@sjcrh/proteinpaint-client 2.189.0 → 2.190.0

package/dist/chunk-WQ3U6X4Q.js

@@ -1,269 +0,0 @@
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  pointer_default,
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// dom/svgSeriesTips.js
-function getSeriesTip(line, rect, _tip = null) {
-  const tip = _tip || new Menu({ padding: "5px" });
-  line.style("display", "none");
-  const rectNode = rect.style("fill", "transparent").node();
-  function mouseOver(event) {
-    const m = pointer_default(event, rectNode);
-    const mx = m[0];
-    const xVal = +opts.xScale.invert(mx).toFixed(opts.decimals);
-    const x = opts.xScale(xVal);
-    line.style("display", "").attr("stroke", "#aaa").attr("stroke-dasharray", 4).attr("x1", x).attr("x2", x);
-    const seriesHtmls = [];
-    for (const series of opts.serieses) {
-      const data = series.data;
-      const data_x = data.map((d) => d.x);
-      if (xVal >= Math.min(...data_x) && xVal <= Math.max(...data_x)) {
-        const max = Math.max(...data_x.filter((x2) => x2 <= xVal));
-        const timepoint = data.find((d) => d.x == max);
-        if (timepoint) seriesHtmls.push(timepoint.html);
-      }
-    }
-    if (seriesHtmls.length) {
-      tip.show(event.clientX, event.clientY).d.html(`<span>${opts.xTitleLabel}: ${xVal}</span><br>` + seriesHtmls.map((d) => d).join(opts.separator));
-    } else {
-      tip.hide();
-    }
-  }
-  rect.on("mouseover", mouseOver).on("mousemove", mouseOver).on("mouseout", () => {
-    line.style("display", "none");
-    tip.hide();
-  });
-  const opts = {
-    separator: "<br>",
-    decimals: 1
-  };
-  return {
-    /*
-    			Will update the length of the vertical line
-    			and reassign optional data values
-    
-    			!!! MUST call api.update() before the expected mouseover event,
-    			so that the line will have the proper length and the mouse
-    			position could be computed with .xScale !!! 
-    
-    			_opts{}
-    			.xScale					required
-    										the d3-scale object that was used for the rect dimensions
-    										
-    			.xTitleLabel			required
-    										title of x-axis
-    										will be used as label of x-value in tooltip
-    
-    			.serieses[{data}] 		required
-    										array of series objects, assumed to be visibly rendered
-    							
-    				.data[{x, html}]	required
-    										array of data objects
-    										the series data that is currently rendered in the chart
-    					
-    					.x 				required, float
-    										the datapoint's actual, unscaled x value
-    					
-    					.html   		required, string
-    										the HTML to display in the tooltip if this datapoint's 
-    										x value matched the vertical line's position
-    
-    			.separator				optional, string
-    										the html to be used to join the series html strings when displayed in the tooltip
-    
-    			.decimals				optional, number
-    										number of decimal places of the datapoint's x-value
-    										will control the precision of the vertical line
-    		*/
-    update(_opts = {}) {
-      Object.assign(opts, _opts);
-      const x = rect.attr("x");
-      const y = rect.attr("y");
-      line.attr("x1", x).attr("x2", x).attr("y1", y).attr("y2", rect.attr("height") - y);
-    },
-    /*
-    	detroy to help minimize memory leaks
-    	from elements and event handlers not being garbage collected
-    	because of non-deactivated references
-    */
-    destroy() {
-      rect.on("mouseover", null).on("mousemove", null).on("mouseout", null);
-    }
-  };
-}
-
-// dom/renderAtRisk.js
-function renderAtRiskG({ g, s, chart, order, term2toColor, onSerieClick }) {
-  const bySeries = {};
-  const xTickValues = chart.xTickValues.filter((xTick) => xTick >= chart.xMin);
-  for (const series of chart.visibleSerieses) {
-    const counts = [];
-    let i = 0, d = series.data[0], prev = d, nCensored = 0;
-    for (const time of xTickValues) {
-      while (d && d.x < time) {
-        nCensored += d.ncensor;
-        prev = d;
-        i++;
-        d = series.data[i];
-      }
-      if (d && d.x === time) {
-        counts.push([time, d.nrisk, nCensored]);
-      } else {
-        counts.push([time, prev.nrisk - prev.nevent - prev.ncensor, nCensored]);
-      }
-    }
-    bySeries[series.seriesId] = counts;
-  }
-  const y = s.svgh - s.svgPadding.top - s.svgPadding.bottom + 60;
-  const seriesOrder = order || chart.serieses.map((s2) => s2.seriesId);
-  let data;
-  g.selectAll(".sjpp-atrisk-title").remove();
-  if (s.atRiskVisible) {
-    data = Object.keys(bySeries).sort((a, b) => seriesOrder.indexOf(a) - seriesOrder.indexOf(b));
-    const addYoffset = chart.serieses.length == 1 && !chart.serieses[0].seriesId;
-    const titleg = g.append("text").attr("class", "sjpp-atrisk-title").attr("transform", `translate(${s.atRiskLabelOffset}, ${addYoffset ? 2 * s.axisTitleFontSize : 0})`).attr("text-anchor", "end").attr("font-size", `${s.axisTitleFontSize - 4}px`).attr("cursor", chart.serieses.length == 1 ? "pointer" : "default").text("Number at risk").on("click", chart.serieses.length == 1 ? (e) => onSerieClick({ seriesId: "" }, e.clientX, e.clientY) : null);
-    if (term2toColor[""]) titleg.style("fill", s.defaultColor);
-    titleg.append("tspan").attr("x", 0).attr("y", s.axisTitleFontSize - 4).text("(# censored)");
-  } else {
-    data = [];
-  }
-  const sg = g.attr("transform", `translate(0,${y})`).selectAll(":scope > g").data(data, (seriesId) => seriesId);
-  sg.exit().remove();
-  sg.each(function(seriesId, i) {
-    const y2 = (i + 1) * (2 * s.axisTitleFontSize);
-    const g2 = select_default(this).attr("transform", `translate(0,${y2})`).attr("fill", term2toColor[""] ? s.defaultColor : term2toColor[seriesId].adjusted);
-    renderAtRiskTick(g2.select(":scope>g"), chart, xTickValues, s, seriesId, bySeries[seriesId]);
-  });
-  sg.enter().append("g").each(function(seriesId, i) {
-    const y2 = (i + 1) * (2 * s.axisTitleFontSize);
-    const g2 = select_default(this).attr("transform", `translate(0,${y2})`).attr("fill", term2toColor[""] ? s.defaultColor : term2toColor[seriesId].adjusted).on("click", (e) => onSerieClick({ seriesId }, e.clientX, e.clientY));
-    const sObj = chart.serieses.find((s2) => s2.seriesId === seriesId);
-    g2.append("text").attr("data-testid", "sjpp-atrisk-seriesId").attr("transform", `translate(${s.atRiskLabelOffset}, 0)`).attr("text-anchor", "end").attr("font-size", `${s.axisTitleFontSize - 4}px`).attr("cursor", "pointer").datum({ seriesId }).text(seriesId && seriesId != "*" ? sObj.seriesLabel || seriesId : "");
-    renderAtRiskTick(g2.append("g"), chart, xTickValues, s, seriesId, bySeries[seriesId]);
-  });
-}
-function renderAtRiskTick(g, chart, xTickValues, s, seriesId, series) {
-  const reversed = series.slice().reverse();
-  const data = xTickValues.map((tickVal) => {
-    if (tickVal === 0) return { seriesId, tickVal, atRisk: series[0][1], nCensored: series[0][2] };
-    const d = reversed.find((d2) => d2[0] <= tickVal);
-    return { seriesId, tickVal, atRisk: d[1], nCensored: d[2] };
-  });
-  const text = g.selectAll("text").data(data);
-  text.exit().remove();
-  text.attr("transform", (d) => `translate(${chart.xScale(d.tickVal)},0)`).attr("text-anchor", "middle").attr("font-size", `${s.axisTitleFontSize - 4}px`).attr("cursor", "pointer").each(renderAtRiskLabel);
-  text.enter().append("text").attr("transform", (d) => `translate(${chart.xScale(d.tickVal)},0)`).attr("text-anchor", "middle").attr("font-size", `${s.axisTitleFontSize - 4}px`).attr("cursor", "pointer").each(renderAtRiskLabel);
-  function renderAtRiskLabel(d) {
-    const tspans = select_default(this).selectAll("tspan").data([d.atRisk, `(${d.nCensored})`]);
-    tspans.exit().remove();
-    tspans.attr("y", (d2, i) => i === 0 ? 0 : i * (s.axisTitleFontSize - 4)).text((d2) => d2);
-    tspans.enter().append("tspan").attr("x", 0).attr("y", (d2, i) => i === 0 ? 0 : i * (s.axisTitleFontSize - 4)).text((d2) => d2);
-  }
-}
-
-// dom/renderPvalueTable.js
-function renderPvalues({
-  title,
-  titleTestid,
-  holder,
-  plot,
-  tests,
-  s,
-  bins,
-  tip,
-  setActiveMenu,
-  updateHiddenPvalues
-}) {
-  let fontSize;
-  if (s.axisTitleFontSize) {
-    fontSize = s.axisTitleFontSize - 2;
-  } else fontSize = 15;
-  const maxPvalsToShow = 10;
-  holder.selectAll("*").remove();
-  if (!plot) {
-    throw `plot type '${plot}' not recognized`;
-  }
-  holder.append("div").style("padding-bottom", "5px").style("font-size", fontSize + "px").style("font-weight", "bold").attr("data-testid", titleTestid || "sjpp-pvalueTable-title").text(title);
-  const tablediv = holder.append("div").style("border", "1px solid #ccc");
-  if (plot == "violin" && tests.pvalues.length > maxPvalsToShow || tests.length > maxPvalsToShow) {
-    tablediv.style("overflow", "auto").style("height", "220px");
-  }
-  const visibleTests = s.hiddenPvalues ? tests.filter((t) => !s.hiddenPvalues.find((p) => p.series1.id === t.series1.id && p.series2.id === t.series2.id)) : tests;
-  if (plot == "violin" ? visibleTests.pvalues.length : visibleTests.length) {
-    const binOrder = bins && bins.length > 0 ? bins.map((b) => b.label) : null;
-    if (binOrder) {
-      for (const test of visibleTests) {
-        const orderedSeries = [test.series1.id, test.series2.id].sort(
-          (a, b) => binOrder.indexOf(a) - binOrder.indexOf(b)
-        );
-        if (test.series2.id == orderedSeries[0]) {
-          test.series1_new = test.series2;
-          test.series2_new = test.series1;
-          test.series1 = test.series1_new;
-          test.series2 = test.series2_new;
-          delete test.series1_new;
-          delete test.series2_new;
-        }
-      }
-      visibleTests.sort(
-        (a, b) => binOrder.indexOf(a.series1.id) - binOrder.indexOf(b.series1.id) || binOrder.indexOf(a.series2.id) - binOrder.indexOf(b.series2.id)
-      );
-    }
-    const table = tablediv.append("table").style("width", "100%");
-    table.append("thead").append("tr").selectAll("td").data(["Group 1", "Group 2", "P-value"]).enter().append("td").style("padding", "1px 8px 1px 2px").style("color", "#555").style("position", "sticky").style("top", "0px").style("background", "white").style("font-size", fontSize + "px").text((column) => column);
-    const tbody = table.append("tbody");
-    const tr = tbody.selectAll("tr").data(plot == "violin" ? visibleTests.pvalues : visibleTests).enter().append("tr").attr("class", `pp-${plot}-chartLegends-pvalue`);
-    if (plot == "survival") {
-      tr.on("click", (event, t) => {
-        const hiddenPvalues = s.hiddenPvalues.slice();
-        hiddenPvalues.push(t);
-        updateHiddenPvalues(hiddenPvalues);
-      });
-    }
-    tr.selectAll("td").data((d) => [d.series1, d.series2, d.pvalue]).enter().append("td").attr("aria-label", plot ? "Click to hide a p-value" : "").style("color", plot == "violin" ? "black" : (d) => d.color).style("padding", "1px 8px 1px 2px").style("font-size", fontSize + "px").style("cursor", plot == "survival" ? "pointer" : "auto").text((d) => plot == "violin" ? d : d.text);
-    if (plot == "cuminc") {
-      if (visibleTests.find((test) => test.permutation)) {
-        holder.append("div").style("margin-top", "10px").style("font-size", fontSize - 2 + "px").text("*computed by permutation of Gray's test statistic");
-      }
-    }
-  }
-  if (plot == "survival") {
-    const hiddenTests = tests.filter(
-      (t) => s.hiddenPvalues.find((p) => p.series1.id === t.series1.id && p.series2.id === t.series2.id)
-    );
-    if (hiddenTests.length) {
-      holder.append("div").style("color", "#aaa").style("cursor", "pointer").html(`<span style='color:#aaa; font-weight:400'><span>Hidden tests (${hiddenTests.length})</span>`).on("click", (event) => {
-        tip.clear();
-        const divs = tip.d.append("div").selectAll("div").data(hiddenTests).enter().append("div").each(function(d) {
-          setActiveMenu(true);
-          const div = select_default(this);
-          div.append("input").attr("type", "checkbox").style("margin-right", "5px");
-          div.append("span").html(`${d.series1.id} vs ${d.series2.id}`);
-        });
-        tip.d.append("button").html("Show checked test(s)").on("click", () => {
-          const hiddenPvalues = [];
-          divs.filter(function() {
-            return !select_default(this.firstChild).property("checked");
-          }).each((d) => hiddenPvalues.push(d));
-          updateHiddenPvalues(hiddenPvalues);
-          tip.hide();
-        });
-        tip.show(event.clientX, event.clientY);
-      });
-    }
-    if (s.maxTimeToEvent && visibleTests.length) {
-      holder.append("div").style("margin-top", "10px").style("font-size", fontSize - 2 + "px").text((visibleTests.length > 1 ? "p-values are" : "p-value is") + " computed with all survival data");
-    }
-  }
-}
-
-export {
-  getSeriesTip,
-  renderAtRiskG,
-  renderPvalues
-};
-//# sourceMappingURL=chunk-WQ3U6X4Q.js.map

package/dist/chunk-WQ3U6X4Q.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../dom/svgSeriesTips.js", "../dom/renderAtRisk.js", "../dom/renderPvalueTable.js"],
-  "sourcesContent": ["import { Menu } from '#dom/menu'\nimport { pointer } from 'd3-selection'\n\n/*\n\tWill create a multi-series tooltip that follows\n \tthe cursor with a moving vertical line\n \tover a chart's plot area\n\n\tArguments:\n\tline \trequired, \n\t\t\t\ta d3-wrapped svg.line element, to be used as the moving vertical line\n\t\t\t\t\n\t\t\t\t!!! NOTE: this line must be immediately under the rect element to avoid\n\t\t\t\tflickering and other undesired behavior !!!\n\n\t\t\t\tthis line must already be styled with stroke, etc\n\t\t\t\tonly the line's visibility and positions will be modified on mouseOver()\n\t\t\t\tthe length will also be adjusted in the returned API's update() method\n\t\n\trect \trequired, \n\t\t\t\ta d3-wrapped svg.rect element, which covers the plot area\n\t      in order to capture mouse events for this tooltip\n\t      !!! will be styled with fill: 'transparent' !!!\n\n\t_tip  optional,\n\t\t\t\ta client.Menu instance\n\n\tReturns\n\tan API object (see the specs at the end of this function)\n*/\nexport function getSeriesTip(line, rect, _tip = null) {\n\tconst tip = _tip || new Menu({ padding: '5px' })\n\tline.style('display', 'none')\n\n\tconst rectNode = rect.style('fill', 'transparent').node()\n\n\tfunction mouseOver(event) {\n\t\tconst m = pointer(event, rectNode)\n\t\tconst mx = m[0]\n\t\tconst xVal = +opts.xScale.invert(mx).toFixed(opts.decimals)\n\t\tconst x = opts.xScale(xVal) /* + 0.5*/ // do not add a small float value here; otherwise, the line will not match up with the data\n\n\t\tline.style('display', '').attr('stroke', '#aaa').attr('stroke-dasharray', 4).attr('x1', x).attr('x2', x)\n\n\t\tconst seriesHtmls = []\n\t\tfor (const series of opts.serieses) {\n\t\t\tconst data = series.data\n\t\t\tconst data_x = data.map(d => d.x)\n\t\t\tif (xVal >= Math.min(...data_x) && xVal <= Math.max(...data_x)) {\n\t\t\t\t// xVal is within range of the series\n\t\t\t\t// determine max timepoint that is less than or\n\t\t\t\t// equal to xVal\n\t\t\t\tconst max = Math.max(...data_x.filter(x => x <= xVal))\n\t\t\t\t// store html of this timepoint\n\t\t\t\tconst timepoint = data.find(d => d.x == max)\n\t\t\t\tif (timepoint) seriesHtmls.push(timepoint.html)\n\t\t\t}\n\t\t}\n\n\t\tif (seriesHtmls.length) {\n\t\t\ttip\n\t\t\t\t.show(event.clientX, event.clientY)\n\t\t\t\t.d.html(`<span>${opts.xTitleLabel}: ${xVal}</span><br>` + seriesHtmls.map(d => d).join(opts.separator))\n\t\t} else {\n\t\t\ttip.hide()\n\t\t}\n\t}\n\n\trect\n\t\t.on('mouseover', mouseOver)\n\t\t.on('mousemove', mouseOver)\n\t\t.on('mouseout', () => {\n\t\t\tline.style('display', 'none')\n\t\t\ttip.hide()\n\t\t})\n\n\tconst opts = {\n\t\tseparator: '<br>',\n\t\tdecimals: 1\n\t}\n\n\t/*\n\t\tThe API object for this tooltip is returned below\n\t*/\n\treturn {\n\t\t/*\n\t\t\tWill update the length of the vertical line\n\t\t\tand reassign optional data values\n\n\t\t\t!!! MUST call api.update() before the expected mouseover event,\n\t\t\tso that the line will have the proper length and the mouse\n\t\t\tposition could be computed with .xScale !!! \n\n\t\t\t_opts{}\n\t\t\t.xScale\t\t\t\t\trequired\n\t\t\t\t\t\t\t\t\t\tthe d3-scale object that was used for the rect dimensions\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t.xTitleLabel\t\t\trequired\n\t\t\t\t\t\t\t\t\t\ttitle of x-axis\n\t\t\t\t\t\t\t\t\t\twill be used as label of x-value in tooltip\n\n\t\t\t.serieses[{data}] \t\trequired\n\t\t\t\t\t\t\t\t\t\tarray of series objects, assumed to be visibly rendered\n\t\t\t\t\t\t\t\n\t\t\t\t.data[{x, html}]\trequired\n\t\t\t\t\t\t\t\t\t\tarray of data objects\n\t\t\t\t\t\t\t\t\t\tthe series data that is currently rendered in the chart\n\t\t\t\t\t\n\t\t\t\t\t.x \t\t\t\trequired, float\n\t\t\t\t\t\t\t\t\t\tthe datapoint's actual, unscaled x value\n\t\t\t\t\t\n\t\t\t\t\t.html   \t\trequired, string\n\t\t\t\t\t\t\t\t\t\tthe HTML to display in the tooltip if this datapoint's \n\t\t\t\t\t\t\t\t\t\tx value matched the vertical line's position\n\n\t\t\t.separator\t\t\t\toptional, string\n\t\t\t\t\t\t\t\t\t\tthe html to be used to join the series html strings when displayed in the tooltip\n\n\t\t\t.decimals\t\t\t\toptional, number\n\t\t\t\t\t\t\t\t\t\tnumber of decimal places of the datapoint's x-value\n\t\t\t\t\t\t\t\t\t\twill control the precision of the vertical line\n\t\t*/\n\t\tupdate(_opts = {}) {\n\t\t\tObject.assign(opts, _opts)\n\t\t\tconst x = rect.attr('x')\n\t\t\tconst y = rect.attr('y')\n\t\t\tline\n\t\t\t\t.attr('x1', x)\n\t\t\t\t.attr('x2', x)\n\t\t\t\t.attr('y1', y)\n\t\t\t\t.attr('y2', rect.attr('height') - y)\n\t\t},\n\n\t\t/*\n\t\t\tdetroy to help minimize memory leaks\n\t\t\tfrom elements and event handlers not being garbage collected\n\t\t\tbecause of non-deactivated references\n\t\t*/\n\t\tdestroy() {\n\t\t\trect.on('mouseover', null).on('mousemove', null).on('mouseout', null)\n\t\t}\n\t}\n}\n", "import { select } from 'd3-selection'\n\n/*\nrender at-risk counts at x-axis tick values\n\nused by survival plot and cuminc plot\n\ninput parameter:\n{\n    g: selection\n    s: {} self.settings\n    chart: {} chart object\n    order: [] array of series ids to specify series order\n    term2toColor: {} map term2 values to colors\n}\n*/\n\nexport function renderAtRiskG({ g, s, chart, order, term2toColor, onSerieClick }) {\n\tconst bySeries = {}\n\n\t// do not compute at-risk counts of tick values that are\n\t// smaller than the first timepoint of the chart\n\t// e.g. if all curves start at 5 years, we do not want\n\t// to compute at-risk counts at tick value 0\n\tconst xTickValues = chart.xTickValues.filter(xTick => xTick >= chart.xMin)\n\n\t// compute at-risk counts of filtered tick values\n\tfor (const series of chart.visibleSerieses) {\n\t\tconst counts = []\n\t\tlet i = 0,\n\t\t\td = series.data[0],\n\t\t\tprev = d, // prev = \"previous\" data point\n\t\t\tnCensored = 0\n\n\t\t// for each x-axis tick value, find and use the data that applies\n\t\tfor (const time of xTickValues) {\n\t\t\twhile (d && d.x < time) {\n\t\t\t\tnCensored += d.ncensor\n\t\t\t\tprev = d\n\t\t\t\ti++\n\t\t\t\td = series.data[i]\n\t\t\t}\n\n\t\t\t// prev will become last timepoint before tick value\n\t\t\t// for example, if tick value is 10 and timepoint A is at time 8.5, timepoint B is at time 9.2, timepoint C is at 9.8, and timepoint D is at time 10.2, then prev will be set to the timepoint C\n\t\t\t// the at-risk count at tick value 10 will then be the nrisk at prev minus any events/censored exits that occurred at prev\n\n\t\t\tif (d && d.x === time) {\n\t\t\t\t// iterated timepoint is equal to tick value\n\t\t\t\t// can use nrisk of timepoint as the nrisk of tick value\n\t\t\t\tcounts.push([time, d.nrisk, nCensored])\n\t\t\t} else {\n\t\t\t\t// iterated timepoint does not equal tick value\n\t\t\t\t// use the nrisk of prev minus any events/censored exits\n\t\t\t\t// at prev as the nrisk of tick value\n\t\t\t\tcounts.push([time, prev.nrisk - prev.nevent - prev.ncensor, nCensored])\n\t\t\t}\n\t\t}\n\t\tbySeries[series.seriesId] = counts\n\t}\n\n\tconst y = s.svgh - s.svgPadding.top - s.svgPadding.bottom + 60 // make y-offset option???\n\t// fully rerender, later may reuse previously rendered elements\n\t// g.selectAll('*').remove()\n\n\tconst seriesOrder = order || chart.serieses.map(s => s.seriesId)\n\n\tlet data\n\tg.selectAll('.sjpp-atrisk-title').remove()\n\tif (s.atRiskVisible) {\n\t\t// at-risk counts are visible\n\t\t// sort the data\n\t\tdata = Object.keys(bySeries).sort((a, b) => seriesOrder.indexOf(a) - seriesOrder.indexOf(b))\n\t\t// render the title\n\t\t// add a y offset to title if there is no series id\n\t\tconst addYoffset = chart.serieses.length == 1 && !chart.serieses[0].seriesId\n\t\tconst titleg = g\n\t\t\t.append('text')\n\t\t\t.attr('class', 'sjpp-atrisk-title')\n\t\t\t.attr('transform', `translate(${s.atRiskLabelOffset}, ${addYoffset ? 2 * s.axisTitleFontSize : 0})`)\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('font-size', `${s.axisTitleFontSize - 4}px`)\n\t\t\t.attr('cursor', chart.serieses.length == 1 ? 'pointer' : 'default')\n\t\t\t.text('Number at risk')\n\t\t\t.on('click', chart.serieses.length == 1 ? e => onSerieClick({ seriesId: '' }, e.clientX, e.clientY) : null)\n\t\tif (term2toColor['']) titleg.style('fill', s.defaultColor)\n\t\ttitleg\n\t\t\t.append('tspan')\n\t\t\t.attr('x', 0)\n\t\t\t.attr('y', s.axisTitleFontSize - 4)\n\t\t\t.text('(# censored)')\n\t} else {\n\t\t// at-risk counts are not visible\n\t\t// empty the data\n\t\tdata = []\n\t}\n\n\t// render at-risk counts\n\tconst sg = g\n\t\t.attr('transform', `translate(0,${y})`)\n\t\t.selectAll(':scope > g')\n\t\t.data(data, seriesId => seriesId)\n\n\tsg.exit().remove()\n\n\tsg.each(function (seriesId, i) {\n\t\tconst y = (i + 1) * (2 * s.axisTitleFontSize)\n\t\tconst g = select(this)\n\t\t\t.attr('transform', `translate(0,${y})`)\n\t\t\t.attr('fill', term2toColor[''] ? s.defaultColor : term2toColor[seriesId].adjusted) // TODO: attached series color to the data of 'sg'\n\t\trenderAtRiskTick(g.select(':scope>g'), chart, xTickValues, s, seriesId, bySeries[seriesId])\n\t})\n\n\tsg.enter()\n\t\t.append('g')\n\t\t.each(function (seriesId, i) {\n\t\t\tconst y = (i + 1) * (2 * s.axisTitleFontSize)\n\t\t\tconst g = select(this)\n\t\t\t\t.attr('transform', `translate(0,${y})`)\n\t\t\t\t.attr('fill', term2toColor[''] ? s.defaultColor : term2toColor[seriesId].adjusted)\n\t\t\t\t.on('click', e => onSerieClick({ seriesId }, e.clientX, e.clientY))\n\n\t\t\tconst sObj = chart.serieses.find(s => s.seriesId === seriesId)\n\t\t\tg.append('text')\n\t\t\t\t.attr('data-testid', 'sjpp-atrisk-seriesId')\n\t\t\t\t.attr('transform', `translate(${s.atRiskLabelOffset}, 0)`)\n\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t.attr('font-size', `${s.axisTitleFontSize - 4}px`)\n\t\t\t\t.attr('cursor', 'pointer')\n\t\t\t\t.datum({ seriesId })\n\t\t\t\t.text(seriesId && seriesId != '*' ? sObj.seriesLabel || seriesId : '')\n\n\t\t\trenderAtRiskTick(g.append('g'), chart, xTickValues, s, seriesId, bySeries[seriesId])\n\t\t})\n}\n\nfunction renderAtRiskTick(g, chart, xTickValues, s, seriesId, series) {\n\tconst reversed = series.slice().reverse()\n\tconst data = xTickValues.map(tickVal => {\n\t\tif (tickVal === 0) return { seriesId, tickVal, atRisk: series[0][1], nCensored: series[0][2] }\n\t\tconst d = reversed.find(d => d[0] <= tickVal)\n\t\treturn { seriesId, tickVal, atRisk: d[1], nCensored: d[2] }\n\t})\n\n\tconst text = g.selectAll('text').data(data)\n\ttext.exit().remove()\n\ttext\n\t\t.attr('transform', d => `translate(${chart.xScale(d.tickVal)},0)`)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', `${s.axisTitleFontSize - 4}px`)\n\t\t.attr('cursor', 'pointer')\n\t\t.each(renderAtRiskLabel)\n\ttext\n\t\t.enter()\n\t\t.append('text')\n\t\t.attr('transform', d => `translate(${chart.xScale(d.tickVal)},0)`)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', `${s.axisTitleFontSize - 4}px`)\n\t\t.attr('cursor', 'pointer')\n\t\t.each(renderAtRiskLabel)\n\n\tfunction renderAtRiskLabel(d) {\n\t\tconst tspans = select(this)\n\t\t\t.selectAll('tspan')\n\t\t\t.data([d.atRisk, `(${d.nCensored})`])\n\n\t\ttspans.exit().remove()\n\n\t\ttspans.attr('y', (d, i) => (i === 0 ? 0 : i * (s.axisTitleFontSize - 4))).text(d => d)\n\n\t\ttspans\n\t\t\t.enter()\n\t\t\t.append('tspan')\n\t\t\t.attr('x', 0)\n\t\t\t.attr('y', (d, i) => (i === 0 ? 0 : i * (s.axisTitleFontSize - 4)))\n\t\t\t.text(d => d)\n\t}\n}\n", "import { select } from 'd3-selection'\n\n/*\nrender a table of p-values\n\nused by survival plot and cuminc plot\n\ninput parameter:\n{\n\ttitle: 'str' value specified by user,\n\ttitleTestid: overrides default testid\n    holder: holder div,\n    plot: plot type ('survial' or 'cuminc'),\n    tests: [] chart tests,\n    s: {} self.settings,\n    bins: [] self.refs.bins,\n    tip: self.app.tip,\n    setActiveMenu: callback for setting self.activeMenu,\n    updateHiddenPvalues: callback for updating s.hiddenPvalues\n}\n*/\n\nexport function renderPvalues({\n\ttitle,\n\ttitleTestid,\n\tholder,\n\tplot,\n\ttests,\n\ts,\n\tbins,\n\ttip,\n\tsetActiveMenu,\n\tupdateHiddenPvalues\n}) {\n\tlet fontSize\n\n\tif (s.axisTitleFontSize) {\n\t\tfontSize = s.axisTitleFontSize - 2\n\t} else fontSize = 15\n\tconst maxPvalsToShow = 10\n\n\tholder.selectAll('*').remove()\n\n\t// title div\n\tif (!plot) {\n\t\tthrow `plot type '${plot}' not recognized`\n\t}\n\n\tholder\n\t\t.append('div')\n\t\t.style('padding-bottom', '5px')\n\t\t.style('font-size', fontSize + 'px')\n\t\t.style('font-weight', 'bold')\n\t\t.attr('data-testid', titleTestid || 'sjpp-pvalueTable-title')\n\t\t.text(title)\n\n\t// table div\n\t// need separate divs for title and table\n\t// to support table scrolling\n\tconst tablediv = holder.append('div').style('border', '1px solid #ccc')\n\tif ((plot == 'violin' && tests.pvalues.length > maxPvalsToShow) || tests.length > maxPvalsToShow) {\n\t\ttablediv.style('overflow', 'auto').style('height', '220px')\n\t}\n\t// in survival plot, individual tests can be hidden by s.hiddenPvalues\n\t// in cuminc plot, s.hiddenPvalues is not defined\n\tconst visibleTests = s.hiddenPvalues\n\t\t? tests.filter(t => !s.hiddenPvalues.find(p => p.series1.id === t.series1.id && p.series2.id === t.series2.id))\n\t\t: tests\n\n\tif (plot == 'violin' ? visibleTests.pvalues.length : visibleTests.length) {\n\t\tconst binOrder = bins && bins.length > 0 ? bins.map(b => b.label) : null\n\t\tif (binOrder) {\n\t\t\t// series are numeric bins\n\t\t\t// the tests of these series should be sorted as follows\n\n\t\t\t// within each test, series 1 should have a smaller bin\n\t\t\t// value than series 2\n\t\t\tfor (const test of visibleTests) {\n\t\t\t\tconst orderedSeries = [test.series1.id, test.series2.id].sort(\n\t\t\t\t\t(a, b) => binOrder.indexOf(a) - binOrder.indexOf(b)\n\t\t\t\t)\n\t\t\t\tif (test.series2.id == orderedSeries[0]) {\n\t\t\t\t\ttest.series1_new = test.series2\n\t\t\t\t\ttest.series2_new = test.series1\n\t\t\t\t\ttest.series1 = test.series1_new\n\t\t\t\t\ttest.series2 = test.series2_new\n\t\t\t\t\tdelete test.series1_new\n\t\t\t\t\tdelete test.series2_new\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// then sort tests first by series1 then by series2\n\t\t\tvisibleTests.sort(\n\t\t\t\t(a, b) =>\n\t\t\t\t\tbinOrder.indexOf(a.series1.id) - binOrder.indexOf(b.series1.id) ||\n\t\t\t\t\tbinOrder.indexOf(a.series2.id) - binOrder.indexOf(b.series2.id)\n\t\t\t)\n\t\t}\n\n\t\t// table\n\t\tconst table = tablediv.append('table').style('width', '100%')\n\n\t\t// table header\n\t\ttable\n\t\t\t.append('thead')\n\t\t\t.append('tr')\n\t\t\t.selectAll('td')\n\t\t\t.data(['Group 1', 'Group 2', 'P-value'])\n\t\t\t.enter()\n\t\t\t.append('td')\n\t\t\t.style('padding', '1px 8px 1px 2px')\n\t\t\t.style('color', '#555')\n\t\t\t.style('position', 'sticky')\n\t\t\t.style('top', '0px')\n\t\t\t.style('background', 'white')\n\t\t\t.style('font-size', fontSize + 'px')\n\t\t\t.text(column => column)\n\n\t\t// table rows\n\t\tconst tbody = table.append('tbody')\n\n\t\tconst tr = tbody\n\t\t\t.selectAll('tr')\n\t\t\t.data(plot == 'violin' ? visibleTests.pvalues : visibleTests)\n\t\t\t.enter()\n\t\t\t.append('tr')\n\t\t\t.attr('class', `pp-${plot}-chartLegends-pvalue`)\n\n\t\tif (plot == 'survival') {\n\t\t\ttr.on('click', (event, t) => {\n\t\t\t\tconst hiddenPvalues = s.hiddenPvalues.slice()\n\t\t\t\thiddenPvalues.push(t)\n\t\t\t\tupdateHiddenPvalues(hiddenPvalues)\n\t\t\t})\n\t\t}\n\n\t\t// table cells\n\t\ttr.selectAll('td')\n\t\t\t.data(d => [d.series1, d.series2, d.pvalue])\n\t\t\t.enter()\n\t\t\t.append('td')\n\t\t\t.attr('aria-label', plot ? 'Click to hide a p-value' : '')\n\t\t\t.style('color', plot == 'violin' ? 'black' : d => d.color)\n\t\t\t.style('padding', '1px 8px 1px 2px')\n\t\t\t.style('font-size', fontSize + 'px')\n\t\t\t.style('cursor', plot == 'survival' ? 'pointer' : 'auto')\n\t\t\t.text(d => (plot == 'violin' ? d : d.text))\n\n\t\t// footnote div\n\t\tif (plot == 'cuminc') {\n\t\t\tif (visibleTests.find(test => test.permutation)) {\n\t\t\t\tholder\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('margin-top', '10px')\n\t\t\t\t\t.style('font-size', fontSize - 2 + 'px')\n\t\t\t\t\t.text(\"*computed by permutation of Gray's test statistic\")\n\t\t\t}\n\t\t}\n\t}\n\n\tif (plot == 'survival') {\n\t\t// features specific to survival plot\n\t\tconst hiddenTests = tests.filter(t =>\n\t\t\ts.hiddenPvalues.find(p => p.series1.id === t.series1.id && p.series2.id === t.series2.id)\n\t\t)\n\t\tif (hiddenTests.length) {\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.style('color', '#aaa')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.html(`<span style='color:#aaa; font-weight:400'><span>Hidden tests (${hiddenTests.length})</span>`)\n\t\t\t\t.on('click', event => {\n\t\t\t\t\ttip.clear()\n\t\t\t\t\tconst divs = tip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.selectAll('div')\n\t\t\t\t\t\t.data(hiddenTests)\n\t\t\t\t\t\t.enter()\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.each(function (d) {\n\t\t\t\t\t\t\tsetActiveMenu(true)\n\t\t\t\t\t\t\tconst div = select(this)\n\t\t\t\t\t\t\tdiv.append('input').attr('type', 'checkbox').style('margin-right', '5px')\n\t\t\t\t\t\t\tdiv.append('span').html(`${d.series1.id} vs ${d.series2.id}`)\n\t\t\t\t\t\t})\n\n\t\t\t\t\ttip.d\n\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t.html('Show checked test(s)')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tconst hiddenPvalues = []\n\t\t\t\t\t\t\tdivs\n\t\t\t\t\t\t\t\t.filter(function () {\n\t\t\t\t\t\t\t\t\treturn !select(this.firstChild).property('checked')\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\t.each(d => hiddenPvalues.push(d))\n\t\t\t\t\t\t\tupdateHiddenPvalues(hiddenPvalues)\n\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t})\n\n\t\t\t\t\ttip.show(event.clientX, event.clientY)\n\t\t\t\t})\n\t\t}\n\n\t\t//footnote: pvalue is still computed with all survival data when Survival Time Visualized is set\n\t\tif (s.maxTimeToEvent && visibleTests.length) {\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin-top', '10px')\n\t\t\t\t.style('font-size', fontSize - 2 + 'px')\n\t\t\t\t.text((visibleTests.length > 1 ? 'p-values are' : 'p-value is') + ' computed with all survival data')\n\t\t}\n\t}\n}\n"],
-  "mappings": 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-  "names": ["x", "s", "y", "g", "d"]
-}

package/dist/chunk-WUFPZPXB.js

@@ -1,293 +0,0 @@
-import {
-  first_genetrack_tolist,
-  gmmode,
-  sayerror
-} from "./chunk-6P5OGWFW.js";
-import {
-  dofetch3
-} from "./chunk-CV575475.js";
-import {
-  codon_stop,
-  nt2aa,
-  proteinDomainColorScale
-} from "./chunk-EBKERML3.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// common/snp.js
-async function string2snp(genome, str) {
-  const data = await dofetch3("snp", {
-    method: "POST",
-    body: JSON.stringify({ byName: true, genome: genome.name, lst: [str] })
-  });
-  if (data.error) throw data.error;
-  if (!data.results || data.results.length == 0) throw str + ": not a SNP";
-  for (const i of data.results) {
-    const chr = genome.chrlookup[i.chrom.toUpperCase()];
-    if (chr && chr.major) {
-      return {
-        chr: i.chrom,
-        start: i.chromStart,
-        stop: i.chromEnd
-      };
-    }
-  }
-  const r = data.results[0];
-  return {
-    chr: r.chrom,
-    start: r.chromStart,
-    stop: r.chromEnd
-  };
-}
-
-// src/block.init.js
-async function block_init_default(arg) {
-  if (!arg.holder) throw "No holder for block.init";
-  if (!arg.genome) throw "no genome";
-  if (arg.holder instanceof Element) arg.holder = select_default(arg.holder);
-  if (!arg.tklst) arg.tklst = [];
-  if (arg.query) {
-    await step1_findgm(arg);
-    return;
-  }
-  if (arg.model && arg.allmodels) {
-    await step2_getseq(arg);
-    return;
-  }
-}
-async function step1_findgm(arg) {
-  const wait = arg.holder.append("p").style("font-size", "2em").style("color", "#858585").text("Searching for " + arg.query + " ...");
-  const data = await dofetch3("genelookup", {
-    body: { deep: 1, input: arg.query, genome: arg.genome.name }
-  });
-  if (!data) throw "querying genes: server error";
-  if (data.error) throw "error querying genes: " + data.error;
-  if (!data.gmlst || data.gmlst.length == 0) {
-    if (arg.genome.hasSNP) {
-      try {
-        const r = await string2snp(arg.genome, arg.query);
-        wait.remove();
-        const par = {
-          genome: arg.genome,
-          holder: arg.holder,
-          chr: r.chr,
-          start: Math.max(0, r.start - 300),
-          stop: r.start + 300,
-          nobox: true,
-          tklst: arg.tklst,
-          debugmode: arg.debugmode
-        };
-        first_genetrack_tolist(arg.genome, par.tklst);
-        const b = await import("./block-W2QR2O43.js");
-        const block = new b.Block(par);
-        block.addhlregion(r.chr, r.start, r.stop - 1);
-      } catch (e) {
-        wait.text("Not a gene or SNP: " + arg.query);
-      }
-    } else {
-      wait.text("No match to gene: " + arg.query);
-    }
-    return;
-  }
-  wait.remove();
-  arg.allmodels = data.gmlst;
-  for (const m of arg.allmodels) {
-    if (m.isoform.toUpperCase() == (data.found_isoform ? data.found_isoform.toUpperCase() : arg.query.toUpperCase())) {
-      arg.model = m;
-      await step2_getseq(arg);
-      return;
-    }
-  }
-  const defaultisoforms = [];
-  for (const m of arg.allmodels) {
-    if (!m.isoform) throw "isoform missing from one gene model: " + JSON.stringify(m);
-    const n = m.isoform.toUpperCase();
-    if (arg.genome.isoformcache.has(n)) {
-      let nothas = true;
-      for (const m2 of arg.genome.isoformcache.get(n)) {
-        if (m2.chr == m.chr && m2.start == m.start && m2.stop == m.stop && m2.strand == m.strand) {
-          nothas = false;
-          break;
-        }
-      }
-      if (nothas) {
-        arg.genome.isoformcache.get(n).push(m);
-      }
-    } else {
-      arg.genome.isoformcache.set(n, [m]);
-    }
-    if (m.isoform.toUpperCase() == arg.query.toUpperCase()) {
-      defaultisoforms.push(m);
-      break;
-    }
-    if (m.isdefault) {
-      defaultisoforms.push(m);
-    }
-  }
-  if (defaultisoforms.length == 1) {
-    arg.model = defaultisoforms[0];
-  } else if (defaultisoforms.length > 1) {
-    for (const m of defaultisoforms) {
-      if (m.chr == "chrY") {
-        continue;
-      }
-      const chr = arg.genome.chrlookup[m.chr.toUpperCase()];
-      if (!chr) {
-        continue;
-      }
-      if (!chr.major) {
-        continue;
-      }
-      arg.model = m;
-      break;
-    }
-    if (!arg.model) {
-      arg.model = defaultisoforms[0];
-    }
-  }
-  if (!arg.model) {
-    arg.model = arg.allmodels[0];
-  }
-  await step2_getseq(arg);
-}
-async function step2_getseq(arg) {
-  if (arg.model.genomicseq) {
-    checker();
-    step2_getpdomain(arg);
-    return;
-  }
-  const par = {
-    genome: arg.genome.name,
-    coord: arg.model.chr + ":" + (arg.model.start + 1) + "-" + arg.model.stop
-  };
-  const data = await dofetch3("ntseq", { method: "POST", body: JSON.stringify(par) });
-  if (!data) throw "getting sequence: server error";
-  if (data.error) throw "getting sequence: " + data.error;
-  if (!data.seq) throw "no nt seq???";
-  arg.model.genomicseq = data.seq.toUpperCase();
-  arg.model.aaseq = nt2aa(arg.model);
-  checker();
-  await step2_getpdomain(arg);
-  function checker() {
-    if (arg.model.aaseq) {
-      const stop = arg.model.aaseq.indexOf(codon_stop);
-      const cdslen = arg.model.cdslen - (arg.model.startCodonFrame ? 3 - arg.model.startCodonFrame : 0);
-      if (stop != -1 && stop < cdslen / 3 - 1) {
-        sayerror(arg.holder, "Translating " + arg.model.isoform + " ends at " + stop + " AA, expecting " + cdslen / 3);
-      }
-    }
-  }
-}
-async function step2_getpdomain(arg) {
-  const isoform2gm = /* @__PURE__ */ new Map();
-  for (const m of arg.allmodels) {
-    if (!m.pdomains) {
-      m.pdomains = [];
-      m.domain_hidden = {};
-      if (!isoform2gm.has(m.isoform)) isoform2gm.set(m.isoform, []);
-      isoform2gm.get(m.isoform).push(m);
-    }
-  }
-  if (isoform2gm.size == 0) {
-    await step3(arg);
-    return;
-  }
-  const data = await dofetch3("pdomain", {
-    method: "POST",
-    body: JSON.stringify({ genome: arg.genome.name, isoforms: [...isoform2gm.keys()] })
-  });
-  if (data.error) throw "error getting protein domain: " + data.error;
-  if (!Array.isArray(data.lst)) throw ".lst[] not array";
-  for (const a of data.lst) {
-    for (const m of isoform2gm.get(a.name)) {
-      m.pdomains = a.pdomains;
-    }
-  }
-  if (arg.geneDomains) {
-    if (typeof arg.geneDomains != "object") throw "geneDomains not object";
-    for (const isoform in arg.geneDomains) {
-      const lst = isoform2gm.get(isoform);
-      if (!lst) throw `unknown isoform ${isoform} from geneDomains{}`;
-      for (const g of lst) {
-        if (!g.pdomains) g.pdomains = [];
-        if (!Array.isArray(arg.geneDomains[isoform])) throw `geneDomains[${isoform}] not array`;
-        for (const b of arg.geneDomains[isoform]) {
-          if (typeof b != "object") throw "element from geneDomains[] not object";
-          if (!Number.isInteger(b.start)) throw "start not integer from geneDomains[]";
-          if (!Number.isInteger(b.stop)) throw "stop not integer from geneDomains[]";
-          if (b.start > b.stop) throw "start>stop from geneDomains[]";
-          if (!b.name) b.name = "Custom domain";
-          if (!g.pdomains.find((a) => a.start == b.start && a.stop == b.stop && a.name == b.name)) g.pdomains.push(b);
-        }
-      }
-    }
-  }
-  const s = proteinDomainColorScale();
-  for (const lst of isoform2gm.values()) {
-    for (const g of lst) {
-      for (const d of g.pdomains || []) {
-        if (!d.color) d.color = s(d.name + d.description);
-      }
-    }
-  }
-  await step3(arg);
-}
-async function step3(arg) {
-  let mode = arg.gmmode;
-  if (!mode) {
-    if (arg.model.cdslen) {
-      mode = gmmode.protein;
-    } else {
-      mode = gmmode.exononly;
-    }
-  }
-  if (arg.dataset) {
-    if (!Array.isArray(arg.dataset)) throw "dataset is not array";
-    for (const dsname of arg.dataset) {
-      if (arg.genome.datasets[dsname] && !arg.genome.datasets[dsname].legacyDsIsUninitiated) continue;
-      const d = await dofetch3(`getDataset?genome=${arg.genome.name}&dsname=${dsname}`);
-      if (d.error) throw `invalid name from dataset[]: ${d.error}`;
-      if (!d.ds) throw ".ds missing";
-      const ds = arg.genome.datasets[d.ds.label];
-      Object.assign(ds, d.ds);
-      const _ = await import("./legacyDataset-SWJCAWIR.js");
-      _.validate_oldds(ds);
-      delete ds.legacyDsIsUninitiated;
-    }
-  }
-  const b = await import("./block-W2QR2O43.js");
-  arg.__blockInstance = new b.Block({
-    genome: arg.genome,
-    holder: arg.holder,
-    nobox: true,
-    usegm: arg.model,
-    gmstackheight: 37,
-    allgm: arg.allmodels,
-    datasetlst: arg.dataset,
-    legacyDsFilter: arg.legacyDsFilter,
-    mset: arg.mset,
-    hlaachange: arg.hlaachange,
-    hlvariants: arg.hlvariants,
-    hlregions: arg.hlregions,
-    gmmode: mode,
-    hidedatasetexpression: arg.hidedatasetexpression,
-    hidegenecontrol: arg.hidegenecontrol,
-    hidegenelegend: arg.hidegenelegend,
-    variantPageCall_snv: arg.variantPageCall_snv,
-    datasetqueries: arg.datasetqueries,
-    samplecart: arg.samplecart,
-    debugmode: arg.debugmode,
-    tklst: arg.tklst,
-    mclassOverride: arg.mclassOverride,
-    hide_dsHandles: arg.hide_dsHandles,
-    onloadalltk_always: arg.onloadalltk_always,
-    onAddRemoveTk: arg.onAddRemoveTk
-  });
-}
-
-export {
-  string2snp,
-  block_init_default
-};
-//# sourceMappingURL=chunk-WUFPZPXB.js.map