@sjcrh/proteinpaint-client 2.200.0 → 2.201.0

package/dist/chunk-OTTMHVYH.js

@@ -1,787 +0,0 @@
-import {
-  sample_match_termvaluesetting
-} from "./chunk-GNS6CQMA.js";
-import {
-  boxplot_getvalue,
-  compute_bins
-} from "./chunk-MPSLUEI4.js";
-import {
-  isNumeric
-} from "./chunk-JNITUVXP.js";
-import {
-  __commonJS,
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// ../node_modules/partjson/dist/partjson.umd.js
-var require_partjson_umd = __commonJS({
-  "../node_modules/partjson/dist/partjson.umd.js"(exports, module) {
-    !(function(t, e) {
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-          const r2 = (t3, e3) => t3 ? t3[e3] : void 0;
-          return (t3) => s3.reduce(r2, t3);
-        }
-        {
-          const t3 = e2.slice(1);
-          return (e3) => e3[t3];
-        }
-      }, "=": function(t2, e2, s2) {
-        const r2 = e2.slice(1).split(t2.delimit).reduce((t3, e3) => t3 && e3 in t3 ? t3[e3] : void 0, t2.opts["="]);
-        if (r2) return (t3) => r2;
-        s2.errors.push(["val", "MISSING-EXTERNAL-SUBS"]);
-      }, "@": function(t2, e2, s2) {
-        if (!t2.reserved.opts.includes(e2)) {
-          if ("@" == e2 || e2 == "@" + t2.delimit) return (t3, e3) => e3.self;
-          if (e2.includes(t2.delimit)) {
-            const r2 = e2.split(t2.delimit), o2 = (r3, o3) => {
-              if ("@" == o3[0] && o3.length > 1 && !t2.reserved.contexts.includes(o3)) return s2.errors.push(["val", "UNRECOGNIZED-CONTEXT-" + e2, s2.lineage.join(".") + "." + o3]), [null, null];
-              const [i2, n2] = r3;
-              return i2 && o3 ? "@" == o3 ? [n2.self, n2] : "@values" == o3 ? [Object.values(i2), n2] : "@" == o3[0] ? [n2[o3.slice(1)], t2.contexts.get(n2[o3.slice(1)])] : [i2[o3], t2.contexts.get(i2[o3])] : [null, null];
-            };
-            return (t3, e3) => r2.reduce(o2, [e3.self, e3])[0];
-          }
-          if (t2.reserved.contexts.includes(e2)) {
-            const t3 = e2.slice(1);
-            return (e3, s3) => s3[t3];
-          }
-          s2.errors.push(["val", "UNRECOGNIZED-CONTEXT-" + e2]);
-        }
-      }, "&": function(t2, e2, s2) {
-        const r2 = e2.slice(1).split(t2.delimit), o2 = r2.shift();
-        if (r2.length) {
-          if (1 == r2.length) {
-            const e3 = r2[0];
-            return () => {
-              const s3 = t2.joins.get(o2);
-              return s3 ? s3[e3] : null;
-            };
-          }
-          {
-            const e3 = (t3, e4) => t3 ? t3[e4] : null;
-            t2.joins.get(o2);
-            return (s3) => r2.reduce(e3, t2.joins.get(o2));
-          }
-        }
-        return () => t2.joins.get(o2);
-      } }, n = { "": function(t2, e2, s2) {
-        return t2;
-      }, "()": function(t2, e2, s2) {
-        if ("=" == s2.subs) {
-          const r2 = t2();
-          return "function" != typeof r2 ? void e2.errors.push(["val", "NOT-A-FUNCTION", s2.subs + s2.term + s2.conv]) : r2;
-        }
-        return (s3, r2) => {
-          const o2 = t2(s3, r2);
-          if ("function" == typeof o2) return o2(s3, r2);
-          e2.errors.push(["val", "NOT-A-FUNCTION", s3]);
-        };
-      } };
-      n["[]"] = n[""], n["(]"] = n["()"];
-      var l = Object.freeze({ __proto__: null, default: function(t2, e2, s2, r2) {
-        const [l2, c2, p] = o(t2, r2);
-        if (t2.reserved.opts.includes(l2)) return [];
-        const h = l2 + p.conv;
-        if (e2.ignore = h in s2 ? s2[h] : s2["@"], p.skip && "~" != p.skip) return i[p.skip](t2, l2, e2), [];
-        if (p.subs in i) {
-          const s3 = i[p.subs](t2, l2, e2);
-          return s3 ? [n[p.conv](s3, e2, p), p] : [];
-        }
-        return e2.errors.push(["val", "UNSUPPORTED-SYMBOL-" + p.subs]), [];
-      }, parseTerm: o, subs: i, conv: n });
-      class c {
-        constructor(o2 = {}) {
-          this.defaultOpts = { template: {}, seed: "{}", "=": {} }, this.opts = Object.assign(this.defaultOpts, o2), this.delimit = ".", this.subsSymbols = ["$", "=", "@", "&"], this.convSymbols = ["()", "[]", "(]"], this.aggrSymbols = ["+", "-", "<", ">"], this.timePost = ["_0:", "_1:", "_2:", "_3:", "_4:", "_5:", "_6:", "_7:", "_8:", "_9:"], this.timeSymbols = [":__", "_:_", "__:", ...this.timePost], this.skipSymbols = ["#", "*", "~"], this.steps = [":__", "", "_:_"], this.errors = new r(this), this.reserved = new t(this), this.keyFiller = new e(this), this.valFiller = new s(this), this.commentedTerms = /* @__PURE__ */ new Map(), this.joins = /* @__PURE__ */ new Map(), this.fillers = /* @__PURE__ */ new Map(), this.contexts = /* @__PURE__ */ new Map(), this.temps = /* @__PURE__ */ new Map(), this.refresh();
-        }
-        refresh(t2 = {}) {
-          this.times = { start: +/* @__PURE__ */ new Date() }, Object.assign(this.opts, t2), "string" != typeof this.opts.template && (this.opts.template = JSON.stringify(this.opts.template));
-          const e2 = JSON.parse(this.opts.template);
-          this.errors.clear(e2["@errmode"]), e2["@delimit"] && (this.delimit = e2["@delimit"]), this.commentedTerms.clear(), this.joins.clear(), this.fillers.clear(), this.contexts.clear(), this.temps.clear(), delete this.tree, this.tree = this.setResultContext(this.opts.seed), this.focusTemplate = /* @__PURE__ */ Object.create(null), this.parseTemplate(e2, { "@": this.reserved.notDefined }), this.times.parse = +/* @__PURE__ */ new Date() - this.times.start, Object.keys(this.focusTemplate).length ? (this.parseTemplate(this.focusTemplate, { "@": this.reserved.notDefined }), this.template = this.focusTemplate) : this.template = e2, this.postLoopTerms = /* @__PURE__ */ Object.create(null), this.done = [], this.opts.data && this.add(this.opts.data, false), this.errors.log(this.fillers);
-        }
-        setResultContext(t2, e2 = null, s2 = null, r2 = false, o2, i2 = null, n2 = null) {
-          const l2 = null !== e2 && e2 in s2 ? s2[e2] : JSON.parse(t2);
-          if (this.contexts.has(l2)) return l2;
-          const c2 = { branch: e2, parent: s2, context: this.contexts.get(s2), self: l2, root: this.tree ? this.tree : l2, joins: this.joins, errors: [], key: o2 };
-          if (r2 && (c2.tracker = /* @__PURE__ */ new Map()), i2 && n2) {
-            const t3 = this.fillers.get(n2);
-            if (!t3["@before"](i2, c2)) return;
-            if (t3["@join"] && !t3["@join"](i2, c2)) return;
-          }
-          return this.contexts.set(l2, c2), null !== e2 && (s2[e2] = l2), l2;
-        }
-        parseTemplate(t2, e2, s2 = []) {
-          const r2 = /* @__PURE__ */ Object.create(null);
-          r2.inputs = /* @__PURE__ */ Object.create(null), r2["@before"] = this.reserved.trueFxn, r2["@after"] = this.reserved.trueFxn, r2.postTerms = {}, r2.errors = [];
-          const i2 = this.reserved["@ignore"](t2, e2, r2);
-          r2["@ignore"] = i2, this.fillers.set(t2, r2);
-          const n2 = this.steps.map((t3) => []);
-          for (const e3 in t2) {
-            const [l2, c2, p, h] = o(this, e3), u = t2[e3], a = r2.inputs[e3] = { term: e3, subterm: l2, symbols: c2, keyTokens: p, templateVal: u, lineage: [...s2, e3], inheritedIgnore: i2, errors: [] };
-            "@()" == c2 ? this.reserved.setFxn(l2, a, r2, u) : (a.keyFxn = this.keyFiller.getFxn(a, i2), a.keyFxn && (a.valFxn = this.valFiller.getFxn(a, i2), "__:" == p.time || this.timePost.includes(p.time) ? (r2.postTerms[p.time] || (r2.postTerms[p.time] = []), r2.postTerms[p.time].includes(e3) || r2.postTerms[p.time].push(e3)) : n2[h].push(e3)));
-          }
-          r2.steps = n2.filter((t3) => t3.length);
-        }
-        add(t2, e2 = true) {
-          this.times.start || (this.times.start = +/* @__PURE__ */ new Date()), e2 && this.errors.clear(), this.joins.clear();
-          for (const e3 of t2) if (this.split) for (const t3 of this.split(e3)) this.processRow(t3, this.template, this.tree), this.joins.clear();
-          else this.processRow(e3, this.template, this.tree), this.joins.clear();
-          this.processResult(this.tree);
-          for (const t3 of this.timePost) if (this.postLoopTerms[t3]) for (const e3 of this.postLoopTerms[t3]) this.postLoop(e3.self, e3, t3);
-          for (const t3 of this.done) t3.done(t3.self, t3);
-          for (const [t3, e3] of this.temps) for (const s2 of e3) delete t3[s2];
-          this.times.total = +/* @__PURE__ */ new Date() - this.times.start, delete this.times.start, e2 && this.errors.log();
-        }
-        processRow(t2, e2, s2) {
-          const r2 = this.contexts.get(s2), o2 = this.fillers.get(e2);
-          if (r2.filler = o2, o2["@before"](t2, r2) && (!o2["@join"] || o2["@join"](t2, r2))) {
-            for (const e3 of o2.steps) for (const i2 of e3) {
-              const e4 = o2.inputs[i2];
-              if (e4.keyFxn && e4.valFxn) {
-                const o3 = e4.keyFxn(t2, r2);
-                for (const i3 of o3) e4.valFxn(t2, i3, s2, r2), "~" == e4.keyTokens.skip && (this.temps.has(s2) || this.temps.set(s2, /* @__PURE__ */ new Set()), this.temps.get(s2).add(i3));
-              }
-            }
-            o2["@after"](t2, r2), o2["@dist"] && o2["@dist"](r2), o2["@done"] && !this.done.includes(r2) && (r2.done = o2["@done"], this.done.push(r2));
-            for (const t3 in o2.postTerms) this.postLoopTerms[t3] || (this.postLoopTerms[t3] = []), this.postLoopTerms[t3].includes(r2) || this.postLoopTerms[t3].push(r2);
-            return true;
-          }
-        }
-        postLoop(t2, e2, s2 = "__:") {
-          if (e2 && e2.filler && e2.filler.postTerms[s2]) for (const r2 of e2.filler.postTerms[s2]) {
-            const s3 = e2.filler.inputs[r2];
-            if (s3.keyFxn && s3.valFxn) {
-              const r3 = s3.keyFxn(null, e2);
-              for (const o2 of r3) s3.valFxn(null, o2, t2, e2);
-            }
-          }
-        }
-        processResult(t2) {
-          const e2 = this.contexts.get(t2);
-          this.postLoop(t2, e2, "__:");
-          for (const e3 in t2) {
-            const s2 = t2[e3];
-            if (s2) {
-              if (Array.isArray(s2) || s2 instanceof Set || s2 instanceof Map) for (const t3 of s2) "object" == typeof t3 && this.processResult(t3);
-              else if ("object" == typeof s2) {
-                const t3 = this.contexts.get(s2);
-                t3 && t3["@dist"] && t3["@dist"](s2), this.processResult(s2);
-              }
-            }
-          }
-          e2 && e2.filler && this.errors.markErrors(t2, e2);
-        }
-        copyResult(t2, e2 = {}) {
-          if (arguments.length && void 0 === t2) return;
-          const s2 = arguments.length ? t2 : this.tree;
-          for (const t3 in s2) {
-            const r2 = s2[t3];
-            if (r2 instanceof Set || r2 instanceof Map) e2[t3] = [...r2];
-            else if (Array.isArray(r2)) {
-              e2[t3] = [];
-              for (const s3 of r2) if (Array.isArray(s3)) {
-                const r3 = [];
-                e2[t3].push(r3), this.copyResult(s3, r3);
-              } else if (s3 && "object" == typeof s3) {
-                const r3 = /* @__PURE__ */ Object.create(null);
-                e2[t3].push(r3), this.copyResult(s3, r3);
-              } else e2[t3] = JSON.parse(JSON.stringify(r2));
-            } else r2 && "object" == typeof r2 ? (e2[t3] = /* @__PURE__ */ Object.create(null), this.copyResult(r2, e2[t3])) : e2[t3] = JSON.parse(JSON.stringify(r2));
-          }
-          return e2;
-        }
-      }
-      return c.prototype.converter = l, c;
-    });
-  }
-});
-
-// plots/barchart.data.js
-var import_partjson = __toESM(require_partjson_umd(), 1);
-function getBarchartData(_q, data) {
-  const q = JSON.parse(JSON.stringify(_q));
-  if (!q.term1) q.term1 = q.term ? q.term : {};
-  if (!q.term1_q) q.term1_q = {};
-  if (!q.term0) q.term0 = {};
-  if (!q.term0_q) q.term0_q = {};
-  if (!q.term2) q.term2 = {};
-  if (!q.term2_q) q.term2_q = {};
-  if (!q.filter) q.filter = { type: "tvslst", join: "", lst: [] };
-  const pj = getCharts(q, data);
-  return pj.tree.results;
-}
-var templateBar = JSON.stringify({
-  "@before()": "=prep()",
-  "@join()": {
-    idVal: "=idVal()"
-  },
-  results: {
-    "_2:maxAcrossCharts": "=maxAcrossCharts()",
-    charts: [
-      {
-        chartId: "@key",
-        total: "+1",
-        "_1:maxSeriesTotal": "=maxSeriesTotal()",
-        "@done()": "=filterEmptySeries()",
-        serieses: [
-          {
-            total: "+1",
-            seriesId: "@key",
-            max: "<&idVal.dataVal",
-            // needed by client-side boxplot renderer
-            "~values": ["&idVal.dataVal", 0],
-            "~sum": "+&idVal.dataVal",
-            "__:boxplot": "=boxplot()",
-            "~samples": ["$sample", "set"],
-            //'__:AF': '=getAF()',
-            data: [
-              {
-                dataId: "@key",
-                total: "+1"
-                //samples: ['$sample']
-              },
-              "&idVal.dataId[]"
-            ]
-          },
-          "&idVal.seriesId[]"
-        ]
-      },
-      "&idVal.chartId[]"
-    ],
-    "~sum": "+&idVal.seriesVal",
-    "~values": ["&idVal.seriesVal", 0],
-    "__:boxplot": "=boxplot()",
-    refs: {
-      cols: ["&idVal.seriesId[]"],
-      colgrps: ["-"],
-      rows: ["&idVal.dataId[]"],
-      rowgrps: ["-"],
-      col2name: {
-        "&idVal.seriesId[]": {
-          name: "@branch",
-          grp: "-"
-        }
-      },
-      row2name: {
-        "&idVal.dataId[]": {
-          name: "@branch",
-          grp: "-"
-        }
-      },
-      "__:useColOrder": "=useColOrder()",
-      "__:useRowOrder": "=useRowOrder()",
-      "__:bins": "=bins()",
-      //'__:q': '=q()',
-      "@done()": "=sortColsRows()"
-    },
-    "@done()": "=sortCharts()"
-  }
-});
-function getCharts(q, data) {
-  const idValFxns = {
-    categorical: getCategoricalIdVal,
-    integer: getNumericIdVal,
-    float: getNumericIdVal,
-    undefined: getUndefinedIdVal
-    // NOTE: condition terms are not currently supported for frontend vocab
-  };
-  return new import_partjson.default({
-    data,
-    seed: `{"values": []}`,
-    // result seed
-    template: templateBar,
-    "=": {
-      idVal(row, context) {
-        const [chartId, chartVal] = idValFxns[q.term0.type](row.data, q.term0, q.term0_q, data);
-        const [seriesId, seriesVal] = idValFxns[q.term1.type](row.data, q.term1, q.term1_q, data);
-        const [dataId, dataVal] = idValFxns[q.term2.type](row.data, q.term2, q.term2_q, data);
-        return {
-          chartId,
-          chartVal,
-          seriesId,
-          seriesVal,
-          dataId,
-          dataVal
-        };
-      },
-      prep(row) {
-        return sample_match_termvaluesetting(row.data, q.filter);
-      },
-      maxSeriesTotal(row, context) {
-        let maxSeriesTotal = 0;
-        for (const grp of context.self.serieses) {
-          if (grp && grp.total > maxSeriesTotal) {
-            maxSeriesTotal = grp.total;
-          }
-        }
-        return maxSeriesTotal;
-      },
-      maxAcrossCharts(row, context) {
-        let maxAcrossCharts = 0;
-        for (const chart of context.self.charts) {
-          if (chart.maxSeriesTotal > maxAcrossCharts) {
-            maxAcrossCharts = chart.maxSeriesTotal;
-          }
-        }
-        return maxAcrossCharts;
-      },
-      boxplot(row, context) {
-        if (!context.self.values || !context.self.values.length) return;
-        const values = context.self.values.filter((d) => d !== null && !isNaN(d));
-        if (!values.length) return;
-        values.sort((i, j) => i - j);
-        const stat = boxplot_getvalue(values);
-        stat.mean = context.self.sum / values.length;
-        let s = 0;
-        for (const v of values) {
-          s += Math.pow(v - stat.mean, 2);
-        }
-        stat.sd = Math.sqrt(s / (values.length - 1));
-        if (isNaN(stat.sd)) stat.sd = null;
-        return stat;
-      },
-      numSamples(row, context) {
-        return context.self.samples.size;
-      },
-      filterEmptySeries(result) {
-        const nonempty = result.serieses.filter((series) => series.total);
-        result.serieses.splice(0, result.serieses.length, ...nonempty);
-      },
-      sortColsRows(result) {
-        if (q.term1_q.orderedLabels) {
-          const labels = q.term1_q.orderedLabels;
-          result.cols.sort((a, b) => labels.indexOf(a) - labels.indexOf(b));
-        }
-        if (q.term2.orderedLabels) {
-          const labels = q.term2_q.orderedLabels;
-          result.rows.sort((a, b) => labels.indexOf(a) - labels.indexOf(b));
-        }
-      },
-      sortCharts(result) {
-      },
-      useColOrder() {
-        return q.term1_q.orderedLabels && q.term1_q.orderedLabels.length > 0;
-      },
-      useRowOrder() {
-        return q.term2_q.orderedLabels && q.term2_q.orderedLabels.length > 0;
-      },
-      bins() {
-        return [q.term0_q, q.term1_q, q.term2_q].map((d) => d.computed_bins);
-      },
-      q() {
-      }
-    }
-  });
-}
-function getCategoricalIdVal(d, term) {
-  const id = "id" in term ? d[term.id] : "-";
-  const value = "id" in term && isNumeric(d[term.id]) ? +d[term.id] : 0;
-  return [[id], value];
-}
-function getNumericIdVal(d, term, q, rows) {
-  if (!("id" in term) || !(term.id in d)) return [[], void 0];
-  if (!q.computed_bins) {
-    const summary = {};
-    rows.map((row) => {
-      if (!isNumeric(row.data[term.id])) return;
-      const v2 = +row.data[term.id];
-      if (!("min" in summary) || summary.min > v2) summary.min = v2;
-      if (!("max" in summary) || summary.max < v2) summary.max = v2;
-    });
-    q.computed_bins = compute_bins(q, (percentiles) => summary);
-    q.orderedLabels = q.computed_bins.map((d2) => d2.label);
-  }
-  const v = d[term.id];
-  if (term.values && v in term.values && term.values[v].uncomputable) {
-    return [[term.values[v].label], void 0];
-  }
-  if (isNumeric(d[term.id])) {
-    const ids = [];
-    for (const b of q.computed_bins) {
-      if (b.startunbounded) {
-        if (v < b.stop) {
-          ids.push(b.label);
-        } else if (b.stopinclusive && v === b.stop) {
-          ids.push(b.label);
-        }
-      } else if (b.stopunbounded) {
-        if (v > b.start) {
-          ids.push(b.label);
-        } else if (b.stopinclusive && v === b.start) {
-          ids.push(b.label);
-        }
-      } else if ((v > b.start || v === b.start && b.startinclusive) && (v < b.stop || v === b.stop && b.stopinclusive)) {
-        ids.push(b.label);
-      }
-      if (ids.length) break;
-    }
-    return [ids, v];
-  }
-  return [[], void 0];
-}
-function getUndefinedIdVal() {
-  return [["-"], void 0];
-}
-function getCategoryData(q, data) {
-  if (!data || !data.length) {
-    return {
-      lst: Object.keys(q.term.values).map((k) => {
-        return { key: k, label: q.term.values[k].label, value: k };
-      })
-    };
-  }
-  const pj = new import_partjson.default({
-    data,
-    template: JSON.stringify({
-      "@before()": "=prep()",
-      "@join()": {
-        idVal: "=idVal()"
-      },
-      results: {
-        "&idVal.id": {
-          samplecount: "+1",
-          ":__key": "&idVal.id",
-          ":__label": "&idVal.id",
-          ":__value": "&idVal.id"
-        }
-      }
-    }),
-    "=": {
-      prep(row) {
-        return sample_match_termvaluesetting(row.data, q.filter);
-      },
-      idVal(row, context) {
-        const [id, value] = getCategoricalIdVal(row.data, q.term);
-        return { id: id[0], value };
-      }
-    }
-  });
-  return { lst: Object.values(pj.tree.results) };
-}
-
-export {
-  require_partjson_umd,
-  getBarchartData,
-  getCategoryData
-};
-//# sourceMappingURL=chunk-OTTMHVYH.js.map