| """Measure one first-load and cached retrieval per indexed source file.""" |
| from contextlib import closing |
| from datetime import datetime, timezone |
| import json |
| import platform |
| import time |
|
|
| import numpy as np |
|
|
| from catalog import ROOT, PROBS |
| from remote_catalog import RemoteCatalog |
|
|
|
|
| def main(): |
| catalog = RemoteCatalog() |
| with closing(catalog.connect()) as conn: |
| ids = [r[0] for r in conn.execute("SELECT min(id) FROM segments GROUP BY object_path ORDER BY object_path")] |
| results = [] |
| for index in ids: |
| record = catalog.records[index] |
| start = time.perf_counter() |
| found = catalog.lookup(record["record_name"]) |
| lookup_ms = (time.perf_counter() - start) * 1000 |
| assert index in found |
| table, cold = catalog.fetch(index) |
| |
| length = record["segment_end_bp"] - record["segment_start_bp"] |
| for column in PROBS: |
| values = table[column][0].values.to_numpy() |
| assert len(values) == length |
| assert np.isfinite(values).all() |
| assert ((values >= 0) & (values <= 1)).all() |
| cached, warm = catalog.fetch(index) |
| assert warm["cache_hit"] and warm["bytes_read"] == 0 and table.equals(cached) |
| start = time.perf_counter() |
| frame, step = catalog.window(index, table=cached) |
| plot_seconds = time.perf_counter() - start |
| assert len(frame) <= 2400 |
| result = {"accession": record["record_name"], "assembly": record["assembly_accession"], |
| "organism": record["organism_name"], "bases": length, |
| "lookup_ms": lookup_ms, "first_load": cold, "cached_load": warm, |
| "plot_seconds": plot_seconds, "plot_bin_bp": step} |
| results.append(result) |
| print(json.dumps(result), flush=True) |
| del table, cached, values |
| report = {"created_at": datetime.now(timezone.utc).isoformat(), |
| "environment": platform.system() + " / Python " + platform.python_version(), |
| "note": "Workspace measurements; not Space latency. Empty app cache before each source's first load; upstream caches uncontrolled. Bytes count returned file ranges, excluding HTTP overhead.", |
| "index_bytes": catalog.path.stat().st_size, "results": results} |
| (ROOT / "data" / "benchmark.json").write_text(json.dumps(report, indent=2) + "\n") |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
