kohulan/chemaudit/chemaudit-batch-validation

ChemAudit Batch Validation

Overview

File-in, file-out bulk validation with three phases:

1. Upload → Celery enqueue — instant job_id response.
2. Processing — per-molecule validation + optional scoring, safety, profiling, standardization. Progress via WebSocket or /status polling.
3. Analytics (opt-in) — scaffold, chemical space, clustering, MMP, taxonomy, similarity search, R-group decomposition. Computed on demand after the base job completes.

All state lives in Redis keyed by job_id. Session cookies scope access (one owner per job).

Deployment limits — check first

curl -sS http://localhost:8000/api/v1/config

Returns {"limits": {"max_batch_size": N, "max_file_size_mb": M}, "deployment_profile": "medium"}. Profiles (small/medium/large/xl/coconut) set these via config/*.yml.

Workflow

1. CSV column detection (optional, CSV/TSV/TXT only)

Before upload, probe a CSV for SMILES and Name columns:

curl -sS -X POST http://localhost:8000/api/v1/batch/detect-columns \
  -F "file=@compounds.csv"

Returns {columns, suggested_smiles, suggested_name, column_samples, row_count_estimate, file_size_mb}.

2. Upload

curl -sS -X POST http://localhost:8000/api/v1/batch/upload \
  -F "file=@compounds.csv" \
  -F "smiles_column=SMILES" \
  -F "name_column=Name" \
  -F "include_extended_safety=false" \
  -F "include_chembl_alerts=false" \
  -F "include_standardization=true" \
  -F "include_profiling=false" \
  -F "include_safety_assessment=false" \
  -F "profile_id=" \
  -F "notification_email="

Accepts .sdf, .csv, .tsv, .txt. Response:

{
  "job_id": "9e3b2c1e-....",
  "status": "pending",
  "total_molecules": 450,
  "message": "Job submitted. Processing 450 molecules."
}

Form fields:

• smiles_column — CSV only; defaults to SMILES.
• name_column — CSV only; optional.
• include_extended_safety — add NIH and ZINC catalogs.
• include_chembl_alerts — add 7 ChEMBL pharma filter sets (BMS, Dundee, Glaxo, Inpharmatica, LINT, MLSMR, SureChEMBL).
• include_standardization — run ChEMBL standardization pipeline per molecule.
• include_profiling — PFI, #stars, Abbott bioavailability, CNS MPO.
• include_safety_assessment — CYP, hERG, bRo5, REOS, complexity panel.
• profile_id — scoring profile ID; adds profile desirability score per molecule.
• notification_email — sends a completion email (validated server-side).

3. Track progress

WebSocket (preferred):

const ws = new WebSocket(`ws://localhost:8000/ws/batch/${job_id}`);
ws.onmessage = (e) => console.log(JSON.parse(e.data));
// Send "ping" to keep alive; server replies "pong".

Messages: {job_id, status, progress, processed, total, eta_seconds}.

Polling:

curl -sS http://localhost:8000/api/v1/batch/<job_id>/status

4. Paginated results

curl -sS "http://localhost:8000/api/v1/batch/<job_id>?page=1&page_size=50&status_filter=error&min_score=0&max_score=40"

Filters: status_filter (success/error), min_score/max_score (0–100), sort_by (index/name/smiles/score/qed/safety/status/issues), sort_dir (asc/desc), issue_filter (failed check name), alert_filter (catalog name).

Stats-only endpoint (cheap, no results array):

curl -sS http://localhost:8000/api/v1/batch/<job_id>/stats

5. On-demand analytics

Get current analytics status and any cached results:

curl -sS http://localhost:8000/api/v1/batch/<job_id>/analytics

Trigger a specific computation:

curl -sS -X POST http://localhost:8000/api/v1/batch/<job_id>/analytics/scaffold
curl -sS -X POST http://localhost:8000/api/v1/batch/<job_id>/analytics/chemical_space \
  -H 'Content-Type: application/json' -d '{"method": "tsne"}'
curl -sS -X POST http://localhost:8000/api/v1/batch/<job_id>/analytics/clustering \
  -H 'Content-Type: application/json' -d '{"cutoff": 0.35}'
curl -sS -X POST http://localhost:8000/api/v1/batch/<job_id>/analytics/mmp \
  -H 'Content-Type: application/json' -d '{"activity_column": "pIC50"}'
curl -sS -X POST http://localhost:8000/api/v1/batch/<job_id>/analytics/similarity_search \
  -H 'Content-Type: application/json' -d '{"query_smiles": "CCO", "top_k": 20}'
curl -sS -X POST http://localhost:8000/api/v1/batch/<job_id>/analytics/rgroup \
  -H 'Content-Type: application/json' -d '{"core_smarts": "c1ccccc1"}'
curl -sS -X POST http://localhost:8000/api/v1/batch/<job_id>/analytics/taxonomy

Supported analysis types: scaffold, chemical_space, mmp, similarity_search, rgroup, clustering, taxonomy.

Clustering cap: Butina clustering is hard-capped at 1,000 molecules (D-06). Subsample or filter first on larger jobs.

Triggering an analysis that's already cached returns already_complete unless params differ (e.g. different method for chemical_space or different cutoff for clustering — those trigger recompute).

6. Pairwise MCS comparison

Between any two molecules in the batch by index:

curl -sS -X POST http://localhost:8000/api/v1/batch/<job_id>/mcs \
  -H 'Content-Type: application/json' \
  -d '{"index_a": 0, "index_b": 17}'

Returns MCS SMARTS, Tanimoto similarity, matched atom/bond counts, property deltas.

7. Subset actions

Apply an operation to a hand-picked subset from the UI or another filter pass:

# Revalidate — creates new batch with the chosen indices
curl -sS -X POST http://localhost:8000/api/v1/batch/<job_id>/subset/revalidate \
  -H 'Content-Type: application/json' \
  -d '{"indices": [0, 3, 17, 42]}'
 
# Rescore with a profile — creates new batch or scores inline
curl -sS -X POST http://localhost:8000/api/v1/batch/<job_id>/subset/rescore \
  -H 'Content-Type: application/json' \
  -d '{"indices": [0, 3, 17], "profile_id": 4}'
 
# Inline rescore (no Celery, sync response)
curl -sS -X POST http://localhost:8000/api/v1/batch/<job_id>/subset/score-inline \
  -H 'Content-Type: application/json' \
  -d '{"indices": [0, 3, 17], "profile_id": 4}'
 
# Export just the subset
curl -sS -X POST http://localhost:8000/api/v1/batch/<job_id>/subset/export \
  -H 'Content-Type: application/json' \
  -d '{"indices": [0, 3, 17], "format": "sdf"}' -o subset.sdf

8. Export — 9 formats

curl -sS "http://localhost:8000/api/v1/batch/<job_id>/export?format=excel&include_images=true&sheet_layout=multi" \
  -o results.xlsx
 
curl -sS "http://localhost:8000/api/v1/batch/<job_id>/export?format=pdf&include_audit=true&sections=validation_summary,score_distribution" \
  -o report.pdf

Formats (details in references/export-formats.md):

Filters: score_min, score_max, status (success/error/warning), indices=0,1,5,23 (GET) or POST body {"indices": [...]} for large selections.

9. Cancel

curl -sS -X DELETE http://localhost:8000/api/v1/batch/<job_id>

Already-completed results are retained.

Examples

Example 1 — "Upload compounds.csv, poll, export failures as SDF"

1. POST /api/v1/batch/upload with the file → capture job_id.
2. Poll GET /api/v1/batch/<job_id>/status until status == "complete".
3. GET /api/v1/batch/<job_id>/export?format=sdf&status=error → save to failures.sdf.

Example 2 — "Scaffold distribution for this library"

1. Upload, wait for complete.
2. POST /api/v1/batch/<job_id>/analytics/scaffold.
3. Poll GET /api/v1/batch/<job_id>/analytics until the scaffold key moves to status: complete.
4. Read scaffold.groups[] and render a Murcko-scaffold frequency chart.

Example 3 — "Cluster at Tanimoto 0.7 and export cluster centroids"

1. Ensure the batch has ≤ 1,000 molecules.
2. POST /api/v1/batch/<job_id>/analytics/clustering with {"cutoff": 0.30} (distance, not similarity — 0.30 distance ≈ 0.70 similarity).
3. Read clustering.clusters[]; each contains centroid_index.
4. Subset-export those indices as CSV.

Rate limits

• /batch/upload: 3/minute.
• /batch/detect-columns: 10/minute.
• /batch/<job_id> (paginated results): 60/minute.
• /batch/<job_id>/status, /stats, DELETE /batch/<job_id>: 10/minute.
• /batch/<job_id>/analytics (status poll): 120/minute.
• /batch/<job_id>/analytics/<type> (trigger): 10/minute.
• /batch/<job_id>/mcs: 30/minute.
• /batch/<job_id>/subset/revalidate, /subset/rescore, /subset/export: 10/minute.
• /batch/<job_id>/subset/score-inline: 30/minute.
• /batch/<job_id>/export (GET and POST): 30/minute.

API key via X-API-Key raises the per-minute tier.

Troubleshooting

400 "File too large" / 400 "File contains N molecules. Maximum allowed is M."

Check /api/v1/config — deployment limits are profile-driven. Split the file or redeploy with a larger profile (./deploy.sh large).

400 "No valid molecules found in file"

CSV column wrong, or every row has a parse error. Run /batch/detect-columns first, or pre-validate with /diagnostics/file-prevalidate (see chemaudit-diagnostics).

400 "Invalid file content. Please check the file format and column names."

Malicious-content scan matched a pattern (script tags, macros). Legitimate hits are rare — audit-logged server-side. Sanitize the source file.

400 "Invalid notification email address"

Pattern-validated; must be a normal user@domain.tld under 254 chars.

404 on /batch/<job_id> a few minutes after completion

Results TTL in Redis is BATCH_RESULT_TTL (default 1 hour). Download exports before expiry or increase the TTL.

400 "Clustering is limited to 1,000 molecules"

D-06 hard cap. Filter (by score, alert, or scaffold) before triggering clustering.

WebSocket closes with code 4003 / 4029

• 4003: session cookie doesn't own the job (uploaded anonymously in a different browser).
• 4029: too many simultaneous WS connections for one job (_WS_MAX_PER_JOB = 10).

Analytics status stuck at computing

The Celery worker crashed mid-task. Trigger the same analysis again — the idempotency guard resets computing to queued when params change; otherwise flush the status key manually.

Further reading

• references/export-formats.md — exhaustive spec of all nine export formats.
• chemaudit-qsar-ready — for ML-dataset curation pipelines on the same file input.
• chemaudit-structure-filter — for generative-chemistry funnel filtering on a SMILES list.
• chemaudit-dataset-intelligence — for dataset health auditing with activity columns.