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Overview

Applications are the foundation of Apigene Copilot. Each application represents an API or service that Copilot can interact with on your behalf. By installing and configuring applications, you enable AI-powered interactions with your tools and services.
Applications list with search and Install Application

What Are Applications?

Applications are API integrations based on OpenAPI specifications. They provide:
  • API Operations: Individual endpoints the AI can call
  • MCP Tools: AI-friendly tools generated from API operations
  • Security Configuration: Authentication and credential management
  • Metadata: Context and descriptions for better AI understanding

Application Lifecycle

Discovery

Browse available applications or add custom ones

Installation

Add the application to your workspace

Configuration

Set up authentication and customize behavior

Usage

Use the application in Copilot conversations

Installing Applications

When you click + Install Application, choose:
  • OpenAPI based — import from URL, file, or Postman collection
  • MCP Server — opens the official native MCP catalog (not an OpenAPI install)

Method 1: From OpenAPI URL

Install applications directly from a URL:
  1. Navigate to Applications page
  2. Click + Install Application button
  3. Choose OpenAPI based, then From URL
  4. Enter the OpenAPI specification URL
  5. Click Install
Supported Formats
  • JSON (.json)
  • YAML (.yaml, .yml)
  • OpenAPI 2.0 (Swagger)
  • OpenAPI 3.0
  • OpenAPI 3.1

Method 2: Upload File

Install from a local OpenAPI specification file:
  1. Navigate to Applications page
  2. Click + Install Application button
  3. Choose OpenAPI based, then From File
  4. Click to select or drag and drop your file
  5. Click Install
File Requirements
  • Valid OpenAPI specification
  • Maximum size: 10MB
  • Formats: JSON or YAML

Method 3: From Postman Collection

Install from a Postman collection. Apigene converts the collection to OpenAPI, then runs the normal application install and reindex flow.
  1. Navigate to Applications+ Install Application
  2. Choose OpenAPI based
  3. Select From Postman
  4. Upload your Postman collection file (JSON)
  5. Wait for conversion and install to finish
  6. Configure Security before making live calls
Conversion depends on collection structure. Nested folders become tags where possible. Review generated operations after install and reindex if tool metadata looks incomplete.

Method 4: Native MCP Server

To connect a remote MCP server instead of an OpenAPI spec:
  1. Choose MCP Server on the install screen, or open MCP in the main nav
  2. Follow Native MCP Servers — official catalog, registry, or custom URL

Installation Process

When you install an OpenAPI-based application, Apigene:
  1. Checks LLM configuration
    • Installing or reindexing an application requires at least one model provider configured for the organization
    • If no provider is configured, complete Settings → AI Models first, then retry
  2. Validates the specification (or converts Postman → OpenAPI first)
  3. Creates agentic metadata
    • Generates tool descriptions
    • Extracts parameter information
    • Creates operation summaries
  4. Initializes configuration
    • Sets up security placeholders
    • Creates default settings
    • Prepares for first use
The installation typically takes 10-30 seconds depending on the API size.

Configuring Applications

After installation, configure your application for use:

General Settings

Access via Applications > [Application Name] > General tab Basic Information
  • API Name: Unique identifier (read-only)
  • API Title: Display name for the application
  • Description: What the application does
  • Version: API version (from specification)
  • Domain URL: Base URL for API calls
Visibility
  • Private: Only you can use it
  • Organization: Available to your team
  • Toggle visibility as needed

Security Configuration

Access via Applications > [Application Name] > Security tab This is the most critical configuration step. Without proper security setup, the application cannot make API calls.

Authentication Types

API Key
Bearer Token
OAuth 2.0
Basic Authentication
Custom Authentication

Security Setup Steps

  1. Identify Authentication Method
    • Check application documentation
    • Look at the Security tab
    • Note required credentials
  2. Obtain Credentials
    • Generate API keys from provider
    • Complete OAuth flow if needed
    • Get service account credentials
  3. Configure in Apigene
    • Enter credentials in Security tab
    • Test connection if available
    • Save configuration
  4. Verify Setup
    • Use application in Copilot
    • Check for authentication errors
    • Update if credentials expire

API Operations

Access via Applications > [Application Name] > Operations tab View and manage all available API endpoints: Operation List
  • Method (GET, POST, PUT, DELETE, etc.)
  • Path (e.g., /api/v1/users)
  • Summary description
  • Tags for organization
Operation Details
  • Full description
  • Parameters (path, query, body)
  • Request examples
  • Response schemas
  • Status codes
Search and Filter
  • Search by operation name
  • Filter by HTTP method
  • Filter by tags
  • Sort by various criteria

MCP Tools Configuration

Access via Applications > [Application Name] > MCP Tools tab MCP (Model Context Protocol) tools are AI-optimized versions of your API operations. Tool Information
  • Tool name (e.g., github_create_issue)
  • Description for AI understanding
  • Required parameters
  • Optional parameters
  • Success criteria
Customization Options
  • Edit tool descriptions
  • Modify parameter hints
  • Add usage examples
  • Set default values
  • Adjust inputs, response handling, and UI templates where available
Tool Generation
  • Automatically created during installation
  • One tool per API operation
  • Can be regenerated via reindex (see below)
  • Updates reflect in Copilot after reindex completes

Reindex and agentic metadata

Reindex regenerates MCP tool metadata from the current OpenAPI specification. Use it when:
  • You updated the OpenAPI spec
  • Tool descriptions look stale or incomplete
  • Install finished but metadata is still generating
  • Postman conversion produced a coarse operation set you refined in the spec
How to reindex
  1. Open Applications → select the application
  2. Use the MCP Tools / metadata area Reindex action
  3. Watch status: queued → in progress → success or failure
  4. Keep an organization model provider configured — reindex requires LLM access for agentic metadata
While reindex runs, the UI may show progress labels such as “Reindexing queued” or “Reindexing in progress”. Do not delete the application mid-run. OpenAPI applications are exposed as Apigene MCP tools for agents and the gateway. That is separate from installing a native MCP server. Programmatic creation of an MCP server record from an API name is also available via the MCP Server API.

Common Parameters

Access via Applications > [Application Name] > Common Parameters tab Set default values for parameters used across multiple operations: Use Cases
  • Organization ID (consistent across all calls)
  • API version preference
  • Response format preferences
  • Default pagination limits
Configuration
  • Parameter name
  • Default value
  • Apply to all operations or specific ones
  • Override in individual calls if needed
Benefits
  • Reduce repetitive input
  • Ensure consistency
  • Simplify Copilot interactions
  • Minimize errors

Managing Applications

Application List

The Applications page shows all installed applications: Information Displayed
  • Application icon (auto-generated from domain)
  • Application name and title
  • Description
  • Security status (configured ✓ / not configured ⚠️)
  • Installation date
Actions
  • Click to view/edit details
  • Delete application
  • Refresh metadata
  • Export configuration

Searching Applications

Use the search bar to find applications:
  • Search by name
  • Search by description
  • Filter results in real-time

Updating Applications

When APIs change, update your applications:
  1. Go to application details
  2. Click Update Specification
  3. Provide new URL or file
  4. Review changes
  5. Save updates
What Gets Updated
  • New operations added
  • Removed operations deprecated
  • Modified parameters reflected
  • Security schemes updated
  • MCP tools regenerated

Deleting Applications

Remove applications you no longer need:
  1. Navigate to Applications page
  2. Find the application
  3. Click the delete icon
  4. Confirm deletion
Impact of Deletion
  • All configuration is removed
  • MCP tools become unavailable
  • Copilot conversations can no longer use it
  • Agents using this application will show errors
  • Historical data is retained

Application Status Indicators

Security Status

✓ Configured (Green)
  • Authentication is set up
  • Application is ready to use
  • API calls will succeed
⚠️ Not Configured (Red)
  • Missing credentials
  • Application cannot make API calls
  • Configuration required
🔄 Needs Update (Yellow)
  • Credentials may be expired
  • Security scheme changed
  • Reconfiguration recommended

Connection Status

Connected (Green)
  • Successfully making API calls
  • Credentials are valid
  • Service is reachable
Failed (Red)
  • Authentication errors
  • Network issues
  • Service unavailable
Untested (Gray)
  • Not yet used in conversations
  • Status unknown
  • Test needed

Best Practices

Installation

Choose Quality Specifications
  • Use official OpenAPI specs when available
  • Verify specification completeness
  • Check for recent updates
Name Consistently
  • Use clear, recognizable names
  • Include version if relevant
  • Follow team naming conventions

Configuration

Secure Credential Management
  • Use service accounts when possible
  • Rotate credentials regularly
  • Don’t share credentials publicly
  • Use environment-specific keys (dev/prod)
Test After Configuration
  • Make a simple API call in Copilot
  • Verify authentication works
  • Check returned data format
  • Confirm permissions are sufficient

Maintenance

Monitor Usage
  • Check Dashboard for application usage
  • Identify unused applications
  • Review API call success rates
  • Monitor for errors
Keep Updated
  • Update specifications when APIs change
  • Review security configurations quarterly
  • Remove deprecated applications
  • Document configuration changes
Optimize Performance
  • Set common parameters to reduce overhead
  • Configure only necessary operations
  • Use appropriate authentication methods
  • Monitor rate limits

Advanced Features

Custom Operation Metadata

Enhance AI understanding of operations:

Parameter Templates

Create reusable parameter sets:

Response Transformation

Configure how responses are displayed:
  • Full Response: Show complete JSON
  • Summary: Show key fields only
  • Custom Format: Define what to extract
  • Error Handling: Custom error messages

Webhook Integration

For supported applications:
  • Configure webhook endpoints
  • Receive real-time updates
  • Trigger automated workflows
  • Enable event-driven actions

Troubleshooting

Installation Fails

Invalid Specification
  • Verify OpenAPI format
  • Use validation tools
  • Check for syntax errors
  • Ensure all required fields present
Network Errors
  • Check URL accessibility
  • Verify no authentication required for spec
  • Try downloading and uploading as file
  • Check firewall settings

Authentication Issues

401 Unauthorized
  • Verify credentials are correct
  • Check if tokens have expired
  • Confirm account has API access
  • Review authentication method
403 Forbidden
  • Check account permissions
  • Verify required scopes granted
  • Contact service administrator
  • Review API access policies

API Calls Failing

Network Errors
  • Check internet connection
  • Verify API service is online
  • Review firewall rules
  • Check for rate limiting
Invalid Parameters
  • Review required vs optional parameters
  • Check parameter data types
  • Verify parameter formats
  • Review API documentation
Response Errors
  • Check API status page
  • Review error messages
  • Verify data format expectations
  • Check for breaking changes in API

Next Steps