@sjcrh/proteinpaint-client 2.210.0 → 2.210.1

package/dist/chunk-KIAMLQ7S.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-SB36AUG7.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-KIAMLQ7S.js.map

package/dist/chunk-LBCIXRI2.js

@@ -1,49 +0,0 @@
-import {
-  runproteinpaint
-} from "./chunk-DSBRHWZ7.js";
-
-// test/front.helpers.js
-var serverData = /* @__PURE__ */ Object.create(null);
-function getRunPp(appname = "", defaultArgs = {}, _host = "http://localhost:3000") {
-  const host = window.testHost || _host;
-  const arg = {
-    host: window.testHost || _host,
-    noheader: 1,
-    nobox: true,
-    debug: 1,
-    norecover: true
-  };
-  if (appname == "mass" || appname == "termdb") {
-    defaultArgs.debounceInterval = 0;
-  }
-  if (appname) arg[appname] = defaultArgs;
-  else copyMerge(arg, defaultArgs);
-  const argStr = JSON.stringify(arg);
-  return function runpp(overrides = {}) {
-    const argCopy = JSON.parse(argStr);
-    if (appname) copyMerge(argCopy[appname], overrides);
-    else copyMerge(argCopy, overrides);
-    if (appname && defaultArgs.fetchOpts) {
-      argCopy[appname].fetchOpts = defaultArgs.fetchOpts;
-    }
-    return runproteinpaint(Object.assign(argCopy, { serverData }));
-  };
-}
-function copyMerge(base, ...args) {
-  const target = typeof base == "string" ? JSON.parse(base) : base;
-  for (const arg of args) {
-    if (arg) {
-      const source = typeof base == "string" ? JSON.parse(JSON.stringify(arg)) : arg;
-      for (const key in source) {
-        if (!target[key] || Array.isArray(target[key]) || typeof target[key] !== "object") target[key] = source[key];
-        else copyMerge(target[key], source[key]);
-      }
-    }
-  }
-  return target;
-}
-
-export {
-  getRunPp
-};
-//# sourceMappingURL=chunk-LBCIXRI2.js.map

package/dist/chunk-MNXL2UV5.js

@@ -1,98 +0,0 @@
-import {
-  keyupEnter
-} from "./chunk-55FABQU2.js";
-import {
-  require_debounce
-} from "./chunk-KV4W2ACA.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import {
-  dofetch,
-  dofetch3
-} from "./chunk-VA57CUC7.js";
-import {
-  __toESM
-} from "./chunk-HS5PO5ZQ.js";
-
-// src/gene.js
-var import_debounce = __toESM(require_debounce(), 1);
-var tip;
-function gene_searchbox(p) {
-  if (!tip) {
-    tip = new Menu({ padding: "" });
-    tip.d.style("z-index", 1e3);
-  }
-  const input = p.div.append("input").attr("placeholder", "Search gene").style("width", p.width || "100px");
-  const printdiv = p.resultdiv || (p.tip ? p.tip.d : tip.d);
-  function fold() {
-    if (p.resultdiv) {
-      p.resultdiv.selectAll("*").remove();
-    } else if (p.tip) {
-      p.tip.hide();
-    } else {
-      tip.hide();
-    }
-  }
-  input.on("keyup", (event) => {
-    const str = event.target.value;
-    if (str.length <= 1) {
-      fold();
-      return;
-    }
-    if (keyupEnter(event)) {
-      const hitgene = printdiv.select(".sja_menuoption");
-      if (hitgene.size() > 0) {
-        p.callback(hitgene.text());
-        fold();
-      }
-      return;
-    }
-    debouncer();
-  });
-  input.node().focus();
-  function genesearch() {
-    dofetch("genelookup", { genome: p.genome, input: input.property("value") }).then((data) => {
-      if (data.error) throw data.error;
-      if (!data.hits) throw ".hits[] missing";
-      if (p.resultdiv) {
-        p.resultdiv.selectAll("*").remove();
-      } else if (p.tip) {
-        p.tip.clear().showunder(input.node());
-      } else {
-        tip.clear().showunder(input.node());
-      }
-      for (const name of data.hits) {
-        printdiv.append("div").attr("class", "sja_menuoption").text(name).on("click", () => {
-          p.callback(name);
-          fold();
-        });
-      }
-    }).catch((err) => {
-      printdiv.append("div").text(err.message || err);
-      if (err.stack) console.log(err.stack);
-    });
-  }
-  const debouncer = (0, import_debounce.debounce)(genesearch, 300);
-}
-function findgenemodel_bysymbol(genome, str) {
-  return dofetch3("genelookup", {
-    body: {
-      deep: 1,
-      input: str,
-      genome
-    }
-  }).then((data) => {
-    if (data.error) throw data.error;
-    if (!data.gmlst || data.gmlst.length == 0) return null;
-    return data.gmlst;
-  }).catch((e) => {
-    throw e;
-  });
-}
-
-export {
-  gene_searchbox,
-  findgenemodel_bysymbol
-};
-//# sourceMappingURL=chunk-MNXL2UV5.js.map

package/dist/chunk-NDOKW2HJ.js

@@ -1,31 +0,0 @@
-import {
-  IN_frame,
-  OUT_frame
-} from "./chunk-SB36AUG7.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-NDOKW2HJ.js.map