@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

package/dist/chunk-22KWZOCN.js

@@ -1,153 +0,0 @@
-import {
-  NumericModes
-} from "./chunk-2UWHV2SB.js";
-
-// plots/proteomeAbundance.js
-function renderAssayAndCohortRadios({
-  holder,
-  assays,
-  selectedProteomeDetails,
-  onChange,
-  assayTitle = "Assay Type",
-  cohortTitle = "Cohort"
-}) {
-  const assayEntries = Object.entries(assays || {});
-  if (!assayEntries.length) {
-    holder.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No proteome assays available.");
-    return {
-      getSelected: () => ({ assay: void 0, cohort: void 0 })
-    };
-  }
-  const initialProteomeDetails = selectedProteomeDetails || {};
-  const assayRadioName = `sjpp-proteome-assay-${Math.random().toString().slice(-6)}`;
-  const cohortRadioName = `sjpp-proteome-cohort-${Math.random().toString().slice(-6)}`;
-  let selectedAssay = assays[initialProteomeDetails.assay] ? initialProteomeDetails.assay : assayEntries[0][0];
-  let selectedCohort = initialProteomeDetails.cohort;
-  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(assayTitle);
-  const assayListDiv = holder.append("div").style("margin-bottom", "10px");
-  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(cohortTitle);
-  const cohortListDiv = holder.append("div");
-  for (const [assayKey] of assayEntries) {
-    const assayLabel = assayListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
-    assayLabel.append("input").attr("type", "radio").attr("name", assayRadioName).attr("value", assayKey).property("checked", assayKey === selectedAssay).style("margin-right", "6px").on("change", () => {
-      selectedAssay = assayKey;
-      selectedCohort = void 0;
-      renderCohortOptions();
-      onChange?.({ assay: selectedAssay, cohort: selectedCohort });
-    });
-    assayLabel.append("span").text(assayKey);
-  }
-  renderCohortOptions();
-  onChange?.({ assay: selectedAssay, cohort: selectedCohort });
-  return {
-    getSelected: () => ({ assay: selectedAssay, cohort: selectedCohort })
-  };
-  function renderCohortOptions() {
-    cohortListDiv.selectAll("*").remove();
-    const cohorts = Object.keys(assays[selectedAssay]?.cohorts || {});
-    if (!cohorts.length) {
-      selectedCohort = void 0;
-      cohortListDiv.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No cohorts available.");
-      return;
-    }
-    if (!selectedCohort || !assays[selectedAssay]?.cohorts?.[selectedCohort]) {
-      selectedCohort = cohorts.includes(initialProteomeDetails.cohort) ? initialProteomeDetails.cohort : cohorts[0];
-    }
-    for (const cohortKey of cohorts) {
-      const cohortLabel = cohortListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
-      cohortLabel.append("input").attr("type", "radio").attr("name", cohortRadioName).attr("value", cohortKey).property("checked", cohortKey === selectedCohort).style("margin-right", "6px").on("change", () => {
-        selectedCohort = cohortKey;
-        onChange?.({ assay: selectedAssay, cohort: selectedCohort });
-      });
-      cohortLabel.append("span").text(cohortKey);
-    }
-  }
-}
-function makeChartBtnMenu(holder, chartsInstance) {
-  chartsInstance.dom.tip.clear();
-  const assays = chartsInstance.state.termdbConfig?.queries?.proteome?.assays || {};
-  const menuDiv = holder.append("div");
-  let selectedProteomeDetails;
-  let launchOption;
-  const syncLaunchButtonState = () => {
-    if (!launchOption) return;
-    if (selectedProteomeDetails?.cohort) launchOption.style("opacity", 1).style("pointer-events", "auto");
-    else launchOption.style("opacity", 0.5).style("pointer-events", "none");
-  };
-  renderAssayAndCohortRadios({
-    holder: menuDiv,
-    assays,
-    onChange: (proteomeDetails) => {
-      selectedProteomeDetails = proteomeDetails;
-      syncLaunchButtonState();
-    }
-  });
-  launchOption = menuDiv.append("button").attr("class", "sjpp_apply_btn sja_filter_tag_btn sja_sharp_border").style("display", "block").style("margin", "10px auto 10px").text("Select Protein").on("click", () => {
-    if (!selectedProteomeDetails?.cohort) return;
-    const { assay, cohort } = selectedProteomeDetails;
-    const assayCohortTitle = `${assay}: ${cohort}`;
-    const chart = {
-      label: "Protein Abundance",
-      chartType: "proteomeAbundance",
-      usecase: {
-        target: "proteomeAbundance",
-        detail: "term",
-        proteomeDetails: { assay, cohort },
-        label: `Assay: ${assay}; Cohort: ${cohort}`
-      },
-      processSelection: (termlst) => termlst,
-      updateActionBySelectedTerms: (action, termlst) => {
-        action.config.assayCohortTitle = assayCohortTitle;
-        const { assay: assay2, cohort: cohort2 } = selectedProteomeDetails;
-        action.config.proteomeDetails = { assay: assay2, cohort: cohort2 };
-        const cohortSelected = chartsInstance.state.termdbConfig.queries.proteome.assays[assay2].cohorts[cohort2];
-        if (cohortSelected.filter) action.config.filter = buildFilter(cohortSelected.filter);
-        const twlst = termlst.map((term) => {
-          const t = structuredClone(term);
-          t.proteomeDetails = { assay: assay2, cohort: cohort2 };
-          return { term: t, q: { mode: NumericModes.continuous } };
-        });
-        if (twlst.length == 1) {
-          action.config.chartType = "summary";
-          action.config.term = twlst[0];
-          if (cohortSelected.overlayTerm) action.config.term2 = { term: structuredClone(cohortSelected.overlayTerm), q: {} };
-          return;
-        }
-        if (twlst.length == 2) {
-          action.config.chartType = "summary";
-          action.config.term = twlst[0];
-          action.config.term2 = twlst[1];
-          return;
-        }
-        action.config.chartType = "hierCluster";
-        action.config.dataType = "proteomeAbundance";
-        action.config.termgroups = [{ name: "Protein Abundance Cluster", lst: twlst, type: "hierCluster" }];
-      }
-    };
-    chartsInstance.dom.tip.clear();
-    chartsInstance.showTree_selectlst(chart);
-  });
-  syncLaunchButtonState();
-}
-function buildFilter(filterConfig) {
-  if (!filterConfig) return;
-  const lst = [];
-  for (const filterTvs of filterConfig) {
-    lst.push({
-      type: "tvs",
-      tvs: filterTvs
-    });
-  }
-  return {
-    type: "tvslst",
-    in: true,
-    join: lst.length > 1 ? "and" : "",
-    lst
-  };
-}
-
-export {
-  renderAssayAndCohortRadios,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=chunk-22KWZOCN.js.map

package/dist/chunk-2K5DSRBJ.js

@@ -1,84 +0,0 @@
-// ../shared/utils/src/tree.js
-var hardcode_root = "root";
-var hierarchy_spacer = "...";
-function stratinput(lst, levels) {
-  const lp = /* @__PURE__ */ Object.create(null);
-  const nodes = /* @__PURE__ */ Object.create(null);
-  const size = /* @__PURE__ */ Object.create(null);
-  for (const m of lst) {
-    for (const [i, lev] of levels.entries()) {
-      const thisv = getkey(m, i, levels);
-      const pav = getkey(m, i - 1, levels);
-      if (!m[lev.k]) {
-        if (i > 0) {
-          size[pav] += 1;
-        }
-        break;
-      }
-      lp[thisv] = pav;
-      if (!(thisv in size)) {
-        size[thisv] = 0;
-      }
-      if (!(thisv in nodes)) {
-        const n = {
-          lst: []
-        };
-        if (lev.full) {
-          n.full = m[lev.full];
-        }
-        n.id0 = levels[0].k;
-        n.v0 = m[levels[0].k];
-        if (i == 1) {
-          n.id1 = levels[1].k;
-          n.v1 = m[levels[1].k];
-        }
-        if (i == 2) {
-          n.id2 = levels[2].k;
-          n.v1 = m[levels[2].k];
-        }
-        nodes[thisv] = n;
-      }
-      nodes[thisv].lst.push(m);
-      if (i == levels.length - 1) {
-        size[thisv] += 1;
-      }
-    }
-  }
-  const nlst = [{ id: hardcode_root, name: hardcode_root }];
-  for (const chid in lp) {
-    const paid = lp[chid];
-    const n = nodes[chid];
-    const fields = chid.split(hierarchy_spacer);
-    nlst.push({
-      id: chid,
-      parentId: paid,
-      lst: n.lst,
-      value: size[chid],
-      name: fields[fields.length - 1],
-      // show this instead of chid
-      full: n.full,
-      id0: n.id0,
-      v0: n.v0,
-      id1: n.id1,
-      v1: n.v1,
-      id2: n.id2,
-      v2: n.v2
-    });
-  }
-  return nlst;
-}
-function getkey(m, i, levels) {
-  const klst = [hardcode_root];
-  for (let j = 0; j < i; j++) {
-    klst.push(m[levels[j].k]);
-  }
-  if (i >= 0) {
-    klst.push(m[levels[i].k]);
-  }
-  return klst.join(hierarchy_spacer);
-}
-
-export {
-  stratinput
-};
-//# sourceMappingURL=chunk-2K5DSRBJ.js.map

package/dist/chunk-2K5DSRBJ.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/tree.js"],
-  "sourcesContent": ["/*\ninput:\n1. list of leaf nodes, e.g. mutation cases, each with a set of key-value pairs\n2. levels of hierarchy in an ordered list\n   each item: { k, full }\n   \"k\" and \"full\" are two attribute keys\n\noutput:\na list of items, as input for d3-hierarchy.stratify\none item for each child-parent relationship in the hierarchy\n{\n\tid:\n\tparentId:\n\tlst:\n\tvalue:\n\tname:\n\tfull:\n\tid0:\n\tv0:\n\tid1:\n\tv1:\n\tid2:\n\tv2:\n}\n\nstrange issue: https://github.com/stjude/proteinpaint/commit/c36004d47d4374d2ade719c6ef9e2b848f0850dc\nusing Map for lp, nodes etc will cause memory issue, thus the use of simple objects\n\nto-do: verify this works after a reorg\n*/\n\nconst hardcode_root = \"root\"\nconst hierarchy_spacer = \"...\"\n\nexport function stratinput(lst, levels) {\n\tconst lp = Object.create(null)\n\t// leaf to parent\n\t// k: HM...BALL...sub\n\t// v: HM...BALL\n\n\tconst nodes = Object.create(null)\n\t/*\n\tk: string id of node, e.g. HM...BALL\n\tv: node\n\t\t.full\n\t\t.lst[]\n\t\t\titems from input\n\t*/\n\n\tconst size = Object.create(null)\n\t// only increment size to leaf nodes, so that root.sum() will work\n\t// k: string id of a node, e.g. HM...BALL\n\t// v: number of items\n\n\tfor (const m of lst) {\n\t\tfor (const [i, lev] of levels.entries()) {\n\t\t\tconst thisv = getkey(m, i, levels)\n\t\t\tconst pav = getkey(m, i - 1, levels)\n\n\t\t\t// as mutations can come as {\"subtype\":\"\"}\n\t\t\t// in the sunburst chart at the subtype level, this mutation should not be counted\n\t\t\t// thus the test with !m[lev.k] rather than !(lev.k in m)\n\t\t\tif (!m[lev.k]) {\n\t\t\t\t// stop at this level\n\t\t\t\t// add count to prev level\n\t\t\t\tif (i > 0) {\n\t\t\t\t\tsize[pav] += 1\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\n\t\t\tlp[thisv] = pav\n\t\t\tif (!(thisv in size)) {\n\t\t\t\tsize[thisv] = 0\n\t\t\t}\n\t\t\tif (!(thisv in nodes)) {\n\t\t\t\tconst n = {\n\t\t\t\t\tlst: [],\n\t\t\t\t}\n\t\t\t\tif (lev.full) {\n\t\t\t\t\tn.full = m[lev.full]\n\t\t\t\t}\n\n\t\t\t\tn.id0 = levels[0].k\n\t\t\t\tn.v0 = m[levels[0].k]\n\t\t\t\tif (i == 1) {\n\t\t\t\t\tn.id1 = levels[1].k\n\t\t\t\t\tn.v1 = m[levels[1].k]\n\t\t\t\t}\n\t\t\t\tif (i == 2) {\n\t\t\t\t\tn.id2 = levels[2].k\n\t\t\t\t\tn.v1 = m[levels[2].k]\n\t\t\t\t}\n\n\t\t\t\tnodes[thisv] = n\n\t\t\t}\n\t\t\tnodes[thisv].lst.push(m)\n\t\t\tif (i == levels.length - 1) {\n\t\t\t\tsize[thisv] += 1\n\t\t\t}\n\t\t}\n\t}\n\n\tconst nlst = [{ id: hardcode_root, name: hardcode_root }]\n\n\tfor (const chid in lp) {\n\t\tconst paid = lp[chid]\n\t\tconst n = nodes[chid]\n\t\tconst fields = chid.split(hierarchy_spacer)\n\t\tnlst.push({\n\t\t\tid: chid,\n\t\t\tparentId: paid,\n\t\t\tlst: n.lst,\n\t\t\tvalue: size[chid],\n\t\t\tname: fields[fields.length - 1], // show this instead of chid\n\t\t\tfull: n.full,\n\t\t\tid0: n.id0,\n\t\t\tv0: n.v0,\n\t\t\tid1: n.id1,\n\t\t\tv1: n.v1,\n\t\t\tid2: n.id2,\n\t\t\tv2: n.v2,\n\t\t})\n\t}\n\treturn nlst\n}\n\nfunction getkey(m, i, levels) {\n\t// if i is 0, return 'root'\n\tconst klst = [hardcode_root]\n\tfor (let j = 0; j < i; j++) {\n\t\tklst.push(m[levels[j].k])\n\t}\n\tif (i >= 0) {\n\t\tklst.push(m[levels[i].k])\n\t}\n\treturn klst.join(hierarchy_spacer)\n}\n"],
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package/dist/chunk-2NQ4TM74.js

@@ -1,48 +0,0 @@
-import {
-  addGeneSearchbox,
-  getSCGEunit
-} from "./chunk-XZZLEHWC.js";
-import {
-  Menu
-} from "./chunk-2SRMRC6L.js";
-import {
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-2UWHV2SB.js";
-
-// termdb/handlers/singleCellGeneExpression.ts
-var SearchHandler = class {
-  init(opts) {
-    this.validateOpts(opts);
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => this.selectGene(geneSearch.geneSymbol, opts.usecase.specialCase.config.sample)
-    });
-  }
-  async selectGene(gene, sample) {
-    if (!gene) throw new Error("No gene selected");
-    const unit = getSCGEunit(this.app.vocabApi);
-    const name = `${gene} ${unit}`;
-    this.callback({ gene, name, type: SINGLECELL_GENE_EXPRESSION, sample });
-  }
-  validateOpts(opts) {
-    if (opts.callback == null) throw new Error("callback is required");
-    if (opts.app == null) throw new Error("app is required");
-    if (opts.holder == null) throw new Error("holder is required");
-    if (opts.genomeObj == null) throw new Error("genomeObj is required");
-    if (opts.usecase == null) throw new Error("usecase is required");
-    if (!opts.usecase?.specialCase?.config?.sample) {
-      throw new Error("usecase.specialCase.config.sample is required for singleCellGeneExpression handler");
-    }
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-2NQ4TM74.js.map