@sjcrh/proteinpaint-client 2.190.2 → 2.191.2

package/dist/chunk-RZGEKL77.js

@@ -0,0 +1,117 @@
+import {
+  copyMerge,
+  getInitFxn
+} from "./chunk-M3J4MINX.js";
+
+// termdb/termInfo.js
+var defaultState = { isVisible: false, term: null };
+var TdbTermInfo = class {
+  /*
+  		Will display background information about a term, 
+  		such as rubric, publication source, description, etc
+  
+  		opts{}
+  			.content_holder: required d3-wrapped DOM element
+  				****TODO: Create menu on the fly if content_holder is not supplied****
+  			
+  			.icon_holder: optional, creates information icon for terms
+  			
+  			.vocabApi: 
+  				- for termInfoInit(), required as opts.vocabApi
+  				- for termInfoComp(), required as part of opts.app
+  				- a vocabulary API that has a getTermInfo() method
+  			
+  			.state{} optional, see defaultState value above
+  				.isVisible: boolean, optional
+  				.term: {id, ...} optional (may be supplied with either getState() or main({state}))
+  	*/
+  constructor(opts) {
+    this.vocabApi = opts.vocabApi || opts.app && opts.app.vocabApi;
+    this.state = Object.assign({}, defaultState, opts.state ? opts.state : {});
+    this.api = this;
+    setInteractivity(this);
+    setRenderers(this);
+    this.initUI(opts);
+  }
+  /*
+  	state: replace 1 or more state values by attribute key
+  */
+  async main(state = {}) {
+    copyMerge(this.state, state);
+    this.dom.content_holder.style("display", this.state.isVisible ? "block" : "none");
+    this.dom.icon_holder.style("background-color", this.state.isVisible ? "darkgray" : "transparent").style("color", this.state.isVisible ? "white" : "#797a7a");
+    if (!this.state.isVisible) return;
+    const data = await this.vocabApi.getTermInfo(this.state.term.id);
+    this.render(data);
+  }
+};
+var termInfoInit = getInitFxn(TdbTermInfo);
+function setRenderers(self) {
+  self.initUI = function(opts) {
+    self.dom = {
+      content_holder: opts.content_holder.style("margin-left", "25px").attr("class", "term_info_div").style("display", self.state.isVisible ? "block" : "none").style("white-space", "normal").style("padding-bottom", "20px"),
+      //Term information/description
+      details: opts.content_holder.append("div"),
+      tbody: opts.content_holder.append("table").append("tbody"),
+      //Information icon button div. Term description appears in content_holder
+      icon_holder: opts.icon_holder.style("margin", "1px 0px 1px 5px").style("padding", "2px 5px").style("font-family", "Times New Roman").style("font-size", "14px").style("font-weight", "bold").style("cursor", "pointer").style("background-color", "transparent").style("color", "#797a7a").style("align-items", "center").style("justify-content", "center").style("border", "none").style("border-radius", "3px").attr("aria-label", "Term Information").html("ⓘ").on("mouseenter", () => {
+        if (self.state.isVisible == true) return;
+        self.dom.icon_holder.style("color", "blue");
+      }).on("mouseleave", () => {
+        if (self.state.isVisible == true) return;
+        self.dom.icon_holder.style("color", "#797a7a");
+      }).on("click", self.toggleDescription)
+    };
+  };
+  self.render = function(data) {
+    if (!data?.terminfo) {
+      self.dom.details.append("div").style("margin-top", "10px").text("No definition found.");
+      return;
+    }
+    self.dom.tbody.selectAll("*").remove();
+    if (data.terminfo.src) {
+      for (let s of data.terminfo.src) {
+        const source_td = self.dom.tbody.append("tr").append("td").style("padding", "5px 0");
+        source_td.append("div").style("font-weight", "bold").text("Source");
+        source_td.append("div").style("margin-left", "20px").text(s.pub);
+        source_td.append("div").style("margin-left", "20px").html(s.title + ":&nbsp;<i>" + s.section + "</i>");
+      }
+    }
+    if (data.terminfo.rubric) {
+      const grade_td = self.dom.tbody.append("tr").append("td").style("padding", "5px 0").append("div").style("font-weight", "bold").text("Grading Rubric").append("ol").style("margin", "0px");
+      for (let grade of data.terminfo.rubric) {
+        grade_td.append("li").style("font-weight", "normal").text(grade);
+      }
+    }
+    self.dom.details.selectAll("*").remove();
+    if (data.terminfo.description) {
+      const header = self.dom.details.append("div").style("padding-top", "20px").style("padding-bottom", "10px").style("font-weight", "bold").text("Description");
+      for (const d of data.terminfo.description) {
+        self.renderDetail(d, self.dom.details.append("div").style("padding-bottom", "3px"));
+      }
+    }
+  };
+  self.renderDetail = function(d, div) {
+    if (Array.isArray(d.value)) {
+      div.append("span").html("<i>" + d.label + "</i>");
+      const section = div.append("div").style("padding-left", "20px");
+      for (const v of d.value) {
+        v.label = "- " + v.label;
+        self.renderDetail(v, section.append("div"));
+      }
+    } else {
+      div.html("<i>" + d.label + ":</i>&nbsp;" + d.value);
+    }
+  };
+}
+function setInteractivity(self) {
+  self.toggleDescription = function() {
+    self.state.isVisible = !self.state.isVisible;
+    self.main({ isVisible: self.state.isVisible });
+  };
+}
+
+export {
+  termInfoInit
+};
+//# sourceMappingURL=chunk-RZGEKL77.js.map

package/dist/chunk-RZY34QRF.js

@@ -0,0 +1,158 @@
+import {
+  appInit
+} from "./chunk-NVX26LFC.js";
+import {
+  showErrorsWithCounter
+} from "./chunk-L4TUTGTA.js";
+import {
+  mclass
+} from "./chunk-EBKERML3.js";
+
+// plots/disco/launch.adhoc.ts
+async function launch(arg, genomeObj, holder) {
+  const [mlst, errors] = await getMlst(arg);
+  if (errors?.length) {
+    return showErrorsWithCounter(errors, holder);
+  }
+  const opts = {
+    holder,
+    vocabApi: {
+      // api is required by plot.app.js, so create a mock one for the adhoc data
+      vocab: { terms: [] },
+      main: () => {
+        return;
+      },
+      getTermdbConfig: () => {
+        return {};
+      }
+    },
+    state: {
+      args: {
+        data: mlst,
+        genome: genomeObj
+      },
+      plots: [
+        {
+          chartType: "Disco",
+          subfolder: "disco",
+          extension: "ts",
+          /** NOTE: Users should only override the settings in the default
+           * settings.Disco:{}, not the entire settings:{} object.*/
+          overrides: { Disco: arg?.settings || {} }
+        }
+      ]
+    }
+  };
+  const plotAppApi = await appInit(opts);
+  return plotAppApi;
+}
+async function getMlst(arg) {
+  if (Array.isArray(arg.mlst)) {
+    return [arg.mlst, null];
+  }
+  const mlst = [];
+  const errors = [];
+  if (arg.snvText) parseSnvText(arg.snvText, mlst, errors);
+  if (arg.svText) parseSvText(arg.svText, mlst, errors);
+  if (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors);
+  return [mlst, errors];
+}
+function parseSnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 5) {
+      errors.push("snv input not equal to 5 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 1,
+        chr: l[0],
+        position: Number(l[1]),
+        gene: l[2],
+        mname: l[3],
+        class: validateMutation(l[4], errors)
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseSvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length < 4 || l.length > 6) {
+      errors.push("sv input not equal to 4 or 6 columns");
+      continue;
+    }
+    let m;
+    try {
+      const length = l.length;
+      if (length == 4) {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          chrB: l[2],
+          posB: Number(l[3])
+        };
+      } else {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          geneA: l[2],
+          chrB: l[3],
+          posB: Number(l[4]),
+          geneB: l[5]
+        };
+      }
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseCnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 4) {
+      errors.push("cnv input not equal to 4 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 4,
+        chr: l[0],
+        start: Number(l[1]),
+        stop: Number(l[2]),
+        value: Number(l[3])
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function validateMutation(mutation, errors) {
+  const mut2check = mutation.toLowerCase();
+  const foundMutation = Object.values(mclass).find(
+    (m) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check
+  );
+  if (foundMutation) {
+    return foundMutation.key;
+  } else {
+    errors.push(`Invalid mutation class: ${mutation}`);
+  }
+}
+
+export {
+  launch
+};
+//# sourceMappingURL=chunk-RZY34QRF.js.map

package/dist/chunk-S4JLRRKK.js

@@ -0,0 +1,287 @@
+import {
+  getColors
+} from "./chunk-EBKERML3.js";
+import {
+  convertUnits,
+  isNumeric,
+  isStrictNumeric
+} from "./chunk-JNITUVXP.js";
+import {
+  format
+} from "./chunk-OAWQ6LOO.js";
+
+// ../shared/utils/dist/src/termdb.bins.js
+function validate_bins(binconfig) {
+  const bc = binconfig;
+  if (!bc || typeof bc !== "object") throw "bin schema must be an object";
+  if (!("type" in bc)) bc.type = "regular-bin";
+  if (bc.type == "custom-bin") {
+    if (!Array.isArray(bc.lst)) throw "binconfig.lst must be an array";
+    if (!bc.lst.length) throw "binconfig.lst must have entries";
+    const first_bin = bc.lst[0];
+    const last_bin = bc.lst[bc.lst.length - 1];
+    for (const bin of bc.lst) {
+      if (!("startinclusive" in bin) && !("stopinclusive" in bin)) {
+        throw "custom bin.startinclusive and/or bin.stopinclusive must be defined";
+      }
+      if (bin == first_bin) {
+        if ("startunbounded" in bin && !bin.startunbounded) {
+          throw `a custom first bin must not set bin.startunbounded to false`;
+        }
+        bin.startunbounded = true;
+        if ("start" in bin) {
+          throw "a custom first bin must not set a bin.start value";
+        }
+        if ("start_percentile" in bin) {
+          throw "the first bin must not set a bin.start_percentile value";
+        }
+        if (!("stop" in bin)) {
+          throw `a custom first bin must define a bin.stop value`;
+        }
+        if (!isStrictNumeric(bin.stop)) {
+          throw `a custom first bin.stop value should be numeric`;
+        }
+      } else if (bin == last_bin) {
+        if (!("start" in bin)) {
+          throw `a custom last bin must define a bin.start value`;
+        }
+        if (!isStrictNumeric(bin.start)) {
+          throw `a custom last bin.start must be numeric`;
+        }
+        if ("stopunbounded" in bin && !bin.stopunbounded) {
+          throw "a custom last bin must not set bin.stopunbounded to false";
+        }
+        bin.stopunbounded = true;
+        if ("stop" in bin) {
+          throw "a custom last bin must not set a bin.stop value";
+        }
+      } else {
+        if (bin.startunbounded || bin.stopunbounded) {
+          throw "bin.startunbounded and bin.stopunbounded must not be set for non-first/non-last bins";
+        }
+        if (!isStrictNumeric(bin.start)) throw "bin.start must be numeric for a non-first bin";
+        if (!isStrictNumeric(bin.stop)) throw "bin.stop must be numeric for a non-last bin";
+      }
+    }
+  } else if (bc.type == "regular-bin") {
+    if (!Number.isFinite(bc.bin_size)) throw "non-numeric bin_size";
+    if (bc.bin_size <= 0) throw "bin_size must be greater than 0";
+    if (!bc.startinclusive && !bc.stopinclusive) {
+      bc.startinclusive = 1;
+      bc.stopinclusive = 0;
+    }
+    if (!bc.first_bin) throw "first_bin{} missing";
+    if (typeof bc.first_bin != "object") throw "first_bin{} is not an object";
+    if (!Object.keys(bc.first_bin).length) throw "first_bin is an empty object";
+    {
+      const b = bc.first_bin;
+      b.startunbounded = true;
+      if (b.stop_percentile) {
+        if (!Number.isInteger(b.stop_percentile)) throw "first_bin.stop_percentile should be integer";
+        if (b.stop_percentile <= 0 || b.stop_percentile >= 100) throw "first_bin.stop_percentile out of bound (0-100)";
+      } else if (!Number.isFinite(b.stop)) {
+        throw "first_bin.stop not a number when stop_percentile is not set";
+      }
+    }
+    if (bc.last_bin) {
+      const b = bc.last_bin;
+      if (b.start_percentile) {
+        if (!Number.isInteger(b.start_percentile)) throw "last_bin.start_percentile should be integer";
+        if (b.start_percentile <= 0 || b.start_percentile >= 100) throw "last_bin.start_percentile out of bound (0-100)";
+      } else if (!Number.isFinite(b.start)) {
+        throw "last_bin.start not a number when start_percentile is not set";
+      }
+      b.stopunbounded = true;
+      if ("stop" in b) {
+        throw "a regular last bin must not set a bin.stop value";
+      }
+    }
+  } else {
+    throw `invalid binconfig.type="${bc.type}"`;
+  }
+}
+var maxNumBins = 100;
+function compute_bins(binconfig, summaryfxn, valueConversion) {
+  const bc = binconfig;
+  validate_bins(bc);
+  if (bc.lst) {
+    if (!Array.isArray(bc.lst)) throw `bc.lst is not an array`;
+    if (bc.lst.length > maxNumBins) throw `bc.lst exceed the maximum of ${maxNumBins} allowed entries`;
+    const k2c2 = getColors(bc.lst.length);
+    for (const bin of bc.lst) bin.color = k2c2(bin.label);
+  }
+  if (bc.type == "custom-bin") return JSON.parse(JSON.stringify(bc.lst));
+  if (typeof summaryfxn != "function") throw "summaryfxn required for modules/termdb.bins.js compute_bins()";
+  const percentiles = target_percentiles(bc);
+  const summary = summaryfxn(percentiles);
+  if (!summary || typeof summary !== "object") throw "invalid returned value by summaryfxn";
+  bc.results = { summary };
+  if (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc);
+  const minFloor = Math.floor(summary.min * 100) / 100;
+  const maxCeil = Math.ceil(summary.max * 100) / 100;
+  const min = bc.first_bin.startunbounded ? minFloor : bc.first_bin.start_percentile ? summary["p" + bc.first_bin.start_percentile] : bc.first_bin.start;
+  let max = maxCeil, last_start, last_stop;
+  if (bc.last_bin) {
+    max = bc.last_bin.stopunbounded ? maxCeil : bc.last_bin.stop_percentile ? summary["p" + bc.last_bin.stop_percentile] : isNumeric(bc.last_bin.stop) && bc.last_bin.stop <= summary.max ? bc.last_bin.stop : maxCeil;
+    last_start = isStrictNumeric(bc.last_bin.start_percentile) ? summary["p" + bc.last_bin.start_percentile] : isStrictNumeric(bc.last_bin.start) ? bc.last_bin.start : void 0;
+    last_stop = bc.last_bin.stopunbounded ? null : bc.last_bin.stop_percentile ? summary["p" + bc.last_bin.stop_percentile] : isStrictNumeric(bc.last_bin.stop) ? bc.last_bin.stop : null;
+  } else if (bc.lst) {
+    const last_bin = bc.lst[bc.lst.length - 1];
+    last_start = last_bin.start;
+    last_stop = "stop" in last_bin && !last_bin.stopunbounded ? last_bin.stop : maxCeil;
+    max = last_stop;
+  } else {
+    last_start = maxCeil;
+    last_stop = maxCeil;
+  }
+  const numericMax = isStrictNumeric(max);
+  const numericLastStart = isStrictNumeric(last_start);
+  const numericLastStop = isStrictNumeric(last_stop);
+  if (!numericMax && !numericLastStart) return [];
+  const bins = [];
+  let currBin = {
+    startunbounded: bc.first_bin.startunbounded,
+    start: bc.first_bin.startunbounded ? void 0 : min,
+    stop: isStrictNumeric(bc.first_bin.stop_percentile) ? +summary["p" + bc.first_bin.stop_percentile] : isStrictNumeric(bc.first_bin.stop) ? +bc.first_bin.stop : min + bc.bin_size,
+    startinclusive: bc.startinclusive,
+    stopinclusive: bc.stopinclusive
+  };
+  if (!isStrictNumeric(currBin.stop)) throw "the computed first_bin.stop is non-numeric" + currBin.stop;
+  while (numericMax && currBin.stop <= max || currBin.startunbounded && !bins.length || currBin.stopunbounded) {
+    bins.push(currBin);
+    if (currBin.stop >= max) {
+      currBin.stopunbounded = true;
+      if (bins.length > 1) {
+        delete currBin.stop;
+      }
+    }
+    currBin.label = get_bin_label(currBin, bc, valueConversion);
+    if (currBin.stopunbounded) break;
+    const upper = currBin.stop + bc.bin_size;
+    const previousStop = currBin.stop;
+    currBin = {
+      startinclusive: bc.startinclusive,
+      stopinclusive: bc.stopinclusive,
+      start: previousStop,
+      stop: numericLastStop && (previousStop == last_start || upper > last_stop) ? last_stop : numericLastStart && upper > last_start && previousStop != last_start ? last_start : upper
+    };
+    if (currBin.stop >= max) {
+      currBin.stop = max;
+      if (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1;
+      if (bc.last_bin && bc.last_bin.stopinclusive) currBin.stopinclusive = 1;
+    }
+    if (numericLastStart && currBin.start == last_start) {
+      if (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1;
+    }
+    if (currBin.start > currBin.stop) {
+      if (numericLastStart && currBin.stop == last_start && bc.last_bin && bc.last_bin.stopunbounded)
+        currBin.stopunbounded = true;
+      else break;
+    }
+    if (bins.length + 1 >= maxNumBins) {
+      delete currBin.stop;
+      currBin.stopunbounded = true;
+      currBin.label = get_bin_label(currBin, bc, valueConversion);
+      if (!bins.includes(currBin)) bins.push(currBin);
+      const hint = "Please increase the bin_size or first bin stop, or have a lower last bin start.";
+      throw new Error(hint + " (max_num_bins_reached)");
+    }
+  }
+  delete bc.binLabelFormatter;
+  if (bins.length > 1) {
+    delete bins[bins.length - 1].stop;
+  }
+  const k2c = getColors(bins.length);
+  for (const bin of bins) bin.color = k2c(bin.label);
+  return bins;
+}
+function getNumDecimalsFormatter(bc) {
+  return "rounding" in bc ? format(bc.rounding) : (d) => d;
+}
+function get_bin_label(bin, binconfig, valueConversion) {
+  if (!bin) return "missing bin.label";
+  if (bin.label) return bin.label;
+  const bc = binconfig;
+  if (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc);
+  if (!bin.startunbounded && !bin.stopunbounded && !("startinclusive" in bin) && !("stopinclusive" in bin)) {
+    if (bc.startinclusive) bin.startinclusive = true;
+    else if (bc.stopinclusive) bin.stopinclusive = true;
+  }
+  const start = bc.use_as == "bins" || bin.start;
+  const stop = bc.use_as == "bins" || bin.stop;
+  let label_offset = 0;
+  if ("label_offset" in bc) {
+    bc.label_offset_ignored = "bin_size" in bc && bc.bin_size < bc.label_offset;
+    if (!bc.label_offset_ignored) label_offset = bc.label_offset;
+  } else if (bc.bin_size === 1 && bc.termtype == "integer") {
+    label_offset = 1;
+  }
+  if (bin.startunbounded) {
+    const oper = bin.stopinclusive ? "\u2264" : "<";
+    const v1 = valueConversion ? convertUnits(stop, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : bc.binLabelFormatter(stop);
+    return oper + v1;
+  }
+  if (bin.stopunbounded || start === stop) {
+    const oper = bin.startinclusive ? "\u2265" : ">";
+    const v0 = valueConversion ? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : bc.binLabelFormatter(start);
+    return oper + v0;
+  }
+  if (label_offset && bin.startinclusive && !bin.stopinclusive) {
+    if (Number.isInteger(bc.bin_size) && Math.abs(start - stop) === label_offset) {
+      return "" + (valueConversion ? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : bc.binLabelFormatter(start));
+    } else {
+      const v0 = valueConversion ? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : bc.binLabelFormatter(start);
+      const v1 = valueConversion ? convertUnits(
+        stop - label_offset,
+        valueConversion.fromUnit,
+        valueConversion.toUnit,
+        valueConversion.scaleFactor,
+        true
+      ) : bc.binLabelFormatter(stop - label_offset);
+      return +v0 >= +v1 ? v0.toString() : v0 + " to " + v1;
+    }
+  } else {
+    const oper0 = bin.startinclusive ? "" : ">";
+    const oper1 = bin.stopinclusive ? "" : "<";
+    const v0 = valueConversion ? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : Number.isInteger(start) ? start : bc.binLabelFormatter(start);
+    const v1 = valueConversion ? convertUnits(stop, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : Number.isInteger(stop) ? stop : bc.binLabelFormatter(stop);
+    if (+v0 >= +v1) {
+      const oper = bin.startinclusive ? "\u2265" : ">";
+      return oper + v0;
+    } else {
+      return oper0 + v0 + " to " + oper1 + v1;
+    }
+  }
+}
+function get_bin_range_equation(bin, binconfig) {
+  const x = '<span style="font-family:Times;font-style:italic;">x</span>';
+  let range_eq;
+  const copy = structuredClone(bin);
+  copy.label = "";
+  const bin_label = get_bin_label(copy, binconfig, void 0);
+  if (bin.startunbounded || bin.stopunbounded) {
+    range_eq = x + " " + bin_label;
+  } else if (bin.startinclusive) {
+    range_eq = bin_label.replace("to <", "\u2264 " + x + " <");
+  } else if (bin.stopinclusive) {
+    range_eq = bin_label.replace(">", "").replace("to", "< " + x + " \u2264");
+  }
+  return range_eq;
+}
+function target_percentiles(binconfig) {
+  const percentiles = [];
+  const f = binconfig.first_bin;
+  if (f && isStrictNumeric(f.start_percentile)) percentiles.push(f.start_percentile);
+  if (f && isStrictNumeric(f.stop_percentile)) percentiles.push(f.stop_percentile);
+  const l = binconfig.last_bin;
+  if (l && isStrictNumeric(l.start_percentile)) percentiles.push(l.start_percentile);
+  if (l && isStrictNumeric(l.stop_percentile)) percentiles.push(l.stop_percentile);
+  return percentiles;
+}
+
+export {
+  compute_bins,
+  get_bin_label,
+  get_bin_range_equation
+};
+//# sourceMappingURL=chunk-S4JLRRKK.js.map

package/dist/chunk-S4JLRRKK.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/utils/src/termdb.bins.ts"],
+  "sourcesContent": ["import { format } from 'd3-format'\nimport { getColors } from './common.js'\nimport { isNumeric, isStrictNumeric, convertUnits } from './helpers.js'\n\nexport default function validate_bins(binconfig) {\n\t// Number.isFinite('1') returns false, which is desired\n\n\tconst bc = binconfig\n\tif (!bc || typeof bc !== 'object') throw 'bin schema must be an object'\n\t// assign default type\n\tif (!('type' in bc)) bc.type = 'regular-bin'\n\n\tif (bc.type == 'custom-bin') {\n\t\tif (!Array.isArray(bc.lst)) throw 'binconfig.lst must be an array'\n\t\tif (!bc.lst.length) throw 'binconfig.lst must have entries'\n\t\tconst first_bin = bc.lst[0]\n\t\tconst last_bin = bc.lst[bc.lst.length - 1]\n\n\t\tfor (const bin of bc.lst) {\n\t\t\tif (!('startinclusive' in bin) && !('stopinclusive' in bin)) {\n\t\t\t\tthrow 'custom bin.startinclusive and/or bin.stopinclusive must be defined'\n\t\t\t}\n\n\t\t\tif (bin == first_bin) {\n\t\t\t\tif ('startunbounded' in bin && !bin.startunbounded) {\n\t\t\t\t\tthrow `a custom first bin must not set bin.startunbounded to false`\n\t\t\t\t}\n\t\t\t\tbin.startunbounded = true\n\t\t\t\tif ('start' in bin) {\n\t\t\t\t\tthrow 'a custom first bin must not set a bin.start value'\n\t\t\t\t}\n\t\t\t\tif ('start_percentile' in bin) {\n\t\t\t\t\tthrow 'the first bin must not set a bin.start_percentile value'\n\t\t\t\t}\n\t\t\t\tif (!('stop' in bin)) {\n\t\t\t\t\tthrow `a custom first bin must define a bin.stop value`\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.stop)) {\n\t\t\t\t\tthrow `a custom first bin.stop value should be numeric`\n\t\t\t\t}\n\t\t\t} else if (bin == last_bin) {\n\t\t\t\tif (!('start' in bin)) {\n\t\t\t\t\tthrow `a custom last bin must define a bin.start value`\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.start)) {\n\t\t\t\t\tthrow `a custom last bin.start must be numeric`\n\t\t\t\t}\n\t\t\t\tif ('stopunbounded' in bin && !bin.stopunbounded) {\n\t\t\t\t\tthrow 'a custom last bin must not set bin.stopunbounded to false'\n\t\t\t\t}\n\t\t\t\tbin.stopunbounded = true\n\t\t\t\tif ('stop' in bin) {\n\t\t\t\t\tthrow 'a custom last bin must not set a bin.stop value'\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tif (bin.startunbounded || bin.stopunbounded) {\n\t\t\t\t\tthrow 'bin.startunbounded and bin.stopunbounded must not be set for non-first/non-last bins'\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.start)) throw 'bin.start must be numeric for a non-first bin'\n\t\t\t\tif (!isStrictNumeric(bin.stop)) throw 'bin.stop must be numeric for a non-last bin'\n\t\t\t}\n\t\t}\n\t} else if (bc.type == 'regular-bin') {\n\t\t// required custom_bin parameter\n\t\tif (!Number.isFinite(bc.bin_size)) throw 'non-numeric bin_size'\n\t\tif (bc.bin_size <= 0) throw 'bin_size must be greater than 0'\n\n\t\tif (!bc.startinclusive && !bc.stopinclusive) {\n\t\t\tbc.startinclusive = 1\n\t\t\tbc.stopinclusive = 0\n\t\t}\n\n\t\tif (!bc.first_bin) throw 'first_bin{} missing'\n\t\tif (typeof bc.first_bin != 'object') throw 'first_bin{} is not an object'\n\t\tif (!Object.keys(bc.first_bin).length) throw 'first_bin is an empty object'\n\n\t\t{\n\t\t\tconst b = bc.first_bin\n\t\t\tb.startunbounded = true\n\t\t\t// requires stop_percentile, or stop\n\t\t\tif (b.stop_percentile) {\n\t\t\t\tif (!Number.isInteger(b.stop_percentile)) throw 'first_bin.stop_percentile should be integer'\n\t\t\t\tif (b.stop_percentile <= 0 || b.stop_percentile >= 100) throw 'first_bin.stop_percentile out of bound (0-100)'\n\t\t\t} else if (!Number.isFinite(b.stop)) {\n\t\t\t\tthrow 'first_bin.stop not a number when stop_percentile is not set'\n\t\t\t}\n\t\t}\n\n\t\tif (bc.last_bin) {\n\t\t\tconst b = bc.last_bin\n\t\t\t// requires start_percentile or start\n\t\t\tif (b.start_percentile) {\n\t\t\t\tif (!Number.isInteger(b.start_percentile)) throw 'last_bin.start_percentile should be integer'\n\t\t\t\tif (b.start_percentile <= 0 || b.start_percentile >= 100) throw 'last_bin.start_percentile out of bound (0-100)'\n\t\t\t} else if (!Number.isFinite(b.start)) {\n\t\t\t\tthrow 'last_bin.start not a number when start_percentile is not set'\n\t\t\t}\n\n\t\t\tb.stopunbounded = true\n\t\t\tif ('stop' in b) {\n\t\t\t\tthrow 'a regular last bin must not set a bin.stop value'\n\t\t\t}\n\t\t}\n\t} else {\n\t\tthrow `invalid binconfig.type=\"${bc.type}\"`\n\t}\n}\n\nconst maxNumBins = 100 // hardcoded limit for now to not stress sqlite\n\nexport function compute_bins(binconfig, summaryfxn, valueConversion) {\n\t/*\n\t  Bins generator\n\t  \n\tbinconfig   \n\t  configuration of bins per the Numerical Binning Scheme\n\n\tsummaryfxn (percentiles)=> return {min, max, pX, pY, ...}\n\t  - required function\n\n\t  - must accept an array of desired percentile values\n\t  and returns an object of computed properties\n\t  {\n\t    min: minimum value\n\t    max: maximum value\n\t    pX: percentile at X value, so p10 will be 10th percentile value\n\t    pY: .. corresponding to the desired percentile values \n\t  }\n\t*/\n\tconst bc = binconfig\n\n\tvalidate_bins(bc)\n\tif (bc.lst) {\n\t\tif (!Array.isArray(bc.lst)) throw `bc.lst is not an array`\n\t\tif (bc.lst.length > maxNumBins) throw `bc.lst exceed the maximum of ${maxNumBins} allowed entries`\n\t\tconst k2c = getColors(bc.lst.length) //to color bins\n\t\tfor (const bin of bc.lst) bin.color = k2c(bin.label)\n\t}\n\tif (bc.type == 'custom-bin') return JSON.parse(JSON.stringify(bc.lst))\n\tif (typeof summaryfxn != 'function') throw 'summaryfxn required for modules/termdb.bins.js compute_bins()'\n\tconst percentiles = target_percentiles(bc)\n\tconst summary = summaryfxn(percentiles)\n\tif (!summary || typeof summary !== 'object') throw 'invalid returned value by summaryfxn'\n\tbc.results = { summary }\n\tif (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc)\n\n\t// round the min and max values for use as bin start and stop\n\t// in the first and last bins, respectively\n\tconst minFloor = Math.floor(summary.min * 100) / 100\n\tconst maxCeil = Math.ceil(summary.max * 100) / 100\n\tconst min = bc.first_bin.startunbounded\n\t\t? minFloor\n\t\t: bc.first_bin.start_percentile\n\t\t? summary['p' + bc.first_bin.start_percentile]\n\t\t: bc.first_bin.start\n\tlet max = maxCeil, // in order to include the max value in the last bin\n\t\tlast_start,\n\t\tlast_stop\n\n\tif (bc.last_bin) {\n\t\tmax = bc.last_bin.stopunbounded\n\t\t\t? maxCeil // in order to include the max value in the last bin\n\t\t\t: bc.last_bin.stop_percentile\n\t\t\t? summary['p' + bc.last_bin.stop_percentile]\n\t\t\t: isNumeric(bc.last_bin.stop) && bc.last_bin.stop <= summary.max // '0.0088' < 0.0088\n\t\t\t? bc.last_bin.stop\n\t\t\t: maxCeil // in order to include the max value in the last bin\n\t\tlast_start = isStrictNumeric(bc.last_bin.start_percentile)\n\t\t\t? summary['p' + bc.last_bin.start_percentile]\n\t\t\t: isStrictNumeric(bc.last_bin.start)\n\t\t\t? bc.last_bin.start\n\t\t\t: undefined\n\t\tlast_stop = bc.last_bin.stopunbounded\n\t\t\t? null\n\t\t\t: bc.last_bin.stop_percentile\n\t\t\t? summary['p' + bc.last_bin.stop_percentile]\n\t\t\t: isStrictNumeric(bc.last_bin.stop)\n\t\t\t? bc.last_bin.stop\n\t\t\t: null\n\t} else if (bc.lst) {\n\t\tconst last_bin = bc.lst[bc.lst.length - 1]\n\t\tlast_start = last_bin.start\n\t\tlast_stop = 'stop' in last_bin && !last_bin.stopunbounded ? last_bin.stop : maxCeil\n\t\tmax = last_stop\n\t} else {\n\t\tlast_start = maxCeil\n\t\tlast_stop = maxCeil\n\t}\n\n\tconst numericMax = isStrictNumeric(max)\n\tconst numericLastStart = isStrictNumeric(last_start)\n\tconst numericLastStop = isStrictNumeric(last_stop)\n\n\tif (!numericMax && !numericLastStart) return [] //throw 'unable to compute the last bin start or stop'\n\n\tconst bins: any[] = []\n\tlet currBin: Record<string, any> = {\n\t\tstartunbounded: bc.first_bin.startunbounded,\n\t\tstart: bc.first_bin.startunbounded ? undefined : min,\n\t\tstop: isStrictNumeric(bc.first_bin.stop_percentile)\n\t\t\t? +summary['p' + bc.first_bin.stop_percentile]\n\t\t\t: isStrictNumeric(bc.first_bin.stop)\n\t\t\t? +bc.first_bin.stop\n\t\t\t: min + bc.bin_size,\n\t\tstartinclusive: bc.startinclusive,\n\t\tstopinclusive: bc.stopinclusive\n\t}\n\n\tif (!isStrictNumeric(currBin.stop)) throw 'the computed first_bin.stop is non-numeric' + currBin.stop\n\n\twhile ((numericMax && currBin.stop <= max) || (currBin.startunbounded && !bins.length) || currBin.stopunbounded) {\n\t\tbins.push(currBin)\n\t\t// force a computed last bin to have stopunbounded true\n\t\tif (currBin.stop >= max) {\n\t\t\tcurrBin.stopunbounded = true\n\t\t\tif (bins.length > 1) {\n\t\t\t\tdelete currBin.stop\n\t\t\t}\n\t\t}\n\t\tcurrBin.label = get_bin_label(currBin, bc, valueConversion)\n\t\tif (currBin.stopunbounded) break\n\n\t\tconst upper = currBin.stop + bc.bin_size\n\t\tconst previousStop = currBin.stop\n\t\tcurrBin = {\n\t\t\tstartinclusive: bc.startinclusive,\n\t\t\tstopinclusive: bc.stopinclusive,\n\t\t\tstart: previousStop,\n\t\t\tstop:\n\t\t\t\tnumericLastStop && (previousStop == last_start || upper > last_stop)\n\t\t\t\t\t? last_stop\n\t\t\t\t\t: numericLastStart && upper > last_start && previousStop != last_start\n\t\t\t\t\t? last_start\n\t\t\t\t\t: upper\n\t\t}\n\n\t\tif (currBin.stop >= max) {\n\t\t\tcurrBin.stop = max\n\t\t\tif (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1\n\t\t\tif (bc.last_bin && bc.last_bin.stopinclusive) currBin.stopinclusive = 1\n\t\t}\n\t\tif (numericLastStart && currBin.start == last_start) {\n\t\t\tif (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1\n\t\t}\n\t\tif (currBin.start > currBin.stop) {\n\t\t\tif (numericLastStart && currBin.stop == last_start && bc.last_bin && bc.last_bin.stopunbounded)\n\t\t\t\tcurrBin.stopunbounded = true\n\t\t\telse break\n\t\t}\n\t\tif (bins.length + 1 >= maxNumBins) {\n\t\t\t// this limit is computed before processing actual numeric values, since\n\t\t\t// the computation with actual values may be problematic when there are lots of bins\n\t\t\tdelete currBin.stop\n\t\t\tcurrBin.stopunbounded = true\n\t\t\tcurrBin.label = get_bin_label(currBin, bc, valueConversion)\n\t\t\tif (!bins.includes(currBin)) bins.push(currBin)\n\t\t\tconst hint = 'Please increase the bin_size or first bin stop, or have a lower last bin start.'\n\t\t\t// throw instead of making the error handling dependent on client code,\n\t\t\t// to make the error behavior consistent across different chart types;\n\t\t\t// previously, the error message was not thrown but assigned as bc.error\n\t\t\tthrow new Error(hint + ' (max_num_bins_reached)')\n\t\t}\n\t}\n\tdelete bc.binLabelFormatter\n\tif (bins.length > 1) {\n\t\tdelete bins[bins.length - 1].stop\n\t}\n\tconst k2c = getColors(bins.length) //to color bins\n\tfor (const bin of bins) bin.color = k2c(bin.label)\n\treturn bins\n}\n\nfunction getNumDecimalsFormatter(bc) {\n\t//return format('rounding' in bc ? bc.rounding : '')\n\treturn 'rounding' in bc ? format(bc.rounding) : d => d // default to labeling using the start/stop value as-is\n}\n\nexport function get_bin_label(bin, binconfig, valueConversion?: any) {\n\t/*\n\t  Generate a numeric bin label given a bin configuration and an optional term valueConversion object\n\t*/\n\tif (!bin) return 'missing bin.label'\n\tif (bin.label) return bin.label\n\n\tconst bc = binconfig\n\tif (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc)\n\tif (!bin.startunbounded && !bin.stopunbounded && !('startinclusive' in bin) && !('stopinclusive' in bin)) {\n\t\tif (bc.startinclusive) bin.startinclusive = true\n\t\telse if (bc.stopinclusive) bin.stopinclusive = true\n\t}\n\n\tconst start = bc.use_as == 'bins' || bin.start\n\tconst stop = bc.use_as == 'bins' || bin.stop\n\n\tlet label_offset = 0\n\tif ('label_offset' in bc) {\n\t\tbc.label_offset_ignored = 'bin_size' in bc && bc.bin_size < bc.label_offset\n\t\tif (!bc.label_offset_ignored) label_offset = bc.label_offset\n\t} else if (bc.bin_size === 1 && bc.termtype == 'integer') {\n\t\tlabel_offset = 1\n\t}\n\n\t// one side-unbounded bins\n\t// label will be \">v\" or \"<v\"\n\tif (bin.startunbounded) {\n\t\tconst oper = bin.stopinclusive ? '\u2264' : '<' // \\u2264\n\t\tconst v1 = valueConversion\n\t\t\t? convertUnits(stop, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t: bc.binLabelFormatter(stop) //bin.startinclusive && label_offset ? stop - label_offset : stop)\n\t\treturn oper + v1\n\t}\n\t// a data value may coincide with the last bin's start\n\tif (bin.stopunbounded || start === stop) {\n\t\tconst oper = bin.startinclusive /*|| label_offset*/ ? '\u2265' : '>' // \\u2265\n\t\tconst v0 = valueConversion\n\t\t\t? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t: bc.binLabelFormatter(start) //bin.startinclusive || start == min ? start : start + label_offset)\n\t\treturn oper + v0\n\t}\n\n\t// two-sided bins\n\tif (label_offset && bin.startinclusive && !bin.stopinclusive) {\n\t\tif (Number.isInteger(bc.bin_size) && Math.abs(start - stop) === label_offset) {\n\t\t\t// make a simpler label when the range simply spans the bin_size\n\t\t\treturn (\n\t\t\t\t'' +\n\t\t\t\t(valueConversion\n\t\t\t\t\t? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t\t\t: bc.binLabelFormatter(start))\n\t\t\t)\n\t\t} else {\n\t\t\tconst v0 = valueConversion\n\t\t\t\t? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t\t: bc.binLabelFormatter(start)\n\t\t\tconst v1 = valueConversion\n\t\t\t\t? convertUnits(\n\t\t\t\t\t\tstop - label_offset,\n\t\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\t\ttrue\n\t\t\t\t  )\n\t\t\t\t: bc.binLabelFormatter(stop - label_offset)\n\t\t\t// ensure that last two bin labels make sense (the last is stopunbounded)\n\t\t\treturn +v0 >= +v1 ? v0.toString() : v0 + ' to ' + v1\n\t\t}\n\t} else {\n\t\t// stop_inclusive || label_offset == 0\n\t\tconst oper0 = bin.startinclusive ? '' : '>'\n\t\tconst oper1 = bin.stopinclusive ? '' : '<'\n\t\tconst v0 = valueConversion\n\t\t\t? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t: Number.isInteger(start)\n\t\t\t? start\n\t\t\t: bc.binLabelFormatter(start)\n\t\tconst v1 = valueConversion\n\t\t\t? convertUnits(stop, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t: Number.isInteger(stop)\n\t\t\t? stop\n\t\t\t: bc.binLabelFormatter(stop)\n\t\t// after rounding the bin labels, the bin start may equal the last bin stop as derived from actual data\n\t\tif (+v0 >= +v1) {\n\t\t\tconst oper = bin.startinclusive ? '\u2265' : '>' // \\u2265\n\t\t\treturn oper + v0\n\t\t} else {\n\t\t\treturn oper0 + v0 + ' to ' + oper1 + v1\n\t\t}\n\t}\n}\n\n// get bin range equation from bin label and bin properties\nexport function get_bin_range_equation(bin, binconfig) {\n\tconst x = '<span style=\"font-family:Times;font-style:italic;\">x</span>'\n\tlet range_eq\n\t// should always use computed (not user-customized) bin label to determine bin range text\n\tconst copy = structuredClone(bin)\n\tcopy.label = '' // mutate only the copy, and not the original bin argument\n\tconst bin_label = get_bin_label(copy, binconfig, undefined)\n\tif (bin.startunbounded || bin.stopunbounded) {\n\t\t// first or last bins, e.g. x \u2264 14 and x > 16\n\t\trange_eq = x + ' ' + bin_label\n\t} else if (bin.startinclusive) {\n\t\t// bins with startinclusive, e.g. 14 \u2264 x < 16\n\t\trange_eq = bin_label.replace('to <', '\u2264 ' + x + ' <')\n\t} else if (bin.stopinclusive) {\n\t\t// bins with stopinclusive, e.g. 14 < x \u2264 16\n\t\trange_eq = bin_label.replace('>', '').replace('to', '< ' + x + ' \u2264')\n\t}\n\treturn range_eq\n}\n\nexport function target_percentiles(binconfig) {\n\tconst percentiles: any[] = []\n\tconst f = binconfig.first_bin\n\tif (f && isStrictNumeric(f.start_percentile)) percentiles.push(f.start_percentile)\n\tif (f && isStrictNumeric(f.stop_percentile)) percentiles.push(f.stop_percentile)\n\tconst l = binconfig.last_bin\n\tif (l && isStrictNumeric(l.start_percentile)) percentiles.push(l.start_percentile)\n\tif (l && isStrictNumeric(l.stop_percentile)) percentiles.push(l.stop_percentile)\n\treturn percentiles\n}\n"],
+  "mappings": 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+  "names": ["k2c"]
+}

package/dist/chunk-SDACELDR.js

@@ -0,0 +1,14 @@
+// src/block.lazyload.js
+var Block;
+async function blocklazyload(arg) {
+  if (!Block) {
+    const b = await import("./block-5V2FCT7Q.js");
+    Block = b.Block;
+  }
+  return new Block(arg);
+}
+
+export {
+  blocklazyload
+};
+//# sourceMappingURL=chunk-SDACELDR.js.map