@sjcrh/proteinpaint-client 2.213.0 → 2.214.0

package/dist/chunk-RU2UHH7M.js

@@ -1,424 +0,0 @@
-import {
-  CATEGORICAL,
-  COHORT,
-  CONDITION,
-  DATE,
-  DNA_METHYLATION,
-  FLOAT,
-  GENE_EXPRESSION,
-  GENE_VARIANT,
-  INTEGER,
-  ISOFORM_EXPRESSION,
-  JUNCTION,
-  METABOLITE_INTENSITY,
-  MULTIVALUE,
-  PROTEOME_ABUNDANCE,
-  PSEUDOBULK,
-  SAMPLELST,
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION,
-  SINGLECELL_NUMERIC_VALUE,
-  SNP,
-  SNP_LIST,
-  SNP_LOCUS,
-  SSGSEA,
-  SURVIVAL,
-  TERM_COLLECTION,
-  TermTypeGroups,
-  dtTerms,
-  dtdnamethylation,
-  dtgeneexpression,
-  dtmetaboliteintensity,
-  dtproteomeabundance,
-  dtssgsea
-} from "./chunk-57Z4VYLM.js";
-
-// ../shared/utils/dist/src/terms.js
-var ROOT_SAMPLE_TYPE = 1;
-var DEFAULT_SAMPLE_TYPE = 2;
-var NumericModes = {
-  continuous: "continuous",
-  discrete: "discrete"
-};
-var dtTermTypes = new Set(dtTerms.map((t) => t.type));
-var TermTypes2Dt = {
-  [GENE_EXPRESSION]: dtgeneexpression,
-  [SSGSEA]: dtssgsea,
-  [DNA_METHYLATION]: dtdnamethylation,
-  [METABOLITE_INTENSITY]: dtmetaboliteintensity,
-  [PROTEOME_ABUNDANCE]: dtproteomeabundance
-};
-var typeGroup = {
-  [CATEGORICAL]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [CONDITION]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [FLOAT]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [INTEGER]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [SAMPLELST]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [SURVIVAL]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [DATE]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [MULTIVALUE]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [GENE_VARIANT]: TermTypeGroups.MUTATION_CNV_FUSION,
-  [SNP]: TermTypeGroups.SNP,
-  [SNP_LIST]: TermTypeGroups.SNP_LIST,
-  [SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,
-  [GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,
-  [ISOFORM_EXPRESSION]: TermTypeGroups.ISOFORM_EXPRESSION,
-  [JUNCTION]: TermTypeGroups.SPLICE_JUNCTION,
-  [SSGSEA]: TermTypeGroups.SSGSEA,
-  [DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,
-  [METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,
-  [PROTEOME_ABUNDANCE]: TermTypeGroups.PROTEOME_ABUNDANCE,
-  [PSEUDOBULK]: TermTypeGroups.PSEUDOBULK,
-  [TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,
-  [SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,
-  [SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION,
-  [SINGLECELL_NUMERIC_VALUE]: TermTypeGroups.SINGLECELL_NUMERIC_VALUE,
-  [COHORT]: TermTypeGroups.COHORT
-};
-var nonDictTypes = /* @__PURE__ */ new Set([
-  SNP,
-  SNP_LIST,
-  SNP_LOCUS,
-  GENE_EXPRESSION,
-  ISOFORM_EXPRESSION,
-  JUNCTION,
-  SSGSEA,
-  DNA_METHYLATION,
-  GENE_VARIANT,
-  METABOLITE_INTENSITY,
-  PROTEOME_ABUNDANCE,
-  PSEUDOBULK,
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION,
-  SINGLECELL_NUMERIC_VALUE,
-  COHORT
-]);
-for (const dtTermType of dtTermTypes) {
-  nonDictTypes.add(dtTermType);
-}
-var numericTypes = /* @__PURE__ */ new Set([
-  INTEGER,
-  FLOAT,
-  GENE_EXPRESSION,
-  ISOFORM_EXPRESSION,
-  JUNCTION,
-  SSGSEA,
-  DNA_METHYLATION,
-  METABOLITE_INTENSITY,
-  PROTEOME_ABUNDANCE,
-  SINGLECELL_GENE_EXPRESSION,
-  SINGLECELL_NUMERIC_VALUE,
-  DATE,
-  PSEUDOBULK
-]);
-var dictionaryNumericTypes = /* @__PURE__ */ new Set([INTEGER, FLOAT, DATE]);
-var categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP]);
-var singleCellTerms = /* @__PURE__ */ new Set([
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION,
-  SINGLECELL_NUMERIC_VALUE
-  /*PSEUDOBULK*/
-]);
-function isSingleCellTerm(term) {
-  if (!term) return false;
-  if (typeof term !== "object") throw new Error("Term is not an object. Did you provide the type instead?");
-  return singleCellTerms.has(term.type);
-}
-function isNumericTerm(term) {
-  if (!term) return false;
-  return numericTypes.has(term.type);
-}
-function isNumericTw(tw) {
-  if (!tw?.term) return false;
-  return isNumericTerm(tw.term) || tw.term.type === TERM_COLLECTION && tw.term.memberType === "numeric" && tw.type === "TermCollectionTWFraction";
-}
-function isCategoricalTerm(term) {
-  if (!term) return false;
-  return categoricalTypes.has(term.type);
-}
-function isDictionaryType(type) {
-  return !isNonDictionaryType(type);
-}
-function isNonDictionaryType(type) {
-  if (!type) throw new Error("Type is not defined");
-  return nonDictTypes.has(type);
-}
-function isNumTermCollection(term) {
-  if (!term || !term.type) throw new Error("Term or term type is not defined");
-  return term.type === TERM_COLLECTION;
-}
-function equals(t1, t2) {
-  if (!t1) throw new Error("First term is not defined ");
-  if (!t2) throw new Error("Second term is not defined ");
-  if (t1.type !== t2.type) return false;
-  if (isDictionaryType(t1.type) && isDictionaryType(t2.type) && t1.type != SAMPLELST) return t1.id === t2.id;
-  switch (t1.type) {
-    case GENE_EXPRESSION:
-      return t1.gene == t2.gene;
-    case ISOFORM_EXPRESSION:
-      return t1.isoform == t2.isoform;
-    case JUNCTION:
-      return t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop && t1.strand == t2.strand;
-    case SSGSEA:
-      return t1.id == t2.id;
-    case DNA_METHYLATION:
-      return t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop;
-    case METABOLITE_INTENSITY:
-    case PROTEOME_ABUNDANCE:
-      return t1.name == t2.name;
-    case GENE_VARIANT:
-      return t1.gene == t2.gene || t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop;
-    // TO DO: Add more cases
-    // case SNP_LIST:
-    // case SNP_LOCUS:
-    // case SAMPLELST:
-    default:
-      return false;
-  }
-}
-function trimGvTermCopy(term, q) {
-  if (term?.type != GENE_VARIANT) return term;
-  delete term.childTerms;
-  if (q?.customset) clearGroupsetParentTerms(q.customset);
-  const lst = term.groupsetting?.lst;
-  if (!lst?.length) return term;
-  if (q?.type == "predefined-groupset") {
-    const idx = q.predefined_groupset_idx;
-    term.groupsetting.lst = lst.map((groupset, i) => i === idx ? groupset : null);
-    clearDtTermMnames(term.groupsetting.lst[idx]);
-    clearGroupsetParentTerms(term.groupsetting.lst[idx]);
-  } else {
-    delete term.groupsetting.lst;
-  }
-  return term;
-}
-function forEachGvTw(obj, callback) {
-  if (!obj || typeof obj != "object") return;
-  if (obj.q && obj.term?.type == GENE_VARIANT) callback(obj);
-  for (const value of Object.values(obj)) forEachGvTw(value, callback);
-}
-function trimGvTermsForSave(obj) {
-  forEachGvTw(obj, (tw) => {
-    delete tw.term.childTerms;
-    delete tw.term.groupsetting;
-    if (tw.q.customset) clearGroupsetParentTerms(tw.q.customset);
-  });
-  return obj;
-}
-function getGvGeneKey(term) {
-  const genes = term?.genes?.length ? term.genes : term ? [term] : [];
-  const keys = genes.map((gene) => {
-    if (getGvGeneKind(gene) == "coord") {
-      const region = getGvQueryRegion(gene);
-      return region ? `${region.chr}:${region.start + 1}-${region.stop}` : void 0;
-    }
-    return gene.gene || gene.name;
-  }).filter((key) => typeof key == "string" && key);
-  if (!keys.length || keys.length != genes.length) return "";
-  return keys.sort().join(",");
-}
-var gvQCacheKeyPrefix = "gv:";
-function getGvQCacheKey(term) {
-  const key = getGvGeneKey(term);
-  return key ? gvQCacheKeyPrefix + key : "";
-}
-function getGvGeneKind(gene) {
-  if (gene?.kind) return gene.kind;
-  if (gene?.gene || gene?.name && !gene.chr) return "gene";
-  if (gene?.chr) return "coord";
-  return void 0;
-}
-function trimGvQForCache(q) {
-  const copy = structuredClone(q);
-  delete copy.isAtomic;
-  delete copy.hiddenValues;
-  delete copy.dtLst;
-  if (copy.customset) {
-    clearDtTermMnames(copy.customset);
-    clearGroupsetParentTerms(copy.customset);
-  }
-  return copy;
-}
-function getGvQueryRegion(gene) {
-  if (!gene?.chr || !Number.isInteger(gene.start) || !Number.isInteger(gene.stop)) return;
-  return { chr: gene.chr, start: gene.start, stop: gene.stop };
-}
-function restoreGvQueryEntry(v, queries) {
-  if (!queries || v?.$q === void 0) return false;
-  Object.assign(v, queries[v.$q]);
-  delete v.$q;
-  return true;
-}
-function matchesGvQueryEntry(entry, v) {
-  if (entry.gene) return entry.gene == v.gene;
-  const r = entry.region;
-  if (r) return !!v.region && r.chr == v.region.chr && r.start == v.region.start && r.stop == v.region.stop;
-  return true;
-}
-function setGroupsetParentTerms(groupset, term) {
-  if (term?.type != GENE_VARIANT) throw "parent of a groupset tvs must be a geneVariant term";
-  const parentTerm = structuredClone(term);
-  delete parentTerm.childTerms;
-  delete parentTerm.groupsetting;
-  walkTvs(groupset, (tvs) => {
-    if (!dtTermTypes.has(tvs.term?.type)) throw `groupset tvs term is not a dt term`;
-    tvs.term.parentTerm = parentTerm;
-  });
-  return groupset;
-}
-function clearGroupsetParentTerms(groupset) {
-  walkTvs(groupset, (tvs) => {
-    if (tvs.term) delete tvs.term.parentTerm;
-  });
-  return groupset;
-}
-function walkTvs(obj, fn) {
-  if (!obj || typeof obj != "object") return;
-  if (obj.type == "tvs" && obj.tvs) {
-    fn(obj.tvs);
-    return;
-  }
-  for (const k in obj) walkTvs(obj[k], fn);
-}
-function getDtsFromGroups(groups) {
-  const dts = /* @__PURE__ */ new Set();
-  for (const group of groups) {
-    for (const dt of getDtsFromFilter(group.filter)) dts.add(dt);
-  }
-  return [...dts];
-}
-function getDtsFromFilter(filter) {
-  const dts = /* @__PURE__ */ new Set();
-  for (const item of filter.lst) {
-    if (item.type == "tvslst") {
-      for (const dt of getDtsFromFilter(item)) dts.add(dt);
-    } else {
-      dts.add(item.tvs.term.dt);
-    }
-  }
-  return dts;
-}
-function clearDtTermMnames(obj) {
-  walkTvs(obj, (tvs) => {
-    if (tvs.term) delete tvs.term.mnames;
-  });
-  return obj;
-}
-function getQuerySampleTypesByTerms(sampleTypesByTerms, querySampleTypes) {
-  if (!sampleTypesByTerms) return;
-  const querySampleTypesByTerms = {};
-  for (const [term, values] of Object.entries(sampleTypesByTerms)) {
-    const queryValues = {};
-    for (const [value, sampleTypes] of Object.entries(values)) {
-      const filteredSampleTypes = sampleTypes.filter((sampleType) => querySampleTypes.includes(sampleType));
-      if (filteredSampleTypes.length) queryValues[value] = filteredSampleTypes;
-    }
-    if (Object.keys(queryValues).length) querySampleTypesByTerms[term] = queryValues;
-  }
-  if (!Object.keys(querySampleTypesByTerms).length) return;
-  return querySampleTypesByTerms;
-}
-var typeMap = {
-  categorical: "Categorical",
-  condition: "Condition",
-  float: "Numerical",
-  integer: "Numerical",
-  date: "Date",
-  geneExpression: "Gene Expression",
-  isoformExpression: "Isoform Expression",
-  [JUNCTION]: "Splice junction",
-  ssGSEA: "Geneset Expression",
-  dnaMethylation: "DNA Methylation",
-  geneVariant: "Gene Variant",
-  metaboliteIntensity: "Metabolite Intensity",
-  proteomeAbundance: "Proteome Abundance",
-  proteomeDAP: "Proteome DAP",
-  multivalue: "Multi Value",
-  singleCellGeneExpression: "Single Cell, Gene Expression",
-  singleCellCellType: "Single Cell, Cell Type",
-  singleCellNumericValue: "Single Cell, Numeric Value",
-  snplocus: "SNP Locus",
-  snp: "SNP",
-  snplst: "SNP List",
-  termCollection: "Term Collection"
-};
-function termItemType(t) {
-  switch (t.type) {
-    case JUNCTION:
-      return "Splice junction";
-    case GENE_EXPRESSION:
-    case SINGLECELL_GENE_EXPRESSION:
-      return "Gene";
-    case ISOFORM_EXPRESSION:
-      return "Isoform";
-    case SSGSEA:
-      return "Gene set";
-    case METABOLITE_INTENSITY:
-      return "Metabolite";
-    // keep adding here
-    default:
-      return "Variable";
-  }
-}
-function termType2label(type) {
-  const s = typeMap[type];
-  if (s) return s;
-  throw new Error("termType2label(): unknown value");
-}
-function getDateFromNumber(value) {
-  const year = Math.floor(value);
-  const january1st = new Date(year, 0, 1);
-  const totalDays = getDaysInYear(year);
-  const time = Math.round((value - year) * totalDays) * oneDayTime;
-  const date = new Date(january1st.getTime() + time);
-  return date;
-}
-var oneDayTime = 24 * 60 * 60 * 1e3;
-function getDateStrFromNumber(value) {
-  const date = getDateFromNumber(value);
-  return date.toLocaleDateString("en-US", {
-    year: "numeric",
-    month: "long"
-  });
-}
-function getDaysInYear(year) {
-  const isLeap = new Date(year, 1, 29).getMonth() === 1;
-  const days = isLeap ? 366 : 365;
-  return days;
-}
-
-export {
-  ROOT_SAMPLE_TYPE,
-  DEFAULT_SAMPLE_TYPE,
-  NumericModes,
-  dtTermTypes,
-  TermTypes2Dt,
-  typeGroup,
-  numericTypes,
-  dictionaryNumericTypes,
-  isSingleCellTerm,
-  isNumericTerm,
-  isNumericTw,
-  isCategoricalTerm,
-  isDictionaryType,
-  isNonDictionaryType,
-  isNumTermCollection,
-  equals,
-  trimGvTermCopy,
-  forEachGvTw,
-  trimGvTermsForSave,
-  gvQCacheKeyPrefix,
-  getGvQCacheKey,
-  trimGvQForCache,
-  restoreGvQueryEntry,
-  matchesGvQueryEntry,
-  setGroupsetParentTerms,
-  getDtsFromGroups,
-  clearDtTermMnames,
-  getQuerySampleTypesByTerms,
-  termItemType,
-  termType2label,
-  getDateFromNumber,
-  getDateStrFromNumber
-};
-//# sourceMappingURL=chunk-RU2UHH7M.js.map

package/dist/chunk-S2PNRIOW.js

@@ -1,123 +0,0 @@
-import {
-  pickCollectionFraction,
-  renderTable
-} from "./chunk-QI6X4V43.js";
-
-// termdb/handlers/termCollection.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    opts.holder.style("display", "");
-    const termlst = opts.details.termlst ?? [];
-    const memberType = opts.details.memberType || opts.details.type;
-    if (opts.termCollectionSelectionMode === "fraction" && memberType === "numeric") {
-      pickCollectionFraction({
-        holder: opts.holder,
-        term: makeTerm(opts.details, termlst, opts.usecase),
-        callback: (tw) => opts.callback(tw)
-      });
-      return;
-    }
-    const tableDiv = opts.holder.append("div");
-    renderTable({
-      columns: [{ label: "VARIABLES" }],
-      rows: termlst.map((t) => {
-        return [{ value: t.name }];
-      }),
-      div: tableDiv,
-      maxWidth: "30vw",
-      maxHeight: "40vh",
-      // the button is disabled while the selection cannot be submitted
-      noButtonCallback: () => updateSelectBtn(),
-      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: () => updateSelectBtn(),
-        striped: false,
-        showHeader: true,
-        //false,
-        selectAll: true,
-        columnButtons: void 0,
-        //Leave until table.js is typed
-        buttons: void 0
-      });
-    }
-    function getRowChecks(div) {
-      const trs = div.select("table").select("tbody").node().querySelectorAll("tr");
-      return [...trs].map((tr) => tr.querySelectorAll("td")[1]?.querySelector("input")?.checked === true);
-    }
-    function getSelectedTermlst() {
-      const checked = getRowChecks(tableDiv);
-      return termlst.filter((term, i) => checked[i]);
-    }
-    function getCategoryKeys() {
-      if (!categoryTable) return void 0;
-      const checked = getRowChecks(categoryTable);
-      return ckSource.map((ck, i) => ({ key: ck.key, shown: checked[i] }));
-    }
-    function getSelectionError() {
-      if (getSelectedTermlst().length < 2) return "Select at least two variables.";
-      if (getCategoryKeys()?.every((ck) => !ck.shown)) return "Select at least one category.";
-      return void 0;
-    }
-    function updateSelectBtn() {
-      if (!selectBtn) return;
-      const error = getSelectionError();
-      selectBtn.property("disabled", Boolean(error)).attr("title", error || null);
-    }
-    const selectBtn = opts.holder.append("div").style("float", "right").style("padding", "6px 20px").append("button").attr("data-testid", "sjpp-term-collection-select").text("Select").on("click", () => {
-      opts.callback({
-        // makeTerm() extracts propsByTermId (color, etc) for the selected terms
-        ...makeTerm(opts.details, getSelectedTermlst(), opts.usecase),
-        categoryKeys: getCategoryKeys()
-      });
-    });
-    updateSelectBtn();
-  }
-};
-function makeTerm(details, termlst, usecase) {
-  const propsByTermId = {};
-  if (details.propsByTermId) {
-    for (const term of termlst) {
-      if (details.propsByTermId[term.id]) propsByTermId[term.id] = details.propsByTermId[term.id];
-    }
-  }
-  return {
-    type: "termCollection",
-    termIds: termlst.map((term) => term.id),
-    termlst,
-    name: details.name,
-    valueTransform: details.valueTransformByPlots?.[usecase?.target],
-    // memberType = ds.cohort.termdb.termCollections[].type for client code
-    memberType: details.memberType || details.type,
-    categoryKeys: details.categoryKeys,
-    isleaf: true,
-    propsByTermId
-  };
-}
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-S2PNRIOW.js.map

package/dist/chunk-SKF6HQ74.js

@@ -1,31 +0,0 @@
-import {
-  IN_frame,
-  OUT_frame
-} from "./chunk-57Z4VYLM.js";
-
-// src/spliceevent.exonskip.getdefault.js
-function spliceevent_exonskip_getdefault_default(events) {
-  let evt2showidx = 0;
-  for (let i = 1; i < events.length; i++) {
-    const e = events[i];
-    const e2show = events[evt2showidx];
-    if (e.isskipexon && e2show.isaltexon) {
-      evt2showidx = i;
-      continue;
-    }
-    if (e.frame == OUT_frame && e2show.framenocheck) {
-      evt2showidx = i;
-      continue;
-    }
-    if (e.frame == IN_frame && e2show.frame != IN_frame) {
-      evt2showidx = i;
-      continue;
-    }
-  }
-  return evt2showidx;
-}
-
-export {
-  spliceevent_exonskip_getdefault_default
-};
-//# sourceMappingURL=chunk-SKF6HQ74.js.map