import { createAssayMatrixTemplate } from './assayMatrixBuilder'
import { idFromName } from './builderIdUtils'
import { createProtocolStepsTemplate } from './protocolStepsBuilder'
import { createReagentListTemplate } from './reagentListBuilder'
import { createSampleSheetTemplate } from './sampleSheetBuilder'
import { presetSampleRecords } from './sampleNormalizers'
import { createTemplateCollection } from './templateEnvelopes'
import type {
  CreateWesternBlotAssayCollectionOptions,
  TemplateCollectionEnvelope,
} from './types'

/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
export function createWesternBlotAssayCollection(
  options: CreateWesternBlotAssayCollectionOptions = {}
): TemplateCollectionEnvelope {
  const sampleRecords = presetSampleRecords(options.samples ?? ['Control', 'Treatment'])
  const loadingControl = options.loadingControl ?? 'ACTB'
  const targetNames = (options.targets ?? ['Target protein']).map(target =>
    typeof target === 'string' ? target : target.name ?? target.id
  )
  const featureNames = loadingControl && !targetNames.includes(loadingControl)
    ? [...targetNames, loadingControl]
    : targetNames
  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })
  const reagentList = createReagentListTemplate({
    reagents: [
      { id: 'primary-antibody', name: 'Primary antibody', kind: 'antibody', storageCondition: '4C' },
      { id: 'secondary-antibody', name: 'Secondary antibody', kind: 'antibody', storageCondition: '4C' },
      { id: 'lysis-buffer', name: 'Lysis buffer', kind: 'buffer', storageCondition: '4C' },
      { id: 'blocking-buffer', name: 'Blocking buffer', kind: 'buffer', storageCondition: '4C' },
      { id: 'wash-buffer', name: 'TBST wash buffer', kind: 'buffer', storageCondition: 'RT' },
      { id: 'substrate', name: 'Detection substrate', kind: 'reagent', storageCondition: '4C' },
    ],
    metadata: { assay: 'western-blot' },
  })
  const protocol = createProtocolStepsTemplate({
    steps: [
      { id: 'lyse-samples', type: 'addition', name: 'Lyse samples', duration: 30 },
      { id: 'run-gel', type: 'custom', name: 'Run SDS-PAGE', duration: 90 },
      { id: 'transfer', type: 'transfer', name: 'Transfer to membrane', duration: 60 },
      { id: 'block', type: 'incubation', name: 'Block membrane', duration: 60 },
      { id: 'primary-antibody', type: 'incubation', name: 'Primary antibody incubation', duration: 960 },
      { id: 'secondary-antibody', type: 'incubation', name: 'Secondary antibody incubation', duration: 60 },
      { id: 'detect', type: 'measurement', name: 'Detect and quantify bands', duration: 30 },
    ],
    metadata: { assay: 'western-blot' },
  })
  const assayMatrix = createAssayMatrixTemplate({
    samples: sampleRecords.map(sample => ({
      sampleId: sample.sampleId,
      name: sample.name,
      group: sample.group,
      metadata: sample.metadata ?? {},
    })),
    features: featureNames.map((feature, index) => ({
      id: idFromName(feature, `feature-${index + 1}`),
      name: feature,
      type: 'protein',
      unit: 'relative intensity',
      metadata: { loadingControl: feature === loadingControl },
    })),
    metadata: { assay: 'western-blot', loadingControl },
  })
  return createTemplateCollection(
    [sampleSheet, reagentList, protocol, assayMatrix],
    { preset: 'western-blot-assay', ...(options.metadata ?? {}) }
  )
}