import { getBioTemplateInfo } from './catalog'
import { createAssayMatrixTemplate } from './assayMatrixBuilder'
import { createCalibrationCurveTemplate } from './calibrationCurveBuilder'
import { createDoseResponseTemplate } from './doseResponseBuilder'
import { createFlowCytometryPanelTemplate } from './flowCytometryPanelBuilder'
import { createInstrumentRunTemplate } from './instrumentRunBuilder'
import { createPlateMapTemplate } from './plateMapBuilder'
import { createProtocolStepsTemplate } from './protocolStepsBuilder'
import { createQpcrPlateTemplate } from './qpcrPlateBuilder'
import { createReagentListTemplate } from './reagentListBuilder'
import { createSamplePrepTemplate } from './samplePrepBuilder'
import { createSampleSheetTemplate } from './sampleSheetBuilder'
import { createTimeCourseTemplate } from './timeCourseBuilder'
import type {
  BioTemplateEnvelope,
  TemplateId,
} 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 createDefaultBioTemplate(templateId: TemplateId | string): BioTemplateEnvelope<unknown> {
  const template = getBioTemplateInfo(templateId)
  if (!template) {
    throw new Error(`Unknown bio template '${templateId}'.`)
  }

  switch (template.template_id) {
    case 'plate-map':
      return createPlateMapTemplate({
        name: 'Plate 1',
        samples: ['Control', 'Treatment'],
      })
    case 'sample-sheet':
      return createSampleSheetTemplate({
        samples: [
          { sampleId: 'S001', name: 'Control 1', group: 'Control' },
          { sampleId: 'S002', name: 'Treatment 1', group: 'Treatment' },
        ],
      })
    case 'sample-prep':
      return createSamplePrepTemplate({
        samples: ['S001', 'S002'],
        prepType: 'extraction',
        outputVolume: 50,
      })
    case 'dose-response':
      return createDoseResponseTemplate({
        compounds: {
          'Compound A': [10, 1, 0.1],
        },
        unit: 'uM',
        replicates: 3,
      })
    case 'calibration-curve':
      return createCalibrationCurveTemplate({
        concentrations: [0.1, 1, 10, 100],
        analyte: 'Analyte',
        unit: 'uM',
      })
    case 'time-course':
      return createTimeCourseTemplate({
        timepoints: [0, 6, 24],
        unit: 'hour',
        conditions: ['Control', 'Treatment'],
        replicates: 3,
      })
    case 'protocol-steps':
      return createProtocolStepsTemplate({
        steps: [
          {
            id: 'seed-cells',
            type: 'addition',
            name: 'Seed cells',
            description: 'Add cells to wells or culture vessels.',
            duration: 15,
          },
          {
            id: 'incubate-overnight',
            type: 'incubation',
            name: 'Incubate overnight',
            duration: 960,
            parameters: { temperature: '37 C', co2: '5%' },
          },
          {
            id: 'measure-readout',
            type: 'measurement',
            name: 'Measure readout',
            duration: 45,
          },
        ],
      })
    case 'assay-matrix':
      return createAssayMatrixTemplate({
        samples: ['S001', 'S002'],
        features: ['Lactate', 'Glucose'],
        values: {
          s001: { lactate: 1.2, glucose: 5.4 },
          s002: { lactate: 2.1, glucose: 4.8 },
        },
      })
    case 'reagent-list':
      return createReagentListTemplate({
        reagents: ['DMSO', 'Compound A', 'Anti-HA antibody'],
      })
    case 'flow-cytometry-panel':
      return createFlowCytometryPanelTemplate({
        markers: ['CD3', 'CD4', 'CD8'],
        instrument: 'BD LSRFortessa',
      })
    case 'instrument-run':
      return createInstrumentRunTemplate({
        items: ['S001', 'S002'],
        instrument: 'LC-MS',
        method: 'Default method',
      })
    case 'qpcr-plate':
      return createQpcrPlateTemplate({
        samples: ['Control', 'Treatment'],
        targets: ['ACTB', 'GAPDH'],
        replicates: 3,
        instrument: 'QuantStudio',
      })
    default:
      throw new Error(`Unknown bio template '${templateId}'.`)
  }
}