| name | boettiger-lab-stack |
| description | Map of the boettiger-lab data-and-agent stack — which GitHub repo owns which piece of the data → STAC → MCP → LLM-agent chain. Use when unsure which repo to edit for a given problem, when routing cross-repo issues, or when the root cause could plausibly be in more than one layer. |
boettiger-lab Stack Map
The stack is a pipeline. Data flows upward; requests flow downward. Each layer has exactly one primary repo. Edit the repo that owns the behavior, not a downstream consumer that works around it.
LLM agent (browser)
│
▼
geo-agent ← client: map + chat UI. static site from CDN.
│ MCP over HTTP
▼
mcp-data-server ← server: DuckDB SQL + STAC tool-use + tile serving
│ reads
▼
STAC catalog on S3 ← metadata about the data: public-data/stac/catalog.json
│ generated by
▼
data-workflows ← pipelines that process datasets and emit STAC JSON
│
▼
raw + CNG data on S3 (Ceph via NRP)
All of this runs on NRP Nautilus (Kubernetes, Ceph S3 under the biodiversity namespace). Platform concerns live in separate skills: nrp-k8s, nrp-s3.
Per-repo ownership
boettiger-lab/geo-agent — client
The browser app. Configured per-deployment by layers-input.json + system-prompt.md + optional k8s/. JavaScript is loaded from CDN; we do not edit it here. If a user-visible bug is in the chat flow, map rendering from configured layers, or the system prompt, it's here. If the fix needs new JS capabilities, that's the upstream geoagent-app repo (CDN source), not this one. See the geo-agent skill for config details.
boettiger-lab/mcp-data-server — server
The MCP server that LLM agents talk to. Owns: DuckDB SQL execution, STAC tool-use (browse_stac_catalog, get_stac_details, get_collection), PMTiles tile proxy, auth, k8s deployment for duckdb-mcp / dev-duckdb-mcp. Reads the STAC catalog at startup. Does NOT own the catalog content — only how it's presented to agents.
boettiger-lab/data-workflows — STAC catalog and dataset pipelines
Generates and maintains the STAC catalog at s3-west.nrp-nautilus.io/public-data/stac/catalog.json and all per-collection stac-collection.json files. Also owns dataset-import workflows and the legacy pipelines that produced the current catalog shape. If a table:columns is wrong, missing, or a collection is structurally malformed, the fix is here, not in mcp-data-server. Note: the repo name is historical — it's really the data-and-catalog repo. See the cng-datasets skill for the current dataset-processing CLI used inside this repo.
boettiger-lab/cng-datasets — dataset-processing CLI
The tool used inside data-workflows for new datasets: URL verification, raw S3 upload, YAML-driven cloud-native conversion (GeoParquet + PMTiles + H3 hex), deployment to NRP. Emits STAC metadata as a side effect. See the cng-datasets skill for the full workflow.
Common cross-repo scenarios
- "The agent gives the wrong column names for dataset X." First check: does
get_stac_details(X) return the right columns? If the STAC has wrong columns → data-workflows. If STAC is fine but the tool output is malformed → mcp-data-server. If the output is fine but the prompt doesn't consume it → geo-agent.
- "The agent didn't find dataset X." Walk the STAC catalog yourself (use the
stac-navigation skill). If X is missing from STAC → data-workflows. If X is present but browse_stac_catalog doesn't surface it → mcp-data-server. If it surfaces but the agent doesn't use it → geo-agent (probably a system-prompt / tool-description issue).
- "MCP startup is slow / pod won't come up." Almost always NRP S3 tail latency.
mcp-data-server fix if the code can bound the load time; nrp-k8s if it's a rollout / admission issue.
- "Catalog shape is weird for this agent use case." Fix the catalog upstream in
data-workflows, don't patch around it in mcp-data-server. Rendering logic should assume a well-formed catalog.
The principle
Edit the repo where the behavior is defined, not a repo that happens to display the symptom. The downstream repos are consumers and should stay thin. When in doubt: trace the data from its source (raw → pipeline → STAC → MCP → agent) and fix the earliest point where the wrong thing enters the chain.
