@morscherlab/mld-sdk 0.7.5 → 0.7.6

package/dist/composables/useAutoGroup.js

@@ -0,0 +1,397 @@
+import { ref, computed } from "vue";
+const DEFAULT_COLORS = [
+  "#3B82F6",
+  "#10B981",
+  "#F59E0B",
+  "#EF4444",
+  "#8B5CF6",
+  "#EC4899",
+  "#06B6D4",
+  "#84CC16",
+  "#F97316",
+  "#6366F1"
+];
+const DELIMITER_CANDIDATES = ["_", "-", "."];
+function analyzeDelimiter(lines) {
+  if (lines.length === 0) {
+    return { delimiter: "_", dominantFieldCount: 1, minFieldCount: 1, consistency: 0 };
+  }
+  let bestDelimiter = "_";
+  let bestConsistency = -1;
+  let bestFieldCount = 1;
+  for (const candidate of DELIMITER_CANDIDATES) {
+    const fieldCounts = lines.map((line) => line.split(candidate).length);
+    const countFrequency = /* @__PURE__ */ new Map();
+    for (const count of fieldCounts) {
+      countFrequency.set(count, (countFrequency.get(count) ?? 0) + 1);
+    }
+    let modeCount = 1;
+    let modeFrequency = 0;
+    for (const [count, freq] of countFrequency) {
+      if (freq > modeFrequency || freq === modeFrequency && count > modeCount) {
+        modeCount = count;
+        modeFrequency = freq;
+      }
+    }
+    const rawConsistency = modeFrequency / lines.length;
+    const consistency = modeCount > 1 ? rawConsistency : 0;
+    if (consistency > bestConsistency || consistency === bestConsistency && DELIMITER_CANDIDATES.indexOf(candidate) < DELIMITER_CANDIDATES.indexOf(bestDelimiter)) {
+      bestDelimiter = candidate;
+      bestConsistency = consistency;
+      bestFieldCount = modeCount;
+    }
+  }
+  const bestFieldCounts = lines.map((line) => line.split(bestDelimiter).length);
+  const multiFieldCounts = bestFieldCounts.filter((c) => c >= 2);
+  const minFieldCount = multiFieldCounts.length > 0 ? Math.min(...multiFieldCounts) : 1;
+  return {
+    delimiter: bestDelimiter,
+    dominantFieldCount: bestFieldCount,
+    minFieldCount,
+    consistency: bestConsistency
+  };
+}
+function detectOutliers(lines, delimiter, minFieldCount) {
+  const outliers = [];
+  for (let i = 0; i < lines.length; i++) {
+    const fieldCount = lines[i].split(delimiter).length;
+    if (fieldCount < minFieldCount) {
+      outliers.push({
+        sample: lines[i],
+        index: i,
+        fieldCount,
+        action: "include"
+      });
+    }
+  }
+  return outliers;
+}
+function extractColumns(samples, delimiter, minFieldCount) {
+  if (samples.length === 0) return [];
+  const suffixCount = minFieldCount - 1;
+  const rows = samples.map((s) => {
+    const parts = s.split(delimiter);
+    const splitAt = parts.length - suffixCount;
+    return [
+      parts.slice(0, splitAt).join(delimiter),
+      ...parts.slice(splitAt)
+    ];
+  });
+  const columnCount = minFieldCount;
+  const columns = [];
+  for (let col = 0; col < columnCount; col++) {
+    const values = rows.map((row) => row[col]);
+    const unique = [...new Set(values)];
+    columns.push({
+      index: col,
+      name: col === 0 ? "Condition" : `Field ${col + 1}`,
+      uniqueValues: unique,
+      cardinality: unique.length,
+      type: col === 0 ? "prefix" : "suffix"
+    });
+  }
+  return columns;
+}
+function parseCSVLine(line) {
+  const result = [];
+  let current = "";
+  let inQuotes = false;
+  for (let i = 0; i < line.length; i++) {
+    const char = line[i];
+    if (char === '"') {
+      inQuotes = !inQuotes;
+    } else if (char === "," && !inQuotes) {
+      result.push(current.trim());
+      current = "";
+    } else {
+      current += char;
+    }
+  }
+  result.push(current.trim());
+  return result;
+}
+function parseCSV(text) {
+  const lines = text.trim().split("\n");
+  if (lines.length < 2) {
+    throw new Error("CSV must have at least a header and one data row");
+  }
+  const headers = parseCSVLine(lines[0]);
+  const rows = [];
+  for (let i = 1; i < lines.length; i++) {
+    const values = parseCSVLine(lines[i]);
+    if (values.length !== headers.length) continue;
+    const row = {};
+    headers.forEach((header, idx) => {
+      row[header] = values[idx];
+    });
+    rows.push(row);
+  }
+  const sampleKeywords = ["sample", "name", "id", "sample_name", "samplename"];
+  const sampleColumn = headers.find((h) => sampleKeywords.includes(h.toLowerCase())) ?? headers[0];
+  return { columns: headers, rows, sampleColumn };
+}
+function computeGroups(allSamples, columns, enabledFields, outlierActions, delimiter, minFieldCount) {
+  const excludedSamples = [];
+  const qcSamples = [];
+  const conformingSamples = [];
+  for (let i = 0; i < allSamples.length; i++) {
+    const action = outlierActions.get(i);
+    if (action === "exclude") {
+      excludedSamples.push(allSamples[i]);
+    } else if (action === "qc") {
+      qcSamples.push(allSamples[i]);
+    } else {
+      conformingSamples.push(allSamples[i]);
+    }
+  }
+  const groupMap = /* @__PURE__ */ new Map();
+  const metadata = [];
+  const enabledIndices = [...enabledFields].sort((a, b) => a - b);
+  const suffixCount = minFieldCount - 1;
+  for (const sample of conformingSamples) {
+    const parts = sample.split(delimiter);
+    const splitAt = Math.max(1, parts.length - suffixCount);
+    const row = [
+      parts.slice(0, splitAt).join(delimiter),
+      ...parts.slice(splitAt)
+    ];
+    const keyParts = [];
+    for (const idx of enabledIndices) {
+      if (idx < row.length && idx < columns.length) {
+        keyParts.push(row[idx]);
+      }
+    }
+    const groupKey = keyParts.join(" / ");
+    if (!groupMap.has(groupKey)) {
+      groupMap.set(groupKey, []);
+    }
+    groupMap.get(groupKey).push(sample);
+    const fields = {};
+    for (const col of columns) {
+      if (col.index < row.length) {
+        fields[col.name] = row[col.index];
+      }
+    }
+    metadata.push({ sampleName: sample, fields, group: groupKey });
+  }
+  const groups = [];
+  let colorIdx = 0;
+  for (const [name, samples] of groupMap) {
+    groups.push({
+      name,
+      color: DEFAULT_COLORS[colorIdx % DEFAULT_COLORS.length],
+      samples
+    });
+    colorIdx++;
+  }
+  if (qcSamples.length > 0) {
+    groups.push({
+      name: "QC",
+      color: "#6B7280",
+      samples: qcSamples
+    });
+    for (const sample of qcSamples) {
+      metadata.push({ sampleName: sample, fields: {}, group: "QC" });
+    }
+  }
+  return { groups, metadata, excludedSamples };
+}
+function useAutoGroup() {
+  const inputMode = ref("paste");
+  const rawText = ref("");
+  const csvData = ref(null);
+  const delimiter = ref("_");
+  const dominantFieldCount = ref(1);
+  const minFieldCount = ref(1);
+  const outliers = ref([]);
+  const fields = ref([]);
+  const fieldNames = ref({});
+  const enabledFields = ref(/* @__PURE__ */ new Set());
+  const samples = computed(() => {
+    if (inputMode.value === "csv" && csvData.value) {
+      return csvData.value.rows.map((r) => r[csvData.value.sampleColumn]);
+    }
+    return rawText.value.split("\n").map((l) => l.trim()).filter((l) => l.length > 0);
+  });
+  const hasOutliers = computed(() => outliers.value.length > 0);
+  const conformingSamples = computed(() => {
+    const outlierIndices = new Set(outliers.value.map((o) => o.index));
+    return samples.value.filter((_, i) => !outlierIndices.has(i));
+  });
+  const outlierActions = computed(() => {
+    const map = /* @__PURE__ */ new Map();
+    for (const o of outliers.value) {
+      map.set(o.index, o.action);
+    }
+    return map;
+  });
+  const effectiveColumns = computed(() => {
+    return fields.value.map((col) => ({
+      ...col,
+      name: fieldNames.value[col.index] ?? col.name
+    }));
+  });
+  const groups = computed(() => {
+    if (effectiveColumns.value.length === 0 || enabledFields.value.size === 0) {
+      return [];
+    }
+    const result2 = computeGroups(
+      samples.value,
+      effectiveColumns.value,
+      enabledFields.value,
+      outlierActions.value,
+      delimiter.value,
+      minFieldCount.value
+    );
+    return result2.groups;
+  });
+  const metadata = computed(() => {
+    if (effectiveColumns.value.length === 0 || enabledFields.value.size === 0) {
+      return [];
+    }
+    return computeGroups(
+      samples.value,
+      effectiveColumns.value,
+      enabledFields.value,
+      outlierActions.value,
+      delimiter.value,
+      minFieldCount.value
+    ).metadata;
+  });
+  const excludedSamples = computed(() => {
+    return computeGroups(
+      samples.value,
+      effectiveColumns.value,
+      enabledFields.value,
+      outlierActions.value,
+      delimiter.value,
+      minFieldCount.value
+    ).excludedSamples;
+  });
+  const result = computed(() => ({
+    groups: groups.value,
+    metadata: metadata.value,
+    excludedSamples: excludedSamples.value
+  }));
+  function parseInput() {
+    if (inputMode.value === "csv" && csvData.value) {
+      parseCsvInput();
+    } else {
+      parsePasteInput();
+    }
+  }
+  function parsePasteInput() {
+    const lines = samples.value;
+    if (lines.length === 0) return;
+    const analysis = analyzeDelimiter(lines);
+    delimiter.value = analysis.delimiter;
+    dominantFieldCount.value = analysis.dominantFieldCount;
+    minFieldCount.value = analysis.minFieldCount;
+    outliers.value = detectOutliers(lines, analysis.delimiter, analysis.minFieldCount);
+    const conforming = lines.filter(
+      (_, i) => !outliers.value.some((o) => o.index === i)
+    );
+    fields.value = extractColumns(conforming, analysis.delimiter, analysis.minFieldCount);
+    fieldNames.value = {};
+    enabledFields.value = new Set(fields.value.map((f) => f.index));
+  }
+  function parseCsvInput() {
+    if (!csvData.value) return;
+    const csv = csvData.value;
+    const nonSampleCols = csv.columns.filter((c) => c !== csv.sampleColumn);
+    fields.value = nonSampleCols.map((col, i) => {
+      const values = csv.rows.map((r) => r[col]);
+      const unique = [...new Set(values)];
+      return {
+        index: i,
+        name: col,
+        uniqueValues: unique,
+        cardinality: unique.length
+      };
+    });
+    outliers.value = [];
+    delimiter.value = ",";
+    dominantFieldCount.value = csv.columns.length;
+    fieldNames.value = {};
+    for (const f of fields.value) {
+      fieldNames.value[f.index] = f.name;
+    }
+    enabledFields.value = new Set(fields.value.map((f) => f.index));
+  }
+  function setOutlierAction(index, action) {
+    const outlier = outliers.value.find((o) => o.index === index);
+    if (outlier) {
+      outlier.action = action;
+      outliers.value = [...outliers.value];
+    }
+  }
+  function setAllOutlierActions(action) {
+    for (const outlier of outliers.value) {
+      outlier.action = action;
+    }
+    outliers.value = [...outliers.value];
+  }
+  function toggleField(index) {
+    const newSet = new Set(enabledFields.value);
+    if (newSet.has(index)) {
+      newSet.delete(index);
+    } else {
+      newSet.add(index);
+    }
+    enabledFields.value = newSet;
+  }
+  function renameField(index, name) {
+    fieldNames.value = { ...fieldNames.value, [index]: name };
+  }
+  function reset() {
+    rawText.value = "";
+    csvData.value = null;
+    delimiter.value = "_";
+    dominantFieldCount.value = 1;
+    minFieldCount.value = 1;
+    outliers.value = [];
+    fields.value = [];
+    fieldNames.value = {};
+    enabledFields.value = /* @__PURE__ */ new Set();
+  }
+  return {
+    // State
+    inputMode,
+    rawText,
+    csvData,
+    delimiter,
+    dominantFieldCount,
+    minFieldCount,
+    outliers,
+    fields,
+    fieldNames,
+    enabledFields,
+    // Computed
+    samples,
+    hasOutliers,
+    conformingSamples,
+    groups,
+    metadata,
+    excludedSamples,
+    result,
+    effectiveColumns,
+    // Actions
+    parseInput,
+    setOutlierAction,
+    setAllOutlierActions,
+    toggleField,
+    renameField,
+    reset
+  };
+}
+export {
+  DEFAULT_COLORS,
+  analyzeDelimiter,
+  computeGroups,
+  detectOutliers,
+  extractColumns,
+  parseCSV,
+  parseCSVLine,
+  useAutoGroup
+};
+//# sourceMappingURL=useAutoGroup.js.map

package/dist/composables/useAutoGroup.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"useAutoGroup.js","sources":["../../src/composables/useAutoGroup.ts"],"sourcesContent":["import { ref, computed } from 'vue'\nimport type {\n  InputMode,\n  OutlierAction,\n  OutlierInfo,\n  ColumnInfo,\n  MetadataRow,\n  AutoGroupResult,\n  ParsedCsvData,\n} from '../types/auto-group'\nimport type { SampleGroup } from '../types/components'\n\nexport const DEFAULT_COLORS = [\n  '#3B82F6', '#10B981', '#F59E0B', '#EF4444', '#8B5CF6',\n  '#EC4899', '#06B6D4', '#84CC16', '#F97316', '#6366F1',\n]\n\nconst DELIMITER_CANDIDATES = ['_', '-', '.'] as const\n\n// --- Pure functions (exported for testing) ---\n\nexport function analyzeDelimiter(lines: string[]): {\n  delimiter: string\n  dominantFieldCount: number\n  minFieldCount: number\n  consistency: number\n} {\n  if (lines.length === 0) {\n    return { delimiter: '_', dominantFieldCount: 1, minFieldCount: 1, consistency: 0 }\n  }\n\n  let bestDelimiter = '_'\n  let bestConsistency = -1\n  let bestFieldCount = 1\n\n  for (const candidate of DELIMITER_CANDIDATES) {\n    const fieldCounts = lines.map(line => line.split(candidate).length)\n    const countFrequency = new Map<number, number>()\n\n    for (const count of fieldCounts) {\n      countFrequency.set(count, (countFrequency.get(count) ?? 0) + 1)\n    }\n\n    // Find mode (most frequent field count)\n    let modeCount = 1\n    let modeFrequency = 0\n    for (const [count, freq] of countFrequency) {\n      if (freq > modeFrequency || (freq === modeFrequency && count > modeCount)) {\n        modeCount = count\n        modeFrequency = freq\n      }\n    }\n\n    const rawConsistency = modeFrequency / lines.length\n    // A delimiter that produces field count 1 didn't actually split anything\n    const consistency = modeCount > 1 ? rawConsistency : 0\n\n    if (\n      consistency > bestConsistency ||\n      (consistency === bestConsistency &&\n        DELIMITER_CANDIDATES.indexOf(candidate) < DELIMITER_CANDIDATES.indexOf(bestDelimiter as typeof candidate))\n    ) {\n      bestDelimiter = candidate\n      bestConsistency = consistency\n      bestFieldCount = modeCount\n    }\n  }\n\n  const bestFieldCounts = lines.map(line => line.split(bestDelimiter).length)\n  const multiFieldCounts = bestFieldCounts.filter(c => c >= 2)\n  const minFieldCount = multiFieldCounts.length > 0 ? Math.min(...multiFieldCounts) : 1\n\n  return {\n    delimiter: bestDelimiter,\n    dominantFieldCount: bestFieldCount,\n    minFieldCount,\n    consistency: bestConsistency,\n  }\n}\n\nexport function detectOutliers(\n  lines: string[],\n  delimiter: string,\n  minFieldCount: number,\n): OutlierInfo[] {\n  const outliers: OutlierInfo[] = []\n\n  for (let i = 0; i < lines.length; i++) {\n    const fieldCount = lines[i].split(delimiter).length\n    if (fieldCount < minFieldCount) {\n      outliers.push({\n        sample: lines[i],\n        index: i,\n        fieldCount,\n        action: 'include',\n      })\n    }\n  }\n\n  return outliers\n}\n\nexport function extractColumns(\n  samples: string[],\n  delimiter: string,\n  minFieldCount: number,\n): ColumnInfo[] {\n  if (samples.length === 0) return []\n\n  const suffixCount = minFieldCount - 1\n  const rows = samples.map(s => {\n    const parts = s.split(delimiter)\n    const splitAt = parts.length - suffixCount\n    return [\n      parts.slice(0, splitAt).join(delimiter),\n      ...parts.slice(splitAt),\n    ]\n  })\n\n  const columnCount = minFieldCount\n  const columns: ColumnInfo[] = []\n  for (let col = 0; col < columnCount; col++) {\n    const values = rows.map(row => row[col])\n    const unique = [...new Set(values)]\n    columns.push({\n      index: col,\n      name: col === 0 ? 'Condition' : `Field ${col + 1}`,\n      uniqueValues: unique,\n      cardinality: unique.length,\n      type: col === 0 ? 'prefix' : 'suffix',\n    })\n  }\n\n  return columns\n}\n\nexport function parseCSVLine(line: string): string[] {\n  const result: string[] = []\n  let current = ''\n  let inQuotes = false\n\n  for (let i = 0; i < line.length; i++) {\n    const char = line[i]\n    if (char === '\"') {\n      inQuotes = !inQuotes\n    } else if (char === ',' && !inQuotes) {\n      result.push(current.trim())\n      current = ''\n    } else {\n      current += char\n    }\n  }\n  result.push(current.trim())\n\n  return result\n}\n\nexport function parseCSV(text: string): ParsedCsvData {\n  const lines = text.trim().split('\\n')\n  if (lines.length < 2) {\n    throw new Error('CSV must have at least a header and one data row')\n  }\n\n  const headers = parseCSVLine(lines[0])\n  const rows: Record<string, string>[] = []\n\n  for (let i = 1; i < lines.length; i++) {\n    const values = parseCSVLine(lines[i])\n    if (values.length !== headers.length) continue\n    const row: Record<string, string> = {}\n    headers.forEach((header, idx) => {\n      row[header] = values[idx]\n    })\n    rows.push(row)\n  }\n\n  // Auto-detect sample column\n  const sampleKeywords = ['sample', 'name', 'id', 'sample_name', 'samplename']\n  const sampleColumn =\n    headers.find(h => sampleKeywords.includes(h.toLowerCase())) ?? headers[0]\n\n  return { columns: headers, rows, sampleColumn }\n}\n\nexport function computeGroups(\n  allSamples: string[],\n  columns: ColumnInfo[],\n  enabledFields: Set<number>,\n  outlierActions: Map<number, OutlierAction>,\n  delimiter: string,\n  minFieldCount: number,\n): { groups: SampleGroup[]; metadata: MetadataRow[]; excludedSamples: string[] } {\n  const excludedSamples: string[] = []\n  const qcSamples: string[] = []\n  const conformingSamples: string[] = []\n\n  for (let i = 0; i < allSamples.length; i++) {\n    const action = outlierActions.get(i)\n    if (action === 'exclude') {\n      excludedSamples.push(allSamples[i])\n    } else if (action === 'qc') {\n      qcSamples.push(allSamples[i])\n    } else {\n      conformingSamples.push(allSamples[i])\n    }\n  }\n\n  // Build group map\n  const groupMap = new Map<string, string[]>()\n  const metadata: MetadataRow[] = []\n  const enabledIndices = [...enabledFields].sort((a, b) => a - b)\n\n  const suffixCount = minFieldCount - 1\n\n  for (const sample of conformingSamples) {\n    const parts = sample.split(delimiter)\n    const splitAt = Math.max(1, parts.length - suffixCount)\n    const row = [\n      parts.slice(0, splitAt).join(delimiter),\n      ...parts.slice(splitAt),\n    ]\n\n    // Build group key from enabled columns\n    const keyParts: string[] = []\n    for (const idx of enabledIndices) {\n      if (idx < row.length && idx < columns.length) {\n        keyParts.push(row[idx])\n      }\n    }\n    const groupKey = keyParts.join(' / ')\n\n    if (!groupMap.has(groupKey)) {\n      groupMap.set(groupKey, [])\n    }\n    groupMap.get(groupKey)!.push(sample)\n\n    // Build metadata row with ALL columns\n    const fields: Record<string, string> = {}\n    for (const col of columns) {\n      if (col.index < row.length) {\n        fields[col.name] = row[col.index]\n      }\n    }\n    metadata.push({ sampleName: sample, fields, group: groupKey })\n  }\n\n  // Convert to SampleGroup[]\n  const groups: SampleGroup[] = []\n  let colorIdx = 0\n  for (const [name, samples] of groupMap) {\n    groups.push({\n      name,\n      color: DEFAULT_COLORS[colorIdx % DEFAULT_COLORS.length],\n      samples,\n    })\n    colorIdx++\n  }\n\n  // QC group\n  if (qcSamples.length > 0) {\n    groups.push({\n      name: 'QC',\n      color: '#6B7280',\n      samples: qcSamples,\n    })\n    for (const sample of qcSamples) {\n      metadata.push({ sampleName: sample, fields: {}, group: 'QC' })\n    }\n  }\n\n  return { groups, metadata, excludedSamples }\n}\n\n// --- Reactive composable ---\n\nexport function useAutoGroup() {\n  const inputMode = ref<InputMode>('paste')\n  const rawText = ref('')\n  const csvData = ref<ParsedCsvData | null>(null)\n  const delimiter = ref('_')\n  const dominantFieldCount = ref(1)\n  const minFieldCount = ref(1)\n  const outliers = ref<OutlierInfo[]>([])\n  const fields = ref<ColumnInfo[]>([])\n  const fieldNames = ref<Record<number, string>>({})\n  const enabledFields = ref(new Set<number>())\n\n  const samples = computed(() => {\n    if (inputMode.value === 'csv' && csvData.value) {\n      return csvData.value.rows.map(r => r[csvData.value!.sampleColumn])\n    }\n    return rawText.value\n      .split('\\n')\n      .map(l => l.trim())\n      .filter(l => l.length > 0)\n  })\n\n  const hasOutliers = computed(() => outliers.value.length > 0)\n\n  const conformingSamples = computed(() => {\n    const outlierIndices = new Set(outliers.value.map(o => o.index))\n    return samples.value.filter((_, i) => !outlierIndices.has(i))\n  })\n\n  const outlierActions = computed(() => {\n    const map = new Map<number, OutlierAction>()\n    for (const o of outliers.value) {\n      map.set(o.index, o.action)\n    }\n    return map\n  })\n\n  const effectiveColumns = computed(() => {\n    return fields.value.map(col => ({\n      ...col,\n      name: fieldNames.value[col.index] ?? col.name,\n    }))\n  })\n\n  const groups = computed(() => {\n    if (effectiveColumns.value.length === 0 || enabledFields.value.size === 0) {\n      return []\n    }\n    const result = computeGroups(\n      samples.value,\n      effectiveColumns.value,\n      enabledFields.value,\n      outlierActions.value,\n      delimiter.value,\n      minFieldCount.value,\n    )\n    return result.groups\n  })\n\n  const metadata = computed(() => {\n    if (effectiveColumns.value.length === 0 || enabledFields.value.size === 0) {\n      return []\n    }\n    return computeGroups(\n      samples.value,\n      effectiveColumns.value,\n      enabledFields.value,\n      outlierActions.value,\n      delimiter.value,\n      minFieldCount.value,\n    ).metadata\n  })\n\n  const excludedSamples = computed(() => {\n    return computeGroups(\n      samples.value,\n      effectiveColumns.value,\n      enabledFields.value,\n      outlierActions.value,\n      delimiter.value,\n      minFieldCount.value,\n    ).excludedSamples\n  })\n\n  const result = computed<AutoGroupResult>(() => ({\n    groups: groups.value,\n    metadata: metadata.value,\n    excludedSamples: excludedSamples.value,\n  }))\n\n  function parseInput() {\n    if (inputMode.value === 'csv' && csvData.value) {\n      parseCsvInput()\n    } else {\n      parsePasteInput()\n    }\n  }\n\n  function parsePasteInput() {\n    const lines = samples.value\n    if (lines.length === 0) return\n\n    const analysis = analyzeDelimiter(lines)\n    delimiter.value = analysis.delimiter\n    dominantFieldCount.value = analysis.dominantFieldCount\n    minFieldCount.value = analysis.minFieldCount\n\n    outliers.value = detectOutliers(lines, analysis.delimiter, analysis.minFieldCount)\n\n    const conforming = lines.filter(\n      (_, i) => !outliers.value.some(o => o.index === i)\n    )\n    fields.value = extractColumns(conforming, analysis.delimiter, analysis.minFieldCount)\n\n    // Reset field names and enable all by default\n    fieldNames.value = {}\n    enabledFields.value = new Set(fields.value.map(f => f.index))\n  }\n\n  function parseCsvInput() {\n    if (!csvData.value) return\n\n    const csv = csvData.value\n    const nonSampleCols = csv.columns.filter(c => c !== csv.sampleColumn)\n\n    fields.value = nonSampleCols.map((col, i) => {\n      const values = csv.rows.map(r => r[col])\n      const unique = [...new Set(values)]\n      return {\n        index: i,\n        name: col,\n        uniqueValues: unique,\n        cardinality: unique.length,\n      }\n    })\n\n    // For CSV, no outliers\n    outliers.value = []\n    delimiter.value = ','\n    dominantFieldCount.value = csv.columns.length\n\n    fieldNames.value = {}\n    for (const f of fields.value) {\n      fieldNames.value[f.index] = f.name\n    }\n    enabledFields.value = new Set(fields.value.map(f => f.index))\n  }\n\n  function setOutlierAction(index: number, action: OutlierAction) {\n    const outlier = outliers.value.find(o => o.index === index)\n    if (outlier) {\n      outlier.action = action\n      // Trigger reactivity\n      outliers.value = [...outliers.value]\n    }\n  }\n\n  function setAllOutlierActions(action: OutlierAction) {\n    for (const outlier of outliers.value) {\n      outlier.action = action\n    }\n    outliers.value = [...outliers.value]\n  }\n\n  function toggleField(index: number) {\n    const newSet = new Set(enabledFields.value)\n    if (newSet.has(index)) {\n      newSet.delete(index)\n    } else {\n      newSet.add(index)\n    }\n    enabledFields.value = newSet\n  }\n\n  function renameField(index: number, name: string) {\n    fieldNames.value = { ...fieldNames.value, [index]: name }\n  }\n\n  function reset() {\n    rawText.value = ''\n    csvData.value = null\n    delimiter.value = '_'\n    dominantFieldCount.value = 1\n    minFieldCount.value = 1\n    outliers.value = []\n    fields.value = []\n    fieldNames.value = {}\n    enabledFields.value = new Set()\n  }\n\n  return {\n    // State\n    inputMode,\n    rawText,\n    csvData,\n    delimiter,\n    dominantFieldCount,\n    minFieldCount,\n    outliers,\n    fields,\n    fieldNames,\n    enabledFields,\n    // Computed\n    samples,\n    hasOutliers,\n    conformingSamples,\n    groups,\n    metadata,\n    excludedSamples,\n    result,\n    effectiveColumns,\n    // Actions\n    parseInput,\n    setOutlierAction,\n    setAllOutlierActions,\n    toggleField,\n    renameField,\n    reset,\n  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package/dist/index.d.ts

@@ -1,5 +1,5 @@
 export { MLDSdk, default } from './install';
-export { BaseButton, BaseInput, BaseTextarea, BaseSelect, BaseCheckbox, BaseToggle, BaseRadioGroup, BaseSlider, ColorSlider, BaseTabs, BaseModal, FormField, DatePicker, TimePicker, TagsInput, NumberInput, FileUploader, AlertBox, ToastNotification, IconButton, ThemeToggle, SettingsButton, CollapsibleCard, AppTopBar, AppSidebar, AppLayout, AppContainer, Skeleton, WellPlate, RackEditor, SampleLegend, PlateMapEditor, ExperimentTimeline, SampleSelector, GroupingModal, GroupAssigner, MoleculeInput, ConcentrationInput, DoseCalculator, ReagentList, SampleHierarchyTree, ProtocolStepEditor, SegmentedControl, MultiSelect, BasePill, DropdownButton, Calendar, DataFrame, LoadingSpinner, Divider, StatusIndicator, ProgressBar, Avatar, EmptyState, Breadcrumb, Tooltip, ConfirmDialog, ChartContainer, SettingsModal, ScientificNumber, ChemicalFormula, FormulaInput, SequenceInput, UnitInput, StepWizard, AuditTrail, BatchProgressList, ExperimentDataViewer, ExperimentCodeBadge, DateTimePicker, TimeRangeInput, ScheduleCalendar, ResourceCard, } from './components';
-export { useApi, useAuth, usePasskey, useTheme, useToast, usePlatformContext, useWellPlateEditor, useConcentrationUnits, useDoseCalculator, useProtocolTemplates, useRackEditor, useChemicalFormula, ATOMIC_WEIGHTS, useSequenceUtils, type ApiClientOptions, type UseWellPlateEditorOptions, type UseWellPlateEditorReturn, type UseRackEditorOptions, type UseRackEditorReturn, type ConcentrationValue, type ConcentrationUnit, type VolumeValue, type VolumeUnit, type StepTemplate, type FormulaParseResult, type FormulaPart, type SequenceType, type SequenceStats, parseTime, formatTime, generateTimeSlots, rangesOverlap, durationMinutes, formatDuration, isTimeInRange, findAvailableSlots, snapToSlot, addMinutes, compareTime, useScheduleDrag, usePluginConfig, type UsePluginConfigReturn, } from './composables';
+export { BaseButton, BaseInput, BaseTextarea, BaseSelect, BaseCheckbox, BaseToggle, BaseRadioGroup, BaseSlider, ColorSlider, BaseTabs, BaseModal, FormField, DatePicker, TimePicker, TagsInput, NumberInput, FileUploader, AlertBox, ToastNotification, IconButton, ThemeToggle, SettingsButton, CollapsibleCard, AppTopBar, AppSidebar, AppLayout, AppContainer, Skeleton, WellPlate, RackEditor, SampleLegend, PlateMapEditor, ExperimentTimeline, SampleSelector, GroupingModal, AutoGroupModal, GroupAssigner, MoleculeInput, ConcentrationInput, DoseCalculator, ReagentList, SampleHierarchyTree, ProtocolStepEditor, SegmentedControl, MultiSelect, BasePill, DropdownButton, Calendar, DataFrame, LoadingSpinner, Divider, StatusIndicator, ProgressBar, Avatar, EmptyState, Breadcrumb, Tooltip, ConfirmDialog, ChartContainer, SettingsModal, ScientificNumber, ChemicalFormula, FormulaInput, SequenceInput, UnitInput, StepWizard, AuditTrail, BatchProgressList, ExperimentDataViewer, ExperimentCodeBadge, DateTimePicker, TimeRangeInput, ScheduleCalendar, ResourceCard, } from './components';
+export { useApi, useAuth, usePasskey, useTheme, useToast, usePlatformContext, useWellPlateEditor, useConcentrationUnits, useDoseCalculator, useProtocolTemplates, useRackEditor, useChemicalFormula, ATOMIC_WEIGHTS, useSequenceUtils, type ApiClientOptions, type UseWellPlateEditorOptions, type UseWellPlateEditorReturn, type UseRackEditorOptions, type UseRackEditorReturn, type ConcentrationValue, type ConcentrationUnit, type VolumeValue, type VolumeUnit, type StepTemplate, type FormulaParseResult, type FormulaPart, type SequenceType, type SequenceStats, parseTime, formatTime, generateTimeSlots, rangesOverlap, durationMinutes, formatDuration, isTimeInRange, findAvailableSlots, snapToSlot, addMinutes, compareTime, useScheduleDrag, usePluginConfig, type UsePluginConfigReturn, useAutoGroup, DEFAULT_COLORS, } from './composables';
 export { useAuthStore, useSettingsStore, colorPalettes, type SettingsState, } from './stores';
-export type { ContainerDirection, ButtonVariant, ButtonSize, InputType, ModalSize, AlertType, Toast, TabItem, SelectOption, RadioOption, FormFieldProps, SidebarToolSection, CollapsibleState, TopBarVariant, TopBarPage, TopBarTab, TopBarTabOption, TopBarSettingsConfig, WellPlateFormat, WellState, WellPlateSelectionMode, Well, HeatmapColorScale, HeatmapConfig, SlotPosition, WellExtendedData, WellEditData, WellEditField, WellLegendItem, Rack, SampleType, PlateMap, PlateMapEditorState, ProtocolStepType, ProtocolStepStatus, ProtocolStep, SampleGroup, GroupItem, FileUploaderMode, SegmentedOption, SegmentedControlVariant, SegmentedControlSize, MultiSelectOption, MultiSelectSize, PillVariant, PillSize, CalendarSelectionMode, CalendarMarker, CalendarDayContext, SortDirection, SortState, DataFrameColumn, PaginationState, SpinnerSize, SpinnerVariant, DividerSpacing, StatusType, ProgressVariant, ProgressSize, AvatarSize, EmptyStateColor, EmptyStateSize, BreadcrumbItem, TooltipPosition, ConfirmVariant, SettingsTab, NumberNotation, TimePickerFormat, TimeRange, ScheduleView, ScheduleEventStatus, ScheduleEvent, ScheduleBlockedSlot, ScheduleSlotContext, ScheduleEventCreateContext, ScheduleEventUpdateContext, ResourceStatus, ResourceSpec, UnitOption, WizardStep, WizardStepState, AuditEntryType, AuditEntry, BatchItemStatus, BatchItem, BatchSummary, AuthConfig, UserInfo, LoginResponse, TokenVerifyResponse, RegisterRequest, UpdateProfileRequest, CredentialInfo, SummaryData, SummarySection, SummarySectionItem, TreeNode, TreeNodeType, PluginInfo, PluginNavItem, PluginSettings, PluginSettingField, PlatformContext, PlatformEventType, PlatformEvent, ThemeMode, ColorPalette, TableDensity, } from './types';
+export type { ContainerDirection, ButtonVariant, ButtonSize, InputType, ModalSize, AlertType, Toast, TabItem, SelectOption, RadioOption, FormFieldProps, SidebarToolSection, CollapsibleState, TopBarVariant, TopBarPage, TopBarTab, TopBarTabOption, TopBarSettingsConfig, WellPlateFormat, WellState, WellPlateSelectionMode, Well, HeatmapColorScale, HeatmapConfig, SlotPosition, WellExtendedData, WellEditData, WellEditField, WellLegendItem, Rack, SampleType, PlateMap, PlateMapEditorState, ProtocolStepType, ProtocolStepStatus, ProtocolStep, SampleGroup, GroupItem, OutlierAction, InputMode, OutlierInfo, ColumnInfo, MetadataRow, AutoGroupResult, ParsedCsvData, FileUploaderMode, SegmentedOption, SegmentedControlVariant, SegmentedControlSize, MultiSelectOption, MultiSelectSize, PillVariant, PillSize, CalendarSelectionMode, CalendarMarker, CalendarDayContext, SortDirection, SortState, DataFrameColumn, PaginationState, SpinnerSize, SpinnerVariant, DividerSpacing, StatusType, ProgressVariant, ProgressSize, AvatarSize, EmptyStateColor, EmptyStateSize, BreadcrumbItem, TooltipPosition, ConfirmVariant, SettingsTab, NumberNotation, TimePickerFormat, TimeRange, ScheduleView, ScheduleEventStatus, ScheduleEvent, ScheduleBlockedSlot, ScheduleSlotContext, ScheduleEventCreateContext, ScheduleEventUpdateContext, ResourceStatus, ResourceSpec, UnitOption, WizardStep, WizardStepState, AuditEntryType, AuditEntry, BatchItemStatus, BatchItem, BatchSummary, AuthConfig, UserInfo, LoginResponse, TokenVerifyResponse, RegisterRequest, UpdateProfileRequest, CredentialInfo, SummaryData, SummarySection, SummarySectionItem, TreeNode, TreeNodeType, PluginInfo, PluginNavItem, PluginSettings, PluginSettingField, PlatformContext, PlatformEventType, PlatformEvent, ThemeMode, ColorPalette, TableDensity, } from './types';

package/dist/index.js

@@ -103,47 +103,49 @@ import { default as default52 } from "./components/SampleSelector.vue.js";
 /* empty css                               */
 import { default as default53 } from "./components/GroupingModal.vue.js";
 /* empty css                              */
-import { default as default54 } from "./components/GroupAssigner.vue.js";
+import { default as default54 } from "./components/AutoGroupModal.vue.js";
+/* empty css                               */
+import { default as default55 } from "./components/GroupAssigner.vue.js";
 /* empty css                              */
-import { default as default55 } from "./components/MoleculeInput.vue.js";
+import { default as default56 } from "./components/MoleculeInput.vue.js";
 /* empty css                              */
-import { default as default56 } from "./components/ConcentrationInput.vue.js";
+import { default as default57 } from "./components/ConcentrationInput.vue.js";
 /* empty css                                   */
-import { default as default57 } from "./components/DoseCalculator.vue.js";
+import { default as default58 } from "./components/DoseCalculator.vue.js";
 /* empty css                               */
-import { default as default58 } from "./components/ReagentList.vue.js";
+import { default as default59 } from "./components/ReagentList.vue.js";
 /* empty css                            */
-import { default as default59 } from "./components/SampleHierarchyTree.vue.js";
+import { default as default60 } from "./components/SampleHierarchyTree.vue.js";
 /* empty css                                    */
-import { default as default60 } from "./components/ProtocolStepEditor.vue.js";
+import { default as default61 } from "./components/ProtocolStepEditor.vue.js";
 /* empty css                                   */
-import { default as default61 } from "./components/ScientificNumber.vue.js";
+import { default as default62 } from "./components/ScientificNumber.vue.js";
 /* empty css                                 */
-import { default as default62 } from "./components/ChemicalFormula.vue.js";
+import { default as default63 } from "./components/ChemicalFormula.vue.js";
 /* empty css                                */
-import { default as default63 } from "./components/FormulaInput.vue.js";
+import { default as default64 } from "./components/FormulaInput.vue.js";
 /* empty css                             */
-import { default as default64 } from "./components/SequenceInput.vue.js";
+import { default as default65 } from "./components/SequenceInput.vue.js";
 /* empty css                              */
-import { default as default65 } from "./components/UnitInput.vue.js";
+import { default as default66 } from "./components/UnitInput.vue.js";
 /* empty css                          */
-import { default as default66 } from "./components/StepWizard.vue.js";
+import { default as default67 } from "./components/StepWizard.vue.js";
 /* empty css                           */
-import { default as default67 } from "./components/AuditTrail.vue.js";
+import { default as default68 } from "./components/AuditTrail.vue.js";
 /* empty css                           */
-import { default as default68 } from "./components/BatchProgressList.vue.js";
+import { default as default69 } from "./components/BatchProgressList.vue.js";
 /* empty css                                  */
-import { default as default69 } from "./components/ExperimentDataViewer.vue.js";
+import { default as default70 } from "./components/ExperimentDataViewer.vue.js";
 /* empty css                                     */
-import { default as default70 } from "./components/ExperimentCodeBadge.vue.js";
+import { default as default71 } from "./components/ExperimentCodeBadge.vue.js";
 /* empty css                                    */
-import { default as default71 } from "./components/DateTimePicker.vue.js";
+import { default as default72 } from "./components/DateTimePicker.vue.js";
 /* empty css                               */
-import { default as default72 } from "./components/TimeRangeInput.vue.js";
+import { default as default73 } from "./components/TimeRangeInput.vue.js";
 /* empty css                               */
-import { default as default73 } from "./components/ScheduleCalendar.vue.js";
+import { default as default74 } from "./components/ScheduleCalendar.vue.js";
 /* empty css                                 */
-import { default as default74 } from "./components/ResourceCard.vue.js";
+import { default as default75 } from "./components/ResourceCard.vue.js";
 /* empty css                             */
 import { useApi } from "./composables/useApi.js";
 import { useAuth } from "./composables/useAuth.js";
@@ -160,6 +162,7 @@ import { ATOMIC_WEIGHTS, useChemicalFormula } from "./composables/useChemicalFor
 import { useSequenceUtils } from "./composables/useSequenceUtils.js";
 import { addMinutes, compareTime, durationMinutes, findAvailableSlots, formatDuration, formatTime, generateTimeSlots, isTimeInRange, parseTime, rangesOverlap, snapToSlot } from "./composables/useTimeUtils.js";
 import { useScheduleDrag } from "./composables/useScheduleDrag.js";
+import { DEFAULT_COLORS, useAutoGroup } from "./composables/useAutoGroup.js";
 import { usePluginConfig } from "./composables/usePluginConfig.js";
 import { useAuthStore } from "./stores/auth.js";
 import { colorPalettes, useSettingsStore } from "./stores/settings.js";
@@ -170,7 +173,8 @@ export {
   default33 as AppLayout,
   default32 as AppSidebar,
   default31 as AppTopBar,
-  default67 as AuditTrail,
+  default68 as AuditTrail,
+  default54 as AutoGroupModal,
   default40 as Avatar,
   default2 as BaseButton,
   default6 as BaseCheckbox,
@@ -183,61 +187,62 @@ export {
   default11 as BaseTabs,
   default4 as BaseTextarea,
   default7 as BaseToggle,
-  default68 as BatchProgressList,
+  default69 as BatchProgressList,
   default42 as Breadcrumb,
   default17 as Calendar,
   default45 as ChartContainer,
-  default62 as ChemicalFormula,
+  default63 as ChemicalFormula,
   default30 as CollapsibleCard,
   default10 as ColorSlider,
-  default56 as ConcentrationInput,
+  default57 as ConcentrationInput,
   default44 as ConfirmDialog,
+  DEFAULT_COLORS,
   default18 as DataFrame,
   default20 as DatePicker,
-  default71 as DateTimePicker,
+  default72 as DateTimePicker,
   default37 as Divider,
-  default57 as DoseCalculator,
+  default58 as DoseCalculator,
   default16 as DropdownButton,
   default41 as EmptyState,
-  default70 as ExperimentCodeBadge,
-  default69 as ExperimentDataViewer,
+  default71 as ExperimentCodeBadge,
+  default70 as ExperimentDataViewer,
   default51 as ExperimentTimeline,
   default24 as FileUploader,
   default19 as FormField,
-  default63 as FormulaInput,
-  default54 as GroupAssigner,
+  default64 as FormulaInput,
+  default55 as GroupAssigner,
   default53 as GroupingModal,
   default27 as IconButton,
   default36 as LoadingSpinner,
   MLDSdk,
-  default55 as MoleculeInput,
+  default56 as MoleculeInput,
   default14 as MultiSelect,
   default23 as NumberInput,
   default50 as PlateMapEditor,
   default39 as ProgressBar,
-  default60 as ProtocolStepEditor,
+  default61 as ProtocolStepEditor,
   default48 as RackEditor,
-  default58 as ReagentList,
-  default74 as ResourceCard,
-  default59 as SampleHierarchyTree,
+  default59 as ReagentList,
+  default75 as ResourceCard,
+  default60 as SampleHierarchyTree,
   default49 as SampleLegend,
   default52 as SampleSelector,
-  default73 as ScheduleCalendar,
-  default61 as ScientificNumber,
+  default74 as ScheduleCalendar,
+  default62 as ScientificNumber,
   default13 as SegmentedControl,
-  default64 as SequenceInput,
+  default65 as SequenceInput,
   default29 as SettingsButton,
   default46 as SettingsModal,
   default35 as Skeleton,
   default38 as StatusIndicator,
-  default66 as StepWizard,
+  default67 as StepWizard,
   default22 as TagsInput,
   default28 as ThemeToggle,
   default21 as TimePicker,
-  default72 as TimeRangeInput,
+  default73 as TimeRangeInput,
   default26 as ToastNotification,
   default43 as Tooltip,
-  default65 as UnitInput,
+  default66 as UnitInput,
   default47 as WellPlate,
   addMinutes,
   colorPalettes,
@@ -255,6 +260,7 @@ export {
   useApi,
   useAuth,
   useAuthStore,
+  useAutoGroup,
   useChemicalFormula,
   useConcentrationUnits,
   useDoseCalculator,

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;"}