@morscherlab/mint-sdk 1.2.0-beta.1 → 1.2.0-beta.3

package/src/__tests__/components/SampleSelector.test.ts

@@ -1,466 +0,0 @@
-import { readFileSync } from 'node:fs'
-import { resolve } from 'node:path'
-import { flushPromises, mount } from '@vue/test-utils'
-import { createPinia } from 'pinia'
-import { describe, expect, it, vi } from 'vitest'
-import AutoGroupModal from '../../components/AutoGroupModal.vue'
-import SampleSelector from '../../components/SampleSelector.vue'
-import SmartGroupFieldRecipe from '../../components/SmartGroupFieldRecipe.vue'
-import type { AutoGroupResult, SampleGroup } from '../../types'
-
-// Wait for the FileReader-backed CSV read (a macrotask, not a microtask) plus
-// the ensuing reactive renders to settle.
-async function settle() {
-  for (let i = 0; i < 3; i++) {
-    await new Promise(resolve => setTimeout(resolve, 0))
-    await flushPromises()
-  }
-}
-
-describe('SampleSelector', () => {
-  it('uses shared list selection for select-all and individual sample toggles', async () => {
-    const wrapper = mount(SampleSelector, {
-      props: {
-        samples: ['S1', 'A very long sample name that gets truncated'],
-        modelValue: [],
-        enableGrouping: false,
-        enableSmartGroup: false,
-      },
-      global: {
-        stubs: {
-          AutoGroupModal: true,
-        },
-      },
-    })
-
-    await wrapper.find('.mint-sample-selector__select-all input').trigger('change')
-    expect(wrapper.emitted('update:modelValue')?.[0]).toEqual([['S1', 'A very long sample name that gets truncated']])
-
-    await wrapper.setProps({ modelValue: ['S1'] })
-    await wrapper.findAll('.mint-sample-selector__flat-item input')[0].trigger('change')
-    expect(wrapper.emitted('update:modelValue')?.[1]).toEqual([[]])
-
-    await wrapper.findAll('.mint-sample-selector__flat-item input')[1].trigger('change')
-    expect(wrapper.emitted('update:modelValue')?.[2]).toEqual([['S1', 'A very long sample name that gets truncated']])
-    expect(wrapper.findAll('.mint-sample-selector__flat-item')[1].attributes('title')).toBe(
-      'A very long sample name that gets truncated',
-    )
-  })
-
-  it('uses shared expansion state for grouped sample sections', async () => {
-    const wrapper = mount(SampleSelector, {
-      props: {
-        samples: ['S1', 'S2'],
-        modelValue: [],
-        groups: [
-          { name: 'Control/A', color: '#3B82F6', samples: ['S1'] },
-          { name: 'Control/B', color: '#06B6D4', samples: ['S2'] },
-        ],
-        enableSmartGroup: false,
-      },
-      global: {
-        stubs: {
-          AutoGroupModal: true,
-        },
-      },
-    })
-
-    expect(wrapper.find('.mint-sample-selector__sample-name').exists()).toBe(false)
-
-    await wrapper.find('.mint-sample-selector__expand-btn').trigger('click')
-
-    expect(wrapper.findAll('.mint-sample-selector__sample-name').map(item => item.text())).toEqual(['S1', 'S2'])
-
-    await wrapper.findAll('.mint-sample-selector__expand-btn')[1].trigger('click')
-
-    expect(wrapper.find('.mint-sample-selector__sample-name').exists()).toBe(false)
-  })
-
-  it('can derive samples directly from experiment design data', () => {
-    const wrapper = mount(SampleSelector, {
-      props: {
-        modelValue: [],
-        designData: {
-          samples: [
-            { sample_name: 'S1', sample_type: 'sample' },
-            { sample_name: 'Blank', sample_type: 'blank' },
-            { sample_name: 'S2', sample_type: 'sample' },
-          ],
-        },
-        enableGrouping: false,
-        enableSmartGroup: false,
-      },
-      global: {
-        stubs: {
-          AutoGroupModal: true,
-        },
-      },
-    })
-
-    expect(wrapper.find('.mint-sample-selector__select-all-count').text()).toBe('2 samples')
-    expect(wrapper.findAll('.mint-sample-selector__flat-name').map(item => item.text())).toEqual(['S1', 'S2'])
-  })
-
-  it('merges smart and manual grouping into one launcher', async () => {
-    const wrapper = mount(SampleSelector, {
-      props: {
-        samples: ['S1', 'S2'],
-        modelValue: [],
-        groups: [],
-      },
-      global: {
-        stubs: {
-          AutoGroupModal: true,
-        },
-      },
-    })
-
-    const labels = wrapper.findAll('.mint-sample-selector__actions-row .mint-sample-selector__action-label')
-    expect(labels.map(label => label.text())).toEqual(['Grouping'])
-    expect(wrapper.findAll('.mint-sample-selector__actions-row > .mint-sample-selector__action-btn')).toHaveLength(2)
-
-    await wrapper.findAllComponents({ name: 'BaseButton' })[0].trigger('click')
-
-    const modal = wrapper.findComponent({ name: 'AutoGroupModal' })
-    expect(modal.props('initialMode')).toBe('auto')
-  })
-
-  it('opens the grouping modal in manual mode', async () => {
-    const wrapper = mount(SampleSelector, {
-      props: {
-        samples: ['S1', 'S2'],
-        modelValue: [],
-        groups: [],
-        enableSmartGroup: false,
-      },
-      global: {
-        stubs: {
-          AutoGroupModal: true,
-        },
-      },
-    })
-
-    const labels = wrapper.findAll('.mint-sample-selector__actions-row .mint-sample-selector__action-label')
-    expect(labels.map(label => label.text())).toEqual(['Grouping'])
-
-    await wrapper.findAllComponents({ name: 'BaseButton' })[0].trigger('click')
-
-    const modal = wrapper.findComponent({ name: 'AutoGroupModal' })
-    expect(modal.props('initialMode')).toBe('manual')
-    expect(modal.props('groups')).toEqual([])
-  })
-})
-
-describe('AutoGroupModal manual workflow', () => {
-  it('assigns selected samples to a manual group and subgroup', async () => {
-    const wrapper = mount(AutoGroupModal, {
-      props: {
-        modelValue: true,
-        initialMode: 'manual',
-        samples: ['S1', 'S2'],
-        groups: [],
-      },
-      global: {
-        plugins: [createPinia()],
-        stubs: {
-          Teleport: true,
-        },
-      },
-    })
-
-    await wrapper.findAll('.mg2-row')[0].trigger('click')
-    const fields = wrapper.findAll('.mg2-bar .mg2-combo input')
-    await fields[0].setValue('Treatment')
-    await fields[1].setValue('Baseline')
-    await wrapper.find('.mg2-bar .sg-btn--primary').trigger('click')
-    await wrapper.find('.sg-foot .mint-button--primary').trigger('click')
-
-    const result = wrapper.emitted('apply')?.at(-1)?.[0] as AutoGroupResult
-    expect(result.groups).toHaveLength(1)
-    expect(result.groups[0]).toMatchObject({
-      name: 'Treatment/Baseline',
-      samples: ['S1'],
-      // A newly-created manual cohort must carry a concrete hex colour (the
-      // first SAMPLE_GROUP_COLOR_OPTIONS swatch), not a `var(--grp-*)` string
-      // that breaks SampleSelector's hex8 tint concatenation.
-      color: '#3B82F6',
-    })
-  })
-
-  it('moves manual selections out of existing groups before assigning them', async () => {
-    const wrapper = mount(AutoGroupModal, {
-      props: {
-        modelValue: true,
-        initialMode: 'manual',
-        samples: ['S1', 'S2'],
-        groups: [
-          { name: 'Control', color: '#3B82F6', samples: ['S1'] },
-          { name: 'Treatment', color: '#10B981', samples: [] },
-        ],
-      },
-      global: {
-        plugins: [createPinia()],
-        stubs: {
-          Teleport: true,
-        },
-      },
-    })
-
-    await wrapper.findAll('.mg2-row')[0].trigger('click')
-    await wrapper.findAll('.mg2-bar .mg2-combo input')[0].setValue('Treatment')
-    await wrapper.find('.mg2-bar .sg-btn--primary').trigger('click')
-    await wrapper.find('.sg-foot .mint-button--primary').trigger('click')
-
-    const result = wrapper.emitted('apply')?.at(-1)?.[0] as AutoGroupResult
-    expect(result.groups).toEqual([
-      { name: 'Control', color: '#3B82F6', samples: [] },
-      { name: 'Treatment', color: '#10B981', samples: ['S1'] },
-    ])
-  })
-
-  it('preserves an existing cohort color when the target is typed manually', async () => {
-    const wrapper = mount(AutoGroupModal, {
-      props: {
-        modelValue: true,
-        initialMode: 'manual',
-        samples: ['S1', 'S2'],
-        groups: [
-          { name: 'Control', color: '#10B981', samples: ['S1'] },
-        ],
-      },
-      global: {
-        plugins: [createPinia()],
-        stubs: {
-          Teleport: true,
-        },
-      },
-    })
-
-    await wrapper.findAll('.mg2-row')[1].trigger('click')
-    await wrapper.findAll('.mg2-bar .mg2-combo input')[0].setValue('Control')
-    await wrapper.find('.mg2-bar .sg-btn--primary').trigger('click')
-    await wrapper.find('.sg-foot .mint-button--primary').trigger('click')
-
-    const result = wrapper.emitted('apply')?.at(-1)?.[0] as AutoGroupResult
-    expect(result.groups).toEqual([
-      { name: 'Control', color: '#10B981', samples: ['S1', 'S2'] },
-    ])
-  })
-})
-
-describe('AutoGroupModal multi-schema auto workflow', () => {
-  it('should keep apply enabled when another sample schema still has a grouping field', async () => {
-    const samples = [
-      ...['5916', '5918', '5919', '5920', '5921'].map((id, index) =>
-        `${id}_batch_project_matrix_subject_${String(index + 1).padStart(3, '0')}`,
-      ),
-      ...Array.from({ length: 5 }, (_, index) =>
-        `sample_1x_${String(index + 1).padStart(3, '0')}`,
-      ),
-      ...Array.from({ length: 5 }, (_, index) =>
-        `sample_2x_${String(index + 6).padStart(3, '0')}`,
-      ),
-      'IQC_Pool_001',
-      'IQC_Pool_002',
-      'IQC_Pool_003',
-    ]
-    const wrapper = mount(AutoGroupModal, {
-      props: {
-        modelValue: true,
-        samples,
-      },
-      global: {
-        plugins: [createPinia()],
-        stubs: {
-          Teleport: true,
-        },
-      },
-    })
-
-    await wrapper.find('.sg-switch').trigger('click')
-
-    expect(wrapper.find('.sg-foot .mint-button--primary').attributes('disabled')).toBeUndefined()
-  })
-
-  it('should scroll the token field list when many fields exceed the modal height', () => {
-    const styles = readFileSync(
-      resolve(process.cwd(), 'src/styles/components/smart-group.css'),
-      'utf8',
-    )
-    const mainPanelStyles = styles.match(/\.sg-body__main\s*\{([^}]*)\}/)?.[1]
-
-    expect(mainPanelStyles).toContain('overflow-y: auto')
-  })
-
-  it('should let the token field panel shrink within the fixed modal body', () => {
-    const styles = readFileSync(
-      resolve(process.cwd(), 'src/styles/components/smart-group.css'),
-      'utf8',
-    )
-    const mainPanelStyles = styles.match(/\.sg-body__main\s*\{([^}]*)\}/)?.[1]
-
-    expect(mainPanelStyles).toContain('min-height: 0')
-  })
-
-  it('should scroll the group preview when generated groups exceed the modal height', () => {
-    const styles = readFileSync(
-      resolve(process.cwd(), 'src/styles/components/smart-group.css'),
-      'utf8',
-    )
-    const sidePanelStyles = styles.match(/\.sg-body__side\s*\{([^}]*)\}/)?.[1]
-
-    expect(sidePanelStyles).toMatch(/min-height:\s*0;[\s\S]*overflow-y:\s*auto;/)
-  })
-})
-
-describe('SampleSelector — QC overlay regression', () => {
-  it('keeps QC samples in the emitted groups via the concat compat rule', async () => {
-    const exp: SampleGroup[] = [
-      { name: 'Kidney', color: '#3B82F6', samples: ['s1', 's2'] },
-    ]
-    const qc: SampleGroup[] = [
-      { name: 'IQC', color: '#6B7280', samples: ['iqc1'] },
-    ]
-    const result: AutoGroupResult = {
-      groups: [...exp, ...qc],
-      experimentalGroups: exp,
-      qcGroups: qc,
-      metadata: [],
-      excludedSamples: [],
-    }
-    const wrapper = mount(SampleSelector, {
-      props: { samples: ['s1', 's2', 'iqc1'], modelValue: [] },
-      global: {
-        stubs: {
-          AutoGroupModal: true,
-        },
-      },
-    })
-    ;(wrapper.vm as unknown as { handleSmartGroupApply: (r: AutoGroupResult) => void })
-      .handleSmartGroupApply(result)
-    const emitted = wrapper.emitted('update:groups')!.at(-1)![0] as SampleGroup[]
-    const allSamples = emitted.flatMap(g => g.samples)
-    expect(allSamples).toContain('iqc1')
-  })
-})
-
-describe('AutoGroupModal CSV upload', () => {
-  it('loads an uploaded CSV into the engine so samples reach both auto and manual modes', async () => {
-    const wrapper = mount(AutoGroupModal, {
-      props: { modelValue: true, samples: [], groups: [] },
-      global: {
-        plugins: [createPinia()],
-        stubs: { Teleport: true },
-      },
-    })
-
-    const csv = 'sample_name,Condition\nS1,Control\nS2,Control\nS3,Treatment\n'
-    const file = new File([csv], 'samples.csv', { type: 'text/csv' })
-    wrapper.findComponent(SmartGroupFieldRecipe).vm.$emit('csv-file', file)
-    await settle()
-
-    // Auto mode: the CSV populated the engine's field cards + grouped all 3 samples.
-    const recipe = wrapper.findComponent(SmartGroupFieldRecipe)
-    expect((recipe.props('fields') as unknown[]).length).toBeGreaterThan(0)
-    const rail = recipe.props('groups') as Array<{ count: number }>
-    expect(rail.reduce((acc, g) => acc + g.count, 0)).toBe(3)
-
-    // Manual mode: the CSV sample names populate the manual list (sourced from
-    // the engine, not props.samples — which is empty here).
-    recipe.vm.$emit('manual')
-    await flushPromises()
-    const names = wrapper.findAll('.mg2-row__name').map(n => n.text())
-    expect(names).toEqual(['S1', 'S2', 'S3'])
-  })
-
-  it('surfaces an error (without throwing) for an empty/header-only CSV, then loads a valid one', async () => {
-    const wrapper = mount(AutoGroupModal, {
-      props: { modelValue: true, samples: [], groups: [] },
-      global: { plugins: [createPinia()], stubs: { Teleport: true } },
-    })
-    const recipe = wrapper.findComponent(SmartGroupFieldRecipe)
-
-    // Header-only CSV → parseCSV throws; onCsvFile must catch + surface the error.
-    recipe.vm.$emit('csv-file', new File(['sample_name\n'], 'bad.csv', { type: 'text/csv' }))
-    await settle()
-    expect(wrapper.find('.sg-host__error').exists()).toBe(true)
-    // Engine left un-mutated: no groups loaded from the bad file.
-    expect((recipe.props('groups') as unknown[]).length).toBe(0)
-
-    // A subsequent valid CSV clears the error and loads.
-    recipe.vm.$emit(
-      'csv-file',
-      new File(['sample_name,Condition\nS1,Control\nS2,Treatment\n'], 'good.csv', { type: 'text/csv' }),
-    )
-    await settle()
-    expect(wrapper.find('.sg-host__error').exists()).toBe(false)
-    const rail = recipe.props('groups') as Array<{ count: number }>
-    expect(rail.reduce((acc, g) => acc + g.count, 0)).toBe(2)
-  })
-})
-
-describe('SmartGroupFieldRecipe CSV menu', () => {
-  it('emits download-template from its menu item', async () => {
-    const wrapper = mount(SmartGroupFieldRecipe)
-    await wrapper.find('.fr-upload').trigger('click')
-    const items = wrapper.findAll('.fr-csv-item')
-    expect(items).toHaveLength(3)
-    await items[1].trigger('click')
-    expect(wrapper.emitted('download-template')).toHaveLength(1)
-  })
-
-  it('emits download-prefilled from its menu item', async () => {
-    const wrapper = mount(SmartGroupFieldRecipe)
-    await wrapper.find('.fr-upload').trigger('click')
-    await wrapper.findAll('.fr-csv-item')[2].trigger('click')
-    expect(wrapper.emitted('download-prefilled')).toHaveLength(1)
-  })
-
-  it('disables the download items (and emits nothing) when canDownloadTemplate is false', async () => {
-    const wrapper = mount(SmartGroupFieldRecipe, { props: { canDownloadTemplate: false } })
-    await wrapper.find('.fr-upload').trigger('click')
-    const items = wrapper.findAll('.fr-csv-item')
-    expect(items[1].attributes('disabled')).toBeDefined()
-    expect(items[2].attributes('disabled')).toBeDefined()
-    await items[1].trigger('click')
-    expect(wrapper.emitted('download-template')).toBeUndefined()
-  })
-})
-
-describe('AutoGroupModal template download wiring', () => {
-  it('maps the menu actions to engine downloadTemplate (blank vs prefilled)', async () => {
-    const blobs: Blob[] = []
-    const origCreate = URL.createObjectURL
-    const origRevoke = URL.revokeObjectURL
-    URL.createObjectURL = vi.fn((b: Blob) => {
-      blobs.push(b)
-      return 'blob:mock'
-    }) as typeof URL.createObjectURL
-    URL.revokeObjectURL = vi.fn() as typeof URL.revokeObjectURL
-    const clickSpy = vi.spyOn(HTMLAnchorElement.prototype, 'click').mockImplementation(() => {})
-    try {
-      const wrapper = mount(AutoGroupModal, {
-        props: { modelValue: true, samples: ['Ctrl_R1', 'Ctrl_R2', 'Drug_R1', 'Drug_R2'], groups: [] },
-        global: { plugins: [createPinia()], stubs: { Teleport: true } },
-      })
-      const recipe = wrapper.findComponent(SmartGroupFieldRecipe)
-      recipe.vm.$emit('download-template')
-      await flushPromises()
-      recipe.vm.$emit('download-prefilled')
-      await flushPromises()
-
-      expect(blobs).toHaveLength(2)
-      const blankText = await blobs[0].text()
-      const prefilledText = await blobs[1].text()
-      // download-template → blank mode: the canonical generic DEFAULT_BLANK_HEADERS.
-      // download-prefilled → prefilled mode: a different, detected-column header.
-      expect(blankText.split('\n')[0]).toBe('sample_name,group,class,replicate,notes')
-      expect(prefilledText.split('\n')[0]).not.toBe(blankText.split('\n')[0])
-      expect(blankText).not.toBe(prefilledText)
-    } finally {
-      URL.createObjectURL = origCreate
-      URL.revokeObjectURL = origRevoke
-      clickSpy.mockRestore()
-    }
-  })
-})

package/src/__tests__/components/SampleSelectorSampleRow.test.ts

@@ -1,40 +0,0 @@
-import { mount } from '@vue/test-utils'
-import { describe, expect, it } from 'vitest'
-import SampleSelectorSampleRow from '../../components/SampleSelectorSampleRow.vue'
-
-describe('SampleSelectorSampleRow', () => {
-  it('renders selected and dragging states', () => {
-    const sampleName = 'A very long sample name that gets truncated in narrow panes'
-    const wrapper = mount(SampleSelectorSampleRow, {
-      props: {
-        sample: sampleName,
-        selected: true,
-        dragging: true,
-        accentColor: '#3B82F6',
-      },
-    })
-
-    expect(wrapper.classes()).toContain('mint-sample-selector__sample--dragging')
-    expect((wrapper.get('input').element as HTMLInputElement).checked).toBe(true)
-    expect(wrapper.get('input').attributes('style')).toContain('accent-color')
-    expect(wrapper.text()).toContain(sampleName)
-    expect(wrapper.attributes('title')).toBe(sampleName)
-    expect(wrapper.attributes('aria-label')).toBe(`Sample: ${sampleName}`)
-  })
-
-  it('emits toggle and remove actions', async () => {
-    const wrapper = mount(SampleSelectorSampleRow, {
-      props: {
-        sample: 'S2',
-        selected: false,
-        removable: true,
-      },
-    })
-
-    await wrapper.get('input').trigger('change')
-    await wrapper.get('button').trigger('click')
-
-    expect(wrapper.emitted('toggle')).toHaveLength(1)
-    expect(wrapper.emitted('remove')).toHaveLength(1)
-  })
-})

package/src/__tests__/components/ScheduleCalendar.test.ts

@@ -1,44 +0,0 @@
-import { mount } from '@vue/test-utils'
-import { describe, expect, it } from 'vitest'
-import ScheduleCalendar from '../../components/ScheduleCalendar.vue'
-
-describe('ScheduleCalendar', () => {
-  it('renders week events with layout styles from the schedule model', () => {
-    const wrapper = mount(ScheduleCalendar, {
-      props: {
-        modelValue: new Date('2024-05-15T12:00:00'),
-        dayStartHour: 6,
-        dayEndHour: 10,
-        slotDuration: 30,
-        showNowIndicator: false,
-        events: [
-          {
-            id: 'run-1',
-            title: 'LCMS run',
-            start: '2024-05-15T07:00:00',
-            end: '2024-05-15T08:30:00',
-          },
-        ],
-      },
-    })
-
-    const event = wrapper.find('.mint-schedule__event')
-    expect(event.exists()).toBe(true)
-    expect(event.find('.mint-schedule__event-title').text()).toBe('LCMS run')
-    expect(event.attributes('style')).toContain('top: 80px')
-    expect(event.attributes('style')).toContain('height: 120px')
-  })
-
-  it('renders the month grid from the extracted calendar layout', () => {
-    const wrapper = mount(ScheduleCalendar, {
-      props: {
-        modelValue: new Date('2024-05-15T12:00:00'),
-        view: 'month',
-      },
-    })
-
-    expect(wrapper.findAll('.mint-schedule__month-weekday')).toHaveLength(7)
-    expect(wrapper.findAll('.mint-schedule__month-cell')).toHaveLength(42)
-    expect(wrapper.find('.mint-schedule__title').text()).toBe('May 2024')
-  })
-})