Panel-design run fails after CZI step: irrelevant CZI matches followed by `parsing error...`

[arashabadi]

Thank you again for sharing SpatialAgent.

I’m trying to design a mouse lung influenza panel, but I have not yet had a successful end-to-end run.
The run reaches the CZI step, returns mostly irrelevant datasets, and then terminates with parsing error....

• Task: 100-gene panel for C57BL/6J mouse lung.
• CZI metadata is available and data_path is correctly set. (Improve notebook UX outside repo root: default data_path causes false CZI metadata missing errors #3 resolved) ... So this is not the previous missing-file issue.

Observed behavior

CZI search executes:

search_czi_datasets({"query": "lung, Mus musculus", "n_datasets": 5})

but top matches can be non-lung tissues (e.g., embryo / skin). Shortly after that step, the agent prints parsing error....

Run stops early; no reliable final panel is produced. but For mouse + lung intent, top CZI results should be lung-relevant mouse datasets and the run should continue normally after CZI retrieval (no parser termination).

Suspected causes

• search_czi_datasets appears to rank embeddings over broad metadata without strict pre-filtering by organism/tissue.
• CZI tool output may be oversized/noisy (print + return duplication), which can increase parser fragility.

Must Fix (I think)

1. Add structured filters in search_czi_datasets (before ranking):
   • organism, tissue, optional disease, strict=True.
   • Filter dataframe first, then rank within filtered rows.
2. Add deterministic fallback when strict filters return no rows:
   • Controlled relaxation + clear warning.
3. Remove duplicate large output payload:
   • Avoid both print(output) and return output for same content.
4. Keep CZI output compact to reduce parser risk.

Should Fix

5. Add ranking guardrails:
   • Strong penalty for organism mismatch.
   • Boost exact/partial tissue match (lung, respiratory).
6. Update panel-design skill to prefer structured CZI constraints over free-text-only queries.