@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/chunk-7PJNKPQB.js

@@ -0,0 +1,275 @@
+import {
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-6PNPHACF.js";
+
+// test/testdata/data.ts
+function getSamplelstTw() {
+  const values = [
+    {
+      sampleId: 42,
+      sample: "2660"
+    },
+    {
+      sampleId: 44,
+      sample: "2688"
+    },
+    {
+      sampleId: 45,
+      sample: "2702"
+    },
+    {
+      sampleId: 46,
+      sample: "2716"
+    },
+    {
+      sampleId: 59,
+      sample: "2898"
+    },
+    {
+      sampleId: 60,
+      sample: "2912"
+    },
+    {
+      sampleId: 67,
+      sample: "3010"
+    },
+    {
+      sampleId: 68,
+      sample: "3024"
+    },
+    {
+      sampleId: 69,
+      sample: "3038"
+    },
+    {
+      sampleId: 70,
+      sample: "3052"
+    },
+    {
+      sampleId: 73,
+      sample: "3094"
+    },
+    {
+      sampleId: 79,
+      sample: "3178"
+    },
+    {
+      sampleId: 80,
+      sample: "3192"
+    }
+  ];
+  return {
+    term: {
+      name: "termdbtest samplelst",
+      type: "samplelst",
+      values: {
+        "Group 1": {
+          key: "Group 1",
+          label: "Group 1",
+          list: values
+        },
+        "Not in Group 1": {
+          key: "Not in Group 1",
+          label: "Not in Group 1",
+          list: values
+        }
+      }
+    },
+    q: {
+      mode: "discrete",
+      groups: [
+        {
+          name: "Group 1",
+          in: true,
+          values
+        },
+        {
+          name: "Not in Group 1",
+          in: false,
+          values
+        }
+      ],
+      isAtomic: true
+    }
+  };
+}
+function getCategoryGroupsetting() {
+  return {
+    id: "diaggrp",
+    q: {
+      type: "custom-groupset",
+      customset: {
+        name: "A versus B",
+        groups: [
+          {
+            name: "Test A",
+            type: "values",
+            values: [{ key: "Acute lymphoblastic leukemia" }, { key: "Wilms tumor" }]
+          },
+          {
+            name: "Test B",
+            type: "values",
+            values: [
+              { key: "Central nervous system (CNS)" },
+              { key: "Acute myeloid leukemia" },
+              { key: "Non-Hodgkin lymphoma" }
+            ]
+          }
+        ]
+      }
+    }
+  };
+}
+function getGenesetMutTw() {
+  return {
+    term: {
+      genes: [
+        { kind: "gene", gene: "TP53", type: "geneVariant" },
+        { kind: "gene", gene: "KRAS", type: "geneVariant" },
+        { kind: "gene", gene: "AKT1", type: "geneVariant" },
+        { kind: "gene", gene: "BCR", type: "geneVariant" }
+      ],
+      type: "geneVariant"
+    },
+    q: { type: "predefined-groupset" }
+  };
+}
+function getGeneVariantTw(position = false) {
+  return {
+    term: {
+      genes: [
+        position ? { kind: "coord", chr: "chr12", start: 25205246, stop: 25250936, name: "KRASregion", type: "geneVariant" } : { kind: "gene", gene: "TP53", type: "geneVariant" }
+      ],
+      type: "geneVariant"
+    },
+    q: { type: "predefined-groupset", predefined_groupset_idx: 0, hiddenValues: {} }
+  };
+}
+function getSsgseaTw(isBin = false) {
+  return {
+    term: { id: "HALLMARK_ADIPOGENESIS", type: "ssGSEA", name: "HALLMARK_ADIPOGENESIS" },
+    q: isBin ? {
+      type: "regular-bin",
+      startinclusive: true,
+      bin_size: 0.2,
+      first_bin: { stop: -0.4 },
+      last_bin: { start: 0.8 },
+      mode: "discrete"
+    } : { mode: "continuous" }
+  };
+}
+function getScgeneexpTw(gene = "KRAS") {
+  return {
+    term: {
+      type: SINGLECELL_GENE_EXPRESSION,
+      id: gene,
+      gene,
+      name: gene,
+      sample: {
+        sID: "1_patient"
+      }
+    },
+    q: {
+      mode: "continuous"
+    }
+  };
+}
+function getScctTw() {
+  return {
+    term: {
+      type: SINGLECELL_CELLTYPE,
+      id: "CellType",
+      name: "Cell Type",
+      sample: {
+        sID: "1_patient"
+      },
+      plot: "UMAP",
+      colorBy: "CellType",
+      values: {
+        T_NK: {
+          key: "T_NK",
+          value: "T_NK"
+        },
+        Blast: {
+          key: "Blast",
+          value: "Blast"
+        },
+        Monocyte: {
+          key: "Monocyte",
+          value: "Monocyte"
+        }
+      },
+      groupsetting: {
+        disabled: false
+      }
+    }
+  };
+}
+function getCategoricalTermcollectionTw() {
+  return {
+    type: "TermCollectionTWQual",
+    term: { type: "termCollection", name: "Assay Availability" }
+  };
+}
+function getAgeCollectionFractionTw() {
+  return {
+    type: "TermCollectionTWFraction",
+    term: {
+      type: "termCollection",
+      termIds: ["agedx", "a_death", "a_ndi", "agelastvisit"],
+      name: "Fake Collection 1",
+      // NOTE this name must match with the termCollection entry in termdbtest
+      memberType: "numeric"
+    },
+    q: {
+      mode: "discrete",
+      numerators: ["a_death"],
+      denominators: ["agedx", "a_death"],
+      type: "custom-bin",
+      lst: [
+        { startunbounded: true, stop: 0.8, label: "<0.8" },
+        { stopunbounded: true, start: 0.8, label: ">0.8" }
+      ]
+    }
+  };
+}
+function getIsoformExpCollectionFractionTw() {
+  return {
+    type: "TermCollectionTWFraction",
+    term: {
+      type: "termCollection",
+      isCustom: true,
+      memberType: "numeric",
+      name: "KRAS Isoforms (TPM)",
+      termlst: [
+        { id: "ENST00000256078", name: "ENST00000256078", type: "isoformExpression", isoform: "ENST00000256078" },
+        { id: "ENST00000311936", name: "ENST00000311936", type: "isoformExpression", isoform: "ENST00000311936" }
+      ]
+    },
+    q: {
+      mode: "discrete",
+      type: "custom-bin",
+      lst: [
+        { startunbounded: true, stop: 0.1, startinclusive: false, stopinclusive: true, label: "low0.1" },
+        { start: 0.1, startinclusive: false, stopinclusive: false, stopunbounded: true, label: "high0.1" }
+      ],
+      denominators: ["ENST00000256078", "ENST00000311936"],
+      numerators: ["ENST00000256078"]
+    }
+  };
+}
+
+export {
+  getSamplelstTw,
+  getCategoryGroupsetting,
+  getGenesetMutTw,
+  getGeneVariantTw,
+  getSsgseaTw,
+  getScgeneexpTw,
+  getScctTw,
+  getCategoricalTermcollectionTw,
+  getAgeCollectionFractionTw,
+  getIsoformExpCollectionFractionTw
+};
+//# sourceMappingURL=chunk-7PJNKPQB.js.map

package/dist/chunk-7PJNKPQB.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../test/testdata/data.ts"],
+  "sourcesContent": ["import * as tt from '#types'\n/* \nexports a set of functions, each returns a TermdbTest-based term/tw/tvs that is complex and lengthy\nthat are used in unit/integration tests so to simplify test and avoid code duplication\n\nfunctions could accept parameters to return customized objects\n\n::NOTE::\n\nif some data contents needs to be changed, better off creating a new function and avoid changing existing one, as multiple tests may be coded against that data\n*/\n\nexport function getSamplelstTw() {\n\tconst values = [\n\t\t{\n\t\t\tsampleId: 42,\n\t\t\tsample: '2660'\n\t\t},\n\t\t{\n\t\t\tsampleId: 44,\n\t\t\tsample: '2688'\n\t\t},\n\t\t{\n\t\t\tsampleId: 45,\n\t\t\tsample: '2702'\n\t\t},\n\t\t{\n\t\t\tsampleId: 46,\n\t\t\tsample: '2716'\n\t\t},\n\t\t{\n\t\t\tsampleId: 59,\n\t\t\tsample: '2898'\n\t\t},\n\t\t{\n\t\t\tsampleId: 60,\n\t\t\tsample: '2912'\n\t\t},\n\t\t{\n\t\t\tsampleId: 67,\n\t\t\tsample: '3010'\n\t\t},\n\t\t{\n\t\t\tsampleId: 68,\n\t\t\tsample: '3024'\n\t\t},\n\t\t{\n\t\t\tsampleId: 69,\n\t\t\tsample: '3038'\n\t\t},\n\t\t{\n\t\t\tsampleId: 70,\n\t\t\tsample: '3052'\n\t\t},\n\t\t{\n\t\t\tsampleId: 73,\n\t\t\tsample: '3094'\n\t\t},\n\t\t{\n\t\t\tsampleId: 79,\n\t\t\tsample: '3178'\n\t\t},\n\t\t{\n\t\t\tsampleId: 80,\n\t\t\tsample: '3192'\n\t\t}\n\t]\n\treturn {\n\t\tterm: {\n\t\t\tname: 'termdbtest samplelst',\n\t\t\ttype: 'samplelst',\n\t\t\tvalues: {\n\t\t\t\t'Group 1': {\n\t\t\t\t\tkey: 'Group 1',\n\t\t\t\t\tlabel: 'Group 1',\n\t\t\t\t\tlist: values\n\t\t\t\t},\n\t\t\t\t'Not in Group 1': {\n\t\t\t\t\tkey: 'Not in Group 1',\n\t\t\t\t\tlabel: 'Not in Group 1',\n\t\t\t\t\tlist: values\n\t\t\t\t}\n\t\t\t}\n\t\t},\n\t\tq: {\n\t\t\tmode: 'discrete',\n\t\t\tgroups: [\n\t\t\t\t{\n\t\t\t\t\tname: 'Group 1',\n\t\t\t\t\tin: true,\n\t\t\t\t\tvalues\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tname: 'Not in Group 1',\n\t\t\t\t\tin: false,\n\t\t\t\t\tvalues\n\t\t\t\t}\n\t\t\t],\n\t\t\tisAtomic: true\n\t\t}\n\t}\n}\n\nexport function getCategoryGroupsetting() {\n\treturn {\n\t\tid: 'diaggrp',\n\t\tq: {\n\t\t\ttype: 'custom-groupset',\n\t\t\tcustomset: {\n\t\t\t\tname: 'A versus B',\n\t\t\t\tgroups: [\n\t\t\t\t\t{\n\t\t\t\t\t\tname: 'Test A',\n\t\t\t\t\t\ttype: 'values',\n\t\t\t\t\t\tvalues: [{ key: 'Acute lymphoblastic leukemia' }, { key: 'Wilms tumor' }]\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tname: 'Test B',\n\t\t\t\t\t\ttype: 'values',\n\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t{ key: 'Central nervous system (CNS)' },\n\t\t\t\t\t\t\t{ key: 'Acute myeloid leukemia' },\n\t\t\t\t\t\t\t{ key: 'Non-Hodgkin lymphoma' }\n\t\t\t\t\t\t]\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function getGenesetMutTw() {\n\treturn {\n\t\tterm: {\n\t\t\tgenes: [\n\t\t\t\t{ kind: 'gene', gene: 'TP53', type: 'geneVariant' },\n\t\t\t\t{ kind: 'gene', gene: 'KRAS', type: 'geneVariant' },\n\t\t\t\t{ kind: 'gene', gene: 'AKT1', type: 'geneVariant' },\n\t\t\t\t{ kind: 'gene', gene: 'BCR', type: 'geneVariant' }\n\t\t\t],\n\t\t\ttype: 'geneVariant'\n\t\t},\n\t\tq: { type: 'predefined-groupset' }\n\t}\n}\n\nexport function getGeneVariantTw(position = false) {\n\treturn {\n\t\tterm: {\n\t\t\tgenes: [\n\t\t\t\tposition\n\t\t\t\t\t? { kind: 'coord', chr: 'chr12', start: 25205246, stop: 25250936, name: 'KRASregion', type: 'geneVariant' }\n\t\t\t\t\t: { kind: 'gene', gene: 'TP53', type: 'geneVariant' }\n\t\t\t],\n\t\t\ttype: 'geneVariant'\n\t\t},\n\t\tq: { type: 'predefined-groupset', predefined_groupset_idx: 0, hiddenValues: {} }\n\t}\n}\n\nexport function getSsgseaTw(isBin = false) {\n\treturn {\n\t\tterm: { id: 'HALLMARK_ADIPOGENESIS', type: 'ssGSEA', name: 'HALLMARK_ADIPOGENESIS' },\n\t\tq: isBin\n\t\t\t? {\n\t\t\t\t\ttype: 'regular-bin',\n\t\t\t\t\tstartinclusive: true,\n\t\t\t\t\tbin_size: 0.2,\n\t\t\t\t\tfirst_bin: { stop: -0.4 },\n\t\t\t\t\tlast_bin: { start: 0.8 },\n\t\t\t\t\tmode: 'discrete'\n\t\t\t  }\n\t\t\t: { mode: 'continuous' }\n\t}\n}\n\nexport function getFilter_agedx(start = 10) {\n\treturn {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin: 'and',\n\t\tlst: [\n\t\t\t{\n\t\t\t\ttag: 'filterUiRoot',\n\t\t\t\ttype: 'tvslst',\n\t\t\t\tjoin: '',\n\t\t\t\tlst: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\tterm: { id: 'agedx', type: 'float', name: 'Age of diagnosis' },\n\t\t\t\t\t\t\tranges: [\n\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\tstart,\n\t\t\t\t\t\t\t\t\tstartinclusive: false,\n\t\t\t\t\t\t\t\t\tstartunbounded: false,\n\t\t\t\t\t\t\t\t\tstop: 16,\n\t\t\t\t\t\t\t\t\tstopinclusive: false,\n\t\t\t\t\t\t\t\t\tstopunbounded: false\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t]\n\t\t\t\t\t\t},\n\t\t\t\t\t\ttype: 'tvs'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t]\n\t}\n}\nexport function getFilter_male() {\n\treturn {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin: 'and',\n\t\tlst: [\n\t\t\t{\n\t\t\t\ttag: 'filterUiRoot',\n\t\t\t\ttype: 'tvslst',\n\t\t\t\tjoin: '',\n\t\t\t\tlst: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\tterm: { id: 'sex' },\n\t\t\t\t\t\t\tvalues: [{ key: '1', label: 'Male' }]\n\t\t\t\t\t\t},\n\t\t\t\t\t\ttype: 'tvs'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t]\n\t}\n}\nexport function getFilter_Hodgkin() {\n\treturn {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin: 'and',\n\t\tlst: [\n\t\t\t{\n\t\t\t\ttag: 'filterUiRoot',\n\t\t\t\ttype: 'tvslst',\n\t\t\t\tjoin: '',\n\t\t\t\tlst: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\tterm: { id: 'diaggrp', type: 'categorical', name: 'diaggrp' },\n\t\t\t\t\t\t\tvalues: [{ key: 'Hodgkin lymphoma', name: 'Hodgkin' }]\n\t\t\t\t\t\t},\n\t\t\t\t\t\ttype: 'tvs'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t]\n\t}\n}\nexport function getFilter_genemutationset(isnot = false) {\n\treturn {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin: 'and',\n\t\tlst: [\n\t\t\t{\n\t\t\t\ttag: 'cohortFilter',\n\t\t\t\ttype: 'tvs',\n\t\t\t\ttvs: { term: { id: 'subcohort', type: 'multivalue' }, values: [{ key: 'ABC', label: 'ABC' }] }\n\t\t\t},\n\t\t\t{\n\t\t\t\ttype: 'tvslst',\n\t\t\t\tin: true,\n\t\t\t\tjoin: '',\n\t\t\t\tlst: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\tid: 'snvindel_somatic',\n\t\t\t\t\t\t\t\tquery: 'snvindel',\n\t\t\t\t\t\t\t\tname: 'SNV/indel (somatic)',\n\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\ttype: 'dtsnvindel',\n\t\t\t\t\t\t\t\tdt: 1,\n\t\t\t\t\t\t\t\tvalues: { M: { label: 'MISSENSE' }, F: { label: 'FRAMESHIFT' }, WT: { label: 'Wildtype' } },\n\t\t\t\t\t\t\t\tname_noOrigin: 'SNV/indel',\n\t\t\t\t\t\t\t\torigin: 'somatic',\n\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\tid: 'HALLMARK_ADIPOGENESIS',\n\t\t\t\t\t\t\t\t\tname: 'HALLMARK_ADIPOGENESIS',\n\t\t\t\t\t\t\t\t\tgenes: [\n\t\t\t\t\t\t\t\t\t\t{ kind: 'gene', id: 'TP53', gene: 'TP53', name: 'TP53', type: 'geneVariant' },\n\t\t\t\t\t\t\t\t\t\t{ kind: 'gene', id: 'AKT1', gene: 'AKT1', name: 'AKT1', type: 'geneVariant' },\n\t\t\t\t\t\t\t\t\t\t{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' },\n\t\t\t\t\t\t\t\t\t\t{ kind: 'gene', id: 'BCR', gene: 'BCR', name: 'BCR', type: 'geneVariant' }\n\t\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t\t{ key: 'M', label: 'MISSENSE', value: 'M', bar_width_frac: null },\n\t\t\t\t\t\t\t\t{ key: 'F', label: 'FRAMESHIFT', value: 'F', bar_width_frac: null }\n\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\tisnot,\n\t\t\t\t\t\t\tgenotype: 'variant',\n\t\t\t\t\t\t\tmcount: 'any'\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t],\n\t\t\t\ttag: 'filterUiRoot'\n\t\t\t}\n\t\t]\n\t}\n}\n\n// for ds using categorical cnv, e.g. gdc or mb\n// TODO shrink size!\n// uses kras which exists in tdbtest, and may be used in integration test\nexport function getCnv_categorical() {\n\treturn {\n\t\tterm: {\n\t\t\ttype: 'geneVariant',\n\t\t\tchildTerms: [\n\t\t\t\t{\n\t\t\t\t\tid: 'snvindel',\n\t\t\t\t\tquery: 'snvindel',\n\t\t\t\t\tname: 'SNV/indel',\n\t\t\t\t\tparent_id: null,\n\t\t\t\t\tisleaf: true,\n\t\t\t\t\ttype: 'dtsnvindel',\n\t\t\t\t\tdt: 1,\n\t\t\t\t\tvalues: {\n\t\t\t\t\t\tM: { key: 'M', label: 'MISSENSE' },\n\t\t\t\t\t\tS: { key: 'S', label: 'SILENT' },\n\t\t\t\t\t\tIntron: { key: 'Intron', label: 'INTRON' },\n\t\t\t\t\t\tD: { key: 'D', label: 'PROTEINDEL' }\n\t\t\t\t\t},\n\t\t\t\t\tname_noOrigin: 'SNV/indel',\n\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tid: 'cnv',\n\t\t\t\t\tquery: 'cnv',\n\t\t\t\t\tname: 'CNV',\n\t\t\t\t\tparent_id: null,\n\t\t\t\t\tisleaf: true,\n\t\t\t\t\ttype: 'dtcnv',\n\t\t\t\t\tdt: 4,\n\t\t\t\t\tvalues: {\n\t\t\t\t\t\tCNV_amplification: { key: 'CNV_amplification', label: 'Amplification' },\n\t\t\t\t\t\tCNV_amp: { key: 'CNV_amp', label: 'Gain' },\n\t\t\t\t\t\tCNV_loss: { key: 'CNV_loss', label: 'Heterozygous Deletion' }\n\t\t\t\t\t},\n\t\t\t\t\tname_noOrigin: 'CNV',\n\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t],\n\t\t\tid: 'KRAS',\n\t\t\tname: 'KRAS',\n\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }],\n\t\t\tgroupsetting: {\n\t\t\t\tdisabled: false,\n\t\t\t\tlst: [\n\t\t\t\t\t{\n\t\t\t\t\t\tname: 'SNV/indel',\n\t\t\t\t\t\tdt: 1,\n\t\t\t\t\t\tgroups: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tname: 'KRAS SNV/indel Mutated',\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'snvindel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tquery: 'snvindel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'SNV/indel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'dtsnvindel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tdt: 1,\n\t\t\t\t\t\t\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tM: { key: 'M', label: 'MISSENSE' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tS: { key: 'S', label: 'SILENT' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tIntron: { key: 'Intron', label: 'INTRON' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tD: { key: 'D', label: 'PROTEINDEL' }\n\t\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\t\tname_noOrigin: 'SNV/indel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t\t\t\t\t\t\t{ key: 'M', label: 'MISSENSE', value: 'M' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t{ key: 'S', label: 'SILENT', value: 'S' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t{ key: 'Intron', label: 'INTRON', value: 'Intron' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t{ key: 'D', label: 'PROTEINDEL', value: 'D' }\n\t\t\t\t\t\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\t\t\t\t\t\tgenotype: 'variant',\n\t\t\t\t\t\t\t\t\t\t\t\tmcount: 'any',\n\t\t\t\t\t\t\t\t\t\t\t\texcludeGeneName: true\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\tcolor: '#e75480'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tname: 'KRAS SNV/indel Wildtype',\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'snvindel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tquery: 'snvindel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'SNV/indel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'dtsnvindel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tdt: 1,\n\t\t\t\t\t\t\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tM: { key: 'M', label: 'MISSENSE' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tS: { key: 'S', label: 'SILENT' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tIntron: { key: 'Intron', label: 'INTRON' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tD: { key: 'D', label: 'PROTEINDEL' }\n\t\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\t\tname_noOrigin: 'SNV/indel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [],\n\t\t\t\t\t\t\t\t\t\t\t\tgenotype: 'wt',\n\t\t\t\t\t\t\t\t\t\t\t\texcludeGeneName: true\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\tcolor: '#D3D3D3'\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tname: 'CNV',\n\t\t\t\t\t\tdt: 4,\n\t\t\t\t\t\tgroups: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tname: 'KRAS CNV Amplification',\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tquery: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'dtcnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tdt: 4,\n\t\t\t\t\t\t\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amplification: { key: 'CNV_amplification', label: 'Amplification' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amp: { key: 'CNV_amp', label: 'Gain' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_loss: { key: 'CNV_loss', label: 'Heterozygous Deletion' }\n\t\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\t\tname_noOrigin: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [{ key: 'CNV_amplification', label: 'Amplification', value: 'CNV_amplification' }],\n\t\t\t\t\t\t\t\t\t\t\t\tgenotype: 'variant',\n\t\t\t\t\t\t\t\t\t\t\t\tmcount: 'any',\n\t\t\t\t\t\t\t\t\t\t\t\texcludeGeneName: true\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\tcolor: '#ff0000'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tname: 'KRAS CNV Gain',\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tquery: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'dtcnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tdt: 4,\n\t\t\t\t\t\t\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amplification: { key: 'CNV_amplification', label: 'Amplification' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amp: { key: 'CNV_amp', label: 'Gain' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_loss: { key: 'CNV_loss', label: 'Heterozygous Deletion' }\n\t\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\t\tname_noOrigin: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [{ key: 'CNV_amp', label: 'Gain', value: 'CNV_amp' }],\n\t\t\t\t\t\t\t\t\t\t\t\tgenotype: 'variant',\n\t\t\t\t\t\t\t\t\t\t\t\tmcount: 'any',\n\t\t\t\t\t\t\t\t\t\t\t\texcludeGeneName: true\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\tcolor: '#e9a3c9'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tname: 'KRAS CNV Heterozygous Deletion',\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tquery: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'dtcnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tdt: 4,\n\t\t\t\t\t\t\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amplification: { key: 'CNV_amplification', label: 'Amplification' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amp: { key: 'CNV_amp', label: 'Gain' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_loss: { key: 'CNV_loss', label: 'Heterozygous Deletion' }\n\t\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\t\tname_noOrigin: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [{ key: 'CNV_loss', label: 'Heterozygous Deletion', value: 'CNV_loss' }],\n\t\t\t\t\t\t\t\t\t\t\t\tgenotype: 'variant',\n\t\t\t\t\t\t\t\t\t\t\t\tmcount: 'any',\n\t\t\t\t\t\t\t\t\t\t\t\texcludeGeneName: true\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\tcolor: '#a1d76a'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tname: 'KRAS CNV Wildtype',\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tquery: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'dtcnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tdt: 4,\n\t\t\t\t\t\t\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amplification: { key: 'CNV_amplification', label: 'Amplification' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amp: { key: 'CNV_amp', label: 'Gain' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_loss: { key: 'CNV_loss', label: 'Heterozygous Deletion' }\n\t\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\t\tname_noOrigin: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [],\n\t\t\t\t\t\t\t\t\t\t\t\tgenotype: 'wt',\n\t\t\t\t\t\t\t\t\t\t\t\texcludeGeneName: true\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\tcolor: '#D3D3D3'\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t},\n\t\tq: { type: 'predefined-groupset', predefined_groupset_idx: 1, cnvMaxLength: 2000000, hiddenValues: {} }\n\t}\n}\n\nexport function getScgeneexpTw(gene = 'KRAS') {\n\treturn {\n\t\tterm: {\n\t\t\ttype: tt.SINGLECELL_GENE_EXPRESSION,\n\t\t\tid: gene,\n\t\t\tgene,\n\t\t\tname: gene,\n\t\t\tsample: {\n\t\t\t\tsID: '1_patient'\n\t\t\t}\n\t\t},\n\t\tq: {\n\t\t\tmode: 'continuous'\n\t\t}\n\t}\n}\nexport function getScctTw() {\n\treturn {\n\t\tterm: {\n\t\t\ttype: tt.SINGLECELL_CELLTYPE,\n\t\t\tid: 'CellType',\n\t\t\tname: 'Cell Type',\n\t\t\tsample: {\n\t\t\t\tsID: '1_patient'\n\t\t\t},\n\t\t\tplot: 'UMAP',\n\t\t\tcolorBy: 'CellType',\n\t\t\tvalues: {\n\t\t\t\tT_NK: {\n\t\t\t\t\tkey: 'T_NK',\n\t\t\t\t\tvalue: 'T_NK'\n\t\t\t\t},\n\t\t\t\tBlast: {\n\t\t\t\t\tkey: 'Blast',\n\t\t\t\t\tvalue: 'Blast'\n\t\t\t\t},\n\t\t\t\tMonocyte: {\n\t\t\t\t\tkey: 'Monocyte',\n\t\t\t\t\tvalue: 'Monocyte'\n\t\t\t\t}\n\t\t\t},\n\t\t\tgroupsetting: {\n\t\t\t\tdisabled: false\n\t\t\t}\n\t\t}\n\t}\n}\n/** TODO: Pseudobulk data is not enabled in TermdbTest!!\n * Do not use until data is available. Capturing structure for\n * clarity during development. */\nexport function getPseudobulkTW(nameId = 'Blast') {\n\treturn {\n\t\tterm: {\n\t\t\ttype: tt.PSEUDOBULK,\n\t\t\tassay: 'geneExpression',\n\t\t\tmemberId: 'CellType',\n\t\t\tname: nameId,\n\t\t\tid: nameId\n\t\t}\n\t}\n}\nexport function getPseudobulkTermCollection(termIds = ['Blast', 'Monocyte', 'T_NK']) {\n\tconst termlst = termIds.map(id => getPseudobulkTW(id).term)\n\n\treturn {\n\t\ttype: 'TermCollectionTWCont',\n\t\tterm: {\n\t\t\ttype: tt.TERM_COLLECTION,\n\t\t\tmemberType: 'numeric',\n\t\t\tid: 'test',\n\t\t\tname: 'Test pseudobulk term collection',\n\t\t\ttermIds,\n\t\t\ttermlst,\n\t\t\tisCustom: true\n\t\t},\n\t\tq: {\n\t\t\tmode: 'continuous',\n\t\t\ttype: 'values',\n\t\t\tlst: []\n\t\t}\n\t}\n}\n\n////////////// following are gdc-specific! may move to separate file\n\nexport function getGdcDiseaseGroupsetting() {\n\treturn {\n\t\tterm: { type: 'categorical', id: 'case.disease_type' },\n\t\tq: {\n\t\t\tmode: 'discrete',\n\t\t\ttype: 'custom-groupset',\n\t\t\thiddenValues: {},\n\t\t\tcustomset: {\n\t\t\t\tgroups: [\n\t\t\t\t\t{ name: 'Excluded categories', type: 'values', uncomputable: true, values: [] },\n\t\t\t\t\t{\n\t\t\t\t\t\tname: 'Group Mix',\n\t\t\t\t\t\ttype: 'values',\n\t\t\t\t\t\tuncomputable: false,\n\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t{ key: 'Ductal and Lobular Neoplasms', label: 'Ductal and Lobular Neoplasms', samplecount: 2829 },\n\t\t\t\t\t\t\t{ key: 'Complex Epithelial Neoplasms', label: 'Complex Epithelial Neoplasms', samplecount: 69 },\n\t\t\t\t\t\t\t{ key: 'Not Applicable', label: 'Not Applicable', samplecount: 9 },\n\t\t\t\t\t\t\t{ key: 'Epithelial Neoplasms, NOS', label: 'Epithelial Neoplasms, NOS', samplecount: 1221 },\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tkey: 'Cystic, Mucinous and Serous Neoplasms',\n\t\t\t\t\t\t\t\tlabel: 'Cystic, Mucinous and Serous Neoplasms',\n\t\t\t\t\t\t\t\tsamplecount: 17\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tkey: 'Adnexal and Skin Appendage Neoplasms',\n\t\t\t\t\t\t\t\tlabel: 'Adnexal and Skin Appendage Neoplasms',\n\t\t\t\t\t\t\t\tsamplecount: 1\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{ key: 'Adenomas and Adenocarcinomas', label: 'Adenomas and Adenocarcinomas', samplecount: 18 },\n\t\t\t\t\t\t\t{ key: 'Squamous Cell Neoplasms', label: 'Squamous Cell Neoplasms', samplecount: 3 },\n\t\t\t\t\t\t\t{ key: 'Nevi and Melanomas', label: 'Nevi and Melanomas', samplecount: 7 },\n\t\t\t\t\t\t\t{ key: 'Basal Cell Neoplasms', label: 'Basal Cell Neoplasms', samplecount: 1 },\n\t\t\t\t\t\t\t{ key: 'Fibroepithelial Neoplasms', label: 'Fibroepithelial Neoplasms', samplecount: 2 },\n\t\t\t\t\t\t\t{ key: 'Neoplasms, NOS', label: 'Neoplasms, NOS', samplecount: 1547 },\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tkey: 'Soft Tissue Tumors and Sarcomas, NOS',\n\t\t\t\t\t\t\t\tlabel: 'Soft Tissue Tumors and Sarcomas, NOS',\n\t\t\t\t\t\t\t\tsamplecount: 30\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{ key: 'Not Reported', label: 'Not Reported', samplecount: 34 },\n\t\t\t\t\t\t\t{ key: 'Meningiomas', label: 'Meningiomas', samplecount: 29 },\n\t\t\t\t\t\t\t{ key: 'Mature B-Cell Lymphomas', label: 'Mature B-Cell Lymphomas', samplecount: 3 },\n\t\t\t\t\t\t\t{ key: 'Lymphoid Leukemias' },\n\t\t\t\t\t\t\t{ key: 'Myeloid Leukemias' },\n\t\t\t\t\t\t\t{ key: 'Acute Lymphoblastic Leukemia' },\n\t\t\t\t\t\t\t{ key: 'Neuroepitheliomatous Neoplasms' },\n\t\t\t\t\t\t\t{ key: 'Complex Mixed and Stromal Neoplasms' }\n\t\t\t\t\t\t]\n\t\t\t\t\t},\n\t\t\t\t\t{ name: 'Group Brain', type: 'values', uncomputable: false, values: [{ key: 'Gliomas', label: 'Gliomas' }] }\n\t\t\t\t]\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function getCategoricalTermcollectionTw() {\n\treturn {\n\t\ttype: 'TermCollectionTWQual',\n\t\tterm: { type: 'termCollection', name: 'Assay Availability' }\n\t}\n}\n\nexport function getAgeCollectionFractionTw() {\n\treturn {\n\t\ttype: 'TermCollectionTWFraction',\n\t\tterm: {\n\t\t\ttype: 'termCollection',\n\t\t\ttermIds: ['agedx', 'a_death', 'a_ndi', 'agelastvisit'],\n\t\t\tname: 'Fake Collection 1', // NOTE this name must match with the termCollection entry in termdbtest\n\t\t\tmemberType: 'numeric'\n\t\t},\n\t\tq: {\n\t\t\tmode: 'discrete',\n\t\t\tnumerators: ['a_death'],\n\t\t\tdenominators: ['agedx', 'a_death'],\n\t\t\ttype: 'custom-bin',\n\t\t\tlst: [\n\t\t\t\t{ startunbounded: true, stop: 0.8, label: '<0.8' },\n\t\t\t\t{ stopunbounded: true, start: 0.8, label: '>0.8' }\n\t\t\t]\n\t\t}\n\t}\n}\nexport function getIsoformExpCollectionFractionTw() {\n\treturn {\n\t\ttype: 'TermCollectionTWFraction',\n\t\tterm: {\n\t\t\ttype: 'termCollection',\n\t\t\tisCustom: true,\n\t\t\tmemberType: 'numeric',\n\t\t\tname: 'KRAS Isoforms (TPM)',\n\t\t\ttermlst: [\n\t\t\t\t{ id: 'ENST00000256078', name: 'ENST00000256078', type: 'isoformExpression', isoform: 'ENST00000256078' },\n\t\t\t\t{ id: 'ENST00000311936', name: 'ENST00000311936', type: 'isoformExpression', isoform: 'ENST00000311936' }\n\t\t\t]\n\t\t},\n\t\tq: {\n\t\t\tmode: 'discrete',\n\t\t\ttype: 'custom-bin',\n\t\t\tlst: [\n\t\t\t\t{ startunbounded: true, stop: 0.1, startinclusive: false, stopinclusive: true, label: 'low0.1' },\n\t\t\t\t{ start: 0.1, startinclusive: false, stopinclusive: false, stopunbounded: true, label: 'high0.1' }\n\t\t\t],\n\t\t\tdenominators: ['ENST00000256078', 'ENST00000311936'],\n\t\t\tnumerators: ['ENST00000256078']\n\t\t}\n\t}\n}\n"],
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+  "names": []
+}

package/dist/chunk-AGLAYNXP.js

@@ -0,0 +1,170 @@
+import {
+  getEmptyCell,
+  maySetEmptyCell,
+  setCellProps
+} from "./chunk-DH3LAQKT.js";
+import {
+  TermTypeGroups
+} from "./chunk-6PNPHACF.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/matrix.serieses.js
+var matrix_serieses_exports = {};
+__export(matrix_serieses_exports, {
+  getSerieses: () => getSerieses
+});
+function getSerieses(data) {
+  const s = this.settings.matrix;
+  const serieses = [];
+  const { colw, dx, dy, xMin, xMax } = this.dimensions;
+  const dvt = this.config.divideBy || {};
+  const divideByTermId = "id" in dvt ? dvt.id : dvt.name;
+  const legendGroups = {};
+  this.colorScaleByTermId = {};
+  for (const t of this.termOrder) {
+    const $id = t.tw.$id;
+    const termid = "id" in t.tw.term ? t.tw.term.id : t.tw.term.name;
+    const isDivideByTerm = termid === divideByTermId;
+    const emptyGridCells = [];
+    const cellht = t.grp.type == "hierCluster" ? s.clusterRowh : dy;
+    const htAdjust = t.grp.type == "hierCluster" ? 0 : t.totalHtAdjustments;
+    const y = s.transpose ? 0 : t.totalIndex * cellht + t.visibleGrpIndex * s.rowgspace + htAdjust;
+    const twSpecificSettings = this.config.settings.matrix.twSpecificSettings;
+    const hoverY0 = (twSpecificSettings[$id]?.contBarGap || 0) + y;
+    const series = {
+      t,
+      tw: t.tw,
+      cells: [],
+      y,
+      hoverY0,
+      hoverY1: hoverY0 + (twSpecificSettings[$id]?.contBarH || cellht)
+    };
+    for (const so of this.unfilteredSampleOrder) {
+      const { totalIndex, grpIndex, row } = so;
+      series.x = !s.transpose ? 0 : t.totalIndex * dx + t.visibleGrpIndex * s.colgspace;
+      const anno = row[$id];
+      const cellTemplate = {
+        s: so,
+        sample: row.sample,
+        tw: t.tw,
+        term: t.tw.term,
+        termid,
+        $id,
+        totalIndex,
+        grpIndex,
+        row,
+        t,
+        seriesY: y
+      };
+      if (!anno) {
+        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
+          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
+          series.cells.push(cell);
+        }
+        continue;
+      }
+      const key = anno.key;
+      const values = anno.filteredValues || anno.values || [anno.value];
+      const numRects = s.cellEncoding == "oncoprint" ? 1 : values.length;
+      const height = !s.transpose ? s.rowh / numRects : colw;
+      const width = !s.transpose ? colw : colw / values.length;
+      const siblingCells = [];
+      if (!anno || !anno.renderedValues?.length) {
+        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
+          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
+          series.cells.push(cell);
+        }
+        continue;
+      }
+      for (const [i, value] of values.entries()) {
+        const cell = Object.assign({ key, siblingCells }, cellTemplate);
+        cell.valueIndex = i;
+        let legend;
+        if (typeof t.tw.setCellProps == "function") {
+          legend = t.tw.setCellProps(cell, anno, value, s, t, this, width, height, dx, dy, i);
+        } else {
+          const cellProps = t.grp.type == "hierCluster" ? setCellProps["hierCluster"] : t.tw.term.type == "samplelst" ? setCellProps["categorical"] : setCellProps[t.tw.term.type];
+          legend = cellProps(cell, t.tw, anno, value, s, t, this, width, height, dx, dy, i);
+        }
+        if (!s.useCanvas && (cell.x + cell.width < xMin || cell.x - cell.width > xMax)) continue;
+        if (legend) {
+          for (const l of [legendGroups, so.grp.legendGroups]) {
+            if (!l) continue;
+            if (!l[legend.group]) {
+              l[legend.group] = {
+                ref: legend.ref,
+                values: {},
+                order: legend.order,
+                $id,
+                origin: legend.entry.origin
+              };
+              if (legend.entry.dt) l[legend.group].dt = [legend.entry.dt];
+            }
+            const lg = l[legend.group];
+            if (lg.dt && !lg.dt.includes(legend.entry.dt)) lg.dt.push(legend.entry.dt);
+            const legendK = legend.entry.origin ? legend.entry.origin + legend.value : legend.value;
+            if (!lg.values[legendK]) {
+              lg.values[legendK] = JSON.parse(JSON.stringify(legend.entry));
+              if (legend.entry.scale) lg.values[legendK].scale = legend.entry.scale;
+            }
+            if (!lg.values[legendK].samples) lg.values[legendK].samples = /* @__PURE__ */ new Set();
+            if (t.tw.term.name === TermTypeGroups.MUTATION_SIGNATURE) {
+              if (value?.value > 0) lg.values[legendK].samples.add(row.sample);
+            } else lg.values[legendK].samples.add(row.sample);
+            if (isDivideByTerm) {
+              lg.values[legend.value].isExcluded = so.grp.isExcluded;
+            }
+          }
+        }
+        if (!so.grp.isExcluded) {
+          if (anno.renderedValues.includes(value)) series.cells.push(cell);
+          siblingCells.push(cell);
+        }
+      }
+      if (s.showGrid == "rect" && !so.grp.isExcluded) {
+        const cell = t.grp.type == "hierCluster" ? getEmptyCell(cellTemplate, s, this.dimensions) : maySetEmptyCell[t.tw.term.type]?.(siblingCells, cellTemplate, s, this.dimensions, this);
+        if (cell) emptyGridCells.push(cell);
+      }
+    }
+    if (emptyGridCells.length) series.cells.unshift(...emptyGridCells);
+    if (series.cells.length) serieses.push(series);
+  }
+  addAllHiddenLegendGroups(legendGroups, this);
+  this.legendData = this.getLegendData(legendGroups, data.refs, this);
+  for (const grp of this.sampleGroups) {
+    grp.legendData = this.getLegendData(grp.legendGroups, data.refs, this);
+  }
+  return serieses;
+}
+function addAllHiddenLegendGroups(legendGroups, self) {
+  for (const valueFilter of self.config.legendValueFilter.lst) {
+    if (valueFilter.tvs.term.type == "categorical" && !legendGroups[valueFilter.tvs.term.$id]) {
+      legendGroups[valueFilter.tvs.term.$id] = {
+        ref: {},
+        values: {},
+        $id: valueFilter.tvs.term.$id
+      };
+    } else if (valueFilter.tvs.term.type == "geneVariant" && !legendGroups[valueFilter.legendGrpName]) {
+      legendGroups[valueFilter.legendGrpName] = {
+        ref: {},
+        values: {},
+        dt: [valueFilter.tvs.values[0].dt],
+        origin: valueFilter.tvs.values[0].origin
+      };
+    } else if ((valueFilter.tvs.term.type == "integer" || valueFilter.tvs.term.type == "float") && !legendGroups[valueFilter.tvs.term.$id]) {
+      legendGroups[valueFilter.tvs.term.$id] = {
+        ref: {},
+        values: {},
+        $id: valueFilter.tvs.term.$id
+      };
+    }
+  }
+}
+
+export {
+  getSerieses,
+  matrix_serieses_exports
+};
+//# sourceMappingURL=chunk-AGLAYNXP.js.map

package/dist/chunk-AGLAYNXP.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/matrix.serieses.js"],
+  "sourcesContent": ["import { setCellProps, getEmptyCell, maySetEmptyCell, setGeneVariantCellProps } from './matrix.cells'\nimport { TermTypes } from '#types'\nimport { TermTypeGroups } from '#shared/common.js'\n\nexport function getSerieses(data) {\n\tconst s = this.settings.matrix\n\tconst serieses = []\n\tconst { colw, dx, dy, xMin, xMax } = this.dimensions\n\tconst dvt = this.config.divideBy || {}\n\tconst divideByTermId = 'id' in dvt ? dvt.id : dvt.name\n\tconst legendGroups = {}\n\tthis.colorScaleByTermId = {}\n\n\tfor (const t of this.termOrder) {\n\t\tconst $id = t.tw.$id\n\t\tconst termid = 'id' in t.tw.term ? t.tw.term.id : t.tw.term.name\n\t\tconst isDivideByTerm = termid === divideByTermId\n\t\tconst emptyGridCells = []\n\t\tconst cellht = t.grp.type == 'hierCluster' ? s.clusterRowh : dy\n\t\tconst htAdjust = t.grp.type == 'hierCluster' ? 0 : t.totalHtAdjustments\n\t\tconst y = s.transpose ? 0 : t.totalIndex * cellht + t.visibleGrpIndex * s.rowgspace + htAdjust\n\t\tconst twSpecificSettings = this.config.settings.matrix.twSpecificSettings\n\t\tconst hoverY0 = (twSpecificSettings[$id]?.contBarGap || 0) + y\n\t\tconst series = {\n\t\t\tt,\n\t\t\ttw: t.tw,\n\t\t\tcells: [],\n\t\t\ty,\n\t\t\thoverY0,\n\t\t\thoverY1: hoverY0 + (twSpecificSettings[$id]?.contBarH || cellht)\n\t\t}\n\n\t\tfor (const so of this.unfilteredSampleOrder) {\n\t\t\tconst { totalIndex, grpIndex, row } = so\n\t\t\tseries.x = !s.transpose ? 0 : t.totalIndex * dx + t.visibleGrpIndex * s.colgspace\n\n\t\t\tconst anno = row[$id]\n\t\t\tconst cellTemplate = {\n\t\t\t\ts: so,\n\t\t\t\tsample: row.sample,\n\t\t\t\ttw: t.tw,\n\t\t\t\tterm: t.tw.term,\n\t\t\t\ttermid,\n\t\t\t\t$id,\n\t\t\t\ttotalIndex,\n\t\t\t\tgrpIndex,\n\t\t\t\trow,\n\t\t\t\tt,\n\t\t\t\tseriesY: y\n\t\t\t}\n\n\t\t\tif (!anno) {\n\t\t\t\tif (!so.grp.isExcluded && (s.useCanvas || so.grp)) {\n\t\t\t\t\tconst cell = getEmptyCell(cellTemplate, s, this.dimensions)\n\t\t\t\t\tseries.cells.push(cell)\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tconst key = anno.key\n\n\t\t\tconst values = anno.filteredValues || anno.values || [anno.value]\n\n\t\t\tconst numRects = s.cellEncoding == 'oncoprint' ? 1 : values.length\n\t\t\tconst height = !s.transpose ? s.rowh / numRects : colw\n\t\t\tconst width = !s.transpose ? colw : colw / values.length\n\t\t\tconst siblingCells = []\n\t\t\tif (!anno || !anno.renderedValues?.length) {\n\t\t\t\tif (!so.grp.isExcluded && (s.useCanvas || so.grp)) {\n\t\t\t\t\tconst cell = getEmptyCell(cellTemplate, s, this.dimensions)\n\t\t\t\t\tseries.cells.push(cell)\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tfor (const [i, value] of values.entries()) {\n\t\t\t\tconst cell = Object.assign({ key, siblingCells }, cellTemplate)\n\t\t\t\tcell.valueIndex = i\n\n\t\t\t\tlet legend\n\t\t\t\tif (typeof t.tw.setCellProps == 'function') {\n\t\t\t\t\t// use extended tw method if present\n\t\t\t\t\tlegend = t.tw.setCellProps(cell, anno, value, s, t, this, width, height, dx, dy, i)\n\t\t\t\t} else {\n\t\t\t\t\t// hierCluster terms have their own setCellProps\n\t\t\t\t\tconst cellProps =\n\t\t\t\t\t\tt.grp.type == 'hierCluster'\n\t\t\t\t\t\t\t? setCellProps['hierCluster']\n\t\t\t\t\t\t\t: t.tw.term.type == 'samplelst'\n\t\t\t\t\t\t\t? setCellProps['categorical']\n\t\t\t\t\t\t\t: setCellProps[t.tw.term.type]\n\n\t\t\t\t\t// will assign x, y, width, height, fill, label, order, etc\n\t\t\t\t\tlegend = cellProps(cell, t.tw, anno, value, s, t, this, width, height, dx, dy, i)\n\t\t\t\t}\n\n\t\t\t\tif (!s.useCanvas && (cell.x + cell.width < xMin || cell.x - cell.width > xMax)) continue\n\t\t\t\tif (legend) {\n\t\t\t\t\tfor (const l of [legendGroups, so.grp.legendGroups]) {\n\t\t\t\t\t\tif (!l) continue\n\t\t\t\t\t\tif (!l[legend.group]) {\n\t\t\t\t\t\t\tl[legend.group] = {\n\t\t\t\t\t\t\t\tref: legend.ref,\n\t\t\t\t\t\t\t\tvalues: {},\n\t\t\t\t\t\t\t\torder: legend.order,\n\t\t\t\t\t\t\t\t$id,\n\t\t\t\t\t\t\t\torigin: legend.entry.origin\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t// legend group dt needs to be an array because a legend group such as Mutations/Consequences\n\t\t\t\t\t\t\t// could have legend items from multiple dts (dt=1, dt=2, dt=5)\n\t\t\t\t\t\t\tif (legend.entry.dt) l[legend.group].dt = [legend.entry.dt]\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tconst lg = l[legend.group]\n\t\t\t\t\t\tif (lg.dt && !lg.dt.includes(legend.entry.dt)) lg.dt.push(legend.entry.dt)\n\t\t\t\t\t\tconst legendK = legend.entry.origin ? legend.entry.origin + legend.value : legend.value\n\n\t\t\t\t\t\tif (!lg.values[legendK]) {\n\t\t\t\t\t\t\tlg.values[legendK] = JSON.parse(JSON.stringify(legend.entry))\n\t\t\t\t\t\t\tif (legend.entry.scale) lg.values[legendK].scale = legend.entry.scale\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (!lg.values[legendK].samples) lg.values[legendK].samples = new Set()\n\t\t\t\t\t\tif (t.tw.term.name === TermTypeGroups.MUTATION_SIGNATURE) {\n\t\t\t\t\t\t\t// for Mutation Signature only count sample when it's signature value > 0\n\t\t\t\t\t\t\tif (value?.value > 0) lg.values[legendK].samples.add(row.sample)\n\t\t\t\t\t\t} else lg.values[legendK].samples.add(row.sample)\n\n\t\t\t\t\t\tif (isDivideByTerm) {\n\t\t\t\t\t\t\tlg.values[legend.value].isExcluded = so.grp.isExcluded\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tif (!so.grp.isExcluded) {\n\t\t\t\t\tif (anno.renderedValues.includes(value)) series.cells.push(cell)\n\t\t\t\t\tsiblingCells.push(cell)\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (s.showGrid == 'rect' && !so.grp.isExcluded) {\n\t\t\t\tconst cell =\n\t\t\t\t\tt.grp.type == 'hierCluster'\n\t\t\t\t\t\t? getEmptyCell(cellTemplate, s, this.dimensions)\n\t\t\t\t\t\t: maySetEmptyCell[t.tw.term.type]?.(siblingCells, cellTemplate, s, this.dimensions, this)\n\t\t\t\tif (cell) emptyGridCells.push(cell)\n\t\t\t}\n\t\t}\n\t\tif (emptyGridCells.length) series.cells.unshift(...emptyGridCells)\n\t\tif (series.cells.length) serieses.push(series)\n\t}\n\n\taddAllHiddenLegendGroups(legendGroups, this)\n\tthis.legendData = this.getLegendData(legendGroups, data.refs, this)\n\tfor (const grp of this.sampleGroups) {\n\t\tgrp.legendData = this.getLegendData(grp.legendGroups, data.refs, this)\n\t}\n\treturn serieses\n}\n\n// Add a legendGroup for the a legend group whose legends are all hidden\nfunction addAllHiddenLegendGroups(legendGroups, self) {\n\tfor (const valueFilter of self.config.legendValueFilter.lst) {\n\t\tif (valueFilter.tvs.term.type == 'categorical' && !legendGroups[valueFilter.tvs.term.$id]) {\n\t\t\tlegendGroups[valueFilter.tvs.term.$id] = {\n\t\t\t\tref: {},\n\t\t\t\tvalues: {},\n\t\t\t\t$id: valueFilter.tvs.term.$id\n\t\t\t}\n\t\t} else if (valueFilter.tvs.term.type == 'geneVariant' && !legendGroups[valueFilter.legendGrpName]) {\n\t\t\tlegendGroups[valueFilter.legendGrpName] = {\n\t\t\t\tref: {},\n\t\t\t\tvalues: {},\n\t\t\t\tdt: [valueFilter.tvs.values[0].dt],\n\t\t\t\torigin: valueFilter.tvs.values[0].origin\n\t\t\t}\n\t\t} else if (\n\t\t\t(valueFilter.tvs.term.type == 'integer' || valueFilter.tvs.term.type == 'float') &&\n\t\t\t!legendGroups[valueFilter.tvs.term.$id]\n\t\t) {\n\t\t\tlegendGroups[valueFilter.tvs.term.$id] = {\n\t\t\t\tref: {},\n\t\t\t\tvalues: {},\n\t\t\t\t$id: valueFilter.tvs.term.$id\n\t\t\t}\n\t\t}\n\t}\n}\n"],
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+}