@sjcrh/proteinpaint-client 2.180.0 → 2.180.1

package/dist/chunk-YMY73A3W.js

@@ -0,0 +1,1201 @@
+import {
+  loadstudycohort
+} from "./chunk-Z3BKMKQR.js";
+import {
+  childCorsMessage,
+  parentCorsMessage
+} from "./chunk-PRZWSBMA.js";
+import {
+  urlmap_default
+} from "./chunk-AQ4OP4GR.js";
+import {
+  block_init_default
+} from "./chunk-DN52ILXL.js";
+import {
+  first_genetrack_tolist,
+  sayerror,
+  tkt
+} from "./chunk-SAHCLNNL.js";
+import {
+  string2pos
+} from "./chunk-HJ6L54YS.js";
+import {
+  dofetch,
+  dofetch2,
+  dofetch3,
+  getSavedToken
+} from "./chunk-KDKY7S5G.js";
+import {
+  copyMerge
+} from "./chunk-MVTCBVSX.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-L62KZOCL.js");
+    return await _.init(arg, app.holder0, app.genomes);
+  }
+  if (arg.launchGdcMatrix) {
+    const _ = await import("./oncomatrix-5TAYUFN7.js");
+    return await _.init(arg, app.holder0, app.genomes);
+  }
+  if (arg.launchGdcHierCluster) {
+    const _ = await import("./geneExpClustering-FBKONWXK.js");
+    return await _.init(arg, app.holder0, app.genomes);
+  }
+  if (arg.launchGdcMaf) {
+    const _ = await import("./maf-4TQPFF46.js");
+    return await _.gdcMAFui(arg, app.holder0);
+  }
+  if (arg.launchGdcGrin2) {
+    const _ = await import("./grin2-A7DYEQOC.js");
+    return await _.gdcGRIN2ui(arg, app.holder0);
+  }
+  if (arg.launchGdcScRNAseq) {
+    const _ = await import("./singlecell-57YOSKNP.js");
+    return await _.init(arg, app.holder0, app.genomes);
+  }
+  if (arg.launchGdcScApp) {
+    const _ = await import("./sc-T2BPIFZ4.js");
+    return await _.init(arg, app.holder0, app.genomes);
+  }
+  if (arg.launchGdcCorrelation) {
+    const _ = await import("./correlation-6VR3QLD5.js");
+    return await _.init(arg, app.holder0, app.genomes);
+  }
+  if (arg.gdcbamslice) {
+    const _ = await import("./bam-AESS7MP3.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-AESS7MP3.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-4TQPFF46.js");
+    const p = {
+      debugmode: arg.debugmode
+    };
+    if (urlp.has("filter0")) p.filter0 = urlp.get("filter0");
+    _.gdcMAFui(p, arg.holder);
+    return true;
+  }
+  if (urlp.has("gdcgrin2")) {
+    const _ = await import("./grin2-A7DYEQOC.js");
+    const p = {
+      debugmode: arg.debugmode
+    };
+    if (urlp.has("filter0")) p.filter0 = urlp.get("filter0");
+    _.gdcGRIN2ui(p, arg.holder);
+    return true;
+  }
+  if (urlp.has("gdccorrelation")) {
+    const _ = await import("./correlation-6VR3QLD5.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("appcard")) {
+    const ad = await import("./adSandbox-7FIAWUBA.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-PP7JFYBG.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-6V52ULRQ.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-6V52ULRQ.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-6V52ULRQ.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-6V52ULRQ.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-GKI7GS7Y.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-FGDYQAVM.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-6BDLX76H.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-6BDLX76H.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-H5ZHOO3F.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-PH3K3TGJ.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;
+    }
+    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-ELXLTPKE.js")).vocabInit({ state: { genome: genomeName, dslabel } });
+    const termdbConfig = await vocabApi.getTermdbConfig();
+    await (await import("./plot.disco-477IKREB.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.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("cnvonly")) tk.hardcodeCnvOnly = true;
+      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-YMY73A3W.js.map