naftiko: 1.0.0-alpha2
info:
  label: Thermo Fisher Scientific Lab Data Management
  description: Workflow capability for laboratory data management combining SampleManager LIMS and NanoDrop Ultra spectrophotometer
    APIs. Covers sample lifecycle, result entry, instrument measurements, and LIMS integration for life science laboratories.
  tags:
  - Life Sciences
  - Laboratory
  - LIMS
  - Spectrophotometry
  - Sample Management
  - Automation
  created: '2026-05-03'
  modified: '2026-05-06'
binds:
- namespace: env
  keys:
    SAMPLEMANAGER_TOKEN: SAMPLEMANAGER_TOKEN
    NANODROP_HOST: NANODROP_HOST
capability:
  consumes:
  - type: http
    namespace: samplemanager
    baseUri: https://{server}:56105/smpwcfrestvgsm
    description: Thermo Scientific SampleManager LIMS REST API.
    authentication:
      type: bearer
      token: '{{SAMPLEMANAGER_TOKEN}}'
    resources:
    - name: samples
      path: /mobile/samples
      description: Laboratory sample records.
      operations:
      - name: get-samples
        method: GET
        description: Retrieve laboratory samples with filtering by status and date.
        inputParameters:
        - name: status
          in: query
          type: string
          required: false
          description: Sample status filter (A, C, X, L).
        - name: from_date
          in: query
          type: string
          required: false
          description: From date filter (YYYY-MM-DD).
        - name: to_date
          in: query
          type: string
          required: false
          description: To date filter (YYYY-MM-DD).
        - name: pagesize
          in: query
          type: integer
          required: false
          description: Records per page.
        - name: page
          in: query
          type: integer
          required: false
          description: Page number.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: sample-by-id
      path: /mobile/samples/{sampleId}
      description: Retrieve a specific sample by identity.
      operations:
      - name: get-sample-by-id
        method: GET
        description: Get details for a specific laboratory sample.
        inputParameters:
        - name: sampleId
          in: path
          type: string
          required: true
          description: Sample identity or barcode.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: sample-results
      path: /mobile/samples/{sampleId}/results
      description: Test results for a sample.
      operations:
      - name: get-sample-results
        method: GET
        description: Get all test results for a specific sample.
        inputParameters:
        - name: sampleId
          in: path
          type: string
          required: true
          description: Sample identity.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: results-entry
      path: /mobile/results
      description: Submit test results.
      operations:
      - name: submit-results
        method: POST
        description: Submit test results for samples in SampleManager.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        body:
          type: json
          data:
            sample_id: '{{tools.sample_id}}'
            results: '{{tools.results}}'
    - name: entity-browse
      path: /mobile/browses/{entity}
      description: Browse SampleManager entities.
      operations:
      - name: browse-entity
        method: GET
        description: Browse records for any SampleManager entity type.
        inputParameters:
        - name: entity
          in: path
          type: string
          required: true
          description: Entity name (SAMPLE, TEST, RESULT, CUSTOMER, etc.).
        - name: criteria
          in: query
          type: string
          required: false
          description: Filter criteria.
        - name: pagesize
          in: query
          type: integer
          required: false
          description: Records per page.
        - name: page
          in: query
          type: integer
          required: false
          description: Page number.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: workflow-trigger
      path: /mobile/workflows/{workflowName}/trigger
      description: Trigger SampleManager workflows.
      operations:
      - name: trigger-workflow
        method: POST
        description: Trigger a named workflow in SampleManager.
        inputParameters:
        - name: workflowName
          in: path
          type: string
          required: true
          description: Workflow name to trigger.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        body:
          type: json
          data: {}
  - type: http
    namespace: nanodrop
    baseUri: http://{{NANODROP_HOST}}:8080
    description: NanoDrop Ultra instrument local REST API.
    resources:
    - name: instrument-status
      path: /api/status
      description: Instrument status and metadata.
      operations:
      - name: get-instrument-status
        method: GET
        description: Get current status and readiness of the NanoDrop Ultra instrument.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: measure
      path: /api/measure
      description: Perform a sample measurement.
      operations:
      - name: perform-measurement
        method: POST
        description: Initiate a sample measurement using the specified method.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        body:
          type: json
          data:
            method: '{{tools.method}}'
            sample_id: '{{tools.sample_id}}'
            sample_name: '{{tools.sample_name}}'
            operator: '{{tools.operator}}'
    - name: measurements
      path: /api/measurements
      description: Stored measurement records.
      operations:
      - name: get-measurements
        method: GET
        description: Retrieve stored measurements with date and method filtering.
        inputParameters:
        - name: from_date
          in: query
          type: string
          required: false
          description: From date filter.
        - name: to_date
          in: query
          type: string
          required: false
          description: To date filter.
        - name: method
          in: query
          type: string
          required: false
          description: Method filter.
        - name: sample_id
          in: query
          type: string
          required: false
          description: Sample ID filter.
        - name: limit
          in: query
          type: integer
          required: false
          description: Maximum records to return.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: measurement-by-id
      path: /api/measurements/{measurementId}
      description: Retrieve a specific measurement with full spectrum data.
      operations:
      - name: get-measurement-by-id
        method: GET
        description: Get full measurement data including spectrum for a specific measurement ID.
        inputParameters:
        - name: measurementId
          in: path
          type: string
          required: true
          description: Unique measurement identifier.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: methods
      path: /api/methods
      description: Available measurement methods.
      operations:
      - name: get-methods
        method: GET
        description: List available measurement methods configured on the instrument.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: export
      path: /api/export
      description: Export measurement data.
      operations:
      - name: export-measurements
        method: POST
        description: Export measurements in CSV, JSON, or XML format for LIMS integration.
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        body:
          type: json
          data:
            format: '{{tools.format}}'
            from_date: '{{tools.from_date}}'
            to_date: '{{tools.to_date}}'
  exposes:
  - type: rest
    port: 8080
    namespace: thermo-fisher-lab-api
    description: Unified REST API for Thermo Fisher Scientific lab data management workflows.
    resources:
    - path: /v1/samples
      name: samples
      description: Laboratory sample management.
      operations:
      - method: GET
        name: list-samples
        description: List laboratory samples from SampleManager LIMS.
        call: samplemanager.get-samples
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/samples/{sampleId}
      name: sample
      description: Individual sample data.
      operations:
      - method: GET
        name: get-sample
        description: Get details for a specific laboratory sample.
        call: samplemanager.get-sample-by-id
        with:
          sampleId: rest.sampleId
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/samples/{sampleId}/results
      name: sample-results
      description: Test results for a sample.
      operations:
      - method: GET
        name: get-sample-results
        description: Get test results for a specific sample.
        call: samplemanager.get-sample-results
        with:
          sampleId: rest.sampleId
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/results
      name: results
      description: Submit test results.
      operations:
      - method: POST
        name: submit-results
        description: Submit test results to SampleManager LIMS.
        call: samplemanager.submit-results
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/entities/{entity}
      name: entities
      description: Browse SampleManager entities.
      operations:
      - method: GET
        name: browse-entity
        description: Browse SampleManager entity records.
        call: samplemanager.browse-entity
        with:
          entity: rest.entity
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/workflows/{workflowName}/trigger
      name: workflow-trigger
      description: Trigger laboratory workflows.
      operations:
      - method: POST
        name: trigger-workflow
        description: Trigger a SampleManager workflow.
        call: samplemanager.trigger-workflow
        with:
          workflowName: rest.workflowName
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/instrument/status
      name: instrument-status
      description: NanoDrop instrument status.
      operations:
      - method: GET
        name: get-instrument-status
        description: Check NanoDrop Ultra instrument readiness.
        call: nanodrop.get-instrument-status
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/spectrophotometry/measurements
      name: spectrophotometry-measurements
      description: NanoDrop spectrophotometric measurements.
      operations:
      - method: GET
        name: list-measurements
        description: List stored NanoDrop measurements.
        call: nanodrop.get-measurements
        outputParameters:
        - type: object
          mapping: $.
      - method: POST
        name: perform-measurement
        description: Perform a NanoDrop measurement.
        call: nanodrop.perform-measurement
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/spectrophotometry/measurements/{measurementId}
      name: spectrophotometry-measurement
      description: Individual NanoDrop measurement with spectrum.
      operations:
      - method: GET
        name: get-measurement
        description: Get full measurement data including absorbance spectrum.
        call: nanodrop.get-measurement-by-id
        with:
          measurementId: rest.measurementId
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/spectrophotometry/export
      name: spectrophotometry-export
      description: Export NanoDrop measurement data.
      operations:
      - method: POST
        name: export-measurements
        description: Export NanoDrop data for LIMS integration.
        call: nanodrop.export-measurements
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    port: 9090
    namespace: thermo-fisher-lab-mcp
    transport: http
    description: MCP server for AI-assisted laboratory data management using Thermo Fisher Scientific APIs.
    tools:
    - name: lims-list-samples
      description: List laboratory samples from SampleManager LIMS with optional status and date filtering.
      hints:
        readOnly: true
        idempotent: true
      call: samplemanager.get-samples
      outputParameters:
      - type: array
        mapping: $.samples
    - name: lims-get-sample
      description: Get details for a specific laboratory sample by identity or barcode.
      hints:
        readOnly: true
        idempotent: true
      call: samplemanager.get-sample-by-id
      with:
        sampleId: tools.sampleId
      outputParameters:
      - type: object
        mapping: $.
    - name: lims-get-sample-results
      description: Get all analytical test results for a specific laboratory sample.
      hints:
        readOnly: true
        idempotent: true
      call: samplemanager.get-sample-results
      with:
        sampleId: tools.sampleId
      outputParameters:
      - type: object
        mapping: $.
    - name: lims-submit-results
      description: Submit analytical test results for samples in SampleManager LIMS.
      hints:
        readOnly: false
      call: samplemanager.submit-results
      outputParameters:
      - type: object
        mapping: $.
    - name: lims-browse-entity
      description: Browse any SampleManager LIMS entity type (SAMPLE, TEST, RESULT, CUSTOMER, BATCH_HEADER, ANALYSIS).
      hints:
        readOnly: true
        idempotent: true
      call: samplemanager.browse-entity
      with:
        entity: tools.entity
      outputParameters:
      - type: object
        mapping: $.
    - name: lims-trigger-workflow
      description: Trigger a named automated workflow in SampleManager LIMS.
      hints:
        readOnly: false
      call: samplemanager.trigger-workflow
      with:
        workflowName: tools.workflowName
      outputParameters:
      - type: object
        mapping: $.
    - name: nanodrop-get-status
      description: Check the operational status and readiness of the NanoDrop Ultra spectrophotometer.
      hints:
        readOnly: true
        idempotent: true
      call: nanodrop.get-instrument-status
      outputParameters:
      - type: object
        mapping: $.
    - name: nanodrop-perform-measurement
      description: Perform a UV-Vis spectrophotometric measurement on loaded sample (DNA, RNA, protein quantification).
      hints:
        readOnly: false
      call: nanodrop.perform-measurement
      outputParameters:
      - type: object
        mapping: $.
    - name: nanodrop-list-measurements
      description: List stored NanoDrop Ultra measurements with concentration, purity ratios, and spectra.
      hints:
        readOnly: true
        idempotent: true
      call: nanodrop.get-measurements
      outputParameters:
      - type: object
        mapping: $.
    - name: nanodrop-get-measurement
      description: Get full NanoDrop measurement data including complete UV-Vis absorbance spectrum.
      hints:
        readOnly: true
        idempotent: true
      call: nanodrop.get-measurement-by-id
      with:
        measurementId: tools.measurementId
      outputParameters:
      - type: object
        mapping: $.
    - name: nanodrop-get-methods
      description: List available measurement methods on the NanoDrop Ultra (DNA-50, RNA-40, Protein A280, etc.).
      hints:
        readOnly: true
        idempotent: true
      call: nanodrop.get-methods
      outputParameters:
      - type: object
        mapping: $.
    - name: nanodrop-export-data
      description: Export NanoDrop Ultra measurements in JSON, CSV, or XML format for LIMS or ELN integration.
      hints:
        readOnly: true
        idempotent: true
      call: nanodrop.export-measurements
      outputParameters:
      - type: object
        mapping: $.