return new Promise((resolve, reject) => {
+    let j = 0;
+    const i = setInterval(() => {
+      if (elem.style.display != "none") {
+        clearInterval(i);
+        resolve(elem);
+      } else {
+        j++;
+        if (j > numRepeats) {
+          reject(`elem did not become visible within 5 seconds`);
+          clearInterval(i);
+        }
+      }
+    }, intervalWait);
+  });
+}
+var TestAppStore = class _TestAppStore extends StoreBase {
+  static type = "store";
+  constructor(opts) {
+    super(opts);
+    this.type = _TestAppStore.type;
+    this.defaultState = {
+      debug: true
+    };
+  }
+  async init() {
+  }
+};
+var storeInit = getStoreInit(TestAppStore);
+var TestApp = class {
+  static type = "app";
+  constructor(opts) {
+    this.type = "app";
+    this.opts = opts;
+    this.fetchOpts = opts.fetchOpts;
+  }
+  async init() {
+    try {
+      this.store = await storeInit({ app: this.api, state: this.opts.state });
+      this.state = await this.store.copyState();
+      if (this.opts.dom) this.dom = this.opts.dom;
+      await this.api.dispatch();
+    } catch (e) {
+      if (e.stack) console.log(e.stack);
+      else throw `TestApp Error: ${e}`;
+    }
+  }
+};
+var testAppInit = getAppInit(TestApp);
+
+export {
+  sleep,
+  detectLst,
+  detectAttr,
+  detectChildAttr,
+  detectStyle,
+  detectChildStyle,
+  detectGt,
+  detectGte,
+  detectOne,
+  whenVisible
+};
+//# sourceMappingURL=chunk-ZIBWLDQI.js.map

package/dist/chunk-ZIBWLDQI.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../test/test.helpers.js"],
+  "sourcesContent": ["import { getAppInit, getStoreInit, StoreBase } from '../rx'\nexport * from './Locator.ts'\n\n/********* EXPORTED ********\nsleep\ndetectLst\ndetectAttr\ndetectChildAttr\ndetectStyle\ndetectChildStyle\ndetectText\ndetectChildText\ndetectGt\ndetectGte\ndetectLt\ndetectLte\ndetectOne\ndetectZero\nwhenGone\nwhenHidden\nwhenVisible\n*/\n\nexport function sleep(ms) {\n\treturn new Promise(resolve => setTimeout(resolve, ms))\n}\n\n//exports.sleep = sleep\n\n/*\n    Detect an asynchronously rendered element\n    NOTE: you can use MutationObserver directly, this is meant for convenience for common use cases\n\n    Argument\n    _opts{}      see the defaults inside the detectLst function\n\n    // options related to the native MutationObserver\n    // see https://developer.mozilla.org/en-US/docs/Web/API/MutationObserver/observe\n    .target      required, the first argument to a MutationObserver instance's observe() method\n                             the DOM element to be observed and where the optional selector will be queried; alias for opts.elem\n    .observe{}   the second argument to a MutationObserver instance's observe() method\n\n    .selector    optional, a valid CSS-selector of the element to be returned under opts.target. \n                             If empty, then opts.target will be returned\n    \n    .matcher()   optional, a function that signals the end of the observer \n                             passed (mutationsList, observer) as arguments\n                             must return an array of zero or more elements to trigger observer.disconnect() \n    .maxTime     optional, max time to wait\n\n    // only used when opts.matcher is not supplied\n    .count       optional, the expected number of detected matching elements to stop the observer\n    .matchAs     optional, how to match the current versus expected counts, '=','>','<','>=','<=' default is '='\n\n    Returns\n    Array of zero or more matched DOM nodes\n*/\n\nexport async function detectLst(_opts = {}) {\n\tconst defaults = {\n\t\ttarget: _opts.target || _opts.elem,\n\t\tselector: _opts.selector,\n\t\tmaxTime: 12000, // default is increased from 5 to 12 specifically for gdc live tests with high latency\n\t\tobserve: {\n\t\t\tchildList: true,\n\t\t\tsubtree: true,\n\t\t\tattributes: true,\n\t\t\tcharacterData: true\n\t\t}\n\t}\n\n\tif (!_opts.matcher) {\n\t\tdefaults.count = 1\n\t\tdefaults.matchAs = '='\n\t}\n\n\tconst opts = Object.assign(defaults, _opts)\n\tif (!opts.target) throw `missing opts.target (alias for opts.elem)` //; console.log(52, opts)\n\n\t//if (!opts.selector) throw `missing opts.selector`\n\t// may defer execution to the next step, to give time for an element to change\n\tif (!opts.trigger && opts.count > 0) await sleep(0)\n\tconst start = Date.now()\n\treturn new Promise((resolve, reject) => {\n\t\tif (!opts.matcher && opts.selector) {\n\t\t\tconst elems = opts.target.querySelectorAll(opts.selector)\n\t\t\tconst matched = matchedCount(elems.length, opts)\n\t\t\tif (matched) {\n\t\t\t\tresolve([...elems])\n\t\t\t\treturn\n\t\t\t}\n\t\t}\n\n\t\tconst callback = mutations => {\n\t\t\tconst elems = opts.selector ? [...opts.target.querySelectorAll(opts.selector)] : [opts.target]\n\t\t\tconst mutated = mutations.filter(m => elems.includes(m.target))\n\t\t\tif (!mutated.length && opts.count !== 0) return\n\t\t\tconst matched = opts.matcher ? opts.matcher(mutated, observer) : matchedCount(elems.length, opts)\n\t\t\tconst expired = Date.now() - start > opts.maxTime\n\t\t\tif (matched || expired) {\n\t\t\t\tobserver.disconnect()\n\t\t\t\tif (t) clearTimeout(t)\n\t\t\t\tif (matched) resolve(Array.isArray(matched) ? matched : elems)\n\t\t\t\telse reject(`test exceeded maxTime=${opts.maxTime}`)\n\t\t\t}\n\t\t}\n\n\t\tconst observer = new MutationObserver(callback)\n\t\tobserver.observe(opts.target, opts.observe)\n\n\t\tlet t\n\t\tif (opts.maxTime) {\n\t\t\tt = setTimeout(() => {\n\t\t\t\tif (opts.count === 0) {\n\t\t\t\t} else reject(`the elem '${opts.target}' did not render within ${opts.maxTime} milliseconds`)\n\t\t\t}, opts.maxTime)\n\t\t}\n\n\t\tif (opts.trigger) opts.trigger()\n\t})\n}\n\n// compare the actual vs expected element counts\nfunction matchedCount(actual, opts) {\n\tconst expected = opts.count\n\tswitch (opts.matchAs) {\n\t\tcase '=':\n\t\t\treturn actual === expected\n\t\tcase '<':\n\t\t\treturn actual < expected\n\t\tcase '<=':\n\t\t\treturn actual <= expected\n\t\tcase '>':\n\t\t\treturn actual > expected\n\t\tcase '>=':\n\t\t\treturn actual >= expected\n\t\tdefault:\n\t\t\tthrow `unknown matchAs='${opts.matchAs}'`\n\t}\n}\n\n/*\n    convenience helpers for detectLst with preconfigured MutationRecord.type, attributeName\n*/\n\nexport async function detectAttr(opts) {\n\tif (!opts.observe) opts.observe = {}\n\topts.observe.attributes = true\n\tconst lst = await detectLst(opts)\n\treturn lst\n}\n\nexport async function detectChildAttr(opts) {\n\tif (!opts.observe) opts.observe = {}\n\topts.observe.subtree = true\n\topts.observe.attributes = true\n\tif (opts.attr) {\n\t\tif (opts.matcher) console.warn(`will not use opts.attr since an opts.matcher is already available`)\n\t\telse {\n\t\t\tif (!('count' in opts)) opts.count = 1\n\t\t\topts.matcher = mutations => {\n\t\t\t\tconst matched = mutations.filter(m => {\n\t\t\t\t\tfor (const key in opts.attr) {\n\t\t\t\t\t\tif (typeof opts.attr[key] === 'function') {\n\t\t\t\t\t\t\tconst value = m.target.getAttribute(key)\n\t\t\t\t\t\t\tif (!opts.attr[key](value)) return false\n\t\t\t\t\t\t} else if (value != opts.attr[key]) {\n\t\t\t\t\t\t\treturn false\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\treturn true\n\t\t\t\t})\n\t\t\t\t// TODO: should accumulate matched counts???\n\t\t\t\tif (matched.length === opts.count) return matched.map(d => d.target)\n\t\t\t}\n\t\t}\n\t}\n\tconst lst = await detectLst(opts)\n\treturn lst\n}\n\nexport async function detectStyle(opts) {\n\tif (!opts.observe) opts.observe = {}\n\topts.observe.attributes = true\n\topts.observe.attributeFilter = ['style']\n\tconst lst = await detectLst(opts)\n\treturn lst\n}\n\nexport async function detectChildStyle(opts) {\n\tif 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