@sjcrh/proteinpaint-client 2.166.0 → 2.167.0

package/dist/chunk-RQUXELHE.js

@@ -1,276 +0,0 @@
-import {
-  parsesample
-} from "./chunk-5TDKRZN5.js";
-import {
-  dtfusionrna,
-  dtsv,
-  mclassfusionrna,
-  mclasssv
-} from "./chunk-ECKWM4HB.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-RQUXELHE.js.map

package/dist/chunk-RYRCMHYR.js

@@ -1,196 +0,0 @@
-import {
-  TermTypeGroups,
-  dtTerms,
-  dtgeneexpression,
-  dtmetaboliteintensity,
-  dtssgsea
-} from "./chunk-ECKWM4HB.js";
-
-// ../shared/utils/src/terms.js
-var ROOT_SAMPLE_TYPE = 1;
-var DEFAULT_SAMPLE_TYPE = 2;
-var NumericModes = {
-  continuous: "continuous",
-  discrete: "discrete"
-};
-var TermTypes = {
-  GENE_VARIANT: "geneVariant",
-  GENE_EXPRESSION: "geneExpression",
-  SSGSEA: "ssGSEA",
-  CATEGORICAL: "categorical",
-  INTEGER: "integer",
-  FLOAT: "float",
-  SNP: "snp",
-  SNP_LIST: "snplst",
-  SNP_LOCUS: "snplocus",
-  CONDITION: "condition",
-  SURVIVAL: "survival",
-  SAMPLELST: "samplelst",
-  METABOLITE_INTENSITY: "metaboliteIntensity",
-  SINGLECELL_GENE_EXPRESSION: "singleCellGeneExpression",
-  SINGLECELL_CELLTYPE: "singleCellCellType",
-  MULTIVALUE: "multivalue",
-  DATE: "date",
-  TERM_COLLECTION: "termCollection"
-};
-var dtTermTypes = new Set(dtTerms.map((t) => t.type));
-for (const dtTermType of dtTermTypes) {
-  TermTypes[dtTermType.toUpperCase()] = dtTermType;
-}
-var NUMERIC_DICTIONARY_TERM = "numericDictTerm";
-var TermTypes2Dt = {
-  [TermTypes.GENE_EXPRESSION]: dtgeneexpression,
-  [TermTypes.SSGSEA]: dtssgsea,
-  [TermTypes.METABOLITE_INTENSITY]: dtmetaboliteintensity
-};
-var typeGroup = {
-  [TermTypes.CATEGORICAL]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [TermTypes.CONDITION]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [TermTypes.FLOAT]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [TermTypes.INTEGER]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [TermTypes.SAMPLELST]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [TermTypes.SURVIVAL]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [TermTypes.GENE_VARIANT]: TermTypeGroups.MUTATION_CNV_FUSION,
-  [TermTypes.SNP]: TermTypeGroups.SNP,
-  [TermTypes.SNP_LIST]: TermTypeGroups.SNP_LIST,
-  [TermTypes.SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,
-  [TermTypes.GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,
-  [TermTypes.SSGSEA]: TermTypeGroups.SSGSEA,
-  [TermTypes.METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,
-  [TermTypes.TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION
-};
-var nonDictTypes = /* @__PURE__ */ new Set([
-  TermTypes.SNP,
-  TermTypes.SNP_LIST,
-  TermTypes.SNP_LOCUS,
-  TermTypes.GENE_EXPRESSION,
-  TermTypes.SSGSEA,
-  TermTypes.GENE_VARIANT,
-  TermTypes.METABOLITE_INTENSITY,
-  TermTypes.SINGLECELL_GENE_EXPRESSION,
-  TermTypes.SINGLECELL_CELLTYPE
-]);
-for (const dtTermType of dtTermTypes) {
-  nonDictTypes.add(TermTypes[dtTermType.toUpperCase()]);
-}
-var numericTypes = /* @__PURE__ */ new Set([
-  TermTypes.INTEGER,
-  TermTypes.FLOAT,
-  TermTypes.GENE_EXPRESSION,
-  TermTypes.SSGSEA,
-  TermTypes.METABOLITE_INTENSITY,
-  TermTypes.SINGLECELL_GENE_EXPRESSION,
-  TermTypes.DATE
-]);
-var annoNumericTypes = /* @__PURE__ */ new Set([TermTypes.INTEGER, TermTypes.FLOAT, TermTypes.DATE]);
-var categoricalTypes = /* @__PURE__ */ new Set([TermTypes.CATEGORICAL, TermTypes.SNP]);
-var singleSampleTerms = /* @__PURE__ */ new Set([TermTypes.SINGLECELL_GENE_EXPRESSION]);
-function isNumericTerm(term) {
-  if (!term) return false;
-  return numericTypes.has(term.type);
-}
-function isCategoricalTerm(term) {
-  if (!term) return false;
-  return categoricalTypes.has(term.type);
-}
-function isDictionaryType(type) {
-  return !isNonDictionaryType(type);
-}
-function isNonDictionaryType(type) {
-  if (!type) throw new Error("Type is not defined");
-  return nonDictTypes.has(type);
-}
-function equals(t1, t2) {
-  if (!t1) throw new Error("First term is not defined ");
-  if (!t2) throw new Error("Second term is not defined ");
-  if (t1.type !== t2.type) return false;
-  if (isDictionaryType(t1.type) && isDictionaryType(t2.type) && t1.type != TermTypes.SAMPLELST) return t1.id === t2.id;
-  switch (t1.type) {
-    case TermTypes.GENE_EXPRESSION:
-      return t1.gene == t2.gene;
-    case TermTypes.SSGSEA:
-      return t1.id == t2.id;
-    case TermTypes.METABOLITE_INTENSITY:
-      return t1.name == t2.name;
-    case TermTypes.GENE_VARIANT:
-      return t1.gene == t2.gene || t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop;
-    // TO DO: Add more cases
-    // case TermTypes.SNP_LIST:
-    // case TermTypes.SNP_LOCUS:
-    // case TermTypes.SAMPLELST:
-    default:
-      return false;
-  }
-}
-var typeMap = {
-  categorical: "Categorical",
-  condition: "Condition",
-  float: "Numerical",
-  integer: "Numerical",
-  geneExpression: "Gene Expression",
-  ssGSEA: "Geneset Expression",
-  geneVariant: "Gene Variant",
-  metaboliteIntensity: "Metabolite Intensity",
-  multiValue: "Multi Value",
-  singleCellGeneExpression: "Single Cell, Gene Expression",
-  singleCellCellType: "Single Cell, Cell Type",
-  snplocus: "SNP Locus",
-  snp: "SNP",
-  snplst: "SNP List",
-  numericDictTerm: "Numeric Dictionary Term",
-  termCollection: "Term Collection"
-};
-function termType2label(type) {
-  return typeMap[type] || "Unknown term type";
-}
-function getDateFromNumber(value) {
-  const year = Math.floor(value);
-  const january1st = new Date(year, 0, 1);
-  const totalDays = getDaysInYear(year);
-  const time = Math.round((value - year) * totalDays) * oneDayTime;
-  const date = new Date(january1st.getTime() + time);
-  return date;
-}
-var oneDayTime = 24 * 60 * 60 * 1e3;
-function getDateStrFromNumber(value) {
-  const date = getDateFromNumber(value);
-  return date.toLocaleDateString("en-US", {
-    year: "numeric",
-    month: "long"
-  });
-}
-function getNumberFromDate(date) {
-  const year = date.getFullYear();
-  const january1st = new Date(year, 0, 1);
-  const diffDays = (date - january1st) / oneDayTime;
-  const daysTotal = getDaysInYear(year);
-  const decimal = diffDays / daysTotal;
-  return year + decimal;
-}
-function getDaysInYear(year) {
-  const isLeap = new Date(year, 1, 29).getMonth() === 1;
-  const days = isLeap ? 366 : 365;
-  return days;
-}
-
-export {
-  ROOT_SAMPLE_TYPE,
-  DEFAULT_SAMPLE_TYPE,
-  NumericModes,
-  TermTypes,
-  dtTermTypes,
-  NUMERIC_DICTIONARY_TERM,
-  TermTypes2Dt,
-  typeGroup,
-  numericTypes,
-  isNumericTerm,
-  isCategoricalTerm,
-  isDictionaryType,
-  isNonDictionaryType,
-  equals,
-  termType2label,
-  getDateFromNumber,
-  getDateStrFromNumber,
-  getNumberFromDate
-};
-//# sourceMappingURL=chunk-RYRCMHYR.js.map