import type { TemplateId, TemplatePresetId } from './types'

import { templateIdentifierMatches, templateSearchMatches } from './lookup'

export interface BioTemplatePresetEntry {
  name: TemplatePresetId
  label: string
  category: 'bio-template-preset'
  purpose: string
  templates: readonly TemplateId[]
  aliases: readonly string[]
  python_import: string
  python_example: string
  frontend_import: string
  frontend_adapters: readonly string[]
  components: readonly string[]
}

/** @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 const bioTemplatePresets = [
  {
    name: 'wellplate-screen',
    label: 'Well-plate screen',
    category: 'bio-template-preset',
    purpose: 'Plate map, sample sheet, and dose-response payloads for plate-based screening assays.',
    templates: ['plate-map', 'sample-sheet', 'dose-response'],
    aliases: [
      'wellplate',
      'well-plate screen',
      'drug screen',
      'plate screen',
      'dose response plate',
      'dose design',
      'dose planner',
    ],
    python_import: 'from mint_sdk.templates import create_wellplate_screen_collection, save_template_collection',
    python_example: 'create_wellplate_screen_collection(samples=["Control", "Treatment"], compounds={"Drug A": [10, 1, 0.1]}, unit="uM")',
    frontend_import: "import { createWellPlateScreenCollection, toPlateMapEditorState, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toPlateMapEditorState', 'toTemplateDataFrame', 'toDoseConditions'],
    components: ['PlateEditor', 'WellPlate', 'DataFrame', 'DoseCalculator'],
  },
  {
    name: 'qpcr-expression',
    label: 'qPCR expression',
    category: 'bio-template-preset',
    purpose: 'Sample metadata and qPCR/ddPCR plate layout for target-expression assays.',
    templates: ['sample-sheet', 'qpcr-plate'],
    aliases: ['qpcr', 'qPCR', 'rt-qpcr', 'ddpcr', 'gene expression', 'primer plate'],
    python_import: 'from mint_sdk.templates import create_qpcr_expression_collection, save_template_collection',
    python_example: 'create_qpcr_expression_collection(samples=["Control", "Treatment"], targets=["ACTB", "GAPDH"], replicates=3)',
    frontend_import: "import { createQpcrExpressionCollection, toQpcrWellPlateWells, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toQpcrDataFrame', 'toQpcrWellPlateWells'],
    components: ['DataFrame', 'WellPlate', 'SampleSelector'],
  },
  {
    name: 'lcms-batch',
    label: 'LC-MS batch',
    category: 'bio-template-preset',
    purpose: 'Sample metadata, instrument queue, and assay matrix payloads for omics acquisition batches.',
    templates: ['sample-sheet', 'instrument-run', 'assay-matrix'],
    aliases: [
      'lcms',
      'lc-ms',
      'mass spec batch',
      'omics batch',
      'metabolomics',
      'metabolism',
      'metabolite profiling',
      'run queue',
      'sequence table',
    ],
    python_import: 'from mint_sdk.templates import create_lcms_batch_collection, save_template_collection',
    python_example: 'create_lcms_batch_collection(samples=["S001", "S002"], features=["Glucose", "Lactate"], instrument="LC-MS")',
    frontend_import: "import { createLcmsBatchCollection, toAssayMatrixSampleOptions, toInstrumentRunDataFrame, toInstrumentRunScheduleEvents, toInstrumentRunSteps, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toInstrumentRunDataFrame', 'toInstrumentRunSteps', 'toInstrumentRunScheduleEvents', 'toAssayMatrixDataFrame', 'toAssayMatrixSampleOptions'],
    components: ['DataFrame', 'ExperimentTimeline', 'ScheduleCalendar', 'ChartContainer', 'SampleSelector'],
  },
  {
    name: 'targeted-metabolomics',
    label: 'Targeted metabolomics',
    category: 'bio-template-preset',
    purpose: 'Sample metadata, extraction prep, internal standards, LC/GC-MS sequence, calibration curve, and metabolite readout matrix for quantitative metabolomics.',
    templates: ['sample-sheet', 'sample-prep', 'reagent-list', 'instrument-run', 'calibration-curve', 'assay-matrix'],
    aliases: [
      'targeted metabolomics',
      'quantitative metabolomics',
      'lc-ms metabolomics',
      'gc-ms metabolomics',
      'targeted lcms',
      'metabolite quantitation',
      'mass spec quantitation',
      'internal standards',
      'peak area ratio',
    ],
    python_import: 'from mint_sdk.templates import create_targeted_metabolomics_collection, save_template_collection',
    python_example: 'create_targeted_metabolomics_collection(samples=["S001", "S002"], metabolites=["Glucose", "Lactate"], internal_standards=["13C Glucose"], instrument="LC-MS")',
    frontend_import: "import { createTargetedMetabolomicsCollection, toInstrumentRunDataFrame, toCalibrationCurveDataFrame, toAssayMatrixDataFrame, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toSamplePrepDataFrame', 'toReagentDataFrame', 'toInstrumentRunDataFrame', 'toInstrumentRunSteps', 'toInstrumentRunScheduleEvents', 'toCalibrationCurveDataFrame', 'toAssayMatrixDataFrame', 'toAssayMatrixSampleOptions'],
    components: ['DataFrame', 'ReagentList', 'ExperimentTimeline', 'ScheduleCalendar', 'FitPanel', 'ChartContainer', 'SampleSelector'],
  },
  {
    name: 'elisa-assay',
    label: 'ELISA assay',
    category: 'bio-template-preset',
    purpose: 'Plate layout, sample metadata, standard curve, and readout matrix for ELISA and plate-reader assays.',
    templates: ['plate-map', 'sample-sheet', 'calibration-curve', 'assay-matrix'],
    aliases: ['elisa', 'plate reader assay', 'standard curve plate', 'absorbance assay', 'immunoassay'],
    python_import: 'from mint_sdk.templates import create_elisa_assay_collection, save_template_collection',
    python_example: 'create_elisa_assay_collection(samples=["Control", "Treatment"], analyte="IL-6", standard_concentrations=[1000, 100, 10, 1], unit="pg/mL")',
    frontend_import: "import { createElisaAssayCollection, toPlateMapEditorState, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toPlateMapEditorState', 'toTemplateDataFrame', 'toCalibrationCurveDataFrame'],
    components: ['PlateEditor', 'WellPlate', 'DataFrame', 'FitPanel', 'ChartContainer'],
  },
  {
    name: 'flow-cytometry-assay',
    label: 'Flow cytometry assay',
    category: 'bio-template-preset',
    purpose: 'Sample metadata, antibody marker panel, compensation controls, and readout matrix for flow-cytometry assays.',
    templates: ['sample-sheet', 'flow-cytometry-panel', 'assay-matrix'],
    aliases: [
      'flow cytometry',
      'facs',
      'facs panel',
      'flow panel',
      'immune phenotyping',
      'immunophenotyping',
    ],
    python_import: 'from mint_sdk.templates import create_flow_cytometry_assay_collection, save_template_collection',
    python_example: 'create_flow_cytometry_assay_collection(samples=["Control", "Treatment"], markers=["CD3", "CD4", "CD8"], instrument="BD LSRFortessa")',
    frontend_import: "import { createFlowCytometryAssayCollection, toFlowPanelDataFrame, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toFlowPanelDataFrame', 'toAssayMatrixDataFrame'],
    components: ['DataFrame', 'SampleSelector', 'ChartContainer'],
  },
  {
    name: 'western-blot-assay',
    label: 'Western blot assay',
    category: 'bio-template-preset',
    purpose: 'Sample metadata, antibody/reagent list, protocol steps, and normalized protein readout matrix for Western blot assays.',
    templates: ['sample-sheet', 'reagent-list', 'protocol-steps', 'assay-matrix'],
    aliases: ['western blot', 'western-blot', 'immunoblot', 'protein blot', 'protein expression'],
    python_import: 'from mint_sdk.templates import create_western_blot_assay_collection, save_template_collection',
    python_example: 'create_western_blot_assay_collection(samples=["Control", "Treatment"], targets=["pERK", "ERK"], loading_control="ACTB")',
    frontend_import: "import { createWesternBlotAssayCollection, toReagentDataFrame, toProtocolDataFrame, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toReagentDataFrame', 'toProtocolDataFrame'],
    components: ['DataFrame', 'ReagentList', 'ExperimentTimeline', 'SampleSelector'],
  },
] as const satisfies readonly BioTemplatePresetEntry[]

/** @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 listBioTemplatePresets(): readonly BioTemplatePresetEntry[] {
  return bioTemplatePresets
}

/** @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 getBioTemplatePresetInfo(name: string): BioTemplatePresetEntry | undefined {
  return bioTemplatePresets.find(entry => {
    const identifiers = [
      entry.name,
      entry.label,
      ...entry.aliases,
    ]
    return templateIdentifierMatches(name, identifiers)
  })
}

/** @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 searchBioTemplatePresets(query: string): readonly BioTemplatePresetEntry[] {
  const normalized = query.trim().toLowerCase()
  if (!normalized) return bioTemplatePresets

  return bioTemplatePresets.filter(entry => templateSearchMatches(normalized, [
    entry.name,
    entry.label,
    entry.purpose,
    entry.python_import,
    entry.python_example,
    entry.frontend_import,
    ...entry.templates,
    ...entry.aliases,
    ...entry.frontend_adapters,
    ...entry.components,
  ]))
}