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

package/src/__tests__/composables/useTemplateCollection.test.ts

@@ -1,147 +0,0 @@
-import { beforeEach, describe, expect, it, vi } from 'vitest'
-
-const mockGet = vi.fn()
-const mockPut = vi.fn()
-const mockDelete = vi.fn()
-const mockUseApi = vi.fn((_options?: unknown) => ({
-  get: mockGet,
-  put: mockPut,
-  delete: mockDelete,
-}))
-
-vi.mock('../../composables/useApi', () => ({
-  useApi: (options: unknown) => mockUseApi(options),
-}))
-
-import { useTemplateCollection } from '../../composables/useTemplateCollection'
-import {
-  createPlateMapTemplate,
-  createSampleSheetTemplate,
-  createTemplateCollection,
-  createWellPlateScreenCollection,
-} from '../../templates'
-import type { PlateMapTemplate, SampleSheetTemplate } from '../../templates'
-
-function setup(options?: Parameters<typeof useTemplateCollection>[0]) {
-  return useTemplateCollection(options)
-}
-
-describe('useTemplateCollection', () => {
-  beforeEach(() => {
-    vi.clearAllMocks()
-    mockGet.mockResolvedValue({})
-    mockPut.mockResolvedValue({})
-    mockDelete.mockResolvedValue({})
-    delete (window as unknown as { __MINT_PLATFORM__?: unknown }).__MINT_PLATFORM__
-    window.history.replaceState({}, '', '/')
-  })
-
-  it('initializes from a template collection envelope', () => {
-    const plate = createPlateMapTemplate({ samples: ['Control', 'Treatment'] })
-    const { templateIds, templates, metadata, hasTemplates, getTemplate, requireTemplate } = setup({
-      initial: createTemplateCollection([plate], { preset: 'unit-test' }),
-    })
-
-    expect(templateIds.value).toEqual(['plate-map'])
-    expect(Object.keys(templates.value)).toEqual(['plate-map'])
-    expect(metadata.value).toEqual({ preset: 'unit-test' })
-    expect(hasTemplates.value).toBe(true)
-    expect(getTemplate<PlateMapTemplate>('plate-map')?.data.samples[1].id).toBe('treatment')
-    expect(requireTemplate<PlateMapTemplate>('plate-map').template_id).toBe('plate-map')
-  })
-
-  it('applies, sets, removes, and resets local templates', () => {
-    const plate = createPlateMapTemplate({ samples: ['Control'] })
-    const sampleSheet = createSampleSheetTemplate({
-      samples: [{ sampleId: 'S001', name: 'Sample 1' }],
-    })
-    const { apply, setTemplate, removeTemplate, reset, templateIds, metadata } = setup({
-      initial: [plate],
-    })
-
-    setTemplate(sampleSheet)
-    expect(templateIds.value).toEqual(['plate-map', 'sample-sheet'])
-
-    expect(removeTemplate('plate-map')).toBe(true)
-    expect(templateIds.value).toEqual(['sample-sheet'])
-    expect(removeTemplate('missing')).toBe(false)
-
-    apply(createTemplateCollection([sampleSheet], { source: 'loaded' }))
-    expect(metadata.value).toEqual({ source: 'loaded' })
-
-    reset()
-    expect(templateIds.value).toEqual(['plate-map'])
-  })
-
-  it('uses fallback metadata only when the payload has none', () => {
-    const plate = createPlateMapTemplate({ samples: ['Control'] })
-    const { apply, metadata } = setup()
-
-    apply(createTemplateCollection([plate], { source: 'payload' }), { source: 'fallback' })
-    expect(metadata.value).toEqual({ source: 'payload' })
-
-    apply([plate], { source: 'fallback' })
-    expect(metadata.value).toEqual({ source: 'fallback' })
-  })
-
-  it('saves the local collection through experiment design_data', async () => {
-    const collection = createWellPlateScreenCollection({
-      samples: ['Control', 'Treatment'],
-      compounds: { Drug: [10, 1] },
-    })
-    const { save, lastSavedAt } = setup({ pluginId: 'p1', initial: collection })
-
-    const ok = await save(42)
-
-    expect(ok).toBe(true)
-    expect(lastSavedAt.value).toBeInstanceOf(Date)
-    expect(mockPut).toHaveBeenCalledWith('/experiments/42/data', {
-      plugin_id: 'p1',
-      data: collection,
-      schema_version: '1.0',
-    })
-  })
-
-  it('loads design_data into the local collection', async () => {
-    const sampleSheet = createSampleSheetTemplate({
-      samples: [
-        { sampleId: 'S001', name: 'Sample 1' },
-        { sampleId: 'S002', name: 'Sample 2' },
-      ],
-    })
-    mockGet.mockResolvedValueOnce(createTemplateCollection([sampleSheet], { source: 'api' }))
-    const { load, templateIds, metadata, requireTemplate, lastLoadedAt } = setup()
-
-    const loaded = await load(7)
-
-    expect(mockGet).toHaveBeenCalledWith('/experiments/7/data')
-    expect(loaded?.metadata).toEqual({ source: 'api' })
-    expect(templateIds.value).toEqual(['sample-sheet'])
-    expect(requireTemplate<SampleSheetTemplate>('sample-sheet').data.samples[1].sampleId).toBe(
-      'S002',
-    )
-    expect(metadata.value).toEqual({ source: 'api' })
-    expect(lastLoadedAt.value).toBeInstanceOf(Date)
-  })
-
-  it('saves the current URL experiment without route plumbing', async () => {
-    window.history.replaceState({}, '', '/plugins/template?experimentId=88')
-    const plate = createPlateMapTemplate({ samples: ['Control'] })
-    const { currentExperimentId, hasCurrentExperiment, saveCurrent } = setup({
-      pluginId: 'p1',
-      initial: [plate],
-    })
-
-    expect(currentExperimentId.value).toBe(88)
-    expect(hasCurrentExperiment.value).toBe(true)
-
-    const ok = await saveCurrent()
-
-    expect(ok).toBe(true)
-    expect(mockPut).toHaveBeenCalledWith('/experiments/88/data', {
-      plugin_id: 'p1',
-      data: createTemplateCollection([plate]),
-      schema_version: '1.0',
-    })
-  })
-})

package/src/__tests__/docs/extractDocsTemplates.test.ts

@@ -1,53 +0,0 @@
-import { describe, expect, it } from 'vitest'
-import { bioTemplateCatalog } from '../../../src/templates/catalog'
-import { bioTemplatePacks } from '../../../src/templates/packs'
-import { bioTemplatePresets } from '../../../src/templates/presets'
-import {
-  extractTemplatePacks,
-  extractTemplatePresets,
-  extractTemplates,
-} from '../../../scripts/extract-docs-templates'
-
-describe('extract docs template helpers', () => {
-  it('maps catalog templates into docs manifest entries', () => {
-    const entry = bioTemplateCatalog[0]!
-    const template = extractTemplates()[0]!
-
-    expect(extractTemplates()).toHaveLength(bioTemplateCatalog.length)
-    expect(template).toMatchObject({
-      name: entry.name,
-      kind: 'template',
-      group: entry.category,
-      source: 'packages/sdk-frontend/src/templates/catalog.ts',
-      description: entry.purpose,
-      template_id: entry.template_id,
-      template_version: entry.template_version,
-      add_command: entry.add_command,
-    })
-  })
-
-  it('maps curated presets and packs into docs manifest entries', () => {
-    const presetEntry = bioTemplatePresets[0]!
-    const preset = extractTemplatePresets()[0]!
-    const packEntry = bioTemplatePacks[0]!
-    const pack = extractTemplatePacks()[0]!
-
-    expect(extractTemplatePresets()).toHaveLength(bioTemplatePresets.length)
-    expect(preset).toMatchObject({
-      name: presetEntry.name,
-      kind: 'template-preset',
-      group: presetEntry.category,
-      source: 'packages/sdk-frontend/src/templates/presets.ts',
-      templates: presetEntry.templates,
-    })
-    expect(extractTemplatePacks()).toHaveLength(bioTemplatePacks.length)
-    expect(pack).toMatchObject({
-      name: packEntry.name,
-      kind: 'template-pack',
-      group: packEntry.category,
-      source: 'packages/sdk-frontend/src/templates/packs.ts',
-      add_command: packEntry.add_command,
-      docs_command: packEntry.docs_command,
-    })
-  })
-})

package/src/__tests__/fixtures/templates/dose-response.json

@@ -1,81 +0,0 @@
-{
-  "template_id": "dose-response",
-  "template_version": "1.0",
-  "kind": "experiment-design",
-  "data": {
-    "compounds": [
-      {
-        "id": "drug-a",
-        "name": "Drug A",
-        "concentrations": [10, 1, 0.1],
-        "metadata": {
-          "color": "#10B981"
-        }
-      }
-    ],
-    "unit": "uM",
-    "replicates": 2,
-    "controls": [
-      {
-        "id": "dmso",
-        "name": "DMSO",
-        "role": "vehicle",
-        "vehicle": "DMSO",
-        "metadata": {}
-      }
-    ],
-    "layout": {
-      "plates": [
-        {
-          "id": "plate-1",
-          "name": "Dose response plate",
-          "format": 96,
-          "wells": {
-            "A1": {
-              "id": "A1",
-              "row": 0,
-              "col": 0,
-              "state": "filled",
-              "sampleType": "dmso",
-              "metadata": {
-                "role": "vehicle"
-              }
-            },
-            "A2": {
-              "id": "A2",
-              "row": 0,
-              "col": 1,
-              "state": "filled",
-              "sampleType": "drug-a",
-              "value": 10,
-              "metadata": {
-                "compound": "Drug A",
-                "concentration": 10
-              }
-            }
-          }
-        }
-      ],
-      "samples": [
-        {
-          "id": "dmso",
-          "name": "DMSO",
-          "color": "#3B82F6"
-        },
-        {
-          "id": "drug-a",
-          "name": "Drug A",
-          "color": "#10B981"
-        }
-      ],
-      "activePlateId": "plate-1",
-      "selectedWells": []
-    },
-    "metadata": {
-      "assay": "cell viability"
-    }
-  },
-  "metadata": {
-    "source": "fixture"
-  }
-}

package/src/__tests__/fixtures/templates/plate-map.json

@@ -1,54 +0,0 @@
-{
-  "template_id": "plate-map",
-  "template_version": "1.0",
-  "kind": "experiment-design",
-  "data": {
-    "plates": [
-      {
-        "id": "plate-1",
-        "name": "Drug screen plate",
-        "format": 96,
-        "wells": {
-          "A1": {
-            "id": "A1",
-            "row": 0,
-            "col": 0,
-            "state": "filled",
-            "sampleType": "dmso",
-            "metadata": {
-              "role": "vehicle"
-            }
-          },
-          "A2": {
-            "id": "A2",
-            "row": 0,
-            "col": 1,
-            "state": "filled",
-            "sampleType": "drug-a",
-            "value": 10,
-            "metadata": {
-              "compound": "Drug A"
-            }
-          }
-        }
-      }
-    ],
-    "samples": [
-      {
-        "id": "dmso",
-        "name": "DMSO",
-        "color": "#3B82F6"
-      },
-      {
-        "id": "drug-a",
-        "name": "Drug A",
-        "color": "#10B981"
-      }
-    ],
-    "activePlateId": "plate-1",
-    "selectedWells": []
-  },
-  "metadata": {
-    "source": "fixture"
-  }
-}

package/src/__tests__/fixtures/templates/qpcr-plate.json

@@ -1,96 +0,0 @@
-{
-  "template_id": "qpcr-plate",
-  "template_version": "1.0",
-  "kind": "experiment-design",
-  "data": {
-    "plateId": "qpcr-plate-1",
-    "format": 96,
-    "samples": [
-      {
-        "sampleId": "control",
-        "name": "Control",
-        "group": "Control",
-        "metadata": {
-          "condition": "baseline"
-        }
-      },
-      {
-        "sampleId": "treatment",
-        "name": "Treatment",
-        "group": "Treatment",
-        "metadata": {
-          "condition": "treated"
-        }
-      }
-    ],
-    "targets": [
-      {
-        "id": "actb",
-        "name": "ACTB",
-        "assayId": "Hs01060665_g1",
-        "reporter": "FAM",
-        "metadata": {}
-      },
-      {
-        "id": "gapdh",
-        "name": "GAPDH",
-        "assayId": "Hs02786624_g1",
-        "reporter": "FAM",
-        "metadata": {}
-      }
-    ],
-    "reactions": [
-      {
-        "id": "control-actb-r1",
-        "wellId": "A1",
-        "sampleId": "control",
-        "targetId": "actb",
-        "replicate": 1,
-        "controlKind": "sample",
-        "cq": 21.4,
-        "flags": [],
-        "metadata": {}
-      },
-      {
-        "id": "control-gapdh-r1",
-        "wellId": "A2",
-        "sampleId": "control",
-        "targetId": "gapdh",
-        "replicate": 1,
-        "controlKind": "sample",
-        "cq": 19.8,
-        "flags": [],
-        "metadata": {}
-      },
-      {
-        "id": "treatment-actb-r1",
-        "wellId": "A3",
-        "sampleId": "treatment",
-        "targetId": "actb",
-        "replicate": 1,
-        "controlKind": "sample",
-        "cq": 24.1,
-        "flags": ["review"],
-        "metadata": {}
-      },
-      {
-        "id": "ntc-actb",
-        "wellId": "A4",
-        "targetId": "actb",
-        "replicate": 1,
-        "controlKind": "no-template",
-        "cq": null,
-        "flags": [],
-        "metadata": {}
-      }
-    ],
-    "instrument": "QuantStudio",
-    "chemistry": "taqman",
-    "metadata": {
-      "assay": "gene expression"
-    }
-  },
-  "metadata": {
-    "source": "fixture"
-  }
-}

package/src/__tests__/fixtures/templates/sample-sheet.json

@@ -1,71 +0,0 @@
-{
-  "template_id": "sample-sheet",
-  "template_version": "1.0",
-  "kind": "experiment-design",
-  "data": {
-    "samples": [
-      {
-        "sampleId": "S001",
-        "name": "Control 1",
-        "group": "Control",
-        "batch": "Batch 1",
-        "replicate": 1,
-        "plateId": "plate-1",
-        "wellId": "A1",
-        "metadata": {
-          "cell_line": "HCT116"
-        }
-      },
-      {
-        "sampleId": "S002",
-        "name": "Drug A 1",
-        "group": "Drug A",
-        "batch": "Batch 1",
-        "replicate": 1,
-        "plateId": "plate-1",
-        "wellId": "A2",
-        "metadata": {
-          "cell_line": "HCT116"
-        }
-      }
-    ],
-    "columns": [
-      {
-        "id": "sample_id",
-        "label": "Sample ID",
-        "type": "string",
-        "required": true,
-        "groupable": false
-      },
-      {
-        "id": "group",
-        "label": "Group",
-        "type": "category",
-        "required": false,
-        "groupable": true
-      },
-      {
-        "id": "cell_line",
-        "label": "Cell Line",
-        "type": "string",
-        "required": false,
-        "groupable": true
-      }
-    ],
-    "groups": [
-      {
-        "name": "Control",
-        "color": "#3B82F6",
-        "samples": ["S001"]
-      },
-      {
-        "name": "Drug A",
-        "color": "#10B981",
-        "samples": ["S002"]
-      }
-    ]
-  },
-  "metadata": {
-    "source": "fixture"
-  }
-}