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Core Concepts

This page explains the fundamental concepts that drive BoCoFlow and help you understand how workflows function.

Workflows​

A workflow in BoCoFlow is a directed graph where:

  • Nodes represent computational operations or data sources/sinks
  • Edges represent the flow of data between nodes
  • Execution follows the dependencies defined by the connections

Workflows are stored as JSON files that contain:

  • The visual layout of nodes
  • Node configurations
  • Connection information
  • Environment settings

Nodes​

Nodes are the building blocks of BoCoFlow workflows. Each node represents a specific operation or function and has:

Node Anatomy​

Node Anatomy

  • Header: Contains the node name and action buttons
  • Ports: Input and output connection points
    • Input ports: Accept data from preceding nodes
    • Output ports: Send data to subsequent nodes
    • Flow ports: Special ports for flow control connections
  • Status indicator: Shows the current execution state

Node Configuration​

Nodes are configured through a configuration modal that appears when you click the ⚙️ icon. Configuration options vary by node type but typically include:

  • File paths: Locations for input/output files
  • Parameters: Processing options
  • Flow variables: Dynamic parameters from flow control nodes

Node Types​

BoCoFlow includes several categories of nodes:

  • I/O Nodes: Read and write data (CSV, text, databases, etc.)
  • Manipulation Nodes: Transform and process data
  • Visualization Nodes: Create visual representations of data
  • Flow Control Nodes: Manage workflow execution and variables

Data Flow​

Data flows through your workflow from one node to the next, following these principles:

  1. Node Execution: When a node executes, it processes input data and produces output data
  2. Data Passing: Output data from one node becomes input data to connected nodes
  3. Formats: Data typically passes as JSON-serialized structures
  4. Caching: Executed node results are cached to avoid redundant computation

Working Directory​

The working directory is a crucial concept in BoCoFlow:

  • It serves as the root location for your workflow project
  • Relative paths in nodes are resolved against this directory
  • Workflow status and execution logs are stored here
  • The directory structure helps maintain portability

Path Handling​

BoCoFlow uses a prefix system to handle file paths:

  • abs: prefix indicates an absolute path on your system
  • rel: prefix indicates a path relative to the working directory

This system ensures workflows can be portable across different environments.

Flow Variables​

Flow variables provide a way to parameterize your workflows:

  • Global flow variables: Available to all nodes in a workflow
  • Local flow variables: Created by flow control nodes and available to downstream nodes
  • Use cases: Controlling file paths, setting processing parameters, creating dynamic workflows

Creating Flow Variables​

  1. Use the "Global Flow Menu" or add flow control nodes
  2. Configure with a variable name and default value
  3. Reference in node configurations

Using Flow Variables​

When configuring a node:

  1. Check the "Use Flow Variable" option for a parameter
  2. Select the desired variable from the dropdown
  3. The variable's value will be used during execution

Execution Model​

BoCoFlow's execution follows a dependency-based model:

  1. Dependency Analysis: The system determines the execution order based on node connections
  2. Selective Execution: Only nodes that need to be executed are processed
  3. Force Execution: The "force_to_run" option allows re-execution even when cached results exist
  4. Status Tracking: Execution status is tracked and visualized for each node

Conda Integration​

BoCoFlow can integrate with Conda environments to manage Python dependencies:

  • Conda Path: Path to your Conda installation
  • Default Environment: The Conda environment to use for node execution
  • Environment Management: Different nodes can use different environments

Next Steps​

Now that you understand the core concepts, learn more about: