@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

package/dist/grin2-Z5O7254R.js

@@ -0,0 +1,1555 @@
+import {
+  make_one_checkbox,
+  renderTable,
+  sayerror,
+  table2col,
+  to_svg
+} from "./chunk-2XPDA6NL.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-GHWHLSUX.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-FN5XPUPH.js";
+import {
+  icons
+} from "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-AY4UBGLC.js";
+import "./chunk-2P6Z7JFC.js";
+import {
+  dofetch3
+} from "./chunk-MYWJQRTD.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-B43MTEYB.js";
+import "./chunk-2T7VYQLY.js";
+import "./chunk-FDK4UJMN.js";
+import {
+  bplen,
+  class2SOterm,
+  dtsnvindel,
+  mclass
+} from "./chunk-X7GDCYND.js";
+import "./chunk-SJC2C77V.js";
+import "./chunk-C3SYSMNE.js";
+import "./chunk-KSGA62R2.js";
+import {
+  axisLeft
+} from "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import {
+  linear
+} from "./chunk-OAWQ6LOO.js";
+import "./chunk-NMBIT4IK.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/grin2/ui-components.ts
+var STYLES = {
+  // Layout styles
+  flexRow: {
+    display: "flex",
+    "align-items": "center",
+    gap: "8px"
+  },
+  gridTwoColumn: {
+    display: "grid",
+    "grid-template-columns": "auto auto",
+    gap: "15px",
+    "max-width": "fit-content"
+  },
+  // Form element styles
+  label: {
+    "font-size": "14px",
+    "font-weight": "500"
+  },
+  numberInput: {
+    padding: "4px 8px",
+    border: "1px solid #ccc",
+    "border-radius": "4px",
+    "font-size": "14px"
+  },
+  checkbox: {
+    margin: "0",
+    cursor: "pointer"
+  },
+  checkboxLabel: {
+    cursor: "pointer",
+    "font-weight": "500"
+  },
+  // Table styles
+  tableHeader: {
+    padding: "12px",
+    "background-color": "#f8f9fa",
+    border: "1px solid #ddd",
+    "font-weight": "bold",
+    "text-align": "left"
+  },
+  tableCell: {
+    padding: "12px",
+    border: "1px solid #ddd",
+    "vertical-align": "top"
+  },
+  optionsTable: {
+    width: "auto",
+    "border-collapse": "collapse",
+    "margin-top": "10px",
+    border: "1px solid #ddd"
+  },
+  // Panel styles
+  infoPanel: {
+    padding: "8px",
+    "background-color": "#f8f9fa",
+    "border-radius": "4px",
+    "border-left": "3px solid #6c757d",
+    "font-size": "12px",
+    color: "#495057",
+    "line-height": "1.4"
+  },
+  // Expandable section styles
+  expandableHeader: {
+    display: "flex",
+    "align-items": "center",
+    gap: "8px",
+    cursor: "pointer",
+    padding: "8px",
+    "border-radius": "4px",
+    transition: "background-color 0.2s"
+  },
+  expandIcon: {
+    "font-size": "12px",
+    transition: "transform 0.2s"
+  },
+  expandableContent: {
+    display: "none",
+    "margin-top": "12px",
+    padding: "12px",
+    "background-color": "#fff",
+    "border-radius": "4px",
+    "box-shadow": "inset 0 1px 3px rgba(0, 0, 0, 0.1)"
+  },
+  expandHeaderText: {
+    "text-decoration": "underline",
+    "font-size": "13px",
+    "font-weight": "500"
+  }
+};
+function applyStyles(selection, styles) {
+  Object.entries(styles).forEach(([property, value]) => {
+    selection.style(property, value);
+  });
+  return selection;
+}
+function createNumberInput(container, config) {
+  const inputContainer = container.append("div");
+  applyStyles(inputContainer, STYLES.flexRow);
+  const label = inputContainer.append("label");
+  applyStyles(label, STYLES.label);
+  if (config.labelWidth) {
+    label.style("min-width", config.labelWidth);
+  }
+  label.text(config.label);
+  const input = inputContainer.append("input").attr("type", "number").attr("value", config.value);
+  applyStyles(input, STYLES.numberInput);
+  if (config.min !== void 0) input.attr("min", config.min);
+  if (config.max !== void 0) input.attr("max", config.max);
+  if (config.step !== void 0) input.attr("step", config.step);
+  if (config.width) input.style("width", config.width);
+  input.on("input", function() {
+    const value = parseFloat(this.value);
+    if (!isNaN(value)) {
+      config.onChange(value);
+    }
+  });
+  return { container: inputContainer, input, label };
+}
+function createCheckbox(container, config) {
+  const checkboxContainer = container.append("div");
+  applyStyles(checkboxContainer, STYLES.flexRow);
+  const checkbox = checkboxContainer.append("input").attr("type", "checkbox").attr("id", config.id).property("checked", config.checked);
+  applyStyles(checkbox, STYLES.checkbox);
+  const label = checkboxContainer.append("label").attr("for", config.id).text(config.label);
+  applyStyles(label, STYLES.checkboxLabel);
+  checkbox.on("change", function() {
+    config.onChange(this.checked);
+  });
+  return { container: checkboxContainer, checkbox, label };
+}
+function createOptionsTable(container) {
+  const table = container.append("table");
+  applyStyles(table, STYLES.optionsTable);
+  return table;
+}
+function createTableHeader(table, columns) {
+  const headerRow = table.append("tr");
+  columns.forEach((columnText, index) => {
+    const th = headerRow.append("th");
+    applyStyles(th, STYLES.tableHeader);
+    if (index === 0) {
+      th.style("width", "200px");
+    }
+    th.text(columnText);
+  });
+  return headerRow;
+}
+function createDataTypeRow(table, config) {
+  const row = table.append("tr");
+  const checkboxCell = row.append("td");
+  applyStyles(checkboxCell, STYLES.tableCell);
+  const { checkbox } = createCheckbox(checkboxCell, {
+    id: config.id,
+    label: config.label,
+    checked: config.checked,
+    onChange: config.onChange
+  });
+  const optionsCell = row.append("td");
+  applyStyles(optionsCell, STYLES.tableCell);
+  const optionsContainer = optionsCell.append("div").style("display", config.checked ? "block" : "none");
+  config.createOptionsContent(optionsContainer);
+  return { row, optionsContainer, checkbox };
+}
+function createInfoPanel(container, config) {
+  const panel = container.append("div");
+  applyStyles(panel, STYLES.infoPanel);
+  if (config.color) {
+    panel.style("border-left-color", config.color);
+  }
+  if (config.title) {
+    panel.append("strong").text(config.title);
+    panel.append("br");
+  }
+  panel.append("span").html(config.content);
+  return panel;
+}
+
+// plots/manhattan/manhattanGDC.ts
+function plotManhattanGDC(div, data, settings, app) {
+  settings = {
+    pngDotRadius: 2,
+    plotWidth: 1e3,
+    plotHeight: 400,
+    yAxisX: 70,
+    yAxisY: 40,
+    yAxisSpace: 40,
+    fontSize: 12,
+    showLegend: true,
+    legendItemWidth: 80,
+    legendDotRadius: 3,
+    legendRightOffset: 15,
+    legendTextOffset: 12,
+    legendVerticalOffset: 4,
+    legendFontSize: 12,
+    showInteractiveDots: true,
+    showDownload: true,
+    interactiveDotRadius: 3,
+    interactiveDotStrokeWidth: 1,
+    ...settings
+  };
+  div.style("position", "relative");
+  const geneTip = new Menu({ padding: "" });
+  const svg = div.append("svg").attr("width", data.plotData.png_width + settings.yAxisX + settings.yAxisSpace).attr("height", data.plotData.png_height + settings.yAxisY * 4);
+  const yAxisG = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`);
+  const yScale = linear().domain([0, data.plotData.y_max]).range([data.plotData.png_height, 0]);
+  yAxisG.call(axisLeft(yScale));
+  svg.append("text").attr("x", -(data.plotData.png_height / 2) - settings.yAxisY).attr("y", settings.yAxisX / 2).attr("transform", "rotate(-90)").attr("text-anchor", "middle").attr("font-size", `${settings.fontSize}px`).attr("fill", "black").text("-log\u2081\u2080(q-value)");
+  svg.append("image").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).attr("width", data.plotData.png_width).attr("height", data.plotData.png_height).attr("href", `data:image/png;base64,${data.pngImg || data.png}`);
+  const xScale = linear().domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer]).range([0, data.plotData.png_width]);
+  if (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {
+    const pointsLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`);
+    pointsLayer.selectAll("circle").data(data.plotData.points).enter().append("circle").attr("cx", (d) => xScale(d.x)).attr("cy", (d) => yScale(d.y)).attr("r", settings.interactiveDotRadius).attr("fill-opacity", 0).attr("stroke", "black").attr("stroke-width", settings.interactiveDotStrokeWidth).attr("stroke-opacity", 0).on("mouseover", (event, d) => {
+      event.target.setAttribute("stroke-opacity", 1);
+      geneTip.clear().show(event.clientX, event.clientY);
+      const table = table2col({
+        holder: geneTip.d.append("div"),
+        margin: "10px"
+      });
+      table.addRow("Gene", d.gene);
+      const [t1, t2] = table.addRow();
+      t1.text("Type");
+      t2.html(`<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`);
+      table.addRow("-log\u2081\u2080(q-value)", d.y.toFixed(3));
+      if (d.nsubj) table.addRow("Subject count", d.nsubj);
+      table.addRow("Chromosome", d.chrom);
+    }).on("mouseout", (event) => {
+      event.target.setAttribute("stroke-opacity", 0);
+      geneTip.hide();
+    }).on("click", (event, d) => {
+      if (app) {
+        app.dispatch({
+          type: "plot_create",
+          config: {
+            chartType: "genomeBrowser",
+            geneSearchResult: { geneSymbol: d.gene }
+          }
+        });
+      }
+    });
+  }
+  if (data.plotData.chrom_data) {
+    const chromLabelY = data.plotData.png_height + settings.yAxisY + 20;
+    Object.entries(data.plotData.chrom_data).forEach(([chrom, chromData]) => {
+      const chromLabel = chrom.replace("chr", "");
+      if (chromLabel === "M") return;
+      const centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center);
+      svg.append("text").attr("x", centerPos).attr("y", chromLabelY).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize - 2}px`).attr("fill", "black").text(chromLabel);
+    });
+  }
+  svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace + data.plotData.png_width / 2).attr("y", data.plotData.png_height + settings.yAxisY + 45).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize}px`).attr("fill", "black").text("Chromosomes");
+  svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace).attr("y", settings.yAxisY / 2).attr("text-anchor", "left").attr("font-weight", "bold").attr("font-size", `${settings.fontSize + 2}px`).attr("fill", "black").text("Manhattan Plot");
+  if (settings.showDownload) {
+    const downloadDiv = div.append("div").style("position", "absolute").style("top", "5px").style("left", `${settings.yAxisX + settings.yAxisSpace + 108}px`).style("z-index", "10").style("background", `${settings.background}`).style("padding", `${settings.padding + 2}px`).style("border-radius", `${settings.borderRadius + 10}px`);
+    icons["download"](downloadDiv, {
+      width: 16,
+      height: 16,
+      title: "Download Manhattan plot",
+      handler: () => {
+        to_svg(
+          svg.node(),
+          `manhattan_plot_${(/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, -5)}`,
+          { apply_dom_styles: true }
+        );
+      }
+    });
+  }
+  const mutationTypes = [...new Set(data.plotData.points.map((p) => p.type))];
+  const legendData = mutationTypes.map((type) => {
+    const point = data.plotData.points.find((p) => p.type === type);
+    return {
+      type: String(type).charAt(0).toUpperCase() + String(type).slice(1),
+      color: point?.color
+    };
+  });
+  if (settings.showLegend && legendData.length > 0) {
+    const legendY = settings.yAxisY / 2;
+    const totalWidth = legendData.length * settings.legendItemWidth;
+    const legendX = settings.yAxisX + settings.yAxisSpace + data.plotData.png_width - totalWidth - settings.legendRightOffset;
+    legendData.forEach((item, i) => {
+      const x = legendX + i * settings.legendItemWidth;
+      svg.append("circle").attr("cx", x + 8).attr("cy", legendY).attr("r", settings.legendDotRadius).attr("fill", item.color).attr("stroke", "black").attr("stroke-width", 1);
+      svg.append("text").attr("x", x + 8 + settings.legendTextOffset).attr("y", legendY + settings.legendVerticalOffset).attr("font-size", `${settings.legendFontSize}px`).attr("fill", "black").text(item.type);
+    });
+  }
+}
+
+// gdc/grin2.ts
+var defaultCheckedClasses = ["M", "F", "N", "StopLost", "StartLost", "L", "I", "D", "ProteinAltering"];
+var skipMAFclasses = ["WT", "Blank", "X"];
+function transformRows(rows, columns) {
+  return rows.map((row) => {
+    const transformedRow = [];
+    for (let i = 0; i < columns.length; i++) {
+      const cellData = row[i];
+      let value = null;
+      if (cellData && cellData.value && Array.isArray(cellData.value)) {
+        value = cellData.value[0];
+      } else if (cellData && "value" in cellData) {
+        value = cellData.value;
+      } else {
+        value = cellData;
+      }
+      transformedRow.push({ value });
+    }
+    return transformedRow;
+  });
+}
+function parseRecordsByCaseData(recordsByCase, excludedByMaxRecord = {}) {
+  const columns = [
+    { label: "Case ID", sortable: true },
+    { label: "MAF Total Processed", sortable: true },
+    { label: "MAF Included", sortable: true },
+    { label: "MAF Excluded by Depth", sortable: true },
+    { label: "MAF Excluded by Alt Count", sortable: true },
+    { label: "MAF Excluded by Consequence", sortable: true },
+    { label: "MAF Skipped Chromosomes", sortable: true },
+    { label: "MAF Excluded by Records Cap", sortable: true },
+    { label: "CNV Total Processed", sortable: true },
+    { label: "CNV Included", sortable: true },
+    { label: "CNV Excluded by Thresholds", sortable: true },
+    { label: "CNV Excluded by Length", sortable: true },
+    { label: "CNV Skipped Chromosomes", sortable: true },
+    { label: "CNV Excluded by Records Cap", sortable: true },
+    { label: "Invalid Rows", sortable: true }
+  ];
+  const rows = [];
+  Object.entries(recordsByCase).forEach(([caseId, caseData]) => {
+    const row = [];
+    row.push({ value: caseId });
+    let parsedData;
+    try {
+      parsedData = typeof caseData === "string" ? JSON.parse(caseData) : caseData;
+    } catch (_e) {
+      parsedData = caseData;
+    }
+    let mafTotalProcessed = 0;
+    let mafIncluded = 0;
+    let mafExcludedByDepth = 0;
+    let mafExcludedByAltCount = 0;
+    let mafExcludedByConsequence = 0;
+    let mafSkippedChromosomes = 0;
+    if (parsedData.maf) {
+      mafTotalProcessed = parsedData.maf.total_processed || 0;
+      mafIncluded = parsedData.maf.total_included || 0;
+      mafExcludedByDepth = parsedData.maf.excluded_by_min_depth || 0;
+      mafExcludedByAltCount = parsedData.maf.excluded_by_min_alt_count || 0;
+      mafExcludedByConsequence = parsedData.maf.excluded_by_consequence_type || 0;
+      if (parsedData.maf.skipped_chromosomes && typeof parsedData.maf.skipped_chromosomes === "object") {
+        mafSkippedChromosomes = Object.values(parsedData.maf.skipped_chromosomes).reduce(
+          (sum, count) => sum + (Number(count) || 0),
+          0
+        );
+      }
+    }
+    row.push({ value: mafTotalProcessed });
+    row.push({ value: mafIncluded });
+    row.push({ value: mafExcludedByDepth });
+    row.push({ value: mafExcludedByAltCount });
+    row.push({ value: mafExcludedByConsequence });
+    if (parsedData.maf?.skipped_chromosomes && Object.keys(parsedData.maf.skipped_chromosomes).length > 0) {
+      const chromosomeEntries = Object.entries(parsedData.maf.skipped_chromosomes);
+      const tableHtml = `
+				<div style="text-align: center;">
+				<table style="border-collapse: collapse; margin: 0 auto; font-size: 11px; border: 1px solid #ddd;">
+					<thead>
+					<tr style="background-color: #f8f9fa;">
+						<th style="border: 1px solid #ddd; padding: 2px 6px;">Chr</th>
+						<th style="border: 1px solid #ddd; padding: 2px 6px;">Count</th>
+					</tr>
+					</thead>
+					<tbody>
+					${chromosomeEntries.map(
+        ([chr, count]) => `<tr>
+						<td style="border: 1px solid #ddd; padding: 2px 6px;">${chr}</td>
+						<td style="border: 1px solid #ddd; padding: 2px 6px; text-align: right;">${count}</td>
+						</tr>`
+      ).join("")}
+					</tbody>
+				</table>
+				</div>
+			`;
+      row.push({
+        html: tableHtml,
+        value: mafSkippedChromosomes,
+        rawData: parsedData.maf.skipped_chromosomes,
+        dataType: "chromosome-details"
+      });
+    } else {
+      row.push({
+        value: mafSkippedChromosomes,
+        rawData: null,
+        dataType: "chromosome-details"
+      });
+    }
+    const mafExcludedByMax = excludedByMaxRecord.maf?.includes(caseId) ? "Yes" : "No";
+    row.push({
+      value: mafExcludedByMax,
+      html: mafExcludedByMax === "Yes" ? `<span style="color: #dc3545; font-weight: bold;">${mafExcludedByMax}</span>` : mafExcludedByMax
+    });
+    let cnvTotalProcessed = 0;
+    let cnvIncluded = 0;
+    let cnvExcludedByThresholds = 0;
+    let cnvExcludedByLength = 0;
+    let cnvSkippedChromosomes = 0;
+    if (parsedData.cnv) {
+      cnvTotalProcessed = parsedData.cnv.total_processed || 0;
+      cnvIncluded = parsedData.cnv.total_included || 0;
+      cnvExcludedByThresholds = (parsedData.cnv.excluded_by_loss_threshold || 0) + (parsedData.cnv.excluded_by_gain_threshold || 0);
+      cnvExcludedByLength = parsedData.cnv.excluded_by_segment_length || 0;
+      if (parsedData.cnv.skipped_chromosomes && typeof parsedData.cnv.skipped_chromosomes === "object") {
+        cnvSkippedChromosomes = Object.values(parsedData.cnv.skipped_chromosomes).reduce(
+          (sum, count) => sum + (Number(count) || 0),
+          0
+        );
+      }
+    }
+    row.push({ value: cnvTotalProcessed });
+    row.push({ value: cnvIncluded });
+    row.push({ value: cnvExcludedByThresholds });
+    row.push({ value: cnvExcludedByLength });
+    if (parsedData.cnv?.skipped_chromosomes && Object.keys(parsedData.cnv.skipped_chromosomes).length > 0) {
+      const chromosomeEntries = Object.entries(parsedData.cnv.skipped_chromosomes);
+      const tableHtml = `
+    <div style="text-align: center;">
+      <table style="border-collapse: collapse; margin: 0 auto; font-size: 11px; border: 1px solid #ddd;">
+        <thead>
+          <tr style="background-color: #f8f9fa;">
+            <th style="border: 1px solid #ddd; padding: 2px 6px;">Chr</th>
+            <th style="border: 1px solid #ddd; padding: 2px 6px;">Count</th>
+          </tr>
+        </thead>
+        <tbody>
+          ${chromosomeEntries.map(
+        ([chr, count]) => `<tr>
+              <td style="border: 1px solid #ddd; padding: 2px 6px;">${chr}</td>
+              <td style="border: 1px solid #ddd; padding: 2px 6px; text-align: right;">${count}</td>
+            </tr>`
+      ).join("")}
+        </tbody>
+      </table>
+    </div>
+  `;
+      row.push({
+        html: tableHtml,
+        value: cnvSkippedChromosomes,
+        rawData: parsedData.cnv.skipped_chromosomes,
+        dataType: "chromosome-details"
+      });
+    } else {
+      row.push({
+        value: cnvSkippedChromosomes,
+        rawData: null,
+        dataType: "chromosome-details"
+      });
+    }
+    const cnvExcludedByMax = excludedByMaxRecord.cnv?.includes(caseId) ? "Yes" : "No";
+    row.push({
+      value: cnvExcludedByMax,
+      html: cnvExcludedByMax === "Yes" ? `<span style="color: #dc3545; font-weight: bold;">${cnvExcludedByMax}</span>` : cnvExcludedByMax
+    });
+    let totalInvalidRows = 0;
+    if (parsedData.maf && parsedData.maf.invalid_rows !== void 0) {
+      totalInvalidRows += Number(parsedData.maf.invalid_rows) || 0;
+    }
+    if (parsedData.cnv && parsedData.cnv.invalid_rows !== void 0) {
+      totalInvalidRows += Number(parsedData.cnv.invalid_rows) || 0;
+    }
+    row.push({ value: totalInvalidRows });
+    rows.push(row);
+  });
+  return { columns, rows };
+}
+function addExpandableFailedFilesToStats(statsContainer, failedFilesInfo) {
+  const expandableContainer = statsContainer.append("div").style("margin-top", "12px");
+  const expandableHeader = expandableContainer.append("div").style("display", "flex").style("align-items", "center").style("gap", "8px").style("cursor", "pointer").style("padding", "8px").style("border-radius", "4px").style("transition", "background-color 0.2s").style("background-color", "rgba(220, 53, 69, 0.1)").style("border", "1px solid rgba(220, 53, 69, 0.2)").on("mouseenter", function() {
+    select_default(this).style("background-color", "rgba(220, 53, 69, 0.15)");
+  }).on("mouseleave", function() {
+    select_default(this).style("background-color", "rgba(220, 53, 69, 0.1)");
+  });
+  const expandIcon = expandableHeader.append("span").style("font-size", "12px").style("color", "#dc3545").style("transition", "transform 0.2s").text("\u25B6");
+  expandableHeader.append("span").style("color", "#dc3545").style("text-decoration", "underline").style("font-size", "13px").style("font-weight", "500").text(`View ${failedFilesInfo.count} failed files details`);
+  if (failedFilesInfo.errorSummary) {
+    const { errorSummary } = failedFilesInfo;
+    const summaryItems = [];
+    if (errorSummary.connectionErrors > 0) {
+      summaryItems.push(`${errorSummary.connectionErrors} connection`);
+    }
+    if (errorSummary.timeoutErrors > 0) {
+      summaryItems.push(`${errorSummary.timeoutErrors} timeout`);
+    }
+    if (errorSummary.serverErrors > 0) {
+      summaryItems.push(`${errorSummary.serverErrors} server`);
+    }
+    if (errorSummary.otherErrors > 0) {
+      summaryItems.push(`${errorSummary.otherErrors} other`);
+    }
+    if (summaryItems.length > 0) {
+      expandableHeader.append("span").style("margin-left", "8px").style("font-size", "12px").style("color", "#666").style("font-weight", "normal").text(`(${summaryItems.join(", ")})`);
+    }
+  }
+  const expandableContent = expandableContainer.append("div").style("display", "none").style("margin-top", "12px").style("padding", "12px").style("background-color", "#fff").style("border", "1px solid #f5c6cb").style("border-radius", "4px").style("box-shadow", "inset 0 1px 3px rgba(0, 0, 0, 0.1)");
+  const tableSection = expandableContent.append("div");
+  tableSection.append("h6").style("margin", "0 0 12px 0").style("color", "#721c24").style("font-size", "14px").style("font-weight", "bold").text("Failed Files Details");
+  const tableContainer = tableSection.append("div").style("max-height", "300px").style("overflow-y", "auto").style("border", "1px solid #dee2e6").style("border-radius", "4px");
+  renderTable({
+    div: tableContainer,
+    columns: failedFilesInfo.tableData.headers.map((header) => ({
+      label: header,
+      sortable: true
+    })),
+    rows: failedFilesInfo.tableData.rows.map((row) => row.map((cell) => ({ value: cell }))),
+    showLines: true,
+    striped: true,
+    showHeader: true,
+    maxHeight: "280px",
+    resize: false,
+    header: {
+      allowSort: true,
+      style: {
+        "background-color": "#f8f9fa",
+        "font-weight": "bold",
+        "border-bottom": "2px solid #dee2e6"
+      }
+    }
+  });
+  expandableContent.append("div").style("margin-top", "12px").style("padding", "8px").style("background-color", "#f8f9fa").style("border-radius", "4px").style("font-size", "12px").style("color", "#495057").style("line-height", "1.4").text("These files could not be downloaded due to network or server issues and were excluded from the analysis.");
+  let isExpanded = false;
+  expandableHeader.on("click", function() {
+    isExpanded = !isExpanded;
+    if (isExpanded) {
+      expandableContent.style("display", "block");
+      expandIcon.style("transform", "rotate(90deg)").text("\u25BC");
+    } else {
+      expandableContent.style("display", "none");
+      expandIcon.style("transform", "rotate(0deg)").text("\u25B6");
+    }
+  });
+}
+function createExpandableDeduplicationSection(container, deduplicationStats) {
+  const duplicatesRemoved = deduplicationStats.duplicatesRemoved || 0;
+  const sizeFilteredCount = deduplicationStats.filteredFiles ? deduplicationStats.filteredFiles.length : 0;
+  const totalExcluded = duplicatesRemoved + sizeFilteredCount;
+  if (totalExcluded === 0) {
+    return;
+  }
+  const expandableContainer = container.append("div").style("margin-top", "8px");
+  const expandableHeader = expandableContainer.append("div").style("display", "flex").style("align-items", "center").style("gap", "8px").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px").style("transition", "background-color 0.2s").style("background-color", "rgba(216, 67, 21, 0.1)").style("border", "1px solid rgba(216, 67, 21, 0.2)").on("mouseenter", function() {
+    select_default(this).style("background-color", "rgba(216, 67, 21, 0.15)");
+  }).on("mouseleave", function() {
+    select_default(this).style("background-color", "rgba(216, 67, 21, 0.1)");
+  });
+  const expandIcon = expandableHeader.append("span").style("font-size", "12px").style("color", "#d84315").style("transition", "transform 0.2s").text("\u25B6");
+  expandableHeader.append("span").style("color", "#d84315").style("text-decoration", "underline").style("font-size", "12px").style("font-weight", "500").text("View excluded files details");
+  const exclusionDetails = [];
+  if (duplicatesRemoved > 0) {
+    exclusionDetails.push(`${duplicatesRemoved} duplicates`);
+  }
+  if (sizeFilteredCount > 0) {
+    exclusionDetails.push(`${sizeFilteredCount} oversized`);
+  }
+  if (exclusionDetails.length > 0) {
+    expandableHeader.append("span").style("margin-left", "8px").style("font-size", "11px").style("color", "#666").style("font-weight", "normal").text(`(${exclusionDetails.join(", ")})`);
+  }
+  const expandableContent = expandableContainer.append("div").style("display", "none").style("margin-top", "8px").style("padding", "12px").style("background-color", "#fff").style("border", "1px solid rgba(216, 67, 21, 0.3)").style("border-radius", "4px").style("box-shadow", "inset 0 1px 3px rgba(0, 0, 0, 0.1)").style("max-height", "400px").style("overflow-y", "auto");
+  if (deduplicationStats.caseDetails && deduplicationStats.caseDetails.length > 0) {
+    const duplicatesSection = expandableContent.append("div").style("margin-bottom", "16px");
+    duplicatesSection.append("h6").style("margin", "0 0 8px 0").style("color", "#d84315").style("font-size", "13px").style("font-weight", "bold").text("Duplicate Files Removed");
+    duplicatesSection.append("p").style("margin", "0 0 12px 0").style("font-size", "12px").style("color", "#666").text(`${deduplicationStats.duplicatesRemoved} duplicate files were removed (largest file kept for each case)`);
+    const duplicatesCasesContainer = duplicatesSection.append("div").style("display", "grid").style("grid-template-columns", "repeat(auto-fill, minmax(300px, 1fr))").style("gap", "8px");
+    deduplicationStats.caseDetails.forEach((caseInfo) => {
+      const caseDiv = duplicatesCasesContainer.append("div").style("padding", "6px 8px").style("background-color", "#fff3e0").style("border-radius", "3px").style("border-left", "3px solid #ff9800");
+      caseDiv.append("div").style("font-size", "12px").style("color", "#333").style("line-height", "1.3").html(
+        `<strong>Case ${caseInfo.caseName}:</strong> Found ${caseInfo.fileCount} MAF files, keeping largest (${bplen(
+          caseInfo.keptFileSize
+        )})`
+      );
+    });
+  }
+  if (deduplicationStats.filteredFiles && deduplicationStats.filteredFiles.length > 0) {
+    if (deduplicationStats.caseDetails && deduplicationStats.caseDetails.length > 0) {
+      expandableContent.append("hr").style("margin", "12px 0").style("border", "none").style("border-top", "1px solid #e0e0e0");
+    }
+    const sizeFilterSection = expandableContent.append("div");
+    sizeFilterSection.append("h6").style("margin", "0 0 8px 0").style("color", "#c62828").style("font-size", "13px").style("font-weight", "bold").text("Files Excluded by Size");
+    sizeFilterSection.append("p").style("margin", "0 0 12px 0").style("font-size", "12px").style("color", "#666").text(`${deduplicationStats.filteredFiles.length} files were excluded for being too large (>${bplen(1e6)})`);
+    const oversizedFilesContainer = sizeFilterSection.append("div").style("display", "grid").style("grid-template-columns", "repeat(auto-fill, minmax(280px, 1fr))").style("gap", "8px");
+    deduplicationStats.filteredFiles.forEach((fileInfo) => {
+      const fileDiv = oversizedFilesContainer.append("div").style("padding", "6px 8px").style("background-color", "#ffebee").style("border-radius", "3px").style("border-left", "3px solid #f44336");
+      fileDiv.append("div").style("font-size", "11px").style("color", "#333").style("margin-bottom", "2px").style("line-height", "1.2").html(`<strong>File ID:</strong> ${fileInfo.fileId}`);
+      fileDiv.append("div").style("font-size", "10px").style("color", "#666").style("line-height", "1.2").text(`Size: ${bplen(fileInfo.fileSize)} - ${fileInfo.reason}`);
+    });
+  }
+  expandableContent.append("div").style("margin-top", "12px").style("padding", "6px 8px").style("background-color", "#f8f9fa").style("border-radius", "4px").style("font-size", "11px").style("color", "#495057").style("line-height", "1.3").text("Files are filtered to ensure optimal performance and avoid duplicates.");
+  let isExpanded = false;
+  expandableHeader.on("click", function() {
+    isExpanded = !isExpanded;
+    if (isExpanded) {
+      expandableContent.style("display", "block");
+      expandIcon.style("transform", "rotate(90deg)").text("\u25BC");
+    } else {
+      expandableContent.style("display", "none");
+      expandIcon.style("transform", "rotate(0deg)").text("\u25B6");
+    }
+  });
+}
+function updateDedupStatus(obj, deduplicationStats) {
+  if (!obj.dedupStatusElement) return;
+  const dedupElement = obj.dedupStatusElement;
+  dedupElement.selectAll("*").remove();
+  if (!deduplicationStats) {
+    dedupElement.style("color", "#666").text("No deduplication data available");
+    return;
+  }
+  const dedupContainer = dedupElement.append("div").style("display", "flex").style("flex-direction", "column").style("gap", "6px");
+  const duplicatesRemoved = deduplicationStats.duplicatesRemoved || 0;
+  const sizeFilteredCount = deduplicationStats.filteredFiles ? deduplicationStats.filteredFiles.length : 0;
+  const totalExcluded = duplicatesRemoved + sizeFilteredCount;
+  const originalTotal = deduplicationStats.originalFileCount + sizeFilteredCount;
+  if (totalExcluded > 0) {
+    const summaryDiv = dedupContainer.append("div").style("font-size", "14px").style("color", "#d84315").style("font-weight", "500");
+    summaryDiv.html(
+      `Found <strong>${originalTotal}</strong> total MAF files, excluded <strong>${totalExcluded}</strong>`
+    );
+    const resultDiv = dedupContainer.append("div").style("font-size", "13px").style("color", "#28a745").style("font-weight", "500");
+    resultDiv.html(`Showing <strong>${deduplicationStats.deduplicatedFileCount}</strong> unique cases`);
+    if (duplicatesRemoved > 0) {
+      resultDiv.append("span").style("color", "#666").style("font-weight", "normal").text(" (largest file per case)");
+    }
+    createExpandableDeduplicationSection(dedupContainer, deduplicationStats);
+  } else {
+    dedupContainer.append("div").style("color", "#28a745").style("font-weight", "500").style("font-size", "14px").html(`All <strong>${deduplicationStats.deduplicatedFileCount}</strong> files included`);
+    dedupContainer.append("div").style("color", "#666").style("font-size", "13px").text("No duplicates or oversized files found");
+  }
+}
+function createMAFOptionsContent(container, obj) {
+  container.selectAll("*").remove();
+  const optionsGrid = container.append("div");
+  applyStyles(optionsGrid, STYLES.gridTwoColumn);
+  optionsGrid.style("margin-top", "10px");
+  createNumberInput(optionsGrid, {
+    label: "Min Total Depth:",
+    value: obj.mafOptions.minTotalDepth || 10,
+    min: 0,
+    step: 1,
+    width: "80px",
+    labelWidth: "140px",
+    onChange: (value) => {
+      if (value >= 0) obj.mafOptions.minTotalDepth = value;
+    }
+  });
+  createNumberInput(optionsGrid, {
+    label: "Min Mutant Allele Count:",
+    value: obj.mafOptions.minAltAlleleCount || 2,
+    min: 0,
+    step: 1,
+    width: "80px",
+    labelWidth: "160px",
+    onChange: (value) => {
+      if (value >= 0) obj.mafOptions.minAltAlleleCount = value;
+    }
+  });
+  createConsequencesSection(optionsGrid, obj);
+  createNumberInput(optionsGrid, {
+    label: "Hypermutator Max Cut Off:",
+    value: obj.mafOptions.hyperMutator || 8e3,
+    min: 0,
+    step: 100,
+    width: "70px",
+    labelWidth: "160px",
+    onChange: (value) => {
+      if (value >= 0) obj.mafOptions.hyperMutator = value;
+    }
+  });
+  createWorkflowSection(optionsGrid);
+  createDeduplicationSection(optionsGrid, obj);
+}
+function createConsequencesSection(optionsGrid, obj) {
+  const consequencesContainer = optionsGrid.append("div").style("display", "flex").style("align-items", "flex-start").style("gap", "8px").style("grid-column", "1 / -1");
+  consequencesContainer.append("label").style("font-size", "14px").style("font-weight", "500").style("min-width", "100px").style("margin-top", "4px").text("Consequences:");
+  const selectionDiv = consequencesContainer.append("div").style("flex", "1");
+  const checkboxContainer = selectionDiv.append("div").style("display", "grid").style("grid-template-columns", "repeat(auto-fit, minmax(200px, 1fr))").style("gap", "8px").style("margin-bottom", "12px");
+  createMutationClassCheckboxes(checkboxContainer, obj);
+  createInfoPanel(selectionDiv, {
+    title: "Mutation Types:",
+    content: `Select the types of mutations to include in your analysis.
+              High-impact mutations (missense, nonsense, frameshift) are selected by default.
+              Silent/synonymous mutations are excluded by default as they don't change protein sequence.`
+  });
+}
+function createMutationClassCheckboxes(container, obj) {
+  const seenLabels = /* @__PURE__ */ new Set();
+  for (const cls in mclass) {
+    if (mclass[cls].dt !== dtsnvindel) continue;
+    if (skipMAFclasses.includes(cls)) continue;
+    const labelText = mclass[cls].label;
+    if (seenLabels.has(labelText)) continue;
+    seenLabels.add(labelText);
+    const isDefaultChecked = defaultCheckedClasses.includes(cls);
+    const checkboxDiv = container.append("div");
+    make_one_checkbox({
+      holder: checkboxDiv,
+      labeltext: labelText,
+      checked: isDefaultChecked,
+      id: `consequence-${cls}`,
+      divstyle: {
+        "font-size": "13px",
+        margin: "0"
+      },
+      callback: async (isChecked) => {
+        if (isChecked) {
+          if (!obj.mafOptions.consequences.includes(cls)) {
+            obj.mafOptions.consequences.push(cls);
+          }
+        } else {
+          obj.mafOptions.consequences = obj.mafOptions.consequences.filter((c) => c !== cls);
+        }
+      }
+    });
+    checkboxDiv.select("label").attr("title", mclass[cls].desc);
+    if (isDefaultChecked && !obj.mafOptions.consequences.includes(cls)) {
+      obj.mafOptions.consequences.push(cls);
+    }
+  }
+}
+function createWorkflowSection(optionsGrid) {
+  const workflowContainer = optionsGrid.append("div");
+  applyStyles(workflowContainer, STYLES.flexRow);
+  workflowContainer.style("grid-column", "1 / -1");
+  const label = workflowContainer.append("label");
+  applyStyles(label, STYLES.label);
+  label.style("min-width", "100px").text("Workflow Type:");
+  workflowContainer.append("span").style("font-size", "14px").style("color", "#666").text("Aliquot Ensemble Somatic Variant Merging and Masking");
+}
+function createDeduplicationSection(optionsGrid, obj) {
+  const dedupContainer = optionsGrid.append("div");
+  applyStyles(dedupContainer, STYLES.flexRow);
+  dedupContainer.style("grid-column", "1 / -1");
+  const label = dedupContainer.append("label");
+  applyStyles(label, STYLES.label);
+  label.style("min-width", "100px").text("Deduplication:");
+  const dedupStatus = dedupContainer.append("span").attr("id", "dedup-status").style("font-size", "14px").style("color", "#666");
+  obj.dedupStatusElement = dedupStatus;
+}
+function createCNVOptionsContent(container, obj) {
+  container.selectAll("*").remove();
+  if (!obj.cnvOptions.dataType) {
+    obj.cnvOptions.dataType = "segment_mean";
+  }
+  const optionsGrid = container.append("div");
+  applyStyles(optionsGrid, STYLES.gridTwoColumn);
+  optionsGrid.style("margin-top", "10px");
+  createDataTypeRadioSection(optionsGrid, obj);
+  createNumberInput(optionsGrid, {
+    label: "Loss Threshold:",
+    value: obj.cnvOptions.lossThreshold || -0.4,
+    min: -10,
+    max: 0,
+    step: 0.1,
+    width: "70px",
+    labelWidth: "120px",
+    onChange: (value) => {
+      if (value <= 0) obj.cnvOptions.lossThreshold = value;
+    }
+  });
+  createNumberInput(optionsGrid, {
+    label: "Gain Threshold:",
+    value: obj.cnvOptions.gainThreshold || 0.3,
+    min: 0,
+    max: 10,
+    step: 0.1,
+    width: "70px",
+    labelWidth: "120px",
+    onChange: (value) => {
+      if (value >= 0) obj.cnvOptions.gainThreshold = value;
+    }
+  });
+  createNumberInput(optionsGrid, {
+    label: "Hypermutator Max Cut Off:",
+    value: obj.cnvOptions.hyperMutator || 500,
+    min: 0,
+    step: 100,
+    width: "70px",
+    labelWidth: "160px",
+    onChange: (value) => {
+      if (value >= 0) obj.cnvOptions.hyperMutator = value;
+    }
+  });
+  createSegmentLengthSection(optionsGrid, obj);
+  createCNVHelpSection(optionsGrid);
+}
+function createDataTypeRadioSection(optionsGrid, obj) {
+  const dataTypeContainer = optionsGrid.append("div");
+  applyStyles(dataTypeContainer, STYLES.flexRow);
+  dataTypeContainer.style("grid-column", "1 / -1");
+  const label = dataTypeContainer.append("label");
+  applyStyles(label, STYLES.label);
+  label.style("min-width", "80px").text("Data Type:");
+  const radioContainer = dataTypeContainer.append("div");
+  applyStyles(radioContainer, STYLES.flexRow);
+  radioContainer.style("gap", "6px");
+  const radio = radioContainer.append("input").attr("type", "radio").attr("id", "cnv-segment-mean").attr("name", "cnv-data-type").attr("value", "segment_mean").property("checked", obj.cnvOptions.dataType === "segment_mean").style("margin", "0").style("cursor", "pointer");
+  radioContainer.append("label").attr("for", "cnv-segment-mean").style("cursor", "pointer").style("font-size", "14px").style("color", "#333").text("Segment mean");
+  radio.on("change", function() {
+    if (this.checked) {
+      obj.cnvOptions.dataType = this.value;
+    }
+  });
+}
+function createSegmentLengthSection(optionsGrid, obj) {
+  const segmentContainer = optionsGrid.append("div");
+  applyStyles(segmentContainer, STYLES.flexRow);
+  segmentContainer.style("grid-column", "1 / -1");
+  const label = segmentContainer.append("label");
+  applyStyles(label, STYLES.label);
+  label.style("min-width", "140px").text("Segment Length Cutoff:");
+  const input = segmentContainer.append("input").attr("type", "number").attr("min", "0").attr("max", "2000000").attr("step", "1000").attr("value", obj.cnvOptions.segLength || 0);
+  applyStyles(input, STYLES.numberInput);
+  input.style("width", "100px");
+  segmentContainer.append("span").style("font-size", "13px").style("color", "#666").text("bp");
+  input.on("input", function() {
+    const value = parseInt(this.value, 10);
+    if (!isNaN(value) && value >= 0) {
+      obj.cnvOptions.segLength = value;
+    }
+  });
+}
+function createCNVHelpSection(optionsGrid) {
+  const helpContainer = optionsGrid.append("div").style("grid-column", "1 / -1").style("margin-top", "8px");
+  createInfoPanel(helpContainer, {
+    title: "CNV Options:",
+    content: `\u2022 Loss Threshold: Log2 ratio for copy number loss (negative values)<br>
+              \u2022 Gain Threshold: Log2 ratio for copy number gain (positive values)<br>
+              \u2022 Hypermutator Max Cut Off: Maximum number of CNVs per case<br>
+              \u2022 Segment Length: Maximum CNV segment size to include (no filter if 0)`
+  });
+}
+function makeControls(obj) {
+  if (!obj.mafOptions) {
+    obj.mafOptions = {
+      minTotalDepth: 10,
+      minAltAlleleCount: 2,
+      consequences: [],
+      hyperMutator: 8e3
+    };
+  }
+  if (!obj.cnvOptions) {
+    obj.cnvOptions = {
+      lossThreshold: -0.4,
+      gainThreshold: 0.3,
+      segLength: 0,
+      hyperMutator: 500
+    };
+  }
+  obj.dataTypeStates = {
+    maf: true,
+    cnv: true,
+    fusion: false
+  };
+  const optionsTable = createOptionsTable(obj.controlDiv);
+  createTableHeader(optionsTable, ["Data Type", "Options"]);
+  const mafRow = createDataTypeRow(optionsTable, {
+    id: "maf-checkbox",
+    label: "MAF (Mutation)",
+    checked: true,
+    onChange: (isChecked) => {
+      obj.dataTypeStates.maf = isChecked;
+      mafRow.optionsContainer.style("display", isChecked ? "block" : "none");
+      obj.updateSubmitButtonState?.();
+    },
+    createOptionsContent: (container) => createMAFOptionsContent(container, obj)
+  });
+  const cnvRow = createDataTypeRow(optionsTable, {
+    id: "cnv-checkbox",
+    label: "CNV (Copy Number)",
+    checked: true,
+    onChange: (isChecked) => {
+      obj.dataTypeStates.cnv = isChecked;
+      cnvRow.optionsContainer.style("display", isChecked ? "block" : "none");
+      if (isChecked) {
+        createCNVOptionsContent(cnvRow.optionsContainer, obj);
+      }
+      obj.updateSubmitButtonState?.();
+    },
+    createOptionsContent: (container) => createCNVOptionsContent(container, obj)
+  });
+  const fusionRow = createDataTypeRow(optionsTable, {
+    id: "fusion-checkbox",
+    label: "Fusion",
+    checked: false,
+    onChange: (isChecked) => {
+      obj.dataTypeStates.fusion = isChecked;
+      fusionRow.optionsContainer.style("display", isChecked ? "block" : "none");
+      obj.updateSubmitButtonState?.();
+    },
+    createOptionsContent: (container) => {
+      container.append("div").style("color", "#666").style("font-style", "italic").text("Please login to access RNA fusion data.");
+    }
+  });
+  createGRIN2InfoRow(optionsTable);
+  createSubmitButton(obj);
+  obj.mafOptionsContainer = mafRow.optionsContainer;
+  obj.cnvOptionsContainer = cnvRow.optionsContainer;
+  obj.fusionOptionsContainer = fusionRow.optionsContainer;
+}
+function createGRIN2InfoRow(optionsTable) {
+  const grin2Row = optionsTable.append("tr");
+  const labelCell = grin2Row.append("td");
+  applyStyles(labelCell, STYLES.tableCell);
+  labelCell.append("div").style("font-weight", "500").style("color", "#333").text("GRIN2 Analysis");
+  const optionsCell = grin2Row.append("td");
+  applyStyles(optionsCell, STYLES.tableCell);
+  optionsCell.append("div").style("color", "#666").text("GRIN2 analysis options will be configured here");
+}
+function createSubmitButton(obj) {
+  const submitButtonContainer = obj.controlDiv.append("div").style("margin-top", "2px").style("margin-bottom", "2px").style("text-align", "left");
+  const submitButton = submitButtonContainer.append("button").attr("id", "submit-options-button").style("margin", "10px 10px 0 0").text("Apply Options & Refresh Files");
+  obj.submitButton = submitButton;
+  submitButton.on("click", function() {
+    if (!this.disabled) {
+      getFilesAndShowTable(obj);
+    }
+  });
+  obj.updateSubmitButtonState = function() {
+    const hasAnyDataTypeSelected = obj.dataTypeStates.maf || obj.dataTypeStates.cnv || obj.dataTypeStates.fusion;
+    if (hasAnyDataTypeSelected) {
+      submitButton.attr("disabled", null).text("Apply Options & Refresh Files");
+    } else {
+      submitButton.attr("disabled", true).text("Select at least one data type");
+    }
+  };
+  obj.updateSubmitButtonState();
+}
+async function getFilesAndShowTable(obj) {
+  obj.tableDiv.selectAll("*").remove();
+  obj.resultDiv.selectAll("*").remove();
+  const wait = obj.tableDiv.append("div").style("margin", "30px 10px 10px 10px").text("Loading...");
+  let result;
+  try {
+    const body = {};
+    if (obj.opts.filter0) body.filter0 = obj.opts.filter0;
+    if (obj.dataTypeStates.maf) {
+      body.mafOptions = {
+        experimentalStrategy: obj.opts.experimentalStrategy || "WXS"
+      };
+    }
+    if (obj.dataTypeStates.cnv) {
+      body.cnvOptions = {
+        dataType: obj.cnvOptions.dataType
+      };
+    }
+    console.log("Request body for GRIN2list:", body);
+    result = await dofetch3("gdc/GRIN2list", { body });
+    console.log("GRIN2list result:", result);
+    if (result.error) throw result.error;
+    if (obj.dataTypeStates.maf && (!result.mafFiles || !Array.isArray(result.mafFiles.files))) {
+      throw "Invalid response: missing mafFiles.files array";
+    }
+    if (obj.dataTypeStates.cnv && (!result.cnvFiles || !Array.isArray(result.cnvFiles.files))) {
+      throw "Invalid response: missing cnvFiles.files array";
+    }
+    const hasMafFiles = result.mafFiles?.files?.length > 0;
+    const hasCnvFiles = result.cnvFiles?.files?.length > 0;
+    if (obj.dataTypeStates.maf && !hasMafFiles) {
+      throw "No MAF files available for the selected criteria.";
+    }
+    if (obj.dataTypeStates.cnv && !hasCnvFiles) {
+      throw "No CNV files available for the selected criteria.";
+    }
+    if (!hasMafFiles && !hasCnvFiles) {
+      throw "No files available for the selected data types.";
+    }
+    if (result.mafFiles && result.mafFiles.deduplicationStats) {
+      updateDedupStatus(obj, result.mafFiles.deduplicationStats);
+    }
+    const cnvFilesByCase = /* @__PURE__ */ new Map();
+    if (obj.dataTypeStates.cnv && result.cnvFiles && result.cnvFiles.files) {
+      for (const cnvFile of result.cnvFiles.files) {
+        const caseId = cnvFile.case_submitter_id;
+        if (!cnvFilesByCase.has(caseId)) {
+          cnvFilesByCase.set(caseId, cnvFile);
+        }
+      }
+    }
+    let filteredFiles = result.mafFiles ? result.mafFiles.files : [];
+    let filteringMessage = "";
+    const mafSelected = obj.dataTypeStates.maf;
+    const cnvSelected = obj.dataTypeStates.cnv;
+    if (mafSelected && cnvSelected) {
+      const originalCount = filteredFiles.length;
+      filteredFiles = filteredFiles.filter((mafFile) => {
+        const caseId = mafFile.case_submitter_id;
+        const hasCnv = cnvFilesByCase.has(caseId);
+        return hasCnv;
+      });
+      const filteredCount = filteredFiles.length;
+      const excludedCount = originalCount - filteredCount;
+      if (excludedCount > 0) {
+        filteringMessage = `Filtered to ${filteredCount} cases with both MAF and CNV files (excluded ${excludedCount} cases with only MAF files)`;
+      } else {
+        filteringMessage = `All ${filteredCount} cases have both MAF and CNV files`;
+      }
+    } else if (cnvSelected && !mafSelected) {
+      const originalCount = filteredFiles.length;
+      filteredFiles = result.cnvFiles ? result.cnvFiles.files : [];
+      const filteredCount = filteredFiles.length;
+      const excludedCount = originalCount - filteredCount;
+      if (excludedCount > 0) {
+        filteringMessage = `Filtered to ${filteredCount} cases with CNV files (excluded ${excludedCount} cases without CNV files)`;
+      }
+    } else if (mafSelected && !cnvSelected) {
+      filteringMessage = `Showing ${filteredFiles.length} cases with MAF files`;
+    }
+    if (filteredFiles.length === 0) {
+      throw "No files match the selected data type criteria. Try adjusting your data type selections.";
+    }
+    const mafFiles = result.mafFiles ? result.mafFiles.files : [];
+    const cnvFiles = result.cnvFiles ? result.cnvFiles.files : [];
+    const mafTotal = result.mafFiles ? result.mafFiles.filesTotal : 0;
+    let statusMessage = "";
+    if (mafSelected && cnvSelected) {
+      if (mafTotal > mafFiles.length) {
+        statusMessage = `Showing first ${mafFiles.length.toLocaleString()} files out of ${mafTotal.toLocaleString()} total.`;
+      } else {
+        statusMessage = `Showing ${filteredFiles.length.toLocaleString()} files.`;
+      }
+    } else if (mafSelected && !cnvSelected) {
+      if (mafTotal > mafFiles.length) {
+        statusMessage = `Showing first ${mafFiles.length.toLocaleString()} MAF files out of ${mafTotal.toLocaleString()} total.`;
+      } else {
+        statusMessage = `Showing ${filteredFiles.length.toLocaleString()} MAF files.`;
+      }
+    } else if (!mafSelected && cnvSelected) {
+      statusMessage = `Showing ${cnvFiles.length.toLocaleString()} CNV files.`;
+    }
+    wait.html(`
+			${statusMessage}<br>
+			${filteringMessage ? `<span style="color: #666; font-style: italic;">${filteringMessage}</span>` : ""}
+		`);
+    const dynamicTableColumns = [
+      { label: "Case", sortable: true },
+      { label: "Project", sortable: true }
+    ];
+    if (obj.dataTypeStates.maf) {
+      dynamicTableColumns.push({ label: "MAF Sample", sortable: false }, {
+        label: "MAF File Size",
+        barplot: { tickFormat: "~s" },
+        sortable: true
+      });
+    }
+    if (obj.dataTypeStates.cnv) {
+      dynamicTableColumns.push({ label: "CNV File ID", sortable: true }, { label: "CNV Sample", sortable: false }, {
+        label: "CNV File Size",
+        barplot: { tickFormat: "~s" },
+        sortable: true
+      });
+    }
+    if (obj.dataTypeStates.fusion) {
+      dynamicTableColumns.push(
+        { label: "Fusion File ID", sortable: true },
+        { label: "Fusion Sample", sortable: false },
+        { label: "Fusion File Size", barplot: { tickFormat: "~s" }, sortable: true }
+      );
+    }
+    const rows = [];
+    for (const f of filteredFiles) {
+      const row = [];
+      row.push(
+        {
+          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 }
+      );
+      if (obj.dataTypeStates.maf) {
+        row.push(
+          {
+            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 }
+        );
+      }
+      if (obj.dataTypeStates.cnv) {
+        const cnvFile = cnvFilesByCase.get(f.case_submitter_id);
+        if (cnvSelected && !cnvFile) {
+          console.warn(`Expected CNV file for case ${f.case_submitter_id} but not found`);
+        }
+        row.push(
+          {
+            html: cnvFile ? `<a href=https://portal.gdc.cancer.gov/files/${cnvFile.id} target=_blank>${cnvFile.id}</a>` : '<span style="color: #dc3545; font-weight: 500;">Missing CNV file</span>',
+            value: cnvFile ? cnvFile.id : "Missing CNV file"
+          },
+          {
+            html: cnvFile && cnvFile.sample_types ? cnvFile.sample_types.map((i) => {
+              return '<span class="sja_mcdot" style="padding:1px 8px;background:#ddd;color:black;white-space:nowrap">' + i + "</span>";
+            }).join(" ") : '<span style="color: #dc3545;">No CNV sample</span>',
+            value: cnvFile && cnvFile.sample_types ? cnvFile.sample_types.join(" ") : "No CNV sample"
+          },
+          {
+            value: cnvFile ? cnvFile.file_size : 0
+          }
+        );
+      }
+      if (obj.dataTypeStates.fusion) {
+        row.push(
+          { html: '<span style="color: #6c757d;">No Fusion file</span>', value: "No Fusion file" },
+          { html: '<span style="color: #6c757d;">No Fusion sample</span>', value: "No Fusion sample" },
+          { value: 0 }
+        );
+      }
+      rows.push(row);
+    }
+    obj.mafTableArg = {
+      rows,
+      columns: dynamicTableColumns,
+      resize: false,
+      div: obj.tableDiv.append("div"),
+      selectAll: true,
+      dataTestId: "sja_FileTable",
+      header: { allowSort: true },
+      selectedRows: [],
+      buttons: [
+        {
+          text: "Run GRIN2 Analysis",
+          onChange: (lst, button) => updateButtonBySelectionChange(lst, button, filteredFiles),
+          callback: (lst, button) => runGRIN2Analysis(lst, button, obj, filteredFiles)
+        }
+      ]
+    };
+    renderTable(obj.mafTableArg);
+  } catch (e) {
+    wait.text(e instanceof Error ? e.message : String(e));
+    if (e instanceof Error && e.stack) console.log(e.stack);
+  }
+  function updateButtonBySelectionChange(lst, button, filteredFiles) {
+    if (obj.busy) {
+      button.property("disabled", true);
+      return;
+    }
+    let sum = 0;
+    for (const i of lst) sum += filteredFiles[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;
+    const mafMaxSize = result.mafFiles ? result.mafFiles.maxTotalSizeCompressed : Infinity;
+    const cnvMaxSize = result.cnvFiles ? result.cnvFiles.maxTotalSizeCompressed : Infinity;
+    const maxSize = Math.min(mafMaxSize, cnvMaxSize);
+    button.innerHTML = sum < maxSize ? `Run GRIN2 Analysis` : `Run GRIN2 Analysis (Large Files)`;
+  }
+  async function runGRIN2Analysis(lst, button, obj2, filteredFiles = result.files) {
+    const mafSelected = obj2.dataTypeStates.maf;
+    const cnvSelected = obj2.dataTypeStates.cnv;
+    const caseFiles = {
+      caseFiles: {}
+    };
+    if (mafSelected) {
+      const soTerms = [];
+      for (const mclassCode of obj2.mafOptions.consequences) {
+        const soTermsForCode = class2SOterm.get(mclassCode) || [];
+        soTerms.push(...soTermsForCode);
+      }
+      caseFiles.mafOptions = {
+        minTotalDepth: obj2.mafOptions.minTotalDepth,
+        minAltAlleleCount: obj2.mafOptions.minAltAlleleCount,
+        consequences: soTerms,
+        hyperMutator: obj2.mafOptions.hyperMutator
+      };
+    }
+    if (cnvSelected) {
+      caseFiles.cnvOptions = {
+        dataType: obj2.cnvOptions.dataType,
+        lossThreshold: obj2.cnvOptions.lossThreshold,
+        gainThreshold: obj2.cnvOptions.gainThreshold,
+        segLength: obj2.cnvOptions.segLength,
+        hyperMutator: obj2.cnvOptions.hyperMutator
+      };
+    }
+    const cnvFilesByCase = /* @__PURE__ */ new Map();
+    if (result.cnvFiles && result.cnvFiles.files) {
+      for (const cnvFile of result.cnvFiles.files) {
+        const caseId = cnvFile.case_submitter_id;
+        if (!cnvFilesByCase.has(caseId)) {
+          cnvFilesByCase.set(caseId, cnvFile);
+        }
+      }
+    }
+    for (const i of lst) {
+      const file = filteredFiles[i];
+      const caseId = file.case_submitter_id;
+      if (!caseFiles.caseFiles[caseId]) {
+        caseFiles.caseFiles[caseId] = {};
+      }
+      const mafSelected2 = obj2.dataTypeStates.maf;
+      const cnvSelected2 = obj2.dataTypeStates.cnv;
+      if (mafSelected2) {
+        caseFiles.caseFiles[caseId].maf = file.id;
+      }
+      if (cnvSelected2) {
+        const cnvFile = cnvFilesByCase.get(caseId);
+        if (cnvFile) {
+          caseFiles.caseFiles[caseId].cnv = cnvFile.id;
+        }
+      }
+    }
+    if (Object.keys(caseFiles.caseFiles).length === 0) return;
+    const oldText = button.innerHTML;
+    button.innerHTML = "Analyzing... Please wait";
+    button.disabled = true;
+    if (obj2.downloadButtonDiv) {
+      obj2.downloadButtonDiv.selectAll("*").remove();
+      obj2.downloadButtonDiv.style("display", "none");
+    }
+    obj2.resultDiv.selectAll("*").remove();
+    try {
+      obj2.busy = true;
+      const response = await dofetch3("gdc/runGRIN2", { body: caseFiles });
+      if (!response) throw "invalid response";
+      if (response.error) throw response.error;
+      console.log("GRIN2 response:", response);
+      if (response.rustResult) {
+      } else {
+        console.log("[GRIN2] No rustResult in response");
+      }
+      const rustData = response.rustResult;
+      let failedFilesInfo = null;
+      let parsedRustResult;
+      let processedData = [];
+      try {
+        parsedRustResult = typeof rustData === "string" ? JSON.parse(rustData) : rustData;
+        if (parsedRustResult) {
+          if (parsedRustResult.successful_data && parsedRustResult.summary) {
+            processedData = parsedRustResult.successful_data;
+            console.log(`[GRIN2] parsedRustResult structure:`, parsedRustResult);
+            if (parsedRustResult.failed_files && parsedRustResult.failed_files.length > 0) {
+              failedFilesInfo = {
+                count: parsedRustResult.failed_files.length,
+                files: parsedRustResult.failed_files,
+                // Create table data for UI display (similar to your deduplication/filter tables)
+                tableData: {
+                  headers: ["Case ID", "Data Type", "Error Type", "Error Details", "Attempts"],
+                  rows: parsedRustResult.failed_files.map((file) => [
+                    file.case_id,
+                    file.data_type,
+                    file.error_type,
+                    file.error_details,
+                    file.attempts_made.toString()
+                  ])
+                },
+                // Error summary for the popup
+                errorSummary: {
+                  connectionErrors: parsedRustResult.failed_files.filter((f) => f.error_type === "connection_error").length,
+                  timeoutErrors: parsedRustResult.failed_files.filter((f) => f.error_type === "timeout_error").length,
+                  serverErrors: parsedRustResult.failed_files.filter((f) => f.error_type === "server_error").length,
+                  otherErrors: parsedRustResult.failed_files.filter(
+                    (f) => !["connection_error", "timeout_error", "server_error"].includes(f.error_type)
+                  ).length
+                }
+              };
+            }
+          }
+          console.log(`[GRIN2] Final processed data contains ${processedData.length.toLocaleString()} characters`);
+        }
+      } catch (parseError) {
+        console.error("[GRIN2] Error parsing Rust result:", parseError);
+        processedData = [];
+        failedFilesInfo = null;
+      }
+      if (!response.resultData.png) throw "png missing";
+      const resultContainer = obj2.resultDiv.append("div").style("text-align", "left").style("margin", "0 auto").style("margin-top", "40px");
+      const plotData = response.resultData;
+      const plotDiv = resultContainer.append("div");
+      plotManhattanGDC(plotDiv, plotData, { yAxisSpace: 0 });
+      resultContainer.node().onerror = () => {
+        resultContainer.select("img").remove();
+        sayerror(resultContainer, "Failed to load image result.");
+      };
+      if (response.topGeneTable && response.topGeneTable.rows && response.topGeneTable.rows.length > 0) {
+        const tableTitle = resultContainer.append("h4").style("margin-bottom", "15px").style("text-align", "left");
+        if (response.totalGenes && response.showingTop) {
+          tableTitle.text(`Top ${response.showingTop} Genes`);
+          resultContainer.append("p").html(
+            `Showing top <strong>${response.showingTop}</strong> genes out of <strong>${response.totalGenes.toLocaleString()}</strong> total genes analyzed.`
+          ).style("color", "#495057").style("font-size", "14px").style("margin", "10px 0 20px 0");
+        } else {
+          tableTitle.text("Top Genes");
+          resultContainer.append("p").style("color", "#495057").style("font-size", "14px").style("margin", "10px 0 20px 0");
+        }
+        const tableContainer = resultContainer.append("div").style("margin-bottom", "20px").style("display", "flex").style("flex", "2");
+        const statsContainer = resultContainer.append("div").style("flex", "1").style("min-width", "250px").style("max-width", "350px");
+        const transformedRows = transformRows(response.topGeneTable.rows, response.topGeneTable.columns);
+        renderTable({
+          div: tableContainer,
+          rows: transformedRows,
+          columns: response.topGeneTable.columns,
+          showLines: true,
+          striped: true,
+          showHeader: true,
+          maxHeight: "500px",
+          maxWidth: "100%",
+          resize: false,
+          header: {
+            allowSort: true,
+            style: {
+              "background-color": "#f8f9fa",
+              "font-weight": "bold",
+              "border-bottom": "2px solid #dee2e6"
+            }
+          },
+          download: {
+            // Enable table download functionality
+            fileName: `GRIN2_TopGenes.tsv`
+          }
+        });
+        if (parsedRustResult?.summary) {
+          const statsPanel = statsContainer.append("div").style("background-color", "#f8f9fa").style("border", "1px solid #dee2e6").style("border-radius", "8px").style("padding", "20px").style("box-shadow", "0 2px 4px rgba(0,0,0,0.1)");
+          statsPanel.append("h5").text("Analysis Summary").style("margin", "0 0 15px 0").style("color", "#343a40").style("font-weight", "bold").style("border-bottom", "2px solid #dee2e6").style("padding-bottom", "8px");
+          if (parsedRustResult && parsedRustResult.summary) {
+            const downloadStats = statsPanel.append("div").style("margin-bottom", "20px");
+            downloadStats.append("h6").text("File Download & Processing").style("margin", "0 0 10px 0").style("color", "#495057").style("font-size", "14px").style("font-weight", "bold");
+            const downloadStatsGrid = downloadStats.append("div").style("display", "grid").style("grid-template-columns", "1fr 1fr").style("gap", "8px").style("font-size", "13px");
+            const totalAttempted = parsedRustResult.summary.total_files;
+            const successful = parsedRustResult.summary.successful_files;
+            const failed = parsedRustResult.summary.failed_files;
+            downloadStatsGrid.append("div").style("color", "#6c757d").text("Total Attempted:");
+            downloadStatsGrid.append("div").style("font-weight", "bold").text(totalAttempted || 0);
+            downloadStatsGrid.append("div").style("color", "#28a745").text("Successfully Downloaded:");
+            downloadStatsGrid.append("div").style("font-weight", "bold").style("color", "#28a745").text(successful || 0);
+            downloadStatsGrid.append("div").style("color", "#dc3545").text("Failed Downloads:");
+            downloadStatsGrid.append("div").style("font-weight", "bold").style("color", "#dc3545").text(failed || 0);
+            if (failedFilesInfo && failedFilesInfo.count > 0) {
+              addExpandableFailedFilesToStats(downloadStats, failedFilesInfo);
+            }
+          }
+          if (response.timing) {
+            const timingStats = statsPanel.append("div").style("margin-bottom", "20px");
+            timingStats.append("h6").text("Timings").style("margin", "0 0 10px 0").style("color", "#495057").style("font-size", "14px").style("font-weight", "bold");
+            const timingStatsGrid = timingStats.append("div").style("display", "grid").style("grid-template-columns", "1fr 1fr").style("gap", "8px").style("font-size", "13px");
+            if (response.timing.rustProcessingTime !== void 0) {
+              timingStatsGrid.append("div").style("color", "#6c757d").text("GDC API Data Query and Parsing (s):");
+              timingStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.timing.rustProcessingTime);
+            }
+            if (response.timing.grin2ProcessingTime !== void 0) {
+              timingStatsGrid.append("div").style("color", "#6c757d").text("GRIN2 Analysis (s):");
+              timingStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.timing.grin2ProcessingTime);
+            }
+            if (response.timing.totalTime !== void 0) {
+              timingStatsGrid.append("div").style("color", "#6c757d").text("Total Processing Time (s):");
+              timingStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.timing.totalTime);
+            }
+          }
+          if (response.rustResult.summary && (response.rustResult.summary.filtered_records !== void 0 || response.rustResult.summary.filtered_maf_records !== void 0 || response.rustResult.summary.filtered_cnv_records !== void 0)) {
+            const filterStats = statsPanel.append("div").style("margin-bottom", "20px");
+            filterStats.append("h6").text("Data Filtering").style("margin", "0 0 10px 0").style("color", "#495057").style("font-size", "14px").style("font-weight", "bold");
+            const filterStatsGrid = filterStats.append("div").style("display", "grid").style("grid-template-columns", "1fr 1fr").style("gap", "8px").style("font-size", "13px");
+            if (response.rustResult.summary.filtered_records !== void 0) {
+              filterStatsGrid.append("div").style("color", "#6c757d").text("Total Number of Excluded Records:");
+              filterStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.rustResult.summary.filtered_records.toLocaleString());
+            }
+            const mafRecords = response.rustResult.summary.included_maf_records || 0;
+            const cnvRecords = response.rustResult.summary.included_cnv_records || 0;
+            const totalIncludedRecords = mafRecords + cnvRecords;
+            filterStatsGrid.append("div").style("color", "#6c757d").text("Total Number of Included Records:");
+            filterStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(totalIncludedRecords.toLocaleString());
+            if (response.rustResult.summary.filtered_maf_records !== void 0) {
+              filterStatsGrid.append("div").style("color", "#6c757d").text("MAF Records Excluded:");
+              filterStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.rustResult.summary.filtered_maf_records.toLocaleString());
+            }
+            if (response.rustResult.summary.included_maf_records !== void 0) {
+              filterStatsGrid.append("div").style("color", "#6c757d").text("MAF Records Included:");
+              filterStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.rustResult.summary.included_maf_records.toLocaleString());
+            }
+            if (response.rustResult.summary.filtered_cnv_records !== void 0) {
+              filterStatsGrid.append("div").style("color", "#6c757d").text("CNV Records Excluded:");
+              filterStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.rustResult.summary.filtered_cnv_records.toLocaleString());
+            }
+            if (response.rustResult.summary.included_cnv_records !== void 0) {
+              filterStatsGrid.append("div").style("color", "#6c757d").text("CNV Records Included:");
+              filterStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.rustResult.summary.included_cnv_records.toLocaleString());
+            }
+            if (response.rustResult.summary.filtered_records_by_case !== void 0) {
+              const { columns, rows } = parseRecordsByCaseData(
+                response.rustResult.summary.filtered_records_by_case,
+                response.rustResult.summary.excluded_by_max_record
+              );
+              const recordsByCaseContainer = filterStats.append("div").style("grid-column", "1 / -1").style("margin-top", "15px");
+              const expandableHeader = recordsByCaseContainer.append("div").style("display", "flex").style("align-items", "center").style("gap", "8px").style("cursor", "pointer").style("padding", "8px").style("border-radius", "4px").style("transition", "background-color 0.2s").style("background-color", "rgba(0, 123, 255, 0.1)").style("border", "1px solid rgba(0, 123, 255, 0.2)").on("mouseenter", function() {
+                select_default(this).style("background-color", "rgba(0, 123, 255, 0.15)");
+              }).on("mouseleave", function() {
+                select_default(this).style("background-color", "rgba(0, 123, 255, 0.1)");
+              });
+              const expandIcon = expandableHeader.append("span").style("font-size", "12px").style("color", "#007bff").style("transition", "transform 0.2s").text("\u25B6");
+              expandableHeader.append("span").style("color", "#007bff").style("text-decoration", "underline").style("font-size", "13px").style("font-weight", "500").text(
+                `View detailed statistics for ${Object.keys(response.rustResult.summary.filtered_records_by_case).length} cases`
+              );
+              const expandableContent = recordsByCaseContainer.append("div").style("display", "none").style("margin-top", "12px");
+              const tableContainer2 = expandableContent.append("div").style("max-height", "400px").style("overflow-y", "auto").style("border", "1px solid #dee2e6").style("border-radius", "4px");
+              renderTable({
+                div: tableContainer2,
+                columns,
+                rows,
+                showLines: true,
+                striped: true,
+                showHeader: true,
+                maxHeight: "380px",
+                resize: false,
+                header: {
+                  allowSort: true,
+                  style: {
+                    "background-color": "#f8f9fa",
+                    "font-weight": "bold",
+                    "border-bottom": "2px solid #dee2e6"
+                  }
+                }
+              });
+              expandableContent.append("div").style("margin-top", "12px").style("padding", "8px").style("background-color", "#f8f9fa").style("border-radius", "4px").style("font-size", "12px").style("color", "#495057").style("line-height", "1.4").text("This table shows analysis statistics per case.");
+              let isExpanded = false;
+              expandableHeader.on("click", function() {
+                isExpanded = !isExpanded;
+                if (isExpanded) {
+                  expandableContent.style("display", "block");
+                  expandIcon.style("transform", "rotate(90deg)").text("\u25BC");
+                } else {
+                  expandableContent.style("display", "none");
+                  expandIcon.style("transform", "rotate(0deg)").text("\u25B6");
+                }
+              });
+            }
+          }
+        }
+        console.log(`Displayed table with ${response.topGeneTable.rows.length} genes`);
+        if (response.totalGenes && response.showingTop && response.totalGenes > response.showingTop) {
+          resultContainer.append("div").style("margin-top", "15px").style("padding", "10px").style("background-color", "#e9ecef").style("border-radius", "4px").style("font-size", "14px").style("max-width", "100%").style("width", "fit-content").style("color", "#495057").html(`
+						<strong>Note:</strong> For performance reasons, only the top ${response.showingTop} 
+						most significant genes are displayed. The complete analysis identified 
+						${response.totalGenes.toLocaleString()} genes total.
+					`);
+        }
+      } else {
+        console.log("No table data received or empty results");
+        resultContainer.append("div").style("padding", "15px").style("background-color", "#fff3cd").style("border", "1px solid #ffeaa7").style("border-radius", "4px").style("margin", "15px 0").style("max-width", "100%").style("width", "fit-content").text("No significant genes found in the analysis.");
+      }
+    } catch (e) {
+      sayerror(obj2.errDiv, e.message || e);
+      if (e.stack) console.log(e.stack);
+    }
+    button.innerHTML = oldText;
+    button.disabled = false;
+    obj2.busy = false;
+  }
+}
+async function gdcGRIN2ui({ filter0, callbacks, debugmode = false }, holder) {
+  if (debugmode) {
+  }
+  try {
+    if (callbacks) {
+      delete callbacks.sjcharts;
+      for (const n in callbacks) {
+        if (typeof callbacks[n] != "function") throw `callbacks.${n} not function`;
+      }
+    }
+    update({ filter0 });
+  } catch (e) {
+    console.log(e);
+    sayerror(holder, e instanceof Error ? e.message : String(e));
+  }
+  async function update({ filter0: filter02 }) {
+    holder.selectAll("*").remove();
+    holder.style("width", "100%").style("max-width", "none");
+    const obj = {
+      errDiv: holder.append("div"),
+      controlDiv: holder.append("div"),
+      tableDiv: holder.append("div").style("width", "100%"),
+      deduplicationInfoDiv: holder.append("div"),
+      downloadButtonDiv: holder.append("div").style("margin-top", "10px").style("display", "none"),
+      resultDiv: holder.append("div").style("margin-top", "20px"),
+      opts: {
+        filter0: filter02,
+        experimentalStrategy: "WXS"
+      },
+      busy: false,
+      // when analyzing, set to true for disabling ui interactivity
+      mafTableArg: null,
+      expStrategyRadio: null
+    };
+    makeControls(obj);
+    await getFilesAndShowTable(obj);
+    callbacks?.postRender?.(publicApi);
+  }
+  const publicApi = { update };
+  return publicApi;
+}
+export {
+  gdcGRIN2ui
+};
+//# sourceMappingURL=grin2-Z5O7254R.js.map