trustgraph/docs/tech-specs/SCHEMA_REFACTORING_PROPOSAL.md
cybermaggedon 89be656990
Release/v1.2 (#457)
* Bump setup.py versions for 1.1

* PoC MCP server (#419)

* Very initial MCP server PoC for TrustGraph

* Put service on port 8000

* Add MCP container and packages to buildout

* Update docs for API/CLI changes in 1.0 (#421)

* Update some API basics for the 0.23/1.0 API change

* Add MCP container push (#425)

* Add command args to the MCP server (#426)

* Host and port parameters

* Added websocket arg

* More docs

* MCP client support (#427)

- MCP client service
- Tool request/response schema
- API gateway support for mcp-tool
- Message translation for tool request & response
- Make mcp-tool using configuration service for information
  about where the MCP services are.

* Feature/react call mcp (#428)

Key Features

  - MCP Tool Integration: Added core MCP tool support with ToolClientSpec and ToolClient classes
  - API Enhancement: New mcp_tool method for flow-specific tool invocation
  - CLI Tooling: New tg-invoke-mcp-tool command for testing MCP integration
  - React Agent Enhancement: Fixed and improved multi-tool invocation capabilities
  - Tool Management: Enhanced CLI for tool configuration and management

Changes

  - Added MCP tool invocation to API with flow-specific integration
  - Implemented ToolClientSpec and ToolClient for tool call handling
  - Updated agent-manager-react to invoke MCP tools with configurable types
  - Enhanced CLI with new commands and improved help text
  - Added comprehensive documentation for new CLI commands
  - Improved tool configuration management

Testing

  - Added tg-invoke-mcp-tool CLI command for isolated MCP integration testing
  - Enhanced agent capability to invoke multiple tools simultaneously

* Test suite executed from CI pipeline (#433)

* Test strategy & test cases

* Unit tests

* Integration tests

* Extending test coverage (#434)

* Contract tests

* Testing embeedings

* Agent unit tests

* Knowledge pipeline tests

* Turn on contract tests

* Increase storage test coverage (#435)

* Fixing storage and adding tests

* PR pipeline only runs quick tests

* Empty configuration is returned as empty list, previously was not in response (#436)

* Update config util to take files as well as command-line text (#437)

* Updated CLI invocation and config model for tools and mcp (#438)

* Updated CLI invocation and config model for tools and mcp

* CLI anomalies

* Tweaked the MCP tool implementation for new model

* Update agent implementation to match the new model

* Fix agent tools, now all tested

* Fixed integration tests

* Fix MCP delete tool params

* Update Python deps to 1.2

* Update to enable knowledge extraction using the agent framework (#439)

* Implement KG extraction agent (kg-extract-agent)

* Using ReAct framework (agent-manager-react)
 
* ReAct manager had an issue when emitting JSON, which conflicts which ReAct manager's own JSON messages, so refactored ReAct manager to use traditional ReAct messages, non-JSON structure.
 
* Minor refactor to take the prompt template client out of prompt-template so it can be more readily used by other modules. kg-extract-agent uses this framework.

* Migrate from setup.py to pyproject.toml (#440)

* Converted setup.py to pyproject.toml

* Modern package infrastructure as recommended by py docs

* Install missing build deps (#441)

* Install missing build deps (#442)

* Implement logging strategy (#444)

* Logging strategy and convert all prints() to logging invocations

* Fix/startup failure (#445)

* Fix loggin startup problems

* Fix logging startup problems (#446)

* Fix logging startup problems (#447)

* Fixed Mistral OCR to use current API (#448)

* Fixed Mistral OCR to use current API

* Added PDF decoder tests

* Fix Mistral OCR ident to be standard pdf-decoder (#450)

* Fix Mistral OCR ident to be standard pdf-decoder

* Correct test

* Schema structure refactor (#451)

* Write schema refactor spec

* Implemented schema refactor spec

* Structure data mvp (#452)

* Structured data tech spec

* Architecture principles

* New schemas

* Updated schemas and specs

* Object extractor

* Add .coveragerc

* New tests

* Cassandra object storage

* Trying to object extraction working, issues exist

* Validate librarian collection (#453)

* Fix token chunker, broken API invocation (#454)

* Fix token chunker, broken API invocation (#455)

* Knowledge load utility CLI (#456)

* Knowledge loader

* More tests
2025-08-18 20:56:09 +01:00

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Markdown

# Schema Directory Refactoring Proposal
## Current Issues
1. **Flat structure** - All schemas in one directory makes it hard to understand relationships
2. **Mixed concerns** - Core types, domain objects, and API contracts all mixed together
3. **Unclear naming** - Files like "object.py", "types.py", "topic.py" don't clearly indicate their purpose
4. **No clear layering** - Can't easily see what depends on what
## Proposed Structure
```
trustgraph-base/trustgraph/schema/
├── __init__.py
├── core/ # Core primitive types used everywhere
│ ├── __init__.py
│ ├── primitives.py # Error, Value, Triple, Field, RowSchema
│ ├── metadata.py # Metadata record
│ └── topic.py # Topic utilities
├── knowledge/ # Knowledge domain models and extraction
│ ├── __init__.py
│ ├── graph.py # EntityContext, EntityEmbeddings, Triples
│ ├── document.py # Document, TextDocument, Chunk
│ ├── knowledge.py # Knowledge extraction types
│ ├── embeddings.py # All embedding-related types (moved from multiple files)
│ └── nlp.py # Definition, Topic, Relationship, Fact types
└── services/ # Service request/response contracts
├── __init__.py
├── llm.py # TextCompletion, Embeddings, Tool requests/responses
├── retrieval.py # GraphRAG, DocumentRAG queries/responses
├── query.py # GraphEmbeddingsRequest/Response, DocumentEmbeddingsRequest/Response
├── agent.py # Agent requests/responses
├── flow.py # Flow requests/responses
├── prompt.py # Prompt service requests/responses
├── config.py # Configuration service
├── library.py # Librarian service
└── lookup.py # Lookup service
```
## Key Changes
1. **Hierarchical organization** - Clear separation between core types, knowledge models, and service contracts
2. **Better naming**:
- `types.py``core/primitives.py` (clearer purpose)
- `object.py` → Split between appropriate files based on actual content
- `documents.py``knowledge/document.py` (singular, consistent)
- `models.py``services/llm.py` (clearer what kind of models)
- `prompt.py` → Split: service parts to `services/prompt.py`, data types to `knowledge/nlp.py`
3. **Logical grouping**:
- All embedding types consolidated in `knowledge/embeddings.py`
- All LLM-related service contracts in `services/llm.py`
- Clear separation of request/response pairs in services directory
- Knowledge extraction types grouped with other knowledge domain models
4. **Dependency clarity**:
- Core types have no dependencies
- Knowledge models depend only on core
- Service contracts can depend on both core and knowledge models
## Migration Benefits
1. **Easier navigation** - Developers can quickly find what they need
2. **Better modularity** - Clear boundaries between different concerns
3. **Simpler imports** - More intuitive import paths
4. **Future-proof** - Easy to add new knowledge types or services without cluttering
## Example Import Changes
```python
# Before
from trustgraph.schema import Error, Triple, GraphEmbeddings, TextCompletionRequest
# After
from trustgraph.schema.core import Error, Triple
from trustgraph.schema.knowledge import GraphEmbeddings
from trustgraph.schema.services import TextCompletionRequest
```
## Implementation Notes
1. Keep backward compatibility by maintaining imports in root `__init__.py`
2. Move files gradually, updating imports as needed
3. Consider adding a `legacy.py` that imports everything for transition period
4. Update documentation to reflect new structure
<function_calls>
<invoke name="TodoWrite">
<parameter name="todos">[{"id": "1", "content": "Examine current schema directory structure", "status": "completed", "priority": "high"}, {"id": "2", "content": "Analyze schema files and their purposes", "status": "completed", "priority": "high"}, {"id": "3", "content": "Propose improved naming and structure", "status": "completed", "priority": "high"}]