import { createAssayMatrixTemplate } from './assayMatrixBuilder'
import { createCalibrationCurveTemplate } from './calibrationCurveBuilder'
import { createInstrumentRunTemplate } from './instrumentRunBuilder'
import { createReagentListTemplate } from './reagentListBuilder'
import { createSamplePrepTemplate } from './samplePrepBuilder'
import { createSampleSheetTemplate } from './sampleSheetBuilder'
import { presetSampleRecords } from './sampleNormalizers'
import {
  firstFeatureName,
  normalizeInternalStandardReagents,
  normalizeMetaboliteFeatures,
  targetedMetabolomicsRunItems,
} from './targetedMetabolomicsHelpers'
import { createTemplateCollection } from './templateEnvelopes'
import type {
  CreateTargetedMetabolomicsCollectionOptions,
  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 createTargetedMetabolomicsCollection(
  options: CreateTargetedMetabolomicsCollectionOptions = {}
): TemplateCollectionEnvelope {
  const sampleRecords = presetSampleRecords(options.samples ?? ['S001', 'S002'])
  const responseUnit = options.responseUnit ?? 'peak area ratio'
  const concentrationUnit = options.concentrationUnit ?? 'uM'
  const metaboliteFeatures = normalizeMetaboliteFeatures(
    options.metabolites ?? ['Glucose', 'Lactate', 'Pyruvate'],
    responseUnit,
  )
  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })
  const samplePrep = createSamplePrepTemplate({
    samples: sampleRecords.map(sample => sample.sampleId),
    prepType: options.prepType ?? 'extraction',
    protocolName: 'Metabolomics sample preparation',
    outputVolume: options.outputVolume ?? 50,
    metadata: { assay: 'targeted-metabolomics' },
  })
  const reagents = createReagentListTemplate({
    reagents: normalizeInternalStandardReagents(
      options.internalStandards ?? ['Stable isotope internal standard mix'],
    ),
    metadata: { assay: 'targeted-metabolomics' },
  })
  const calibrationCurve = createCalibrationCurveTemplate({
    concentrations: options.standardConcentrations ?? [0.1, 1, 10, 100],
    analyte: options.calibrationAnalyte ?? firstFeatureName(metaboliteFeatures, 'Metabolite panel'),
    unit: concentrationUnit,
    responseUnit,
    model: 'linear-weighted-1-x',
    includeQc: options.includeQc,
    metadata: { assay: 'targeted-metabolomics' },
  })
  const instrumentRun = createInstrumentRunTemplate({
    items: targetedMetabolomicsRunItems(
      sampleRecords,
      calibrationCurve.data.points,
      options.includeQc !== false,
    ),
    method: options.method ?? 'Targeted metabolomics',
    instrument: options.instrument ?? 'LC-MS',
    includeBlanks: false,
    includeQc: false,
    metadata: { assay: 'targeted-metabolomics' },
  })
  const assayMatrix = createAssayMatrixTemplate({
    samples: sampleRecords.map(sample => ({
      sampleId: sample.sampleId,
      name: sample.name,
      group: sample.group,
      metadata: sample.metadata ?? {},
    })),
    features: metaboliteFeatures,
    metadata: { assay: 'targeted-metabolomics', responseUnit },
  })
  return createTemplateCollection(
    [sampleSheet, samplePrep, reagents, instrumentRun, calibrationCurve, assayMatrix],
    { preset: 'targeted-metabolomics', ...(options.metadata ?? {}) }
  )
}