@morscherlab/mint-sdk 1.0.0-beta.2 → 1.0.0-beta.4

package/src/templates/catalog.ts

@@ -0,0 +1,245 @@
+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
+}
+
+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: ['PlateMapEditor', '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', 'AutoGroupModal', '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 { toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
+    frontend_adapters: ['toTemplateDataFrame', 'toAssayMatrixDataFrame', 'toAssayMatrixRows', 'toAssayMatrixColumns'],
+    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, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'",
+    frontend_adapters: ['toTemplateDataFrame', 'toInstrumentRunDataFrame', 'toInstrumentRunRows', 'toInstrumentRunColumns'],
+    components: ['DataFrame', '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[]
+
+export function listBioTemplateCatalog(): readonly BioTemplateCatalogEntry[] {
+  return bioTemplateCatalog
+}
+
+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)
+  })
+}
+
+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,
+  ]))
+}