@sjcrh/proteinpaint-client 2.166.0 → 2.167.1

package/dist/maf-YJJO773K.js

@@ -1,448 +0,0 @@
-import {
-  make_radios,
-  renderTable,
-  sayerror,
-  table2col
-} from "./chunk-UT6W4ZZL.js";
-import "./chunk-HJ6L54YS.js";
-import {
-  dofetch3,
-  fileSize
-} from "./chunk-5TDKRZN5.js";
-import "./chunk-RYRCMHYR.js";
-import "./chunk-ECKWM4HB.js";
-import {
-  Menu
-} from "./chunk-NXOWHUR4.js";
-import "./chunk-5MWX5HUZ.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-ICNJQHQZ.js";
-import "./chunk-FYTZCTJC.js";
-import "./chunk-7NTZWOJV.js";
-import "./chunk-OMO754MK.js";
-import "./chunk-RA5EXEHB.js";
-import "./chunk-PMZS3SHH.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-W2IWHXLL.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-UJUXE42U.js";
-import "./chunk-OMR2DT66.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.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.${n} not function`;
-      }
-    }
-    {
-      const cn = /* @__PURE__ */ new Set();
-      for (const c of mafColumns) {
-        if (!c.column) throw ".column missing from an element";
-        if (cn.has(c.column)) throw "duplicate column: " + c.column;
-        cn.add(c.column);
-      }
-    }
-    update({ filter0 });
-  } catch (e) {
-    console.log(e);
-    sayerror(holder, e.message || e);
-  }
-  async function update({ filter0: filter02 }) {
-    holder.selectAll("*").remove();
-    const obj = {
-      errDiv: holder.append("div"),
-      controlDiv: holder.append("div"),
-      tableDiv: holder.append("div"),
-      opts: {
-        filter0: filter02,
-        experimentalStrategy: "WXS"
-      },
-      busy: false,
-      // when downloading, set to true for disabling ui interactivity
-      mafTableArg: null,
-      expStrategyRadio: null
-    };
-    makeControls(obj);
-    await getFilesAndShowTable(obj);
-    callbacks?.postRender?.(publicApi);
-  }
-  const publicApi = { update };
-  return publicApi;
-}
-function makeControls(obj) {
-  const table = table2col({ holder: obj.controlDiv });
-  table.addRow("Access", "Open");
-  table.addRow("Workflow Type", "Aliquot Ensemble Somatic Variant Merging and Masking");
-  {
-    const [td1, td2] = table.addRow("Experimental Strategy");
-    obj.expStrategyRadio = make_radios({
-      holder: td2,
-      options: [
-        { label: "WXS", value: "WXS", checked: obj.opts.experimentalStrategy == "WXS" },
-        {
-          label: "Targeted Sequencing",
-          value: "Targeted Sequencing",
-          checked: obj.opts.experimentalStrategy == "Targeted Sequencing"
-        }
-      ],
-      styles: { display: "inline" },
-      callback: async (value) => {
-        obj.opts.experimentalStrategy = value;
-        await getFilesAndShowTable(obj);
-      }
-    });
-  }
-  {
-    let updateText2 = function() {
-      clickText.text(
-        `${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
-      buttons: [
-        {
-          text: "Aggregate selected MAF files and download",
-          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) {
-    if (obj.busy) {
-      obj.mafTableArg.buttons[0].button.property("disabled", true);
-      return;
-    }
-    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;
-    }
-    select_default(button.parentElement).style("float", "left");
-    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;
-    const oldText = button.innerHTML;
-    button.innerHTML = "Loading... Please wait";
-    button.disabled = true;
-    serverMessage.style("display", "none");
-    let data;
-    try {
-      obj.busy = true;
-      obj.expStrategyRadio.inputs.property("disabled", true);
-      data = await dofetch3("gdc/mafBuild", { body: { fileIdLst, columns: outColumns } });
-      if (!Object.keys(data).length) throw "server returned blank multipart";
-      obj.busy = false;
-      obj.expStrategyRadio.inputs.property("disabled", false);
-    } catch (e) {
-      sayerror(obj.errDiv, e);
-      button.innerHTML = oldText;
-      button.disabled = false;
-      obj.busy = false;
-      obj.expStrategyRadio.property("disabled", false);
-      return;
-    }
-    button.innerHTML = oldText;
-    button.disabled = false;
-    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.${(/* @__PURE__ */ new Date()).toISOString().split("T")[0]}.maf.gz`;
-    a.style.display = "none";
-    document.body.appendChild(a);
-    a.click();
-    document.body.removeChild(a);
-  }
-  function mayCreateServerMessageSpan(button) {
-    if (serverMessage) return;
-    const holder = select_default(button.parentElement);
-    serverMessage = holder.append("span").attr("class", "sja_clbtext").style("display", "none");
-  }
-  function displayRunStatusErrors(errors) {
-    const rows = [];
-    for (const e of errors) {
-      if (typeof e.error != "string") throw ".error=string missing from an entry";
-      if (typeof e.url != "string") throw ".url=string missing from an entry";
-      const l = e.url.split("/");
-      const uuid = l[l.length - 1];
-      const fo = result.files.find((i) => i.id == uuid);
-      if (fo) {
-        rows.push([
-          { html: `<a href=${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-YJJO773K.js.map

package/dist/maf-YJJO773K.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../gdc/maf.js"],
-  "sourcesContent": ["import { dofetch3 } from '#common/dofetch'\nimport { make_radios, renderTable, sayerror, Menu, table2col } from '#dom'\nimport { fileSize } from '#shared/fileSize.js'\nimport { select } from 'd3-selection'\n\n/*\na UI to list open-access maf files from current cohort\nlet user selects some, for the backend to generate an aggregated maf file and download to user\n\nobj {} TODO convert to class and declare properties\n\n*/\n\nconst tip = new Menu()\n\n// list of columns to show in MAF file table\nconst tableColumns = [\n\t{ label: 'Case', sortable: true },\n\t{ label: 'Project', sortable: true },\n\t{ label: 'Samples' },\n\t{ label: 'File Size', barplot: { tickFormat: '~s' }, sortable: true } // barchart column not sortable yet\n]\n\n// list of gdc maf file columns; selected ones are used for output\nconst mafColumns = [\n\t{ column: 'Hugo_Symbol', selected: true },\n\t{ column: 'Entrez_Gene_Id', selected: true },\n\t{ column: 'Center', selected: true },\n\t{ column: 'NCBI_Build', selected: true },\n\t{ column: 'Chromosome', selected: true },\n\t{ column: 'Start_Position', selected: true },\n\t{ column: 'End_Position', selected: true },\n\t{ column: 'Strand', selected: true },\n\t{ column: 'Variant_Classification', selected: true },\n\t{ column: 'Variant_Type', selected: true },\n\t{ column: 'Reference_Allele', selected: true },\n\t{ column: 'Tumor_Seq_Allele1', selected: true },\n\t{ column: 'Tumor_Seq_Allele2', selected: true },\n\t{ column: 'dbSNP_RS', selected: true },\n\t{ column: 'dbSNP_Val_Status', selected: true },\n\t{ column: 'Tumor_Sample_Barcode', selected: true },\n\t{ column: 'Matched_Norm_Sample_Barcode', selected: true },\n\t{ column: 'Match_Norm_Seq_Allele1', selected: true },\n\t{ column: 'Match_Norm_Seq_Allele2', selected: true },\n\t{ column: 'Tumor_Validation_Allele1', selected: true },\n\t{ column: 'Tumor_Validation_Allele2', selected: true },\n\t{ column: 'Match_Norm_Validation_Allele1', selected: true },\n\t{ column: 'Match_Norm_Validation_Allele2', selected: true },\n\t{ column: 'Verification_Status', selected: true },\n\t{ column: 'Validation_Status', selected: true },\n\t{ column: 'Mutation_Status', selected: true },\n\t{ column: 'Sequencing_Phase', selected: true },\n\t{ column: 'Sequence_Source', selected: true },\n\t{ column: 'Validation_Method', selected: true },\n\t{ column: 'Score', selected: true },\n\t{ column: 'BAM_File', selected: true },\n\t{ column: 'Sequencer', selected: true },\n\t{ column: 'Tumor_Sample_UUID', selected: true },\n\t{ column: 'Matched_Norm_Sample_UUID', selected: true },\n\t{ column: 'HGVSc', selected: true },\n\t{ column: 'HGVSp', selected: true },\n\t{ column: 'HGVSp_Short', selected: true },\n\t{ column: 'Transcript_ID', selected: true },\n\t{ column: 'Exon_Number', selected: true },\n\t{ column: 't_depth', selected: true },\n\t{ column: 't_ref_count', selected: true },\n\t{ column: 't_alt_count', selected: true },\n\t{ column: 'n_depth', selected: true },\n\t{ column: 'n_ref_count', selected: true },\n\t{ column: 'n_alt_count', selected: true },\n\t{ column: 'all_effects', selected: true },\n\t{ column: 'Allele', selected: true },\n\t{ column: 'Gene', selected: true },\n\t{ column: 'Feature', selected: true },\n\t{ column: 'Feature_type', selected: true },\n\t{ column: 'One_Consequence', selected: true },\n\t{ column: 'Consequence', selected: true },\n\t{ column: 'cDNA_position', selected: true },\n\t{ column: 'CDS_position', selected: true },\n\t{ column: 'Protein_position', selected: true },\n\t{ column: 'Amino_acids', selected: true },\n\t{ column: 'Codons', selected: true },\n\t{ column: 'Existing_variation', selected: true },\n\t{ column: 'DISTANCE', selected: true },\n\t{ column: 'TRANSCRIPT_STRAND', selected: true },\n\t{ column: 'SYMBOL', selected: true },\n\t{ column: 'SYMBOL_SOURCE', selected: true },\n\t{ column: 'HGNC_ID', selected: true },\n\t{ column: 'BIOTYPE', selected: true },\n\t{ column: 'CANONICAL', selected: true },\n\t{ column: 'CCDS', selected: true },\n\t{ column: 'ENSP', selected: true },\n\t{ column: 'SWISSPROT', selected: true },\n\t{ column: 'TREMBL', selected: true },\n\t{ column: 'UNIPARC', selected: true },\n\t{ column: 'UNIPROT_ISOFORM', selected: true },\n\t{ column: 'RefSeq', selected: true },\n\t{ column: 'MANE', selected: true },\n\t{ column: 'APPRIS', selected: true },\n\t{ column: 'FLAGS', selected: true },\n\t{ column: 'SIFT', selected: true },\n\t{ column: 'PolyPhen', selected: true },\n\t{ column: 'EXON', selected: true },\n\t{ column: 'INTRON', selected: true },\n\t{ column: 'DOMAINS', selected: true },\n\t{ column: '1000G_AF', selected: true },\n\t{ column: '1000G_AFR_AF', selected: true },\n\t{ column: '1000G_AMR_AF', selected: true },\n\t{ column: '1000G_EAS_AF', selected: true },\n\t{ column: '1000G_EUR_AF', selected: true },\n\t{ column: '1000G_SAS_AF', selected: true },\n\t{ column: 'ESP_AA_AF', selected: true },\n\t{ column: 'ESP_EA_AF', selected: true },\n\t{ column: 'gnomAD_AF', selected: true },\n\t{ column: 'gnomAD_AFR_AF', selected: true },\n\t{ column: 'gnomAD_AMR_AF', selected: true },\n\t{ column: 'gnomAD_ASJ_AF', selected: true },\n\t{ column: 'gnomAD_EAS_AF', selected: true },\n\t{ column: 'gnomAD_FIN_AF', selected: true },\n\t{ column: 'gnomAD_NFE_AF', selected: true },\n\t{ column: 'gnomAD_OTH_AF', selected: true },\n\t{ column: 'gnomAD_SAS_AF', selected: true },\n\t{ column: 'MAX_AF', selected: true },\n\t{ column: 'MAX_AF_POPS', selected: true },\n\t{ column: 'gnomAD_non_cancer_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_AFR_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_AMI_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_AMR_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_ASJ_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_EAS_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_FIN_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_MID_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_NFE_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_OTH_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_SAS_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_MAX_AF_adj', selected: true },\n\t{ column: 'gnomAD_non_cancer_MAX_AF_POPS_adj', selected: true },\n\t{ column: 'CLIN_SIG', selected: true },\n\t{ column: 'SOMATIC', selected: true },\n\t{ column: 'PUBMED', selected: true },\n\t{ column: 'TRANSCRIPTION_FACTORS', selected: true },\n\t{ column: 'MOTIF_NAME', selected: true },\n\t{ column: 'MOTIF_POS', selected: true },\n\t{ column: 'HIGH_INF_POS', selected: true },\n\t{ column: 'MOTIF_SCORE_CHANGE', selected: true },\n\t{ column: 'miRNA', selected: true },\n\t{ column: 'IMPACT', selected: true },\n\t{ column: 'PICK', selected: true },\n\t{ column: 'VARIANT_CLASS', selected: true },\n\t{ column: 'TSL', selected: true },\n\t{ column: 'HGVS_OFFSET', selected: true },\n\t{ column: 'PHENO', selected: true },\n\t{ column: 'GENE_PHENO', selected: true },\n\t{ column: 'CONTEXT', selected: true },\n\t{ column: 'case_id', selected: true },\n\t{ column: 'GDC_FILTER', selected: true },\n\t{ column: 'COSMIC', selected: true },\n\t{ column: 'hotspot', selected: true },\n\t{ column: 'tumor_bam_uuid', selected: true },\n\t{ column: 'normal_bam_uuid', selected: true },\n\t{ column: 'RNA_Support', selected: true },\n\t{ column: 'RNA_depth', selected: true },\n\t{ column: 'RNA_ref_count', selected: true },\n\t{ column: 'RNA_alt_count', selected: true },\n\t{ column: 'callers', selected: true }\n]\n\nexport async function gdcMAFui({ filter0, callbacks, debugmode = false }, holder) {\n\ttry {\n\t\tif (callbacks) {\n\t\t\t/* due to src/app.js line 100\n\t\t\tdelete this when that is reshaped to app.sjcharts.callbacks={}\n\t\t\t*/\n\t\t\tdelete callbacks.sjcharts\n\t\t\tfor (const n in callbacks) {\n\t\t\t\tif (typeof callbacks[n] != 'function') throw `callbacks.${n} not function`\n\t\t\t}\n\t\t}\n\t\t{\n\t\t\t// validate column names in case of human err\n\t\t\tconst cn = new Set()\n\t\t\tfor (const c of mafColumns) {\n\t\t\t\tif (!c.column) throw '.column missing from an element'\n\t\t\t\tif (cn.has(c.column)) throw 'duplicate column: ' + c.column\n\t\t\t\tcn.add(c.column)\n\t\t\t}\n\t\t}\n\t\tupdate({ filter0 })\n\t} catch (e) {\n\t\tconsole.log(e)\n\t\tsayerror(holder, e.message || e)\n\t}\n\n\tasync function update({ filter0 }) {\n\t\tholder.selectAll('*').remove()\n\t\t// TODO convert obj to class and declare all properties\n\t\tconst obj = {\n\t\t\terrDiv: holder.append('div'),\n\t\t\tcontrolDiv: holder.append('div'),\n\t\t\ttableDiv: holder.append('div'),\n\t\t\topts: {\n\t\t\t\tfilter0,\n\t\t\t\texperimentalStrategy: 'WXS'\n\t\t\t},\n\t\t\tbusy: false, // when downloading, set to true for disabling ui interactivity\n\t\t\tmafTableArg: null,\n\t\t\texpStrategyRadio: null\n\t\t}\n\t\tmakeControls(obj)\n\t\tawait getFilesAndShowTable(obj)\n\t\tcallbacks?.postRender?.(publicApi)\n\t}\n\n\t// return api to be accessible by react wrapper; will call api.update() to auto refresh cohortmaf UI on GFF cohort change\n\tconst publicApi = { update }\n\treturn publicApi\n}\n\nfunction makeControls(obj) {\n\tconst table = table2col({ holder: obj.controlDiv })\n\ttable.addRow('Access', 'Open')\n\ttable.addRow('Workflow Type', 'Aliquot Ensemble Somatic Variant Merging and Masking')\n\t{\n\t\tconst [td1, td2] = table.addRow('Experimental Strategy')\n\t\tobj.expStrategyRadio = make_radios({\n\t\t\tholder: td2,\n\t\t\toptions: [\n\t\t\t\t{ label: 'WXS', value: 'WXS', checked: obj.opts.experimentalStrategy == 'WXS' },\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Targeted Sequencing',\n\t\t\t\t\tvalue: 'Targeted Sequencing',\n\t\t\t\t\tchecked: obj.opts.experimentalStrategy == 'Targeted Sequencing'\n\t\t\t\t}\n\t\t\t],\n\t\t\tstyles: { display: 'inline' },\n\t\t\tcallback: async value => {\n\t\t\t\tobj.opts.experimentalStrategy = value\n\t\t\t\tawait getFilesAndShowTable(obj)\n\t\t\t}\n\t\t})\n\t}\n\n\t{\n\t\tconst [td1, td2] = table.addRow('Output Columns')\n\t\tconst clickText = td2\n\t\t\t.append('span')\n\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t.on('click', event => {\n\t\t\t\tconst rows = [],\n\t\t\t\t\tselectedRows = []\n\t\t\t\tfor (const [i, c] of mafColumns.entries()) {\n\t\t\t\t\trows.push([{ value: c.column }])\n\t\t\t\t\tif (c.selected) selectedRows.push(i)\n\t\t\t\t}\n\t\t\t\trenderTable({\n\t\t\t\t\tdiv: tip.clear().showunder(event.target).d,\n\t\t\t\t\trows,\n\t\t\t\t\tcolumns: [{ label: 'Column Name' }],\n\t\t\t\t\tselectedRows,\n\t\t\t\t\tnoButtonCallback: (i, n) => {\n\t\t\t\t\t\tmafColumns[i].selected = n.checked\n\t\t\t\t\t\tupdateText()\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t})\n\n\t\tupdateText()\n\n\t\tfunction updateText() {\n\t\t\tclickText.text(\n\t\t\t\t`${mafColumns.reduce((c, i) => c + (i.selected ? 1 : 0), 0)} of ${\n\t\t\t\t\tmafColumns.length\n\t\t\t\t} columns selected. Click to change`\n\t\t\t)\n\t\t}\n\t}\n}\n\nasync function getFilesAndShowTable(obj) {\n\tobj.tableDiv.selectAll('*').remove()\n\tconst wait = obj.tableDiv.append('div').style('margin', '30px 10px 10px 10px').text('Loading...')\n\n\tlet result // convenient for accessing outside of try-catch\n\n\ttry {\n\t\tconst body = {\n\t\t\texperimentalStrategy: obj.opts.experimentalStrategy\n\t\t}\n\t\tif (obj.opts.filter0) body.filter0 = obj.opts.filter0\n\t\tresult = await dofetch3('gdc/maf', { body })\n\t\tif (result.error) throw result.error\n\t\tif (!Array.isArray(result.files)) throw 'result.files[] not array'\n\t\tif (result.files.length == 0) throw 'No MAF files available.'\n\n\t\t// render\n\t\tif (result.filesTotal > result.files.length) {\n\t\t\twait.text(`Showing first ${result.files.length} MAF files out of ${result.filesTotal} total.`)\n\t\t} else {\n\t\t\twait.text(`Showing ${result.files.length} MAF files.`)\n\t\t}\n\n\t\tconst rows = []\n\t\tfor (const f of result.files) {\n\t\t\tconst row = [\n\t\t\t\t{\n\t\t\t\t\thtml: `<a href=https://portal.gdc.cancer.gov/files/${f.id} target=_blank>${f.case_submitter_id}</a>`,\n\t\t\t\t\tvalue: f.case_submitter_id\n\t\t\t\t},\n\t\t\t\t{ value: f.project_id },\n\t\t\t\t{\n\t\t\t\t\thtml: f.sample_types\n\t\t\t\t\t\t.map(i => {\n\t\t\t\t\t\t\treturn (\n\t\t\t\t\t\t\t\t'<span class=\"sja_mcdot\" style=\"padding:1px 8px;background:#ddd;color:black;white-space:nowrap\">' +\n\t\t\t\t\t\t\t\ti +\n\t\t\t\t\t\t\t\t'</span>'\n\t\t\t\t\t\t\t)\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.join(' ')\n\t\t\t\t},\n\t\t\t\t{ value: f.file_size } // do not send in text-formated file size, table sorting won't work\n\t\t\t]\n\t\t\trows.push(row)\n\t\t}\n\n\t\t// tracks table arg, so that the created button DOM element is accessible and can be modified\n\t\tobj.mafTableArg = {\n\t\t\trows,\n\t\t\tcolumns: tableColumns,\n\t\t\tresize: true,\n\t\t\tdiv: obj.tableDiv.append('div'),\n\t\t\tselectAll: true, // comment out for quicker testing\n\t\t\tdataTestId: 'sja_mafFileTable',\n\t\t\theader: { allowSort: true },\n\t\t\tselectedRows: [], //[198], // uncomment out for quicker testing\n\t\t\tbuttons: [\n\t\t\t\t{\n\t\t\t\t\ttext: 'Aggregate selected MAF files and download',\n\t\t\t\t\tonChange: updateButtonBySelectionChange,\n\t\t\t\t\tcallback: submitSelectedFiles\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t\trenderTable(obj.mafTableArg)\n\t} catch (e) {\n\t\twait.text(e.message || e)\n\t\tif (e.stack) console.log(e.stack)\n\t}\n\n\tfunction updateButtonBySelectionChange(lst, button) {\n\t\tif (obj.busy) {\n\t\t\t/* is waiting for server response. do not proceed to alter submit button\n\t\t\tbecause the checkboxes in the maf table cannot be disabled when submission is running,\n\t\t\tthus user can still check and uncheck maf files, that can cause the submit button to be enabled\n\t\t\tthus do below to disable it\n\t\t\t*/\n\t\t\tobj.mafTableArg.buttons[0].button.property('disabled', true)\n\t\t\treturn\n\t\t}\n\n\t\tlet sum = 0\n\t\tfor (const i of lst) sum += result.files[i].file_size\n\t\tif (sum == 0) {\n\t\t\tbutton.innerHTML = 'No file selected'\n\t\t\tbutton.disabled = true\n\t\t\treturn\n\t\t}\n\n\t\t// TEMP fix! later add `buttonsToLeft:true` at line 321; this fix avoid changing table.ts to make it easy to cherrypick for 2.16 gdc release\n\t\tselect(button.parentElement).style('float', 'left')\n\n\t\tbutton.disabled = false\n\t\tbutton.innerHTML =\n\t\t\tsum < result.maxTotalSizeCompressed\n\t\t\t\t? `Download ${fileSize(sum)} compressed MAF data`\n\t\t\t\t: `Download ${fileSize(result.maxTotalSizeCompressed)} compressed MAF data (${fileSize(sum)} selected)`\n\t}\n\n\t/* after table is created, on clicking download btn for first time, create a <span> after download btn,\n\tin order to show server-sent message on problematic files (emtpy, failed, invalid)\n\tscope this <span> for easy access by helpers,\n\tdetect if it is truthy to only create it once\n\t*/\n\tlet serverMessage\n\n\tasync function submitSelectedFiles(lst, button) {\n\t\tconst outColumns = mafColumns.filter(i => i.selected).map(i => i.column)\n\t\tif (outColumns.length == 0) {\n\t\t\twindow.alert('No output columns selected.')\n\t\t\treturn\n\t\t}\n\n\t\tmayCreateServerMessageSpan(button)\n\n\t\tconst fileIdLst = []\n\t\tfor (const i of lst) {\n\t\t\tfileIdLst.push(result.files[i].id)\n\t\t}\n\t\tif (fileIdLst.length == 0) return\n\n\t\tconst oldText = button.innerHTML\n\t\tbutton.innerHTML = 'Loading... Please wait'\n\t\tbutton.disabled = true\n\t\tserverMessage.style('display', 'none')\n\n\t\t// may disable the \"Aggregate\" button here and re-enable later\n\n\t\tlet data\n\t\ttry {\n\t\t\tobj.busy = true\n\t\t\tobj.expStrategyRadio.inputs.property('disabled', true)\n\t\t\tdata = await dofetch3('gdc/mafBuild', { body: { fileIdLst, columns: outColumns } })\n\t\t\tif (!Object.keys(data).length) throw 'server returned blank multipart'\n\t\t\tobj.busy = false\n\t\t\tobj.expStrategyRadio.inputs.property('disabled', false)\n\t\t} catch (e) {\n\t\t\tsayerror(obj.errDiv, e)\n\t\t\tbutton.innerHTML = oldText\n\t\t\tbutton.disabled = false\n\t\t\tobj.busy = false\n\t\t\tobj.expStrategyRadio.property('disabled', false)\n\t\t\treturn\n\t\t}\n\n\t\tbutton.innerHTML = oldText\n\t\tbutton.disabled = false\n\n\t\tif (data.errors?.body) {\n\t\t\t// expect gdc/mafBuild errors to be an array\n\t\t\tconst errors = data.errors.body || []\n\t\t\tif (Array.isArray(errors)) {\n\t\t\t\tconst fileErrors = errors.filter(d => d.url)\n\t\t\t\tif (fileErrors.length) displayRunStatusErrors(fileErrors)\n\t\t\t\tconst nonFileErrors = errors.filter(d => !d.url)\n\t\t\t\tfor (const e of nonFileErrors) sayerror(obj.errDiv, e.error || e.message)\n\t\t\t}\n\t\t}\n\n\t\t// download the file to client\n\t\tif (!data.gzfile) throw 'missing gzfile from response'\n\t\tconst href = URL.createObjectURL(data.gzfile.body)\n\t\t// console.log(394, [octetData?.body.size, href.length, href], octetData)\n\t\tconst a = document.createElement('a')\n\t\ta.href = href\n\t\ta.download = `cohortMAF.${new Date().toISOString().split('T')[0]}.maf.gz`\n\t\ta.style.display = 'none'\n\t\tdocument.body.appendChild(a)\n\t\ta.click()\n\t\tdocument.body.removeChild(a)\n\t}\n\n\tfunction mayCreateServerMessageSpan(button) {\n\t\tif (serverMessage) return // message <span> are already created\n\t\tconst holder = select(button.parentElement)\n\t\tserverMessage = holder.append('span').attr('class', 'sja_clbtext').style('display', 'none')\n\t}\n\n\tfunction displayRunStatusErrors(errors) {\n\t\t// errors[] each ele: {error:str, url:str}\n\t\tconst rows = [] // map errors[] to rows[] to show in table of menu\n\t\tfor (const e of errors) {\n\t\t\tif (typeof e.error != 'string') throw '.error=string missing from an entry'\n\t\t\tif (typeof e.url != 'string') throw '.url=string missing from an entry'\n\t\t\t// url should end in file uuid, which can be used to match with original record of that file\n\t\t\tconst l = e.url.split('/')\n\t\t\tconst uuid = l[l.length - 1]\n\t\t\tconst fo = result.files.find(i => i.id == uuid)\n\t\t\tif (fo) {\n\t\t\t\t// record is found for this failed uuid\n\t\t\t\trows.push([\n\t\t\t\t\t{ html: `<a href=${e.url} target=_blank>${fo.case_submitter_id}</a>` },\n\t\t\t\t\t{ value: fo.project_id },\n\t\t\t\t\t{ value: fileSize(fo.file_size) },\n\t\t\t\t\t{ value: e.error }\n\t\t\t\t])\n\t\t\t} else {\n\t\t\t\t// file is not found; could happen in testing when backend hardcodes a uuid not in result.files[], or even gdc backend changes..\n\t\t\t\trows.push([{ value: uuid }, { value: '?' }, { value: '?' }, { value: e.error }])\n\t\t\t}\n\t\t}\n\t\tserverMessage\n\t\t\t.text(`${errors.length} empty/failed file${errors.length > 1 ? 's' : ''}`)\n\t\t\t.style('display', '')\n\t\t\t.on('click', event => {\n\t\t\t\trenderTable({\n\t\t\t\t\trows,\n\t\t\t\t\tcolumns: [{ column: '' }, { column: '' }, { column: '' }, { column: '' }],\n\t\t\t\t\tshowHeader: false,\n\t\t\t\t\tdiv: tip.clear().showunder(event.target).d\n\t\t\t\t})\n\t\t\t})\n\t}\n}\n"],
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