@morscherlab/mint-sdk 1.0.0-rc.2 → 1.0.0-rc.5

package/src/__tests__/fixtures/auto-group/mixed-lc-ms-batch.txt

@@ -0,0 +1,187 @@
+exp281_260413_YS_H2_400ulES_1ul_071
+exp281_260413_YS_K2_400ulES_1ul_070
+exp281_260413_YS_L2_400ulES_1ul_069
+exp281_260415_SAM_SAH_SAHStandard_5nM_002
+exp281_260415_SAM_SAH_SAHStandard_5nM_093
+exp281_260415_SAM_SAH_SAMstandard_5nM_001
+exp281_260415_SAM_SAH_SAMstandard_5nM_092
+exp281_260415_SAM_SAH_Tissues_ExtractionS_00B
+exp281_260415_SAM_SAH_Tissues_ExtractionS_091
+exp281_260415_SAM_SAH_Tissues_IQC_003
+exp281_260415_SAM_SAH_Tissues_IQC_056
+exp281_260415_SAM_SAH_Tissues_IQC_090
+exp281_260415_SAM_SAH_Tissues_Kidney_M10_085
+exp281_260415_SAM_SAH_Tissues_Kidney_M11_080
+exp281_260415_SAM_SAH_Tissues_Kidney_M12_027
+exp281_260415_SAM_SAH_Tissues_Kidney_M13_048
+exp281_260415_SAM_SAH_Tissues_Kidney_M14_023
+exp281_260415_SAM_SAH_Tissues_Kidney_M15_074
+exp281_260415_SAM_SAH_Tissues_Kidney_M16_088
+exp281_260415_SAM_SAH_Tissues_Kidney_M17_070
+exp281_260415_SAM_SAH_Tissues_Kidney_M18_006
+exp281_260415_SAM_SAH_Tissues_Kidney_M19_033
+exp281_260415_SAM_SAH_Tissues_Kidney_M1_050
+exp281_260415_SAM_SAH_Tissues_Kidney_M20_004
+exp281_260415_SAM_SAH_Tissues_Kidney_M21_061
+exp281_260415_SAM_SAH_Tissues_Kidney_M22_032
+exp281_260415_SAM_SAH_Tissues_Kidney_M23_024
+exp281_260415_SAM_SAH_Tissues_Kidney_M24_040
+exp281_260415_SAM_SAH_Tissues_Kidney_M25_045
+exp281_260415_SAM_SAH_Tissues_Kidney_M26_026
+exp281_260415_SAM_SAH_Tissues_Kidney_M27_067
+exp281_260415_SAM_SAH_Tissues_Kidney_M2_086
+exp281_260415_SAM_SAH_Tissues_Kidney_M3_083
+exp281_260415_SAM_SAH_Tissues_Kidney_M4_068
+exp281_260415_SAM_SAH_Tissues_Kidney_M5_049
+exp281_260415_SAM_SAH_Tissues_Kidney_M6_069
+exp281_260415_SAM_SAH_Tissues_Kidney_M7_054
+exp281_260415_SAM_SAH_Tissues_Kidney_M8_079
+exp281_260415_SAM_SAH_Tissues_Kidney_M9_009
+exp281_260415_SAM_SAH_Tissues_Liver_M10_011
+exp281_260415_SAM_SAH_Tissues_Liver_M11_075
+exp281_260415_SAM_SAH_Tissues_Liver_M12_022
+exp281_260415_SAM_SAH_Tissues_Liver_M13_060
+exp281_260415_SAM_SAH_Tissues_Liver_M14_025
+exp281_260415_SAM_SAH_Tissues_Liver_M15_031
+exp281_260415_SAM_SAH_Tissues_Liver_M16_078
+exp281_260415_SAM_SAH_Tissues_Liver_M17_029
+exp281_260415_SAM_SAH_Tissues_Liver_M18_046
+exp281_260415_SAM_SAH_Tissues_Liver_M19_073
+exp281_260415_SAM_SAH_Tissues_Liver_M1_047
+exp281_260415_SAM_SAH_Tissues_Liver_M20_072
+exp281_260415_SAM_SAH_Tissues_Liver_M21_042
+exp281_260415_SAM_SAH_Tissues_Liver_M22_030
+exp281_260415_SAM_SAH_Tissues_Liver_M23_014
+exp281_260415_SAM_SAH_Tissues_Liver_M24_043
+exp281_260415_SAM_SAH_Tissues_Liver_M25_008
+exp281_260415_SAM_SAH_Tissues_Liver_M26_057
+exp281_260415_SAM_SAH_Tissues_Liver_M27_053
+exp281_260415_SAM_SAH_Tissues_Liver_M2_019
+exp281_260415_SAM_SAH_Tissues_Liver_M3_017
+exp281_260415_SAM_SAH_Tissues_Liver_M4_007
+exp281_260415_SAM_SAH_Tissues_Liver_M5_059
+exp281_260415_SAM_SAH_Tissues_Liver_M6_005
+exp281_260415_SAM_SAH_Tissues_Liver_M7_035
+exp281_260415_SAM_SAH_Tissues_Liver_M8_036
+exp281_260415_SAM_SAH_Tissues_Liver_M9_055
+exp281_260415_SAM_SAH_Tissues_Tumor_M10_037
+exp281_260415_SAM_SAH_Tissues_Tumor_M11_015
+exp281_260415_SAM_SAH_Tissues_Tumor_M12_062
+exp281_260415_SAM_SAH_Tissues_Tumor_M13_087
+exp281_260415_SAM_SAH_Tissues_Tumor_M14_081
+exp281_260415_SAM_SAH_Tissues_Tumor_M15_016
+exp281_260415_SAM_SAH_Tissues_Tumor_M16_013
+exp281_260415_SAM_SAH_Tissues_Tumor_M17_084
+exp281_260415_SAM_SAH_Tissues_Tumor_M18_021
+exp281_260415_SAM_SAH_Tissues_Tumor_M19_064
+exp281_260415_SAM_SAH_Tissues_Tumor_M1_066
+exp281_260415_SAM_SAH_Tissues_Tumor_M20_012
+exp281_260415_SAM_SAH_Tissues_Tumor_M21_038
+exp281_260415_SAM_SAH_Tissues_Tumor_M22_034
+exp281_260415_SAM_SAH_Tissues_Tumor_M23_089
+exp281_260415_SAM_SAH_Tissues_Tumor_M24_028
+exp281_260415_SAM_SAH_Tissues_Tumor_M25_063
+exp281_260415_SAM_SAH_Tissues_Tumor_M26_018
+exp281_260415_SAM_SAH_Tissues_Tumor_M27_082
+exp281_260415_SAM_SAH_Tissues_Tumor_M2_076
+exp281_260415_SAM_SAH_Tissues_Tumor_M3_071
+exp281_260415_SAM_SAH_Tissues_Tumor_M4_041
+exp281_260415_SAM_SAH_Tissues_Tumor_M5_051
+exp281_260415_SAM_SAH_Tissues_Tumor_M6_044
+exp281_260415_SAM_SAH_Tissues_Tumor_M7_065
+exp281_260415_SAM_SAH_Tissues_Tumor_M8_010
+exp281_260415_SAM_SAH_Tissues_Tumor_M9_052
+exp280_260413_SK_ESwithSpikeIn_02
+exp280_260413_SK_ESwithSpikeIn_1to100_Stock_05
+exp280_260413_SK_ESwithSpikeIn_1to100_Stock_10
+exp280_260413_SK_ESwithSpikeIn_1to10_04
+exp280_260413_SK_SAM_5nM_03
+exp280_260413_SK_SAM_5nM_06
+exp280_260413_YS_Experiment_EQC_002
+exp280_260413_YS_Experiment_EQC_067
+exp280_260413_YS_Experiment_EQC_102
+exp280_260413_YS_Experiment_Plasma_M10_031
+exp280_260413_YS_Experiment_Plasma_M10_0dot5ul_061
+exp280_260413_YS_Experiment_Plasma_M10_0dot5ul_097
+exp280_260413_YS_Experiment_Plasma_M11_018
+exp280_260413_YS_Experiment_Plasma_M11_0dot5ul_054
+exp280_260413_YS_Experiment_Plasma_M11_0dot5ul_090
+exp280_260413_YS_Experiment_Plasma_M12_026
+exp280_260413_YS_Experiment_Plasma_M12_0dot5ul_059
+exp280_260413_YS_Experiment_Plasma_M12_0dot5ul_095
+exp280_260413_YS_Experiment_Plasma_M13_027
+exp280_260413_YS_Experiment_Plasma_M13_0dot5ul_037
+exp280_260413_YS_Experiment_Plasma_M13_0dot5ul_073
+exp280_260413_YS_Experiment_Plasma_M14_011
+exp280_260413_YS_Experiment_Plasma_M14_0dot5ul_058
+exp280_260413_YS_Experiment_Plasma_M14_0dot5ul_094
+exp280_260413_YS_Experiment_Plasma_M15_029
+exp280_260413_YS_Experiment_Plasma_M15_0dot5ul_065
+exp280_260413_YS_Experiment_Plasma_M15_0dot5ul_100
+exp280_260413_YS_Experiment_Plasma_M16_024
+exp280_260413_YS_Experiment_Plasma_M16_0dot5ul_048
+exp280_260413_YS_Experiment_Plasma_M16_0dot5ul_084
+exp280_260413_YS_Experiment_Plasma_M17_006
+exp280_260413_YS_Experiment_Plasma_M17_0dot5ul_055
+exp280_260413_YS_Experiment_Plasma_M17_0dot5ul_091
+exp280_260413_YS_Experiment_Plasma_M18_013
+exp280_260413_YS_Experiment_Plasma_M18_0dot5ul_064
+exp280_260413_YS_Experiment_Plasma_M18_0dot5ul_099
+exp280_260413_YS_Experiment_Plasma_M19_030
+exp280_260413_YS_Experiment_Plasma_M19_0dot5ul_051
+exp280_260413_YS_Experiment_Plasma_M19_0dot5ul_087
+exp280_260413_YS_Experiment_Plasma_M1_015
+exp280_260413_YS_Experiment_Plasma_M1_0dot5ul_039
+exp280_260413_YS_Experiment_Plasma_M1_0dot5ul_075
+exp280_260413_YS_Experiment_Plasma_M20_005
+exp280_260413_YS_Experiment_Plasma_M20_0dot5ul_049
+exp280_260413_YS_Experiment_Plasma_M20_0dot5ul_085
+exp280_260413_YS_Experiment_Plasma_M21_004
+exp280_260413_YS_Experiment_Plasma_M21_0dot5ul_050
+exp280_260413_YS_Experiment_Plasma_M21_0dot5ul_086
+exp280_260413_YS_Experiment_Plasma_M22_009
+exp280_260413_YS_Experiment_Plasma_M22_0dot5ul_040
+exp280_260413_YS_Experiment_Plasma_M22_0dot5ul_076
+exp280_260413_YS_Experiment_Plasma_M23_023
+exp280_260413_YS_Experiment_Plasma_M23_0dot5ul_066
+exp280_260413_YS_Experiment_Plasma_M23_0dot5ul_101
+exp280_260413_YS_Experiment_Plasma_M24_003
+exp280_260413_YS_Experiment_Plasma_M24_0dot5ul_042
+exp280_260413_YS_Experiment_Plasma_M24_0dot5ul_078
+exp280_260413_YS_Experiment_Plasma_M25_007
+exp280_260413_YS_Experiment_Plasma_M25_0dot5ul_038
+exp280_260413_YS_Experiment_Plasma_M25_0dot5ul_074
+exp280_260413_YS_Experiment_Plasma_M26_014
+exp280_260413_YS_Experiment_Plasma_M26_0dot5ul_056
+exp280_260413_YS_Experiment_Plasma_M26_0dot5ul_092
+exp280_260413_YS_Experiment_Plasma_M27_032
+exp280_260413_YS_Experiment_Plasma_M27_0dot5ul_063
+exp280_260413_YS_Experiment_Plasma_M27_0dot5ul_098
+exp280_260413_YS_Experiment_Plasma_M2_020
+exp280_260413_YS_Experiment_Plasma_M2_0dot5ul_047
+exp280_260413_YS_Experiment_Plasma_M2_0dot5ul_083
+exp280_260413_YS_Experiment_Plasma_M3_025
+exp280_260413_YS_Experiment_Plasma_M3_0dot5ul_060
+exp280_260413_YS_Experiment_Plasma_M3_0dot5ul_096
+exp280_260413_YS_Experiment_Plasma_M4_008
+exp280_260413_YS_Experiment_Plasma_M4_0dot5ul_045
+exp280_260413_YS_Experiment_Plasma_M4_0dot5ul_081
+exp280_260413_YS_Experiment_Plasma_M5_012
+exp280_260413_YS_Experiment_Plasma_M5_0dot5ul_057
+exp280_260413_YS_Experiment_Plasma_M5_0dot5ul_093
+exp280_260413_YS_Experiment_Plasma_M6_016
+exp280_260413_YS_Experiment_Plasma_M6_0dot5ul_046
+exp280_260413_YS_Experiment_Plasma_M6_0dot5ul_082
+exp280_260413_YS_Experiment_Plasma_M7_017
+exp280_260413_YS_Experiment_Plasma_M7_0dot5ul_041
+exp280_260413_YS_Experiment_Plasma_M7_0dot5ul_077
+exp280_260413_YS_Experiment_Plasma_M8_022
+exp280_260413_YS_Experiment_Plasma_M8_0dot5ul_043
+exp280_260413_YS_Experiment_Plasma_M8_0dot5ul_079
+exp280_260413_YS_Experiment_Plasma_M9_021
+exp280_260413_YS_Experiment_Plasma_M9_0dot5ul_052
+exp280_260413_YS_Experiment_Plasma_M9_0dot5ul_088
+exp280_260413_YS_Experiment_SAH_1nM_036
+exp280_260413_YS_Experiment_SAH_1nM_072
+exp280_260413_YS_Experiment_SAM_1nM_035
+exp280_260413_YS_Experiment_SAM_1nM_071

package/src/components/AppSidebar.vue

@@ -31,9 +31,9 @@ import type { FormEnhancements, FormSchema } from '../types/form-builder'
 import {
   controlsToSectionFormSchemas,
   controlsToSidebarPanels,
-  defineControlModel,
   getControlDefaults,
   mergeControlWorkspaceOptions,
+  resolveControlModel,
   type ControlModel,
   type ControlModelBinding,
   type ControlSchema,
@@ -173,8 +173,7 @@ const resolvedWidth = computed(() => props.width ?? (isAnalysisVariant.value ? '
 const resolvedCollapsible = computed(() => props.collapsible ?? isAnalysisVariant.value)
 
 const resolvedModel = computed<ControlModelBinding | undefined>(() => {
-  if (props.model === undefined) return undefined
-  return isControlModelBinding(props.model) ? props.model : defineControlModel(props.model)
+  return resolveControlModel(props.model)
 })
 
 const resolvedControls = computed<ControlSchema | undefined>(() =>
@@ -297,9 +296,6 @@ function firstVisibleViewId(panels: Record<string, SidebarToolSection[]>): strin
   return ''
 }
 
-function isControlModelBinding(model: ControlModel | ControlModelBinding): model is ControlModelBinding {
-  return 'controls' in model && 'controlOptions' in model
-}
 </script>
 
 <template>

package/src/components/AppTopBar.navigation.ts

@@ -0,0 +1,62 @@
+import type { PageSelectorItem } from '../types/components'
+import type { PluginNavItem } from '../types/platform'
+
+export interface PluginNavPageSelectorOptions {
+  pluginIcon?: string
+  pluginName?: 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-${index + 1}`),
+    label: item.label,
+    to: path,
+    icon: item.icon || options.pluginIcon,
+    hint: item.description || options.pluginName,
+  }
+}
+
+export function currentPagePath(
+  pathname: string | undefined,
+  routePrefix?: string,
+): string | undefined {
+  if (!pathname) return undefined
+  const normalizedPathname = normalizeNavPath(pathname)
+  const normalizedRoutePrefix = normalizeNavPath(routePrefix)
+
+  if (normalizedPathname === normalizedRoutePrefix) return '/'
+  if (
+    normalizedRoutePrefix !== '/' &&
+    normalizedPathname.startsWith(`${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
+}

package/src/components/AppTopBar.vue

@@ -14,7 +14,6 @@ import type {
   AccountMenuItem,
   SettingsTab,
 } from '../types/components'
-import type { PluginNavItem } from '../types/platform'
 import { normalizeItemInput } from '../utils/items'
 import ThemeToggle from './ThemeToggle.vue'
 import SettingsModal from './SettingsModal.vue'
@@ -27,6 +26,10 @@ import AppPluginSwitcher from './AppPluginSwitcher.vue'
 import PluginIcon from './PluginIcon.vue'
 import { usePlatformContext } from '../composables/usePlatformContext'
 import { APP_EXPERIMENT_KEY } from '../composables/useAppExperiment'
+import {
+  currentItemIdFromLocation,
+  pluginNavItemToPageSelectorItem,
+} from './AppTopBar.navigation'
 
 interface Props {
   /** App or plugin title shown in the left title group when no page selector is present. */
@@ -153,7 +156,12 @@ const hasTitleOnly = computed(
 )
 const platformPageSelector = computed<PageSelectorItem[]>(() =>
   hasPlatformPageSelector.value
-    ? plugin.value?.nav_items?.map(pluginNavItemToPageSelectorItem) ?? []
+    ? plugin.value?.nav_items?.map((item, index) =>
+      pluginNavItemToPageSelectorItem(item, index, {
+        pluginIcon: plugin.value?.icon,
+        pluginName: plugin.value?.name,
+      })
+    ) ?? []
     : [],
 )
 const normalizedPageSelector = computed<PageSelectorItem[]>(() =>
@@ -167,50 +175,15 @@ const normalizedSettingsTabs = computed<SettingsTab[]>(() =>
 )
 const effectiveCurrentPageSelectorId = computed(() =>
   props.currentPageSelectorId
-    ?? (hasPlatformPageSelector.value ? currentItemIdFromLocation(normalizedPageSelector.value) : undefined)
+    ?? (hasPlatformPageSelector.value
+      ? currentItemIdFromLocation(
+        normalizedPageSelector.value,
+        typeof window === 'undefined' ? undefined : window.location.pathname,
+        plugin.value?.route_prefix,
+      )
+      : undefined)
     ?? (hasPlatformPageSelector.value ? normalizedPageSelector.value[0]?.id : undefined),
 )
-
-function normalizeNavPath(path?: string): string {
-  const raw = path?.trim() || '/'
-  const prefixed = raw.startsWith('/') ? raw : `/${raw}`
-  return prefixed.replace(/\/+$/, '') || '/'
-}
-
-function pageIdFromPath(path: string, fallback: string): string {
-  const normalized = normalizeNavPath(path)
-  if (normalized === '/') return 'dashboard'
-  return normalized.replace(/^\/+/, '').replace(/\/+/g, '-') || fallback
-}
-
-function pluginNavItemToPageSelectorItem(item: PluginNavItem, index: number): PageSelectorItem {
-  const path = normalizeNavPath(item.path)
-  return {
-    id: item.id || pageIdFromPath(path, `page-${index + 1}`),
-    label: item.label,
-    to: path,
-    icon: item.icon || plugin.value?.icon,
-    hint: item.description || plugin.value?.name,
-  }
-}
-
-function currentPagePath(): string | undefined {
-  if (typeof window === 'undefined') return undefined
-  const pathname = normalizeNavPath(window.location.pathname)
-  const routePrefix = normalizeNavPath(plugin.value?.route_prefix)
-
-  if (pathname === routePrefix) return '/'
-  if (routePrefix !== '/' && pathname.startsWith(`${routePrefix}/`)) {
-    return normalizeNavPath(pathname.slice(routePrefix.length))
-  }
-  return pathname
-}
-
-function currentItemIdFromLocation(pages: Array<Pick<PageSelectorItem, 'id' | 'to' | 'href'>>): string | undefined {
-  const path = currentPagePath()
-  if (!path) return undefined
-  return pages.find((page) => normalizeNavPath(page.to || page.href) === path)?.id
-}
 </script>
 
 <template>

package/src/components/AutoGroupModal.story.vue

@@ -2,6 +2,23 @@
 import { ref } from 'vue'
 import AutoGroupModal from './AutoGroupModal.vue'
 import type { AutoGroupResult } from '../types/auto-group'
+import mixedLcMsRaw from '../__tests__/fixtures/auto-group/mixed-lc-ms-batch.txt?raw'
+
+const mixedLcMsSamples = mixedLcMsRaw.trim().split('\n')
+
+const simpleHomogeneous = [
+  'sample_treated_rep1',
+  'sample_treated_rep2',
+  'sample_ctrl_rep1',
+  'sample_ctrl_rep2',
+]
+
+const numericBinning = [
+  'exp_drugA_0dot1uM_rep1',
+  'exp_drugA_1uM_rep1',
+  'exp_drugA_10uM_rep1',
+  'exp_drugA_100uM_rep1',
+]
 
 // Realistic proteomics-style samples with consistent structure
 const proteomicsSamples = [
@@ -269,5 +286,38 @@ function initState(samples: string[] = proteomicsSamples) {
         />
       </div>
     </Variant>
+
+    <Variant title="Simple homogeneous batch" :init-state="() => ({ isOpen: true })">
+      <template #default="{ state }">
+        <div style="padding: 2rem;">
+          <button v-if="!state.isOpen" type="button" style="padding: 0.5rem 1rem; background: var(--bg-card, #fff); border: 1px solid var(--border-color, #e5e7eb); border-radius: 0.375rem; cursor: pointer; font-size: 0.875rem;" @click="state.isOpen = true">
+            Re-open Modal
+          </button>
+          <AutoGroupModal v-model="state.isOpen" :samples="simpleHomogeneous" />
+        </div>
+      </template>
+    </Variant>
+
+    <Variant title="Mixed LC-MS batch (user fixture)" :init-state="() => ({ isOpen: true })">
+      <template #default="{ state }">
+        <div style="padding: 2rem;">
+          <button v-if="!state.isOpen" type="button" style="padding: 0.5rem 1rem; background: var(--bg-card, #fff); border: 1px solid var(--border-color, #e5e7eb); border-radius: 0.375rem; cursor: pointer; font-size: 0.875rem;" @click="state.isOpen = true">
+            Re-open Modal
+          </button>
+          <AutoGroupModal v-model="state.isOpen" :samples="mixedLcMsSamples" />
+        </div>
+      </template>
+    </Variant>
+
+    <Variant title="Numeric binning (dose curve)" :init-state="() => ({ isOpen: true })">
+      <template #default="{ state }">
+        <div style="padding: 2rem;">
+          <button v-if="!state.isOpen" type="button" style="padding: 0.5rem 1rem; background: var(--bg-card, #fff); border: 1px solid var(--border-color, #e5e7eb); border-radius: 0.375rem; cursor: pointer; font-size: 0.875rem;" @click="state.isOpen = true">
+            Re-open Modal
+          </button>
+          <AutoGroupModal v-model="state.isOpen" :samples="numericBinning" />
+        </div>
+      </template>
+    </Variant>
   </Story>
 </template>