@sjcrh/proteinpaint-client 2.205.0 → 2.206.0

package/dist/chunk-M4XXKTH2.js

@@ -0,0 +1,339 @@
+import {
+  matchesGvQueryEntry
+} from "./chunk-5ILEFNXJ.js";
+import {
+  mclass
+} from "./chunk-IZUYLFOX.js";
+
+// ../shared/utils/dist/src/termCollection.js
+function validateTermCollectionTerm(term) {
+  if (!Array.isArray(term?.termlst) || !term.termlst.length)
+    throw new Error("termCollection requires nonempty term.termlst[]");
+  const memberIds = /* @__PURE__ */ new Set();
+  const types = /* @__PURE__ */ new Set();
+  for (const t of term.termlst) {
+    if (typeof t.id != "string" || !t.id) throw new Error("member term id not non-empty string");
+    if (typeof t.type != "string" || !t.type) throw new Error("member term type not non-empty string");
+    if (memberIds.has(t.id)) throw new Error(`duplicate member term id '${t.id}'`);
+    memberIds.add(t.id);
+    types.add(t.type == "integer" || t.type == "float" ? "numDict" : t.type);
+  }
+  if (types.size > 1) throw new Error("termCollection.termlst[] not allowed to mix multiple term types");
+  return memberIds;
+}
+function validateFractionMembers(numerators, denominators, memberIds) {
+  if (!Array.isArray(denominators) || !denominators.length) throw new Error("fraction requires nonempty denominators[]");
+  if (!Array.isArray(numerators) || !numerators.length) throw new Error("fraction requires nonempty numerators[]");
+  if (new Set(denominators).size !== denominators.length) throw new Error("fraction denominators[] contains duplicates");
+  if (new Set(numerators).size !== numerators.length) throw new Error("fraction numerators[] contains duplicates");
+  for (const id of denominators) {
+    if (typeof id != "string" || !id) throw new Error("fraction denominator id not non-empty string");
+    if (!memberIds.has(id)) throw new Error(`fraction denominator '${id}' is not a collection member`);
+  }
+  for (const id of numerators) {
+    if (typeof id != "string" || !id) throw new Error("fraction numerator id not non-empty string");
+    if (!denominators.includes(id)) throw new Error(`fraction numerator '${id}' is not included in denominators[]`);
+  }
+}
+var FRACTION_TW_TYPE = "TermCollectionTWFraction";
+function isFractionTw(tw) {
+  return tw?.type === FRACTION_TW_TYPE && tw?.term?.type === "termCollection";
+}
+function getFractionTvsTerm(tw) {
+  if (!isFractionTw(tw)) throw new Error("not a fraction termCollection tw");
+  const term = structuredClone(tw.term);
+  const memberIds = term.termlst?.length ? validateTermCollectionTerm(term) : new Set(term.termIds || []);
+  const denominators = tw.q?.denominators?.length ? [...tw.q.denominators] : [...memberIds];
+  const numerators = tw.q?.numerators?.length ? [...tw.q.numerators] : [...denominators];
+  validateFractionMembers(numerators, denominators, memberIds);
+  term.numerators = numerators;
+  term.denominators = denominators;
+  return term;
+}
+function validateTermCollectionFraction(q, term) {
+  const memberIds = validateTermCollectionTerm(term);
+  validateFractionMembers(q?.numerators, q?.denominators, memberIds);
+  if (q.mode === "discrete" && q.type !== "regular-bin" && q.type !== "custom-bin")
+    throw new Error("discrete fraction termCollection requires regular-bin or custom-bin q.type");
+}
+
+// ../shared/utils/dist/src/filter.js
+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;
+}
+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));
+    }
+  }
+}
+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;
+}
+function getWrappedTvslst(lst = [], join = "", $id = null) {
+  const filter = {
+    type: "tvslst",
+    in: true,
+    join,
+    lst
+  };
+  if ($id !== null) filter.$id = $id;
+  return filter;
+}
+function getTvsDenominators(term) {
+  if (Array.isArray(term?.denominators) && term.denominators.length) return term.denominators;
+  return (term?.termlst || []).map((t) => t.id);
+}
+function validateTermCollectionTvs(term) {
+  const memberIds = validateTermCollectionTerm(term);
+  if (!term.numerators) return;
+  validateFractionMembers(term.numerators, getTvsDenominators(term), memberIds);
+}
+
+// ../shared/utils/dist/src/geneVariantFilter.js
+var statusClasses = /* @__PURE__ */ new Set(["WT", "Blank"]);
+function unsupported(what) {
+  return `tw.q.variantFilter does not support ${what}, which qualifies a sample rather than an individual variant. Use a groupset (q.type='custom-groupset') for a sample-level filter.`;
+}
+function validateVariantFilter(filter, term) {
+  if (!filter) return;
+  if (filter.type != "tvslst") throw `tw.q.variantFilter.type must be 'tvslst'`;
+  if (!Array.isArray(filter.lst) || !filter.lst.length) throw "tw.q.variantFilter.lst[] is empty";
+  if (filter.lst.length > 1 && filter.join != "and" && filter.join != "or")
+    throw `tw.q.variantFilter.join must be 'and' or 'or' when lst[] has more than one item`;
+  const dts = term?.childTerms?.length ? new Set(term.childTerms.map((t) => t.dt)) : null;
+  for (const item of filter.lst) {
+    if (item.type == "tvslst") {
+      validateVariantFilter(item, term);
+      continue;
+    }
+    if (item.type != "tvs") throw `unexpected tw.q.variantFilter item.type='${item.type}'`;
+    const tvs = item.tvs;
+    if (!tvs) throw "missing tvs of a tw.q.variantFilter item";
+    if (!Number.isInteger(tvs.term?.dt)) throw "tw.q.variantFilter tvs.term must be a dt term, with an integer .dt";
+    if (dts && !dts.has(tvs.term.dt))
+      throw `tw.q.variantFilter tvs.term.dt=${tvs.term.dt} is not a dt of term '${term.name}'`;
+    if (!Array.isArray(tvs.values) || !tvs.values.length) throw "tw.q.variantFilter tvs.values[] is empty";
+    for (const v of tvs.values) {
+      if (!v.key) throw "a tw.q.variantFilter tvs.values[] entry is missing .key";
+      if (statusClasses.has(v.key))
+        throw `tw.q.variantFilter cannot select the '${v.key}' class, which is a testing status and not a variant`;
+      if (v.partnerBreakpointRange) throw unsupported("partnerBreakpointRange");
+    }
+    if (tvs.genotype && tvs.genotype != "variant") throw unsupported(`genotype='${tvs.genotype}'`);
+    if (tvs.mcount && tvs.mcount != "any") throw unsupported(`mcount='${tvs.mcount}'`);
+    if (tvs.mafFilter) throw unsupported("mafFilter");
+    if (tvs.continuousCnv) throw unsupported("continuousCnv");
+    if (tvs.selfBreakpointRange) throw unsupported("selfBreakpointRange");
+  }
+}
+function getFilterScope(filter, scope = /* @__PURE__ */ new Set()) {
+  for (const item of filter.lst) {
+    if (item.type == "tvslst") getFilterScope(item, scope);
+    else scope.add(`${item.tvs.term.dt}:${item.tvs.term.origin || "*"}`);
+  }
+  return scope;
+}
+function isInScope(v, scope) {
+  return scope.has(`${v.dt}:*`) || scope.has(`${v.dt}:${v.origin || ""}`);
+}
+function matchTvs(v, tvs) {
+  let match = false;
+  if (v.dt == tvs.term.dt && (!tvs.term.origin || v.origin == tvs.term.origin)) {
+    match = tvs.values.some((e) => e.key == v.class && (!e.mname || e.mname == v.mname && matchesGvQueryEntry(e, v)));
+  }
+  return tvs.isnot ? !match : match;
+}
+function matchFilter(v, filter) {
+  const lst = filter.type == "tvslst" ? filter.lst : [filter];
+  let numMatched = 0;
+  for (const item of lst) {
+    const matched = item.type == "tvslst" ? matchFilter(v, item) : matchTvs(v, item.tvs);
+    if (matched) numMatched++;
+    if (filter.join == "or" && numMatched) break;
+  }
+  const pass = filter.join == "or" ? numMatched > 0 : numMatched == lst.length;
+  return filter.in === false ? !pass : pass;
+}
+function filterVariantValues(values, filter) {
+  if (!filter || !values) return values;
+  const scope = getFilterScope(filter);
+  const kept = [];
+  const annotated = /* @__PURE__ */ new Set();
+  const dropped = /* @__PURE__ */ new Map();
+  for (const v of values) {
+    if (!isInScope(v, scope)) continue;
+    const key = `${v.dt}:${v.origin || ""}`;
+    if (statusClasses.has(v.class) || matchFilter(v, filter)) {
+      kept.push(v);
+      annotated.add(key);
+    } else if (!dropped.has(key)) {
+      dropped.set(key, v);
+    }
+  }
+  for (const [key, v] of dropped) {
+    if (annotated.has(key)) continue;
+    const wt = { dt: v.dt, class: "WT", label: mclass.WT.label };
+    if (v.gene) wt.gene = v.gene;
+    if (v.origin) wt.origin = v.origin;
+    kept.push(wt);
+  }
+  return kept;
+}
+function variantFilterLabel(filter, mclassOverride, maxItems = 3) {
+  if (!filter) return "";
+  const entries = [];
+  collect(filter, false);
+  function collect(f, negated) {
+    const flipped = f.in === false ? !negated : negated;
+    for (const item of f.lst) {
+      if (item.type == "tvslst") collect(item, flipped);
+      else if (flipped === !!item.tvs.isnot) entries.push(...item.tvs.values);
+    }
+  }
+  if (!entries.length) return "";
+  const classes = mclass;
+  const names = [
+    ...new Set(entries.map((e) => e.mname || mclassOverride?.[e.key]?.label || classes[e.key]?.label || e.key))
+  ];
+  return names.length > maxItems ? `${names.slice(0, maxItems).join("/")}\u2026` : names.join("/");
+}
+
+export {
+  isFractionTw,
+  getFractionTvsTerm,
+  validateTermCollectionFraction,
+  getFilteredSamples,
+  sample_match_termvaluesetting,
+  getWrappedTvslst,
+  getTvsDenominators,
+  validateTermCollectionTvs,
+  validateVariantFilter,
+  filterVariantValues,
+  variantFilterLabel
+};
+//# sourceMappingURL=chunk-M4XXKTH2.js.map

package/dist/chunk-ME7OF3CS.js

@@ -0,0 +1,176 @@
+import {
+  appInit
+} from "./chunk-KIRZXPMB.js";
+import {
+  showErrorsWithCounter
+} from "./chunk-Q5SK3U2T.js";
+import {
+  mclass
+} from "./chunk-IZUYLFOX.js";
+
+// plots/disco/launch.adhoc.ts
+async function launch(arg, genomeObj, holder) {
+  const [mlst, errors] = await getMlst(arg);
+  if (errors?.length) {
+    return showErrorsWithCounter(errors, holder);
+  }
+  const opts = {
+    holder,
+    vocabApi: {
+      // api is required by plot.app.js, so create a mock one for the adhoc data
+      vocab: { terms: [] },
+      main: () => {
+        return;
+      },
+      getTermdbConfig: () => {
+        return {};
+      }
+    },
+    state: {
+      args: {
+        data: mlst,
+        genome: genomeObj
+      },
+      plots: [
+        {
+          chartType: "Disco",
+          subfolder: "disco",
+          extension: "ts",
+          /** NOTE: Users should only override the settings in the default
+           * settings.Disco:{}, not the entire settings:{} object.*/
+          overrides: { Disco: arg?.settings || {} }
+        }
+      ]
+    }
+  };
+  const plotAppApi = await appInit(opts);
+  return plotAppApi;
+}
+async function getMlst(arg) {
+  if (Array.isArray(arg.mlst)) {
+    return [arg.mlst, null];
+  }
+  const mlst = [];
+  const errors = [];
+  if (arg.snvText) parseSnvText(arg.snvText, mlst, errors);
+  if (arg.svText) parseSvText(arg.svText, mlst, errors);
+  if (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors);
+  return [mlst, errors];
+}
+function parseSnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (![5, 7, 9].includes(l.length)) {
+      errors.push("snv input not equal to 5, 7, or 9 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 1,
+        chr: l[0],
+        position: Number(l[1]),
+        gene: l[2],
+        mname: l[3],
+        class: validateMutation(l[4], errors)
+      };
+      const vafs = parseOptionalVafs(l, errors);
+      if (vafs.length) m.vafs = vafs;
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseOptionalVafs(line, errors) {
+  const vafs = [];
+  const addVaf = (id, totalIndex, altIndex) => {
+    if (line.length <= altIndex) return;
+    const totalCount = Number(line[totalIndex]);
+    const altCount = Number(line[altIndex]);
+    if (!Number.isInteger(totalCount) || !Number.isInteger(altCount) || totalCount <= 0 || altCount < 0 || altCount > totalCount) {
+      errors.push(`${id} total/alt counts must be integers with total > 0, alt >= 0, and alt cannot exceed total`);
+      return;
+    }
+    vafs.push({ id, totalCount, altCount });
+  };
+  addVaf("DNA", 5, 6);
+  addVaf("RNA", 7, 8);
+  return vafs;
+}
+function parseSvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length < 4 || l.length > 6) {
+      errors.push("sv input not equal to 4 or 6 columns");
+      continue;
+    }
+    let m;
+    try {
+      const length = l.length;
+      if (length == 4) {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          chrB: l[2],
+          posB: Number(l[3])
+        };
+      } else {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          geneA: l[2],
+          chrB: l[3],
+          posB: Number(l[4]),
+          geneB: l[5]
+        };
+      }
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseCnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 4) {
+      errors.push("cnv input not equal to 4 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 4,
+        chr: l[0],
+        start: Number(l[1]),
+        stop: Number(l[2]),
+        value: Number(l[3])
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function validateMutation(mutation, errors) {
+  const mut2check = mutation.toLowerCase();
+  const foundMutation = Object.values(mclass).find(
+    (m) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check
+  );
+  if (foundMutation) {
+    return foundMutation.key;
+  } else {
+    errors.push(`Invalid mutation class: ${mutation}`);
+  }
+}
+
+export {
+  launch
+};
+//# sourceMappingURL=chunk-ME7OF3CS.js.map