@sjcrh/proteinpaint-client 2.197.0 → 2.198.0

package/dist/chunk-MCXQL4W2.js

@@ -1,226 +0,0 @@
-import {
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-M2PPUO4E.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" }
-  };
-}
-
-export {
-  getSamplelstTw,
-  getCategoryGroupsetting,
-  getGenesetMutTw,
-  getGeneVariantTw,
-  getSsgseaTw,
-  getScgeneexpTw,
-  getScctTw,
-  getCategoricalTermcollectionTw
-};
-//# sourceMappingURL=chunk-MCXQL4W2.js.map

package/dist/chunk-MCXQL4W2.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../test/testdata/data.ts"],
-  "sourcesContent": ["import * as tt from '#shared/terms.js'\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: 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'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\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: 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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 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