Debugging playbook#

This page is a step-by-step debugging runbook for Cellucid Python developers and power users.

It is optimized for two outcomes:

you can fix the issue yourself, or
you can file a bug report that a maintainer can act on without guessing.

Step 0 — Identify which mode you are in#

Everything downstream depends on this.

Pick the closest match:

Mode A: Export folder#

you ran cellucid.prepare(...) and have a directory export.
you start the viewer with cellucid serve ./export_dir or cellucid.show("./export_dir").

Mode B: AnnData server#

you are serving .h5ad/.zarr or an in-memory AnnData.
you start the viewer with cellucid serve ./data.h5ad --dataset-name "My dataset" --dataset-id my-dataset or cellucid.show_anndata(...).

Mode C: Notebook embedding#

you are in Jupyter/VSCode/Colab.
you see an iframe (or a blank output where you expected an iframe).

Step 1 — Confirm the server is alive#

Open a terminal (or use curl from wherever the server is running) and check:

curl -s http://127.0.0.1:8765/_cellucid/health
curl -s http://127.0.0.1:8765/_cellucid/info

If these fail:

your server is not running, crashed, or the port is wrong.

If the port differs, find it in:

the CLI banner output, or
viewer.server_url (notebook), or
server.url (Python).

Step 2 — Confirm the viewer UI assets can load#

Start the viewer/server. Source-generation errors occur before the HTTP server binds and identify the failing inventory, object, verification, or filesystem operation.

Fix options:

ensure access to the configured web_source_url,
correct the exact source response or inventory contract, and
pass a writable web_cache_dir.

See: Server mode architecture, endpoints, and security and Configuration, environment variables, and logging.

Step 3 — Confirm dataset endpoints return data#

Export folder mode#

Check that the directory contains:

dataset_identity.json
obs_manifest.json
at least one points_*d.bin or points_*d.bin.gz

Then probe:

curl -I http://127.0.0.1:<port>/dataset_identity.json
curl -I http://127.0.0.1:<port>/obs_manifest.json
curl -I http://127.0.0.1:<port>/points_3d.bin
curl -I http://127.0.0.1:<port>/points_3d.bin.gz

(One of the two points paths should exist depending on compression.)

AnnData server mode#

Probe:

curl -I http://127.0.0.1:<port>/dataset_identity.json
curl -I http://127.0.0.1:<port>/obs_manifest.json
curl -I http://127.0.0.1:<port>/points_3d.bin

If you want to test gene/obs endpoints, pick a known key and try:

curl -I http://127.0.0.1:<port>/var/FOXP1.values.f32
curl -I http://127.0.0.1:<port>/obs/cell_type.codes.u8

Step 4 — Use browser DevTools (network + console)#

This is the fastest way to distinguish:

server failures (404/500),
format/schema issues (manifest parse errors),
and frontend/UI issues.

4.1 Network tab checklist#

In browser DevTools → Network:

filter for _cellucid:
- /_cellucid/health should be 200
- /_cellucid/info should be 200
filter for obs_manifest.json and var_manifest.json:
- should be 200 and have JSON content
look for 404s:
- missing .gz files often means a partial export / compression mismatch
look for CORS errors:
- “CORS blocked” usually means origin mismatch or a proxy issue

4.2 Console tab checklist#

In DevTools → Console:

copy/paste the first relevant error (don’t paraphrase)
look for:
- “Failed to fetch”
- “CORS blocked”
- JSON parse errors (manifest schema mismatch)

If you suspect web-app internal bugs, also consult:

Debugging playbook

Step 5 — Notebook-specific debugging (`viewer.debug_connection()`)#

If you have a viewer object (Jupyter/VSCode/Colab), run:

report = viewer.debug_connection()
report

The report includes:

server health/info probes,
dataset_identity_probes, keyed by every dataset declared by the server, preserving each exact dataset id/path and recording failures per dataset,
whether the viewer is displayed,
web UI cache status + build id,
a Python→frontend ping/pong roundtrip,
a frontend “debug snapshot” (URL/origin/userAgent as seen by the iframe),
and recent accepted-event counts grouped by exact event type.

If you are filing a bug report, paste the report as JSON:

import json
print(json.dumps(report, indent=2, default=str))

Common failure patterns (fast diagnosis)#

Pattern: “Viewer UI loads, but data is missing”#

Export folder mode:

manifests might reference files that don’t exist (partial export)
exact identifier/path mismatch
.gz mismatch (exported compressed, but viewer requests uncompressed or vice versa)

AnnData server mode:

route for that path may not exist (wrong filename/ext)
adapter could be raising internally (check server logs)

Start with:

Pattern: “Hooks don’t fire”#

Confirm in browser Network tab:

POST /_cellucid/events is happening and returns 200.

If it is not happening:

frontend may not be configured for notebook mode,
iframe may be blocked by proxy/mixed-content issues.

If it is happening:

viewerId may mismatch (stale iframe vs new viewer),
Python viewer may have been stopped/garbage-collected.