@sjcrh/proteinpaint-client 2.212.0 → 2.213.0

package/dist/maf-2TFOOAIF.js

@@ -1,455 +0,0 @@
-import {
-  fileDateStamp,
-  make_radios,
-  renderTable,
-  sayerror,
-  table2col
-} from "./chunk-VHDYIOWU.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-5WIA4KFA.js";
-import {
-  Menu
-} from "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3,
-  fileSize
-} from "./chunk-RMUK3TLD.js";
-import "./chunk-HH5JKOE6.js";
-import "./chunk-RU2UHH7M.js";
-import "./chunk-57Z4VYLM.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.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.${fileDateStamp()}.maf.gz`;
-      a.style.display = "none";
-      document.body.appendChild(a);
-      a.click();
-      document.body.removeChild(a);
-    } catch (e) {
-      sayerror(obj.errDiv, e);
-    } finally {
-      button.innerHTML = oldText;
-      obj.holder.style("pointer-events", "auto").style("opacity", 1);
-    }
-  }
-  function mayCreateServerMessageSpan(button) {
-    if (serverMessage) return;
-    const holder = select_default(button.parentElement);
-    serverMessage = holder.append("span").attr("class", "sja_clbtext").style("display", "none");
-  }
-  function displayRunStatusErrors(errors) {
-    const rows = [];
-    for (const e of errors) {
-      if (typeof e.error != "string") throw ".error=string missing from an entry";
-      if (typeof e.url != "string") throw ".url=string missing from an entry";
-      const l = e.url.split("/");
-      const uuid = l[l.length - 1];
-      const fo = result.files.find((i) => i.id == uuid);
-      if (fo) {
-        rows.push([
-          { html: `<a href=${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-2TFOOAIF.js.map