@sjcrh/proteinpaint-client 2.203.0 → 2.203.1

package/dist/chunk-4KUGV44F.js

@@ -1,397 +0,0 @@
-import {
-  CNVkey2order
-} from "./chunk-TRWFL52W.js";
-import {
-  TermTypes,
-  colorScaleMap,
-  dtcnv,
-  dtfusionrna,
-  dtgeneexpression,
-  dtsnvindel,
-  dtsv
-} from "./chunk-4QBRVM4V.js";
-import {
-  convertUnits
-} from "./chunk-W5J3LTYS.js";
-
-// plots/matrix/matrix.cells.js
-function setNumericCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
-  const key = anno.key;
-  const values = tw.term.values || {};
-  cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : key;
-  cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || anno.color || values[anno.key]?.color || self.data.refs.byTermId?.[tw.$id]?.bins?.find((b) => anno.key == b.name)?.color;
-  cell.order = t.ref.bins ? t.ref.bins.findIndex((bin) => bin.name == key) : 0;
-  if (tw.q?.mode == "continuous") {
-    const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
-    if (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {};
-    const twSettings = twSpecificSettings[tw.$id];
-    if (!twSettings.contBarH) twSettings.contBarH = s.barh;
-    if (!("gap" in twSettings)) twSettings.contBarGap = 4;
-    const specialValue = tw.term.values?.[cell.key];
-    if (specialValue?.uncomputable) {
-      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-      cell.y = height * i;
-      cell.height = twSettings.contBarH;
-      cell.fill = "transparent";
-      const group = tw.legend?.group || tw.$id;
-      return;
-    }
-    cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.contBarColor || "#555";
-    if (s.transpose) {
-      cell.height = t.scale(cell.key);
-      cell.x = twSettings.contBarGap;
-    } else {
-      const vc = cell.term.valueConversion;
-      let renderV = vc ? cell.key * vc.scaleFactor : cell.key;
-      if (tw.q.convert2ZScore) {
-        renderV = (renderV - t.mean) / t.std;
-        cell.fill = renderV > 0 ? "#FF6666" : "#6666FF";
-        cell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`;
-      }
-      cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : tw.term.unit ? `${cell.key.toFixed(2)} ${tw.term.unit}` : cell.key.toFixed(2);
-      cell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV);
-      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-      cell.y = renderV >= 0 ? t.counts.posMaxHt + twSettings.contBarGap - cell.height : t.counts.posMaxHt + twSettings.contBarGap;
-      cell.convertedValueLabel = !vc ? "" : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-    }
-  } else {
-    cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-    cell.y = height * i;
-    const group = tw.legend?.group || tw.$id;
-    return { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } };
-  }
-}
-function setSurvivalCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
-  const key = tw.q?.mode == "continuous" ? anno.value : anno.key;
-  cell.key = key;
-  cell.label = tw.q?.mode == "continuous" ? tw.term.unit ? `${key} ${tw.term.unit}` : key : tw.term.values?.[key].label ? tw.term.values?.[key].label : "Exit code: " + key;
-  cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || (key == 1 ? "#a1a3a6" : "#a3c88b");
-  cell.order = 0;
-  if (tw.q?.mode == "continuous") {
-    const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
-    if (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {};
-    const twSettings = twSpecificSettings[tw.$id];
-    if (!twSettings.contBarH) twSettings.contBarH = s.barh;
-    if (!("gap" in twSettings)) twSettings.contBarGap = 4;
-    cell.exitCodeKey = tw.term.values?.[anno.key].label || "Exit code: " + anno.key;
-    cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[anno.key]?.color || (anno.key == 1 ? "#a1a3a6" : "#a3c88b");
-    if (s.transpose) {
-      cell.height = t.scale(cell.key);
-      cell.x = twSettings.contBarGap;
-    } else {
-      const vc = cell.term.valueConversion;
-      let renderV = vc ? cell.key * vc.scaleFactor : cell.key;
-      if (tw.q.convert2ZScore) {
-        renderV = (renderV - t.mean) / t.std;
-        cell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`;
-      }
-      cell.label = tw.term.unit ? `${cell.key.toFixed(2)} ${tw.term.unit}` : cell.key.toFixed(2);
-      cell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV);
-      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-      cell.y = renderV >= 0 ? t.counts.posMaxHt + twSettings.contBarGap - cell.height : t.counts.posMaxHt + twSettings.contBarGap;
-      cell.convertedValueLabel = !vc ? "" : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-    }
-  } else {
-    const vc = cell.term.valueConversion;
-    cell.timeToEventKey = vc ? convertUnits(anno.value, vc.fromUnit, vc.toUnit, vc.scaleFactor) : anno.value.toFixed(2);
-    cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-    cell.y = height * i;
-    const group = tw.legend?.group || tw.$id;
-    return { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } };
-  }
-}
-function setCategoricalCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
-  const values = tw.term.values || {};
-  const key = anno.key;
-  cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : key;
-  cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || anno.color || values[anno.key]?.color;
-  cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-  cell.y = height * i;
-  const group = tw.legend?.group || tw.$id;
-  return { ref: t.ref, group, value: anno.key, entry: { key, label: cell.label, fill: cell.fill } };
-}
-function setMultivalueCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
-  const key = value?.key ?? anno.key;
-  const values = tw.term.values || {};
-  cell.key = key;
-  cell.label = values[key]?.label || key;
-  cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || values[key]?.color;
-  cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-  cell.y = height * i;
-  const group = tw.legend?.group || tw.$id;
-  return { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } };
-}
-function setGeneVariantCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
-  if (tw.q?.type == "predefined-groupset" || tw.q?.type == "custom-groupset") {
-    cell.label = value;
-    const groupset = tw.q.type == "custom-groupset" ? tw.q.customset : tw.term.groupsetting.lst[tw.q.predefined_groupset_idx];
-    if (!groupset) throw "groupset not found";
-    const group = groupset.groups.find((group2) => group2.name == value);
-    if (!group) throw "group not found";
-    cell.fill = group.color;
-    cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-    cell.y = height * i;
-    return {
-      ref: t.ref,
-      group: tw.legend?.group || tw.$id,
-      value,
-      entry: { key: anno.key, label: cell.label, fill: cell.fill }
-    };
-  } else {
-    const values = anno.renderedValues || anno.filteredValues || anno.values || [anno.value];
-    const colorFromq = tw.q?.values && tw.q?.values[value.class]?.color;
-    cell.label = value.label || self.mclass[value.class].label;
-    cell.fill = self.getValueColor?.(value.value) || colorFromq || value.color || self.mclass[value.class]?.color;
-    cell.class = value.class;
-    cell.value = value;
-    const colw = self.dimensions.colw;
-    if (s.cellEncoding == "") {
-      cell.height = s.rowh / values.length;
-      cell.width = colw;
-      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-      cell.y = height * i;
-    } else if (value.dt == dtsnvindel || value.dt == dtfusionrna || value.dt == dtsv) {
-      if (s.cellEncoding == "single") {
-        cell.height = s.rowh;
-        cell.width = colw;
-        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-        cell.y = 0;
-      } else {
-        const divisor = 3;
-        cell.height = s.rowh / divisor;
-        cell.width = colw;
-        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-        cell.y = height * 0.33333;
-        if (s.oncoPrintSNVindelCellBorder) {
-          cell.border = true;
-        }
-      }
-    } else if (value.dt == dtcnv || value.dt == dtgeneexpression) {
-      cell.height = s.rowh;
-      cell.width = colw;
-      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-      cell.y = 0;
-    } else {
-      throw `cannot set cell props for dt='${value.dt}'`;
-    }
-    if (value.class == "Blank" || value.class == "WT") {
-      cell.label = `${self.dt2label[value.dt]} ${cell.label}`;
-    }
-    const byDt = self.state.termdbConfig.assayAvailability?.byDt;
-    const order = CNVkey2order(value.class);
-    if (value.dt == dtcnv) {
-      if (t.scales && value.class.startsWith("CNV_")) {
-        const {
-          /*maxLoss,*/
-          maxGain,
-          minLoss,
-          /*minGain,*/
-          absMax
-        } = t.scales;
-        value.scaledValue = value.value < 0 ? value.value / -absMax : value.value / absMax;
-        cell.fill = value.value < 0 ? t.scales.loss(value.scaledValue) : t.scales.gain(value.scaledValue);
-        return {
-          ref: t.ref,
-          group: "CNV",
-          value: value.class,
-          order: -1,
-          entry: {
-            key: value.class,
-            label: cell.label,
-            scale: value.class == "CNV_loss" ? t.scales.loss : t.scales.gain,
-            domain: t.domain ? t.domain : value.class == "CNV_loss" ? [0, -minLoss] : [0, maxGain],
-            colors: t.range,
-            scales: value.dt == 4 && t.scales,
-            minLabel: 0,
-            maxLabel: value.class == "CNV_loss" ? minLoss : maxGain,
-            order,
-            dt: value.dt,
-            origin: value.origin
-          }
-        };
-      } else {
-        const group = "CNV";
-        return {
-          ref: t.ref,
-          group,
-          value: value.class,
-          order: -1,
-          entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
-        };
-      }
-    } else if (value.dt == dtfusionrna && byDt?.[dtfusionrna]) {
-      const group = "Fusion RNA";
-      return {
-        ref: t.ref,
-        group,
-        value: value.class,
-        order: -1,
-        entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
-      };
-    } else if (value.dt == dtsv && byDt?.[dtsv]) {
-      const group = "Structural Variation";
-      return {
-        ref: t.ref,
-        group,
-        value: value.class,
-        order: -1,
-        entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
-      };
-    } else if (value.dt == dtgeneexpression) {
-      return {
-        ref: t.ref,
-        group: self.config.settings.hierCluster?.termGroupName || "Gene Expression",
-        value: value.class,
-        order: -1,
-        entry: {
-          key: value.class,
-          label: "",
-          scale: self.geneExpValues.scale,
-          domain: [0, 0.5, 1],
-          minLabel: self.geneExpValues.min,
-          maxLabel: self.geneExpValues.max,
-          order,
-          dt: value.dt,
-          origin: value.origin
-        }
-      };
-    } else {
-      const controlLabels = self.settings.matrix.controlLabels;
-      const group = tw.legend?.group || (value.origin ? `${value.origin[0].toUpperCase() + value.origin.slice(1)} ${controlLabels.Mutations}` : controlLabels.Mutations);
-      return {
-        ref: t.ref,
-        group,
-        value: value.class,
-        order: -2,
-        entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
-      };
-    }
-  }
-}
-function setHierClusterCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
-  const values = anno.renderedValues || anno.filteredValues || anno.values || [anno.value];
-  cell.label = value.value;
-  cell.fill = self.getValueColor?.(value.value);
-  cell.value = value;
-  const colw = self.dimensions.colw;
-  cell.height = s.clusterRowh;
-  cell.width = colw;
-  cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-  cell.y = height * i;
-  const hierCluster = self.config.settings.hierCluster;
-  let groupName;
-  if (hierCluster?.termGroupName) {
-    groupName = hierCluster.termGroupName;
-  } else if (tw.term.type == "geneExpression") {
-    groupName = "Gene Expression";
-    const unit = self.app.vocabApi.termdbConfig.queries?.geneExpression?.unit;
-    if (hierCluster?.zScoreTransformation) groupName += " (Z-score)";
-    else if (unit) groupName += ` (${unit})`;
-  } else if (tw.term.type == "metaboliteIntensity") {
-    groupName = "Intensity";
-  } else if (tw.term.type == "proteomeAbundance") {
-    groupName = "Protein Abundance";
-  } else {
-    groupName = "Heatmap color scale";
-  }
-  return {
-    ref: t.ref,
-    group: groupName,
-    order: -1,
-    entry: {
-      label: "",
-      scale: self.hierClusterValues.scale,
-      domain: colorScaleMap[self.settings.hierCluster.colorScale].domain,
-      minLabel: self.hierClusterValues.min,
-      maxLabel: self.hierClusterValues.max,
-      order: 0,
-      dt: value.dt
-    }
-  };
-}
-function getEmptyCell(cellTemplate, s, d) {
-  const cell = Object.assign({}, cellTemplate);
-  cell.fill = s.cellbg;
-  cell.height = s.rowh;
-  cell.width = d.colw;
-  cell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace;
-  cell.y = 0;
-  return cell;
-}
-var setCellProps = {
-  // some of these have been replaced by addOns{setCellProps} in matrix.xtw.ts,
-  // but leaving here for now since non-classed tw's may still use these
-  categorical: setCategoricalCellProps,
-  condition: setCategoricalCellProps,
-  multivalue: setMultivalueCellProps,
-  integer: setNumericCellProps,
-  float: setNumericCellProps,
-  survival: setSurvivalCellProps,
-  geneVariant: setGeneVariantCellProps,
-  hierCluster: setHierClusterCellProps,
-  [TermTypes.GENE_EXPRESSION]: setNumericCellProps,
-  [TermTypes.METABOLITE_INTENSITY]: setNumericCellProps,
-  [TermTypes.PROTEOME_ABUNDANCE]: setNumericCellProps
-  //termCollection: setTermCollectionCellProps
-};
-var maySetEmptyCell = {
-  geneVariant: setVariantEmptyCell,
-  integer: setNumericEmptyCell,
-  float: setNumericEmptyCell,
-  categorical: setDefaultEmptyCell,
-  condition: setDefaultEmptyCell,
-  multivalue: setDefaultEmptyCell,
-  survival: setNumericEmptyCell,
-  [TermTypes.GENE_EXPRESSION]: setNumericEmptyCell,
-  [TermTypes.METABOLITE_INTENSITY]: setNumericEmptyCell,
-  [TermTypes.PROTEOME_ABUNDANCE]: setNumericEmptyCell
-};
-function setVariantEmptyCell(siblingCells, cellTemplate, s, d) {
-  if (siblingCells.find((c) => c.value.dt == dtcnv)) return;
-  const cell = Object.assign({}, cellTemplate);
-  cell.fill = s.cellbg;
-  cell.height = s.rowh;
-  cell.width = d.colw;
-  cell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace;
-  cell.y = 0;
-  return cell;
-}
-function setNumericEmptyCell(siblingCells, cellTemplate, s, d, self) {
-  const q = cellTemplate.tw.q;
-  if (q.mode != "continuous") {
-    if (siblingCells.length) return;
-    setDefaultEmptyCell(siblingCells, cellTemplate, s, d);
-  } else {
-    if (q?.mode != "continuous") return;
-    const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
-    const twSettings = twSpecificSettings[cellTemplate.$id];
-    const h = twSettings ? twSettings.contBarH + 2 * twSettings.contBarGap : s.rowh;
-    if (cellTemplate.height >= h) return;
-    const cell = Object.assign({}, cellTemplate);
-    cell.fill = s.cellbg;
-    cell.height = h || s.rowh;
-    cell.width = d.colw;
-    cell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace;
-    cell.y = 0;
-    return cell;
-  }
-}
-function setDefaultEmptyCell(siblingCells, cellTemplate, s, d) {
-  if (siblingCells.length) return;
-  const cell = Object.assign({}, cellTemplate);
-  cell.fill = s.cellbg;
-  cell.height = s.rowh;
-  cell.width = d.colw;
-  cell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace;
-  cell.y = 0;
-  return cell;
-}
-
-export {
-  setGeneVariantCellProps,
-  setHierClusterCellProps,
-  getEmptyCell,
-  setCellProps,
-  maySetEmptyCell
-};
-//# sourceMappingURL=chunk-4KUGV44F.js.map

package/dist/chunk-4WF3XDQP.js

@@ -1,220 +0,0 @@
-// ../shared/utils/dist/src/termCollection.js
-function validateTermCollectionTerm(term) {
-  if (!Array.isArray(term?.termlst) || !term.termlst.length)
-    throw new Error("termCollection requires nonempty term.termlst[]");
-  const memberIds = /* @__PURE__ */ new Set();
-  const types = /* @__PURE__ */ new Set();
-  for (const t of term.termlst) {
-    if (typeof t.id != "string" || !t.id) throw new Error("member term id not non-empty string");
-    if (typeof t.type != "string" || !t.type) throw new Error("member term type not non-empty string");
-    if (memberIds.has(t.id)) throw new Error(`duplicate member term id '${t.id}'`);
-    memberIds.add(t.id);
-    types.add(t.type == "integer" || t.type == "float" ? "numDict" : t.type);
-  }
-  if (types.size > 1) throw new Error("termCollection.termlst[] not allowed to mix multiple term types");
-  return memberIds;
-}
-function validateFractionMembers(numerators, denominators, memberIds) {
-  if (!Array.isArray(denominators) || !denominators.length) throw new Error("fraction requires nonempty denominators[]");
-  if (!Array.isArray(numerators) || !numerators.length) throw new Error("fraction requires nonempty numerators[]");
-  if (new Set(denominators).size !== denominators.length) throw new Error("fraction denominators[] contains duplicates");
-  if (new Set(numerators).size !== numerators.length) throw new Error("fraction numerators[] contains duplicates");
-  for (const id of denominators) {
-    if (typeof id != "string" || !id) throw new Error("fraction denominator id not non-empty string");
-    if (!memberIds.has(id)) throw new Error(`fraction denominator '${id}' is not a collection member`);
-  }
-  for (const id of numerators) {
-    if (typeof id != "string" || !id) throw new Error("fraction numerator id not non-empty string");
-    if (!denominators.includes(id)) throw new Error(`fraction numerator '${id}' is not included in denominators[]`);
-  }
-}
-var FRACTION_TW_TYPE = "TermCollectionTWFraction";
-function isFractionTw(tw) {
-  return tw?.type === FRACTION_TW_TYPE && tw?.term?.type === "termCollection";
-}
-function getFractionTvsTerm(tw) {
-  if (!isFractionTw(tw)) throw new Error("not a fraction termCollection tw");
-  const term = structuredClone(tw.term);
-  const memberIds = term.termlst?.length ? validateTermCollectionTerm(term) : new Set(term.termIds || []);
-  const denominators = tw.q?.denominators?.length ? [...tw.q.denominators] : [...memberIds];
-  const numerators = tw.q?.numerators?.length ? [...tw.q.numerators] : [...denominators];
-  validateFractionMembers(numerators, denominators, memberIds);
-  term.numerators = numerators;
-  term.denominators = denominators;
-  return term;
-}
-function validateTermCollectionFraction(q, term) {
-  const memberIds = validateTermCollectionTerm(term);
-  validateFractionMembers(q?.numerators, q?.denominators, memberIds);
-  if (q.mode === "discrete" && q.type !== "regular-bin" && q.type !== "custom-bin")
-    throw new Error("discrete fraction termCollection requires regular-bin or custom-bin q.type");
-}
-
-// ../shared/utils/dist/src/filter.js
-function getFilteredSamples(sampleAnno, filter) {
-  setDatasetAnnotations(filter);
-  const samples = /* @__PURE__ */ new Set();
-  for (const anno of sampleAnno) {
-    if (samples.has(anno.sample)) continue;
-    const data = anno.s || anno.data;
-    if (data && sample_match_termvaluesetting(data, filter)) {
-      samples.add(anno.sample);
-    }
-  }
-  return samples;
-}
-function sample_match_termvaluesetting(row, filter, _term = null, sample = null) {
-  const lst = filter.type == "tvslst" ? filter.lst : [filter];
-  let numberofmatchedterms = 0;
-  for (const item of lst) {
-    if ("type" in item && item.type == "tvslst") {
-      if (sample_match_termvaluesetting(row, item, _term, sample)) {
-        numberofmatchedterms++;
-      }
-    } else {
-      const itemCopy = JSON.parse(JSON.stringify(item));
-      const t = itemCopy.tvs;
-      if (_term && t.term) {
-        if (!(_term.name == t.term.name && _term.type == t.term.type)) {
-          numberofmatchedterms++;
-          continue;
-        }
-      }
-      let samplevalue;
-      if (_term && !t.term) {
-        if (t.term$type && t.term$type !== _term.type) {
-          numberofmatchedterms++;
-          continue;
-        }
-        t.term = _term;
-        samplevalue = typeof row === "object" && t.term.id in row ? row[t.term.id] : row;
-      } else if (sample && t.term.$id) {
-        samplevalue = sample[t.term.$id].value;
-      } else {
-        samplevalue = t.term.id in row ? row[t.term.id] : row;
-      }
-      setDatasetAnnotations(itemCopy);
-      let thistermmatch;
-      if (t.term.type == "categorical") {
-        if (samplevalue === void 0) continue;
-        thistermmatch = t.valueset.has(samplevalue);
-      } else if (t.term.type == "integer" || t.term.type == "float") {
-        if (samplevalue === void 0) continue;
-        for (const range of t.ranges) {
-          if ("value" in range) {
-            thistermmatch = samplevalue === range.value;
-            if (thistermmatch) break;
-          } else if (samplevalue == range.name) {
-            thistermmatch = true;
-            break;
-          } else {
-            if (t.term.values) {
-              const v = t.term.values[samplevalue.toString()];
-              if (v && v.uncomputable) {
-                continue;
-              }
-            }
-            let left, right;
-            if (range.startunbounded) {
-              left = true;
-            } else if ("start" in range) {
-              if (range.startinclusive) {
-                left = samplevalue >= range.start;
-              } else {
-                left = samplevalue > range.start;
-              }
-            }
-            if (range.stopunbounded) {
-              right = true;
-            } else if ("stop" in range) {
-              if (range.stopinclusive) {
-                right = samplevalue <= range.stop;
-              } else {
-                right = samplevalue < range.stop;
-              }
-            }
-            thistermmatch = left && right;
-          }
-          if (thistermmatch) break;
-        }
-      } else if (t.term.type == "condition") {
-        const key = getPrecomputedKey(t);
-        const anno = samplevalue && samplevalue[key];
-        if (anno) {
-          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
-        }
-      } else if (t.term.type == "geneVariant") {
-        const svalues = samplevalue.values || [samplevalue];
-        for (const sv of svalues) {
-          thistermmatch = t.values.find(
-            (v) => v.dt == sv.dt && (!v.origin || sv.origin == v.origin) && (!v.mclasslst || v.mclasslst.includes(sv.class))
-          ) && true;
-          if (thistermmatch) break;
-        }
-      } else {
-        throw "unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]";
-      }
-      if (t.isnot) {
-        thistermmatch = !thistermmatch;
-      }
-      if (thistermmatch) numberofmatchedterms++;
-    }
-    if (filter.join == "or") {
-      if (numberofmatchedterms && filter.in) return true;
-      if (!numberofmatchedterms && !filter.in) return true;
-    }
-  }
-  if (!("in" in filter)) filter.in = true;
-  return filter.in == (numberofmatchedterms == lst.length);
-}
-function setDatasetAnnotations(item, ds = null) {
-  if (item.type == "tvslst") {
-    for (const subitem of item.lst) {
-      setDatasetAnnotations(subitem, ds);
-    }
-  } else {
-    if (ds && typeof ds.setAnnoByTermId == "function") {
-      ds.setAnnoByTermId(item.tvs.term.id);
-    }
-    if (item.tvs.term.type == "categorical") {
-      const tvsAny = item.tvs;
-      tvsAny.valueset = new Set(tvsAny.values.map((i) => i.key));
-    }
-  }
-}
-function getPrecomputedKey(q) {
-  const precomputedKey = q.bar_by_children && q.value_by_max_grade ? "childrenAtMaxGrade" : q.bar_by_children && q.value_by_most_recent ? "childrenAtMostRecent" : q.bar_by_children && q.value_by_computable_grade ? "children" : q.bar_by_grade && q.value_by_max_grade ? "maxGrade" : q.bar_by_grade && q.value_by_most_recent ? "mostRecentGrades" : q.bar_by_grade && q.value_by_computable_grade ? "computableGrades" : "";
-  if (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`;
-  return precomputedKey;
-}
-function getWrappedTvslst(lst = [], join = "", $id = null) {
-  const filter = {
-    type: "tvslst",
-    in: true,
-    join,
-    lst
-  };
-  if ($id !== null) filter.$id = $id;
-  return filter;
-}
-function getTvsDenominators(term) {
-  if (Array.isArray(term?.denominators) && term.denominators.length) return term.denominators;
-  return (term?.termlst || []).map((t) => t.id);
-}
-function validateTermCollectionTvs(term) {
-  const memberIds = validateTermCollectionTerm(term);
-  if (!term.numerators) return;
-  validateFractionMembers(term.numerators, getTvsDenominators(term), memberIds);
-}
-
-export {
-  isFractionTw,
-  getFractionTvsTerm,
-  validateTermCollectionFraction,
-  getFilteredSamples,
-  sample_match_termvaluesetting,
-  getWrappedTvslst,
-  getTvsDenominators,
-  validateTermCollectionTvs
-};
-//# sourceMappingURL=chunk-4WF3XDQP.js.map

package/dist/chunk-4WF3XDQP.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/termCollection.ts", "../../shared/utils/src/filter.ts"],
-  "sourcesContent": ["import type { TermCollectionQFraction } from '#types'\n\ntype CollectionMemberLike = {\n\tid?: string\n\tname?: string\n\ttype?: string\n}\n\nexport type CollectionTermLike = {\n\ttermlst: CollectionMemberLike[]\n\t/** numerator/denominator member ids of a filter tvs, mirroring q.numerators[]/q.denominators[]\n\tof a fraction tw. only used by validateTermCollectionTvs() */\n\tnumerators?: string[]\n\tdenominators?: string[]\n}\n\n/** Validate the term obj of a termCollection, shared by the fraction tw and the filter tvs.\nReturns the set of member term ids, for validating id arrays e.g. numerators. */\nexport function validateTermCollectionTerm(term: CollectionTermLike): Set<string> {\n\tif (!Array.isArray(term?.termlst) || !term.termlst.length)\n\t\tthrow new Error('termCollection requires nonempty term.termlst[]')\n\tconst memberIds: Set<string> = new Set()\n\tconst types: Set<string> = new Set() // term types of member terms\n\tfor (const t of term.termlst) {\n\t\tif (typeof t.id != 'string' || !t.id) throw new Error('member term id not non-empty string') // id required for validating id arrays e.g. numerators\n\t\tif (typeof t.type != 'string' || !t.type) throw new Error('member term type not non-empty string')\n\t\tif (memberIds.has(t.id)) throw new Error(`duplicate member term id '${t.id}'`)\n\t\tmemberIds.add(t.id)\n\n\t\t// allow integer/float to be mixed in one collection\n\t\ttypes.add(t.type == 'integer' || t.type == 'float' ? 'numDict' : t.type)\n\t}\n\tif (types.size > 1) throw new Error('termCollection.termlst[] not allowed to mix multiple term types')\n\treturn memberIds\n}\n\n/** Validate the numerator/denominator member selection of a fraction, shared by the q{} of a\nfraction tw and the term of a filter tvs. Both lists are member term ids of the collection.\nmemberIds is returned by validateTermCollectionTerm() */\nexport function validateFractionMembers(numerators: string[], denominators: string[], memberIds: Set<string>): void {\n\tif (!Array.isArray(denominators) || !denominators.length) throw new Error('fraction requires nonempty denominators[]')\n\tif (!Array.isArray(numerators) || !numerators.length) throw new Error('fraction requires nonempty numerators[]')\n\tif (new Set(denominators).size !== denominators.length) throw new Error('fraction denominators[] contains duplicates')\n\tif (new Set(numerators).size !== numerators.length) throw new Error('fraction numerators[] contains duplicates')\n\tfor (const id of denominators) {\n\t\tif (typeof id != 'string' || !id) throw new Error('fraction denominator id not non-empty string')\n\t\tif (!memberIds.has(id)) throw new Error(`fraction denominator '${id}' is not a collection member`)\n\t}\n\tfor (const id of numerators) {\n\t\tif (typeof id != 'string' || !id) throw new Error('fraction numerator id not non-empty string')\n\t\t// no need to test against memberIds: denominators[] is already a subset of it\n\t\tif (!denominators.includes(id)) throw new Error(`fraction numerator '${id}' is not included in denominators[]`)\n\t}\n}\n\n/** tw.type of a termCollection that resolves to one numeric value per sample, the fraction\nof the numerator members over the denominator ones */\nexport const FRACTION_TW_TYPE = 'TermCollectionTWFraction'\n\n/** True when a tw is a fraction termCollection */\nexport function isFractionTw(tw: any): boolean {\n\treturn tw?.type === FRACTION_TW_TYPE && tw?.term?.type === 'termCollection'\n}\n\n/** Build the tvs.term for filtering on a fraction termCollection, e.g. from a clicked bar\nor a brushed violin. The member selection of a tw lives in q{}, but a tvs is standalone:\nthe server filter and the filter ui both read numerators[]/denominators[] from tvs.term.\nReturns a copy, so that editing the filter later does not mutate the plot term.\n@param tw a filled fraction termCollection tw\n@throws Error if the tw or its member selection is invalid */\nexport function getFractionTvsTerm(tw: any): CollectionTermLike {\n\tif (!isFractionTw(tw)) throw new Error('not a fraction termCollection tw')\n\tconst term = structuredClone(tw.term)\n\t// a min copy tw may carry termIds[] instead of the full termlst[]\n\tconst memberIds = term.termlst?.length ? validateTermCollectionTerm(term) : new Set<string>(term.termIds || [])\n\tconst denominators = tw.q?.denominators?.length ? [...tw.q.denominators] : [...memberIds]\n\tconst numerators = tw.q?.numerators?.length ? [...tw.q.numerators] : [...denominators]\n\tvalidateFractionMembers(numerators, denominators, memberIds)\n\tterm.numerators = numerators\n\tterm.denominators = denominators\n\treturn term\n}\n\n/** Validate the member selection and binning discriminator for a fraction term collection. */\nexport function validateTermCollectionFraction(q: TermCollectionQFraction, term: CollectionTermLike): void {\n\tconst memberIds = validateTermCollectionTerm(term)\n\tvalidateFractionMembers(q?.numerators, q?.denominators, memberIds)\n\tif (q.mode === 'discrete' && q.type !== 'regular-bin' && q.type !== 'custom-bin')\n\t\tthrow new Error('discrete fraction termCollection requires regular-bin or custom-bin q.type')\n}\n", "import type { Filter, Tvs } from '#types'\nimport { validateTermCollectionTerm, validateFractionMembers, type CollectionTermLike } from './termCollection.js'\n\n/**\n * Sample annotation structure\n */\nexport interface SampleAnnotation {\n\tsample: string | number\n\ts?: Record<string, any>\n\tdata?: Record<string, any>\n}\n\n/**\n * Dataset with annotation functionality\n */\nexport interface Dataset {\n\tsetAnnoByTermId?: (termId: string) => void\n}\n\n/**\n * Filters an array of sample annotations and returns a Set of matching sample names\n * @param sampleAnno Array of sample annotations\n * @param filter Nested filter structure as used in the termdbapp\n * @returns Set of sample names that match the filter\n */\nexport function getFilteredSamples(sampleAnno: SampleAnnotation[], filter: Filter): Set<string | number> {\n\tsetDatasetAnnotations(filter)\n\n\tconst samples = new Set<string | number>()\n\tfor (const anno of sampleAnno) {\n\t\tif (samples.has(anno.sample)) continue\n\t\tconst data = anno.s || anno.data\n\t\tif (data && sample_match_termvaluesetting(data, filter)) {\n\t\t\tsamples.add(anno.sample)\n\t\t}\n\t}\n\treturn samples\n}\n\n/**\n * Given a value from a sample's annotation of a term, return true if a value matches the filter\n * @param row Sample annotation data\n * @param filter Filter structure or single tvs item\n * @param _term Optional term to filter by\n * @param sample Optional sample data\n * @returns True if the sample matches the filter\n */\nexport function sample_match_termvaluesetting(\n\trow: any,\n\tfilter: Filter,\n\t_term: any = null,\n\tsample: any = null\n): boolean {\n\tconst lst = filter.type == 'tvslst' ? filter.lst : [filter]\n\tlet numberofmatchedterms = 0\n\n\t/* for AND, require all terms to match */\n\tfor (const item of lst) {\n\t\tif ('type' in item && item.type == 'tvslst') {\n\t\t\tif (sample_match_termvaluesetting(row, item, _term, sample)) {\n\t\t\t\tnumberofmatchedterms++\n\t\t\t}\n\t\t} else {\n\t\t\tconst itemCopy = JSON.parse(JSON.stringify(item))\n\t\t\tconst t = itemCopy.tvs\n\n\t\t\tif (_term && t.term) {\n\t\t\t\tif (!(_term.name == t.term.name && _term.type == t.term.type)) {\n\t\t\t\t\t// for an filter from \"this.config.legendValueFilter\", if the filter is not for the tw\n\t\t\t\t\t// (not the same type and name), ignore the filter.\n\t\t\t\t\tnumberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tlet samplevalue\n\t\t\tif (_term && !t.term) {\n\t\t\t\tif (t.term$type && t.term$type !== _term.type) {\n\t\t\t\t\t//when the filter is not for the term being tested, ignore the filter\n\t\t\t\t\tnumberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tt.term = _term\n\t\t\t\tsamplevalue = typeof row === 'object' && t.term.id in row ? row[t.term.id] : row\n\t\t\t} else if (sample && t.term.$id) {\n\t\t\t\tsamplevalue = sample[t.term.$id].value\n\t\t\t} else {\n\t\t\t\tsamplevalue = t.term.id in row ? row[t.term.id] : row\n\t\t\t}\n\t\t\tsetDatasetAnnotations(itemCopy)\n\t\t\tlet thistermmatch\n\n\t\t\tif (t.term.type == 'categorical') {\n\t\t\t\tif (samplevalue === undefined) continue // this sample has no anno for this term, do not count\n\t\t\t\tthistermmatch = t.valueset.has(samplevalue)\n\t\t\t} else if (t.term.type == 'integer' || t.term.type == 'float') {\n\t\t\t\tif (samplevalue === undefined) continue // this sample has no anno for this term, do not count\n\t\t\t\tfor (const range of t.ranges) {\n\t\t\t\t\tif ('value' in range) {\n\t\t\t\t\t\tthistermmatch = samplevalue === range.value\n\t\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t\t} else if (samplevalue == range.name) {\n\t\t\t\t\t\tthistermmatch = true\n\t\t\t\t\t\tbreak\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// actual range\n\t\t\t\t\t\tif (t.term.values) {\n\t\t\t\t\t\t\tconst v = t.term.values[samplevalue.toString()]\n\t\t\t\t\t\t\tif (v && v.uncomputable) {\n\t\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tlet left, right\n\t\t\t\t\t\tif (range.startunbounded) {\n\t\t\t\t\t\t\tleft = true\n\t\t\t\t\t\t} else if ('start' in range) {\n\t\t\t\t\t\t\tif (range.startinclusive) {\n\t\t\t\t\t\t\t\tleft = samplevalue >= range.start\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tleft = samplevalue > range.start\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (range.stopunbounded) {\n\t\t\t\t\t\t\tright = true\n\t\t\t\t\t\t} else if ('stop' in range) {\n\t\t\t\t\t\t\tif (range.stopinclusive) {\n\t\t\t\t\t\t\t\tright = samplevalue <= range.stop\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tright = samplevalue < range.stop\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthistermmatch = left && right\n\t\t\t\t\t}\n\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t}\n\t\t\t} else if (t.term.type == 'condition') {\n\t\t\t\tconst key = getPrecomputedKey(t)\n\t\t\t\tconst anno = samplevalue && samplevalue[key]\n\t\t\t\tif (anno) {\n\t\t\t\t\tthistermmatch = Array.isArray(anno)\n\t\t\t\t\t\t? t.values.find((d: any) => anno.includes(d.key))\n\t\t\t\t\t\t: t.values.find((d: any) => d.key == anno)\n\t\t\t\t}\n\t\t\t} else if (t.term.type == 'geneVariant') {\n\t\t\t\t/*\n\t\t\t\tsamplevalue.values here can be an array or only one of the entries \n\t\t\t\t[\n\t\t\t\t\t{ dt: 1, class: 'WT', _SAMPLEID_: 21, origin: 'germline' },\n\t\t\t\t\t{ dt: 1, class: 'WT', _SAMPLEID_: 21, origin: 'somatic' },\n\t\t\t\t\t{ dt: 2, class: 'Blank', _SAMPLEID_: 21 },\n\t\t\t\t\t{ dt: 4, class: 'WT', _SAMPLEID_: 21 }\n\t\t\t\t]\n\t\t\t\t*/\n\t\t\t\t/* tvs.values is an array that stores classes (for each available dt) that have/haven't been crossed out by the user at this round of edit-and-apply, e.g.\n          [\n            {dt: 1, mclassLst: ['WT'], mclassExcludeLst: ['Blank'], origin: 'germline'}\n            {dt: 1, mclassLst: ['Blank', 'WT', 'M'], mclassExcludeLst:[], origin:'somatic'},\n            {dt: 2, mclassLst: ['Blank', 'WT'], mclassExcludeLst:[]}\n            {dt: 4, mclassLst: ['WT', 'CNV_loss'], mclassExcludeLst:[]}\n          ]\n        */\n\t\t\t\tconst svalues = samplevalue.values || [samplevalue]\n\t\t\t\tfor (const sv of svalues) {\n\t\t\t\t\tthistermmatch =\n\t\t\t\t\t\tt.values.find(\n\t\t\t\t\t\t\t(v: any) =>\n\t\t\t\t\t\t\t\tv.dt == sv.dt &&\n\t\t\t\t\t\t\t\t(!v.origin || sv.origin == v.origin) &&\n\t\t\t\t\t\t\t\t(!v.mclasslst || v.mclasslst.includes(sv.class))\n\t\t\t\t\t\t) && true\n\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tthrow 'unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]'\n\t\t\t}\n\n\t\t\tif (t.isnot) {\n\t\t\t\tthistermmatch = !thistermmatch\n\t\t\t}\n\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t}\n\n\t\t// if one tvslst is matched with an \"or\" (Set UNION), then sample is okay\n\t\tif (filter.join == 'or') {\n\t\t\tif (numberofmatchedterms && filter.in) return true\n\t\t\tif (!numberofmatchedterms && !filter.in) return true\n\t\t}\n\t}\n\t// for join=\"and\" (Set intersection)\n\tif (!('in' in filter)) (filter as any).in = true // casting to any avoids tsc err despite it's typed!\n\treturn filter.in == (numberofmatchedterms == lst.length)\n}\n\n/**\n * Recursively processes filter items and sets dataset annotations\n * @param item Filter item to process\n * @param ds Optional dataset with annotation functionality\n */\nexport function setDatasetAnnotations(item: Filter | { type: 'tvs'; tvs: Tvs }, ds: Dataset | null = null): void {\n\tif (item.type == 'tvslst') {\n\t\tfor (const subitem of item.lst) {\n\t\t\tsetDatasetAnnotations(subitem, ds)\n\t\t}\n\t} else {\n\t\tif (ds && typeof ds.setAnnoByTermId == 'function') {\n\t\t\tds.setAnnoByTermId(item.tvs.term.id)\n\t\t}\n\t\tif (item.tvs.term.type == 'categorical') {\n\t\t\tconst tvsAny = item.tvs as any\n\t\t\ttvsAny.valueset = new Set(tvsAny.values.map((i: any) => i.key))\n\t\t}\n\t}\n}\n\n/**\n * Gets the precomputed key for a condition term based on bar_by and value_by settings\n */\nfunction getPrecomputedKey(q: any): string {\n\tconst precomputedKey =\n\t\tq.bar_by_children && q.value_by_max_grade\n\t\t\t? 'childrenAtMaxGrade'\n\t\t\t: q.bar_by_children && q.value_by_most_recent\n\t\t\t? 'childrenAtMostRecent'\n\t\t\t: q.bar_by_children && q.value_by_computable_grade\n\t\t\t? 'children'\n\t\t\t: q.bar_by_grade && q.value_by_max_grade\n\t\t\t? 'maxGrade'\n\t\t\t: q.bar_by_grade && q.value_by_most_recent\n\t\t\t? 'mostRecentGrades'\n\t\t\t: q.bar_by_grade && q.value_by_computable_grade\n\t\t\t? 'computableGrades'\n\t\t\t: ''\n\tif (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`\n\treturn precomputedKey\n}\n\n/**\n * Joins a list of filters into the first filter with \"and\", returns joined filter\n * Used by caller app to join hidden filters into a visible filter\n * @param lst List of filters to join\n * @returns The joined filter\n */\nexport function filterJoin(lst: Filter[]): Filter | undefined {\n\tif (!lst || lst.length == 0) return\n\tlet f = JSON.parse(JSON.stringify(lst[0]))\n\tif (lst.length == 1) return f\n\t// more than 1 item, will join\n\tif (f.lst.length < 2) {\n\t\tif (f.join !== '') throw 'filter.join must be an empty string \"\" when filter.lst.length < 2'\n\t\tf.join = 'and'\n\t} else if (f.join == 'or') {\n\t\t// f is \"or\", wrap it with another root layer of \"and\"\n\t\tf = {\n\t\t\ttype: 'tvslst',\n\t\t\tjoin: 'and',\n\t\t\tin: true,\n\t\t\tlst: [f]\n\t\t}\n\t} else if (f.join != 'and') {\n\t\tthrow 'filter.join must be either \"and\" or \"or\" when .lst length > 1'\n\t}\n\t// now, f.join should be \"and\"\n\t// if the argument lst[0].join == \"and\",\n\t// then the f.in boolean value is reused\n\tfor (let i = 1; i < lst.length; i++) {\n\t\tconst f2 = JSON.parse(JSON.stringify(lst[i]))\n\t\tif (f2.join == 'or') f.lst.push(f2)\n\t\telse f.lst.push(...f2.lst)\n\t}\n\t// if f ends up single-tvs item (from joining single tvs to empty filter), need to set join to '' per filter spec\n\tif (f.lst.length == 1 && f.lst[0].type == 'tvs') {\n\t\tf.join = ''\n\t}\n\treturn f\n}\n\n/**\n * Creates a wrapped tvslst (term value settings list) filter object\n * @param lst List of filter items\n * @param join Join operation (and/or)\n * @param $id Optional filter ID\n * @returns Wrapped filter object\n */\nexport function getWrappedTvslst(lst: Filter['lst'] = [], join: string = '', $id: string | null = null): Filter {\n\tconst filter: Filter = {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin,\n\t\tlst\n\t}\n\tif ($id !== null) filter.$id = $id\n\treturn filter\n}\n\nexport function getTvsDenominators(term: any): string[] {\n\t/* Denominator term ids of a termCollection tvs, which reduces the collection to a\n\tpercentage. term.denominators[] is explicit, matching q.denominators[] of a fraction\n\ttermCollection tw. 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