@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

package/dist/chunk-EF37UZY6.js

@@ -0,0 +1,37 @@
+import {
+  addGeneSearchbox,
+  getGEunit
+} from "./chunk-2XPDA6NL.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  TermTypes
+} from "./chunk-FDK4UJMN.js";
+
+// termdb/handlers/geneExpression.ts
+var SearchHandler = class {
+  init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: holder,
+      searchOnly: "gene",
+      callback: () => this.selectGene(geneSearch.geneSymbol)
+    });
+  }
+  async selectGene(gene) {
+    const unit = getGEunit(this.app.vocabApi);
+    const name = `${gene} ${unit}`;
+    if (!gene) throw new Error("No gene selected");
+    this.callback({ gene, name, type: TermTypes.GENE_EXPRESSION });
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-EF37UZY6.js.map

package/dist/chunk-ESXMS7FW.js

@@ -0,0 +1,229 @@
+import {
+  keyupEnter
+} from "./chunk-2XPDA6NL.js";
+import {
+  get_bin_label,
+  get_bin_range_equation
+} from "./chunk-2T7VYQLY.js";
+
+// termsetting/handlers/NumCustomBinEditor.ts
+var NumCustomBinEditor = class {
+  constructor(editHandler) {
+    this.dom = {};
+    this.editHandler = editHandler;
+    this.opts = editHandler.opts;
+    this.tw = editHandler.tw;
+    this.termsetting = editHandler.termsetting;
+  }
+  async render(div) {
+    if (this.q?.type != "custom-bin") this.q = this.getDefaultQ();
+    await this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+    if (this.dom.inputsDiv) {
+      if (this.editHandler.dom.binsDiv?.node().contains(this.dom.inputsDiv.node())) return;
+      else {
+        this.dom.inputsDiv.remove();
+        delete this.dom.inputsDiv;
+      }
+    }
+    this.dom.inputsDiv = div.append("div").style("display", "flex").style("width", "100%");
+    this.renderCustomBinInputs();
+  }
+  getBoundaryOpts() {
+    return {
+      values: this.q.lst.slice(1).map((bin) => ({ x: bin.startunbounded ? bin.stop : bin.start, isDraggable: true })),
+      callback: (d, value) => {
+        const boundaryValues = this.q.lst.slice(1).map((d2) => "start" in d2 ? d2.start : "");
+        boundaryValues[d.index] = value;
+        this.dom.customBinBoundaryInput.text(boundaryValues.join(",\n"));
+        this.handleInputChange("drag");
+        return 0;
+      }
+    };
+  }
+  getDefaultQ() {
+    if (this.tw.q.mode == "discrete" && this.tw.q.type == "custom-bin") {
+      const copy = JSON.parse(JSON.stringify(this.tw.q));
+      copy.lst.forEach((bin) => {
+        if (!bin.label) bin.label = get_bin_label(bin, this.tw.q, this.tw.term.valueConversion);
+        bin.range = get_bin_range_equation(bin, this.tw.q);
+      });
+      return copy;
+    }
+    const { min, max } = this.editHandler.handler.density_data;
+    const defaultCustomBoundary = (
+      /* when no sample is annotated by this term,
+      minvalue and maxvalue are both null
+      setting defaultCustomBoundary to arbitrary "0" will allow existing UI to work
+      but remains to be evaluated if is really okay to use 0
+      */
+      !Number.isFinite(min) || !Number.isFinite(max) ? 0 : (
+        // minvalue and maxvalue is valid number
+        max != min ? min + (max - min) / 2 : max
+      )
+    );
+    const firstBin = {
+      startunbounded: true,
+      startinclusive: false,
+      stopinclusive: false,
+      stop: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
+    };
+    const lastBin = {
+      stopunbounded: true,
+      startinclusive: true,
+      stopinclusive: false,
+      start: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
+    };
+    return {
+      mode: "discrete",
+      type: "custom-bin",
+      lst: [
+        // Type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' is not assignable to type 'StartUnboundedBin | FullyBoundedBin'.
+        // Property 'start' is missing in type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' but required in type 'FullyBoundedBin'.
+        {
+          ...firstBin,
+          label: get_bin_label(firstBin, this.tw.q, this.tw.term.valueConversion),
+          range: get_bin_range_equation(firstBin, this.tw.q)
+        },
+        {
+          ...lastBin,
+          label: get_bin_label(lastBin, this.tw.q, this.tw.term.valueConversion),
+          range: get_bin_range_equation(lastBin, this.tw.q)
+        }
+        //satisfies StopUnboundedBin
+      ]
+    };
+  }
+  /******************* Functions for Numerical Custom size bins *******************/
+  renderCustomBinInputs() {
+    const q = this.q;
+    const boundaryDiv = this.dom.inputsDiv.append("div").style("margin-right", "20px");
+    this.dom.rangeAndLabelDiv = this.dom.inputsDiv.append("div");
+    boundaryDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Bin boundaries");
+    this.dom.customBinBoundaryInput = boundaryDiv.append("textarea").style("width", "100px").style("height", "70px").text(
+      q.lst.slice(1).map((d) => "start" in d ? d.start : "").join("\n")
+    ).on("change", () => this.handleInputChange()).on("keyup", async (event) => {
+      if (!keyupEnter(event) && event.key != 8 && event.key != "Enter") return;
+      if (!this.dom.inputsDiv.selectAll("input").node().value) return;
+      this.handleInputChange();
+    });
+    boundaryDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
+    this.renderBoundaryInputDivs();
+  }
+  renderBoundaryInputDivs() {
+    const data = this.q.lst;
+    const holder = this.dom.rangeAndLabelDiv;
+    holder.selectAll("*").remove();
+    const grid = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center");
+    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
+    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Bin label");
+    for (const d of data) {
+      grid.append("div").attr("name", "range").html(d.range);
+      grid.append("div").append("input").attr("type", "text").style("margin", "2px 0px").property("value", d.label).on("change", function() {
+        d.label = this.value;
+      });
+    }
+    this.dom.customBinRanges = this.dom.inputsDiv.selectAll('div[name="range"]').data(data);
+    this.dom.customBinLabelInput = this.dom.inputsDiv.selectAll("input").data(data);
+  }
+  handleInputChange(eventType = "") {
+    const self = this.tw;
+    const inputs = this.dom.inputsDiv.selectAll("input");
+    inputs.property("value", "");
+    const data = this.processCustomBinInputs();
+    if (data == void 0) {
+      return;
+    }
+    if (self.q.hiddenValues) this.tw.q.hiddenValues = self.q.hiddenValues;
+    if (this.binsChanged(data, this.q.lst)) {
+      this.q.lst = data;
+    }
+    this.renderBoundaryInputDivs();
+    if (eventType != "drag") this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+  binsChanged(data, qlst) {
+    if (data.length != qlst.length) return true;
+    if (Object.keys(data[0]).length !== Object.keys(qlst[0]).length) return true;
+    for (const [i, bin] of qlst.entries()) {
+      for (const k of Object.keys(bin)) {
+        if (bin[k] && bin[k] !== data[i][k]) {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+  processCustomBinInputs() {
+    const self = this.termsetting;
+    const startinclusive = this.editHandler.boundaryInclusion == "startinclusive";
+    const stopinclusive = this.editHandler.boundaryInclusion == "stopinclusive";
+    const inputs = this.dom.inputsDiv.node().querySelectorAll("input");
+    const inputData = this.dom.customBinBoundaryInput.property("value").split("\n").filter((d) => d != "" && !isNaN(d));
+    const trackBins = new Set(inputData);
+    if (!trackBins.size) return this.tw.q.lst;
+    const sortedBins = Array.from(trackBins).map(Number).sort((a, b) => a - b);
+    const data = [
+      // first bin: StartUnbounded type
+      {
+        startunbounded: true,
+        stop: sortedBins[0],
+        startinclusive: false,
+        stopinclusive,
+        label: inputs[0].value
+      }
+    ];
+    if (!data[0].label) data[0].label = get_bin_label(data[0], self.q, self.term.valueConversion);
+    if (!data[0].range) data[0].range = get_bin_range_equation(data[0], self.q);
+    for (const [i, d] of sortedBins.entries()) {
+      let bin;
+      const label = inputs[i + 1]?.value || "";
+      if (i !== trackBins.size - 1) {
+        bin = {
+          start: +d,
+          startinclusive,
+          stopinclusive,
+          stop: sortedBins[i + 1],
+          label
+          //range: ''
+        };
+      } else {
+        bin = {
+          start: +d,
+          startinclusive,
+          stopinclusive: false,
+          stopunbounded: true,
+          label
+          //range: ''
+        };
+      }
+      if (bin.label === "" || bin.label === void 0) bin.label = get_bin_label(bin, self.q, self.term.valueConversion);
+      if (bin.range === "" || bin.range === void 0) bin.range = get_bin_range_equation(bin, self.q);
+      data.push(bin);
+    }
+    return data;
+  }
+  getEditedQ(destroyDom = true) {
+    const lst = this.processCustomBinInputs();
+    if (destroyDom) {
+      for (const name of Object.keys(this.dom)) {
+        this.dom[name].remove();
+        delete this.dom[name];
+      }
+    }
+    return {
+      mode: "discrete",
+      type: "custom-bin",
+      lst
+    };
+  }
+  undoEdits() {
+    this.q = this.getDefaultQ();
+    this.dom.inputsDiv.selectAll("*").remove();
+    this.renderCustomBinInputs();
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+};
+
+export {
+  NumCustomBinEditor
+};
+//# sourceMappingURL=chunk-ESXMS7FW.js.map

package/dist/chunk-FDK4UJMN.js

@@ -0,0 +1,263 @@
+import {
+  TermTypeGroups,
+  dtTerms,
+  dtdnamethylation,
+  dtgeneexpression,
+  dtmetaboliteintensity,
+  dtproteomeabundance,
+  dtssgsea
+} from "./chunk-X7GDCYND.js";
+
+// ../shared/utils/dist/src/terms.js
+var ROOT_SAMPLE_TYPE = 1;
+var DEFAULT_SAMPLE_TYPE = 2;
+var NumericModes = {
+  continuous: "continuous",
+  discrete: "discrete"
+};
+var CATEGORICAL = "categorical";
+var CONDITION = "condition";
+var DATE = "date";
+var DNA_METHYLATION = "dnaMethylation";
+var FLOAT = "float";
+var GENE_VARIANT = "geneVariant";
+var GENE_EXPRESSION = "geneExpression";
+var ISOFORM_EXPRESSION = "isoformExpression";
+var INTEGER = "integer";
+var METABOLITE_INTENSITY = "metaboliteIntensity";
+var MULTIVALUE = "multivalue";
+var SAMPLELST = "samplelst";
+var SINGLECELL_CELLTYPE = "singleCellCellType";
+var SINGLECELL_GENE_EXPRESSION = "singleCellGeneExpression";
+var SNP = "snp";
+var SNP_LIST = "snplst";
+var SNP_LOCUS = "snplocus";
+var SSGSEA = "ssGSEA";
+var SURVIVAL = "survival";
+var TERM_COLLECTION = "termCollection";
+var PROTEOME_ABUNDANCE = "proteomeAbundance";
+var PROTEOME_DAP = "proteomeDAP";
+var TermTypes = {
+  GENE_VARIANT,
+  GENE_EXPRESSION,
+  ISOFORM_EXPRESSION,
+  SSGSEA,
+  DNA_METHYLATION,
+  CATEGORICAL,
+  INTEGER,
+  FLOAT,
+  SNP,
+  SNP_LIST,
+  SNP_LOCUS,
+  CONDITION,
+  SURVIVAL,
+  SAMPLELST,
+  METABOLITE_INTENSITY,
+  PROTEOME_ABUNDANCE,
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION,
+  MULTIVALUE,
+  DATE,
+  TERM_COLLECTION
+};
+var dtTermTypes = new Set(dtTerms.map((t) => t.type));
+for (const dtTermType of dtTermTypes) {
+  TermTypes[dtTermType.toUpperCase()] = dtTermType;
+}
+var NUMERIC_DICTIONARY_TERM = "numericDictTerm";
+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,
+  [SSGSEA]: TermTypeGroups.SSGSEA,
+  [DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,
+  [METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,
+  [PROTEOME_ABUNDANCE]: TermTypeGroups.PROTEOME_ABUNDANCE,
+  [TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,
+  [SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,
+  [SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION
+};
+var nonDictTypes = /* @__PURE__ */ new Set([
+  SNP,
+  SNP_LIST,
+  SNP_LOCUS,
+  GENE_EXPRESSION,
+  ISOFORM_EXPRESSION,
+  SSGSEA,
+  DNA_METHYLATION,
+  GENE_VARIANT,
+  METABOLITE_INTENSITY,
+  PROTEOME_ABUNDANCE,
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION
+]);
+for (const dtTermType of dtTermTypes) {
+  nonDictTypes.add(TermTypes[dtTermType.toUpperCase()]);
+}
+var numericTypes = /* @__PURE__ */ new Set([
+  INTEGER,
+  FLOAT,
+  GENE_EXPRESSION,
+  ISOFORM_EXPRESSION,
+  SSGSEA,
+  DNA_METHYLATION,
+  METABOLITE_INTENSITY,
+  PROTEOME_ABUNDANCE,
+  SINGLECELL_GENE_EXPRESSION,
+  DATE
+]);
+var categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP]);
+var singleCellTerms = /* @__PURE__ */ new Set([SINGLECELL_CELLTYPE, SINGLECELL_GENE_EXPRESSION]);
+function isSingleCellTerm(term) {
+  if (!term) return false;
+  return singleCellTerms.has(term.type);
+}
+function isNumericTerm(term) {
+  if (!term) return false;
+  return numericTypes.has(term.type);
+}
+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 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;
+  }
+}
+var typeMap = {
+  categorical: "Categorical",
+  condition: "Condition",
+  float: "Numerical",
+  integer: "Numerical",
+  geneExpression: "Gene Expression",
+  isoformExpression: "Isoform Expression",
+  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",
+  snplocus: "SNP Locus",
+  snp: "SNP",
+  snplst: "SNP List",
+  numericDictTerm: "Numeric Dictionary Term",
+  termCollection: "Term Collection"
+};
+function termType2label(type) {
+  return typeMap[type] || "Unknown term type";
+}
+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,
+  CATEGORICAL,
+  DATE,
+  DNA_METHYLATION,
+  FLOAT,
+  GENE_VARIANT,
+  GENE_EXPRESSION,
+  ISOFORM_EXPRESSION,
+  INTEGER,
+  METABOLITE_INTENSITY,
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION,
+  SNP,
+  SSGSEA,
+  TERM_COLLECTION,
+  PROTEOME_ABUNDANCE,
+  PROTEOME_DAP,
+  TermTypes,
+  dtTermTypes,
+  NUMERIC_DICTIONARY_TERM,
+  TermTypes2Dt,
+  typeGroup,
+  numericTypes,
+  isSingleCellTerm,
+  isNumericTerm,
+  isCategoricalTerm,
+  isDictionaryType,
+  isNonDictionaryType,
+  isNumTermCollection,
+  equals,
+  termType2label,
+  getDateFromNumber,
+  getDateStrFromNumber
+};
+//# sourceMappingURL=chunk-FDK4UJMN.js.map

package/dist/chunk-FDK4UJMN.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/utils/src/terms.ts"],
+  "sourcesContent": ["import type { Term } from '#types'\nimport {\n\tdtgeneexpression,\n\tdtssgsea,\n\tdtdnamethylation,\n\tdtmetaboliteintensity,\n\tdtproteomeabundance,\n\tTermTypeGroups,\n\tdtTerms\n} from './common.js'\n\n// moved TermTypeGroups to `server/src/common.js`, so now has to re-export\nexport { TermTypeGroups } from './common.js'\n\n/*\nFor datasets with multiple types of samples the ROOT_SAMPLE_TYPE is used to represent the root sample type, for example, \nthe type patient, that has one or more samples associated to it. This should be the id used as sample_type, when generating the db to identify the root samples\nin sampleidmap or the terms annotating root samples in the terms table.\nThe samples associated to a patient have annotations that are specific to a timepoint, for example, the age of the patient,\nthe doses of the drugs the patient was taking at the time of the data collection, etc. These annotations are associated to a sample.\n*/\nexport const ROOT_SAMPLE_TYPE = 1\n\n//For datasets with one sample type the DEFAULT_SAMPLE_TYPE is used to represent the sample type\nexport const DEFAULT_SAMPLE_TYPE = 2\n\nexport const NumericModes = {\n\tcontinuous: 'continuous',\n\tdiscrete: 'discrete'\n}\n\nexport const CATEGORICAL = 'categorical'\nexport const CONDITION = 'condition'\nexport const DATE = 'date'\nexport const DNA_METHYLATION = 'dnaMethylation'\nexport const FLOAT = 'float'\nexport const GENE_VARIANT = 'geneVariant'\nexport const GENE_EXPRESSION = 'geneExpression'\nexport const ISOFORM_EXPRESSION = 'isoformExpression'\nexport const INTEGER = 'integer'\nexport const METABOLITE_INTENSITY = 'metaboliteIntensity'\nexport const MULTIVALUE = 'multivalue'\nexport const SAMPLELST = 'samplelst'\nexport const SINGLECELL_CELLTYPE = 'singleCellCellType'\nexport const SINGLECELL_GENE_EXPRESSION = 'singleCellGeneExpression'\nexport const SNP = 'snp'\nexport const SNP_LIST = 'snplst'\nexport const SNP_LOCUS = 'snplocus'\nexport const SSGSEA = 'ssGSEA'\nexport const SURVIVAL = 'survival'\nexport const TERM_COLLECTION = 'termCollection'\nexport const PROTEOME_ABUNDANCE = 'proteomeAbundance'\nexport const PROTEOME_DAP = 'proteomeDAP'\n\n//Term types should be used gradually using these constants instead of hardcoding the values,\n// eg: type == CATEGORICAL instead of type == 'categorical'\nexport const TermTypes: { [key: string]: string } = {\n\tGENE_VARIANT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tCATEGORICAL,\n\tINTEGER,\n\tFLOAT,\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tCONDITION,\n\tSURVIVAL,\n\tSAMPLELST,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tMULTIVALUE,\n\tDATE,\n\tTERM_COLLECTION\n}\nexport const dtTermTypes: Set<string> = new Set(dtTerms.map((t: any) => t.type))\nfor (const dtTermType of dtTermTypes) {\n\tTermTypes[dtTermType.toUpperCase()] = dtTermType\n}\n\nexport const NUMERIC_DICTIONARY_TERM = 'numericDictTerm'\n\nexport const TermTypes2Dt = {\n\t[GENE_EXPRESSION]: dtgeneexpression,\n\t[SSGSEA]: dtssgsea,\n\t[DNA_METHYLATION]: dtdnamethylation,\n\t[METABOLITE_INTENSITY]: dtmetaboliteintensity,\n\t[PROTEOME_ABUNDANCE]: dtproteomeabundance\n}\n\n// maps term type to group (as is shown as toggles in search ui)\nexport const typeGroup = {\n\t[CATEGORICAL]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[CONDITION]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[FLOAT]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[INTEGER]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[SAMPLELST]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[SURVIVAL]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[DATE]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[MULTIVALUE]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[GENE_VARIANT]: TermTypeGroups.MUTATION_CNV_FUSION,\n\t[SNP]: TermTypeGroups.SNP,\n\t[SNP_LIST]: TermTypeGroups.SNP_LIST,\n\t[SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,\n\t[GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,\n\t[ISOFORM_EXPRESSION]: TermTypeGroups.ISOFORM_EXPRESSION,\n\t[SSGSEA]: TermTypeGroups.SSGSEA,\n\t[DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,\n\t[METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,\n\t[PROTEOME_ABUNDANCE]: TermTypeGroups.PROTEOME_ABUNDANCE,\n\t[TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,\n\t[SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,\n\t[SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION\n}\n\nconst nonDictTypes = new Set([\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tGENE_VARIANT,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION\n])\n\nfor (const dtTermType of dtTermTypes) {\n\tnonDictTypes.add(TermTypes[dtTermType.toUpperCase()])\n}\n\nexport const numericTypes = new Set([\n\tINTEGER,\n\tFLOAT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tDATE\n])\n\n// available termdb numeric table names used as anno_<term.type>,\n// for example anno_integer, anno_float, anno_date\nexport const annoNumericTypes = new Set([INTEGER, FLOAT, DATE])\n\nconst categoricalTypes = new Set([CATEGORICAL, SNP])\n\nconst singleCellTerms = new Set([SINGLECELL_CELLTYPE, SINGLECELL_GENE_EXPRESSION])\n\nexport function isSingleCellTerm(term: any) {\n\tif (!term) return false\n\treturn singleCellTerms.has(term.type)\n}\nexport function isNumericTerm(term: Term) {\n\tif (!term) return false\n\treturn numericTypes.has(term.type)\n}\nexport function isCategoricalTerm(term: Term) {\n\tif (!term) return false\n\treturn categoricalTypes.has(term.type)\n}\n\nexport function isDictionaryType(type: string) {\n\treturn !isNonDictionaryType(type)\n}\n\nexport function isNonDictionaryType(type: string) {\n\tif (!type) throw new Error('Type is not defined')\n\treturn nonDictTypes.has(type)\n}\n\nexport function isNumTermCollection(term: Term) {\n\tif (!term || !term.type) throw new Error('Term or term type is not defined')\n\t//Enable this check when memberType is added to term collection\n\t// return term.type === TERM_COLLECTION && term.memberType == 'numeric'\n\treturn term.type === TERM_COLLECTION\n}\n\nexport function equals(t1: any, t2: any) {\n\tif (!t1) throw new Error('First term is not defined ')\n\tif (!t2) throw new Error('Second term is not defined ')\n\tif (t1.type !== t2.type) return false //term types are different\n\tif (isDictionaryType(t1.type) && isDictionaryType(t2.type) && t1.type != SAMPLELST) return t1.id === t2.id\n\tswitch (t1.type) {\n\t\tcase GENE_EXPRESSION:\n\t\t\treturn t1.gene == t2.gene\n\t\tcase ISOFORM_EXPRESSION:\n\t\t\treturn t1.isoform == t2.isoform\n\t\tcase SSGSEA:\n\t\t\treturn t1.id == t2.id\n\t\tcase DNA_METHYLATION:\n\t\t\treturn t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop\n\t\tcase METABOLITE_INTENSITY:\n\t\tcase PROTEOME_ABUNDANCE:\n\t\t\treturn t1.name == t2.name\n\t\tcase GENE_VARIANT:\n\t\t\treturn t1.gene == t2.gene || (t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop)\n\n\t\t// TO DO: Add more cases\n\t\t// case SNP_LIST:\n\t\t// case SNP_LOCUS:\n\t\t// case SAMPLELST:\n\n\t\tdefault:\n\t\t\treturn false\n\t}\n}\n\nexport function getBin(lst: any[], value: number) {\n\tlet bin = lst.findIndex(\n\t\tb => (b.startunbounded && value < b.stop) || (b.startunbounded && b.stopinclusive && value == b.stop)\n\t)\n\tif (bin == -1)\n\t\tbin = lst.findIndex(\n\t\t\tb => (b.stopunbounded && value > b.start) || (b.stopunbounded && b.startinclusive && value == b.start)\n\t\t)\n\tif (bin == -1)\n\t\tbin = lst.findIndex(\n\t\t\tb =>\n\t\t\t\t(value > b.start && value < b.stop) ||\n\t\t\t\t(b.startinclusive && value == b.start) ||\n\t\t\t\t(b.stopinclusive && value == b.stop)\n\t\t)\n\treturn bin\n}\n//Terms may  have a sample type associated to them, in datasets with multiple types of samples.\n//For example the gender is associated to the patient while the age is associated to the type sample. This function is used\n//for example when calling getData or getFilter, to return either the parent or the child samples, depending on the use case.\nexport function getSampleType(term: any, ds: any) {\n\tif (!term) return null\n\t//non dict terms annotate only samples, eg: gene expression, metabolite intensity, gene variant.\n\t//Their sample type is the default sample type that may or may not have a parent type, depending on the dataset\n\tif (term.type && isNonDictionaryType(term.type)) return DEFAULT_SAMPLE_TYPE\n\t//dictionary terms may annotate different types of samples, eg: patient and sample or mouse and crop.\n\tif (term.id) return ds.cohort.termdb.term2SampleType.get(term.id)\n\tif (term.type == 'samplelst') {\n\t\tconst key = Object.keys(term.values)[0]\n\t\tconst sampleId = term.values[key].list[0]?.sampleId\n\t\tif (sampleId) return ds.sampleId2Type.get(Number(sampleId) || sampleId)\n\t\telse return DEFAULT_SAMPLE_TYPE\n\t}\n\t// samplelst or non dict terms\n\treturn DEFAULT_SAMPLE_TYPE //later own term needs to know what type annotates based on the samples\n}\n\nexport function getParentType(types: Set<string>, ds: any) {\n\tif (Object.keys(ds.cohort.termdb.sampleTypes).length == 0) return null //dataset only has one type of sample\n\tconst ids = Array.from(types)\n\tif (!ids || ids.length == 0) return null\n\tfor (const id of ids) {\n\t\tconst typeObj = ds.cohort.termdb.sampleTypes[id]\n\t\tif (!typeObj) continue\n\t\tif (typeObj.parent_id == null) return id //this is the root type\n\t\t//if my parent is in the list, then I am not the parent\n\t\tif (ids.includes(typeObj.parent_id)) continue\n\t\telse return typeObj.parent_id //my parent is not in the list, so I am the parent\n\t}\n\treturn null //no parent found\n}\n\n//Returns human readable label for each term type; label is just for printing and not computing\nconst typeMap: { [key: string]: string } = {\n\tcategorical: 'Categorical',\n\tcondition: 'Condition',\n\tfloat: 'Numerical',\n\tinteger: 'Numerical',\n\tgeneExpression: 'Gene Expression',\n\tisoformExpression: 'Isoform Expression',\n\tssGSEA: 'Geneset Expression',\n\tdnaMethylation: 'DNA Methylation',\n\tgeneVariant: 'Gene Variant',\n\tmetaboliteIntensity: 'Metabolite Intensity',\n\tproteomeAbundance: 'Proteome Abundance',\n\tproteomeDAP: 'Proteome DAP',\n\tmultivalue: 'Multi Value',\n\tsingleCellGeneExpression: 'Single Cell, Gene Expression',\n\tsingleCellCellType: 'Single Cell, Cell Type',\n\tsnplocus: 'SNP Locus',\n\tsnp: 'SNP',\n\tsnplst: 'SNP List',\n\tnumericDictTerm: 'Numeric Dictionary Term',\n\ttermCollection: 'Term Collection'\n}\n\nexport function termType2label(type: string) {\n\treturn typeMap[type] || 'Unknown term type'\n}\n\nexport function getDateFromNumber(value: number) {\n\tconst year = Math.floor(value)\n\tconst january1st = new Date(year, 0, 1)\n\tconst totalDays = getDaysInYear(year)\n\tconst time = Math.round((value - year) * totalDays) * oneDayTime\n\tconst date = new Date(january1st.getTime() + time)\n\treturn date\n}\n/*\nValue is a decimal year.\nA decimal year is a way of expressing a date or time period as a year with a decimal part, where the decimal portion \nrepresents the fraction of the year that has elapsed. \nExample:\n2025.0 represents the beginning of the year 2025. \n2025.5 represents the middle of the year 2025. \n */\nconst oneDayTime = 24 * 60 * 60 * 1000\n\nexport function getDateStrFromNumber(value: number) {\n\tconst date = getDateFromNumber(value)\n\n\t//Omit day to  deidentify the patients\n\treturn date.toLocaleDateString('en-US', {\n\t\tyear: 'numeric',\n\t\tmonth: 'long'\n\t})\n}\n\n//The value returned is a decimal year\n//A decimal year is a way of expressing a date or time period as a year with a decimal part, where the decimal portion\n//represents the fraction of the year that has elapsed.\nexport function getNumberFromDateStr(str: string) {\n\tconst date = new Date(str)\n\treturn getNumberFromDate(date)\n}\n\nexport function getNumberFromDate(date: Date) {\n\tconst year = date.getFullYear()\n\tconst january1st: Date = new Date(year, 0, 1)\n\tconst diffDays = (date.getTime() - january1st.getTime()) / oneDayTime\n\tconst daysTotal = getDaysInYear(year)\n\tconst decimal = diffDays / daysTotal\n\treturn year + decimal\n}\n\nexport function getDaysInYear(year: number) {\n\tconst isLeap = new Date(year, 1, 29).getMonth() === 1\n\tconst days = isLeap ? 366 : 365\n\treturn days\n}\n"],
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