@sjcrh/proteinpaint-client 2.207.0 → 2.207.1

package/dist/chunk-JV5AGMUC.js

@@ -1,123 +0,0 @@
-import {
-  pickCollectionFraction,
-  renderTable
-} from "./chunk-NQDF3U2C.js";
-
-// termdb/handlers/termCollection.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    opts.holder.style("display", "");
-    const termlst = opts.details.termlst ?? [];
-    const memberType = opts.details.memberType || opts.details.type;
-    if (opts.termCollectionSelectionMode === "fraction" && memberType === "numeric") {
-      pickCollectionFraction({
-        holder: opts.holder,
-        term: makeTerm(opts.details, termlst, opts.usecase),
-        callback: (tw) => opts.callback(tw)
-      });
-      return;
-    }
-    const tableDiv = opts.holder.append("div");
-    renderTable({
-      columns: [{ label: "VARIABLES" }],
-      rows: termlst.map((t) => {
-        return [{ value: t.name }];
-      }),
-      div: tableDiv,
-      maxWidth: "30vw",
-      maxHeight: "40vh",
-      // the button is disabled while the selection cannot be submitted
-      noButtonCallback: () => updateSelectBtn(),
-      striped: false,
-      showHeader: true,
-      //false,
-      selectAll: true,
-      columnButtons: void 0,
-      //Leave until table.js is typed
-      buttons: void 0
-    });
-    let categoryTable;
-    let ckSource = [];
-    if (opts.details.categoryKeys) {
-      ckSource = opts.details.categoryKeys;
-      const categoryDiv = opts.holder.append("div").style("margin-top", "15px");
-      const values = opts.details.termlst[0].values || {};
-      categoryTable = categoryDiv.append("div");
-      renderTable({
-        columns: [{ label: "CATEGORIES" }],
-        rows: ckSource.map((ck) => {
-          return [{ value: values[ck.key]?.label ?? ck.key, checked: ck.shown }];
-        }),
-        div: categoryTable,
-        maxWidth: "30vw",
-        maxHeight: "40vh",
-        noButtonCallback: () => updateSelectBtn(),
-        striped: false,
-        showHeader: true,
-        //false,
-        selectAll: true,
-        columnButtons: void 0,
-        //Leave until table.js is typed
-        buttons: void 0
-      });
-    }
-    function getRowChecks(div) {
-      const trs = div.select("table").select("tbody").node().querySelectorAll("tr");
-      return [...trs].map((tr) => tr.querySelectorAll("td")[1]?.querySelector("input")?.checked === true);
-    }
-    function getSelectedTermlst() {
-      const checked = getRowChecks(tableDiv);
-      return termlst.filter((term, i) => checked[i]);
-    }
-    function getCategoryKeys() {
-      if (!categoryTable) return void 0;
-      const checked = getRowChecks(categoryTable);
-      return ckSource.map((ck, i) => ({ key: ck.key, shown: checked[i] }));
-    }
-    function getSelectionError() {
-      if (getSelectedTermlst().length < 2) return "Select at least two variables.";
-      if (getCategoryKeys()?.every((ck) => !ck.shown)) return "Select at least one category.";
-      return void 0;
-    }
-    function updateSelectBtn() {
-      if (!selectBtn) return;
-      const error = getSelectionError();
-      selectBtn.property("disabled", Boolean(error)).attr("title", error || null);
-    }
-    const selectBtn = opts.holder.append("div").style("float", "right").style("padding", "6px 20px").append("button").attr("data-testid", "sjpp-term-collection-select").text("Select").on("click", () => {
-      opts.callback({
-        // makeTerm() extracts propsByTermId (color, etc) for the selected terms
-        ...makeTerm(opts.details, getSelectedTermlst(), opts.usecase),
-        categoryKeys: getCategoryKeys()
-      });
-    });
-    updateSelectBtn();
-  }
-};
-function makeTerm(details, termlst, usecase) {
-  const propsByTermId = {};
-  if (details.propsByTermId) {
-    for (const term of termlst) {
-      if (details.propsByTermId[term.id]) propsByTermId[term.id] = details.propsByTermId[term.id];
-    }
-  }
-  return {
-    type: "termCollection",
-    termIds: termlst.map((term) => term.id),
-    termlst,
-    name: details.name,
-    valueTransform: details.valueTransformByPlots?.[usecase?.target],
-    // memberType = ds.cohort.termdb.termCollections[].type for client code
-    memberType: details.memberType || details.type,
-    categoryKeys: details.categoryKeys,
-    isleaf: true,
-    propsByTermId
-  };
-}
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-JV5AGMUC.js.map

package/dist/chunk-KUHCBPKU.js

@@ -1,446 +0,0 @@
-import {
-  schemeCategory20
-} from "./chunk-V2OJLJSK.js";
-import {
-  isNumericTerm
-} from "./chunk-HZ3TCGBK.js";
-import {
-  dtcnv,
-  dtsnvindel
-} from "./chunk-IZUYLFOX.js";
-import {
-  category10_default
-} from "./chunk-Z2ZITHT4.js";
-import {
-  linear,
-  ordinal
-} from "./chunk-4OLM3KSB.js";
-import {
-  __export
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/matrix/matrix.legend.js
-var matrix_legend_exports = {};
-__export(matrix_legend_exports, {
-  CNVkey2order: () => CNVkey2order,
-  getLegendData: () => getLegendData,
-  getLegendItemText: () => getLegendItemText
-});
-function getLegendData(legendGroups, refs, self) {
-  const s = this.settings.matrix;
-  const legendData = [];
-  const dvt = this.config.divideBy || {};
-  const dvtId = dvt && "id" in dvt ? dvt.id : dvt.name;
-  for (const $id in legendGroups) {
-    const legend = legendGroups[$id];
-    if ($id == "Consequences") {
-      for (const f of this.config.legendValueFilter.lst) {
-        if (f.tvs.term.type !== "geneVariant") continue;
-        if (f.legendGrpName != $id) continue;
-        if (f.tvs.legendFilterType == "geneVariant_soft" && f.filteredOutCats.length == 0) {
-          continue;
-        }
-        for (const v of f.tvs.values) {
-          for (const key of v.mclasslst) {
-            const legendk = v.origin ? v.origin + key : key;
-            legend.values[legendk] = {
-              key,
-              dt: v.dt,
-              origin: v.origin,
-              label: v.label || self.mclass[key].label,
-              fill: v.color || self.mclass[key]?.color,
-              order: CNVkey2order(key),
-              crossedOut: f.tvs.legendFilterType == "geneVariant_hard" ? true : false,
-              greyedOut: f.tvs.legendFilterType == "geneVariant_soft" ? true : false
-            };
-          }
-        }
-      }
-      const keys2 = Object.keys(legend.values);
-      if (!keys2.length) continue;
-      legendData.unshift({
-        name: "Consequences",
-        order: legend.order,
-        $id: legend.$id,
-        dt: legend.dt,
-        origin: legend.origin,
-        items: keys2.map((key, i) => {
-          const item = legend.values[key];
-          const count = item.samples?.size;
-          return {
-            termid: "Consequences",
-            key: item.key,
-            text: this.getLegendItemText(item, count, {}, s),
-            color: item.fill,
-            order: i,
-            border: "1px solid #ccc",
-            count,
-            isLegendItem: true,
-            dt: item.dt,
-            crossedOut: item.crossedOut,
-            greyedOut: item.greyedOut,
-            origin: item.origin
-          };
-        })
-      });
-      legendData[0].items.sort((a, b) => a.text < b.text ? -1 : 1);
-      continue;
-    }
-    const t = $id == dvtId ? { tw: dvt } : this.termOrder.find((t2) => t2.tw.$id == $id || t2.tw.legend?.group == $id) || {
-      tw: { term: { id: $id, name: $id, type: $id === "CNV" ? "geneVariant" : "" } }
-    };
-    for (const f of this.config.legendValueFilter.lst) {
-      const name = t.tw.legend?.group || t.tw.label || t.tw.term.name;
-      if (f.legendGrpName != $id && f.legendGrpName != name && f.tvs.term.name != name) continue;
-      if (f.tvs.term.type == "geneVariant") {
-        for (const v of f.tvs.values) {
-          if (legend.dt && !legend.dt.includes(v.dt)) legend.dt.push(v.dt);
-          if (f.tvs.legendFilterType == "geneVariant_soft" && f.filteredOutCats.length == 0) {
-            continue;
-          }
-          for (const key of v.mclasslst) {
-            const legendk = v.origin ? v.origin + key : key;
-            legend.values[legendk] = {
-              key,
-              dt: v.dt,
-              origin: v.origin,
-              label: v.label || self.mclass[key]?.label || "Gain and loss",
-              fill: v.color || self.mclass[key]?.color,
-              order: CNVkey2order(key),
-              crossedOut: f.tvs.legendFilterType == "geneVariant_hard" ? true : false,
-              greyedOut: f.tvs.legendFilterType == "geneVariant_soft" ? true : false
-            };
-          }
-        }
-      } else {
-        if (isNumericTerm(f.tvs.term)) {
-          if (t.ref?.bins) {
-            for (const v of f.tvs.ranges) {
-              const termValues = t.ref.bins;
-              legend.values[v.name] = {
-                key: v.name,
-                label: termValues?.find((vl) => vl.name == v.name)?.name || v.name,
-                fill: termValues?.find((vl) => vl.name == v.name)?.color,
-                crossedOut: true
-              };
-            }
-          }
-        } else if (f.tvs.term.type == "survival") {
-          for (const v of f.tvs.values) {
-            const termValues = t.tw.term.values;
-            legend.values[v.key] = {
-              key: v.key,
-              label: termValues?.[v.key]?.label || "Exit code: " + v.key,
-              fill: v.key == 1 ? "#ff7f0e" : "#1f77b4",
-              crossedOut: true
-            };
-          }
-        } else {
-          for (const v of f.tvs.values) {
-            const termValues = t.tw.term.values;
-            legend.values[v.key] = {
-              key: v.key,
-              label: termValues?.[v.key]?.label || v.key,
-              fill: termValues?.[v.key]?.color,
-              crossedOut: true
-            };
-          }
-        }
-      }
-    }
-    const keys = Object.keys(legend.values).sort();
-    const hasScale = Object.values(legend.values).find((v) => v.scale);
-    if (hasScale) {
-      if (legend === legendGroups?.CNV) {
-        const gain = legend.values["CNV_amp"];
-        const loss = legend.values["CNV_loss"];
-        if (gain?.scale && loss?.scale) {
-          const colors = loss.scales?.legend.range;
-          const domain = loss.scales?.legend.domain;
-          const setLegendAttr = (item) => {
-            return {
-              $id,
-              domain: item.scales.legend.domain,
-              key: item.key,
-              isLegendItem: true,
-              minLabel: domain[0],
-              //item.minLoss, // item.maxLabel,
-              maxLabel: domain.slice(-1)[0],
-              //item.maxGain, // item.maxLabel,
-              scale: item.scale,
-              termid: "CNV"
-            };
-          };
-          const numericInputs = {
-            cutoffMode: s.cnvValues.cutoffMode,
-            defaultPercentile: s.cnvValues.defaultPercentile,
-            percentile: s.cnvValues.percentile,
-            callback: async (obj) => {
-              const cValues = self.config.settings.matrix.cnvValues;
-              if (obj.cutoffMode == "fixed") {
-                if (cValues.min == null) cValues.min = domain[0];
-                if (cValues.max == null) cValues.max = domain[domain.length - 1];
-                if (obj.min != cValues.min) obj.max = Math.abs(obj.min);
-                else obj.min = -obj.max;
-              }
-              self.config.settings.matrix.cnvValues = {
-                defaultPercentile: self.config.settings.matrix.cnvValues.defaultPercentile,
-                cutoffMode: obj.cutoffMode,
-                min: obj.min,
-                max: obj.max,
-                percentile: obj.percentile
-              };
-              await self.app.dispatch({
-                type: "plot_edit",
-                id: self.opts.id,
-                config: self.config
-              });
-            }
-          };
-          legend.values.CNV_gain_loss = {
-            key: $id,
-            label: "Gain and Loss",
-            dt: dtcnv,
-            order: -1,
-            domain,
-            name: "CNV gain/loss",
-            scale: linear().domain(domain).range(colors),
-            scales: loss.scales,
-            //Prevent the colors and domain recalculating below
-            minLabel: domain[0],
-            //loss.maxLabel,
-            maxLabel: domain.slice(-1)[0],
-            labels: { left: "Loss", right: "Gain" },
-            parents: [Object.assign(setLegendAttr(loss), loss), Object.assign(setLegendAttr(gain), gain)],
-            samples: /* @__PURE__ */ new Set([...gain.samples, ...loss.samples]),
-            numericInputs
-          };
-          delete legend.values[gain.key];
-          delete legend.values[loss.key];
-          keys.splice(keys.indexOf(gain.key), 1);
-          keys.splice(keys.indexOf(loss.key), 1);
-          keys.push("CNV_gain_loss");
-        }
-      }
-      const legendGrpLabelMaxChars = s.legendGrpLabelMaxChars || 26;
-      legendData.push({
-        name: $id.length < legendGrpLabelMaxChars ? $id : $id.slice(0, legendGrpLabelMaxChars) + "...",
-        //name:$id,
-        order: legend.order,
-        $id: legend.$id,
-        dt: legend.dt,
-        origin: legend.origin,
-        hasScale,
-        items: keys.map((key, i) => {
-          const item = legend.values[key];
-          const count = item.samples?.size;
-          if (item.scale) {
-            const colors = item.scales?.legend?.range || getColors(item);
-            const domain = item.scales?.legend?.domain || setColorScaleDomain(item.minLabel, item.maxLabel, item.domain, colors);
-            const opts = {
-              termid: $id,
-              key: item.key,
-              text: this.getLegendItemText(item, count, t, s),
-              width: 100,
-              scale: item.scale,
-              colors,
-              domain,
-              order: "order" in item ? item.order : i,
-              count,
-              isLegendItem: true,
-              dt: item.dt,
-              crossedOut: item.crossedOut,
-              greyedOut: item.greyedOut,
-              origin: item.origin,
-              parents: item.parents,
-              labels: item.labels
-            };
-            if (item.numericInputs) {
-              opts.numericInputs = item.numericInputs;
-            }
-            return opts;
-          } else {
-            return {
-              termid: $id,
-              key: item.key,
-              text: this.getLegendItemText(item, count, t, s),
-              color: item.fill || this.colorScaleByTermId[$id](key),
-              order: "order" in item ? item.order : i,
-              count,
-              isLegendItem: true,
-              dt: item.dt,
-              crossedOut: item.crossedOut,
-              greyedOut: item.greyedOut,
-              origin: item.origin
-            };
-          }
-        })
-      });
-    } else {
-      const grp = $id;
-      const term = t.tw.term;
-      const ref = legend.ref;
-      if (ref.bins)
-        keys.sort((a, b) => ref.bins.findIndex((bin) => bin.name === a) - ref.bins.findIndex((bin) => bin.name === b));
-      else if (ref.keyOrder) keys.sort((a, b) => ref.keyOrder.indexOf(a) - ref.keyOrder.indexOf(b));
-      if (!this.colorScaleByTermId[grp])
-        this.colorScaleByTermId[grp] = keys.length < 11 ? ordinal(category10_default) : ordinal(schemeCategory20);
-      const name = t.tw.legend?.group || t.tw.label || term.name;
-      const legendGrpLabelMaxChars = s.legendGrpLabelMaxChars || 26;
-      legendData.push({
-        name: name.length < legendGrpLabelMaxChars ? name : name.slice(0, legendGrpLabelMaxChars) + "...",
-        order: legend.order,
-        $id: legend.$id,
-        dt: legend.dt,
-        origin: legend.origin,
-        items: keys.map((key, i) => {
-          const item = legend.values[key];
-          const count = item.samples?.size;
-          return {
-            $id,
-            termid: term.id || term.name,
-            key: item.key,
-            text: this.getLegendItemText(item, count, t, s),
-            color: t.scale || item.fill || this.colorScaleByTermId[grp](key),
-            order: "order" in item ? item.order : i,
-            count,
-            isExcluded: item.isExcluded,
-            //onClickCallback: this.handleLegendItemClick,
-            isLegendItem: true,
-            dt: item.dt,
-            crossedOut: item.crossedOut,
-            greyedOut: item.greyedOut,
-            origin: item.origin
-          };
-        })
-      });
-    }
-  }
-  for (const grpFilter of self.config.legendGrpFilter.lst) {
-    if (grpFilter.dt.length == 1 && grpFilter.dt[0] == 4 && !legendData.filter((l) => l.dt)?.find((l) => l.dt.length == 1 && l.dt[0] == 4)) {
-      legendData.push({
-        name: "CNV",
-        dt: grpFilter.dt,
-        origin: grpFilter.origin,
-        crossedOut: true,
-        items: grpFilter.filteredOutCats.map((fc) => {
-          return {
-            dt: 4,
-            termid: "CNV",
-            origin: grpFilter.origin,
-            key: fc,
-            text: self.mclass[fc].label,
-            color: self.mclass[fc]?.color,
-            isLegendItem: true
-          };
-        })
-      });
-    } else if (grpFilter.dt.includes(dtsnvindel)) {
-      const controlLabels = self.settings.matrix.controlLabels;
-      const groupName = grpFilter.origin ? `${grpFilter.origin[0].toUpperCase() + grpFilter.origin.slice(1)} ${controlLabels.Mutations}` : controlLabels.Mutations;
-      if (!legendData.filter((l) => l.dt)?.find((l) => l.dt.includes(dtsnvindel) && l.origin == grpFilter.origin)) {
-        legendData.push({
-          name: groupName,
-          dt: grpFilter.dt,
-          origin: grpFilter.origin,
-          crossedOut: true,
-          items: grpFilter.filteredOutCats.map((fc) => {
-            return {
-              dt: self.mclass[fc].dt,
-              origin: grpFilter.origin,
-              termid: groupName,
-              key: fc,
-              text: self.mclass[fc].label,
-              color: self.mclass[fc]?.color,
-              isLegendItem: true
-            };
-          })
-        });
-      }
-    } else if (grpFilter.dt.length == 1 && grpFilter.dt[0] == 2 && !legendData.filter((l) => l.dt)?.find((l) => l.dt.length == 1 && l.dt[0] == 2)) {
-      legendData.push({
-        name: "Fusion RNA",
-        dt: grpFilter.dt,
-        origin: grpFilter.origin,
-        crossedOut: true,
-        items: grpFilter.filteredOutCats.map((fc) => {
-          return {
-            dt: 2,
-            origin: grpFilter.origin,
-            termid: "Fusion RNA",
-            key: fc,
-            text: self.mclass[fc].label,
-            color: self.mclass[fc]?.color,
-            isLegendItem: true
-          };
-        })
-      });
-    } else if (grpFilter.dt.length == 1 && grpFilter.dt[0] == 5 && !legendData.filter((l) => l.dt)?.find((l) => l.dt.length == 1 && l.dt[0] == 5)) {
-      legendData.push({
-        name: "Structural Variation",
-        dt: grpFilter.dt,
-        origin: grpFilter.origin,
-        crossedOut: true,
-        items: grpFilter.filteredOutCats.map((fc) => {
-          return {
-            dt: 5,
-            origin: grpFilter.origin,
-            termid: "Structural Variation",
-            key: fc,
-            text: self.mclass[fc].label,
-            color: self.mclass[fc]?.color,
-            isLegendItem: true
-          };
-        })
-      });
-    }
-  }
-  for (const itemsGrp of legendData) {
-    itemsGrp.items.sort((a, b) => {
-      const getStatusOrder = (item) => {
-        if (!item.greyedOut && !item.crossedOut) return 0;
-        if (item.greyedOut && !item.crossedOut) return 1;
-        if (item.crossedOut) return 2;
-        return 3;
-      };
-      return getStatusOrder(a) - getStatusOrder(b);
-    });
-  }
-  return legendData.sort(
-    (a, b) => a.crossedOut && b.crossedOut ? 0 : a.crossedOut ? 1 : b.crossedOut ? -1 : a.order && b.order ? a.order - b.order : a.order ? -1 : b.order ? 1 : 0
-  );
-}
-function getLegendItemText(item, count, t, s) {
-  if (item.crossedOut || item.greyedOut) {
-    return item.label;
-  }
-  let text = item.label;
-  const notes = [count];
-  if (item.isExcluded) notes.push("hidden");
-  if (t?.tw?.term?.type == "geneVariant" && s.geneVariantCountSamplesSkipMclass.includes(item.key))
-    notes.push("not counted");
-  if (!notes.length) return text;
-  return text += ` (${notes.join(", ")})`;
-}
-function setColorScaleDomain(min, max, domain, colors) {
-  if (domain[0] === min && domain[domain.length - 1] === max) return domain;
-  const step = (max - min) / (colors.length - 1);
-  return colors.map((_, i) => {
-    if (i === (colors.length - 1) / 2 && min < 0 && max > 0) return 0;
-    return min + step * i;
-  });
-}
-function getColors(item) {
-  return item.domain?.map((c) => item.scale(c)) || item.scale.range();
-}
-function CNVkey2order(key) {
-  return key == "CNV_homozygous_deletion" ? -5 : key == "CNV_amplification" ? -4 : key == "CNV_loss" ? -3 : key == "CNV_amp" ? -2 : key == "CNV_loh" ? -1 : 0;
-}
-
-export {
-  getLegendData,
-  getLegendItemText,
-  CNVkey2order,
-  matrix_legend_exports
-};
-//# sourceMappingURL=chunk-KUHCBPKU.js.map

package/dist/chunk-L32KMIC3.js

@@ -1,54 +0,0 @@
-import {
-  getColors
-} from "./chunk-IZUYLFOX.js";
-
-// termdb/handlers/junction.customTerm.ts
-var junctionCustomTermSource = "junction";
-function makeJunctionCustomTerm(junctions, eventlabel) {
-  if (!junctions.length) throw new Error("junctions[] is empty");
-  if (!eventlabel) {
-    const term = junctions[0];
-    return {
-      id: `junction:${term.id}`,
-      name: term.name,
-      source: junctionCustomTermSource,
-      tw: {
-        term,
-        q: { mode: "continuous" }
-      }
-    };
-  }
-  const termlst = [...new Map(junctions.map((term) => [term.id, term])).values()];
-  const colorScale = getColors(termlst.length);
-  const termIds = termlst.map((term) => term.id);
-  return {
-    id: `junction-event:${eventlabel}`,
-    name: eventlabel,
-    source: junctionCustomTermSource,
-    eventlabel,
-    tw: {
-      term: {
-        type: "termCollection",
-        isCustom: true,
-        memberType: "numeric",
-        name: eventlabel,
-        termIds,
-        termlst,
-        propsByTermId: Object.fromEntries(termlst.map((term) => [term.id, { color: colorScale(term.id) }])),
-        isleaf: true
-      },
-      q: {
-        mode: "continuous",
-        type: "values",
-        lst: termIds,
-        numerators: termIds
-      }
-    }
-  };
-}
-
-export {
-  junctionCustomTermSource,
-  makeJunctionCustomTerm
-};
-//# sourceMappingURL=chunk-L32KMIC3.js.map