@sjcrh/proteinpaint-client 2.193.0 → 2.195.0

package/dist/maf-MBX3S3LS.js

@@ -0,0 +1,459 @@
+import {
+  make_radios,
+  renderTable,
+  sayerror,
+  table2col
+} from "./chunk-LYULXXGR.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-CPMOBFFR.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-B4VBTVVQ.js";
+import "./chunk-IQTEW3SK.js";
+import {
+  dofetch3,
+  fileSize
+} from "./chunk-MNPTPENH.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.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.${n} not function`;
+      }
+    }
+    {
+      const cn = /* @__PURE__ */ new Set();
+      for (const c of mafColumns) {
+        if (!c.column) throw ".column missing from an element";
+        if (cn.has(c.column)) throw "duplicate column: " + c.column;
+        cn.add(c.column);
+      }
+    }
+    update({ filter0 });
+  } catch (e) {
+    console.log(e);
+    sayerror(holder, e.message || e);
+  }
+  async function update({ filter0: filter02 }) {
+    holder.selectAll("*").remove();
+    const obj = {
+      holder,
+      errDiv: holder.append("div"),
+      controlDiv: holder.append("div"),
+      tableDiv: holder.append("div"),
+      opts: {
+        filter0: filter02,
+        experimentalStrategy: "WXS"
+      },
+      mafTableArg: null
+    };
+    makeControls(obj);
+    await getFilesAndShowTable(obj);
+    callbacks?.postRender?.(publicApi);
+  }
+  const publicApi = { update };
+  return publicApi;
+}
+function makeControls(obj) {
+  const table = table2col({ holder: obj.controlDiv });
+  table.addRow("Access", "Open");
+  table.addRow("Workflow Type", "Aliquot Ensemble Somatic Variant Merging and Masking");
+  {
+    const [td1, td2] = table.addRow("Experimental Strategy");
+    make_radios({
+      holder: td2,
+      options: [
+        {
+          label: "WXS",
+          value: "WXS",
+          checked: obj.opts.experimentalStrategy == "WXS",
+          testid: "sjpp-gdcmaf-radio-wxs"
+        },
+        {
+          label: "Targeted Sequencing",
+          value: "Targeted Sequencing",
+          checked: obj.opts.experimentalStrategy == "Targeted Sequencing",
+          testid: "sjpp-gdcmaf-radio-targeted"
+        }
+      ],
+      styles: { display: "inline" },
+      callback: async (value) => {
+        obj.opts.experimentalStrategy = value;
+        await getFilesAndShowTable(obj);
+      }
+    });
+  }
+  {
+    let updateText2 = function() {
+      clickText.text(
+        `${mafColumns.reduce((c, i) => c + (i.selected ? 1 : 0), 0).toLocaleString()} of ${mafColumns.length.toLocaleString()} columns selected. Click to change`
+      );
+    };
+    var updateText = updateText2;
+    const [td1, td2] = table.addRow("Output Columns");
+    const clickText = td2.append("span").attr("data-testid", "sjpp-gdcmaf-columnhandle").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,
+        // keep the header "select all" checkbox in sync with the rows: tick it when every
+        // column is currently selected (e.g. the all-selected default state)
+        selectAll: selectedRows.length === mafColumns.length,
+        dataTestId: "sjpp-gdcmaf-columnTableUi",
+        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.toLocaleString()} MAF files out of ${result.filesTotal.toLocaleString()} total.`
+      );
+    } else {
+      wait.text(`Showing ${result.files.length.toLocaleString()} MAF files.`);
+    }
+    const rows = [];
+    for (const f of result.files) {
+      const row = [
+        {
+          html: `<a href=https://portal.gdc.cancer.gov/files/${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: "sjpp-gdcmaf-maffiletable-" + obj.opts.experimentalStrategy,
+      header: { allowSort: true },
+      selectedRows: [],
+      //[198], // uncomment out for quicker testing
+      buttonsToLeft: true,
+      buttons: [
+        {
+          text: " ",
+          // table.ts requires this
+          onChange: updateButtonBySelectionChange,
+          callback: submitSelectedFiles,
+          dataTestId: "sjpp-gdcmaf-submitBtn"
+        }
+      ]
+    };
+    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.status == "error" || data.error) throw data.error || data.message || "server error building MAF";
+      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 (nonFileErrors.length) return;
+        }
+      }
+      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-MBX3S3LS.js.map

package/dist/maf-MBX3S3LS.js.map

@@ -0,0 +1,7 @@
+{
+  "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\tholder,\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\tmafTableArg: 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\tmake_radios({\n\t\t\tholder: td2,\n\t\t\toptions: [\n\t\t\t\t{\n\t\t\t\t\tlabel: 'WXS',\n\t\t\t\t\tvalue: 'WXS',\n\t\t\t\t\tchecked: obj.opts.experimentalStrategy == 'WXS',\n\t\t\t\t\ttestid: 'sjpp-gdcmaf-radio-wxs'\n\t\t\t\t},\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\ttestid: 'sjpp-gdcmaf-radio-targeted'\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('data-testid', 'sjpp-gdcmaf-columnhandle')\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\t// keep the header \"select all\" checkbox in sync with the rows: tick it when every\n\t\t\t\t\t// column is currently selected (e.g. the all-selected default state)\n\t\t\t\t\tselectAll: selectedRows.length === mafColumns.length,\n\t\t\t\t\tdataTestId: 'sjpp-gdcmaf-columnTableUi',\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\n\t\t\t\t\t.reduce((c, i) => c + (i.selected ? 1 : 0), 0)\n\t\t\t\t\t.toLocaleString()} of ${mafColumns.length.toLocaleString()} 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(\n\t\t\t\t`Showing first ${result.files.length.toLocaleString()} MAF files out of ${result.filesTotal.toLocaleString()} total.`\n\t\t\t)\n\t\t} else {\n\t\t\twait.text(`Showing ${result.files.length.toLocaleString()} MAF files.`)\n\t\t}\n\n\t\tconst rows = []\n\t\tfor (const f of result.files) {\n\t\t\tconst row = [\n\t\t\t\t{\n\t\t\t\t\thtml: `<a href=https://portal.gdc.cancer.gov/files/${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: 'sjpp-gdcmaf-maffiletable-' + obj.opts.experimentalStrategy,\n\t\t\theader: { allowSort: true },\n\t\t\tselectedRows: [], //[198], // uncomment out for quicker testing\n\t\t\tbuttonsToLeft: true,\n\t\t\tbuttons: [\n\t\t\t\t{\n\t\t\t\t\ttext: ' ', // table.ts requires this\n\t\t\t\t\tonChange: updateButtonBySelectionChange,\n\t\t\t\t\tcallback: submitSelectedFiles,\n\t\t\t\t\tdataTestId: 'sjpp-gdcmaf-submitBtn'\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\t// note that button is generated by renderTable()\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\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\tobj.holder.style('pointer-events', 'none').style('opacity', 0.5)\n\t\tconst oldText = button.innerHTML\n\t\tbutton.innerHTML = 'Loading... Please wait'\n\t\tserverMessage.style('display', 'none')\n\n\t\tlet data\n\t\ttry {\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\n\t\t\t// A JSON (non-multipart) response means buildMaf failed before it could start streaming the\n\t\t\t// file \u2014 e.g. no files under the size limit, or a GDC metadata-query error. Surface the\n\t\t\t// server's actual message instead of falling through to the misleading 'missing gzfile'.\n\t\t\t// (A successful multipart response is keyed by part name \u2014 gzfile/errors \u2014 and has no\n\t\t\t// top-level .error/.status, so this only catches the JSON error shape.)\n\t\t\tif (data.status == 'error' || data.error) throw data.error || data.message || 'server error building MAF'\n\n\t\t\tif (data.errors?.body) {\n\t\t\t\t// expect gdc/mafBuild errors to be an array\n\t\t\t\tconst errors = data.errors.body || []\n\t\t\t\tif (Array.isArray(errors)) {\n\t\t\t\t\tconst fileErrors = errors.filter(d => d.url)\n\t\t\t\t\tif (fileErrors.length) displayRunStatusErrors(fileErrors)\n\t\t\t\t\tconst nonFileErrors = errors.filter(d => !d.url)\n\t\t\t\t\tfor (const e of nonFileErrors) sayerror(obj.errDiv, e.error || e.message)\n\t\t\t\t\t// A non-file (build-level) error \u2014 e.g. the server-side timeout backstop \u2014 means the\n\t\t\t\t\t// cohort MAF is incomplete/invalid. Surface the error and do NOT download the partial\n\t\t\t\t\t// file. (Per-file errors alone are non-fatal: the partial cohort still downloads below.)\n\t\t\t\t\tif (nonFileErrors.length) return\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// download the file to client\n\t\t\tif (!data.gzfile) throw 'missing gzfile from response'\n\t\t\tconst href = URL.createObjectURL(data.gzfile.body)\n\t\t\tconst a = document.createElement('a')\n\t\t\ta.href = href\n\t\t\ta.download = `cohortMAF.${new Date().toISOString().split('T')[0]}.maf.gz`\n\t\t\ta.style.display = 'none'\n\t\t\tdocument.body.appendChild(a)\n\t\t\ta.click()\n\t\t\tdocument.body.removeChild(a)\n\t\t} catch (e) {\n\t\t\tsayerror(obj.errDiv, e)\n\t\t} finally {\n\t\t\tbutton.innerHTML = oldText\n\t\t\tobj.holder.style('pointer-events', 'auto').style('opacity', 1)\n\t\t}\n\t}\n\n\tfunction mayCreateServerMessageSpan(button) {\n\t\tif (serverMessage) return // message <span> are already created\n\t\tconst holder = select(button.parentElement)\n\t\tserverMessage = holder.append('span').attr('class', 'sja_clbtext').style('display', 'none')\n\t}\n\n\tfunction displayRunStatusErrors(errors) {\n\t\t// errors[] each ele: {error:str, url:str}\n\t\tconst rows = [] // map errors[] to rows[] to show in table of menu\n\t\tfor (const e of errors) {\n\t\t\tif (typeof e.error != 'string') throw '.error=string missing from an entry'\n\t\t\tif (typeof e.url != 'string') throw '.url=string missing from an entry'\n\t\t\t// url should end in file uuid, which can be used to match with original record of that file\n\t\t\tconst l = e.url.split('/')\n\t\t\tconst uuid = l[l.length - 1]\n\t\t\tconst fo = result.files.find(i => i.id == uuid)\n\t\t\tif (fo) {\n\t\t\t\t// record is found for this failed uuid\n\t\t\t\trows.push([\n\t\t\t\t\t{ html: `<a href=${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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+}