@morscherlab/mint-sdk 1.3.0 → 1.3.1

package/src/composables/useAutoGroup.ts

@@ -16,21 +16,21 @@ import type {
   ValueOps,
 } from '../types/auto-group'
 import {
+  GROUPING_FIELD_ROLES,
   buildClassSchema,
   classKey,
   composeGroups,
   composeTemplate,
   detectClass,
-  expandGroupsWithReplicates,
-  expandTreeWithReplicates,
   findMerges,
-  pickPrimaryDelimiter,
-  preGroupReplicates,
+  isExperimentalKind,
   restoreFingerprint,
   serializeFingerprint,
   splitByTokenLength,
-  splitMulti,
-  type ReplicatePreGrouping,
+  splitColumns,
+  tokenizeBatch,
+  type Delimiter,
+  type ExperimentHeader,
   type TemplateOptions,
 } from './autoGroup'
 import { unwrapExperimentDesignData } from './experimentDesignData'
@@ -82,12 +82,10 @@ export function useAutoGroup() {
   })
 
   const tokenized = ref<string[][]>([])
-  const delimiter = ref<'_' | '-' | '.'>('_')
-  // Replicate pre-grouping: strip injection-number / T<n> / B<n> / Rep<n> markers,
-  // collapse samples with the same base name into one "row" for tokenisation,
-  // then expand the resulting groups back to the original samples in `result`.
-  // null when the paste path hasn't run (CSV path keeps the old behaviour for now).
-  const preGrouping = ref<ReplicatePreGrouping | null>(null)
+  const delimiter = ref<Delimiter>('_')
+  // Experiment code / date / operator that all pasted names share. Empty for
+  // CSV and experiment input.
+  const experiment = ref<ExperimentHeader>({})
 
   function parseInput() {
     if ((inputMode.value === 'csv' || inputMode.value === 'experiment') && csvData.value) {
@@ -98,9 +96,7 @@ export function useAutoGroup() {
   }
 
   function parseInputFromCsv() {
-    // CSV input already exposes structured columns, so replicate pre-grouping
-    // isn't needed (and would interfere with header-aware role inference).
-    preGrouping.value = null
+    experiment.value = {}
     const csv = csvData.value!
     const nonSampleCols = csv.columns.filter(c => c !== csv.sampleColumn && c !== 'sample_type')
     if (nonSampleCols.length === 0) {
@@ -146,47 +142,54 @@ export function useAutoGroup() {
     if (lines.length === 0) {
       classes.value = []
       schemas.value = {}
-      preGrouping.value = null
+      experiment.value = {}
       return
     }
-    // Replicate pre-pass: strip _T<n> / _B<n> / _Rep<n> markers, then collapse
-    // samples whose stripped names match into one base entry. The trailing
-    // injection / run-order number is deliberately NOT stripped here — it
-    // survives tokenisation and is surfaced as a 'run-order' column below. The
-    // tokenize → classify → split-by-length → schema pipeline runs on the
-    // *base* names; the `result` computed expands each resulting group back to
-    // the original samples via `expandGroupsWithReplicates`.
-    const pre = preGroupReplicates(lines)
-    preGrouping.value = pre
-
-    const d = pickPrimaryDelimiter(pre.baseNames)
-    delimiter.value = d
-    tokenized.value = pre.baseNames.map(l => splitMulti(l, d))
-    // sampleTypeHints align to original samples, so pick the first sample's
-    // hint per base group as the representative hint.
-    const hints = pre.membersByBase.map(members => sampleTypeHints.value[members[0]])
-    // Classify by sample type, THEN split each class by token length so every
-    // member of a class shares the same field count. This keeps the per-class
-    // token matrix rectangular, so column index N means the same field for
-    // every sample and the trailing injection number lands in its own column.
+    // One token row for each sample. Replicate tokens, sample numbers and the
+    // injection number stay in the row and get a column role below
+    // ('replicate', 'id', 'run-order'), which keeps them out of the default
+    // group key. Nothing is removed from a name before the user sees it.
+    const batch = tokenizeBatch(lines)
+    delimiter.value = batch.delimiter
+    experiment.value = batch.experiment
+    const tokens = batch.rows
+    // Classify by sample type, THEN split each experimental class by token
+    // length so every member of a class shares the same field count. This
+    // keeps the per-class token matrix rectangular, so column index N means
+    // the same field for every sample.
     const detected = splitByTokenLength(
-      detectClass(tokenized.value, { sampleTypeHints: hints }),
-      tokenized.value,
+      detectClass(tokens, { sampleTypeHints: sampleTypeHints.value, sharedPrefix: batch.sharedPrefix }),
+      tokens,
     )
-    classes.value = detected
     const newSchemas: Record<string, ClassSchema> = {}
     for (const cls of detected) {
-      const memberTokens = cls.members.map(i => tokenized.value[i])
-      newSchemas[classKey(cls)] = {
-        ...buildClassSchema(
-          memberTokens,
-          cls.kind,
-          cls.subKind,
-          cls.classTagPositions,
-        ),
-        tokenLength: cls.tokenLength,
+      let memberTokens = cls.members.map(i => tokens[i])
+      let tailPositions: number[] = []
+      const experimental = isExperimentalKind(cls.kind)
+      if (experimental) {
+        // Tokens that hold two fields (`2-1`, `C1`) become two columns.
+        const split = splitColumns(memberTokens)
+        cls.members.forEach((member, row) => { tokens[member] = split.rows[row] })
+        cls.classTagPositions = split.origin.flatMap((source, index) =>
+          cls.classTagPositions.includes(source) ? [index] : [],
+        )
+        memberTokens = split.rows
+        tailPositions = split.tail
       }
+      const schema = buildClassSchema(
+        memberTokens,
+        cls.kind,
+        cls.subKind,
+        cls.classTagPositions,
+        tailPositions,
+      )
+      // A QC-kind class is one group named by the class label, also when the
+      // user routes it into the groups.
+      if (!experimental) schema.groupBy = []
+      newSchemas[classKey(cls)] = { ...schema, tokenLength: cls.tokenLength }
     }
+    tokenized.value = tokens
+    classes.value = detected
     schemas.value = newSchemas
     if (detected.length > 0) {
       activeClassKey.value = classKey(detected[0])
@@ -206,41 +209,20 @@ export function useAutoGroup() {
     return findMerges(schema, memberTokens)
   })
 
-  const result = computed<AutoGroupResult>(() => {
-    const pre = preGrouping.value
-    const composed = composeGroups({
+  function composeWith(withSchemas: Record<string, ClassSchema>): AutoGroupResult {
+    return composeGroups({
       tokenizedSamples: tokenized.value,
-      // After the pre-pass, sampleNames passed to compose are the *base* names
-      // (one per replicate group); fall back to the original samples when
-      // pre-grouping hasn't run (e.g. the CSV path or empty input).
-      sampleNames: pre ? pre.baseNames : samples.value,
-      schemas: schemas.value,
+      sampleNames: samples.value,
+      schemas: withSchemas,
       classes: classes.value,
       prefixClassLabels: !(csvData.value && (inputMode.value === 'csv' || inputMode.value === 'experiment')),
       missingGroupName: csvData.value && (inputMode.value === 'csv' || inputMode.value === 'experiment')
         ? STRUCTURED_MISSING_GROUP
         : undefined,
     })
-    if (!pre) return composed
-    // Expand each group's `samples` from base names back to the original
-    // sample names so the Preview panel shows real filenames, not stripped
-    // bases, and so `metadata` reflects each input row exactly once.
-    return {
-      ...composed,
-      groups: expandGroupsWithReplicates(composed.groups, pre),
-      experimentalGroups: composed.experimentalGroups
-        ? expandGroupsWithReplicates(composed.experimentalGroups, pre)
-        : undefined,
-      qcGroups: composed.qcGroups
-        ? expandGroupsWithReplicates(composed.qcGroups, pre)
-        : undefined,
-      // The tree is built over base names too; expand its leaves to the original
-      // samples so it agrees with the flat experimental-groups panel.
-      groupTree: composed.groupTree
-        ? expandTreeWithReplicates(composed.groupTree, pre)
-        : composed.groupTree,
-    }
-  })
+  }
+
+  const result = computed<AutoGroupResult>(() => composeWith(schemas.value))
 
   const fingerprint = computed<SchemaFingerprint>(() =>
     serializeFingerprint(result.value.schemas ?? []),
@@ -316,9 +298,11 @@ export function useAutoGroup() {
   // the same field at a different position.
   function schemasExposing(fieldKey: string): { key: string; index: number }[] {
     return Object.entries(schemas.value).flatMap(([key, schema]) => {
+      // An overlay class is one group; its columns are not grouping fields.
+      if (!isExperimentalKind(schema.classKind)) return []
       const col = schema.columns.find(c =>
         (c.displayName ?? c.name) === fieldKey
-        && (c.role === 'factor' || c.role === 'replicate' || schema.groupBy.includes(c.index)),
+        && (GROUPING_FIELD_ROLES.has(c.role) || schema.groupBy.includes(c.index)),
       )
       return col ? [{ key, index: col.index }] : []
     })
@@ -345,6 +329,34 @@ export function useAutoGroup() {
     }
   }
 
+  /**
+   * Rename a grouping field in every class exposing it. A blank name, or a
+   * name that a column of any experimental class has, changes nothing: the
+   * name is the field's identity across classes, and the cards merge by it.
+   */
+  function renameGroupByField(fieldKey: string, name: string) {
+    const next = name.trim()
+    const targets = schemasExposing(fieldKey)
+    if (!next || next === fieldKey || targets.length === 0) return
+    const taken = Object.values(schemas.value).some(schema =>
+      isExperimentalKind(schema.classKind) && schema.columns.some(c => (c.displayName ?? c.name) === next),
+    )
+    if (taken) return
+    for (const { key, index } of targets) setColumnName(key, index, next)
+  }
+
+  /** Number of experimental groups that remain when the field is switched off in every class. */
+  function groupCountWithout(fieldKey: string): number {
+    const targets = new Map(schemasExposing(fieldKey).map(({ key, index }) => [key, index]))
+    const without = Object.fromEntries(
+      Object.entries(schemas.value).map(([key, schema]) => [
+        key,
+        targets.has(key) ? { ...schema, groupBy: schema.groupBy.filter(i => i !== targets.get(key)) } : schema,
+      ]),
+    )
+    return composeWith(without).experimentalGroups?.length ?? 0
+  }
+
   /**
    * Move a grouping field in the active schema, then project that visible field
    * order across every class. Class-only fields keep their relative order after
@@ -575,6 +587,7 @@ export function useAutoGroup() {
     schemas.value = {}
     activeClassKey.value = ''
     tokenized.value = []
+    experiment.value = {}
     outliers.value = []
     sampleTypeHints.value = []
   }
@@ -583,7 +596,7 @@ export function useAutoGroup() {
     // State
     inputMode, rawText, csvData, sampleTypeHints,
     classes, schemas, activeClassKey,
-    delimiter, dominantFieldCount, minFieldCount,
+    delimiter, experiment, dominantFieldCount, minFieldCount,
     // Computed
     samples, tokenized, activeSchema, suggestions,
     groups, qcGroups, metadata, excludedSamples, result, fingerprint,
@@ -592,7 +605,7 @@ export function useAutoGroup() {
     canDownloadTemplate,
     // Mutators
     setClassDisposition, setClassDispositions, toggleGroupBy, moveGroupBy,
-    toggleGroupByField, moveGroupByField,
+    toggleGroupByField, moveGroupByField, renameGroupByField, groupCountWithout,
     setRole, setColumnName, setValueOps, setBinning,
     mergeColumns, loadFingerprint,
     // Actions

package/src/permissions.ts

@@ -95,9 +95,10 @@ export function canAccessPlugin(
   user: PermissionUser | null | undefined,
   pluginName: string | null | undefined,
 ): boolean {
-  if (!pluginName) return true
+  if (!pluginName || isAdminUser(user)) return true
   const access = getRoleInfo(user)?.plugin_access
-  if (!access || access === 'all') return true
+  // As on the platform: a value that is not null, 'all' or a list allows no plugin.
+  if (access == null || access === 'all') return true
   return Array.isArray(access) && access.includes(pluginName)
 }
 

package/src/styles/components/smart-group.css

@@ -160,22 +160,6 @@
 }
 .sg-field__toggle { grid-row: 1 / 3; grid-column: 2; align-self: center; }
 
-/* toggle switch */
-.sg-switch {
-  position: relative; width: 1.65rem; height: 0.95rem;
-  border-radius: 9999px; background: var(--bg-tertiary);
-  border: none; cursor: pointer; flex-shrink: 0;
-  transition: background 0.15s ease;
-}
-.sg-switch.on { background: var(--color-primary); }
-.sg-switch::after {
-  content: ''; position: absolute; top: 0.125rem; left: 0.125rem;
-  width: 0.7rem; height: 0.7rem; border-radius: 9999px;
-  background: #fff; box-shadow: 0 1px 2px rgb(0 0 0 / 0.25);
-  transition: transform 0.15s ease;
-}
-.sg-switch.on::after { transform: translateX(0.7rem); }
-
 /* ==========================================================================
    Shared — live group preview (right rail)
    ========================================================================== */
@@ -229,18 +213,8 @@
   font-size: 0.6875rem; font-weight: 600;
   color: var(--text-secondary);
 }
-.sg-qc__route {
-  margin-left: auto;
-  font: inherit; font-size: 0.75rem; font-weight: 500;
-  color: var(--text-secondary);
-  padding: 0.1875rem 1.5rem 0.1875rem 0.5rem;
-  background: var(--bg-secondary);
-  background-image: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' fill='none' viewBox='0 0 20 20'%3e%3cpath stroke='%2394a3b8' stroke-linecap='round' stroke-linejoin='round' stroke-width='1.5' d='M6 8l4 4 4-4'/%3e%3c/svg%3e");
-  background-position: right 0.25rem center; background-repeat: no-repeat;
-  background-size: 1.1em 1.1em;
-  border: 1px solid var(--border-color); border-radius: var(--radius-sm);
-  appearance: none; cursor: pointer;
-}
+.fr-qc__route { margin-left: auto; }
+.fr-qc__chips { display: flex; flex-wrap: wrap; gap: 0.25rem; }
 .sg-qc__chip {
   display: inline-flex; align-items: center; gap: 0.375rem;
   padding: 0.25rem 0.5rem; border-radius: var(--radius);
@@ -287,47 +261,85 @@
 /* ==========================================================================
    Field Recipe refinements (layered on the shared chrome above)
    ========================================================================== */
+/* Section label above the anatomy and each field list. */
+.fr-label { font-size: 0.75rem; font-weight: 600; color: var(--text-secondary); }
+
+/* One-line field row: [grip] [layer] name [rename] values [hint] [toggle]. */
 .fr .sg-field {
-  grid-template-columns: 1fr auto;
-  grid-template-rows: auto auto;
-  row-gap: 0.25rem;
-  padding: 0.5rem 0.75rem;
+  display: flex; align-items: center; gap: 0.5rem;
+  padding: 0.375rem 0.625rem;
 }
-.fr-field__head { display: flex; align-items: center; gap: 0.5rem; }
-.fr .sg-field__role { margin-left: 0; }
-.fr .sg-field__vals { grid-column: 1 / 2; grid-row: 2; }
-.fr-switch { grid-column: 2; grid-row: 1 / 3; align-self: center; }
-
-/* Layer-order controls: which hierarchy layer this field forms, plus reorder. */
-.sg-field__order {
-  grid-column: 1 / 3;
-  display: flex; align-items: center; gap: 0.25rem;
+.fr .sg-field__name { white-space: nowrap; }
+.fr .sg-field__role { margin-left: 0; white-space: nowrap; }
+.fr .sg-field__vals { flex: 1; min-width: 0; }
+.fr-row__grip,
+.fr-row__rename {
+  display: inline-flex; align-items: center; justify-content: center;
+  width: 1.25rem; height: 1.25rem; padding: 0; flex-shrink: 0;
+  border: none; border-radius: var(--radius-sm); background: none;
+  color: var(--text-muted); cursor: pointer;
+  transition: background 0.15s ease, color 0.15s ease;
 }
-.sg-field__layer {
-  font-size: 0.6875rem; font-weight: 600;
-  color: var(--color-primary);
-  padding: 0.0625rem 0.375rem; border-radius: 9999px;
-  background: var(--color-primary-soft);
-  margin-right: auto;
+.fr-row__grip { cursor: grab; }
+.fr-row__grip:hover,
+.fr-row__rename:hover { color: var(--text-primary); background: var(--bg-hover); }
+.fr-row__grip:focus-visible,
+.fr-row__rename:focus-visible { outline: none; box-shadow: var(--focus-ring-soft); }
+/* Which hierarchy layer this field forms (1 = the sample selector's major group). */
+.fr-row__layer {
+  display: inline-grid; place-items: center; flex-shrink: 0;
+  width: 1.25rem; height: 1.25rem; border-radius: 9999px;
+  border: 1px solid var(--color-primary);
+  background: var(--bg-secondary); color: var(--_ink-primary);
+  font-size: 0.6875rem; font-weight: 700; font-variant-numeric: tabular-nums;
+}
+.fr-row__name-input {
+  width: 9rem; padding: 0.0625rem 0.375rem;
+  font: inherit; font-size: 0.875rem; font-weight: 600; color: var(--text-primary);
+  border: 1px solid var(--color-primary); border-radius: var(--radius-sm);
+  background: var(--bg-secondary);
 }
-.sg-field__order-btn {
-  display: inline-flex; align-items: center; justify-content: center;
-  width: 1.25rem; height: 1.25rem; padding: 0;
-  border: 1px solid var(--border-color); border-radius: 0.375rem;
-  background: var(--bg-primary); color: var(--text-secondary);
-  cursor: pointer; transition: background 0.15s ease, color 0.15s ease;
+.fr-row__name-input:focus-visible { outline: none; box-shadow: var(--focus-ring-soft); }
+/* Groups that remain when this field is switched off. */
+.fr-row__hint {
+  font-size: 0.75rem; font-weight: 500; color: var(--text-secondary-strong);
+  white-space: nowrap; font-variant-numeric: tabular-nums;
 }
-.sg-field__order-btn:hover:not(:disabled) { background: var(--bg-tertiary); color: var(--text-primary); }
-.sg-field__order-btn:disabled { opacity: 0.4; cursor: default; }
+/* The message is dark text (AA on the tinted row); the input border carries the error colour. */
+.fr-row__error { font-size: 0.75rem; font-weight: 600; color: var(--text-primary); white-space: nowrap; }
+.fr-row__name-input[aria-invalid='true'] { border-color: var(--_ink-error); box-shadow: var(--focus-ring-error); }
+.fr-row--dragging { opacity: 0.5; }
+.fr-row--over { box-shadow: inset 0 2px 0 var(--color-primary); }
 
-/* Replicate-on: the field card itself warns instead of silently shattering. */
+/* Replicate-on: the field row itself warns instead of silently shattering. */
 .fr-field--warn.sg-field--on {
   border-color: var(--mint-warning-border);
   background: var(--mint-warning-bg);
 }
-.fr-field--warn.sg-field--on .fr-switch.on { background: var(--mint-warning); }
-.fr-field--warn.sg-field--on .sg-field__role--rep {
-  color: #fff; background: var(--mint-warning);
+.fr-field--warn.sg-field--on .fr-row__layer { border-color: var(--mint-warning); color: var(--text-primary); }
+
+/* Name anatomy: the tokens of one example sample and the role of each. */
+.fr-anatomy { display: flex; flex-direction: column; gap: 0.375rem; }
+.fr-anatomy__tokens { display: flex; flex-wrap: wrap; gap: 0.375rem 0.5rem; }
+.fr-token { display: inline-flex; flex-direction: column; align-items: center; gap: 0.125rem; }
+.fr-token__text {
+  font-family: var(--font-mono); font-size: 0.75rem; font-weight: 500;
+  padding: 0.125rem 0.375rem; border-radius: var(--radius-sm);
+  border: 1px solid var(--border-color); background: var(--bg-tertiary);
+  color: var(--text-secondary-strong);
+}
+.fr-token__caption { font-size: 0.6875rem; color: var(--text-secondary-strong); white-space: nowrap; }
+.fr-token--on .fr-token__text {
+  border-color: var(--color-primary); background: var(--color-primary-soft);
+  color: var(--text-primary);
+}
+.fr-token--on .fr-token__caption { color: var(--_ink-primary); font-weight: 700; }
+.fr-token--off .fr-token__text { border-style: dashed; background: transparent; }
+
+/* No samples: say what to do. */
+.fr-blank {
+  display: flex; flex-direction: column; align-items: flex-start; gap: 0.5rem;
+  padding: 1rem 0;
 }
 
 /* Neutral (no-selection) summary variant. */
@@ -652,29 +664,6 @@ html.dark .sg-summary code { background: rgba(255, 255, 255, 0.1); }
   background: var(--bg-tertiary); color: var(--text-primary); border-color: var(--text-muted);
 }
 .fr-upload:focus-visible { outline: none; box-shadow: var(--focus-ring-soft); }
-.fr-csv { position: relative; }
-.fr-csv-menu {
-  position: absolute; top: calc(100% + 0.25rem); right: 0; z-index: 10;
-  min-width: 11rem; padding: 0.25rem;
-  display: flex; flex-direction: column; gap: 0.0625rem;
-  background: var(--bg-secondary);
-  border: 1px solid var(--border-color); border-radius: var(--radius-md);
-  box-shadow: var(--shadow-lg);
-}
-.fr-csv-item {
-  display: flex; align-items: center; gap: 0.5rem;
-  font: inherit; font-size: 0.8125rem; font-weight: 500; text-align: left;
-  color: var(--text-primary); cursor: pointer;
-  padding: 0.4375rem 0.5rem; border: none; border-radius: var(--radius);
-  background: none; transition: background 0.12s ease, color 0.12s ease;
-}
-.fr-csv-item:hover { background: var(--bg-hover); }
-.fr-csv-item:disabled {
-  /* disabled cue: muted colour + struck label + not-allowed, not opacity alone */
-  color: var(--text-muted); cursor: not-allowed; opacity: 0.7;
-  text-decoration: line-through; text-decoration-color: var(--text-muted);
-}
-.fr-csv-item:disabled:hover { background: none; }
 /* anchor the drop overlay to the main panel */
 .sg-body__main { position: relative; }
 .fr-dropzone {

package/src/types/auto-group.ts

@@ -61,6 +61,7 @@ export type ColumnRole =
   | 'factor'
   | 'replicate'
   | 'run-order'
+  | 'id'
   | 'numeric'
   | 'class-tag'
   | 'ignore'