@sjcrh/proteinpaint-client 2.182.1 → 2.183.1

package/dist/chunk-6ITDJ5UR.js

@@ -1,261 +0,0 @@
-import {
-  TermTypeGroups,
-  dtTerms,
-  dtdnamethylation,
-  dtgeneexpression,
-  dtmetaboliteintensity,
-  dtproteomeabundance,
-  dtssgsea
-} from "./chunk-XYFDBYOY.js";
-
-// ../shared/utils/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 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 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",
-  multivalue: "Multi Value",
-  singleCellGeneExpression: "Single Cell, Gene Expression",
-  singleCellCellType: "Single Cell, Cell Type",
-  snplocus: "SNP Locus",
-  snp: "SNP",
-  snplst: "SNP List",
-  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,
-  TermTypes,
-  dtTermTypes,
-  TermTypes2Dt,
-  typeGroup,
-  numericTypes,
-  isSingleCellTerm,
-  isNumericTerm,
-  isCategoricalTerm,
-  isDictionaryType,
-  isNonDictionaryType,
-  isNumTermCollection,
-  equals,
-  termType2label,
-  getDateFromNumber,
-  getDateStrFromNumber
-};
-//# sourceMappingURL=chunk-6ITDJ5UR.js.map

package/dist/chunk-6ITDJ5UR.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/terms.js"],
-  "sourcesContent": ["import {\n\tdtgeneexpression,\n\tdtssgsea,\n\tdtdnamethylation,\n\tdtmetaboliteintensity,\n\tdtproteomeabundance,\n\tTermTypeGroups,\n\tdtTerms,\n} from \"./common.js\"\nimport { TermTypeGroups as TermTypeGroups2 } from \"./common.js\"\nconst ROOT_SAMPLE_TYPE = 1\nconst DEFAULT_SAMPLE_TYPE = 2\nconst NumericModes = {\n\tcontinuous: \"continuous\",\n\tdiscrete: \"discrete\",\n}\nconst CATEGORICAL = \"categorical\"\nconst CONDITION = \"condition\"\nconst DATE = \"date\"\nconst DNA_METHYLATION = \"dnaMethylation\"\nconst FLOAT = \"float\"\nconst GENE_VARIANT = \"geneVariant\"\nconst GENE_EXPRESSION = \"geneExpression\"\nconst ISOFORM_EXPRESSION = \"isoformExpression\"\nconst INTEGER = \"integer\"\nconst METABOLITE_INTENSITY = \"metaboliteIntensity\"\nconst MULTIVALUE = \"multivalue\"\nconst SAMPLELST = \"samplelst\"\nconst SINGLECELL_CELLTYPE = \"singleCellCellType\"\nconst SINGLECELL_GENE_EXPRESSION = \"singleCellGeneExpression\"\nconst SNP = \"snp\"\nconst SNP_LIST = \"snplst\"\nconst SNP_LOCUS = \"snplocus\"\nconst SSGSEA = \"ssGSEA\"\nconst SURVIVAL = \"survival\"\nconst TERM_COLLECTION = \"termCollection\"\nconst PROTEOME_ABUNDANCE = \"proteomeAbundance\"\nconst TermTypes = {\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}\nconst dtTermTypes = new Set(dtTerms.map((t) => t.type))\nfor (const dtTermType of dtTermTypes) {\n\tTermTypes[dtTermType.toUpperCase()] = dtTermType\n}\nconst 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}\nconst 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}\nconst nonDictTypes = /* @__PURE__ */ 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])\nfor (const dtTermType of dtTermTypes) {\n\tnonDictTypes.add(TermTypes[dtTermType.toUpperCase()])\n}\nconst numericTypes = /* @__PURE__ */ 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])\nconst annoNumericTypes = /* @__PURE__ */ new Set([INTEGER, FLOAT, DATE])\nconst categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP])\nconst singleCellTerms = /* @__PURE__ */ new Set([\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n])\nfunction isSingleCellTerm(term) {\n\tif (!term) return false\n\treturn singleCellTerms.has(term.type)\n}\nfunction isNumericTerm(term) {\n\tif (!term) return false\n\treturn numericTypes.has(term.type)\n}\nfunction isCategoricalTerm(term) {\n\tif (!term) return false\n\treturn categoricalTypes.has(term.type)\n}\nfunction isDictionaryType(type) {\n\treturn !isNonDictionaryType(type)\n}\nfunction isNonDictionaryType(type) {\n\tif (!type) throw new Error(\"Type is not defined\")\n\treturn nonDictTypes.has(type)\n}\nfunction isNumTermCollection(term) {\n\tif (!term || !term.type) throw new Error(\"Term or term type is not defined\")\n\treturn term.type === TERM_COLLECTION\n}\nfunction equals(t1, t2) {\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\n\tif (\n\t\tisDictionaryType(t1.type) &&\n\t\tisDictionaryType(t2.type) &&\n\t\tt1.type != SAMPLELST\n\t)\n\t\treturn 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 (\n\t\t\t\tt1.gene == t2.gene ||\n\t\t\t\t(t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop)\n\t\t\t)\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\t\tdefault:\n\t\t\treturn false\n\t}\n}\nfunction getBin(lst, value) {\n\tlet bin = lst.findIndex(\n\t\t(b) =>\n\t\t\t(b.startunbounded && value < b.stop) ||\n\t\t\t(b.startunbounded && b.stopinclusive && value == b.stop)\n\t)\n\tif (bin == -1)\n\t\tbin = lst.findIndex(\n\t\t\t(b) =>\n\t\t\t\t(b.stopunbounded && value > b.start) ||\n\t\t\t\t(b.stopunbounded && b.startinclusive && value == b.start)\n\t\t)\n\tif (bin == -1)\n\t\tbin = lst.findIndex(\n\t\t\t(b) =>\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}\nfunction getSampleType(term, ds) {\n\tif (!term) return null\n\tif (term.type && isNonDictionaryType(term.type)) return DEFAULT_SAMPLE_TYPE\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\treturn DEFAULT_SAMPLE_TYPE\n}\nfunction getParentType(types, ds) {\n\tif (Object.keys(ds.cohort.termdb.sampleTypes).length == 0) return null\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\n\t\tif (ids.includes(typeObj.parent_id)) continue\n\t\telse return typeObj.parent_id\n\t}\n\treturn null\n}\nconst typeMap = {\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\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\ttermCollection: \"Term Collection\",\n}\nfunction termType2label(type) {\n\treturn typeMap[type] || \"Unknown term type\"\n}\nfunction getDateFromNumber(value) {\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}\nconst oneDayTime = 24 * 60 * 60 * 1e3\nfunction getDateStrFromNumber(value) {\n\tconst date = getDateFromNumber(value)\n\treturn date.toLocaleDateString(\"en-US\", {\n\t\tyear: \"numeric\",\n\t\tmonth: \"long\",\n\t})\n}\nfunction getNumberFromDateStr(str) {\n\tconst date = new Date(str)\n\treturn getNumberFromDate(date)\n}\nfunction getNumberFromDate(date) {\n\tconst year = date.getFullYear()\n\tconst january1st = 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}\nfunction getDaysInYear(year) {\n\tconst isLeap = new Date(year, 1, 29).getMonth() === 1\n\tconst days = isLeap ? 366 : 365\n\treturn days\n}\nexport {\n\tCATEGORICAL,\n\tCONDITION,\n\tDATE,\n\tDEFAULT_SAMPLE_TYPE,\n\tDNA_METHYLATION,\n\tFLOAT,\n\tGENE_EXPRESSION,\n\tGENE_VARIANT,\n\tINTEGER,\n\tISOFORM_EXPRESSION,\n\tMETABOLITE_INTENSITY,\n\tMULTIVALUE,\n\tNumericModes,\n\tPROTEOME_ABUNDANCE,\n\tROOT_SAMPLE_TYPE,\n\tSAMPLELST,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tSSGSEA,\n\tSURVIVAL,\n\tTERM_COLLECTION,\n\tTermTypeGroups2 as TermTypeGroups,\n\tTermTypes,\n\tTermTypes2Dt,\n\tannoNumericTypes,\n\tdtTermTypes,\n\tequals,\n\tgetBin,\n\tgetDateFromNumber,\n\tgetDateStrFromNumber,\n\tgetDaysInYear,\n\tgetNumberFromDate,\n\tgetNumberFromDateStr,\n\tgetParentType,\n\tgetSampleType,\n\tisCategoricalTerm,\n\tisDictionaryType,\n\tisNonDictionaryType,\n\tisNumTermCollection,\n\tisNumericTerm,\n\tisSingleCellTerm,\n\tnumericTypes,\n\ttermType2label,\n\ttypeGroup,\n}\n"],
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-  "names": []
-}

package/dist/chunk-6VLA5NEW.js

@@ -1,335 +0,0 @@
-import {
-  storeInit
-} from "./chunk-ZTKQLABY.js";
-import {
-  summaryInit
-} from "./chunk-LRMV5DNW.js";
-import {
-  navInit
-} from "./chunk-NV5XWADG.js";
-import {
-  AppBase,
-  downloadSVGsAsPdf,
-  filterRxCompInit,
-  newSandboxDiv,
-  sayerror,
-  vocabInit
-} from "./chunk-NVB7MQLH.js";
-import {
-  importPlot
-} from "./chunk-4JON7TLI.js";
-import {
-  Menu
-} from "./chunk-A6TQGNDQ.js";
-import {
-  AppApi,
-  getCompInit,
-  multiInit
-} from "./chunk-MVTCBVSX.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-
-// mass/plot.js
-var MassPlot = class _MassPlot {
-  static type = "plot";
-  constructor(opts) {
-    this.type = _MassPlot.type;
-    setRenderers(this);
-    this.initUi(opts);
-  }
-  reactsTo(action) {
-    if (action.type.includes("cache_termq")) return true;
-    if (action.type.endsWith("_group")) return true;
-    if (action.type.startsWith("plot_")) {
-      return action.id === this.id || action.id == this.parentId || action.config?.parentId === this.id || action.parentId === this.id;
-    }
-    if (action.type.startsWith("filter")) return true;
-    if (action.type.startsWith("cohort")) return true;
-    if (action.type == "app_refresh") return true;
-    if (action.type.endsWith("customTerm")) return true;
-  }
-  // !!! NOTE: This getState() method is reused by the plot-specific recover component.
-  // When logging something within getState, it may have been called by either the plot or recover instance
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      termfilter: appState.termfilter,
-      config,
-      groups: appState.groups,
-      // quick fix to skip history tracking as needed
-      _scope_: appState._scope_
-    };
-  }
-  async main() {
-    this.dom.errdiv.style("display", "none").style("background-color", "rgba(255,100,100,0.2)").html("");
-    if (!this.components) await this.setComponents(this.opts);
-  }
-  async setComponents(opts) {
-    const _ = await importPlot(opts.chartType);
-    const promises = {
-      // recover: recoverInit({
-      // 	app: this.app,
-      // 	holder: this.dom.localRecoverDiv,
-      // 	getState: appState => this.getState(appState),
-      // 	reactsTo: action =>
-      // 		action.id == this.id &&
-      // 		(action.type == 'plot_edit' || action.type == 'plot_nestedEdits') &&
-      // 		action._track_ != 'none',
-      // 	plot_id: this.id,
-      // 	maxHistoryLen: 10,
-      // 	hideLabel: true
-      // }),
-      chart: _.componentInit({
-        app: this.app,
-        holder: this.dom.viz,
-        header: this.dom.paneTitleDiv,
-        id: this.id,
-        plotDiv: select_default(this.dom.holder.app_div.node().parentNode),
-        /******* reason for passing plotDiv to chart ********
-        				- this plot instance may allow to launch a new plot as a persistent sandbox
-        				  inside mass plotDiv, maintaining the uniform plot appearance despite it's ad-hoc
-        				  the new plot is not a formal mass plot type, and cannot be done via app.dispatch()
-        				  thus the need to directly access plotDiv
-        				- example: mds3 tk from genome browser can launch disco etc
-        				- having access to plotDiv may offer flexibility for the plot to do stuff
-        
-        				since plot.js has no access to mass app .dom.plotDiv in which all apps are shown,
-        				this workarounds gets the parent node of sandbox.app_div which is app.dom.plotDiv
-        				*/
-        getFilterImage: async () => this.components.filter.getFilterImage()
-      })
-    };
-    if (!this.state.config.hidePlotFilter)
-      promises.filter = filterRxCompInit({
-        app: this.app,
-        vocabApi: this.app.vocabApi,
-        parentId: this.id,
-        holder: this.dom.filterDiv,
-        hideLabel: true,
-        emptyLabel: "+Add new filter",
-        callback: (filter) => {
-          this.app.dispatch({
-            id: this.id,
-            type: "plot_edit",
-            config: { filter }
-          });
-        }
-      });
-    this.components = await multiInit(promises);
-  }
-  destroy() {
-    this.dom.holder.app_div.selectAll("*").remove();
-    this.dom.holder.app_div.remove();
-    for (const key in this.dom) {
-      delete this.dom[key];
-    }
-  }
-};
-var plotInit = getCompInit(MassPlot);
-function setRenderers(self) {
-  self.initUi = function(opts) {
-    const holder = opts.holder;
-    opts.holder.app_div.attr("data-testid", "sjpp-massplot-sandbox-" + opts.chartType);
-    holder.header.style("padding", 0);
-    try {
-      self.dom = {
-        tip: new Menu({ padding: "0px" }),
-        holder,
-        paneTitleDiv: holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px").style("vertical-align", "sub"),
-        localRecoverDiv: holder.header.append("div").style("display", "inline-block"),
-        filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9),
-        body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
-        // will hold no data notice or the page title in multichart views
-        errdiv: holder.body.append("div").style("display", "none").style("padding", "5px").style("background-color", "rgba(255,100,100,0.2)"),
-        // dom.viz will hold the rendered view
-        viz: holder.body.append("div")
-      };
-    } catch (e) {
-      self.dom.errdiv.style("display", "none").text(e);
-    }
-  };
-}
-
-// mass/app.ts
-var MassApp = class extends AppBase {
-  // expected class-specific props
-  constructor(opts, api) {
-    super(opts);
-    this.components = {};
-    this.wasDestroyed = false;
-    this.api = api;
-    if (opts.addLoginCallback) {
-      opts.addLoginCallback(() => this.api.dispatch({ type: "app_refresh" }));
-    }
-    this.type = "app";
-    this.dom = {
-      holder: opts.holder,
-      // do not modify holder style
-      topbar: opts.holder.append("div"),
-      errdiv: opts.holder.append("div"),
-      plotDiv: opts.holder.append("div")
-    };
-    this.plotIdToSandboxId = {};
-  }
-  static {
-    this.type = "app";
-  }
-  async preApiFreeze(api) {
-    try {
-      api.tip = new Menu({ padding: "5px" });
-      api.tip.d.on("keyup", (event) => {
-        if (event.key == "Escape") api.tip.hide();
-      });
-      api.printError = (e) => this.printError(e);
-      api.vocabApi = await vocabInit({
-        app: api,
-        state: { vocab: this.opts.state.vocab },
-        fetchOpts: this.opts.fetchOpts,
-        getDatasetAccessToken: this.opts.getDatasetAccessToken
-      });
-      api.hasWebGL = function() {
-        try {
-          const canvas = document.createElement("canvas");
-          return !!(window.WebGLRenderingContext && (canvas.getContext("webgl") || canvas.getContext("experimental-webgl")));
-        } catch (_) {
-          return false;
-        }
-      };
-      this.opts.state.vocab = api.vocabApi.vocab;
-    } catch (e) {
-      console.log(`preApiFreeze error`, e);
-      throw e;
-    }
-  }
-  async init() {
-    try {
-      const debounceInterval = "debounceInterval" in this.opts ? this.opts.debounceInterval : 0;
-      const embeddedSessionState = this.opts.embeddedSessionState;
-      if (embeddedSessionState) {
-        Object.assign(this.opts.state, embeddedSessionState);
-      }
-      this.store = await storeInit({ app: this.api, state: this.opts.state, debounceInterval });
-      this.state = await this.store.copyState();
-      this.components = {};
-      if (this.state.nav.header_mode != "hidden") {
-        this.components.nav = await navInit({
-          app: this.api,
-          holder: this.dom.topbar,
-          header_mode: this.state && this.state.nav && this.state.nav.header_mode,
-          vocab: this.state.vocab,
-          massSessionDuration: this.state.termdbConfig.massSessionDuration,
-          // this.opts.massSessionDuration
-          pkgver: this.opts.pkgver,
-          downloadPlots: () => {
-            this.downloadPlots();
-          }
-        });
-      }
-      this.components.plots = {};
-      if (this.opts.app?.doNotAwaitInitRender) {
-        this.api.dispatch();
-      } else {
-        await this.api.dispatch();
-      }
-    } catch (e) {
-      this.printError(e);
-      throw e;
-    }
-  }
-  async main() {
-    await this.api.vocabApi.main();
-    this.dom.plotDiv?.style(
-      "display",
-      this.state.nav?.header_mode != "hidden" && this.state.nav?.activeTab == 0 ? "none" : "block"
-    );
-    const newPlots = {};
-    let sandbox;
-    for (const plot of this.state.plots) {
-      if (plot.parentId) continue;
-      if (this.components.plots && !(plot.id in this.components.plots)) {
-        sandbox = newSandboxDiv(this.dom.plotDiv, {
-          close: () => {
-            this.api.dispatch({
-              type: "plot_delete",
-              id: plot.id
-            });
-          },
-          plotId: plot.id,
-          beforePlotId: plot.insertBefore || null,
-          style: {
-            width: "98.5%"
-          }
-        });
-        if (plot.chartType == "summary")
-          newPlots[plot.id] = summaryInit(Object.assign({ app: this.api, holder: sandbox }, plot));
-        else newPlots[plot.id] = plotInit(Object.assign({ app: this.api, holder: sandbox }, plot));
-      }
-    }
-    const numNewPlots = Object.keys(newPlots).length;
-    if (numNewPlots) {
-      await Promise.all(Object.values(newPlots));
-      for (const plotId in newPlots) {
-        this.components.plots[plotId] = await newPlots[plotId];
-      }
-    }
-    for (const plotId in this.components.plots) {
-      if (!this.state.plots.find((p) => p.id === plotId)) {
-        this.components.plots[plotId].destroy();
-        delete this.components.plots[plotId];
-      }
-    }
-  }
-  printError(e) {
-    const errdiv = e.errdiv || this.dom.errdiv;
-    if (errdiv) errdiv.style("display", "").html("").style("background-color", "");
-    sayerror(errdiv || this.opts.holder, "Error: " + (e.message || e.error || e));
-    if (e.stack) console.log(e.stack);
-    this.bus.emit("error");
-    if (this.opts?.debug) console.trace("Trace from MassApp.printError() call");
-  }
-  skipPrevActionAbort(action) {
-    if (!action) return false;
-    if (action.type.startsWith("filter")) return false;
-    if (action.type.startsWith("cohort")) return false;
-    if (action.type == "app_refresh") {
-      if (action.subactions) {
-        return action.subactions.find((a) => a.type.startsWith("filter") || a.type.startsWith("cohort")) ? false : true;
-      }
-    }
-    return true;
-  }
-  async downloadPlots() {
-    const chartImagesAll = [];
-    let i = 1;
-    const values = Object.values(this.components.plots);
-    for (const plot of values) {
-      const chart = plot.type == "plot" ? plot.getComponents("chart") : plot;
-      const chartImages = chart.getChartImages ? chart.getChartImages() : null;
-      if (!chartImages) {
-        console.log(`The ${chart.type} does not support downloading images yet`);
-        continue;
-      }
-      for (const chartImage of chartImages) {
-        if (values.length > 1) chartImage.name = `${i}. ${chartImage.name}`;
-        chartImagesAll.push(chartImage);
-      }
-      i++;
-    }
-    if (chartImagesAll.length > 0) {
-      const filters = [];
-      const globalFilterImg = await this.components.nav.getComponents("filter").getFilterImage();
-      if (globalFilterImg) filters.push(globalFilterImg);
-      downloadSVGsAsPdf(chartImagesAll, "plots", "landscape", filters);
-    } else alert("No chart images available for download");
-  }
-};
-var appInit = AppApi.getInitFxn(MassApp);
-
-export {
-  appInit
-};
-//# sourceMappingURL=chunk-6VLA5NEW.js.map