Thermo Fisher Scientific Lab Data Management

naftiko: "1.0.0-alpha1"

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: "2026-05-03"

binds:
  - namespace: env
    keys:
      SAMPLEMANAGER_TOKEN: SAMPLEMANAGER_TOKEN
      NANODROP_HOST: NANODROP_HOST

capability:
  consumes:
    - import: samplemanager
      location: ./shared/samplemanager-lims.yaml
    - import: nanodrop
      location: ./shared/nanodrop-ultra.yaml

  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: "$."