@sjcrh/proteinpaint-client 2.226.0 → 2.227.1

package/dist/chunk-EARMOT6Q.js

@@ -1,176 +0,0 @@
-import {
-  appInit
-} from "./chunk-4WFXCUT4.js";
-import {
-  showErrorsWithCounter
-} from "./chunk-DPWSIN62.js";
-import {
-  mclass
-} from "./chunk-2N345NXD.js";
-
-// plots/disco/launch.adhoc.ts
-async function launch(arg, genomeObj, holder) {
-  const [mlst, errors] = await getMlst(arg);
-  if (errors?.length) {
-    return showErrorsWithCounter(errors, holder);
-  }
-  const opts = {
-    holder,
-    vocabApi: {
-      // api is required by plot.app.js, so create a mock one for the adhoc data
-      vocab: { terms: [] },
-      main: () => {
-        return;
-      },
-      getTermdbConfig: () => {
-        return {};
-      }
-    },
-    state: {
-      args: {
-        data: mlst,
-        genome: genomeObj
-      },
-      plots: [
-        {
-          chartType: "Disco",
-          subfolder: "disco",
-          extension: "ts",
-          /** NOTE: Users should only override the settings in the default
-           * settings.Disco:{}, not the entire settings:{} object.*/
-          overrides: { Disco: arg?.settings || {} }
-        }
-      ]
-    }
-  };
-  const plotAppApi = await appInit(opts);
-  return plotAppApi;
-}
-async function getMlst(arg) {
-  if (Array.isArray(arg.mlst)) {
-    return [arg.mlst, null];
-  }
-  const mlst = [];
-  const errors = [];
-  if (arg.snvText) parseSnvText(arg.snvText, mlst, errors);
-  if (arg.svText) parseSvText(arg.svText, mlst, errors);
-  if (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors);
-  return [mlst, errors];
-}
-function parseSnvText(text, mlst, errors) {
-  for (const line of text.trim().split("\n")) {
-    const l = line.trim().split("	");
-    if (![5, 7, 9].includes(l.length)) {
-      errors.push("snv input not equal to 5, 7, or 9 columns");
-      continue;
-    }
-    let m;
-    try {
-      m = {
-        dt: 1,
-        chr: l[0],
-        position: Number(l[1]),
-        gene: l[2],
-        mname: l[3],
-        class: validateMutation(l[4], errors)
-      };
-      const vafs = parseOptionalVafs(l, errors);
-      if (vafs.length) m.vafs = vafs;
-    } catch (e) {
-      errors.push(e);
-      continue;
-    }
-    mlst.push(m);
-  }
-}
-function parseOptionalVafs(line, errors) {
-  const vafs = [];
-  const addVaf = (id, totalIndex, altIndex) => {
-    if (line.length <= altIndex) return;
-    const totalCount = Number(line[totalIndex]);
-    const altCount = Number(line[altIndex]);
-    if (!Number.isInteger(totalCount) || !Number.isInteger(altCount) || totalCount <= 0 || altCount < 0 || altCount > totalCount) {
-      errors.push(`${id} total/alt counts must be integers with total > 0, alt >= 0, and alt cannot exceed total`);
-      return;
-    }
-    vafs.push({ id, totalCount, altCount });
-  };
-  addVaf("DNA", 5, 6);
-  addVaf("RNA", 7, 8);
-  return vafs;
-}
-function parseSvText(text, mlst, errors) {
-  for (const line of text.trim().split("\n")) {
-    const l = line.trim().split("	");
-    if (l.length < 4 || l.length > 6) {
-      errors.push("sv input not equal to 4 or 6 columns");
-      continue;
-    }
-    let m;
-    try {
-      const length = l.length;
-      if (length == 4) {
-        m = {
-          dt: 2,
-          chrA: l[0],
-          posA: Number(l[1]),
-          chrB: l[2],
-          posB: Number(l[3])
-        };
-      } else {
-        m = {
-          dt: 2,
-          chrA: l[0],
-          posA: Number(l[1]),
-          geneA: l[2],
-          chrB: l[3],
-          posB: Number(l[4]),
-          geneB: l[5]
-        };
-      }
-    } catch (e) {
-      errors.push(e);
-      continue;
-    }
-    mlst.push(m);
-  }
-}
-function parseCnvText(text, mlst, errors) {
-  for (const line of text.trim().split("\n")) {
-    const l = line.trim().split("	");
-    if (l.length != 4) {
-      errors.push("cnv input not equal to 4 columns");
-      continue;
-    }
-    let m;
-    try {
-      m = {
-        dt: 4,
-        chr: l[0],
-        start: Number(l[1]),
-        stop: Number(l[2]),
-        value: Number(l[3])
-      };
-    } catch (e) {
-      errors.push(e);
-      continue;
-    }
-    mlst.push(m);
-  }
-}
-function validateMutation(mutation, errors) {
-  const mut2check = mutation.toLowerCase();
-  const foundMutation = Object.values(mclass).find(
-    (m) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check
-  );
-  if (foundMutation) {
-    return foundMutation.key;
-  } else {
-    errors.push(`Invalid mutation class: ${mutation}`);
-  }
-}
-
-export {
-  launch
-};
-//# sourceMappingURL=chunk-EARMOT6Q.js.map

package/dist/chunk-EARMOT6Q.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/disco/launch.adhoc.ts"],
-  "sourcesContent": ["import type { Genome } from '#types'\nimport type { Selection } from 'd3-selection'\nimport { appInit } from '../plot.app'\nimport { showErrorsWithCounter } from '../../dom/sayerror'\nimport { mclass } from '#shared/common.js'\n\ntype SnvEntry = {\n\tdt: 1\n\tchr: string\n\tposition: number\n\tgene: string\n\tmname: string\n\tclass: string\n\tvafs?: Array<{ id: string; totalCount: number; altCount: number }>\n}\ntype CnvEntry = {\n\tdt: 4\n\tchr: string\n\tstart: number\n\tstop: number\n\tvalue: number\n}\ntype SvEntry4Cols = {\n\tdt: number\n\tchrA: string\n\tposA: number\n\tchrB: string\n\tposB: number\n}\n\ntype SvEntry6Cols = {\n\tdt: number\n\tchrA: string\n\tposA: number\n\tgeneA: string\n\tchrB: string\n\tposB: number\n\tgeneB: string\n}\n\ntype SvEntry = SvEntry4Cols | SvEntry6Cols\n\ntype MutationListEntry = SnvEntry | CnvEntry | SvEntry\n\n/** When disco is embedded, the arguments below are nested under arg.disco */\nexport type DiscoPlotArgs = {\n\t/**optional array of preparsed mutation events, from runpp() */\n\tmlst?: MutationListEntry[]\n\n\t/**tabular text of snv data, with follow columns.\n\t1. chr\n\t2. position\n\t3. gene\n\t4. aachange\n\t5. class\n\tOptionally, provide DNA total/alt read counts in columns 6-7 and RNA total/alt \n\tread counts in columns 8-9.\n\teach line is parsed into an object:\n\t{dt:1, chr:, position:, gene:, class:} */\n\tsnvText?: string\n\t/**tp path to a text file of same content as snvText */\n\tsnvFile?: string\n\t/**url of a text file of same content as snvText */\n\tsnvUrl?: string\n\n\t/**tabular text of sv/fusion data, with follow columns\n\t1. chrA\n\t2. posA\n\t3. geneA\n\t4. chrB\n\t5. posB\n\t6. geneB\n\teach line is parsed into an object:\n\t{dt:2, chrA, posA, geneA, chrB, posB, geneB} */\n\tsvText?: string\n\tsvFile?: string\n\tsvUrl?: string\n\n\t/**tabular text of cnv data, with following columns\n\t1. chr\n\t2. start\n\t3. stop\n\t4. value\n\teach line is parsed into an object\n\t{chr, start, stop, value} */\n\tcnvText?: string\n\tcnvFile?: string\n\tcnvUrl?: string\n\tsettings?: any\n}\n\n//... more datatypes can be added later\n\n/**\n * parse input data into mlst[] and pass to disco\n * TODO display data error on ui\n * TODO later make this script a native part of disco, so that runpp() directly invokes plot.app.js...\n * @param arg\n * @param genomeObj\n * @param holder\n * @returns\n */\n\nexport async function launch(arg: DiscoPlotArgs, genomeObj: Genome, holder: Selection<HTMLDivElement, any, any, any>) {\n\tconst [mlst, errors] = await getMlst(arg)\n\n\tif (errors?.length) {\n\t\treturn showErrorsWithCounter(errors, holder)\n\t}\n\n\tconst opts = {\n\t\tholder,\n\t\tvocabApi: {\n\t\t\t// api is required by plot.app.js, so create a mock one for the adhoc data\n\t\t\tvocab: { terms: [] },\n\t\t\tmain: () => {\n\t\t\t\treturn //fix so linter doesn't yell while this is in development\n\t\t\t},\n\t\t\tgetTermdbConfig: () => {\n\t\t\t\treturn {}\n\t\t\t}\n\t\t},\n\t\tstate: {\n\t\t\targs: {\n\t\t\t\tdata: mlst,\n\t\t\t\tgenome: genomeObj\n\t\t\t},\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'Disco',\n\t\t\t\t\tsubfolder: 'disco',\n\t\t\t\t\textension: 'ts',\n\t\t\t\t\t/** NOTE: Users should only override the settings in the default\n\t\t\t\t\t * settings.Disco:{}, not the entire settings:{} object.*/\n\t\t\t\t\toverrides: { Disco: arg?.settings || {} }\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n\n\tconst plotAppApi = await appInit(opts)\n\treturn plotAppApi\n}\n\n/**\n * from multiple possible data sources, parse mutation events and put everything into one array and return, for disco rendering\n * app drawer will supply data for \"snvText, svText, cnvText\"\n * while the \"File\" and \"Url\" can come from url parameters e.g. host?disco=1&snvFile=path/to/file\n * @param arg\n * @returns\n */\nasync function getMlst(arg: DiscoPlotArgs): Promise<[MutationListEntry[], string[] | null]> {\n\tif (Array.isArray(arg.mlst)) {\n\t\t// has preformatted in runpp()\n\t\treturn [arg.mlst, null]\n\t}\n\n\t// parse data from text and files and append to one mlst[] array\n\tconst mlst = [] as MutationListEntry[]\n\tconst errors = [] as string[]\n\n\tif (arg.snvText) parseSnvText(arg.snvText, mlst, errors)\n\tif (arg.svText) parseSvText(arg.svText, mlst, errors)\n\tif (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors)\n\n\t// if (arg.snvFile) {\n\t// }\n\t// if (arg.snvUrl) {\n\t// }\n\t// if (arg.svFile) {\n\t// }\n\t// if (arg.svUrl) {\n\t// }\n\t// if (arg.cnvFile) {\n\t// }\n\t// if (arg.cnvUrl) {\n\t// }\n\n\treturn [mlst, errors]\n}\n\nfunction parseSnvText(text: string, mlst: MutationListEntry[], errors: string[]) {\n\t// TODO share a parser for snvindel text file with samples (with header line and non-fixed columns), but should not require sample here\n\tfor (const line of text.trim().split('\\n')) {\n\t\tconst l = line.trim().split('\\t')\n\n\t\tif (![5, 7, 9].includes(l.length)) {\n\t\t\terrors.push('snv input not equal to 5, 7, or 9 columns')\n\t\t\tcontinue\n\t\t}\n\n\t\tlet m: SnvEntry\n\t\ttry {\n\t\t\tm = {\n\t\t\t\tdt: 1,\n\t\t\t\tchr: l[0],\n\t\t\t\tposition: Number(l[1]),\n\t\t\t\tgene: l[2],\n\t\t\t\tmname: l[3],\n\t\t\t\tclass: validateMutation(l[4], errors)\n\t\t\t}\n\t\t\tconst vafs = parseOptionalVafs(l, errors)\n\t\t\tif (vafs.length) m.vafs = vafs\n\t\t} catch (e: any) {\n\t\t\terrors.push(e)\n\t\t\tcontinue\n\t\t}\n\t\tmlst.push(m)\n\t}\n}\n\nfunction parseOptionalVafs(line: string[], errors: string[]) {\n\tconst vafs: Array<{ id: string; totalCount: number; altCount: number }> = []\n\tconst addVaf = (id: string, totalIndex: number, altIndex: number) => {\n\t\tif (line.length <= altIndex) return\n\t\tconst totalCount = Number(line[totalIndex])\n\t\tconst altCount = Number(line[altIndex])\n\t\tif (\n\t\t\t!Number.isInteger(totalCount) ||\n\t\t\t!Number.isInteger(altCount) ||\n\t\t\ttotalCount <= 0 ||\n\t\t\taltCount < 0 ||\n\t\t\taltCount > totalCount\n\t\t) {\n\t\t\terrors.push(`${id} total/alt counts must be integers with total > 0, alt >= 0, and alt cannot exceed total`)\n\t\t\treturn\n\t\t}\n\n\t\tvafs.push({ id, totalCount, altCount })\n\t}\n\n\taddVaf('DNA', 5, 6)\n\taddVaf('RNA', 7, 8)\n\treturn vafs\n}\n\nfunction parseSvText(text: string, mlst: MutationListEntry[], errors: string[]) {\n\tfor (const line of text.trim().split('\\n')) {\n\t\tconst l = line.trim().split('\\t')\n\t\tif (l.length < 4 || l.length > 6) {\n\t\t\terrors.push('sv input not equal to 4 or 6 columns')\n\t\t\tcontinue\n\t\t}\n\t\tlet m: SvEntry\n\t\ttry {\n\t\t\tconst length: number = l.length\n\t\t\tif (length == 4) {\n\t\t\t\tm = {\n\t\t\t\t\tdt: 2,\n\t\t\t\t\tchrA: l[0],\n\t\t\t\t\tposA: Number(l[1]),\n\t\t\t\t\tchrB: l[2],\n\t\t\t\t\tposB: Number(l[3])\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tm = {\n\t\t\t\t\tdt: 2,\n\t\t\t\t\tchrA: l[0],\n\t\t\t\t\tposA: Number(l[1]),\n\t\t\t\t\tgeneA: l[2],\n\t\t\t\t\tchrB: l[3],\n\t\t\t\t\tposB: Number(l[4]),\n\t\t\t\t\tgeneB: l[5]\n\t\t\t\t}\n\t\t\t}\n\t\t} catch (e: any) {\n\t\t\terrors.push(e)\n\t\t\tcontinue\n\t\t}\n\t\tmlst.push(m)\n\t}\n}\n\nfunction parseCnvText(text: string, mlst: MutationListEntry[], errors: string[]) {\n\tfor (const line of text.trim().split('\\n')) {\n\t\tconst l = line.trim().split('\\t')\n\t\tif (l.length != 4) {\n\t\t\terrors.push('cnv input not equal to 4 columns')\n\t\t\tcontinue\n\t\t}\n\t\tlet m: CnvEntry\n\t\ttry {\n\t\t\tm = {\n\t\t\t\tdt: 4,\n\t\t\t\tchr: l[0],\n\t\t\t\tstart: Number(l[1]),\n\t\t\t\tstop: Number(l[2]),\n\t\t\t\tvalue: Number(l[3])\n\t\t\t}\n\t\t} catch (e: any) {\n\t\t\terrors.push(e)\n\t\t\tcontinue\n\t\t}\n\t\tmlst.push(m)\n\t}\n}\n\nfunction validateMutation(mutation: string, errors: string[]) {\n\tconst mut2check = mutation.toLowerCase()\n\tconst foundMutation = Object.values(mclass).find(\n\t\t(m: any) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check\n\t) as any\n\tif (foundMutation) {\n\t\treturn foundMutation.key\n\t} else {\n\t\terrors.push(`Invalid mutation class: ${mutation}`)\n\t}\n}\n"],
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