@sjcrh/proteinpaint-client 2.210.1 → 2.211.0

package/dist/chunk-TGTCOCPF.js

@@ -1,1278 +0,0 @@
-import {
-  loadstudycohort
-} from "./chunk-HGXSYPU6.js";
-import {
-  childCorsMessage,
-  parentCorsMessage
-} from "./chunk-PRZWSBMA.js";
-import {
-  block_init_default
-} from "./chunk-BX3P73XH.js";
-import {
-  urlmap_default
-} from "./chunk-4FTH4L3A.js";
-import {
-  first_genetrack_tolist,
-  sayerror,
-  tkt
-} from "./chunk-CSAS3PVJ.js";
-import {
-  string2pos
-} from "./chunk-HJ6L54YS.js";
-import {
-  dofetch,
-  dofetch2,
-  dofetch3,
-  getSavedToken
-} from "./chunk-VTHZGUSZ.js";
-import {
-  copyMerge
-} from "./chunk-WINIL2KN.js";
-
-// src/app.mdsjson.js
-async function init_mdsjson(file_str, url_str) {
-  let json_files = [], json_urls = [];
-  if (file_str && file_str.includes(",")) json_files = file_str.split(",");
-  else if (file_str) json_files.push(file_str);
-  else if (url_str && url_str.includes(",")) json_urls = url_str.split(",");
-  else if (url_str) json_urls.push(url_str);
-  const tklst = [];
-  if (json_files.length) {
-    const json_url = void 0;
-    for (const json_file of json_files) {
-      tklst.push(await tklst_pipeline(json_file, json_url));
-    }
-  } else if (json_urls.length) {
-    const json_file = void 0;
-    for (const json_url of json_urls) {
-      tklst.push(await tklst_pipeline(json_file, json_url));
-    }
-  }
-  return tklst;
-}
-async function tklst_pipeline(json_file, json_url) {
-  const obj = await mdsjson_parse(json_file, json_url);
-  validate_mdsjson(obj);
-  const tk = get_json_tk(obj);
-  return tk;
-}
-async function mdsjson_parse(json_file, json_url) {
-  if (json_file !== void 0 && json_file == "") throw ".jsonfile missing";
-  if (json_url !== void 0 && json_url == "") throw ".jsonurl missing";
-  let tmp;
-  if (json_file !== void 0) tmp = await dofetch("textfile", { file: json_file });
-  else if (json_url !== void 0) tmp = await dofetch("urltextfile", { url: json_url });
-  if (tmp.error) {
-    throw tmp.error;
-  }
-  return JSON.parse(tmp.text);
-}
-function validate_mdsjson(obj) {
-  if (!obj) throw "file is missing";
-  if (!obj.type) throw "dataset type is missing";
-  const svcnvfile = obj.svcnvfile || obj.svcnvurl;
-  const vcffile = obj.vcffile || obj.vcfurl;
-  if (!svcnvfile && !vcffile) throw "vcf or cnv file/url is required";
-  if (Object.keys(obj).filter((x) => x.includes("expression")).length) {
-    if (!obj.expressionfile && !obj.expressionurl) throw "expression file/url is missing";
-  }
-  if (Object.keys(obj).filter((x) => x.includes("rnabam")).length) {
-    if (!obj.rnabamfile && !obj.rnabamurl) throw "rnabam file/url is missing";
-  }
-  if (obj.sampleset) {
-    for (const sample of obj.sampleset) {
-      if (obj.sampleset.length != 1 && !sample.name) throw "sampleset name is missing";
-      if (!sample.samples) throw "sampleset samples[] is missing";
-    }
-  }
-  if (obj.sample2assaytrack) {
-    for (const [sample, assaylst] of Object.entries(obj.sample2assaytrack)) {
-      if (!assaylst.length) throw "assay[] missing for " + sample;
-      for (const assay of assaylst) {
-        if (!assay.name) throw "assay name is missing for " + sample;
-        if (!assay.type) throw "assay type is missing for " + sample;
-      }
-    }
-  }
-  if (obj.groupsamplebyattr) {
-    if (!obj.groupsamplebyattr.attrlst) return ".attrlst[] missing from groupsamplebyattr";
-    if (obj.groupsamplebyattr.attrlst.length == 0) return "groupsamplebyattr.attrlst[] empty array";
-    for (const attr of obj.groupsamplebyattr.attrlst) {
-      if (!attr.k) return "k missing from one of groupsamplebyattr.attrlst[]";
-    }
-    if (obj.groupsamplebyattr.sortgroupby) {
-      if (!obj.groupsamplebyattr.sortgroupby.key) return ".key missing from .sortgroupby";
-      if (!obj.groupsamplebyattr.sortgroupby.order) return ".order[] missing from .sortgroupby";
-      if (!Array.isArray(obj.groupsamplebyattr.sortgroupby.order)) return ".order must be an array";
-    }
-    if (!obj.groupsamplebyattr.attrnamespacer) obj.groupsamplebyattr.attrnamespacer = ", ";
-  }
-  if (obj.fixedgeneexpression) {
-    for (const gene of obj.fixedgeneexpression) {
-      if (!gene.gene) throw "gene missing in fixedgeneexpression array";
-    }
-  }
-  if (obj.vcf) {
-    if (!obj.vcf.hiddenclass) throw "hiddenclasses[] missing from .vcf";
-  }
-}
-function get_json_tk(tkobj) {
-  const track = {
-    type: tkobj.type,
-    name: tkobj.name
-  };
-  if (tkobj.isdense == "true" || tkobj.isdense == true || tkobj.isfull === false) track.isdense = true;
-  else if (tkobj.isfull) track.isfull = true;
-  if (tkobj.svcnvfile) track.file = tkobj.svcnvfile;
-  else if (tkobj.svcnvurl) track.url = tkobj.svcnvurl;
-  if (Object.keys(tkobj).filter((x) => x.includes("expression")).length) {
-    track.checkexpressionrank = {
-      file: tkobj.expressionfile,
-      url: tkobj.expressionurl
-    };
-  }
-  if (Object.keys(tkobj).filter((x) => x.includes("vcf")).length) {
-    track.checkvcf = {
-      file: tkobj.vcffile,
-      url: tkobj.vcfurl
-    };
-  }
-  if (tkobj.vcf) {
-    if (tkobj.vcf.hiddenclass) {
-      track.vcf = [];
-      track.vcf.hiddenclass = tkobj.vcf.hiddenclass;
-    }
-  }
-  if (Object.keys(tkobj).filter((x) => x.includes("rnabam")).length) {
-    track.checkrnabam = {
-      file: tkobj.rnabamfile,
-      url: tkobj.rnabamurl
-    };
-  }
-  if (tkobj.sampleset) {
-    track.sampleset = tkobj.sampleset;
-  }
-  if (tkobj.sample2assaytrack) {
-    track.sample2assaytrack = tkobj.sample2assaytrack;
-  }
-  if (tkobj.groupsamplebyattr) {
-    track.groupsamplebyattr = tkobj.groupsamplebyattr;
-  }
-  track.fixedgeneexpression = tkobj.fixedgeneexpression;
-  track.getallsamples = tkobj.getallsamples;
-  track.valueCutoff = tkobj.cnvValueCutoff !== void 0 ? tkobj.cnvValueCutoff : void 0;
-  track.bplengthUpperLimit = tkobj.cnvLengthUpperLimit !== void 0 ? tkobj.cnvLengthUpperLimit : void 0;
-  track.segmeanValueCutoff = tkobj.segmeanValueCutoff !== void 0 ? tkobj.segmeanValueCutoff : void 0;
-  track.lohLengthUpperLimit = tkobj.lohLengthUpperLimit !== void 0 ? tkobj.lohLengthUpperLimit : void 0;
-  track.multihidelabel_vcf = tkobj.multihidelabel_vcf !== void 0 ? tkobj.multihidelabel_vcf : void 0;
-  track.multihidelabel_fusion = tkobj.multihidelabel_fusion !== void 0 ? tkobj.multihidelabel_fusion : void 0;
-  track.multihidelabel_sv = tkobj.multihidelabel_sv !== void 0 ? tkobj.multihidelabel_sv : void 0;
-  track.legend_vorigin = tkobj.legend_vorigin;
-  return track;
-}
-async function get_scatterplot_data(json_file, json_url) {
-  let data = {};
-  const obj = await mdsjson_parse(json_file, json_url);
-  data.mdssamplescatterplot = obj;
-  return data;
-}
-
-// gdc/launch.ts
-async function mayLaunchGdcPlotFromRunpp(arg, app) {
-  if (arg.geneSearch4GDCmds3) {
-    const _ = await import("./lollipop-SL2F5G6K.js");
-    return await _.init(arg, app.holder0, app.genomes);
-  }
-  if (arg.launchIdc) {
-    const _ = await import("./IDCViewer-DQXAORHT.js");
-    return await _.init(arg, app.holder0);
-  }
-  if (arg.launchGdcGb) {
-    const _ = await import("./gb-PHJ2SM5D.js");
-    return await _.init(arg, app.holder0, app.genomes);
-  }
-  if (arg.launchGdcMatrix) {
-    const _ = await import("./oncomatrix-COK76MJN.js");
-    return await _.init(arg, app.holder0, app.genomes);
-  }
-  if (arg.launchGdcHierCluster) {
-    const _ = await import("./geneExpClustering-OXZJHEPD.js");
-    return await _.init(arg, app.holder0, app.genomes);
-  }
-  if (arg.launchGdcMaf) {
-    const _ = await import("./maf-FRYGN5GR.js");
-    return await _.gdcMAFui(arg, app.holder0);
-  }
-  if (arg.launchGdcGrin2) {
-    const _ = await import("./grin2-3T6KRC34.js");
-    return await _.gdcGRIN2ui(arg, app.holder0, app.genomes);
-  }
-  if (arg.launchGdcScRNAseq) {
-    const _ = await import("./singlecell-PEIEFXVU.js");
-    return await _.init(arg, app.holder0, app.genomes);
-  }
-  if (arg.launchGdcScApp) {
-    const _ = await import("./sc-2BUOXML2.js");
-    return await _.init(arg, app.holder0, app.genomes);
-  }
-  if (arg.launchGdcCorrelation) {
-    const _ = await import("./correlation-X6GB6ITK.js");
-    return await _.init(arg, app.holder0, app.genomes);
-  }
-  if (arg.launchGdcScatter) {
-    const _ = await import("./scatter-CPEIVL3K.js");
-    return await _.init(arg, app.holder0, app.genomes);
-  }
-  if (arg.launchGdcDE) {
-    const _ = await import("./DE-BI7DHHW4.js");
-    return await _.init(arg, app.holder0, app.genomes);
-  }
-  if (arg.launchGdcDM) {
-    const _ = await import("./DM-62TEJA3C.js");
-    return await _.init(arg, app.holder0, app.genomes);
-  }
-  if (arg.gdcbamslice) {
-    const _ = await import("./bam-ESRPS4TQ.js");
-    arg.gdcbamslice.filter0 = arg.filter0;
-    return await _.bamsliceui(arg.gdcbamslice, app.holder0, app.genomes);
-  }
-}
-async function mayLaunchGdcPlotFromUrlparam(urlp, arg) {
-  if (urlp.has("gdcbamslice")) {
-    const _ = await import("./bam-ESRPS4TQ.js");
-    _.bamsliceui(
-      {
-        debugmode: arg.debugmode,
-        stream2download: urlp.has("stream2download")
-        // for testing only, launch the app in "download mode", will not visualize
-      },
-      arg.holder,
-      arg.genomes
-    );
-    return true;
-  }
-  if (urlp.has("gdcmaf")) {
-    const _ = await import("./maf-FRYGN5GR.js");
-    const p = {
-      debugmode: arg.debugmode
-    };
-    if (urlp.has("filter0")) p.filter0 = urlp.get("filter0");
-    _.gdcMAFui(p, arg.holder);
-    return true;
-  }
-  if (urlp.has("gdcidc")) {
-    const _ = await import("./IDCViewer-DQXAORHT.js");
-    const p = {
-      filter0: urlp.get("filter0")
-    };
-    return await _.init(p, arg.holder);
-  }
-  if (urlp.has("gdcgrin2")) {
-    const _ = await import("./grin2-3T6KRC34.js");
-    const p = {
-      debugmode: arg.debugmode
-    };
-    if (urlp.has("filter0")) p.filter0 = urlp.get("filter0");
-    _.gdcGRIN2ui(p, arg.holder, arg.genomes);
-    return true;
-  }
-  if (urlp.has("gdccorrelation")) {
-    const _ = await import("./correlation-X6GB6ITK.js");
-    const p = {
-      debugmode: arg.debugmode
-    };
-    if (urlp.has("filter0")) p.filter0 = urlp.get("filter0");
-    _.init(p, arg.holder, arg.genomes);
-    return true;
-  }
-}
-
-// src/app.parseurl.js
-async function parse(arg) {
-  const urlp = urlmap_default();
-  const features = JSON.parse(sessionStorage.getItem("optionalFeatures"));
-  if (urlp.has("image_file")) {
-    const _ = await import("./wsi.direct-K2J6GGWY.js");
-    const cellTypesValue = urlp.get("cell_types");
-    const cellTypeFilter = !cellTypesValue || cellTypesValue == 1 ? void 0 : (Array.isArray(cellTypesValue) ? cellTypesValue : String(cellTypesValue).split(",")).map((t) => String(t).trim()).filter(Boolean);
-    await _.init(
-      {
-        slide: urlp.get("image_file"),
-        // optional: consolidated spatial .h5ad, tpmasterdir-relative — the
-        // single source of boundaries, annotations and expression
-        spatialData: urlp.get("spatial_data"),
-        // optional: show overlays only within the n most zoomed-in levels
-        annotationLevel: urlp.get("annotation_level"),
-        // optional: fill cell boundaries with one color per gene (comma-
-        // separated list), shaded by the per-cell count from the h5ad
-        geneExpression: urlp.get("gene_expression"),
-        // optional: sum per-cell counts over these genes into ONE overlay
-        geneGroups: urlp.get("gene_groups"),
-        // optional: fill cells by their annotated type (list built above)
-        showCellTypes: urlp.has("cell_types"),
-        cellTypeFilter
-      },
-      arg.holder
-    );
-    return;
-  }
-  if (urlp.has("appcard")) {
-    const ad = await import("./adSandbox-S3JP7XF3.js");
-    const cardJsonFile = urlp.get("appcard");
-    const example = urlp.get("example");
-    const re = await dofetch2("/cards/index.json");
-    arg.app.drawer.opts.genomes = arg.genomes;
-    arg.app.drawer.opts.fromApp = true;
-    arg.app.drawer.opts.app = {
-      cardsPath: "cards"
-    };
-    const element = re.elements.findIndex(
-      (t) => t.sandboxJson == cardJsonFile || t.sandboxHtml == cardJsonFile || t.name.toUpperCase().includes(cardJsonFile.toUpperCase())
-    );
-    if (re.elements[element]?.configFeature) {
-      if (!features[re.elements[element].configFeature]) {
-        sayerror(arg.holder, `This track or app is not enabled on this site.`);
-        return;
-      }
-    }
-    if (example) {
-      arg.app.drawer.opts.example = example;
-    }
-    if (element <= 0) {
-      const nestedCards = [...re.elements.filter((e) => e.type == "nestedCard")];
-      let element2, c;
-      nestedCards.findIndex((t) => {
-        for (const [i, child] of t.children.entries()) {
-          if (child.sandboxJson == cardJsonFile || child.sandboxHtml == cardJsonFile || child.name.toUpperCase().includes(cardJsonFile.toUpperCase())) {
-            element2 = t;
-            c = i;
-          }
-        }
-      });
-      if (!element2) {
-        sayerror(arg.holder, `Invalid app card.`);
-        return;
-      }
-      ad.openSandbox(element2.children[c], arg.app.drawer.opts);
-    } else {
-      ad.openSandbox(re.elements[element], arg.app.drawer.opts);
-    }
-    return;
-  }
-  if (await mayLaunchGdcPlotFromUrlparam(urlp, arg)) return;
-  if (urlp.has("termdb")) {
-    const value = urlp.get("termdb");
-    const state = typeof value === "string" ? JSON.parse(value) : value;
-    const opts = {
-      holder: arg.holder,
-      state: copyMerge(state, arg.state || {})
-    };
-    const _ = await import("./app-ZNSUUOFJ.js");
-    const subapp = _.appInit(opts);
-    return subapp;
-  }
-  if (urlp.has("massnative")) {
-    const value = urlp.get("massnative");
-    const [genomename, dslabel] = value.split(",");
-    if (!genomename || !dslabel) throw 'value is not "genome,dslabel"';
-    const opts = {
-      holder: arg.holder,
-      genome: arg.genomes[genomename],
-      state: copyMerge(
-        {
-          genome: genomename,
-          dslabel
-        },
-        arg.state || {}
-      ),
-      pkgver: arg.app.pkgver,
-      launchDate: arg.app.launchDate
-    };
-    if (!opts.genome) throw "invalid genome";
-    childCorsMessage(opts);
-    const _ = await import("./app-2MERLGNJ.js");
-    const subapp = await _.appInit(opts);
-    return subapp;
-  }
-  if (urlp.has("mass")) {
-    const value = urlp.get("mass");
-    const state = typeof value === "string" ? JSON.parse(value) : value;
-    const opts = {
-      debug: arg.app.debugmode,
-      holder: arg.holder,
-      state: copyMerge(state, arg.state || {}),
-      pkgver: arg.app.pkgver,
-      launchDate: arg.app.launchDate
-    };
-    if (state.genome) {
-      opts.genome = arg.genomes[state.genome];
-    } else if (state?.vocab?.genome) {
-      opts.genome = arg.genomes[state.vocab.genome];
-    }
-    childCorsMessage(opts);
-    const _ = await import("./app-2MERLGNJ.js");
-    const subapp = await _.appInit(opts);
-    return subapp;
-  }
-  if (urlp.has("mass-session-file") || urlp.has("mass-session-url")) {
-    let opts;
-    if (urlp.has("mass-session-file")) {
-      const file = urlp.get("mass-session-file");
-      const d = await dofetch3(`/textfile`, {
-        method: "POST",
-        body: JSON.stringify({ file })
-      });
-      if (typeof d != "object") throw "data not object";
-      if (d.error) throw d.error;
-      if (!d.text) throw "data.text missing";
-      const state = JSON.parse(d.text);
-      if (features.overrideEmbedderHostInMassSession) {
-        state.embedder.host = features.overrideEmbedderHostInMassSession;
-        state.embedder.origin = "http://" + features.overrideEmbedderHostInMassSession;
-        state.embedder.href = `http://${features.overrideEmbedderHostInMassSession}/`;
-      }
-      if (state.embedder?.origin && state.embedder.origin != window.location.origin) {
-        parentCorsMessage({ state });
-        return;
-      }
-      opts = {
-        debug: arg.app.debugmode,
-        holder: arg.holder,
-        state,
-        genome: arg.genomes[state.vocab.genome],
-        pkgver: arg.app.pkgver,
-        launchDate: arg.app.launchDate
-      };
-    } else if (urlp.has("mass-session-url")) {
-      const url = urlp.get("mass-session-url");
-      const d = await dofetch3("/urltextfile", {
-        method: "POST",
-        body: JSON.stringify({ url })
-      });
-      if (typeof d != "object") throw "data not object";
-      if (d.error) throw d.error;
-      if (!d.text) throw "data.text missing";
-      const state = JSON.parse(d.text);
-      if (state.embedder?.origin && state.embedder.origin != window.location.origin) {
-        parentCorsMessage({ state });
-        return;
-      }
-      opts = {
-        debug: arg.app.debugmode,
-        holder: arg.holder,
-        state: copyMerge(state, arg.state || {}),
-        genome: arg.genomes[state.vocab.genome],
-        pkgver: arg.app.pkgver,
-        launchDate: arg.app.launchDate
-      };
-    }
-    const _ = await import("./app-2MERLGNJ.js");
-    const subapp = _.appInit(opts);
-    return subapp;
-  }
-  if (urlp.has("mass-session-id")) {
-    const id = urlp.get("mass-session-id");
-    const src = urlp.get("src");
-    let res;
-    if (src == "browser") {
-      const json = localStorage.getItem("savedMassSessions");
-      const savedSessions = JSON.parse(json);
-      res = { state: savedSessions[id] };
-    } else {
-      const fetchOpts = { headers: {}, body: { id } };
-      if (src == "cred") {
-        const dslabel = urlp.get("dslabel");
-        const route = urlp.get("route");
-        fetchOpts.body.dslabel = dslabel;
-        fetchOpts.body.route = route;
-        fetchOpts.body.route = route;
-        const jwt = getSavedToken(dslabel, route);
-        if (jwt) fetchOpts.headers.authorization = `Bearer ${btoa(jwt)}`;
-      }
-      res = await dofetch3(`/massSession`, fetchOpts);
-      if (res.error) throw res.error;
-    }
-    const embedder = res.state?.embedder;
-    if (embedder?.origin && embedder.origin != window.location.origin) {
-      parentCorsMessage(res);
-      return;
-    }
-    const opts = {
-      debug: arg.app.debugmode,
-      holder: arg.holder,
-      state: copyMerge(res.state, arg.state || {}),
-      genome: arg.genomes[res.state.vocab.genome],
-      sessionDaysLeft: res.sessionDaysLeft,
-      sessionId: id,
-      pkgver: arg.app.pkgver,
-      launchDate: arg.app.launchDate
-    };
-    const _ = await import("./app-2MERLGNJ.js");
-    const subapp = _.appInit(opts);
-    return subapp;
-  }
-  if (urlp.has("genome") && arg.selectgenome) {
-    const n = urlp.get("genome");
-    const genome_options = [...arg.selectgenome.node().childNodes];
-    const selectedIndex = genome_options.findIndex((d) => d.value == n);
-    if (selectedIndex == -1) {
-      sayerror(
-        arg.holder,
-        `Invalid genome: ${n}. Please provide an available genome from this list: ${genome_options.map((d) => d.value).join(", ").replace(/,(?=[^,]*$)/, ", or")}`
-      );
-      return;
-    }
-    arg.selectgenome.node().selectedIndex = selectedIndex;
-    arg.selectgenome.node().dispatchEvent(new Event("change"));
-  }
-  if (urlp.has("hicfile") || urlp.has("hicurl")) {
-    let file, url, name;
-    if (urlp.has("hicfile")) {
-      file = urlp.get("hicfile");
-      name = file.split("/").pop();
-    } else {
-      url = urlp.get("hicurl");
-      name = url.split("/").pop();
-    }
-    const gn = urlp.get("genome");
-    if (!gn) throw "genome is required for hic";
-    const genome = arg.genomes[gn];
-    if (!genome) throw "invalid genome";
-    const hic = {
-      genome,
-      file,
-      url,
-      name,
-      //.basename(file || url),
-      hostURL: arg.hostURL,
-      enzyme: urlp.get("enzyme"),
-      holder: arg.holder
-    };
-    const _ = await import("./HicApp-APDL5POY.js");
-    await _.hicInit(hic);
-    return;
-  }
-  if (urlp.has("singlecell")) {
-    if (!urlp.has("genome")) throw '"genome" is required for "singlecell"';
-    const genomename = urlp.get("genome");
-    const genomeobj = arg.genomes[genomename];
-    if (!genomeobj) throw "invalid genome: " + genomename;
-    const _ = await import("./singlecell-NKPTXVHW.js");
-    _.init(
-      {
-        genome: genomeobj,
-        jsonfile: urlp.get("singlecell")
-      },
-      arg.holder
-    );
-    return;
-  }
-  if (urlp.has("mavbfile")) {
-    if (!urlp.has("genome")) throw '"genome" is required for "mavb"';
-    const genomename = urlp.get("genome");
-    const genome = arg.genomes[genomename];
-    if (!genome) throw "invalid genome: " + genomename;
-    const _ = await import("./mavb-3CL5OHWB.js");
-    _.mavbparseinput(
-      {
-        genome,
-        hostURL: arg.hostURL,
-        file: urlp.get("mavbfile")
-      },
-      () => {
-      },
-      arg.holder,
-      arg.jwt
-    );
-    return;
-  }
-  if (urlp.has("mavburl")) {
-    if (!urlp.has("genome")) throw '"genome" is required for "mavb"';
-    const genomename = urlp.get("genome");
-    const genome = arg.genomes[genomename];
-    if (!genome) throw "invalid genome: " + genomename;
-    const _ = await import("./mavb-3CL5OHWB.js");
-    _.mavbparseinput(
-      {
-        genome,
-        hostURL: arg.hostURL,
-        url: urlp.get("mavburl")
-      },
-      () => {
-      },
-      arg.holder,
-      arg.jwt
-    );
-    return;
-  }
-  if (urlp.has("scatterplot")) {
-    if (!urlp.has("genome")) throw '"genome" is required for "scatterplot"';
-    const genomename = urlp.get("genome");
-    const genome = arg.genomes[genomename];
-    if (!genome) throw "invalid genome: " + genomename;
-    let plot_data;
-    if (urlp.has("mdsjson") || urlp.has("mdsjsonurl")) {
-      const url_str = urlp.get("mdsjsonurl");
-      const file_str = urlp.get("mdsjson");
-      plot_data = await get_scatterplot_data(file_str, url_str);
-    }
-    if (urlp.has("tsnejson")) {
-      const file_str = urlp.get("tsnejson");
-      const data = await dofetch("textfile", { file: file_str });
-      if (data.error) throw data.error;
-      else if (data.text) {
-        plot_data = {
-          mdssamplescatterplot: {
-            analysisdata: JSON.parse(data.text)
-          }
-        };
-      }
-    }
-    plot_data.mdssamplescatterplot.genome = genome;
-    const _ = await import("./mds.samplescatterplot-X6CXMY4C.js");
-    _.init(plot_data.mdssamplescatterplot, arg.holder, false);
-    return;
-  }
-  if (urlp.has("block")) {
-    if (!urlp.has("genome")) throw "missing genome for block";
-    const genomename = urlp.get("genome");
-    const genomeobj = arg.genomes[genomename];
-    if (!genomeobj) throw "invalid genome: " + genomename;
-    const par = {
-      nobox: 1,
-      hostURL: arg.hostURL,
-      jwt: arg.jwt,
-      holder: arg.holder,
-      genome: genomeobj,
-      dogtag: genomename,
-      debugmode: arg.debugmode
-    };
-    let position = null;
-    let rglst = null;
-    if (urlp.has("position")) {
-      const lst = urlp.get("position").split(";");
-      if (lst[0]) {
-        const tmp = lst[0].split(/[:-]/);
-        const chr = tmp[0];
-        const start = Number.parseInt(tmp[1]);
-        const stop = Number.parseInt(tmp[2]);
-        if (!chr) throw "chr missing";
-        if (Number.isNaN(start) || Number.isNaN(stop)) throw "Invalid start/stop value in position";
-        position = { chr, start, stop };
-      }
-      const subpanels = [];
-      for (let i = 1; i < lst.length; i++) {
-        if (!lst[i]) continue;
-        const tmp = lst[i].split(/[:-]/);
-        const chr = tmp[0];
-        const start = Number.parseInt(tmp[1]);
-        const stop = Number.parseInt(tmp[2]);
-        if (!chr) throw "subpanel chr missing";
-        if (Number.isNaN(start) || Number.isNaN(stop)) throw "Invalid start/stop value in subpanel position";
-        subpanels.push({
-          chr,
-          start,
-          stop,
-          width: 600,
-          leftborder: "rgba(200,0,0,.1)",
-          leftpad: 5
-        });
-      }
-      if (subpanels.length) {
-        par.subpanels = subpanels;
-      }
-    }
-    if (urlp.has("regions")) {
-      rglst = [];
-      for (const s of urlp.get("regions").split(",")) {
-        const l = s.split(/[:-]/);
-        const chr = l[0];
-        const start = Number.parseInt(l[1]);
-        const stop = Number.parseInt(l[2]);
-        if (Number.isNaN(start) || Number.isNaN(stop)) throw "Invalid start/stop value in regions";
-        rglst.push({ chr: l[0], start, stop });
-      }
-    }
-    if (!position && !rglst) {
-      if (genomeobj.defaultcoord) {
-        position = {
-          chr: genomeobj.defaultcoord.chr,
-          start: genomeobj.defaultcoord.start,
-          stop: genomeobj.defaultcoord.stop
-        };
-      }
-    }
-    if (position) {
-      par.chr = position.chr;
-      par.start = position.start;
-      par.stop = position.stop;
-    } else if (rglst) {
-      par.rglst = rglst;
-    }
-    if (urlp.has("hlregion")) {
-      const lst = [];
-      for (const t of urlp.get("hlregion").split(",")) {
-        const pos = string2pos(t, genomeobj, true);
-        if (pos) lst.push(pos);
-      }
-      if (lst.length) par.hlregions = lst;
-    }
-    par.datasetqueries = may_get_officialmds(urlp);
-    par.tklst = await get_tklst(urlp, genomeobj);
-    first_genetrack_tolist(arg.genomes[genomename], par.tklst);
-    mayAddBedjfilterbyname(urlp, par.tklst);
-    const b = await import("./block-GEG4UUOU.js");
-    new b.Block(par);
-    return;
-  }
-  if (urlp.has("gene")) {
-    const str = urlp.get("gene");
-    if (str.length == 0) throw "zero length query string";
-    const par = {
-      hostURL: arg.hostURL,
-      query: str,
-      holder: arg.holder,
-      variantPageCall_snv: arg.variantPageCall_snv,
-      samplecart: arg.samplecart,
-      debugmode: arg.debugmode
-    };
-    {
-      let genomename;
-      for (let n in arg.genomes) {
-        if (arg.genomes[n].isdefault) {
-          genomename = n;
-          break;
-        }
-      }
-      if (urlp.has("genome")) {
-        genomename = urlp.get("genome");
-      }
-      if (!genomename) throw "No genome, and none set as default";
-      par.genome = arg.genomes[genomename];
-      if (!par.genome) throw "invalid genome: " + genomename;
-    }
-    let ds = null;
-    if (urlp.has("dataset")) {
-      par.dataset = urlp.get("dataset").split(",");
-    }
-    if (urlp.has("hlaachange")) {
-      par.hlaachange = /* @__PURE__ */ new Map();
-      for (const s of urlp.get("hlaachange").split(",")) {
-        par.hlaachange.set(s, false);
-      }
-    }
-    if (urlp.has("hlregion")) {
-      const lst = [];
-      for (const t of urlp.get("hlregion").split(",")) {
-        const pos = string2pos(t, par.genome, true);
-        if (pos) lst.push(pos);
-      }
-      if (lst.length) par.hlregions = lst;
-    }
-    if (urlp.has("aarange")) {
-      const [a, b] = urlp.get("aarange").split(",").map(Number);
-      if (Number.isInteger(a) && Number.isInteger(b) && a > 0 && b > a) {
-        par.aarange = [a, b];
-      } else {
-        throw "invalid aarange";
-      }
-    }
-    par.tklst = await get_tklst(urlp, par.genome);
-    mayAddBedjfilterbyname(urlp, par.tklst);
-    par.datasetqueries = may_get_officialmds(urlp);
-    await block_init_default(par);
-    return;
-  }
-  if (urlp.has("disco")) {
-    const genomeName = urlp.get("genome");
-    const genome = arg.genomes[genomeName];
-    if (!genome) throw "genome missing";
-    const dslabel = urlp.get("dslabel");
-    if (!dslabel) throw "dslabel missing";
-    const sample_id = urlp.get("sample");
-    if (!sample_id) throw "sample_id missing";
-    const vocabApi = (await import("./vocabulary-HCPEIO2P.js")).vocabInit({ state: { genome: genomeName, dslabel } });
-    const termdbConfig = await vocabApi.getTermdbConfig();
-    await (await import("./plot.disco-H4P4B6QS.js")).default(termdbConfig, dslabel, { sample_id }, arg.holder, genome);
-    return;
-  }
-  if (urlp.has("study")) {
-    const v = urlp.get("study");
-    if (v != "") {
-      loadstudycohort(
-        arg.genomes,
-        v,
-        arg.holder,
-        arg.hostURL,
-        void 0,
-        // jwt
-        false,
-        // no show
-        arg.app || {
-          debugmode: arg.debugmode,
-          instanceTracker: arg.instanceTracker || {},
-          callbacks: arg.callbacks || {}
-        }
-      );
-    }
-  }
-}
-function may_get_officialmds(urlp) {
-  if (!urlp.has("mds")) return;
-  const tmp = urlp.get("mds").split(",");
-  if (tmp[0] && tmp[1]) {
-    const dataset = { dataset: tmp[0], querykey: tmp[1] };
-    if (urlp.has("sample")) {
-      dataset.singlesample = { name: urlp.get("sample") };
-      dataset.getsampletrackquickfix = true;
-    }
-    return [dataset];
-  }
-  return;
-}
-async function get_tklst(urlp, genomeobj) {
-  const tklst = [];
-  for (const [key, value] of urlp) {
-    const tks = await mayGetTkobj(key, value, urlp, genomeobj);
-    if (!tks) continue;
-    if (Array.isArray(tks)) tklst.push(...tks);
-    else tklst.push(tks);
-  }
-  for (const t of tklst) {
-    if ((t.type == "mds3" || t.type == "j2") && t.dslabel) continue;
-    t.iscustom = true;
-  }
-  if (urlp.has("isdense")) {
-    tklst.filter((t) => t.type == tkt.mdssvcnv).forEach((t) => {
-      t.isdense = true;
-      t.isfull = false;
-    });
-  }
-  if (urlp.has("sample")) {
-    tklst.filter((t) => t.type == tkt.mdssvcnv).forEach((t) => {
-      t.singlesample = { name: urlp.get("sample") };
-      t.getsampletrackquickfix = true;
-    });
-  }
-  return tklst;
-}
-async function mayGetTkobj(key, value, urlp, genomeobj) {
-  if (key == "mds3") {
-    const lst = value.split(",");
-    const tks = [];
-    for (const n of lst) {
-      const tk = {
-        type: tkt.mds3,
-        dslabel: n
-      };
-      if (urlp.has("token")) tk.token = urlp.get("token");
-      if (urlp.has("filterobj")) tk.filterObj = urlp.get("filterobj");
-      if (urlp.has("filter0")) tk.filter0 = urlp.get("filter0");
-      if (urlp.has("cnvonly")) tk.hardcodeCnvOnly = true;
-      if (urlp.has("snvindelonly")) tk.snvIndelOnly = true;
-      tks.push(tk);
-    }
-    return tks;
-  }
-  if (key == "j2") {
-    const lst = value.split(",");
-    const tks = [];
-    for (const n of lst) {
-      const tk = {
-        type: tkt.j2,
-        dslabel: n
-      };
-      if (urlp.has("token")) tk.token = urlp.get("token");
-      if (urlp.has("filter")) tk.filter = urlp.get("filter");
-      if (urlp.has("filter0")) tk.filter0 = urlp.get("filter0");
-      tks.push(tk);
-    }
-    return tks;
-  }
-  if (key == "mds3bcffile") {
-    const [tkname, bcffile] = value.split(",");
-    let tk;
-    if (tkname && bcffile) {
-      tk = {
-        type: tkt.mds3,
-        name: tkname,
-        bcf: { file: bcffile }
-      };
-    }
-    return tk;
-  }
-  if (key == "mds3bcfurl") {
-    const [tkname, url, indexURL] = value.split(",");
-    let tk;
-    if (tkname && url) {
-      tk = {
-        type: tkt.mds3,
-        name: tkname,
-        bcf: { url, indexURL }
-      };
-    }
-    return tk;
-  }
-  if (key == "arcfile") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: tkt.hicstraw,
-          name: lst[i],
-          bedfile: lst[i + 1],
-          mode_hm: false,
-          mode_arc: true
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "mdsjson" || key == "mdsjsonurl") {
-    let url_str, file_str;
-    if (key == "mdsjson") file_str = value;
-    else url_str = value;
-    return await init_mdsjson(file_str, url_str);
-  }
-  if (key == "tkjsonfile") {
-    const re = await dofetch("textfile", { file: value });
-    if (re.error) throw re.error;
-    if (!re.text) throw ".text missing";
-    const lst = JSON.parse(re.text);
-    const tks = [];
-    for (const i of lst) {
-      if (i.isfacet) {
-        if (!genomeobj.tkset) genomeobj.tkset = [];
-        if (!i.tracks) throw ".tracks[] missing from a facet table";
-        if (!Array.isArray(i.tracks)) throw ".tracks[] not an array from a facet table";
-        i.tklst = i.tracks;
-        delete i.tracks;
-        for (const t of i.tklst) {
-          if (!t.assay) throw ".assay missing from a facet track";
-          if (!t.sample) throw ".sample missing from a facet track";
-          t.tkid = Math.random().toString();
-        }
-        genomeobj.tkset.push(i);
-      } else {
-        tks.push(i);
-      }
-    }
-    return tks;
-  }
-  if (key == "bamfile") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: tkt.bam,
-          name: lst[i],
-          file: lst[i + 1]
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "bamurl") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: tkt.bam,
-          name: lst[i],
-          url: lst[i + 1]
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "bedjfile") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: tkt.bedj,
-          name: lst[i],
-          file: lst[i + 1]
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "bedjurl") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: tkt.bedj,
-          name: lst[i],
-          url: lst[i + 1]
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "hictkfile" || key == "hictkurl") {
-    const isfile = key == "hictkfile";
-    const lst = value.split(",");
-    const norm = urlp.has("hictknorm") ? urlp.get("hictknorm").split(",") : null;
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 3) {
-      if (lst[i] && lst[i + 1] && lst[i + 2]) {
-        const t = {
-          type: tkt.hicstraw,
-          name: lst[i],
-          enzyme: lst[i + 1],
-          normalizationmethod: norm ? norm[i / 3] : null
-        };
-        if (isfile) {
-          t.file = lst[i + 2];
-        } else {
-          t.url = lst[i + 2];
-        }
-        tks.push(t);
-      }
-    }
-    return tks;
-  }
-  if (key == "ldfile") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: tkt.ld,
-          name: lst[i],
-          file: lst[i + 1]
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "bigwigfile") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: tkt.bigwig,
-          name: lst[i],
-          file: lst[i + 1],
-          scale: { auto: 1 }
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "bigwigurl") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: tkt.bigwig,
-          name: lst[i],
-          url: lst[i + 1],
-          scale: { auto: 1 }
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "junctionfile") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: tkt.junction,
-          name: lst[i],
-          tracks: [
-            {
-              file: lst[i + 1]
-            }
-          ]
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "junctionurl") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: tkt.junction,
-          name: lst[i],
-          tracks: [
-            {
-              url: lst[i + 1]
-            }
-          ]
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "aicheckfile") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: "aicheck",
-          name: lst[i],
-          file: lst[i + 1]
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "bampilefile") {
-    const lst = value.split(",");
-    let links = null;
-    if (urlp.has("bampilelink")) {
-      links = urlp.get("bampilelink").split(",").map(decodeURIComponent);
-    }
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        const tk = {
-          type: tkt.bampile,
-          name: lst[i],
-          file: lst[i + 1]
-        };
-        if (links && links[i / 2]) {
-          tk.link = links[i / 2];
-        }
-        tks.push(tk);
-      }
-    }
-    return tks;
-  }
-  if (key == "svcnvfpkmurl") {
-    const lst = value.split(",");
-    const name = lst[0];
-    const type2url = {};
-    for (let i = 1; i < lst.length; i += 2) {
-      type2url[lst[i]] = lst[i + 1];
-    }
-    let tk;
-    if (type2url.svcnv || type2url.vcf) {
-      tk = {
-        type: tkt.mdssvcnv,
-        name
-      };
-      if (type2url.svcnv) {
-        tk.url = type2url.svcnv;
-      }
-      if (type2url.vcf) {
-        tk.checkvcf = {
-          url: type2url.vcf,
-          indexURL: type2url.vcfindex
-        };
-      }
-      if (type2url.fpkm) {
-        tk.checkexpressionrank = {
-          datatype: "FPKM",
-          url: type2url.fpkm,
-          indexURL: type2url.fpkmindex
-        };
-      }
-    }
-    return tk;
-  }
-  if (key == "svcnvfpkmfile") {
-    const lst = value.split(",");
-    const name = lst[0];
-    const type2file = {};
-    for (let i = 1; i < lst.length; i += 2) {
-      type2file[lst[i]] = lst[i + 1];
-    }
-    let tk;
-    if (type2file.svcnv || type2file.vcf) {
-      tk = {
-        type: tkt.mdssvcnv,
-        name
-      };
-      if (type2file.svcnv) {
-        tk.file = type2file.svcnv;
-      }
-      if (type2file.vcf) {
-        tk.checkvcf = {
-          file: type2file.vcf
-        };
-      }
-      if (type2file.fpkm) {
-        tk.checkexpressionrank = {
-          datatype: "FPKM",
-          file: type2file.fpkm
-        };
-      }
-    }
-    return tk;
-  }
-  if (key == "mdsjunctionfile") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: "mdsjunction",
-          name: lst[i],
-          file: lst[i + 1]
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "junctionmatrix") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: "mdsjunction",
-          name: lst[i],
-          file2: lst[i + 1]
-          // quick fix to support new file type
-        });
-      }
-    }
-    return tks;
-  }
-  if (key == "junctionrnapeg") {
-    const lst = value.split(",");
-    const tks = [];
-    for (let i = 0; i < lst.length; i += 2) {
-      if (lst[i] && lst[i + 1]) {
-        tks.push({
-          type: tkt.junction,
-          name: lst[i],
-          tracks: [{ rnapegfile: lst[i + 1] }]
-        });
-      }
-    }
-    return tks;
-  }
-}
-function mayAddBedjfilterbyname(urlp, tklst) {
-  if (urlp.has("bedjfilterbyname")) {
-    for (const t of tklst) {
-      if (t.type == "bedj") t.filterByName = urlp.get("bedjfilterbyname");
-    }
-  }
-}
-
-export {
-  init_mdsjson,
-  mayLaunchGdcPlotFromRunpp,
-  parse,
-  get_tklst
-};
-//# sourceMappingURL=chunk-TGTCOCPF.js.map