@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/chunk-KZFOWI7N.js

@@ -1,52 +0,0 @@
-import {
-  plotColor
-} from "./chunk-XRVBHNCW.js";
-
-// plots/scatter/settings/defaults.ts
-function getDefaultScatterSettings(opts = {}) {
-  const overrides = opts?.overrides || {};
-  const defaults = {
-    size: 0.8,
-    minShapeSize: 0.5,
-    maxShapeSize: 4,
-    scaleDotOrder: "Ascending",
-    refSize: 0.8,
-    svgw: 600,
-    svgh: 600,
-    svgd: 600,
-    axisTitleFontSize: 16,
-    showAxes: true,
-    showRef: true,
-    opacity: 0.6,
-    defaultColor: plotColor,
-    regression: "None",
-    fov: 50,
-    threeSize: 5e-3,
-    threeFOV: 70,
-    //ColorScale settings
-    colorScaleMode: "auto",
-    colorScalePercentile: 95,
-    colorScaleMinFixed: null,
-    colorScaleMaxFixed: null,
-    //3D Plot settings
-    showContour: false,
-    colorContours: false,
-    contourBandwidth: 30,
-    contourThresholds: 10,
-    duration: 500,
-    useGlobalMinMax: true,
-    saveZoomTransform: false,
-    // Axis scale settings
-    minXScale: null,
-    maxXScale: null,
-    minYScale: null,
-    maxYScale: null,
-    itemLabel: opts?.singleCellPlot ? "Cell" : "Sample"
-  };
-  return Object.assign(defaults, overrides);
-}
-
-export {
-  getDefaultScatterSettings
-};
-//# sourceMappingURL=chunk-KZFOWI7N.js.map

package/dist/chunk-LJS24D4U.js

@@ -1,50 +0,0 @@
-import {
-  addGeneSearchbox,
-  getSCGEunit
-} from "./chunk-KBYRXJ6Y.js";
-import {
-  Menu
-} from "./chunk-A6TQGNDQ.js";
-import {
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-SOED2SLH.js";
-
-// termdb/handlers/singleCellGeneExpression.ts
-var SearchHandler = class {
-  init(opts) {
-    this.validateOpts(opts);
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => this.selectGene(geneSearch.geneSymbol, opts.usecase?.specialCase?.config?.sample)
-    });
-  }
-  /**TODO: scge tw handler will validate that a sample is included. Need to resolve issue
-   * with sample info not included.*/
-  async selectGene(gene, sample) {
-    if (!gene) throw new Error("No gene selected");
-    const unit = getSCGEunit(this.app.vocabApi);
-    const name = `${gene} ${unit}`;
-    this.callback({ gene, name, type: SINGLECELL_GENE_EXPRESSION, sample });
-  }
-  validateOpts(opts) {
-    if (opts.callback == null) throw new Error("callback is required");
-    if (opts.app == null) throw new Error("app is required");
-    if (opts.holder == null) throw new Error("holder is required");
-    if (opts.genomeObj == null) throw new Error("genomeObj is required");
-    if (opts.usecase == null) throw new Error("usecase is required");
-    if (!opts.usecase?.specialCase?.config?.sample) {
-      throw new Error("usecase.specialCase.config.sample is required for singleCellGeneExpression handler");
-    }
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-LJS24D4U.js.map

package/dist/chunk-LKFYRQOH.js

@@ -1,226 +0,0 @@
-import {
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-SOED2SLH.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: "scRNA",
-      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-LKFYRQOH.js.map

package/dist/chunk-LKFYRQOH.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() {\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' },\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: 10,\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_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: 'scRNA',\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: '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"],
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-  "names": []
-}

package/dist/chunk-LXQ6DLAR.js

@@ -1,217 +0,0 @@
-import {
-  dofetch,
-  dofetch2
-} from "./chunk-RCYTUKAJ.js";
-import {
-  contigNameNoChr2
-} from "./chunk-XRVBHNCW.js";
-
-// tracks/hic/data/parseData.ts
-async function hicParseFile(hic, debugmode, errList = []) {
-  if (debugmode) window["hic"] = hic;
-  if (hic.tklst) {
-    const lst = [];
-    for (const t of hic.tklst) {
-      if (!t.type) {
-        errList.push("type missing from one of the tracks accompanying HiC");
-      } else {
-        t.iscustom = true;
-        lst.push(t);
-      }
-    }
-    if (lst.length) {
-      hic.tklst = lst;
-    } else {
-      delete hic.tklst;
-    }
-  }
-  if (hic.enzyme) {
-    if (hic.genome.hicenzymefragment) {
-      let frag = null;
-      for (const f of hic.genome.hicenzymefragment) {
-        if (f.enzyme == hic.enzyme) {
-          frag = f;
-          break;
-        }
-      }
-      if (frag) {
-        hic.enzymefile = frag.file;
-      } else {
-        errList.push("unknown enzyme: " + hic.enzyme);
-        delete hic.enzyme;
-      }
-    } else {
-      errList.push("no enzyme fragment information available for this genome");
-      delete hic.enzyme;
-    }
-  }
-  try {
-    if (hic.sv && hic.sv.file) {
-      const re = await dofetch(hic.hostURL + "/textfile", {
-        method: "POST",
-        body: JSON.stringify({ file: hic.sv.file, jwt: hic.jwt })
-      });
-      const data2 = re.json();
-      const [err2, header, items] = parseSV(data2.text);
-      if (err2) throw { message: "Error parsing SV: " + err2 };
-      hic.sv.header = header;
-      hic.sv.items = items;
-    }
-    const data = await dofetch2("hicstat?" + (hic.file ? "file=" + hic.file : "url=" + hic.url));
-    if (data.error) {
-      errList.push(data.error);
-      return;
-    }
-    const err = hicparsestat(hic, data.out);
-    if (err) throw { message: err };
-  } catch (err) {
-    errList.push(err.message || err);
-    if (err.stack) {
-      console.log(err.stack);
-    }
-  }
-  return hic;
-}
-function parseSV(txt) {
-  const lines = txt.trim().split(/\r?\n/);
-  const [err, header] = parseSVheader(lines[0]);
-  if (err) return ["header error: " + err];
-  const items = [];
-  for (let i = 1; i < lines.length; i++) {
-    const line = lines[i];
-    if (line[0] == "#") continue;
-    const [e, m] = parseSVline(line, header);
-    if (e) return ["line " + (i + 1) + " error: " + e];
-    items.push(m);
-  }
-  return [null, header, items];
-}
-function parseSVheader(line) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid file header for fusions";
-  const htry = (...lst) => {
-    for (const a of lst) {
-      const j = header.indexOf(a);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("chr_a", "chr1", "chra");
-  if (i == -1) return "chr_A missing from header";
-  header[i] = "chr1";
-  i = htry("chr_b", "chr2", "chrb");
-  if (i == -1) return "chr_B missing from header";
-  header[i] = "chr2";
-  i = htry("pos_a", "position_a", "position1", "posa");
-  if (i == -1) return "pos_a missing from header";
-  header[i] = "position1";
-  i = htry("pos_b", "position_b", "position2", "posb");
-  if (i == -1) return "pos_b missing from header";
-  header[i] = "position2";
-  i = htry("strand_a", "orta", "orienta");
-  if (i == -1) return "strand_a missing from header";
-  header[i] = "strand1";
-  i = htry("strand_b", "ortb", "orientb");
-  if (i == -1) return "strand_b missing from header";
-  header[i] = "strand2";
-  i = htry("numreadsa");
-  if (i != -1) header[i] = "reads1";
-  i = htry("numreadsb");
-  if (i != -1) header[i] = "reads2";
-  return [null, header];
-}
-function parseSVline(line, header) {
-  const lst = line.split("	");
-  const m = {};
-  for (let j = 0; j < header.length; j++) {
-    m[header[j]] = lst[j];
-  }
-  if (!m.chr1) return ["missing chr1"];
-  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
-    m.chr1 = "chr" + m.chr1;
-  }
-  if (!m.chr2) return ["missing chr2"];
-  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
-    m.chr2 = "chr" + m.chr2;
-  }
-  if (!m.position1) return ["missing position1"];
-  let v = Number.parseInt(m.position1);
-  if (Number.isNaN(v) || v <= 0) return ["position1 invalid value"];
-  m.position1 = v;
-  if (!m.position2) return ["missing position2"];
-  v = Number.parseInt(m.position2);
-  if (Number.isNaN(v) || v <= 0) return ["position2 invalid value"];
-  m.position2 = v;
-  if (m.reads1) {
-    v = Number.parseInt(m.reads1);
-    if (Number.isNaN(v)) return ["reads1 invalid value"];
-    m.reads1 = v;
-  }
-  if (m.reads2) {
-    v = Number.parseInt(m.reads2);
-    if (Number.isNaN(v)) return ["reads2 invalid value"];
-    m.reads2 = v;
-  }
-  return [null, m];
-}
-function hicparsestat(hic, j) {
-  if (!j) return "cannot stat hic file";
-  hic.normalization = j.normalization;
-  hic.version = j.version;
-  if (!j.Chromosomes) return "Chromosomes not found in file stat";
-  if (!Array.isArray(j.chrorder)) return ".chrorder[] missing";
-  if (j.chrorder.length == 0) return ".chrorder[] empty array";
-  hic.chrorder = j.chrorder;
-  if (!j["Base pair-delimited resolutions"]) return "Base pair-delimited resolutions not found in file stat";
-  if (!Array.isArray(j["Base pair-delimited resolutions"])) return "Base pair-delimited resolutions should be array";
-  hic.bpresolution = j["Base pair-delimited resolutions"];
-  if (!j["Fragment-delimited resolutions"]) return "Fragment-delimited resolutions not found in file stat";
-  if (!Array.isArray(j["Fragment-delimited resolutions"])) return "Fragment-delimited resolutions is not array";
-  hic.fragresolution = j["Fragment-delimited resolutions"];
-  const chrlst = [];
-  for (const chr in j.Chromosomes) {
-    chrlst.push(chr);
-  }
-  const [nochrcount, haschrcount] = contigNameNoChr2(hic.genome, chrlst);
-  if (nochrcount + haschrcount == 0) return "chromosome names do not match with genome build";
-  if (nochrcount > 0) {
-    hic.nochr = true;
-    for (let i = 0; i < hic.chrorder.length; i++) hic.chrorder[i] = "chr" + hic.chrorder[i];
-  }
-  hic.chrlst = [];
-  for (const chr of hic.genome.majorchrorder) {
-    const c2 = hic.nochr ? chr.replace("chr", "") : chr;
-    if (chrlst.indexOf(c2) != -1) {
-      hic.chrlst.push(chr);
-    }
-  }
-}
-function hicparsefragdata(items) {
-  const id2coord = /* @__PURE__ */ new Map();
-  let min = null, max;
-  for (const i of items) {
-    if (!i.rest || !i.rest[0]) {
-      return ["items[].rest data problem"];
-    }
-    const id = Number.parseInt(i.rest[0]);
-    if (Number.isNaN(id)) {
-      return [i.start + "." + i.stop + " invalid fragment id: " + i.rest[0]];
-    }
-    id2coord.set(id, [i.start, i.stop]);
-    if (min == null) {
-      min = id;
-      max = id;
-    } else {
-      min = Math.min(min, id);
-      max = Math.max(max, id);
-    }
-  }
-  return [null, id2coord, min, max];
-}
-
-export {
-  hicParseFile,
-  hicparsestat,
-  hicparsefragdata
-};
-//# sourceMappingURL=chunk-LXQ6DLAR.js.map