[Bug]: Multi-source + autoentities + MCP: `describe_entities` returns `NoEntitiesConfigured`

[mishu85]

What happened?

Context

I'm building an NPM package that exposes multiple enterprise SQL Server databases through a single MCP (Model Context Protocol) server using Data API Builder (DAB). The goal is to allow AI agents like GitHub Copilot to query hundreds of tables across multiple databases dynamically without manually mapping each table.

I'm using:

• DAB 2.0.9 with multi-source configuration
• autoentities pattern (%.%) to discover all tables in all schemas at runtime
• MCP stdio mode to expose database entities as MCP tools

The Bug

When using multi-source configuration with multiple child configs containing autoentities, DAB successfully starts and loads all entities during initialization, but the MCP describe_entities tool returns NoEntitiesConfigured error.

What Works ✅

• Single database with autoentities + MCP works perfectly
• Each child config tested individually returns hundreds of entities via describe_entities
• Multi-source with parent + 1 child works
• dab validate shows entities are discovered correctly for all configs

What Fails ❌

• Multi-source with parent + 2 or more children: describe_entities returns no entities
• The error message: "No entities are configured in the runtime configuration."
• This happens despite DAB logging "Successfully completed runtime initialization"

Steps to Reproduce

1. Create parent config (dab-config.json):

{
  "data-source": {
    "database-type": "mssql",
    "connection-string": "@env('DATABASE1_CONNSTRING')"
  },
  "data-source-files": [
    "databases/database1/dab-config.json",
    "databases/database2/dab-config.json",
    "databases/database3/dab-config.json"
  ],
  "runtime": {
    "rest": { "enabled": false },
    "graphql": { "enabled": false },
    "mcp": {
      "enabled": true,
      "dml-tools": {
        "describe-entities": true,
        "read-records": true,
        "aggregate-records": true
      }
    },
    "host": { "mode": "production" }
  },
  "entities": {}
}

2. Create child config (databases/database1/dab-config.json):

{
  "$schema": "https://github.com/Azure/data-api-builder/releases/latest/download/dab.draft.schema.json",
  "data-source": {
    "database-type": "mssql",
    "connection-string": "@env('DATABASE1_CONNSTRING')"
  },
  "autoentities": {
    "db1": {
      "patterns": {
        "include": ["%.%"],
        "exclude": [],
        "name": "db1_{schema}_{object}"
      },
      "template": {
        "rest": { "enabled": false },
        "graphql": { "enabled": false },
        "mcp": { "dml-tools": true }
      },
      "permissions": [
        { "role": "anonymous", "actions": [{ "action": "read" }] }
      ]
    }
  }
}

3. Start DAB:

dab start --mcp-stdio --config dab-config.json --verbose

Output:

info: Azure.DataApiBuilder.Service.Startup[0]
      Successfully completed runtime initialization.

4. Send MCP initialize request:

{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"test","version":"1.0"}}}

Response: ✅ Success

{"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2024-11-05","capabilities":{"tools":{"listChanged":true},"logging":{}},"serverInfo":{"name":"SQL MCP Server","version":"2.0.9"}}}

5. Call describe_entities:

{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"describe_entities","arguments":{"nameOnly":true}}}

Response: ❌ Error

{
  "toolName": "describe_entities",
  "status": "error",
  "error": {
    "type": "NoEntitiesConfigured",
    "message": "No entities are configured in the runtime configuration."
  }
}

Expected Behavior

describe_entities should return all entities discovered from child configs via autoentities, with prefixes like:

• db1_schema_table
• db2_schema_table
• db3_schema_table

Actual Behavior

NoEntitiesConfigured error is returned, despite:

• All configs loading successfully
• Entities being discovered during validation (dab validate shows hundreds of entities)
• Startup completing without errors

Analysis

The bug appears to be in DAB's config merging logic for multi-source mode. When merging parent + multiple children:

1. autoentities successfully discover entities in each child config
2. DAB starts and reports successful initialization
3. But the merged runtime configuration exposed to MCP contains no entities
4. MCP's describe_entities tool sees an empty entity list

Single child works because no complex merging is needed. Multiple children fail because autoentities from children don't propagate to the merged runtime configuration that MCP queries.

Environment

• DAB Version: 2.0.9
• Database: SQL Server 2022 (RTM-CU13-GDR)
• OS: Windows
• Node.js: v25.6.0
• MCP Inspector: v0.22.0

Workaround

Run separate DAB instances per database instead of using multi-source, and configure multiple MCP servers in the consumer.

Impact

This prevents using DAB's multi-source feature with autoentities in MCP mode, requiring manual entity mapping or separate server instances per database.

Version

2.0.9

What database are you using?

Azure SQL

What hosting model are you using?

No response

Which API approach are you accessing DAB through?

No response

Relevant log output

info: Azure.DataApiBuilder.Service.Startup[0]
      Successfully completed runtime initialization.
{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"test","version":"1.0"}}}
{"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2024-11-05","capabilities":{"tools":{"listChanged":true},"logging":{}},"serverInfo":{"name":"SQL MCP Server","version":"2.0.9"}}}
{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"describe_entities","arguments":{"nameOnly":true}}}
{"jsonrpc":"2.0","id":2,"result":{"content":[{"Type":"text","text":"{\r\n  \u0022toolName\u0022: \u0022describe_entities\u0022,\r\n  \u0022status\u0022: \u0022error\u0022,\r\n  \u0022error\u0022: {\r\n    \u0022type\u0022: \u0022NoEntitiesConfigured\u0022,\r\n    \u0022message\u0022: \u0022No entities are configured in the runtime configuration.\u0022\r\n  }\r\n}","type":"text"}],"isError":true}}

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