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View and modify Thoth configuration settings. Use when user wants to change API keys, paths, search settings, or other configuration options.
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| name | settings-management |
| description | View and modify Thoth configuration settings. Use when user wants to change API keys, paths, search settings, or other configuration options. |
| tools | ["view_settings","update_settings","validate_settings","reset_settings","migrate_settings"] |
Manage Thoth configuration including API credentials, file paths, search parameters, and system behavior. Settings are stored in thoth.settings.json and persist across sessions.
The settings system provides:
| Tool | Purpose | When to Use |
|---|---|---|
view_settings | Display current configuration | Check current values |
update_settings | Modify settings | Change configuration |
validate_settings | Check settings validity | After changes or troubleshooting |
reset_settings | Restore defaults | Fix broken configuration |
migrate_settings | Import from environment | First-time setup |
api){
"api": {
"openai_api_key": "sk-...",
"anthropic_api_key": "sk-ant-...",
"semantic_scholar_api_key": "...",
"openalex_email": "user@example.com"
}
}
paths){
"paths": {
"vault_path": "/path/to/obsidian/vault",
"pdf_directory": "thoth/papers/pdfs",
"data_directory": "thoth/data",
"backup_directory": "thoth/backups"
}
}
rag){
"rag": {
"embedding_model": "text-embedding-3-small",
"chunk_size": 1000,
"chunk_overlap": 200,
"collection_name": "thoth_articles"
}
}
search){
"search": {
"default_limit": 10,
"min_relevance": 0.7,
"hybrid_search": true,
"sources": ["semantic_scholar", "openalex", "arxiv"]
}
}
discovery){
"discovery": {
"default_max_papers": 50,
"default_relevance_threshold": 0.7,
"auto_discovery_enabled": false,
"discovery_interval_hours": 24
}
}
database){
"database": {
"connection_string": "postgresql://...",
"pool_size": 5
}
}
view_settings()
→ Returns complete settings object
view_settings(section="api")
→ Returns only API configuration
view_settings(section="paths")
→ Returns only path configuration
view_settings(section="rag", key="embedding_model")
→ Returns: "text-embedding-3-small"
update_settings(
section="search",
updates={"default_limit": 20}
)
update_settings(
section="rag",
updates={
"chunk_size": 1200,
"chunk_overlap": 300
}
)
validate_settings()
→ Returns validation results
Example output:
{
"valid": true,
"warnings": [
"semantic_scholar_api_key not set - rate limits will apply"
],
"errors": []
}
| Issue | Solution |
|---|---|
| Missing required field | Set the field with update_settings |
| Invalid path | Check path exists and is accessible |
| Invalid API key format | Verify key is correctly copied |
| Invalid value type | Check expected type in schema |
reset_settings(section="search")
→ Restores search settings to defaults
reset_settings(all=true)
→ Restores entire configuration to defaults
Warning: Reset will overwrite current values. Consider backup first.
For first-time setup or transitioning from .env files:
migrate_settings()
→ Imports settings from environment variables
Migrated:
- OPENAI_API_KEY → api.openai_api_key
- VAULT_PATH → paths.vault_path
- POSTGRES_URL → database.connection_string
...
User: "I moved my Obsidian vault to a new location"
1. View current path
view_settings(section="paths", key="vault_path")
→ /old/path/to/vault
2. Update path
update_settings(
section="paths",
updates={"vault_path": "/new/path/to/vault"}
)
3. Validate
validate_settings()
→ valid: true
4. Response:
"Updated your vault path to /new/path/to/vault.
Changes are saved and will take effect immediately."
User: "I need to set up my Semantic Scholar API key"
1. Get current state
view_settings(section="api")
→ Shows current API keys (masked)
2. Update key
update_settings(
section="api",
updates={"semantic_scholar_api_key": "user-provided-key"}
)
3. Validate
validate_settings()
→ Check for warnings/errors
4. Response:
"Semantic Scholar API key configured.
You'll now have higher rate limits for paper discovery."
User: "My searches are returning too few results"
1. Check current search settings
view_settings(section="search")
→ default_limit: 10, min_relevance: 0.8
2. Adjust settings
update_settings(
section="search",
updates={
"default_limit": 25,
"min_relevance": 0.6,
"hybrid_search": true
}
)
3. Response:
"Search settings updated:
- Results limit: 10 → 25
- Relevance threshold: 0.8 → 0.6 (more inclusive)
- Hybrid search: enabled (combines semantic + keyword)
Try your search again - you should see more results."
User: "I just installed Thoth, help me configure it"
1. Try migration from environment
migrate_settings()
→ Imported 5 settings from environment
2. Check for missing required settings
validate_settings()
→ warnings: ["vault_path not set"]
3. Set required paths
update_settings(
section="paths",
updates={
"vault_path": "/path/to/obsidian/vault",
"pdf_directory": "thoth/papers/pdfs"
}
)
4. Verify API keys
view_settings(section="api")
→ Check which keys are configured
5. Response:
"Initial configuration complete!
Configured:
✓ OpenAI API key
✓ Vault path
✓ PDF directory
Optional (not configured):
- Semantic Scholar API key (higher rate limits)
- Anthropic API key (alternative LLM)
You can now start using Thoth. Would you like me to:
- Run a test search to verify everything works?
- Help you import existing PDFs?"
| Setting | Section | Purpose |
|---|---|---|
openai_api_key | api | LLM and embeddings |
vault_path | paths | Obsidian vault location |
| Setting | Section | Default | Purpose |
|---|---|---|---|
pdf_directory | paths | thoth/papers/pdfs | PDF storage |
chunk_size | rag | 1000 | RAG chunk size |
min_relevance | search | 0.7 | Search threshold |
| Setting | Section | Purpose |
|---|---|---|
semantic_scholar_api_key | api | Higher rate limits |
anthropic_api_key | api | Alternative LLM |
auto_discovery_enabled | discovery | Background searches |
thoth.settings.json1. Validate settings: validate_settings()
2. Check for errors in validation output
3. Restart services if required
4. For RAG changes, run reindex
1. Try validate_settings() for specific errors
2. Reset specific section: reset_settings(section="broken_section")
3. As last resort: reset_settings(all=true)
1. Check if migration was run: migrate_settings()
2. Verify file permissions on settings file
3. Check for typos in section/key names
Initialize a new user's research assistant. Use this on first interaction or when user asks to "get started", "set up", or "introduce yourself". Also use when you don't know the user's research interests or the human memory block still has placeholder text.
Walk the user through new Thoth features since their last onboarding or update. Use when the user asks "what's new", "what changed", or "what can you do now". Also use after check_whats_new returns updates to walk through them.
Create, manage, and iterate on research plan documents in the Obsidian vault. Use when the user asks for a research plan, literature review roadmap, or when you need to formalize your own working research strategy.
Conduct deep analysis of research papers, synthesize literature, and generate comprehensive reviews. Use when user needs thorough paper analysis, literature reviews, or cross-paper synthesis.
Manage external knowledge collections (textbooks, lecture notes, background material) and search them to support research. Use when user wants to upload reference material or query foundational knowledge.
Answer questions using your existing research collection and external knowledge. Use when user asks questions about papers they have, wants summaries, or seeks insights from their knowledge base.