@sjcrh/proteinpaint-client 2.176.1-0 → 2.177.0

package/dist/lollipop-QJHPSEYN.js

@@ -0,0 +1,163 @@
+import {
+  block_init_default
+} from "./chunk-7B6CB6XY.js";
+import {
+  addGeneSearchbox,
+  first_genetrack_tolist
+} from "./chunk-2JTKLLXN.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-POVVC3BE.js";
+import {
+  Menu
+} from "./chunk-CXMZYVZT.js";
+import {
+  dofetch3
+} from "./chunk-3JKV3JII.js";
+import "./chunk-UWOYHXHE.js";
+import "./chunk-DK5V6E5X.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-SSFOXHYJ.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-2YLLYUYO.js";
+import "./chunk-YPPAQW54.js";
+import "./chunk-NPOWNTGW.js";
+import "./chunk-TPK3G44P.js";
+import "./chunk-6TKSYIQW.js";
+import "./chunk-BEWDIM6H.js";
+import "./chunk-OMZHTBFI.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-733PDAIR.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-UJUXE42U.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// gdc/lollipop.js
+var tip = new Menu({ padding: "" });
+async function init(arg, holder, genomes) {
+  const useGenome = arg.genome || "hg38";
+  const useDslabel = arg.dslabel || "GDC";
+  const genome = genomes[useGenome];
+  if (!genome) throw useGenome + " missing";
+  if (arg.geneSearch4GDCmds3.onloadalltk_always && typeof arg.geneSearch4GDCmds3.onloadalltk_always != "function")
+    throw "arg.geneSearch4GDCmds3.onloadalltk_always not function";
+  if (arg.geneSearch4GDCmds3.postRender && typeof arg.geneSearch4GDCmds3.postRender != "function")
+    throw "arg.geneSearch4GDCmds3.postRender not function";
+  holder.selectAll(".sja_lollipop_holder").remove();
+  const mainDiv = holder.append("div").attr("class", "sja_lollipop_holder");
+  const geneInputDiv = mainDiv.append("div").style("margin-left", "20px");
+  geneInputDiv.append("div").text(
+    arg.geneSearch4GDCmds3.hardcodeCnvOnly ? `To view ${useDslabel} CNV segments over a gene or region, enter genomic position (chr11:108195437-108267444), dbSNP accesion, or gene name (MYC).` : `To view ${useDslabel} mutations on a gene, enter one of gene symbol (MYC), alias (c-Myc), GENCODE accession (ENSG00000136997, ENST00000621592), or RefSeq accession (NM_002467).`
+  );
+  const graphDiv = mainDiv.append("div").attr("class", "sja_geneSearch4GDCmds3_blockdiv");
+  const searchOpt = {
+    genome,
+    tip,
+    row: geneInputDiv,
+    callback: launchView,
+    geneSymbol: arg.geneSymbol,
+    triggerSearch: arg.geneSymbol && arg.geneSearch4GDCmds3?.hardcodeCnvOnly == true,
+    hideInputBeforeCallback: arg.geneSearch4GDCmds3?.hardcodeCnvOnly == true
+  };
+  if (!arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
+    searchOpt.searchOnly = "gene";
+  }
+  const coordInput = addGeneSearchbox(searchOpt);
+  let userSelection;
+  await arg.geneSearch4GDCmds3.postRender?.({ tip });
+  if (arg.state) {
+    if (arg.state.userSelection) launchView(false, arg.state.userSelection);
+    delete arg.state;
+  }
+  async function launchView(triggeredByInput = true, userSelection2) {
+    const pa = {
+      // param for instantiating block
+      genome,
+      holder: graphDiv,
+      gmmode: "exon only",
+      nobox: 1,
+      hide_dsHandles: arg.hide_dsHandles,
+      onloadalltk_always: arg.geneSearch4GDCmds3.onloadalltk_always
+    };
+    if (arg.tracks) {
+      pa.tklst = arg.tracks;
+    } else {
+      const tk = {
+        type: "mds3",
+        dslabel: useDslabel,
+        allow2selectSamples: arg.allow2selectSamples,
+        filter0: arg.filter0
+      };
+      pa.tklst = [tk];
+      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
+        tk.hardcodeCnvOnly = 1;
+        delete pa.gmmode;
+        first_genetrack_tolist(pa.genome, pa.tklst);
+      }
+    }
+    if (userSelection2) {
+      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
+        if (typeof userSelection2 != "object") throw "userSelection not object when pa.block is true";
+        pa.chr = userSelection2.chr;
+        pa.start = userSelection2.start;
+        pa.stop = userSelection2.stop;
+        if (!pa.chr || !Number.isInteger(pa.start) || !Number.isInteger(pa.stop))
+          throw "userSelection not {chr,start,stop}";
+      } else {
+        if (typeof userSelection2 != "string") throw "userSelection should be string when pa.block is not true";
+        pa.query = userSelection2;
+      }
+    } else {
+      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
+        if (!coordInput.chr || !Number.isInteger(coordInput.start) || !Number.isInteger(coordInput.stop)) {
+          if (triggeredByInput) throw "coordInput.chr/start/stop missing";
+        }
+        pa.chr = coordInput.chr;
+        pa.start = coordInput.start;
+        pa.stop = coordInput.stop;
+      } else {
+        if (!coordInput.geneSymbol) {
+          if (triggeredByInput) throw "coordInput.geneSymbol missing";
+        }
+        const gmlst = (await dofetch3(`genelookup?deep=1&input=${coordInput.geneSymbol}&genome=${useGenome}`)).gmlst;
+        if (!Array.isArray(gmlst) || gmlst.length == 0) throw "gmlst is not non-empty array";
+        pa.query = getSelectedIsoform(coordInput, gmlst);
+        if (gmlst.some((i) => i.coding)) pa.gmmode = "protein";
+      }
+    }
+    graphDiv.selectAll("*").remove();
+    if (!arg.geneSearch4GDCmds3.hardcodeCnvOnly) return await block_init_default(pa);
+    const _ = await import("./block-UT6PNRVU.js");
+    return new _.Block(pa);
+  }
+  const api = {
+    update: (_arg) => {
+      Object.assign(arg, _arg);
+      launchView(false);
+    },
+    getState: () => ({ userSelection })
+  };
+  return api;
+}
+function getSelectedIsoform(coordInput, gmlst) {
+  if (coordInput.fromWhat) {
+    if (gmlst.some((i) => i.isoform.toUpperCase() == coordInput.fromWhat.toUpperCase())) {
+      return coordInput.fromWhat;
+    }
+    if (coordInput.fromWhat.toUpperCase().startsWith("ENSG")) {
+      for (const i of gmlst) {
+        if (i.isdefault && i.isoform.startsWith("ENST")) return i.isoform;
+      }
+    }
+  }
+  const defaultIsoform = gmlst.find((i) => i.isdefault);
+  if (defaultIsoform) return defaultIsoform.isoform;
+  return gmlst[0].isoform;
+}
+export {
+  init
+};
+//# sourceMappingURL=lollipop-QJHPSEYN.js.map

package/dist/maf-QRGRW2O4.js

@@ -0,0 +1,439 @@
+import {
+  make_radios,
+  renderTable,
+  sayerror,
+  table2col
+} from "./chunk-2JTKLLXN.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-POVVC3BE.js";
+import {
+  Menu
+} from "./chunk-CXMZYVZT.js";
+import {
+  dofetch3,
+  fileSize
+} from "./chunk-3JKV3JII.js";
+import "./chunk-UWOYHXHE.js";
+import "./chunk-DK5V6E5X.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-SSFOXHYJ.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-2YLLYUYO.js";
+import "./chunk-YPPAQW54.js";
+import "./chunk-NPOWNTGW.js";
+import "./chunk-TPK3G44P.js";
+import "./chunk-6TKSYIQW.js";
+import "./chunk-BEWDIM6H.js";
+import "./chunk-OMZHTBFI.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-733PDAIR.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-UJUXE42U.js";
+import "./chunk-OMR2DT66.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// gdc/maf.js
+var tip = new Menu();
+var tableColumns = [
+  { label: "Case", sortable: true },
+  { label: "Project", sortable: true },
+  { label: "Samples" },
+  { label: "File Size", barplot: { tickFormat: "~s" }, sortable: true }
+  // barchart column not sortable yet
+];
+var mafColumns = [
+  { column: "Hugo_Symbol", selected: true },
+  { column: "Entrez_Gene_Id", selected: true },
+  { column: "Center", selected: true },
+  { column: "NCBI_Build", selected: true },
+  { column: "Chromosome", selected: true },
+  { column: "Start_Position", selected: true },
+  { column: "End_Position", selected: true },
+  { column: "Strand", selected: true },
+  { column: "Variant_Classification", selected: true },
+  { column: "Variant_Type", selected: true },
+  { column: "Reference_Allele", selected: true },
+  { column: "Tumor_Seq_Allele1", selected: true },
+  { column: "Tumor_Seq_Allele2", selected: true },
+  { column: "dbSNP_RS", selected: true },
+  { column: "dbSNP_Val_Status", selected: true },
+  { column: "Tumor_Sample_Barcode", selected: true },
+  { column: "Matched_Norm_Sample_Barcode", selected: true },
+  { column: "Match_Norm_Seq_Allele1", selected: true },
+  { column: "Match_Norm_Seq_Allele2", selected: true },
+  { column: "Tumor_Validation_Allele1", selected: true },
+  { column: "Tumor_Validation_Allele2", selected: true },
+  { column: "Match_Norm_Validation_Allele1", selected: true },
+  { column: "Match_Norm_Validation_Allele2", selected: true },
+  { column: "Verification_Status", selected: true },
+  { column: "Validation_Status", selected: true },
+  { column: "Mutation_Status", selected: true },
+  { column: "Sequencing_Phase", selected: true },
+  { column: "Sequence_Source", selected: true },
+  { column: "Validation_Method", selected: true },
+  { column: "Score", selected: true },
+  { column: "BAM_File", selected: true },
+  { column: "Sequencer", selected: true },
+  { column: "Tumor_Sample_UUID", selected: true },
+  { column: "Matched_Norm_Sample_UUID", selected: true },
+  { column: "HGVSc", selected: true },
+  { column: "HGVSp", selected: true },
+  { column: "HGVSp_Short", selected: true },
+  { column: "Transcript_ID", selected: true },
+  { column: "Exon_Number", selected: true },
+  { column: "t_depth", selected: true },
+  { column: "t_ref_count", selected: true },
+  { column: "t_alt_count", selected: true },
+  { column: "n_depth", selected: true },
+  { column: "n_ref_count", selected: true },
+  { column: "n_alt_count", selected: true },
+  { column: "all_effects", selected: true },
+  { column: "Allele", selected: true },
+  { column: "Gene", selected: true },
+  { column: "Feature", selected: true },
+  { column: "Feature_type", selected: true },
+  { column: "One_Consequence", selected: true },
+  { column: "Consequence", selected: true },
+  { column: "cDNA_position", selected: true },
+  { column: "CDS_position", selected: true },
+  { column: "Protein_position", selected: true },
+  { column: "Amino_acids", selected: true },
+  { column: "Codons", selected: true },
+  { column: "Existing_variation", selected: true },
+  { column: "DISTANCE", selected: true },
+  { column: "TRANSCRIPT_STRAND", selected: true },
+  { column: "SYMBOL", selected: true },
+  { column: "SYMBOL_SOURCE", selected: true },
+  { column: "HGNC_ID", selected: true },
+  { column: "BIOTYPE", selected: true },
+  { column: "CANONICAL", selected: true },
+  { column: "CCDS", selected: true },
+  { column: "ENSP", selected: true },
+  { column: "SWISSPROT", selected: true },
+  { column: "TREMBL", selected: true },
+  { column: "UNIPARC", selected: true },
+  { column: "UNIPROT_ISOFORM", selected: true },
+  { column: "RefSeq", selected: true },
+  { column: "MANE", selected: true },
+  { column: "APPRIS", selected: true },
+  { column: "FLAGS", selected: true },
+  { column: "SIFT", selected: true },
+  { column: "PolyPhen", selected: true },
+  { column: "EXON", selected: true },
+  { column: "INTRON", selected: true },
+  { column: "DOMAINS", selected: true },
+  { column: "1000G_AF", selected: true },
+  { column: "1000G_AFR_AF", selected: true },
+  { column: "1000G_AMR_AF", selected: true },
+  { column: "1000G_EAS_AF", selected: true },
+  { column: "1000G_EUR_AF", selected: true },
+  { column: "1000G_SAS_AF", selected: true },
+  { column: "ESP_AA_AF", selected: true },
+  { column: "ESP_EA_AF", selected: true },
+  { column: "gnomAD_AF", selected: true },
+  { column: "gnomAD_AFR_AF", selected: true },
+  { column: "gnomAD_AMR_AF", selected: true },
+  { column: "gnomAD_ASJ_AF", selected: true },
+  { column: "gnomAD_EAS_AF", selected: true },
+  { column: "gnomAD_FIN_AF", selected: true },
+  { column: "gnomAD_NFE_AF", selected: true },
+  { column: "gnomAD_OTH_AF", selected: true },
+  { column: "gnomAD_SAS_AF", selected: true },
+  { column: "MAX_AF", selected: true },
+  { column: "MAX_AF_POPS", selected: true },
+  { column: "gnomAD_non_cancer_AF", selected: true },
+  { column: "gnomAD_non_cancer_AFR_AF", selected: true },
+  { column: "gnomAD_non_cancer_AMI_AF", selected: true },
+  { column: "gnomAD_non_cancer_AMR_AF", selected: true },
+  { column: "gnomAD_non_cancer_ASJ_AF", selected: true },
+  { column: "gnomAD_non_cancer_EAS_AF", selected: true },
+  { column: "gnomAD_non_cancer_FIN_AF", selected: true },
+  { column: "gnomAD_non_cancer_MID_AF", selected: true },
+  { column: "gnomAD_non_cancer_NFE_AF", selected: true },
+  { column: "gnomAD_non_cancer_OTH_AF", selected: true },
+  { column: "gnomAD_non_cancer_SAS_AF", selected: true },
+  { column: "gnomAD_non_cancer_MAX_AF_adj", selected: true },
+  { column: "gnomAD_non_cancer_MAX_AF_POPS_adj", selected: true },
+  { column: "CLIN_SIG", selected: true },
+  { column: "SOMATIC", selected: true },
+  { column: "PUBMED", selected: true },
+  { column: "TRANSCRIPTION_FACTORS", selected: true },
+  { column: "MOTIF_NAME", selected: true },
+  { column: "MOTIF_POS", selected: true },
+  { column: "HIGH_INF_POS", selected: true },
+  { column: "MOTIF_SCORE_CHANGE", selected: true },
+  { column: "miRNA", selected: true },
+  { column: "IMPACT", selected: true },
+  { column: "PICK", selected: true },
+  { column: "VARIANT_CLASS", selected: true },
+  { column: "TSL", selected: true },
+  { column: "HGVS_OFFSET", selected: true },
+  { column: "PHENO", selected: true },
+  { column: "GENE_PHENO", selected: true },
+  { column: "CONTEXT", selected: true },
+  { column: "case_id", selected: true },
+  { column: "GDC_FILTER", selected: true },
+  { column: "COSMIC", selected: true },
+  { column: "hotspot", selected: true },
+  { column: "tumor_bam_uuid", selected: true },
+  { column: "normal_bam_uuid", selected: true },
+  { column: "RNA_Support", selected: true },
+  { column: "RNA_depth", selected: true },
+  { column: "RNA_ref_count", selected: true },
+  { column: "RNA_alt_count", selected: true },
+  { column: "callers", selected: true }
+];
+async function gdcMAFui({ filter0, callbacks, debugmode = false }, holder) {
+  try {
+    if (callbacks) {
+      delete callbacks.sjcharts;
+      for (const n in callbacks) {
+        if (typeof callbacks[n] != "function") throw `callbacks.${n} not function`;
+      }
+    }
+    {
+      const cn = /* @__PURE__ */ new Set();
+      for (const c of mafColumns) {
+        if (!c.column) throw ".column missing from an element";
+        if (cn.has(c.column)) throw "duplicate column: " + c.column;
+        cn.add(c.column);
+      }
+    }
+    update({ filter0 });
+  } catch (e) {
+    console.log(e);
+    sayerror(holder, e.message || e);
+  }
+  async function update({ filter0: filter02 }) {
+    holder.selectAll("*").remove();
+    const obj = {
+      holder,
+      errDiv: holder.append("div"),
+      controlDiv: holder.append("div"),
+      tableDiv: holder.append("div"),
+      opts: {
+        filter0: filter02,
+        experimentalStrategy: "WXS"
+      },
+      mafTableArg: null
+    };
+    makeControls(obj);
+    await getFilesAndShowTable(obj);
+    callbacks?.postRender?.(publicApi);
+  }
+  const publicApi = { update };
+  return publicApi;
+}
+function makeControls(obj) {
+  const table = table2col({ holder: obj.controlDiv });
+  table.addRow("Access", "Open");
+  table.addRow("Workflow Type", "Aliquot Ensemble Somatic Variant Merging and Masking");
+  {
+    const [td1, td2] = table.addRow("Experimental Strategy");
+    make_radios({
+      holder: td2,
+      options: [
+        { label: "WXS", value: "WXS", checked: obj.opts.experimentalStrategy == "WXS" },
+        {
+          label: "Targeted Sequencing",
+          value: "Targeted Sequencing",
+          checked: obj.opts.experimentalStrategy == "Targeted Sequencing"
+        }
+      ],
+      styles: { display: "inline" },
+      callback: async (value) => {
+        obj.opts.experimentalStrategy = value;
+        await getFilesAndShowTable(obj);
+      }
+    });
+  }
+  {
+    let updateText2 = function() {
+      clickText.text(
+        `${mafColumns.reduce((c, i) => c + (i.selected ? 1 : 0), 0)} of ${mafColumns.length} columns selected. Click to change`
+      );
+    };
+    var updateText = updateText2;
+    const [td1, td2] = table.addRow("Output Columns");
+    const clickText = td2.append("span").attr("class", "sja_clbtext").on("click", (event) => {
+      const rows = [], selectedRows = [];
+      for (const [i, c] of mafColumns.entries()) {
+        rows.push([{ value: c.column }]);
+        if (c.selected) selectedRows.push(i);
+      }
+      renderTable({
+        div: tip.clear().showunder(event.target).d,
+        rows,
+        columns: [{ label: "Column Name" }],
+        selectedRows,
+        noButtonCallback: (i, n) => {
+          mafColumns[i].selected = n.checked;
+          updateText2();
+        }
+      });
+    });
+    updateText2();
+  }
+}
+async function getFilesAndShowTable(obj) {
+  obj.tableDiv.selectAll("*").remove();
+  const wait = obj.tableDiv.append("div").style("margin", "30px 10px 10px 10px").text("Loading...");
+  let result;
+  try {
+    const body = {
+      experimentalStrategy: obj.opts.experimentalStrategy
+    };
+    if (obj.opts.filter0) body.filter0 = obj.opts.filter0;
+    result = await dofetch3("gdc/maf", { body });
+    if (result.error) throw result.error;
+    if (!Array.isArray(result.files)) throw "result.files[] not array";
+    if (result.files.length == 0) throw "No MAF files available.";
+    if (result.filesTotal > result.files.length) {
+      wait.text(`Showing first ${result.files.length} MAF files out of ${result.filesTotal} total.`);
+    } else {
+      wait.text(`Showing ${result.files.length} MAF files.`);
+    }
+    const rows = [];
+    for (const f of result.files) {
+      const row = [
+        {
+          html: `<a href=https://portal.gdc.cancer.gov/files/${f.id} target=_blank>${f.case_submitter_id}</a>`,
+          value: f.case_submitter_id
+        },
+        { value: f.project_id },
+        {
+          html: f.sample_types.map((i) => {
+            return '<span class="sja_mcdot" style="padding:1px 8px;background:#ddd;color:black;white-space:nowrap">' + i + "</span>";
+          }).join(" ")
+        },
+        { value: f.file_size }
+        // do not send in text-formated file size, table sorting won't work
+      ];
+      rows.push(row);
+    }
+    obj.mafTableArg = {
+      rows,
+      columns: tableColumns,
+      resize: true,
+      div: obj.tableDiv.append("div"),
+      selectAll: true,
+      // comment out for quicker testing
+      dataTestId: "sja_mafFileTable",
+      header: { allowSort: true },
+      selectedRows: [],
+      //[198], // uncomment out for quicker testing
+      buttonsToLeft: true,
+      buttons: [
+        {
+          text: " ",
+          // table.ts requires this
+          onChange: updateButtonBySelectionChange,
+          callback: submitSelectedFiles
+        }
+      ]
+    };
+    renderTable(obj.mafTableArg);
+  } catch (e) {
+    wait.text(e.message || e);
+    if (e.stack) console.log(e.stack);
+  }
+  function updateButtonBySelectionChange(lst, button) {
+    let sum = 0;
+    for (const i of lst) sum += result.files[i].file_size;
+    if (sum == 0) {
+      button.innerHTML = "No file selected";
+      button.disabled = true;
+      return;
+    }
+    button.disabled = false;
+    button.innerHTML = sum < result.maxTotalSizeCompressed ? `Download ${fileSize(sum)} compressed MAF data` : `Download ${fileSize(result.maxTotalSizeCompressed)} compressed MAF data (${fileSize(sum)} selected)`;
+  }
+  let serverMessage;
+  async function submitSelectedFiles(lst, button) {
+    const outColumns = mafColumns.filter((i) => i.selected).map((i) => i.column);
+    if (outColumns.length == 0) {
+      window.alert("No output columns selected.");
+      return;
+    }
+    mayCreateServerMessageSpan(button);
+    const fileIdLst = [];
+    for (const i of lst) {
+      fileIdLst.push(result.files[i].id);
+    }
+    if (fileIdLst.length == 0) return;
+    obj.holder.style("pointer-events", "none").style("opacity", 0.5);
+    const oldText = button.innerHTML;
+    button.innerHTML = "Loading... Please wait";
+    serverMessage.style("display", "none");
+    let data;
+    try {
+      data = await dofetch3("gdc/mafBuild", { body: { fileIdLst, columns: outColumns } });
+      if (!Object.keys(data).length) throw "server returned blank multipart";
+      if (data.errors?.body) {
+        const errors = data.errors.body || [];
+        if (Array.isArray(errors)) {
+          const fileErrors = errors.filter((d) => d.url);
+          if (fileErrors.length) displayRunStatusErrors(fileErrors);
+          const nonFileErrors = errors.filter((d) => !d.url);
+          for (const e of nonFileErrors) sayerror(obj.errDiv, e.error || e.message);
+        }
+      }
+      if (!data.gzfile) throw "missing gzfile from response";
+      const href = URL.createObjectURL(data.gzfile.body);
+      const a = document.createElement("a");
+      a.href = href;
+      a.download = `cohortMAF.${(/* @__PURE__ */ new Date()).toISOString().split("T")[0]}.maf.gz`;
+      a.style.display = "none";
+      document.body.appendChild(a);
+      a.click();
+      document.body.removeChild(a);
+    } catch (e) {
+      sayerror(obj.errDiv, e);
+    } finally {
+      button.innerHTML = oldText;
+      obj.holder.style("pointer-events", "auto").style("opacity", 1);
+    }
+  }
+  function mayCreateServerMessageSpan(button) {
+    if (serverMessage) return;
+    const holder = select_default(button.parentElement);
+    serverMessage = holder.append("span").attr("class", "sja_clbtext").style("display", "none");
+  }
+  function displayRunStatusErrors(errors) {
+    const rows = [];
+    for (const e of errors) {
+      if (typeof e.error != "string") throw ".error=string missing from an entry";
+      if (typeof e.url != "string") throw ".url=string missing from an entry";
+      const l = e.url.split("/");
+      const uuid = l[l.length - 1];
+      const fo = result.files.find((i) => i.id == uuid);
+      if (fo) {
+        rows.push([
+          { html: `<a href=${e.url} target=_blank>${fo.case_submitter_id}</a>` },
+          { value: fo.project_id },
+          { value: fileSize(fo.file_size) },
+          { value: e.error }
+        ]);
+      } else {
+        rows.push([{ value: uuid }, { value: "?" }, { value: "?" }, { value: e.error }]);
+      }
+    }
+    serverMessage.text(`${errors.length} empty/failed file${errors.length > 1 ? "s" : ""}`).style("display", "").on("click", (event) => {
+      renderTable({
+        rows,
+        columns: [{ column: "" }, { column: "" }, { column: "" }, { column: "" }],
+        showHeader: false,
+        div: tip.clear().showunder(event.target).d
+      });
+    });
+  }
+}
+export {
+  gdcMAFui
+};
+//# sourceMappingURL=maf-QRGRW2O4.js.map