@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/chunk-MSW7OS2O.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/utils/src/bulk.sv.js"],
+  "sourcesContent": ["import * as bulk from \"./bulk.js\"\nimport * as common from \"./common.js\"\n\n/////////////////////////////////\n//\n// client/server shared\n//\n/////////////////////////////////\n\n// work for both sv/fusion\n// must tell if the data is fusion or sv\n\nexport function parseheader(line, flag, issv) {\n\tconst header = line.toLowerCase().split(\"\\t\")\n\tif (header.length <= 1) return \"invalid file header for fusions\"\n\tconst htry = (...lst) => {\n\t\tfor (const a of lst) {\n\t\t\tconst j = header.indexOf(a)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry(\"gene_a\", \"gene1\", \"genea\")\n\tif (i == -1) return \"gene_a missing from header\"\n\theader[i] = \"gene1\"\n\ti = htry(\"gene_b\", \"gene2\", \"geneb\")\n\tif (i == -1) return \"gene_b missing from header\"\n\theader[i] = \"gene2\"\n\ti = htry(\"chr_a\", \"chr1\", \"chra\")\n\tif (i == -1) return \"chr_a missing from header\"\n\theader[i] = \"chr1\"\n\ti = htry(\"chr_b\", \"chr2\", \"chrb\")\n\tif (i == -1) return \"chr_b missing from header\"\n\theader[i] = \"chr2\"\n\ti = htry(\"pos_a\", \"position_a\", \"position1\", \"posa\")\n\tif (i == -1) return \"pos_a missing from header\"\n\theader[i] = \"position1\"\n\ti = htry(\"pos_b\", \"position_b\", \"position2\", \"posb\")\n\tif (i == -1) return \"pos_b missing from header\"\n\theader[i] = \"position2\"\n\ti = htry(\"isoform_a\", \"refseq_a\", \"refseq1\", \"isoform1\", \"sv_refseqa\")\n\tif (i == -1) return \"isoform_a missing from header\"\n\theader[i] = \"isoform1\"\n\ti = htry(\"isoform_b\", \"refseq_b\", \"refseq2\", \"isoform2\", \"sv_refseqb\")\n\tif (i == -1) return \"isoform_b missing from header\"\n\theader[i] = \"isoform2\"\n\ti = htry(\"strand_a\", \"orta\")\n\tif (i == -1) return \"strand_a missing from header\"\n\theader[i] = \"strand1\"\n\ti = htry(\"strand_b\", \"ortb\")\n\tif (i == -1) return \"strand_b missing from header\"\n\theader[i] = \"strand2\"\n\t// optional\n\ti = htry(\"sample\", \"sample_name\", \"tumor_sample_barcode\")\n\tif (i != -1) header[i] = \"sample\"\n\ti = htry(\"patient\", \"donor\", \"target_case_id\")\n\tif (i != -1) header[i] = \"patient\"\n\ti = htry(\"sampletype\", \"sample type\", \"sample_type\")\n\tif (i != -1) header[i] = \"sampletype\"\n\ti = htry(\"disease\")\n\tif (i != -1) header[i] = \"disease\"\n\ti = htry(\"origin\")\n\tif (i != -1) header[i] = \"origin\"\n\tif (issv) {\n\t\tflag.sv.loaded = true\n\t\tflag.sv.header = header\n\t} else {\n\t\tflag.fusion.loaded = true\n\t\tflag.fusion.header = header\n\t}\n\treturn false\n}\n\nexport function parseline(i, line, flag, issv) {\n\tif (line == \"\" || line[0] == \"#\") return\n\tconst lst = line.split(\"\\t\")\n\tconst m = {}\n\tconst header = issv ? flag.sv.header : flag.fusion.header\n\tconst badlines = issv ? flag.sv.badlines : flag.fusion.badlines\n\n\tfor (let j = 0; j < header.length; j++) {\n\t\tm[header[j]] = lst[j]\n\t}\n\tif (!m.chr1) {\n\t\tbadlines.push([i, \"missing chr1\", lst])\n\t\treturn\n\t}\n\tif (m.chr1.toLowerCase().indexOf(\"chr\") != 0) {\n\t\tm.chr1 = \"chr\" + m.chr1\n\t}\n\tif (!m.chr2) {\n\t\tbadlines.push([i, \"missing chr2\", lst])\n\t\treturn\n\t}\n\tif (m.chr2.toLowerCase().indexOf(\"chr\") != 0) {\n\t\tm.chr2 = \"chr\" + m.chr2\n\t}\n\tlet v = m.position1\n\tif (!v) {\n\t\tbadlines.push([i, \"missing position1\", lst])\n\t\treturn\n\t}\n\tlet v2 = Number.parseInt(v)\n\tif (Number.isNaN(v2) || v2 <= 0) {\n\t\tbadlines.push([i, \"invalid value for position1\", lst])\n\t\treturn\n\t}\n\tm.position1 = v2\n\tv = m.position2\n\tif (!v) {\n\t\tbadlines.push([i, \"missing position2\", lst])\n\t\treturn\n\t}\n\tv2 = Number.parseInt(v)\n\tif (Number.isNaN(v2) || v2 <= 0) {\n\t\tbadlines.push([i, \"invalid value for position2\", lst])\n\t\treturn\n\t}\n\tm.position2 = v2\n\tif (bulk.parsesample(m, flag, i, lst, badlines)) {\n\t\treturn\n\t}\n\tif (m.isoform1 && m.isoform1.indexOf(\",\") != -1) {\n\t\tconst lst2 = m.isoform1.split(\",\")\n\t\tm.isoform1 = undefined\n\t\tfor (const t of lst2) {\n\t\t\tif (t != \"\") m.isoform1 = t\n\t\t}\n\t}\n\tif (m.isoform2 && m.isoform2.indexOf(\",\") != -1) {\n\t\tconst lst2 = m.isoform2.split(\",\")\n\t\tm.isoform2 = undefined\n\t\tfor (const t of lst2) {\n\t\t\tif (t != \"\") m.isoform2 = t\n\t\t}\n\t}\n\tif (!m.gene1) {\n\t\tm.isoform1 = undefined\n\t}\n\tif (!m.gene2) {\n\t\tm.isoform2 = undefined\n\t}\n\tif (m.gene1) {\n\t\t// put data under gene1\n\t\tflag.good++\n\t\tconst m2 = {\n\t\t\tdt: issv ? common.dtsv : common.dtfusionrna,\n\t\t\tclass: issv ? common.mclasssv : common.mclassfusionrna,\n\t\t\tisoform: m.isoform1,\n\t\t\tmname: m.gene2 || m.chr2,\n\t\t\tsample: m.sample,\n\t\t\tpatient: m.patient,\n\t\t\tsampletype: m.sampletype,\n\t\t\torigin: m.origin,\n\t\t\tdisease: m.disease,\n\t\t\tpairlst: [\n\t\t\t\t{\n\t\t\t\t\ta: {\n\t\t\t\t\t\tname: m.gene1,\n\t\t\t\t\t\tisoform: m.isoform1,\n\t\t\t\t\t\tstrand: m.strand1,\n\t\t\t\t\t\tchr: m.chr1,\n\t\t\t\t\t\tposition: m.position1,\n\t\t\t\t\t},\n\t\t\t\t\tb: {\n\t\t\t\t\t\tname: m.gene2,\n\t\t\t\t\t\tisoform: m.isoform2,\n\t\t\t\t\t\tstrand: m.strand2,\n\t\t\t\t\t\tchr: m.chr2,\n\t\t\t\t\t\tposition: m.position2,\n\t\t\t\t\t},\n\t\t\t\t},\n\t\t\t],\n\t\t}\n\t\tconst n = flag.geneToUpper ? m.gene1.toUpperCase() : m.gene1\n\t\tif (!flag.data[n]) {\n\t\t\tflag.data[n] = []\n\t\t}\n\t\tflag.data[n].push(m2)\n\t}\n\tif (m.gene2 && m.gene2 != m.gene1) {\n\t\t// put data under gene2\n\t\tflag.good++\n\t\tconst m2 = {\n\t\t\tdt: issv ? common.dtsv : common.dtfusionrna,\n\t\t\tclass: issv ? common.mclasssv : common.mclassfusionrna,\n\t\t\tisoform: m.isoform2,\n\t\t\tmname: m.gene1 || m.chr1,\n\t\t\tsample: m.sample,\n\t\t\tpatient: m.patient,\n\t\t\tsampletype: m.sampletype,\n\t\t\torigin: m.origin,\n\t\t\tdisease: m.disease,\n\t\t\tpairlst: [\n\t\t\t\t{\n\t\t\t\t\ta: {\n\t\t\t\t\t\tname: m.gene1,\n\t\t\t\t\t\tisoform: m.isoform1,\n\t\t\t\t\t\tstrand: m.strand1,\n\t\t\t\t\t\tchr: m.chr1,\n\t\t\t\t\t\tposition: m.position1,\n\t\t\t\t\t},\n\t\t\t\t\tb: {\n\t\t\t\t\t\tname: m.gene2,\n\t\t\t\t\t\tisoform: m.isoform2,\n\t\t\t\t\t\tstrand: m.strand2,\n\t\t\t\t\t\tchr: m.chr2,\n\t\t\t\t\t\tposition: m.position2,\n\t\t\t\t\t},\n\t\t\t\t},\n\t\t\t],\n\t\t}\n\t\tconst n = flag.geneToUpper ? m.gene2.toUpperCase() : m.gene2\n\t\tif (!flag.data[n]) {\n\t\t\tflag.data[n] = []\n\t\t}\n\t\tflag.data[n].push(m2)\n\t}\n}\n\nexport function duplicate(m) {\n\tconst n = {}\n\tfor (const k in m) {\n\t\tif (k == \"pairlst\") continue\n\t\tconst v = m[k]\n\t\tconst type = typeof v\n\t\tif (type == \"object\") {\n\t\t\tcontinue\n\t\t}\n\t\tn[k] = v\n\t}\n\tif (m.pairlst) {\n\t\tn.pairlst = []\n\t\tfor (const pair of m.pairlst) {\n\t\t\tconst p = {}\n\t\t\tfor (const k in pair) {\n\t\t\t\tif (k == \"a\" || k == \"b\" || k == \"interstitial\") {\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tp[k] = pair[k]\n\t\t\t}\n\t\t\tif (pair.a) {\n\t\t\t\tp.a = {}\n\t\t\t\tfor (const k in pair.a) {\n\t\t\t\t\tconst v = pair.a[k]\n\t\t\t\t\tif (typeof v == \"object\") {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tp.a[k] = v\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (pair.b) {\n\t\t\t\tp.b = {}\n\t\t\t\tfor (const k in pair.b) {\n\t\t\t\t\tconst v = pair.b[k]\n\t\t\t\t\tif (typeof v == \"object\") {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tp.b[k] = v\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (pair.interstitial) {\n\t\t\t\tp.interstitial = {}\n\t\t\t\tfor (const k in pair.interstitial) {\n\t\t\t\t\tconst v = pair.interstitial[k]\n\t\t\t\t\tif (typeof v == \"object\") {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tp.interstitial[k] = v\n\t\t\t\t}\n\t\t\t}\n\t\t\tn.pairlst.push(p)\n\t\t}\n\t}\n\treturn n\n}\n"],
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+  "names": []
+}

package/dist/chunk-MVCGSYS2.js

@@ -0,0 +1,50 @@
+import {
+  addGeneSearchbox,
+  getSCGEunit
+} from "./chunk-YWUVCXFS.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-EGWVYY7K.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)
+    });
+  }
+  /**TODO: scge tw handler will validate that a sample is included. Need to resolve issue
+   * with sample info not included.*/
+  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-MVCGSYS2.js.map

package/dist/chunk-N2HBIQKU.js

@@ -0,0 +1,102 @@
+import {
+  renderTable
+} from "./chunk-YWUVCXFS.js";
+
+// termdb/handlers/termCollection.ts
+var SearchHandler = class {
+  async init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    opts.holder.style("display", "");
+    const tableDiv = opts.holder.append("div");
+    const termlst = opts.details.termlst ?? [];
+    renderTable({
+      columns: [{ label: "VARIABLES" }],
+      rows: termlst.map((t) => {
+        return [{ value: t.name }];
+      }),
+      div: tableDiv,
+      maxWidth: "30vw",
+      maxHeight: "40vh",
+      noButtonCallback: () => {
+      },
+      // FIXME to supply a real callback
+      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: () => {
+        },
+        // FIXME to supply a real callback
+        striped: false,
+        showHeader: true,
+        //false,
+        selectAll: true,
+        columnButtons: void 0,
+        //Leave until table.js is typed
+        buttons: void 0
+      });
+    }
+    opts.holder.append("div").style("float", "right").style("padding", "6px 20px").append("button").attr("class", "sjpp_apply_btn sja_filter_tag_btn").text("Select").on("click", () => {
+      const trs = tableDiv.select("table").select("tbody").node().querySelectorAll("tr");
+      const selectedTermlst = termlst.filter((term, i) => {
+        const checked = trs[i]?.querySelectorAll("td")[1]?.querySelector("input")?.checked;
+        return checked === true;
+      });
+      if (selectedTermlst.length === 0) {
+        alert("Please select at least one term");
+        return;
+      }
+      const propsByTermId = {};
+      if (opts.details.propsByTermId) {
+        for (const t of selectedTermlst) {
+          if (opts.details.propsByTermId[t.id]) propsByTermId[t.id] = opts.details.propsByTermId[t.id];
+        }
+      }
+      let categoryKeys;
+      if (categoryTable) {
+        const trs2 = categoryTable.select("table").select("tbody").node().querySelectorAll("tr");
+        categoryKeys = ckSource.map((ck, i) => {
+          const checked = trs2[i].querySelectorAll("td")[1].querySelector("input")?.checked;
+          return { key: ck.key, shown: !!checked };
+        });
+      }
+      opts.callback({
+        type: "termCollection",
+        termIds: selectedTermlst.map((i) => i.id),
+        termlst: selectedTermlst,
+        name: opts.details.name,
+        valueTransform: opts.details.valueTransformByPlots?.[opts.usecase.target],
+        // memberType = ds.cohort.termdb.termCollections[].type for client code
+        memberType: opts.details.memberType || opts.details.type,
+        categoryKeys,
+        isleaf: true,
+        propsByTermId
+      });
+    });
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-N2HBIQKU.js.map

package/dist/chunk-NL3DVEVX.js

@@ -0,0 +1,158 @@
+import {
+  appInit
+} from "./chunk-K7XWZSQA.js";
+import {
+  showErrorsWithCounter
+} from "./chunk-YWUVCXFS.js";
+import {
+  mclass
+} from "./chunk-AMYSEKPF.js";
+
+// plots/disco/launch.adhoc.ts
+async function launch(arg, genomeObj, holder) {
+  const [mlst, errors] = await getMlst(arg);
+  if (errors?.length) {
+    return showErrorsWithCounter(errors, holder);
+  }
+  const opts = {
+    holder,
+    vocabApi: {
+      // api is required by plot.app.js, so create a mock one for the adhoc data
+      vocab: { terms: [] },
+      main: () => {
+        return;
+      },
+      getTermdbConfig: () => {
+        return {};
+      }
+    },
+    state: {
+      args: {
+        data: mlst,
+        genome: genomeObj
+      },
+      plots: [
+        {
+          chartType: "Disco",
+          subfolder: "disco",
+          extension: "ts",
+          /** NOTE: Users should only override the settings in the default
+           * settings.Disco:{}, not the entire settings:{} object.*/
+          overrides: { Disco: arg?.settings || {} }
+        }
+      ]
+    }
+  };
+  const plotAppApi = await appInit(opts);
+  return plotAppApi;
+}
+async function getMlst(arg) {
+  if (Array.isArray(arg.mlst)) {
+    return [arg.mlst, null];
+  }
+  const mlst = [];
+  const errors = [];
+  if (arg.snvText) parseSnvText(arg.snvText, mlst, errors);
+  if (arg.svText) parseSvText(arg.svText, mlst, errors);
+  if (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors);
+  return [mlst, errors];
+}
+function parseSnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 5) {
+      errors.push("snv input not equal to 5 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 1,
+        chr: l[0],
+        position: Number(l[1]),
+        gene: l[2],
+        mname: l[3],
+        class: validateMutation(l[4], errors)
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseSvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length < 4 || l.length > 6) {
+      errors.push("sv input not equal to 4 or 6 columns");
+      continue;
+    }
+    let m;
+    try {
+      const length = l.length;
+      if (length == 4) {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          chrB: l[2],
+          posB: Number(l[3])
+        };
+      } else {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          geneA: l[2],
+          chrB: l[3],
+          posB: Number(l[4]),
+          geneB: l[5]
+        };
+      }
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseCnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 4) {
+      errors.push("cnv input not equal to 4 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 4,
+        chr: l[0],
+        start: Number(l[1]),
+        stop: Number(l[2]),
+        value: Number(l[3])
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function validateMutation(mutation, errors) {
+  const mut2check = mutation.toLowerCase();
+  const foundMutation = Object.values(mclass).find(
+    (m) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check
+  );
+  if (foundMutation) {
+    return foundMutation.key;
+  } else {
+    errors.push(`Invalid mutation class: ${mutation}`);
+  }
+}
+
+export {
+  launch
+};
+//# sourceMappingURL=chunk-NL3DVEVX.js.map