naftiko: 1.0.0-alpha2
info:
  label: Scispot Lab Data Management
  description: Unified capability for managing laboratory data across Scispot's LIMS, ELN, sample tracking, sequence management,
    and container manifests. Enables computational biologists, lab automation engineers, and data scientists to programmatically
    access and manipulate all lab data in one unified workflow interface with REST and MCP adapters.
  tags:
  - Laboratory
  - LIMS
  - ELN
  - Life Science
  - Biotech
  - Samples
  - Sequences
  - Automation
  created: '2026-05-02'
  modified: '2026-05-06'
binds:
- namespace: env
  keys:
    SCISPOT_API_KEY: SCISPOT_API_KEY
capability:
  consumes:
  - type: http
    namespace: scispot
    baseUri: https://api.scispot.com/v1
    description: Scispot laboratory data platform API
    authentication:
      type: apikey
      key: apiKey
      value: '{{SCISPOT_API_KEY}}'
      placement: header
    resources:
    - name: labsheets
      path: /labsheets
      description: List all labsheets in the workspace
      operations:
      - name: list-labsheets
        method: GET
        description: Retrieve all LIMS-style data tables
        inputParameters:
        - name: page
          in: query
          type: integer
          required: false
          description: Page number
        - name: limit
          in: query
          type: integer
          required: false
          description: Results per page
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: labsheet-rows
      path: /labsheets/{labsheetId}/rows
      description: Manage rows within a specific labsheet
      operations:
      - name: get-labsheet-rows
        method: GET
        description: Retrieve all rows from a labsheet
        inputParameters:
        - name: labsheetId
          in: path
          type: string
          required: true
          description: Labsheet identifier
        - name: page
          in: query
          type: integer
          required: false
          description: Page number
        - name: limit
          in: query
          type: integer
          required: false
          description: Rows per page
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
      - name: add-labsheet-row
        method: POST
        description: Add a new data row to a labsheet
        inputParameters:
        - name: labsheetId
          in: path
          type: string
          required: true
          description: Labsheet identifier
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        body:
          type: json
          data:
            barcode: '{{tools.barcode}}'
            data: '{{tools.data}}'
    - name: labsheet-row
      path: /labsheets/{labsheetId}/rows/{rowId}
      description: Manage a specific labsheet row
      operations:
      - name: get-labsheet-row
        method: GET
        description: Get a specific row by ID
        inputParameters:
        - name: labsheetId
          in: path
          type: string
          required: true
          description: Labsheet identifier
        - name: rowId
          in: path
          type: string
          required: true
          description: Row identifier
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
      - name: update-labsheet-row
        method: PUT
        description: Update an existing labsheet row
        inputParameters:
        - name: labsheetId
          in: path
          type: string
          required: true
          description: Labsheet identifier
        - name: rowId
          in: path
          type: string
          required: true
          description: Row identifier
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        body:
          type: json
          data:
            data: '{{tools.data}}'
      - name: delete-labsheet-row
        method: DELETE
        description: Delete a row from a labsheet
        inputParameters:
        - name: labsheetId
          in: path
          type: string
          required: true
          description: Labsheet identifier
        - name: rowId
          in: path
          type: string
          required: true
          description: Row identifier
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: barcode-search
      path: /results/search/{barcode}
      description: Search results by barcode
      operations:
      - name: search-by-barcode
        method: GET
        description: Find all records associated with a barcode
        inputParameters:
        - name: barcode
          in: path
          type: string
          required: true
          description: Barcode identifier
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: eln-notebooks
      path: /eln/notebooks
      description: Manage ELN notebooks
      operations:
      - name: list-notebooks
        method: GET
        description: List all ELN notebooks
        inputParameters:
        - name: page
          in: query
          type: integer
          required: false
          description: Page number
        - name: limit
          in: query
          type: integer
          required: false
          description: Results per page
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: notebook-entries
      path: /eln/notebooks/{notebookId}/entries
      description: Manage entries within an ELN notebook
      operations:
      - name: list-notebook-entries
        method: GET
        description: List all entries in a notebook
        inputParameters:
        - name: notebookId
          in: path
          type: string
          required: true
          description: Notebook identifier
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
      - name: create-notebook-entry
        method: POST
        description: Create a new notebook entry (experiment, protocol, or observation)
        inputParameters:
        - name: notebookId
          in: path
          type: string
          required: true
          description: Notebook identifier
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        body:
          type: json
          data:
            title: '{{tools.title}}'
            type: '{{tools.entry_type}}'
            content: '{{tools.content}}'
    - name: manifests
      path: /manifests
      description: Manage physical container manifests
      operations:
      - name: list-manifests
        method: GET
        description: List all manifests (plates, boxes, racks)
        inputParameters:
        - name: type
          in: query
          type: string
          required: false
          description: Container type filter (plate, box, rack)
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
      - name: create-manifest
        method: POST
        description: Create a new physical container manifest
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        body:
          type: json
          data:
            name: '{{tools.name}}'
            type: '{{tools.container_type}}'
            barcode: '{{tools.barcode}}'
    - name: manifest-detail
      path: /manifests/{manifestId}
      description: Get a specific manifest by ID
      operations:
      - name: get-manifest
        method: GET
        description: Retrieve a single manifest with its contents
        inputParameters:
        - name: manifestId
          in: path
          type: string
          required: true
          description: Manifest identifier
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: sequences
      path: /sequences
      description: Manage biological sequences
      operations:
      - name: list-sequences
        method: GET
        description: List all biological sequences (DNA, RNA, protein, chemical)
        inputParameters:
        - name: type
          in: query
          type: string
          required: false
          description: Sequence type filter (dna, rna, protein, chemical)
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
      - name: create-sequence
        method: POST
        description: Add a new biological sequence with annotations
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        body:
          type: json
          data:
            name: '{{tools.name}}'
            type: '{{tools.sequence_type}}'
            sequence: '{{tools.sequence}}'
    - name: sequence-detail
      path: /sequences/{sequenceId}
      description: Manage a specific sequence by ID
      operations:
      - name: get-sequence
        method: GET
        description: Retrieve a single sequence with annotations
        inputParameters:
        - name: sequenceId
          in: path
          type: string
          required: true
          description: Sequence identifier
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
      - name: update-sequence
        method: PUT
        description: Update an existing biological sequence
        inputParameters:
        - name: sequenceId
          in: path
          type: string
          required: true
          description: Sequence identifier
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        body:
          type: json
          data:
            name: '{{tools.name}}'
            sequence: '{{tools.sequence}}'
  exposes:
  - type: rest
    port: 8080
    namespace: scispot-lab-management-api
    description: Unified REST API for Scispot lab data management workflows.
    resources:
    - path: /v1/labsheets
      name: labsheets
      description: LIMS labsheet management
      operations:
      - method: GET
        name: list-labsheets
        description: List all LIMS labsheets in the workspace
        call: scispot.list-labsheets
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/labsheets/{labsheetId}/rows
      name: labsheet-rows
      description: Labsheet row data management
      operations:
      - method: GET
        name: get-labsheet-rows
        description: Retrieve all data rows from a labsheet
        call: scispot.get-labsheet-rows
        with:
          labsheetId: rest.labsheetId
        outputParameters:
        - type: object
          mapping: $.
      - method: POST
        name: add-labsheet-row
        description: Add a new row to a labsheet
        call: scispot.add-labsheet-row
        with:
          labsheetId: rest.labsheetId
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/labsheets/{labsheetId}/rows/{rowId}
      name: labsheet-row
      description: Individual labsheet row operations
      operations:
      - method: GET
        name: get-labsheet-row
        description: Get a specific row by ID
        call: scispot.get-labsheet-row
        with:
          labsheetId: rest.labsheetId
          rowId: rest.rowId
        outputParameters:
        - type: object
          mapping: $.
      - method: PUT
        name: update-labsheet-row
        description: Update an existing labsheet row
        call: scispot.update-labsheet-row
        with:
          labsheetId: rest.labsheetId
          rowId: rest.rowId
        outputParameters:
        - type: object
          mapping: $.
      - method: DELETE
        name: delete-labsheet-row
        description: Delete a labsheet row
        call: scispot.delete-labsheet-row
        with:
          labsheetId: rest.labsheetId
          rowId: rest.rowId
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/samples/search/{barcode}
      name: barcode-lookup
      description: Sample lookup by barcode
      operations:
      - method: GET
        name: search-by-barcode
        description: Find all records associated with a sample barcode
        call: scispot.search-by-barcode
        with:
          barcode: rest.barcode
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/notebooks
      name: notebooks
      description: ELN notebook management
      operations:
      - method: GET
        name: list-notebooks
        description: List all Electronic Lab Notebooks
        call: scispot.list-notebooks
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/notebooks/{notebookId}/entries
      name: notebook-entries
      description: ELN notebook entry management
      operations:
      - method: GET
        name: list-notebook-entries
        description: List entries in a notebook
        call: scispot.list-notebook-entries
        with:
          notebookId: rest.notebookId
        outputParameters:
        - type: object
          mapping: $.
      - method: POST
        name: create-notebook-entry
        description: Create a new notebook entry
        call: scispot.create-notebook-entry
        with:
          notebookId: rest.notebookId
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/manifests
      name: manifests
      description: Container manifest management (plates, boxes, racks)
      operations:
      - method: GET
        name: list-manifests
        description: List all physical container manifests
        call: scispot.list-manifests
        outputParameters:
        - type: object
          mapping: $.
      - method: POST
        name: create-manifest
        description: Create a new physical container manifest
        call: scispot.create-manifest
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/manifests/{manifestId}
      name: manifest-detail
      description: Individual manifest operations
      operations:
      - method: GET
        name: get-manifest
        description: Get a specific manifest with its contents
        call: scispot.get-manifest
        with:
          manifestId: rest.manifestId
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/sequences
      name: sequences
      description: Biological sequence management
      operations:
      - method: GET
        name: list-sequences
        description: List all biological sequences
        call: scispot.list-sequences
        outputParameters:
        - type: object
          mapping: $.
      - method: POST
        name: create-sequence
        description: Add a new biological sequence
        call: scispot.create-sequence
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/sequences/{sequenceId}
      name: sequence-detail
      description: Individual sequence operations
      operations:
      - method: GET
        name: get-sequence
        description: Get a specific sequence with annotations
        call: scispot.get-sequence
        with:
          sequenceId: rest.sequenceId
        outputParameters:
        - type: object
          mapping: $.
      - method: PUT
        name: update-sequence
        description: Update a biological sequence
        call: scispot.update-sequence
        with:
          sequenceId: rest.sequenceId
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    port: 9090
    namespace: scispot-lab-management-mcp
    transport: http
    description: MCP server for AI-assisted lab data management using Scispot.
    tools:
    - name: list-labsheets
      description: List all LIMS labsheets (data tables) in the Scispot workspace. Labsheets are used for sample registries,
        assay results, inventory tracking, and any structured lab data.
      hints:
        readOnly: true
        idempotent: true
      call: scispot.list-labsheets
      outputParameters:
      - type: object
        mapping: $.
    - name: get-labsheet-rows
      description: Retrieve all data rows from a specific Scispot labsheet. Returns the full dataset with all column values
        for each row in the specified LIMS table.
      hints:
        readOnly: true
        idempotent: true
      call: scispot.get-labsheet-rows
      with:
        labsheetId: tools.labsheetId
      outputParameters:
      - type: object
        mapping: $.
    - name: add-labsheet-row
      description: Add a new data row to a Scispot labsheet. Supports barcode assignment and custom column values. Use for
        sample registration, assay result entry, and inventory updates.
      hints:
        readOnly: false
        destructive: false
        idempotent: false
      call: scispot.add-labsheet-row
      with:
        labsheetId: tools.labsheetId
        barcode: tools.barcode
        data: tools.data
      outputParameters:
      - type: object
        mapping: $.
    - name: update-labsheet-row
      description: Update an existing row in a Scispot labsheet with new column values. Used for updating sample status, adding
        results, or correcting data.
      hints:
        readOnly: false
        destructive: false
        idempotent: true
      call: scispot.update-labsheet-row
      with:
        labsheetId: tools.labsheetId
        rowId: tools.rowId
        data: tools.data
      outputParameters:
      - type: object
        mapping: $.
    - name: delete-labsheet-row
      description: Delete a row from a Scispot labsheet. Use with caution as this permanently removes the record from the
        LIMS.
      hints:
        readOnly: false
        destructive: true
        idempotent: true
      call: scispot.delete-labsheet-row
      with:
        labsheetId: tools.labsheetId
        rowId: tools.rowId
      outputParameters:
      - type: object
        mapping: $.
    - name: search-by-barcode
      description: Search all Scispot data by sample barcode. Returns all records across labsheets and experiments associated
        with the specified barcode.
      hints:
        readOnly: true
        idempotent: true
      call: scispot.search-by-barcode
      with:
        barcode: tools.barcode
      outputParameters:
      - type: object
        mapping: $.
    - name: list-notebooks
      description: List all Electronic Lab Notebook (ELN) notebooks in the Scispot workspace. Notebooks contain experimental
        protocols, observations, and research notes.
      hints:
        readOnly: true
        idempotent: true
      call: scispot.list-notebooks
      outputParameters:
      - type: object
        mapping: $.
    - name: create-notebook-entry
      description: Create a new entry in a Scispot ELN notebook. Entries can be experiments, protocol executions, observations,
        or research notes.
      hints:
        readOnly: false
        destructive: false
        idempotent: false
      call: scispot.create-notebook-entry
      with:
        notebookId: tools.notebookId
        title: tools.title
        entry_type: tools.entry_type
        content: tools.content
      outputParameters:
      - type: object
        mapping: $.
    - name: list-manifests
      description: List all physical container manifests (plates, boxes, racks) in the Scispot workspace. Manifests track
        sample storage organization.
      hints:
        readOnly: true
        idempotent: true
      call: scispot.list-manifests
      outputParameters:
      - type: object
        mapping: $.
    - name: create-manifest
      description: Create a new physical container manifest (plate, box, or rack) in Scispot for organizing and tracking sample
        storage.
      hints:
        readOnly: false
        destructive: false
        idempotent: false
      call: scispot.create-manifest
      with:
        name: tools.name
        container_type: tools.container_type
        barcode: tools.barcode
      outputParameters:
      - type: object
        mapping: $.
    - name: list-sequences
      description: List all biological sequences (DNA, RNA, protein, chemical) stored in the Scispot workspace with their
        metadata and annotations.
      hints:
        readOnly: true
        idempotent: true
      call: scispot.list-sequences
      outputParameters:
      - type: object
        mapping: $.
    - name: create-sequence
      description: Add a new biological sequence to the Scispot database. Supports DNA, RNA, protein, and chemical structure
        sequences with full annotation support.
      hints:
        readOnly: false
        destructive: false
        idempotent: false
      call: scispot.create-sequence
      with:
        name: tools.name
        sequence_type: tools.sequence_type
        sequence: tools.sequence
      outputParameters:
      - type: object
        mapping: $.
    - name: get-sequence
      description: Retrieve a specific biological sequence by ID including its full sequence string, annotations, features,
        and associated metadata.
      hints:
        readOnly: true
        idempotent: true
      call: scispot.get-sequence
      with:
        sequenceId: tools.sequenceId
      outputParameters:
      - type: object
        mapping: $.