@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/chunk-6BB43SIB.js

@@ -1,102 +0,0 @@
-import {
-  renderTable
-} from "./chunk-5VOPABBA.js";
-
-// termdb/handlers/termCollection.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    opts.holder.style("display", "");
-    const tableDiv = opts.holder.append("div");
-    const termlst = opts.details.termlst ?? [];
-    renderTable({
-      columns: [{ label: "VARIABLES" }],
-      rows: termlst.map((t) => {
-        return [{ value: t.name }];
-      }),
-      div: tableDiv,
-      maxWidth: "30vw",
-      maxHeight: "40vh",
-      noButtonCallback: () => {
-      },
-      // FIXME to supply a real callback
-      striped: false,
-      showHeader: true,
-      //false,
-      selectAll: true,
-      columnButtons: void 0,
-      //Leave until table.js is typed
-      buttons: void 0
-    });
-    let categoryTable;
-    let ckSource = [];
-    if (opts.details.categoryKeys) {
-      ckSource = opts.details.categoryKeys;
-      const categoryDiv = opts.holder.append("div").style("margin-top", "15px");
-      const values = opts.details.termlst[0].values || {};
-      categoryTable = categoryDiv.append("div");
-      renderTable({
-        columns: [{ label: "CATEGORIES" }],
-        rows: ckSource.map((ck) => {
-          return [{ value: values[ck.key]?.label ?? ck.key, checked: ck.shown }];
-        }),
-        div: categoryTable,
-        maxWidth: "30vw",
-        maxHeight: "40vh",
-        noButtonCallback: () => {
-        },
-        // FIXME to supply a real callback
-        striped: false,
-        showHeader: true,
-        //false,
-        selectAll: true,
-        columnButtons: void 0,
-        //Leave until table.js is typed
-        buttons: void 0
-      });
-    }
-    opts.holder.append("div").style("float", "right").style("padding", "6px 20px").append("button").attr("class", "sjpp_apply_btn sja_filter_tag_btn").text("Select").on("click", () => {
-      const trs = tableDiv.select("table").select("tbody").node().querySelectorAll("tr");
-      const selectedTermlst = termlst.filter((term, i) => {
-        const checked = trs[i]?.querySelectorAll("td")[1]?.querySelector("input")?.checked;
-        return checked === true;
-      });
-      if (selectedTermlst.length === 0) {
-        alert("Please select at least one term");
-        return;
-      }
-      const propsByTermId = {};
-      if (opts.details.propsByTermId) {
-        for (const t of selectedTermlst) {
-          if (opts.details.propsByTermId[t.id]) propsByTermId[t.id] = opts.details.propsByTermId[t.id];
-        }
-      }
-      let categoryKeys;
-      if (categoryTable) {
-        const trs2 = categoryTable.select("table").select("tbody").node().querySelectorAll("tr");
-        categoryKeys = ckSource.map((ck, i) => {
-          const checked = trs2[i].querySelectorAll("td")[1].querySelector("input")?.checked;
-          return { key: ck.key, shown: !!checked };
-        });
-      }
-      opts.callback({
-        type: "termCollection",
-        termIds: selectedTermlst.map((i) => i.id),
-        termlst: selectedTermlst,
-        name: opts.details.name,
-        valueTransform: opts.details.valueTransformByPlots?.[opts.usecase.target],
-        // memberType = ds.cohort.termdb.termCollections[].type for client code
-        memberType: opts.details.memberType || opts.details.type,
-        categoryKeys,
-        isleaf: true,
-        propsByTermId
-      });
-    });
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-6BB43SIB.js.map

package/dist/chunk-6BB43SIB.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termdb/handlers/termCollection.ts"],
-  "sourcesContent": ["import { renderTable } from '#dom'\nimport type { CategoryKey } from '#types'\n\nexport class SearchHandler {\n\tcallback: any\n\tapp: any\n\n\tasync init(opts) {\n\t\t// opts.details is the term object for term collection\n\t\tthis.callback = opts.callback\n\t\tthis.app = opts.app\n\n\t\topts.holder.style('display', '')\n\t\tconst tableDiv = opts.holder.append('div')\n\n\t\tconst termlst = opts.details.termlst ?? []\n\t\trenderTable({\n\t\t\tcolumns: [{ label: 'VARIABLES' }],\n\t\t\trows: termlst.map(t => {\n\t\t\t\treturn [{ value: t.name }]\n\t\t\t}),\n\t\t\tdiv: tableDiv,\n\t\t\tmaxWidth: '30vw',\n\t\t\tmaxHeight: '40vh',\n\t\t\tnoButtonCallback: () => {}, // FIXME to supply a real callback\n\t\t\tstriped: false,\n\t\t\tshowHeader: true, //false,\n\t\t\tselectAll: true,\n\t\t\tcolumnButtons: undefined, //Leave until table.js is typed\n\t\t\tbuttons: undefined\n\t\t})\n\n\t\tlet categoryTable\n\t\tlet ckSource: CategoryKey[] = []\n\t\tif (opts.details.categoryKeys) {\n\t\t\t// later, if there's just one category, simply show a disabled checked box for this category and no longer uncheckable\n\t\t\tckSource = opts.details.categoryKeys as CategoryKey[]\n\t\t\tconst categoryDiv = opts.holder.append('div').style('margin-top', '15px')\n\t\t\tconst values = opts.details.termlst[0].values || {}\n\t\t\tcategoryTable = categoryDiv.append('div')\n\t\t\trenderTable({\n\t\t\t\tcolumns: [{ label: 'CATEGORIES' }],\n\t\t\t\trows: ckSource.map((ck: CategoryKey) => {\n\t\t\t\t\treturn [{ value: values[ck.key]?.label ?? ck.key, checked: ck.shown }]\n\t\t\t\t}),\n\t\t\t\tdiv: categoryTable,\n\t\t\t\tmaxWidth: '30vw',\n\t\t\t\tmaxHeight: '40vh',\n\t\t\t\tnoButtonCallback: () => {}, // FIXME to supply a real callback\n\t\t\t\tstriped: false,\n\t\t\t\tshowHeader: true, //false,\n\t\t\t\tselectAll: true,\n\t\t\t\tcolumnButtons: undefined, //Leave until table.js is typed\n\t\t\t\tbuttons: undefined\n\t\t\t})\n\t\t}\n\n\t\t// FIXME backward code!!!!\n\t\topts.holder\n\t\t\t.append('div')\n\t\t\t.style('float', 'right')\n\t\t\t.style('padding', '6px 20px')\n\t\t\t.append('button')\n\t\t\t.attr('class', 'sjpp_apply_btn sja_filter_tag_btn')\n\t\t\t.text('Select')\n\t\t\t.on('click', () => {\n\t\t\t\tconst trs = tableDiv.select('table').select('tbody').node().querySelectorAll('tr')\n\t\t\t\tconst selectedTermlst = termlst.filter((term, i) => {\n\t\t\t\t\tconst checked = trs[i]?.querySelectorAll('td')[1]?.querySelector('input')?.checked\n\t\t\t\t\treturn checked === true\n\t\t\t\t})\n\t\t\t\tif (selectedTermlst.length === 0) {\n\t\t\t\t\talert('Please select at least one term')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst propsByTermId = {}\n\t\t\t\tif (opts.details.propsByTermId) {\n\t\t\t\t\t// extract properties (like color, etc) for the selected terms\n\t\t\t\t\tfor (const t of selectedTermlst) {\n\t\t\t\t\t\tif (opts.details.propsByTermId[t.id]) propsByTermId[t.id] = opts.details.propsByTermId[t.id]\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tlet categoryKeys\n\t\t\t\tif (categoryTable) {\n\t\t\t\t\tconst trs = categoryTable.select('table').select('tbody').node().querySelectorAll('tr')\n\t\t\t\t\tcategoryKeys = ckSource.map((ck: CategoryKey, i: number) => {\n\t\t\t\t\t\tconst checked = trs[i].querySelectorAll('td')[1].querySelector('input')?.checked\n\t\t\t\t\t\treturn { key: ck.key, shown: !!checked }\n\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\topts.callback({\n\t\t\t\t\ttype: 'termCollection',\n\t\t\t\t\ttermIds: selectedTermlst.map(i => i.id),\n\t\t\t\t\ttermlst: selectedTermlst,\n\t\t\t\t\tname: opts.details.name,\n\t\t\t\t\tvalueTransform: opts.details.valueTransformByPlots?.[opts.usecase.target],\n\t\t\t\t\t// memberType = ds.cohort.termdb.termCollections[].type for client code\n\t\t\t\t\tmemberType: opts.details.memberType || opts.details.type,\n\t\t\t\t\tcategoryKeys,\n\t\t\t\t\tisleaf: true,\n\t\t\t\t\tpropsByTermId\n\t\t\t\t})\n\t\t\t})\n\t}\n}\n"],
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-  "names": ["trs"]
-}

package/dist/chunk-7IYJZZQI.js

@@ -1,167 +0,0 @@
-// ../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 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");
-  }
-}
-
-export {
-  getFilteredSamples,
-  sample_match_termvaluesetting,
-  getWrappedTvslst,
-  validateTermCollectionTvs
-};
-//# sourceMappingURL=chunk-7IYJZZQI.js.map

package/dist/chunk-7IYJZZQI.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/filter.ts"],
-  "sourcesContent": ["import type { Filter, Tvs } from '#types'\n\n/**\n * Sample annotation structure\n */\nexport interface SampleAnnotation {\n\tsample: string | number\n\ts?: Record<string, any>\n\tdata?: Record<string, any>\n}\n\n/**\n * Dataset with annotation functionality\n */\nexport interface Dataset {\n\tsetAnnoByTermId?: (termId: string) => void\n}\n\n/**\n * Filters an array of sample annotations and returns a Set of matching sample names\n * @param sampleAnno Array of sample annotations\n * @param filter Nested filter structure as used in the termdbapp\n * @returns Set of sample names that match the filter\n */\nexport function getFilteredSamples(sampleAnno: SampleAnnotation[], filter: Filter): Set<string | number> {\n\tsetDatasetAnnotations(filter)\n\n\tconst samples = new Set<string | number>()\n\tfor (const anno of sampleAnno) {\n\t\tif (samples.has(anno.sample)) continue\n\t\tconst data = anno.s || anno.data\n\t\tif (data && sample_match_termvaluesetting(data, filter)) {\n\t\t\tsamples.add(anno.sample)\n\t\t}\n\t}\n\treturn samples\n}\n\n/**\n * Given a value from a sample's annotation of a term, return true if a value matches the filter\n * @param row Sample annotation data\n * @param filter Filter structure or single tvs item\n * @param _term Optional term to filter by\n * @param sample Optional sample data\n * @returns True if the sample matches the filter\n */\nexport function sample_match_termvaluesetting(\n\trow: any,\n\tfilter: Filter,\n\t_term: any = null,\n\tsample: any = null\n): boolean {\n\tconst lst = filter.type == 'tvslst' ? filter.lst : [filter]\n\tlet numberofmatchedterms = 0\n\n\t/* for AND, require all terms to match */\n\tfor (const item of lst) {\n\t\tif ('type' in item && item.type == 'tvslst') {\n\t\t\tif (sample_match_termvaluesetting(row, item, _term, sample)) {\n\t\t\t\tnumberofmatchedterms++\n\t\t\t}\n\t\t} else {\n\t\t\tconst itemCopy = JSON.parse(JSON.stringify(item))\n\t\t\tconst t = itemCopy.tvs\n\n\t\t\tif (_term && t.term) {\n\t\t\t\tif (!(_term.name == t.term.name && _term.type == t.term.type)) {\n\t\t\t\t\t// for an filter from \"this.config.legendValueFilter\", if the filter is not for the tw\n\t\t\t\t\t// (not the same type and name), ignore the filter.\n\t\t\t\t\tnumberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tlet samplevalue\n\t\t\tif (_term && !t.term) {\n\t\t\t\tif (t.term$type && t.term$type !== _term.type) {\n\t\t\t\t\t//when the filter is not for the term being tested, ignore the filter\n\t\t\t\t\tnumberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tt.term = _term\n\t\t\t\tsamplevalue = typeof row === 'object' && t.term.id in row ? row[t.term.id] : row\n\t\t\t} else if (sample && t.term.$id) {\n\t\t\t\tsamplevalue = sample[t.term.$id].value\n\t\t\t} else {\n\t\t\t\tsamplevalue = t.term.id in row ? row[t.term.id] : row\n\t\t\t}\n\t\t\tsetDatasetAnnotations(itemCopy)\n\t\t\tlet thistermmatch\n\n\t\t\tif (t.term.type == 'categorical') {\n\t\t\t\tif (samplevalue === undefined) continue // this sample has no anno for this term, do not count\n\t\t\t\tthistermmatch = t.valueset.has(samplevalue)\n\t\t\t} else if (t.term.type == 'integer' || t.term.type == 'float') {\n\t\t\t\tif (samplevalue === undefined) continue // this sample has no anno for this term, do not count\n\t\t\t\tfor (const range of t.ranges) {\n\t\t\t\t\tif ('value' in range) {\n\t\t\t\t\t\tthistermmatch = samplevalue === range.value\n\t\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t\t} else if (samplevalue == range.name) {\n\t\t\t\t\t\tthistermmatch = true\n\t\t\t\t\t\tbreak\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// actual range\n\t\t\t\t\t\tif (t.term.values) {\n\t\t\t\t\t\t\tconst v = t.term.values[samplevalue.toString()]\n\t\t\t\t\t\t\tif (v && v.uncomputable) {\n\t\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tlet left, right\n\t\t\t\t\t\tif (range.startunbounded) {\n\t\t\t\t\t\t\tleft = true\n\t\t\t\t\t\t} else if ('start' in range) {\n\t\t\t\t\t\t\tif (range.startinclusive) {\n\t\t\t\t\t\t\t\tleft = samplevalue >= range.start\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tleft = samplevalue > range.start\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (range.stopunbounded) {\n\t\t\t\t\t\t\tright = true\n\t\t\t\t\t\t} else if ('stop' in range) {\n\t\t\t\t\t\t\tif (range.stopinclusive) {\n\t\t\t\t\t\t\t\tright = samplevalue <= range.stop\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tright = samplevalue < range.stop\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthistermmatch = left && right\n\t\t\t\t\t}\n\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t}\n\t\t\t} else if (t.term.type == 'condition') {\n\t\t\t\tconst key = getPrecomputedKey(t)\n\t\t\t\tconst anno = samplevalue && samplevalue[key]\n\t\t\t\tif (anno) {\n\t\t\t\t\tthistermmatch = Array.isArray(anno)\n\t\t\t\t\t\t? t.values.find((d: any) => anno.includes(d.key))\n\t\t\t\t\t\t: t.values.find((d: any) => d.key == anno)\n\t\t\t\t}\n\t\t\t} else if (t.term.type == 'geneVariant') {\n\t\t\t\t/*\n\t\t\t\tsamplevalue.values here can be an array or only one of the entries \n\t\t\t\t[\n\t\t\t\t\t{ dt: 1, class: 'WT', _SAMPLEID_: 21, origin: 'germline' },\n\t\t\t\t\t{ dt: 1, class: 'WT', _SAMPLEID_: 21, origin: 'somatic' },\n\t\t\t\t\t{ dt: 2, class: 'Blank', _SAMPLEID_: 21 },\n\t\t\t\t\t{ dt: 4, class: 'WT', _SAMPLEID_: 21 }\n\t\t\t\t]\n\t\t\t\t*/\n\t\t\t\t/* tvs.values is an array that stores classes (for each available dt) that have/haven't been crossed out by the user at this round of edit-and-apply, e.g.\n          [\n            {dt: 1, mclassLst: ['WT'], mclassExcludeLst: ['Blank'], origin: 'germline'}\n            {dt: 1, mclassLst: ['Blank', 'WT', 'M'], mclassExcludeLst:[], origin:'somatic'},\n            {dt: 2, mclassLst: ['Blank', 'WT'], mclassExcludeLst:[]}\n            {dt: 4, mclassLst: ['WT', 'CNV_loss'], mclassExcludeLst:[]}\n          ]\n        */\n\t\t\t\tconst svalues = samplevalue.values || [samplevalue]\n\t\t\t\tfor (const sv of svalues) {\n\t\t\t\t\tthistermmatch =\n\t\t\t\t\t\tt.values.find(\n\t\t\t\t\t\t\t(v: any) =>\n\t\t\t\t\t\t\t\tv.dt == sv.dt &&\n\t\t\t\t\t\t\t\t(!v.origin || sv.origin == v.origin) &&\n\t\t\t\t\t\t\t\t(!v.mclasslst || v.mclasslst.includes(sv.class))\n\t\t\t\t\t\t) && true\n\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tthrow 'unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]'\n\t\t\t}\n\n\t\t\tif (t.isnot) {\n\t\t\t\tthistermmatch = !thistermmatch\n\t\t\t}\n\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t}\n\n\t\t// if one tvslst is matched with an \"or\" (Set UNION), then sample is okay\n\t\tif (filter.join == 'or') {\n\t\t\tif (numberofmatchedterms && filter.in) return true\n\t\t\tif (!numberofmatchedterms && !filter.in) return true\n\t\t}\n\t}\n\t// for join=\"and\" (Set intersection)\n\tif (!('in' in filter)) (filter as any).in = true // casting to any avoids tsc err despite it's typed!\n\treturn filter.in == (numberofmatchedterms == lst.length)\n}\n\n/**\n * Recursively processes filter items and sets dataset annotations\n * @param item Filter item to process\n * @param ds Optional dataset with annotation functionality\n */\nexport function setDatasetAnnotations(item: Filter | { type: 'tvs'; tvs: Tvs }, ds: Dataset | null = null): void {\n\tif (item.type == 'tvslst') {\n\t\tfor (const subitem of item.lst) {\n\t\t\tsetDatasetAnnotations(subitem, ds)\n\t\t}\n\t} else {\n\t\tif (ds && typeof ds.setAnnoByTermId == 'function') {\n\t\t\tds.setAnnoByTermId(item.tvs.term.id)\n\t\t}\n\t\tif (item.tvs.term.type == 'categorical') {\n\t\t\tconst tvsAny = item.tvs as any\n\t\t\ttvsAny.valueset = new Set(tvsAny.values.map((i: any) => i.key))\n\t\t}\n\t}\n}\n\n/**\n * Gets the precomputed key for a condition term based on bar_by and value_by settings\n */\nfunction getPrecomputedKey(q: any): string {\n\tconst precomputedKey =\n\t\tq.bar_by_children && q.value_by_max_grade\n\t\t\t? 'childrenAtMaxGrade'\n\t\t\t: q.bar_by_children && q.value_by_most_recent\n\t\t\t? 'childrenAtMostRecent'\n\t\t\t: q.bar_by_children && q.value_by_computable_grade\n\t\t\t? 'children'\n\t\t\t: q.bar_by_grade && q.value_by_max_grade\n\t\t\t? 'maxGrade'\n\t\t\t: q.bar_by_grade && q.value_by_most_recent\n\t\t\t? 'mostRecentGrades'\n\t\t\t: q.bar_by_grade && q.value_by_computable_grade\n\t\t\t? 'computableGrades'\n\t\t\t: ''\n\tif (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`\n\treturn precomputedKey\n}\n\n/**\n * Joins a list of filters into the first filter with \"and\", returns joined filter\n * Used by caller app to join hidden filters into a visible filter\n * @param lst List of filters to join\n * @returns The joined filter\n */\nexport function filterJoin(lst: Filter[]): Filter | undefined {\n\tif (!lst || lst.length == 0) return\n\tlet f = JSON.parse(JSON.stringify(lst[0]))\n\tif (lst.length == 1) return f\n\t// more than 1 item, will join\n\tif (f.lst.length < 2) {\n\t\tif (f.join !== '') throw 'filter.join must be an empty string \"\" when filter.lst.length < 2'\n\t\tf.join = 'and'\n\t} else if (f.join == 'or') {\n\t\t// f is \"or\", wrap it with another root layer of \"and\"\n\t\tf = {\n\t\t\ttype: 'tvslst',\n\t\t\tjoin: 'and',\n\t\t\tin: true,\n\t\t\tlst: [f]\n\t\t}\n\t} else if (f.join != 'and') {\n\t\tthrow 'filter.join must be either \"and\" or \"or\" when .lst length > 1'\n\t}\n\t// now, f.join should be \"and\"\n\t// if the argument lst[0].join == \"and\",\n\t// then the f.in boolean value is reused\n\tfor (let i = 1; i < lst.length; i++) {\n\t\tconst f2 = JSON.parse(JSON.stringify(lst[i]))\n\t\tif (f2.join == 'or') f.lst.push(f2)\n\t\telse f.lst.push(...f2.lst)\n\t}\n\t// if f ends up single-tvs item (from joining single tvs to empty filter), need to set join to '' per filter spec\n\tif (f.lst.length == 1 && f.lst[0].type == 'tvs') {\n\t\tf.join = ''\n\t}\n\treturn f\n}\n\n/**\n * Creates a wrapped tvslst (term value settings list) filter object\n * @param lst List of filter items\n * @param join Join operation (and/or)\n * @param $id Optional filter ID\n * @returns Wrapped filter object\n */\nexport function getWrappedTvslst(lst: Filter['lst'] = [], join: string = '', $id: string | null = null): Filter {\n\tconst filter: Filter = {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin,\n\t\tlst\n\t}\n\tif ($id !== null) filter.$id = $id\n\treturn filter\n}\n\n/**\n * Validates numerator and denominator term collections\n * @param lst1 Numerator list of term ids\n * @param lst2 Denominator list of term ids\n * @throws Error if validation fails\n */\nexport function validateTermCollectionTvs(lst1: any[], lst2: any[]): void {\n\t// lst1/lst2: numerator and denominator. both are lists of term ids\n\tif (!Array.isArray(lst1)) throw new Error('numerator not array')\n\tif (!Array.isArray(lst2)) throw new Error('denominator not array')\n\tif (lst1.length == 0) throw new Error('numerator empty')\n\tif (lst2.length == 0) throw new Error('denominator empty')\n\tif (lst1.length > lst2.length) throw new Error('numerator longer than denominator')\n\tfor (const s of lst1) {\n\t\tif (typeof s != 'string') throw new Error('one of numerator not string')\n\t\tif (!s) throw new Error('empty string in numerator')\n\t\tif (!lst2.includes(s)) throw new Error('one of numerator not in denominator')\n\t}\n}\n"],
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-}

package/dist/chunk-7OHRR2IE.js

@@ -1,276 +0,0 @@
-import {
-  parsesample
-} from "./chunk-M6EF3WVV.js";
-import {
-  dtfusionrna,
-  dtsv,
-  mclassfusionrna,
-  mclasssv
-} from "./chunk-2X6W4E3W.js";
-
-// ../shared/utils/dist/src/bulk.sv.js
-function parseheader(line, flag, issv) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid file header for fusions";
-  const htry = (...lst) => {
-    for (const a of lst) {
-      const j = header.indexOf(a);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("gene_a", "gene1", "genea");
-  if (i == -1) return "gene_a missing from header";
-  header[i] = "gene1";
-  i = htry("gene_b", "gene2", "geneb");
-  if (i == -1) return "gene_b missing from header";
-  header[i] = "gene2";
-  i = htry("chr_a", "chr1", "chra");
-  if (i == -1) return "chr_a missing from header";
-  header[i] = "chr1";
-  i = htry("chr_b", "chr2", "chrb");
-  if (i == -1) return "chr_b missing from header";
-  header[i] = "chr2";
-  i = htry("pos_a", "position_a", "position1", "posa");
-  if (i == -1) return "pos_a missing from header";
-  header[i] = "position1";
-  i = htry("pos_b", "position_b", "position2", "posb");
-  if (i == -1) return "pos_b missing from header";
-  header[i] = "position2";
-  i = htry("isoform_a", "refseq_a", "refseq1", "isoform1", "sv_refseqa");
-  if (i == -1) return "isoform_a missing from header";
-  header[i] = "isoform1";
-  i = htry("isoform_b", "refseq_b", "refseq2", "isoform2", "sv_refseqb");
-  if (i == -1) return "isoform_b missing from header";
-  header[i] = "isoform2";
-  i = htry("strand_a", "orta");
-  if (i == -1) return "strand_a missing from header";
-  header[i] = "strand1";
-  i = htry("strand_b", "ortb");
-  if (i == -1) return "strand_b missing from header";
-  header[i] = "strand2";
-  i = htry("sample", "sample_name", "tumor_sample_barcode");
-  if (i != -1) header[i] = "sample";
-  i = htry("patient", "donor", "target_case_id");
-  if (i != -1) header[i] = "patient";
-  i = htry("sampletype", "sample type", "sample_type");
-  if (i != -1) header[i] = "sampletype";
-  i = htry("disease");
-  if (i != -1) header[i] = "disease";
-  i = htry("origin");
-  if (i != -1) header[i] = "origin";
-  if (issv) {
-    flag.sv.loaded = true;
-    flag.sv.header = header;
-  } else {
-    flag.fusion.loaded = true;
-    flag.fusion.header = header;
-  }
-  return false;
-}
-function parseline(i, line, flag, issv) {
-  if (line == "" || line[0] == "#") return;
-  const lst = line.split("	");
-  const m = {};
-  const header = issv ? flag.sv.header : flag.fusion.header;
-  const badlines = issv ? flag.sv.badlines : flag.fusion.badlines;
-  for (let j = 0; j < header.length; j++) {
-    m[header[j]] = lst[j];
-  }
-  if (!m.chr1) {
-    badlines.push([i, "missing chr1", lst]);
-    return;
-  }
-  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
-    m.chr1 = "chr" + m.chr1;
-  }
-  if (!m.chr2) {
-    badlines.push([i, "missing chr2", lst]);
-    return;
-  }
-  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
-    m.chr2 = "chr" + m.chr2;
-  }
-  let v = m.position1;
-  if (!v) {
-    badlines.push([i, "missing position1", lst]);
-    return;
-  }
-  let v2 = Number.parseInt(v);
-  if (Number.isNaN(v2) || v2 <= 0) {
-    badlines.push([i, "invalid value for position1", lst]);
-    return;
-  }
-  m.position1 = v2;
-  v = m.position2;
-  if (!v) {
-    badlines.push([i, "missing position2", lst]);
-    return;
-  }
-  v2 = Number.parseInt(v);
-  if (Number.isNaN(v2) || v2 <= 0) {
-    badlines.push([i, "invalid value for position2", lst]);
-    return;
-  }
-  m.position2 = v2;
-  if (parsesample(m, flag, i, lst)) {
-    return;
-  }
-  if (m.isoform1 && m.isoform1.indexOf(",") != -1) {
-    const lst2 = m.isoform1.split(",");
-    m.isoform1 = void 0;
-    for (const t of lst2) {
-      if (t != "") m.isoform1 = t;
-    }
-  }
-  if (m.isoform2 && m.isoform2.indexOf(",") != -1) {
-    const lst2 = m.isoform2.split(",");
-    m.isoform2 = void 0;
-    for (const t of lst2) {
-      if (t != "") m.isoform2 = t;
-    }
-  }
-  if (!m.gene1) {
-    m.isoform1 = void 0;
-  }
-  if (!m.gene2) {
-    m.isoform2 = void 0;
-  }
-  if (m.gene1) {
-    flag.good++;
-    const m2 = {
-      dt: issv ? dtsv : dtfusionrna,
-      class: issv ? mclasssv : mclassfusionrna,
-      isoform: m.isoform1,
-      mname: m.gene2 || m.chr2,
-      sample: m.sample,
-      patient: m.patient,
-      sampletype: m.sampletype,
-      origin: m.origin,
-      disease: m.disease,
-      pairlst: [
-        {
-          a: {
-            name: m.gene1,
-            isoform: m.isoform1,
-            strand: m.strand1,
-            chr: m.chr1,
-            position: m.position1
-          },
-          b: {
-            name: m.gene2,
-            isoform: m.isoform2,
-            strand: m.strand2,
-            chr: m.chr2,
-            position: m.position2
-          }
-        }
-      ]
-    };
-    const n = flag.geneToUpper ? m.gene1.toUpperCase() : m.gene1;
-    if (!flag.data[n]) {
-      flag.data[n] = [];
-    }
-    flag.data[n].push(m2);
-  }
-  if (m.gene2 && m.gene2 != m.gene1) {
-    flag.good++;
-    const m2 = {
-      dt: issv ? dtsv : dtfusionrna,
-      class: issv ? mclasssv : mclassfusionrna,
-      isoform: m.isoform2,
-      mname: m.gene1 || m.chr1,
-      sample: m.sample,
-      patient: m.patient,
-      sampletype: m.sampletype,
-      origin: m.origin,
-      disease: m.disease,
-      pairlst: [
-        {
-          a: {
-            name: m.gene1,
-            isoform: m.isoform1,
-            strand: m.strand1,
-            chr: m.chr1,
-            position: m.position1
-          },
-          b: {
-            name: m.gene2,
-            isoform: m.isoform2,
-            strand: m.strand2,
-            chr: m.chr2,
-            position: m.position2
-          }
-        }
-      ]
-    };
-    const n = flag.geneToUpper ? m.gene2.toUpperCase() : m.gene2;
-    if (!flag.data[n]) {
-      flag.data[n] = [];
-    }
-    flag.data[n].push(m2);
-  }
-}
-function duplicate(m) {
-  const n = {};
-  for (const k in m) {
-    if (k == "pairlst") continue;
-    const v = m[k];
-    const type = typeof v;
-    if (type == "object") {
-      continue;
-    }
-    n[k] = v;
-  }
-  if (m.pairlst) {
-    n.pairlst = [];
-    for (const pair of m.pairlst) {
-      const p = {};
-      for (const k in pair) {
-        if (k == "a" || k == "b" || k == "interstitial") {
-          continue;
-        }
-        p[k] = pair[k];
-      }
-      if (pair.a) {
-        p.a = {};
-        for (const k in pair.a) {
-          const v = pair.a[k];
-          if (typeof v == "object") {
-            continue;
-          }
-          p.a[k] = v;
-        }
-      }
-      if (pair.b) {
-        p.b = {};
-        for (const k in pair.b) {
-          const v = pair.b[k];
-          if (typeof v == "object") {
-            continue;
-          }
-          p.b[k] = v;
-        }
-      }
-      if (pair.interstitial) {
-        p.interstitial = {};
-        for (const k in pair.interstitial) {
-          const v = pair.interstitial[k];
-          if (typeof v == "object") {
-            continue;
-          }
-          p.interstitial[k] = v;
-        }
-      }
-      n.pairlst.push(p);
-    }
-  }
-  return n;
-}
-
-export {
-  parseheader,
-  parseline,
-  duplicate
-};
-//# sourceMappingURL=chunk-7OHRR2IE.js.map