import type { TemplateId } from './types'

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

export interface BioTemplateCatalogEntry {
  name: TemplateId
  template_id: TemplateId
  template_version: string
  label: string
  category: 'bio-data'
  purpose: string
  aliases: readonly string[]
  python_import: string
  python_example: string
  frontend_import: string
  frontend_adapters: readonly string[]
  components: readonly string[]
  add_command: 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 bioTemplateCatalog = [
  {
    name: 'plate-map',
    template_id: 'plate-map',
    template_version: '1.0',
    label: 'Plate map',
    category: 'bio-data',
    purpose: 'Plate layout, wells, sample assignments, and sample legend data.',
    aliases: ['wellplate', 'well-plate', 'plate layout', 'plate-map editor'],
    python_import: 'from mint_sdk.templates import PlateMapTemplate, save_template',
    python_example: 'PlateMapTemplate.create_96_well(name="Plate 1", samples=["Control", "Treatment"])',
    frontend_import: "import { toPlateMapEditorState, toWellPlateWells } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toPlateMapEditorState', 'toWellPlateWells'],
    components: ['PlateEditor', 'WellPlate', 'SampleLegend'],
    add_command: 'mint add data-template plate-map --page',
  },
  {
    name: 'sample-sheet',
    template_id: 'sample-sheet',
    template_version: '1.0',
    label: 'Sample sheet',
    category: 'bio-data',
    purpose: 'Tabular sample metadata, display columns, and group definitions.',
    aliases: ['sample metadata', 'sample table', 'metadata sheet', 'csv samples'],
    python_import: 'from mint_sdk.templates import SampleSheetTemplate, save_template',
    python_example: 'SampleSheetTemplate.from_rows([{"sample_id": "S001", "name": "Control 1", "group": "Control"}])',
    frontend_import: "import { toTemplateDataFrame, toSampleOptions } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toSampleDataFrame', 'toSampleRows', 'toSampleColumns', 'toSampleOptions'],
    components: ['DataFrame', 'SampleSelector', 'GroupAssigner'],
    add_command: 'mint add data-template sample-sheet --page',
  },
  {
    name: 'sample-prep',
    template_id: 'sample-prep',
    template_version: '1.0',
    label: 'Sample prep',
    category: 'bio-data',
    purpose: 'Extraction, dilution, normalization, transfer, source/destination, volume, reagent, and status steps.',
    aliases: ['sample preparation', 'extraction', 'dilution', 'normalization', 'prep steps'],
    python_import: 'from mint_sdk.templates import SamplePrepTemplate, save_template',
    python_example: 'SamplePrepTemplate.create(["S001", "S002"], prep_type="extraction", output_volume=50)',
    frontend_import: "import { toSamplePrepDataFrame, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toSamplePrepDataFrame', 'toSamplePrepRows', 'toSamplePrepColumns'],
    components: ['DataFrame', 'ProtocolStepEditor', 'SampleSelector', 'WellPlate'],
    add_command: 'mint add data-template sample-prep --page',
  },
  {
    name: 'dose-response',
    template_id: 'dose-response',
    template_version: '1.0',
    label: 'Dose response',
    category: 'bio-data',
    purpose: 'Compounds, concentration series, controls, replicates, and optional plate layout.',
    aliases: [
      'drug response',
      'concentration series',
      'dose curve',
      'dose design',
      'dose planner',
      'dose calculator',
      'drp',
    ],
    python_import: 'from mint_sdk.templates import ControlDefinition, DoseResponseTemplate, save_template',
    python_example: 'DoseResponseTemplate.create({"Compound A": [10, 1, 0.1]}, unit="uM", replicates=3)',
    frontend_import: "import { toDoseConditions, toDoseLayoutState } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toDoseConditions', 'toDoseLayoutState'],
    components: ['DoseCalculator', 'ReagentEditor', 'WellPlate'],
    add_command: 'mint add data-template dose-response --page',
  },
  {
    name: 'calibration-curve',
    template_id: 'calibration-curve',
    template_version: '1.0',
    label: 'Calibration curve',
    category: 'bio-data',
    purpose: 'Standard curves, blank/QC points, fitted model settings, and acceptance thresholds.',
    aliases: ['standard curve', 'calibration', 'quantitation', 'qc acceptance', 'calibrator'],
    python_import: 'from mint_sdk.templates import CalibrationCurveTemplate, save_template',
    python_example: 'CalibrationCurveTemplate.create([0.1, 1, 10, 100], analyte="Glucose", unit="uM")',
    frontend_import: "import { toCalibrationCurveDataFrame, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toCalibrationCurveDataFrame', 'toCalibrationCurveRows', 'toCalibrationCurveColumns'],
    components: ['DataFrame', 'FitPanel', 'ChartContainer'],
    add_command: 'mint add data-template calibration-curve --page',
  },
  {
    name: 'time-course',
    template_id: 'time-course',
    template_version: '1.0',
    label: 'Time course',
    category: 'bio-data',
    purpose: 'Longitudinal time points, conditions, replicates, and scheduled samples.',
    aliases: ['longitudinal', 'time series', 'sampling schedule', 'kinetics'],
    python_import: 'from mint_sdk.templates import TimeCourseTemplate, save_template',
    python_example: 'TimeCourseTemplate.create([0, 6, 24], unit="hour", conditions=["Control", "Treatment"], replicates=3)',
    frontend_import: "import { toTemplateDataFrame, toTimeCourseSteps } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toTimeCourseDataFrame', 'toTimeCourseRows', 'toTimeCourseSteps', 'toTimeCourseColumns'],
    components: ['ExperimentTimeline', 'DataFrame', 'ScheduleCalendar'],
    add_command: 'mint add data-template time-course --page',
  },
  {
    name: 'protocol-steps',
    template_id: 'protocol-steps',
    template_version: '1.0',
    label: 'Protocol steps',
    category: 'bio-data',
    purpose: 'Ordered experiment protocol steps, durations, statuses, and run-sheet parameters.',
    aliases: ['protocol', 'run sheet', 'workflow', 'method steps', 'sop'],
    python_import: 'from mint_sdk.templates import ProtocolStepsTemplate, save_template',
    python_example: 'ProtocolStepsTemplate.create(["Seed cells", "Add treatment", "Measure viability"])',
    frontend_import: "import { toProtocolSteps, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toProtocolSteps', 'toProtocolDataFrame'],
    components: ['ExperimentTimeline', 'ProtocolStepEditor', 'DataFrame'],
    add_command: 'mint add data-template protocol-steps --page',
  },
  {
    name: 'assay-matrix',
    template_id: 'assay-matrix',
    template_version: '1.0',
    label: 'Assay matrix',
    category: 'bio-data',
    purpose: 'Sample-by-feature measurement matrices for omics, plate-reader, and marker assays.',
    aliases: ['omics matrix', 'measurement matrix', 'readout matrix', 'feature table'],
    python_import: 'from mint_sdk.templates import AssayMatrixTemplate, save_template',
    python_example: 'AssayMatrixTemplate.create(samples=["S001", "S002"], features=["Lactate", "Glucose"])',
    frontend_import: "import { toAssayMatrixSampleOptions, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toAssayMatrixDataFrame', 'toAssayMatrixRows', 'toAssayMatrixColumns', 'toAssayMatrixSampleOptions'],
    components: ['DataFrame', 'ChartContainer', 'SampleSelector'],
    add_command: 'mint add data-template assay-matrix --page',
  },
  {
    name: 'reagent-list',
    template_id: 'reagent-list',
    template_version: '1.0',
    label: 'Reagent list',
    category: 'bio-data',
    purpose: 'Experiment reagents, catalog numbers, lots, storage, locations, and stock status.',
    aliases: ['reagents', 'inventory', 'antibodies', 'primers', 'compound stocks'],
    python_import: 'from mint_sdk.templates import ReagentListTemplate, save_template',
    python_example: 'ReagentListTemplate.create(["DMSO", "Compound A", "Anti-HA antibody"])',
    frontend_import: "import { toReagentListItems, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toReagentDataFrame', 'toReagentListItems'],
    components: ['ReagentList', 'DataFrame', 'ReagentEditor'],
    add_command: 'mint add data-template reagent-list --page',
  },
  {
    name: 'flow-cytometry-panel',
    template_id: 'flow-cytometry-panel',
    template_version: '1.0',
    label: 'Flow cytometry panel',
    category: 'bio-data',
    purpose: 'Flow-cytometry markers, fluorophores, detectors, compensation controls, and panel metadata.',
    aliases: ['flow panel', 'facs panel', 'cytometry panel', 'antibody panel'],
    python_import: 'from mint_sdk.templates import FlowCytometryPanelTemplate, save_template',
    python_example: 'FlowCytometryPanelTemplate.create(["CD3", "CD4", "CD8"], instrument="BD LSRFortessa")',
    frontend_import: "import { toFlowPanelDataFrame, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toFlowPanelDataFrame', 'toFlowPanelRows', 'toFlowPanelColumns'],
    components: ['DataFrame', 'ReagentList', 'SampleSelector'],
    add_command: 'mint add data-template flow-cytometry-panel --page',
  },
  {
    name: 'instrument-run',
    template_id: 'instrument-run',
    template_version: '1.0',
    label: 'Instrument run',
    category: 'bio-data',
    purpose: 'Instrument sequence tables, sample queues, methods, QC, blanks, and acquisition status.',
    aliases: ['run queue', 'sequence table', 'sample queue', 'lcms run', 'instrument sequence', 'batch run'],
    python_import: 'from mint_sdk.templates import InstrumentRunTemplate, save_template',
    python_example: 'InstrumentRunTemplate.create(["S001", "S002"], instrument="LC-MS")',
    frontend_import: "import { toInstrumentRunDataFrame, toInstrumentRunScheduleEvents, toInstrumentRunSteps, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toInstrumentRunDataFrame', 'toInstrumentRunRows', 'toInstrumentRunColumns', 'toInstrumentRunSteps', 'toInstrumentRunScheduleEvents'],
    components: ['DataFrame', 'ExperimentTimeline', 'ScheduleCalendar', 'SampleSelector'],
    add_command: 'mint add data-template instrument-run --page',
  },
  {
    name: 'qpcr-plate',
    template_id: 'qpcr-plate',
    template_version: '1.0',
    label: 'qPCR plate',
    category: 'bio-data',
    purpose: 'qPCR/ddPCR plate layouts, samples, targets, replicate reactions, controls, and Cq fields.',
    aliases: ['qpcr', 'qPCR', 'ddpcr', 'rt-qpcr', 'gene expression', 'primer plate'],
    python_import: 'from mint_sdk.templates import QpcrPlateTemplate, save_template',
    python_example: 'QpcrPlateTemplate.create(samples=["Control", "Treatment"], targets=["ACTB", "GAPDH"], replicates=3)',
    frontend_import: "import { toQpcrDataFrame, toQpcrWellPlateWells, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
    frontend_adapters: ['toTemplateDataFrame', 'toQpcrDataFrame', 'toQpcrRows', 'toQpcrColumns', 'toQpcrWellPlateWells'],
    components: ['DataFrame', 'WellPlate', 'SampleSelector'],
    add_command: 'mint add data-template qpcr-plate --page',
  },
] as const satisfies readonly BioTemplateCatalogEntry[]

/** @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 listBioTemplateCatalog(): readonly BioTemplateCatalogEntry[] {
  return bioTemplateCatalog
}

/** @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 getBioTemplateInfo(name: string): BioTemplateCatalogEntry | undefined {
  return bioTemplateCatalog.find(entry => {
    const identifiers = [
      entry.name,
      entry.template_id,
      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 searchBioTemplateCatalog(query: string): readonly BioTemplateCatalogEntry[] {
  const normalized = query.trim().toLowerCase()
  if (!normalized) return bioTemplateCatalog

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