@morscherlab/mint-sdk 1.3.9 → 1.4.0-beta.2

package/src/__tests__/templates/templatesDeprecation.test.ts

@@ -1,78 +0,0 @@
-import { dirname, resolve } from 'node:path'
-import { fileURLToPath } from 'node:url'
-import { beforeAll, describe, expect, it } from 'vitest'
-import ts from 'typescript'
-
-const TEMPLATES_INDEX = resolve(dirname(fileURLToPath(import.meta.url)), '../../templates/index.ts')
-const COMPONENTS_INDEX = resolve(dirname(fileURLToPath(import.meta.url)), '../../components/index.ts')
-const COMPOSABLES_DIR = resolve(dirname(fileURLToPath(import.meta.url)), '../../composables')
-
-// Composables removed in MINT 1.4 with the templates and sample grouping.
-const REMOVED_COMPOSABLE_FILES = [
-  'useBioTemplateComponents.ts',
-  'useBioTemplateControls.ts',
-  'useBioTemplatePackWorkspace.ts',
-  'useBioTemplatePresetWorkspace.ts',
-  'useBioTemplateWorkspace.ts',
-  'useTemplateCollection.ts',
-  'useExperimentSave.ts',
-  'useGroupAssignment.ts',
-].map(file => resolve(COMPOSABLES_DIR, file))
-
-// One program for every file: building one per file took longer than the test timeout on CI.
-let program: ts.Program
-let checker: ts.TypeChecker
-
-beforeAll(() => {
-  program = ts.createProgram([TEMPLATES_INDEX, COMPONENTS_INDEX, ...REMOVED_COMPOSABLE_FILES], {
-    target: ts.ScriptTarget.ES2022,
-    module: ts.ModuleKind.ESNext,
-    moduleResolution: ts.ModuleResolutionKind.Bundler,
-    noEmit: true,
-  })
-  checker = program.getTypeChecker()
-}, 60_000)
-
-function exportsOf(file: string): ts.Symbol[] {
-  return checker.getExportsOfModule(checker.getSymbolAtLocation(program.getSourceFile(file)!)!)
-}
-
-function isDeprecated(symbol: ts.Symbol): boolean {
-  return symbol.getJsDocTags(checker).some(tag => tag.name === 'deprecated')
-}
-
-// TypeScript ignores @deprecated on `export { ... } from` blocks; an import
-// site only shows the deprecation when the original declaration carries it.
-function undeprecatedValueExports(file: string): string[] {
-  return exportsOf(file)
-    .map(symbol => (symbol.flags & ts.SymbolFlags.Alias ? checker.getAliasedSymbol(symbol) : symbol))
-    .filter(symbol => symbol.flags & ts.SymbolFlags.Value)
-    .filter(symbol => !isDeprecated(symbol))
-    .map(symbol => symbol.getName())
-}
-
-describe('templates deprecation', () => {
-  it('should expose deprecated component tags to TypeScript consumers', () => {
-    const names = ['BioTemplateRenderer', 'SmartGroupModal', 'DoseDesignWorkspaceView']
-    const tagged = exportsOf(COMPONENTS_INDEX).filter(isDeprecated).map(symbol => symbol.getName())
-
-    expect(names.filter(name => !tagged.includes(name))).toEqual([])
-  })
-
-  it('should not tag components that stay public in MINT 1.4', () => {
-    const names = ['SampleSelector', 'SequenceProgressBar', 'InstrumentStateBadge']
-    const tagged = exportsOf(COMPONENTS_INDEX).filter(isDeprecated).map(symbol => symbol.getName())
-
-    expect(names.filter(name => tagged.includes(name))).toEqual([])
-  })
-
-  it('should tag every template value export when the templates move out in MINT 1.4', () => {
-    expect(undeprecatedValueExports(TEMPLATES_INDEX)).toEqual([])
-  })
-
-  it('should tag every value export of the template and grouping composables when they are removed in MINT 1.4', () => {
-    const untagged = REMOVED_COMPOSABLE_FILES.flatMap(undeprecatedValueExports)
-
-    expect(untagged).toEqual([])
-  })
-})

package/src/__tests__/utils/lcms.test.ts

@@ -1,73 +0,0 @@
-import { describe, expect, it } from 'vitest'
-import {
-  basenameFromWindowsPath,
-  extractLcmsCommonPrefix,
-  extractLcmsSampleName,
-  inferLcmsPlateTypeFromWellIds,
-  lcmsWellIdFromPosition,
-  reconstructLcmsPlateCellsFromSequenceItems,
-} from '../../lcms'
-
-describe('lcms utilities', () => {
-  it('extracts common prefixes and sample names from Xcalibur file names', () => {
-    const prefix = extractLcmsCommonPrefix([
-      'Batch_01_NEG_S1_001',
-      'Batch_01_NEG_S2_002',
-      'Batch_01_NEG_QC_003',
-    ])
-
-    expect(prefix).toBe('Batch_01')
-    expect(extractLcmsSampleName('Batch_01_NEG_S1_001', prefix)).toBe('S1')
-  })
-
-  it('infers plate type from well geometry', () => {
-    expect(lcmsWellIdFromPosition('R:A1')).toBe('A1')
-    expect(inferLcmsPlateTypeFromWellIds(['A1', 'F9'])).toBe('54vial')
-    expect(inferLcmsPlateTypeFromWellIds(['A1', 'H12'])).toBe('96well')
-  })
-
-  it('reconstructs plate cells from sequence items while skipping controls', () => {
-    const result = reconstructLcmsPlateCellsFromSequenceItems([
-      {
-        sample_type: 'Unknown',
-        file_name: 'Batch_NEG_S1_001',
-        sample_id: 'R:A1',
-        path: '',
-        instrument_method: 'C:\\Methods\\neg.meth',
-        position: 'R:A1',
-        injection_volume: 5,
-      },
-      {
-        sample_type: 'Unknown',
-        file_name: 'Batch_NEG_S2_002',
-        sample_id: 'R:H12',
-        path: '',
-        instrument_method: 'C:\\Methods\\neg.meth',
-        position: 'R:H12',
-        injection_volume: 5,
-      },
-      {
-        sample_type: 'Blank',
-        file_name: 'Batch_NEG_Blank_003',
-        sample_id: 'R:F9',
-        path: '',
-        instrument_method: 'C:\\Methods\\neg.meth',
-        position: 'R:F9',
-        injection_volume: 5,
-      },
-    ])
-
-    expect(result).toEqual({
-      plateType: '96well',
-      cells: [
-        { row: 'A', column: 1, sample_name: 'S1' },
-        { row: 'H', column: 12, sample_name: 'S2' },
-      ],
-    })
-  })
-
-  it('extracts basenames from Windows and POSIX paths', () => {
-    expect(basenameFromWindowsPath('C:\\Methods\\neg.meth')).toBe('neg.meth')
-    expect(basenameFromWindowsPath('/methods/pos.meth')).toBe('pos.meth')
-  })
-})

package/src/__tests__/utils/rack.test.ts

@@ -1,120 +0,0 @@
-import { describe, expect, it } from 'vitest'
-import {
-  createLcmsControlWellEditData,
-  getLcmsDefaultControlWellId,
-  lcmsPlateCellsToRacks,
-  rackToLcmsPlateCells,
-} from '../../utils/rack'
-import type { Rack } from '../../types'
-
-describe('rack LCMS adapters', () => {
-  it('converts LCMS plate cells into rack wells grouped by slot', () => {
-    const racks = lcmsPlateCellsToRacks([
-      {
-        row: 'A',
-        column: 1,
-        sample_name: 'S1',
-        sample_type: 'sample',
-        injection_volume: 7,
-        slot: 'G',
-      },
-      {
-        row: 'H',
-        column: 10,
-        sample_name: 'IQC',
-        sample_type: 'iqc',
-        injection_count: 2,
-        slot: 'R',
-      },
-    ])
-
-    expect(racks.map(rack => rack.slot)).toEqual(['R', 'G'])
-    expect(racks[0]).toMatchObject({
-      id: 'rack-R',
-      format: 96,
-      wells: {
-        H10: {
-          sampleType: 'iqc',
-          metadata: {
-            label: 'IQC',
-            injectionVolume: 5,
-            injectionCount: 2,
-          },
-        },
-      },
-    })
-    expect(racks[1].wells.A1?.metadata).toMatchObject({
-      label: 'S1',
-      injectionVolume: 7,
-    })
-  })
-
-  it('flattens rack wells back to LCMS plate cells with slot metadata', () => {
-    const rack: Rack = {
-      id: 'rack-R',
-      name: 'Rack R',
-      format: 54,
-      slot: 'R',
-      injectionVolume: 5,
-      wells: {
-        A1: {
-          id: 'A1',
-          state: 'filled',
-          sampleType: 'sample',
-          metadata: {
-            label: 'S1',
-            injectionVolume: 7,
-            injectionCount: 3,
-            customMethod: 'C:\\Methods\\custom.meth',
-          },
-        },
-        F7: {
-          id: 'F7',
-          state: 'filled',
-          sampleType: 'iqc',
-          metadata: {
-            label: 'IQC',
-          },
-        },
-      },
-    }
-
-    expect(rackToLcmsPlateCells(rack)).toEqual([
-      {
-        row: 'A',
-        column: 1,
-        sample_name: 'S1',
-        sample_type: 'sample',
-        injection_volume: 7,
-        injection_count: 3,
-        custom_method: 'C:\\Methods\\custom.meth',
-        slot: 'R',
-      },
-      {
-        row: 'F',
-        column: 7,
-        sample_name: 'IQC',
-        sample_type: 'iqc',
-        injection_volume: 5,
-        injection_count: 1,
-        custom_method: null,
-        slot: 'R',
-      },
-    ])
-  })
-
-  it('exposes LCMS default control well edit data', () => {
-    expect(getLcmsDefaultControlWellId('54vial', 'iqc')).toBe('F7')
-    expect(createLcmsControlWellEditData('qc', {
-      plateType: '96well',
-      injectionVolume: 8,
-    })).toEqual({
-      wellId: 'H11',
-      label: 'QC',
-      sampleType: 'qc',
-      injectionVolume: 8,
-      injectionCount: 1,
-      customMethod: '',
-    })
-  })
-})

package/src/components/AppAvatarMenu.story.vue

@@ -1,155 +0,0 @@
-<script setup lang="ts">
-import AppAvatarMenu from './AppAvatarMenu.vue'
-import type { AccountMenuItem } from '../types'
-
-function handleSelect(item: AccountMenuItem) {
-  console.log('Selected:', item.id)
-}
-
-function handleSignOut() {
-  console.log('Sign out')
-}
-
-const basicItems: AccountMenuItem[] = [
-  { id: 'profile', label: 'Profile' },
-  { id: 'settings', label: 'Settings' },
-]
-
-const richItems: AccountMenuItem[] = [
-  { id: 'profile', label: 'Profile' },
-  { id: 'settings', label: 'Settings' },
-  { id: 'divider-1', divider: true, label: '' },
-  { id: 'admin', label: 'Admin panel' },
-  { id: 'billing', label: 'Billing', rightLabel: 'Pro' },
-]
-
-const devToolsItems: AccountMenuItem[] = [
-  { id: 'profile', label: 'Profile' },
-  { id: 'divider-1', divider: true, label: '' },
-  { id: 'api-keys', label: 'API keys' },
-  { id: 'webhooks', label: 'Webhooks' },
-  { id: 'docs', label: 'Documentation', href: 'https://docs.morscher.lab' },
-]
-
-function initState() {
-  return {
-    userName: 'Estrella',
-    userInitial: '',
-    userEmail: 'estrella@morscher.lab',
-    showSignOut: true,
-    signOutLabel: 'Sign out',
-  }
-}
-</script>
-
-<template>
-  <Story title="Layout/AppAvatarMenu">
-    <Variant title="Pill with name (primary)">
-      <!-- Default pattern used in the platform topbar: avatar circle +
-           username text, matching GitHub / Linear / Notion conventions. -->
-      <div style="padding: 2rem; display: flex; justify-content: flex-start; background: var(--bg-primary); min-height: 8rem;">
-        <AppAvatarMenu
-          user-name="Estrella"
-          user-email="estrella@morscher.lab"
-          :items="basicItems"
-          @select="handleSelect"
-          @sign-out="handleSignOut"
-        />
-      </div>
-    </Variant>
-
-    <Variant title="Avatar only (no username)">
-      <!-- What renders in dev/signed-out mode — the name span v-if hides
-           when `user-name` is absent, leaving just the gradient chip. -->
-      <div style="padding: 2rem; display: flex; justify-content: flex-start; background: var(--bg-primary); min-height: 8rem;">
-        <AppAvatarMenu
-          :items="basicItems"
-          :show-sign-out="false"
-          @select="handleSelect"
-        />
-      </div>
-    </Variant>
-
-    <Variant title="With email in panel header">
-      <div style="padding: 2rem; display: flex; justify-content: flex-start; background: var(--bg-primary); min-height: 12rem;">
-        <AppAvatarMenu
-          user-name="Estrella"
-          user-email="estrella@morscher.lab"
-          :items="richItems"
-          @select="handleSelect"
-          @sign-out="handleSignOut"
-        />
-      </div>
-    </Variant>
-
-    <Variant title="With divider + right-labels">
-      <div style="padding: 2rem; display: flex; justify-content: flex-start; background: var(--bg-primary); min-height: 12rem;">
-        <AppAvatarMenu
-          user-name="Ada Lovelace"
-          user-initial="AL"
-          user-email="ada@morscher.lab"
-          :items="richItems"
-          @select="handleSelect"
-          @sign-out="handleSignOut"
-        />
-      </div>
-    </Variant>
-
-    <Variant title="Developer tools menu">
-      <!-- Menu items with `href` render as anchor tags that open external
-           documentation links in a new tab. -->
-      <div style="padding: 2rem; display: flex; justify-content: flex-start; background: var(--bg-primary); min-height: 12rem;">
-        <AppAvatarMenu
-          user-name="Marie Curie"
-          user-email="marie@morscher.lab"
-          :items="devToolsItems"
-          sign-out-label="End session"
-          @select="handleSelect"
-          @sign-out="handleSignOut"
-        />
-      </div>
-    </Variant>
-
-    <Variant title="Custom avatar slot">
-      <!-- Consumers can override the avatar chip content (e.g., an image,
-           an emoji, an icon) while keeping the pill trigger + dropdown. -->
-      <div style="padding: 2rem; display: flex; justify-content: flex-start; background: var(--bg-primary); min-height: 8rem;">
-        <AppAvatarMenu
-          user-name="Rosalind Franklin"
-          :items="basicItems"
-          @select="handleSelect"
-          @sign-out="handleSignOut"
-        >
-          <template #avatar>
-            <span style="font-size: 0.875rem;">🧬</span>
-          </template>
-        </AppAvatarMenu>
-      </div>
-    </Variant>
-
-    <Variant title="Playground" :init-state="initState">
-      <template #default="{ state }">
-        <div style="padding: 2rem; display: flex; justify-content: flex-start; background: var(--bg-primary); min-height: 10rem;">
-          <AppAvatarMenu
-            :user-name="state.userName"
-            :user-initial="state.userInitial"
-            :user-email="state.userEmail"
-            :items="basicItems"
-            :show-sign-out="state.showSignOut"
-            :sign-out-label="state.signOutLabel"
-            @select="handleSelect"
-            @sign-out="handleSignOut"
-          />
-        </div>
-      </template>
-
-      <template #controls="{ state }">
-        <HstText v-model="state.userName" title="User name" />
-        <HstText v-model="state.userInitial" title="User initial (override)" />
-        <HstText v-model="state.userEmail" title="User email" />
-        <HstCheckbox v-model="state.showSignOut" title="Show sign out" />
-        <HstText v-model="state.signOutLabel" title="Sign out label" />
-      </template>
-    </Variant>
-  </Story>
-</template>

package/src/components/AppAvatarMenu.vue

@@ -1,154 +0,0 @@
-<script setup lang="ts">
-/** Avatar-triggered dropdown with user name/email header, configurable menu items, dividers, and a sign-out action. */
-import { computed, ref, useTemplateRef } from 'vue'
-import { useDropdownState } from '../composables/useDropdownState'
-import { useMenuKeyboard } from '../composables/useMenuKeyboard'
-import type { AccountMenuItem } from '../types/components'
-import ActionItemInternal from './internal/ActionItemInternal.vue'
-
-interface Props {
-  userName?: string
-  userInitial?: string
-  userEmail?: string
-  items?: AccountMenuItem[]
-  showSignOut?: boolean
-  signOutLabel?: string
-}
-
-const props = withDefaults(defineProps<Props>(), {
-  items: () => [] as AccountMenuItem[],
-  showSignOut: true,
-  signOutLabel: 'Sign out',
-})
-
-const emit = defineEmits<{
-  select: [item: AccountMenuItem]
-  'sign-out': []
-  'menu-open': []
-  'menu-close': []
-}>()
-
-const { isOpen, open, close, toggle } = useDropdownState({
-  rootRef: useTemplateRef<HTMLElement>('root'),
-  triggerRef: useTemplateRef<HTMLElement>('trigger'),
-  onOpen: () => emit('menu-open'),
-  onClose: () => emit('menu-close'),
-})
-
-const panelRef = ref<HTMLElement | null>(null)
-
-function menuItems(): HTMLElement[] {
-  if (!panelRef.value) return []
-  return Array.from(panelRef.value.querySelectorAll<HTMLElement>('[role="menuitem"]'))
-}
-
-const { handleTriggerKeydown, handlePanelKeydown } = useMenuKeyboard({
-  items: menuItems,
-  isOpen: () => isOpen.value,
-  open,
-  close,
-})
-
-const initials = computed(() => {
-  if (props.userInitial) return props.userInitial.slice(0, 2).toUpperCase()
-  if (props.userName) {
-    const parts = props.userName.trim().split(/\s+/).filter(Boolean)
-    const first = parts[0]
-    if (!first) return 'U'
-    const second = parts[1]
-    if (second) return (first.charAt(0) + second.charAt(0)).toUpperCase()
-    return first.slice(0, 2).toUpperCase()
-  }
-  return 'U'
-})
-
-function closeSilently() {
-  isOpen.value = false
-}
-
-function handleSelect(item: AccountMenuItem) {
-  if (item.divider) return
-  emit('select', item)
-  close()
-}
-
-function handleSignOut() {
-  emit('sign-out')
-  close()
-}
-</script>
-
-<template>
-  <div ref="root" class="mint-avatar-menu">
-    <button
-      ref="trigger"
-      type="button"
-      class="mint-avatar-menu__trigger"
-      :class="{ 'mint-avatar-menu__trigger--open': isOpen }"
-      :aria-expanded="isOpen"
-      aria-haspopup="menu"
-      :title="userName ? `${userName} · Account menu` : 'Account menu'"
-      @click.stop="toggle"
-      @keydown="handleTriggerKeydown"
-    >
-      <span class="mint-avatar-menu__avatar">
-        <slot name="avatar" :initials="initials">
-          {{ initials }}
-        </slot>
-      </span>
-      <span v-if="userName" class="mint-avatar-menu__name">{{ userName }}</span>
-    </button>
-
-    <div
-      v-if="isOpen"
-      ref="panelRef"
-      class="mint-popover mint-avatar-menu__panel"
-      role="menu"
-      @keydown="handlePanelKeydown"
-    >
-      <div v-if="userName || userEmail" class="mint-avatar-menu__header">
-        <div v-if="userName" class="mint-avatar-menu__user-name">{{ userName }}</div>
-        <div v-if="userEmail" class="mint-avatar-menu__user-email">{{ userEmail }}</div>
-      </div>
-
-      <slot name="items" :close="closeSilently">
-        <template v-for="item in items" :key="item.id">
-          <div v-if="item.divider" class="mint-menu-separator mint-avatar-menu__divider" role="separator" />
-          <ActionItemInternal
-            v-else
-            :href="item.href"
-            :to="item.to"
-            :class="['mint-menu-item mint-avatar-menu__item', { 'mint-menu-item--danger mint-avatar-menu__item--danger': item.danger }]"
-            role="menuitem"
-            @click="handleSelect(item)"
-          >
-            <span v-if="item.icon" class="mint-avatar-menu__item-icon">
-              <slot name="item-icon" :item="item" />
-            </span>
-            <span class="mint-avatar-menu__item-label">{{ item.label }}</span>
-            <span v-if="item.rightLabel" class="mint-menu-item__meta mint-avatar-menu__item-right">{{ item.rightLabel }}</span>
-          </ActionItemInternal>
-        </template>
-      </slot>
-
-      <template v-if="showSignOut">
-        <div class="mint-menu-separator mint-avatar-menu__divider" role="separator" />
-        <button
-          type="button"
-          class="mint-menu-item mint-menu-item--danger mint-avatar-menu__item mint-avatar-menu__item--danger"
-          role="menuitem"
-          @click="handleSignOut"
-        >
-          <span class="mint-avatar-menu__item-icon" aria-hidden="true">
-            <svg viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
-              <path d="M9 21H5a2 2 0 0 1-2-2V5a2 2 0 0 1 2-2h4" />
-              <polyline points="16 17 21 12 16 7" />
-              <line x1="21" y1="12" x2="9" y2="12" />
-            </svg>
-          </span>
-          <span class="mint-avatar-menu__item-label">{{ signOutLabel }}</span>
-        </button>
-      </template>
-    </div>
-  </div>
-</template>

package/src/components/AppTopBar.navigation.ts

@@ -1,60 +0,0 @@
-import type { PageSelectorItem } from '../types/components'
-import type { PluginNavItem } from '../types/platform'
-
-export interface PluginNavPageSelectorOptions {
-  pluginIcon?: string
-}
-
-export function normalizeNavPath(path?: string): string {
-  const raw = path?.trim() || '/'
-  const prefixed = raw.startsWith('/') ? raw : `/${raw}`
-  return prefixed.replace(/\/+$/, '') || '/'
-}
-
-export function pageIdFromPath(path: string, fallback: string): string {
-  const normalized = normalizeNavPath(path)
-  if (normalized === '/') return 'dashboard'
-  return normalized.replace(/^\/+/, '').replace(/\/+/g, '-') || fallback
-}
-
-export function pluginNavItemToPageSelectorItem(
-  item: PluginNavItem,
-  index: number,
-  options: PluginNavPageSelectorOptions = {},
-): PageSelectorItem {
-  const path = normalizeNavPath(item.path)
-  return {
-    id: item.id || pageIdFromPath(path, `page-${index + 1}`),
-    label: item.label,
-    to: path,
-    icon: item.icon || options.pluginIcon,
-  }
-}
-
-export function currentPagePath(
-  pathname: string | undefined,
-  routePrefix?: string,
-): string | undefined {
-  if (!pathname) return undefined
-  const normalizedPathname = normalizeNavPath(pathname)
-  const normalizedRoutePrefix = normalizeNavPath(routePrefix)
-
-  if (normalizedPathname === normalizedRoutePrefix) return '/'
-  if (
-    normalizedRoutePrefix !== '/' &&
-    normalizedPathname.startsWith(`${normalizedRoutePrefix}/`)
-  ) {
-    return normalizeNavPath(normalizedPathname.slice(normalizedRoutePrefix.length))
-  }
-  return normalizedPathname
-}
-
-export function currentItemIdFromLocation(
-  pages: Array<Pick<PageSelectorItem, 'id' | 'to' | 'href'>>,
-  pathname: string | undefined,
-  routePrefix?: string,
-): string | undefined {
-  const path = currentPagePath(pathname, routePrefix)
-  if (!path) return undefined
-  return pages.find((page) => normalizeNavPath(page.to || page.href) === path)?.id
-}