System health check - determines if RSpace server is accessible and running

Usage: Call this first to verify connectivity before other operations Returns: Status message from RSpace server

Retrieves recent RSpace documents with pagination

Usage: Get overview of recent documents for browsing/selection Limit: Maximum 200 documents per call for performance Returns: List of document metadata (not full content)

Retrieves complete content of a single document

Usage: Get full document text for reading/analysis Parameters: doc_id can be numeric ID or string globalId (e.g., "SD12345") Returns: Full document with concatenated field content

Updates existing RSpace document content and metadata

Usage: Modify document name, tags, or field content Fields format: [{"id": field_id, "content": "new HTML content"}] Returns: Updated document information

Generic search tool for RSpace documents with flexible search options

Usage: Search across all your RSpace documents using various criteria

Parameters:

• query: The search term(s) to look for

• search_type: "simple" for basic search, "advanced" for multi-criteria search

• query_types: List of search types to use (for advanced search):

  • "global": Search across all document content and metadata

  • "fullText": Search within document text content

  • "tag": Search by document tags

  • "name": Search by document names/titles

  • "created": Search by creation date (use ISO format like "2024-01-01")

  • "lastModified": Search by modification date

  • "form": Search by form type

  • "attachment": Search by attachments

• operator: "and" (all criteria must match) or "or" (any criteria can match)

• order_by: Sort results by field (e.g., "lastModified desc", "name asc")

• page_number: Page number for pagination (0-based)

• page_size: Number of results per page (max 200)

• include_content: Whether to fetch full document content (slower but more complete)

Returns: Dictionary with search results and metadata

Examples:

• Simple text search: search_documents("PCR protocol")

• Search by tags: search_documents("experiment", search_type="advanced", query_types=["tag"])

• Multi-criteria search: search_documents("DNA", search_type="advanced", query_types=["fullText", "tag"], operator="or")

Search documents by specific tags

Usage: Find documents tagged with specific keywords

Parameters:

• tags: List of tags to search for

• operator: "and" (document must have all tags) or "or" (document can have any tag)

• order_by: Sort results by field

• page_number: Page number for pagination

• page_size: Number of results per page

Returns: Dictionary with search results

Example: search_by_tags(["PCR", "protocol"], operator="and")

Search for recently modified documents

Usage: Find documents modified within a specific timeframe

Parameters:

• days_back: Number of days to look back

• query: Optional text search within recent documents

• page_size: Number of results to return

Returns: Dictionary with recent documents

Example: search_recent_documents(7, "experiment")

Advanced content-based document search

Usage: Find documents containing specific content terms

Parameters:

• content_terms: List of terms that should appear in document content

• operator: "and" (all terms must appear) or "or" (any term can appear)

• exclude_terms: Optional list of terms to exclude from results

• order_by: Sort results by field

• page_size: Number of results to return

Returns: Dictionary with search results

Example: find_documents_by_content(["DNA", "extraction"], operator="and")

Creates a new electronic lab notebook

Usage: Organize related experiments/entries under a single notebook Returns: Created notebook information including ID for adding entries

Adds a new entry to an existing notebook

Usage: Add experimental procedures, results, or observations to a notebook Content: Supports both HTML and plain text formatting Returns: Created entry information

Adds tags to documents for organization and searchability

Usage: Categorize documents by project, experiment type, etc. Tags: Use consistent naming for better organization Returns: Updated document with new tags

Changes the name/title of a document or notebook entry

Usage: Update document titles for better organization Returns: Updated document information

Lists available custom forms for structured document creation

Usage: Browse available templates before creating structured documents Filtering: Use query parameter to search form names/descriptions Returns: Paginated list of form metadata

Retrieves detailed information about a specific form template

Usage: Examine form structure before creating documents or new forms Returns: Complete form definition including field specifications

Creates a new custom form template for structured data entry

Usage: Define reusable templates for experiments, protocols, reports Fields structure: [ { "name": "Field Name", "type": "String|Text|Number|Radio|Date|Choice", "mandatory": True/False, "defaultValue": "optional default" } ] Returns: Created form information (form will be in NEW state)

Makes a form available for creating documents

Usage: Activate form after creation/modification Note: Forms must be published before they can be used for document creation Returns: Updated form status

Hides a form from document creation interface

Usage: Temporarily disable forms without deletion Returns: Updated form status

Shares form with user's groups for collaborative use

Usage: Make custom forms available to team members Returns: Updated sharing status

Removes form sharing with groups

Usage: Make form private again Returns: Updated sharing status

Permanently deletes a form template

Usage: Remove unused forms (only works for forms in NEW state) Warning: This operation cannot be undone Returns: Deletion confirmation

Creates a structured document using a form template

Usage: Generate documents with predefined structure and validation Fields: Pre-populate form fields with initial data Returns: Created document information

Retrieves audit trail of all actions performed in RSpace

Usage: Monitor document access, modifications, and user activity Filtering options:

• username: Filter by specific user actions

• global_id: Filter by specific document

• date_from/date_to: ISO8601 format date range

Returns: Chronological list of system events

Downloads file attachments from RSpace documents

Usage: Retrieve images, data files, or other attachments Parameters:

• file_id: Numeric ID of the file attachment

• file_path: Local filesystem path where file should be saved

Returns: Download status and file information

Uploads a file to RSpace and attaches it to a document as a proper file attachment

Usage: One-step process to upload any file and attach it to an RSpace document File types: Supports all file types (images, PDFs, data files, protocols, etc.) Attachment: Creates proper RSpace file attachment, not just a link

Parameters:

• document_id: RSpace document ID (numeric or global ID like "SD12345")

• file_path: Path to the file to upload (e.g., "data/results.pdf")

• caption: Optional caption that appears with the attachment

• description: Optional description for the uploaded file

Returns: Upload confirmation and document update information

Creates a new sample in the inventory system

Usage: Register new samples with metadata and quantity tracking Subsamples: Automatically creates specified number of subsample aliquots Quantity: Tracks total amount with specified units (ml, mg, μl, etc.)

Returns: Created sample information including generated subsample IDs

Retrieves complete information about a specific sample

Usage: Get detailed sample metadata, location, and subsample information Parameters: sample_id can be numeric ID or global ID (e.g., "SA12345") Returns: Full sample details including all subsamples

Lists samples in the inventory with pagination and sorting

Usage: Browse sample collection, find recent additions Sorting: Options include "lastModified", "name", "created" Returns: Paginated list of sample metadata

Creates an exact copy of an existing sample

Usage: Replicate samples for parallel experiments or backup Returns: New sample information with fresh ID and subsamples

Divides a subsample into multiple new subsamples

Usage: Create aliquots for distribution or different experiments Quantity: If specified, each new subsample gets this amount Returns: Information about newly created subsamples

Adds annotations or observations to a specific subsample

Usage: Record experimental notes, observations, or handling instructions Returns: Updated subsample information with new note

Searches across all inventory items using text query

Usage: Find samples, containers, or templates by name, tags, or description Result types: 'SAMPLE', 'SUBSAMPLE', 'CONTAINER', 'TEMPLATE' (or None for all) Returns: Matching items with relevance scoring

Creates a simple list-based container for organizing inventory

Usage: Create folders, boxes, or other containers without specific positioning Storage permissions: Configure what types of items can be stored Hierarchy: Optionally nest within another container

Returns: Created container information with storage settings

Creates a grid-based container with specific positioning

Usage: Create microplates, freezer boxes, or other position-specific storage Dimensions: Define exact grid size (e.g., 8x12 for 96-well plate) Positioning: Items placed at specific coordinates (row, column)

Returns: Created container information with grid specifications

Retrieves container information with optional content listing

Usage: Examine container properties and optionally see what's inside Performance: Set include_content=False for faster queries on large containers Returns: Container details and optionally contained items

Lists top-level containers (not nested within other containers)

Usage: Browse main container organization structure Returns: Paginated list of root-level containers

Retrieves all available workbenches (virtual workspaces)

Usage: Find available workspaces for organizing current work Workbenches: Special containers representing physical or logical workspaces Returns: List of all workbench containers

Moves multiple items to a list-based container

Usage: Organize items in simple containers without specific positioning Items: Can move both samples/subsamples and other containers Returns: Success status and results for each moved item

Moves items to grid container, filling positions row by row

Usage: Systematic filling of plates, boxes, or other gridded containers Auto-positioning: Automatically calculates next available positions Dimensions: Auto-detected from container if not provided

Returns: Success status and final positions of moved items

Moves items to grid container, filling positions column by column

Usage: Alternative filling pattern for specific experimental layouts Auto-positioning: Fills down columns before moving to next column Returns: Success status and final positions of moved items

Places items at specific coordinates within a grid container

Usage: Precise positioning for experimental layouts or protocols Coordinates: Each item gets an exact (row, column) position Validation: Ensures equal number of items and positions

Returns: Success status and confirmation of final positions

Creates a reusable template for sample creation

Usage: Standardize sample creation with predefined fields and validation Template data: Define field structure, default values, and constraints Returns: Created template information for future sample generation

Retrieves detailed information about a sample template

Usage: Examine template structure before using for sample creation Returns: Complete template definition including field specifications

Lists available sample templates for reuse

Usage: Browse existing templates before creating new samples Returns: Paginated list of template metadata

Changes the name of any inventory item

Usage: Rename samples, subsamples, containers, or templates Universal: Works with any inventory item type Returns: Updated item information with new name

Adds custom metadata fields to inventory items

Usage: Extend items with experiment-specific or project-specific data Field format: [{"name": "Field Name", "type": "text|number", "content": "value"}] Types: 'text' for strings, 'number' for numeric values

Returns: Updated item with new custom fields

Generates scannable barcodes for inventory items

Usage: Create physical labels for sample tracking and identification Types: 'BARCODE' for standard linear barcodes, 'QR' for QR codes Returns: Binary barcode image data for printing or display

Retrieves container metadata without content for fast queries

Usage: Quick container information lookup without performance impact Performance: Avoids loading large content lists for better response times Returns: Container metadata only (name, type, capacity, etc.)

Retrieves only the items stored in a container

Usage: Get container contents without metadata overhead Performance: Focused query for container content analysis Returns: List of contained items with minimal metadata

Creates multiple samples efficiently in a single operation

Usage: High-performance sample creation for large datasets Performance: Much faster than individual create_sample calls Format: List of sample definition dictionaries

Note: Implementation should use batch API endpoints when available Returns: Results for all created samples with error handling

Retrieves recent samples with minimal data for dashboard views

Usage: Quick overview of recent activity without full sample details Performance: Optimized for dashboard and summary displays Filtering: Configurable time window and result count

Returns: Lightweight sample list with essential information only