@sjcrh/proteinpaint-client 2.216.0 → 2.217.0

package/dist/maf-W6SF6BJS.js

@@ -0,0 +1,451 @@
+import {
+  fileDateStamp,
+  make_radios,
+  renderTable,
+  sayerror,
+  table2col
+} from "./chunk-NNDKYTUV.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-HWNQOADC.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import "./chunk-PLFPXOGX.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import {
+  dofetch3,
+  fileSize
+} from "./chunk-BIJOXCLN.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-L2WOLNZK.js";
+import "./chunk-AMW5LCUB.js";
+import "./chunk-ZPWBYHNE.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.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-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-W6SF6BJS.js.map