@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/chunk-MSW7OS2O.js

@@ -1,276 +0,0 @@
-import {
-  parsesample
-} from "./chunk-6ZCHECOT.js";
-import {
-  dtfusionrna,
-  dtsv,
-  mclassfusionrna,
-  mclasssv
-} from "./chunk-AMYSEKPF.js";
-
-// ../shared/utils/src/bulk.sv.js
-function parseheader(line, flag, issv) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid file header for fusions";
-  const htry = (...lst) => {
-    for (const a of lst) {
-      const j = header.indexOf(a);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("gene_a", "gene1", "genea");
-  if (i == -1) return "gene_a missing from header";
-  header[i] = "gene1";
-  i = htry("gene_b", "gene2", "geneb");
-  if (i == -1) return "gene_b missing from header";
-  header[i] = "gene2";
-  i = htry("chr_a", "chr1", "chra");
-  if (i == -1) return "chr_a missing from header";
-  header[i] = "chr1";
-  i = htry("chr_b", "chr2", "chrb");
-  if (i == -1) return "chr_b missing from header";
-  header[i] = "chr2";
-  i = htry("pos_a", "position_a", "position1", "posa");
-  if (i == -1) return "pos_a missing from header";
-  header[i] = "position1";
-  i = htry("pos_b", "position_b", "position2", "posb");
-  if (i == -1) return "pos_b missing from header";
-  header[i] = "position2";
-  i = htry("isoform_a", "refseq_a", "refseq1", "isoform1", "sv_refseqa");
-  if (i == -1) return "isoform_a missing from header";
-  header[i] = "isoform1";
-  i = htry("isoform_b", "refseq_b", "refseq2", "isoform2", "sv_refseqb");
-  if (i == -1) return "isoform_b missing from header";
-  header[i] = "isoform2";
-  i = htry("strand_a", "orta");
-  if (i == -1) return "strand_a missing from header";
-  header[i] = "strand1";
-  i = htry("strand_b", "ortb");
-  if (i == -1) return "strand_b missing from header";
-  header[i] = "strand2";
-  i = htry("sample", "sample_name", "tumor_sample_barcode");
-  if (i != -1) header[i] = "sample";
-  i = htry("patient", "donor", "target_case_id");
-  if (i != -1) header[i] = "patient";
-  i = htry("sampletype", "sample type", "sample_type");
-  if (i != -1) header[i] = "sampletype";
-  i = htry("disease");
-  if (i != -1) header[i] = "disease";
-  i = htry("origin");
-  if (i != -1) header[i] = "origin";
-  if (issv) {
-    flag.sv.loaded = true;
-    flag.sv.header = header;
-  } else {
-    flag.fusion.loaded = true;
-    flag.fusion.header = header;
-  }
-  return false;
-}
-function parseline(i, line, flag, issv) {
-  if (line == "" || line[0] == "#") return;
-  const lst = line.split("	");
-  const m = {};
-  const header = issv ? flag.sv.header : flag.fusion.header;
-  const badlines = issv ? flag.sv.badlines : flag.fusion.badlines;
-  for (let j = 0; j < header.length; j++) {
-    m[header[j]] = lst[j];
-  }
-  if (!m.chr1) {
-    badlines.push([i, "missing chr1", lst]);
-    return;
-  }
-  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
-    m.chr1 = "chr" + m.chr1;
-  }
-  if (!m.chr2) {
-    badlines.push([i, "missing chr2", lst]);
-    return;
-  }
-  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
-    m.chr2 = "chr" + m.chr2;
-  }
-  let v = m.position1;
-  if (!v) {
-    badlines.push([i, "missing position1", lst]);
-    return;
-  }
-  let v2 = Number.parseInt(v);
-  if (Number.isNaN(v2) || v2 <= 0) {
-    badlines.push([i, "invalid value for position1", lst]);
-    return;
-  }
-  m.position1 = v2;
-  v = m.position2;
-  if (!v) {
-    badlines.push([i, "missing position2", lst]);
-    return;
-  }
-  v2 = Number.parseInt(v);
-  if (Number.isNaN(v2) || v2 <= 0) {
-    badlines.push([i, "invalid value for position2", lst]);
-    return;
-  }
-  m.position2 = v2;
-  if (parsesample(m, flag, i, lst, badlines)) {
-    return;
-  }
-  if (m.isoform1 && m.isoform1.indexOf(",") != -1) {
-    const lst2 = m.isoform1.split(",");
-    m.isoform1 = void 0;
-    for (const t of lst2) {
-      if (t != "") m.isoform1 = t;
-    }
-  }
-  if (m.isoform2 && m.isoform2.indexOf(",") != -1) {
-    const lst2 = m.isoform2.split(",");
-    m.isoform2 = void 0;
-    for (const t of lst2) {
-      if (t != "") m.isoform2 = t;
-    }
-  }
-  if (!m.gene1) {
-    m.isoform1 = void 0;
-  }
-  if (!m.gene2) {
-    m.isoform2 = void 0;
-  }
-  if (m.gene1) {
-    flag.good++;
-    const m2 = {
-      dt: issv ? dtsv : dtfusionrna,
-      class: issv ? mclasssv : mclassfusionrna,
-      isoform: m.isoform1,
-      mname: m.gene2 || m.chr2,
-      sample: m.sample,
-      patient: m.patient,
-      sampletype: m.sampletype,
-      origin: m.origin,
-      disease: m.disease,
-      pairlst: [
-        {
-          a: {
-            name: m.gene1,
-            isoform: m.isoform1,
-            strand: m.strand1,
-            chr: m.chr1,
-            position: m.position1
-          },
-          b: {
-            name: m.gene2,
-            isoform: m.isoform2,
-            strand: m.strand2,
-            chr: m.chr2,
-            position: m.position2
-          }
-        }
-      ]
-    };
-    const n = flag.geneToUpper ? m.gene1.toUpperCase() : m.gene1;
-    if (!flag.data[n]) {
-      flag.data[n] = [];
-    }
-    flag.data[n].push(m2);
-  }
-  if (m.gene2 && m.gene2 != m.gene1) {
-    flag.good++;
-    const m2 = {
-      dt: issv ? dtsv : dtfusionrna,
-      class: issv ? mclasssv : mclassfusionrna,
-      isoform: m.isoform2,
-      mname: m.gene1 || m.chr1,
-      sample: m.sample,
-      patient: m.patient,
-      sampletype: m.sampletype,
-      origin: m.origin,
-      disease: m.disease,
-      pairlst: [
-        {
-          a: {
-            name: m.gene1,
-            isoform: m.isoform1,
-            strand: m.strand1,
-            chr: m.chr1,
-            position: m.position1
-          },
-          b: {
-            name: m.gene2,
-            isoform: m.isoform2,
-            strand: m.strand2,
-            chr: m.chr2,
-            position: m.position2
-          }
-        }
-      ]
-    };
-    const n = flag.geneToUpper ? m.gene2.toUpperCase() : m.gene2;
-    if (!flag.data[n]) {
-      flag.data[n] = [];
-    }
-    flag.data[n].push(m2);
-  }
-}
-function duplicate(m) {
-  const n = {};
-  for (const k in m) {
-    if (k == "pairlst") continue;
-    const v = m[k];
-    const type = typeof v;
-    if (type == "object") {
-      continue;
-    }
-    n[k] = v;
-  }
-  if (m.pairlst) {
-    n.pairlst = [];
-    for (const pair of m.pairlst) {
-      const p = {};
-      for (const k in pair) {
-        if (k == "a" || k == "b" || k == "interstitial") {
-          continue;
-        }
-        p[k] = pair[k];
-      }
-      if (pair.a) {
-        p.a = {};
-        for (const k in pair.a) {
-          const v = pair.a[k];
-          if (typeof v == "object") {
-            continue;
-          }
-          p.a[k] = v;
-        }
-      }
-      if (pair.b) {
-        p.b = {};
-        for (const k in pair.b) {
-          const v = pair.b[k];
-          if (typeof v == "object") {
-            continue;
-          }
-          p.b[k] = v;
-        }
-      }
-      if (pair.interstitial) {
-        p.interstitial = {};
-        for (const k in pair.interstitial) {
-          const v = pair.interstitial[k];
-          if (typeof v == "object") {
-            continue;
-          }
-          p.interstitial[k] = v;
-        }
-      }
-      n.pairlst.push(p);
-    }
-  }
-  return n;
-}
-
-export {
-  parseheader,
-  parseline,
-  duplicate
-};
-//# sourceMappingURL=chunk-MSW7OS2O.js.map

package/dist/chunk-MVCGSYS2.js

@@ -1,50 +0,0 @@
-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

@@ -1,102 +0,0 @@
-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

@@ -1,158 +0,0 @@
-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