@sjcrh/proteinpaint-shared 2.187.0 → 2.188.1

package/dist/src/termdb.usecase.js

@@ -0,0 +1,239 @@
+import {
+  TermTypes,
+  isNumericTerm,
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION,
+  ISOFORM_EXPRESSION
+} from "./terms.js";
+const graphableTypes = /* @__PURE__ */ new Set([
+  "categorical",
+  "integer",
+  "float",
+  "condition",
+  "survival",
+  "snplst",
+  "snplocus",
+  "geneVariant",
+  "samplelst",
+  "geneExpression",
+  ISOFORM_EXPRESSION,
+  "dtcnv",
+  "dtsnvindel",
+  "dtfusion",
+  "dtsv",
+  "date",
+  TermTypes.SSGSEA,
+  TermTypes.DNA_METHYLATION,
+  TermTypes.METABOLITE_INTENSITY,
+  TermTypes.PROTEOME_ABUNDANCE,
+  SINGLECELL_GENE_EXPRESSION,
+  SINGLECELL_CELLTYPE,
+  TermTypes.SNP,
+  TermTypes.TERM_COLLECTION
+]);
+function isUsableTerm(term, _usecase, termdbConfig, ds) {
+  const usecase = _usecase || {};
+  if (typeof ds?.usecase?.[usecase.target] == "function") {
+    return ds.usecase[usecase.target](term, usecase);
+  }
+  const uses = /* @__PURE__ */ new Set();
+  const child_types = term.child_types || [];
+  switch (usecase.target) {
+    case "barchart":
+    case "violin":
+    case "boxplot":
+    case "summary":
+      if (term.type && term.type !== "survival") uses.add("plot");
+      if (hasAllowedChildTypes(child_types, ["survival"])) uses.add("branch");
+      return uses;
+    case "summaryInput":
+      if (usecase.detail === "term2" || usecase.detail == "term0") {
+        if (term.type && term.type !== "survival") uses.add("plot");
+        if (hasAllowedChildTypes(child_types, ["survival"])) uses.add("branch");
+        return uses;
+      } else {
+        if (graphableTypes.has(term.type)) uses.add("plot");
+        if (!term.isleaf) uses.add("branch");
+        return uses;
+      }
+    case "matrix":
+      if (term.type) uses.add("plot");
+      if (!term.isleaf) uses.add("branch");
+      return uses;
+    case "table":
+      if (usecase.detail == "term") uses.add("plot");
+      if (child_types.length > 1) uses.add("branch");
+      return uses;
+    case "sampleScatter":
+      if (usecase.detail == "numeric") {
+        if (isNumericTerm(term)) {
+          uses.add("plot");
+        }
+        if (hasNumericChild(child_types)) uses.add("branch");
+      } else {
+        if (graphableTypes.has(term.type)) uses.add("plot");
+        if (!term.isleaf) uses.add("branch");
+      }
+      return uses;
+    case "runChart2":
+      if (usecase.detail == "date" || usecase.detail == "xtw") {
+        if (term.type == "date") {
+          uses.add("plot");
+        }
+        if (child_types.includes("date")) uses.add("branch");
+      } else if (usecase.detail == "numeric") {
+        if (isNumericTerm(term) && term.type != "date") {
+          uses.add("plot");
+        }
+        if (hasNumericChild(child_types)) uses.add("branch");
+      } else {
+        if (graphableTypes.has(term.type)) uses.add("plot");
+        if (!term.isleaf) uses.add("branch");
+      }
+      return uses;
+    case "numericDictTermCluster":
+      if (!usecase.detail?.exclude?.includes(term.id)) {
+        if (isNumericTerm(term)) {
+          uses.add("plot");
+        }
+        if (hasNumericChild(child_types)) {
+          uses.add("branch");
+        }
+      }
+      return uses;
+    case "termCollections":
+      if (usecase.detail?.termIds?.includes(term.id)) uses.add("plot");
+      if (usecase.detail?.branchIds?.includes(term.id)) uses.add("branch");
+      return uses;
+    case "profileForms":
+      if (!term.isleaf) {
+        const ancestors = term.id.split("__").length;
+        if (ancestors == 3) {
+          uses.add("plot");
+        } else if (ancestors < 3) uses.add("branch");
+      }
+      return uses;
+    case "profileForms2": {
+      if (term.isleaf) return uses;
+      const allowed = termdbConfig?.plotConfigByCohort?.[usecase.cohort]?.profileForms2?.domains;
+      if (!allowed) return uses;
+      const ancestors = term.id.split("__").length;
+      const subtype = usecase.subtype;
+      if (ancestors == 3) {
+        if (allowed.find((d) => d.id === term.id)?.plotTypes?.includes(subtype)) uses.add("plot");
+      } else if (ancestors < 3) {
+        const prefix = term.id + "__";
+        if (allowed.some((d) => d.id.startsWith(prefix) && d.plotTypes.includes(subtype))) {
+          uses.add("branch");
+        }
+      }
+      return uses;
+    }
+    // case 'boxplot':
+    // 	if (term.type == 'float' || term.type == 'integer') uses.add('plot')
+    // 	if (usecase.detail === 'term2' && hasNumericChild(child_types)) uses.add('branch')
+    // 	return uses
+    case "cuminc":
+      if (usecase.detail == "term") {
+        if (term.type == "condition") uses.add("plot");
+        if (child_types.includes("condition")) uses.add("branch");
+        return uses;
+      }
+      if (usecase.detail === "term2" || usecase.detail == "term0") {
+        if (term.type && term.type != "condition" && term.type != "survival") uses.add("plot");
+        if (hasAllowedChildTypes(child_types, ["condition", "survival"])) uses.add("branch");
+        return uses;
+      }
+      return uses;
+    case "survival":
+      if (usecase.detail == "term") {
+        if (term.type == "survival") uses.add("plot");
+        if (child_types.includes("survival")) uses.add("branch");
+        return uses;
+      }
+      if (usecase.detail === "term2" || usecase.detail == "term0") {
+        if (term.type && term.type != "survival") uses.add("plot");
+        if (hasAllowedChildTypes(child_types, ["survival"])) uses.add("branch");
+        return uses;
+      }
+      return uses;
+    case "regression":
+      if (usecase.detail == "outcome") {
+        if (usecase.regressionType == "linear") {
+          if (term.type == "float" || term.type == "integer") uses.add("plot");
+          if (hasNumericChild(child_types)) uses.add("branch");
+          return uses;
+        }
+        if (usecase.regressionType == "logistic") {
+          if (term.type && term.type != "survival") uses.add("plot");
+          if (hasAllowedChildTypes(child_types, ["survival"])) uses.add("branch");
+          return uses;
+        } else if (usecase.regressionType == "cox") {
+          if (term.type == "condition" || term.type == "survival") uses.add("plot");
+          if (child_types.includes("condition") || child_types.includes("survival")) uses.add("branch");
+          return uses;
+        }
+      }
+      if (usecase.detail == "independent") {
+        if (term.type == "float" || term.type == "integer" || term.type == "categorical" || term.type == "samplelst")
+          uses.add("plot");
+        if (hasChildTypes(child_types, ["categorical", "float", "integer"])) uses.add("branch");
+        return uses;
+      }
+      return uses;
+    case "filter": {
+      const exlst = termdbConfig?.excludedTermtypeByTarget?.filter;
+      if (exlst) {
+        if (graphableTypes.has(term.type) && !exlst.includes(term.type)) uses.add("plot");
+        if (child_types.find((t) => !exlst.includes(t))) uses.add("branch");
+        return uses;
+      }
+      if (graphableTypes.has(term.type)) uses.add("plot");
+      if (!term.isleaf) uses.add("branch");
+      return uses;
+    }
+    case "correlationVolcano":
+      if (usecase.detail == "numeric") {
+        if (isNumericTerm(term)) {
+          uses.add("plot");
+        }
+        if (hasNumericChild(child_types)) uses.add("branch");
+      } else {
+        if (graphableTypes.has(term.type)) uses.add("plot");
+        if (!term.isleaf) uses.add("branch");
+      }
+      return uses;
+    case "proteinView":
+      if (term.type == TermTypes.PROTEOME_ABUNDANCE) uses.add("plot");
+      if (child_types.includes(TermTypes.PROTEOME_ABUNDANCE)) uses.add("branch");
+      return uses;
+    default:
+      if (graphableTypes.has(term.type)) uses.add("plot");
+      if (!term.isleaf) uses.add("branch");
+      return uses;
+  }
+}
+function hasAllowedChildTypes(child_types, excluded_types) {
+  if (!child_types.length) {
+    return false;
+  }
+  if (!excluded_types?.length) {
+    return true;
+  }
+  if (child_types.some((type) => !excluded_types.includes(type))) {
+    return true;
+  }
+}
+function hasNumericChild(child_types) {
+  return child_types.includes("float") || child_types.includes("integer");
+}
+function hasChildTypes(child_types, expected_types) {
+  for (const a of expected_types) {
+    if (child_types.includes(a)) return true;
+  }
+}
+export {
+  graphableTypes,
+  isUsableTerm
+};
+//# sourceMappingURL=termdb.usecase.js.map

package/dist/src/termdb.usecase.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/termdb.usecase.js"],
+  "sourcesContent": ["import {\n\tTermTypes,\n\tisNumericTerm,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tISOFORM_EXPRESSION\n} from './terms.js'\n\nexport const graphableTypes = new Set([\n\t'categorical',\n\t'integer',\n\t'float',\n\t'condition',\n\t'survival',\n\t'snplst',\n\t'snplocus',\n\t'geneVariant',\n\t'samplelst',\n\t'geneExpression',\n\tISOFORM_EXPRESSION,\n\t'dtcnv',\n\t'dtsnvindel',\n\t'dtfusion',\n\t'dtsv',\n\t'date',\n\tTermTypes.SSGSEA,\n\tTermTypes.DNA_METHYLATION,\n\tTermTypes.METABOLITE_INTENSITY,\n\tTermTypes.PROTEOME_ABUNDANCE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tSINGLECELL_CELLTYPE,\n\tTermTypes.SNP,\n\tTermTypes.TERM_COLLECTION\n])\n\n/*\nisUsableTerm() will\n\n\t- centralize the \"allowed term\" logic\n\twhich can be intricate or dataset-specific \n\tfor certain terms or contexts\n\t- make it easy to handle new term types\n\nArguments:\n\n\tterm {}\n\t\t.type: 'categorical', etc.\n\t\t.child_types: []\n\t\n\t_usecase {}\n\t\t.target (REQUIRED): 'barchart', 'regression', etc\n\t\t\t- used as a switch-case \"router\" for additional use-specific logic\n\t\t\t- other parameters, if applicable, are described in the route \"handler\" \n\t\t.detail \n\t\t  - a more specific detailed use case\n\t\n\n\ttermdbConfig\n\t\toptional. provides ds overrides on default rules via excludedTermtypeByTarget. for use on client\n\n\tds\n\t\toptional. provides ds overrides when the function runs on backend\n\t\tserver-side dataset object that can supply overrides (in the form of functions) to the use case logic,\n\t\tfor example, to apply role-based allowed term uses or performance-related restrictions\n\t\tto ancestor terms when a use case aggregates too many data points for a given chart type\n\nReturns\n\n\ta Set{} with zero or more of the following strings:\n\t- 'plot' if the term can be used in a plot chartType\n\t- 'branch' if the term can be used only as an expandable tree branch, but not in a plot\n\t- an empty Set means that the term has no valid uses, i.e, it cannot be used either for plotting or as a tree branch\n*/\nexport function isUsableTerm(term, _usecase, termdbConfig, ds) {\n\tconst usecase = _usecase || {}\n\n\t// may apply dataset specific override filter for a use case\n\tif (typeof ds?.usecase?.[usecase.target] == 'function') {\n\t\treturn ds.usecase[usecase.target](term, usecase)\n\t}\n\n\t// if (term.isprivate && !user.roleCanUse(term)) return false\n\n\tconst uses = new Set()\n\t// note: expects term.child_types to be null if term.isleaf == true\n\tconst child_types = term.child_types || []\n\t// default handling\n\tswitch (usecase.target) {\n\t\tcase 'barchart':\n\t\tcase 'violin':\n\t\tcase 'boxplot':\n\t\tcase 'summary':\n\t\t\tif (term.type && term.type !== 'survival') uses.add('plot')\n\t\t\tif (hasAllowedChildTypes(child_types, ['survival'])) uses.add('branch')\n\t\t\treturn uses\n\n\t\tcase 'summaryInput':\n\t\t\tif (usecase.detail === 'term2' || usecase.detail == 'term0') {\n\t\t\t\tif (term.type && term.type !== 'survival') uses.add('plot')\n\t\t\t\tif (hasAllowedChildTypes(child_types, ['survival'])) uses.add('branch')\n\t\t\t\treturn uses\n\t\t\t} else {\n\t\t\t\tif (graphableTypes.has(term.type)) uses.add('plot')\n\t\t\t\tif (!term.isleaf) uses.add('branch')\n\t\t\t\treturn uses\n\t\t\t}\n\n\t\tcase 'matrix':\n\t\t\tif (term.type) uses.add('plot')\n\t\t\tif (!term.isleaf) uses.add('branch')\n\t\t\treturn uses\n\n\t\tcase 'table':\n\t\t\tif (usecase.detail == 'term') uses.add('plot')\n\t\t\tif (child_types.length > 1) uses.add('branch')\n\t\t\treturn uses\n\n\t\tcase 'sampleScatter':\n\t\t\tif (usecase.detail == 'numeric') {\n\t\t\t\tif (isNumericTerm(term)) {\n\t\t\t\t\tuses.add('plot')\n\t\t\t\t}\n\t\t\t\tif (hasNumericChild(child_types)) uses.add('branch')\n\t\t\t}\n\t\t\t// Commenting out for now. May need later for another single\n\t\t\t// cell term. Revisit logic at that time.\n\t\t\t// else if (usecase?.specialCase?.type == 'singleCell') {\n\t\t\t// \t\tif (term.type && term.type.startsWith('singleCell')) {\n\t\t\t// \t\t\tif (term.plot && term.plot == usecase.specialCase?.config.name) {\n\t\t\t// \t\t\t\tuses.add('plot')\n\t\t\t// \t\t\t}\n\t\t\t// \t\t}\n\t\t\t// }\n\t\t\telse {\n\t\t\t\tif (graphableTypes.has(term.type)) uses.add('plot')\n\t\t\t\tif (!term.isleaf) uses.add('branch')\n\t\t\t}\n\t\t\treturn uses\n\t\tcase 'runChart2':\n\t\t\tif (usecase.detail == 'date' || usecase.detail == 'xtw') {\n\t\t\t\tif (term.type == 'date') {\n\t\t\t\t\tuses.add('plot')\n\t\t\t\t}\n\t\t\t\tif (child_types.includes('date')) uses.add('branch')\n\t\t\t} else if (usecase.detail == 'numeric') {\n\t\t\t\tif (isNumericTerm(term) && term.type != 'date') {\n\t\t\t\t\tuses.add('plot')\n\t\t\t\t}\n\t\t\t\tif (hasNumericChild(child_types)) uses.add('branch')\n\t\t\t} else {\n\t\t\t\tif (graphableTypes.has(term.type)) uses.add('plot')\n\t\t\t\tif (!term.isleaf) uses.add('branch')\n\t\t\t}\n\t\t\treturn uses\n\n\t\tcase 'numericDictTermCluster':\n\t\t\tif (!usecase.detail?.exclude?.includes(term.id)) {\n\t\t\t\tif (isNumericTerm(term)) {\n\t\t\t\t\tuses.add('plot')\n\t\t\t\t}\n\t\t\t\tif (hasNumericChild(child_types)) {\n\t\t\t\t\tuses.add('branch')\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn uses\n\n\t\tcase 'termCollections':\n\t\t\tif (usecase.detail?.termIds?.includes(term.id)) uses.add('plot')\n\t\t\tif (usecase.detail?.branchIds?.includes(term.id)) uses.add('branch')\n\t\t\treturn uses\n\n\t\tcase 'profileForms':\n\t\t\tif (!term.isleaf) {\n\t\t\t\tconst ancestors = term.id.split('__').length //depends on using the __ naming convension!\n\t\t\t\tif (ancestors == 3) {\n\t\t\t\t\t// 3rd level term is a domain, we show the templates associated to this domain\n\t\t\t\t\tuses.add('plot')\n\t\t\t\t} else if (ancestors < 3) uses.add('branch')\n\t\t\t}\n\t\t\treturn uses\n\n\t\tcase 'profileForms2': {\n\t\t\t// Picker (forms2.ts makeChartBtnMenu) sets usecase.cohort + usecase.subtype.\n\t\t\t// Reads the per-cohort domains list directly from the dataset config at\n\t\t\t// plotConfigByCohort[cohort].profileForms2.domains \u2014 each entry is { id, plotTypes }.\n\t\t\tif (term.isleaf) return uses\n\t\t\tconst allowed = termdbConfig?.plotConfigByCohort?.[usecase.cohort]?.profileForms2?.domains\n\t\t\tif (!allowed) return uses\n\t\t\tconst ancestors = term.id.split('__').length\n\t\t\tconst subtype = usecase.subtype\n\t\t\tif (ancestors == 3) {\n\t\t\t\tif (allowed.find(d => d.id === term.id)?.plotTypes?.includes(subtype)) uses.add('plot')\n\t\t\t} else if (ancestors < 3) {\n\t\t\t\tconst prefix = term.id + '__'\n\t\t\t\tif (allowed.some(d => d.id.startsWith(prefix) && d.plotTypes.includes(subtype))) {\n\t\t\t\t\tuses.add('branch')\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn uses\n\t\t}\n\n\t\t// case 'boxplot':\n\t\t// \tif (term.type == 'float' || term.type == 'integer') uses.add('plot')\n\t\t// \tif (usecase.detail === 'term2' && hasNumericChild(child_types)) uses.add('branch')\n\t\t// \treturn uses\n\n\t\tcase 'cuminc':\n\t\t\tif (usecase.detail == 'term') {\n\t\t\t\tif (term.type == 'condition') uses.add('plot')\n\t\t\t\tif (child_types.includes('condition')) uses.add('branch')\n\t\t\t\treturn uses\n\t\t\t}\n\t\t\tif (usecase.detail === 'term2' || usecase.detail == 'term0') {\n\t\t\t\tif (term.type && term.type != 'condition' && term.type != 'survival') uses.add('plot')\n\t\t\t\tif (hasAllowedChildTypes(child_types, ['condition', 'survival'])) uses.add('branch')\n\t\t\t\treturn uses\n\t\t\t}\n\t\t\treturn uses\n\n\t\tcase 'survival':\n\t\t\tif (usecase.detail == 'term') {\n\t\t\t\tif (term.type == 'survival') uses.add('plot')\n\t\t\t\tif (child_types.includes('survival')) uses.add('branch')\n\t\t\t\treturn uses\n\t\t\t}\n\t\t\tif (usecase.detail === 'term2' || usecase.detail == 'term0') {\n\t\t\t\tif (term.type && term.type != 'survival') uses.add('plot')\n\t\t\t\tif (hasAllowedChildTypes(child_types, ['survival'])) uses.add('branch')\n\t\t\t\treturn uses\n\t\t\t}\n\t\t\treturn uses\n\n\t\tcase 'regression':\n\t\t\tif (usecase.detail == 'outcome') {\n\t\t\t\tif (usecase.regressionType == 'linear') {\n\t\t\t\t\tif (term.type == 'float' || term.type == 'integer') uses.add('plot')\n\t\t\t\t\tif (hasNumericChild(child_types)) uses.add('branch')\n\t\t\t\t\treturn uses\n\t\t\t\t}\n\t\t\t\tif (usecase.regressionType == 'logistic') {\n\t\t\t\t\tif (term.type && term.type != 'survival') uses.add('plot')\n\t\t\t\t\tif (hasAllowedChildTypes(child_types, ['survival'])) uses.add('branch')\n\t\t\t\t\treturn uses\n\t\t\t\t} else if (usecase.regressionType == 'cox') {\n\t\t\t\t\tif (term.type == 'condition' || term.type == 'survival') uses.add('plot')\n\t\t\t\t\tif (child_types.includes('condition') || child_types.includes('survival')) uses.add('branch')\n\t\t\t\t\treturn uses\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (usecase.detail == 'independent') {\n\t\t\t\tif (term.type == 'float' || term.type == 'integer' || term.type == 'categorical' || term.type == 'samplelst')\n\t\t\t\t\tuses.add('plot')\n\t\t\t\tif (hasChildTypes(child_types, ['categorical', 'float', 'integer'])) uses.add('branch')\n\t\t\t\treturn uses\n\t\t\t}\n\t\t\treturn uses\n\n\t\tcase 'filter': {\n\t\t\t// apply \"exlst\" to other targets as needed\n\t\t\tconst exlst = termdbConfig?.excludedTermtypeByTarget?.filter\n\t\t\tif (exlst) {\n\t\t\t\tif (graphableTypes.has(term.type) && !exlst.includes(term.type)) uses.add('plot')\n\t\t\t\tif (child_types.find(t => !exlst.includes(t))) uses.add('branch') // there's a non-excluded child type, allow branch to show\n\t\t\t\treturn uses\n\t\t\t}\n\t\t\t// no specific rule for filter. use default rules\n\t\t\tif (graphableTypes.has(term.type)) uses.add('plot')\n\t\t\tif (!term.isleaf) uses.add('branch')\n\t\t\treturn uses\n\t\t}\n\n\t\tcase 'correlationVolcano':\n\t\t\tif (usecase.detail == 'numeric') {\n\t\t\t\tif (isNumericTerm(term)) {\n\t\t\t\t\tuses.add('plot')\n\t\t\t\t}\n\t\t\t\tif (hasNumericChild(child_types)) uses.add('branch')\n\t\t\t} else {\n\t\t\t\tif (graphableTypes.has(term.type)) uses.add('plot')\n\t\t\t\tif (!term.isleaf) uses.add('branch')\n\t\t\t}\n\t\t\treturn uses\n\n\t\tcase 'proteinView':\n\t\t\tif (term.type == TermTypes.PROTEOME_ABUNDANCE) uses.add('plot')\n\t\t\tif (child_types.includes(TermTypes.PROTEOME_ABUNDANCE)) uses.add('branch')\n\t\t\treturn uses\n\n\t\tdefault:\n\t\t\tif (graphableTypes.has(term.type)) uses.add('plot')\n\t\t\tif (!term.isleaf) uses.add('branch')\n\t\t\treturn uses\n\t}\n}\n\n// determine if the term has at least one child type that\n// is not excluded\nfunction hasAllowedChildTypes(child_types, excluded_types) {\n\tif (!child_types.length) {\n\t\t// term does not have children\n\t\treturn false\n\t}\n\tif (!excluded_types?.length) {\n\t\t// no excluded types\n\t\treturn true\n\t}\n\tif (child_types.some(type => !excluded_types.includes(type))) {\n\t\t// at least one child type is not excluded\n\t\treturn true\n\t}\n}\n\nfunction hasNumericChild(child_types) {\n\treturn child_types.includes('float') || child_types.includes('integer')\n}\n\nfunction hasChildTypes(child_types, expected_types) {\n\tfor (const a of expected_types) {\n\t\tif (child_types.includes(a)) return true\n\t}\n}\n"],
+  "mappings": 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+  "names": []
+}

package/dist/src/terms.d.ts

@@ -0,0 +1,83 @@
+import type { Term } from '#types';
+export { TermTypeGroups } from './common.js';
+export declare const ROOT_SAMPLE_TYPE = 1;
+export declare const DEFAULT_SAMPLE_TYPE = 2;
+export declare const NumericModes: {
+    continuous: string;
+    discrete: string;
+};
+export declare const CATEGORICAL = "categorical";
+export declare const CONDITION = "condition";
+export declare const DATE = "date";
+export declare const DNA_METHYLATION = "dnaMethylation";
+export declare const FLOAT = "float";
+export declare const GENE_VARIANT = "geneVariant";
+export declare const GENE_EXPRESSION = "geneExpression";
+export declare const ISOFORM_EXPRESSION = "isoformExpression";
+export declare const INTEGER = "integer";
+export declare const METABOLITE_INTENSITY = "metaboliteIntensity";
+export declare const MULTIVALUE = "multivalue";
+export declare const SAMPLELST = "samplelst";
+export declare const SINGLECELL_CELLTYPE = "singleCellCellType";
+export declare const SINGLECELL_GENE_EXPRESSION = "singleCellGeneExpression";
+export declare const SNP = "snp";
+export declare const SNP_LIST = "snplst";
+export declare const SNP_LOCUS = "snplocus";
+export declare const SSGSEA = "ssGSEA";
+export declare const SURVIVAL = "survival";
+export declare const TERM_COLLECTION = "termCollection";
+export declare const PROTEOME_ABUNDANCE = "proteomeAbundance";
+export declare const PROTEOME_DAP = "proteomeDAP";
+export declare const TermTypes: {
+    [key: string]: string;
+};
+export declare const dtTermTypes: Set<string>;
+export declare const NUMERIC_DICTIONARY_TERM = "numericDictTerm";
+export declare const TermTypes2Dt: {
+    geneExpression: any;
+    ssGSEA: any;
+    dnaMethylation: any;
+    metaboliteIntensity: any;
+    proteomeAbundance: any;
+};
+export declare const typeGroup: {
+    categorical: any;
+    condition: any;
+    float: any;
+    integer: any;
+    samplelst: any;
+    survival: any;
+    date: any;
+    multivalue: any;
+    geneVariant: any;
+    snp: any;
+    snplst: any;
+    snplocus: any;
+    geneExpression: any;
+    isoformExpression: any;
+    ssGSEA: any;
+    dnaMethylation: any;
+    metaboliteIntensity: any;
+    proteomeAbundance: any;
+    termCollection: any;
+    singleCellCellType: any;
+    singleCellGeneExpression: any;
+};
+export declare const numericTypes: Set<string>;
+export declare const annoNumericTypes: Set<string>;
+export declare function isSingleCellTerm(term: any): boolean;
+export declare function isNumericTerm(term: Term): boolean;
+export declare function isCategoricalTerm(term: Term): boolean;
+export declare function isDictionaryType(type: string): boolean;
+export declare function isNonDictionaryType(type: string): boolean;
+export declare function isNumTermCollection(term: Term): boolean;
+export declare function equals(t1: any, t2: any): boolean;
+export declare function getBin(lst: any[], value: number): number;
+export declare function getSampleType(term: any, ds: any): any;
+export declare function getParentType(types: Set<string>, ds: any): any;
+export declare function termType2label(type: string): string;
+export declare function getDateFromNumber(value: number): Date;
+export declare function getDateStrFromNumber(value: number): string;
+export declare function getNumberFromDateStr(str: string): number;
+export declare function getNumberFromDate(date: Date): number;
+export declare function getDaysInYear(year: number): 366 | 365;

package/dist/src/terms.js

@@ -0,0 +1,327 @@
+import {
+  dtgeneexpression,
+  dtssgsea,
+  dtdnamethylation,
+  dtmetaboliteintensity,
+  dtproteomeabundance,
+  TermTypeGroups,
+  dtTerms
+} from "./common.js";
+import { TermTypeGroups as TermTypeGroups2 } from "./common.js";
+const ROOT_SAMPLE_TYPE = 1;
+const DEFAULT_SAMPLE_TYPE = 2;
+const NumericModes = {
+  continuous: "continuous",
+  discrete: "discrete"
+};
+const CATEGORICAL = "categorical";
+const CONDITION = "condition";
+const DATE = "date";
+const DNA_METHYLATION = "dnaMethylation";
+const FLOAT = "float";
+const GENE_VARIANT = "geneVariant";
+const GENE_EXPRESSION = "geneExpression";
+const ISOFORM_EXPRESSION = "isoformExpression";
+const INTEGER = "integer";
+const METABOLITE_INTENSITY = "metaboliteIntensity";
+const MULTIVALUE = "multivalue";
+const SAMPLELST = "samplelst";
+const SINGLECELL_CELLTYPE = "singleCellCellType";
+const SINGLECELL_GENE_EXPRESSION = "singleCellGeneExpression";
+const SNP = "snp";
+const SNP_LIST = "snplst";
+const SNP_LOCUS = "snplocus";
+const SSGSEA = "ssGSEA";
+const SURVIVAL = "survival";
+const TERM_COLLECTION = "termCollection";
+const PROTEOME_ABUNDANCE = "proteomeAbundance";
+const PROTEOME_DAP = "proteomeDAP";
+const 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
+};
+const dtTermTypes = new Set(dtTerms.map((t) => t.type));
+for (const dtTermType of dtTermTypes) {
+  TermTypes[dtTermType.toUpperCase()] = dtTermType;
+}
+const NUMERIC_DICTIONARY_TERM = "numericDictTerm";
+const TermTypes2Dt = {
+  [GENE_EXPRESSION]: dtgeneexpression,
+  [SSGSEA]: dtssgsea,
+  [DNA_METHYLATION]: dtdnamethylation,
+  [METABOLITE_INTENSITY]: dtmetaboliteintensity,
+  [PROTEOME_ABUNDANCE]: dtproteomeabundance
+};
+const 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
+};
+const 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()]);
+}
+const numericTypes = /* @__PURE__ */ new Set([
+  INTEGER,
+  FLOAT,
+  GENE_EXPRESSION,
+  ISOFORM_EXPRESSION,
+  SSGSEA,
+  DNA_METHYLATION,
+  METABOLITE_INTENSITY,
+  PROTEOME_ABUNDANCE,
+  SINGLECELL_GENE_EXPRESSION,
+  DATE
+]);
+const annoNumericTypes = /* @__PURE__ */ new Set([INTEGER, FLOAT, DATE]);
+const categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP]);
+const 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;
+  }
+}
+function getBin(lst, value) {
+  let bin = lst.findIndex(
+    (b) => b.startunbounded && value < b.stop || b.startunbounded && b.stopinclusive && value == b.stop
+  );
+  if (bin == -1)
+    bin = lst.findIndex(
+      (b) => b.stopunbounded && value > b.start || b.stopunbounded && b.startinclusive && value == b.start
+    );
+  if (bin == -1)
+    bin = lst.findIndex(
+      (b) => value > b.start && value < b.stop || b.startinclusive && value == b.start || b.stopinclusive && value == b.stop
+    );
+  return bin;
+}
+function getSampleType(term, ds) {
+  if (!term) return null;
+  if (term.type && isNonDictionaryType(term.type)) return DEFAULT_SAMPLE_TYPE;
+  if (term.id) return ds.cohort.termdb.term2SampleType.get(term.id);
+  if (term.type == "samplelst") {
+    const key = Object.keys(term.values)[0];
+    const sampleId = term.values[key].list[0]?.sampleId;
+    if (sampleId) return ds.sampleId2Type.get(Number(sampleId) || sampleId);
+    else return DEFAULT_SAMPLE_TYPE;
+  }
+  return DEFAULT_SAMPLE_TYPE;
+}
+function getParentType(types, ds) {
+  if (Object.keys(ds.cohort.termdb.sampleTypes).length == 0) return null;
+  const ids = Array.from(types);
+  if (!ids || ids.length == 0) return null;
+  for (const id of ids) {
+    const typeObj = ds.cohort.termdb.sampleTypes[id];
+    if (!typeObj) continue;
+    if (typeObj.parent_id == null) return id;
+    if (ids.includes(typeObj.parent_id)) continue;
+    else return typeObj.parent_id;
+  }
+  return null;
+}
+const 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;
+}
+const oneDayTime = 24 * 60 * 60 * 1e3;
+function getDateStrFromNumber(value) {
+  const date = getDateFromNumber(value);
+  return date.toLocaleDateString("en-US", {
+    year: "numeric",
+    month: "long"
+  });
+}
+function getNumberFromDateStr(str) {
+  const date = new Date(str);
+  return getNumberFromDate(date);
+}
+function getNumberFromDate(date) {
+  const year = date.getFullYear();
+  const january1st = new Date(year, 0, 1);
+  const diffDays = (date.getTime() - january1st.getTime()) / oneDayTime;
+  const daysTotal = getDaysInYear(year);
+  const decimal = diffDays / daysTotal;
+  return year + decimal;
+}
+function getDaysInYear(year) {
+  const isLeap = new Date(year, 1, 29).getMonth() === 1;
+  const days = isLeap ? 366 : 365;
+  return days;
+}
+export {
+  CATEGORICAL,
+  CONDITION,
+  DATE,
+  DEFAULT_SAMPLE_TYPE,
+  DNA_METHYLATION,
+  FLOAT,
+  GENE_EXPRESSION,
+  GENE_VARIANT,
+  INTEGER,
+  ISOFORM_EXPRESSION,
+  METABOLITE_INTENSITY,
+  MULTIVALUE,
+  NUMERIC_DICTIONARY_TERM,
+  NumericModes,
+  PROTEOME_ABUNDANCE,
+  PROTEOME_DAP,
+  ROOT_SAMPLE_TYPE,
+  SAMPLELST,
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION,
+  SNP,
+  SNP_LIST,
+  SNP_LOCUS,
+  SSGSEA,
+  SURVIVAL,
+  TERM_COLLECTION,
+  TermTypeGroups2 as TermTypeGroups,
+  TermTypes,
+  TermTypes2Dt,
+  annoNumericTypes,
+  dtTermTypes,
+  equals,
+  getBin,
+  getDateFromNumber,
+  getDateStrFromNumber,
+  getDaysInYear,
+  getNumberFromDate,
+  getNumberFromDateStr,
+  getParentType,
+  getSampleType,
+  isCategoricalTerm,
+  isDictionaryType,
+  isNonDictionaryType,
+  isNumTermCollection,
+  isNumericTerm,
+  isSingleCellTerm,
+  numericTypes,
+  termType2label,
+  typeGroup
+};
+//# sourceMappingURL=terms.js.map