cfd2b848b9ee185619c7e677269329964d147327 braney Mon Apr 27 16:10:16 2026 -0700 quickLiftBench: switch to saved-session comparisons, refs #37445 Replace the per-track URL-builder schema (db/track/hubUrl + positions list) with saved-session refs of the form `user/sessionName`. Each variant loads a saved session and renders at the session's own saved region; native and quickLifted sessions live on different assemblies, so identical chr:start-end ranges would not be biologically equivalent. Drop hgt.reset=1 from the URL: it re-applied default-track visibility, defeating hideTracks=1. Cart isolation comes from a fresh requests.Session() per case (new hgsid -> fresh cart). Headline metric is total_ms, parsed from the "Overall total time" footer span; load_ms_sum and draw_ms_sum are summed across per-track rows. Add bench1_hgwdev and bench1_rr cases pointing at the first real native/lifted session pair (Brianraney/benchQuickNative1 vs benchQuickList1). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/utils/qa/quickLiftBench/quickLiftBench.py src/utils/qa/quickLiftBench/quickLiftBench.py index b962586e3f8..d3ebc098ff9 100755 --- src/utils/qa/quickLiftBench/quickLiftBench.py +++ src/utils/qa/quickLiftBench/quickLiftBench.py @@ -1,86 +1,92 @@ #!/usr/bin/env python3 """ -quickLiftBench.py - Benchmark hgTracks render times for quickLifted tracks vs -their non-lifted counterparts. - -Drives a YAML-configured set of benchmark cases, hits hgTracks with -?measureTiming=1, parses per-track loadTime/drawTime out of the response, and -writes TSV results suitable for inclusion in a quickLift performance paper. - -For each case, multiple variants (e.g. native vs lifted) are timed at multiple -positions across multiple iterations. Output is one TSV row per (case, variant, -position, iteration) plus a per-(case, position) summary with median/p90 and -lifted/native ratios. +quickLiftBench.py - Benchmark hgTracks render time for two saved sessions on +the same server. + +Each case names two (or more) variants, each variant is a saved-session +reference of the form "user/sessionName". The runner loads the session, applies +a position from the case, and times the hgTracks render with measureTiming=1. + +Output is one TSV row per (case, variant, position, iteration) plus a +per-(case, position) summary with median/p90 and pairwise ratios. The headline +metric is `total_ms`, taken from the "Overall total time" timing span emitted +by hgTracks. `load_ms_sum` and `draw_ms_sum` are the sums across all visible +tracks from the printTrackTiming() table. """ import argparse import csv import os import re import statistics import sys import time from datetime import datetime from urllib.parse import urlencode import requests import yaml -# Regex over the extracted trackTiming span text. The HTML inside looks like: -# track, load time, draw time, total (first window)<br /> -# shortLabel, 12, 8, 20<br /> +# A row of the printTrackTiming() table: shortLabel, load, draw, total TRACK_TIMING_ROW_RE = re.compile( r"^\s*([^,<>]+?)\s*,\s*(\d+)\s*,\s*(\d+)\s*,\s*(\d+)\s*$" ) -# <span class='trackTiming'> ... </span> -- there can be more than one (composite -# subtracks emit their own). We grab the first block, which contains the per-track -# table. +# <span class='trackTiming'> ... </span>. The opening span is never explicitly +# closed by printTrackTiming(); the regex's non-greedy match terminates at the +# first subsequent </span> from an unrelated span (e.g. the trailing +# 'timing' span for "Time to write and close cart"). TRACK_TIMING_SPAN_RE = re.compile( r"<span class=['\"]trackTiming['\"]>(.*?)</span>", re.DOTALL | re.IGNORECASE, ) -# <span class='timing'>label: NNN millis<BR></span> +# <span class='timing'>label: NNN millis<BR></span> -- per-phase timings. +# Also matches the "Overall total time" footer span which uses <br /> (XHTML). TIMING_SPAN_RE = re.compile( - r"<span class=['\"]timing['\"]>(.+?):\s*(\d+)\s*millis<BR></span>", + r"<span class=['\"]timing['\"]>(.+?):\s*(\d+)\s*millis(?:<br\s*/?>)?\s*</span>", re.DOTALL | re.IGNORECASE, ) +OVERALL_TIMING_LABEL = "Overall total time" + def parse_args(): p = argparse.ArgumentParser( - description="Benchmark quickLift vs native track render times.", + description=( + "Benchmark hgTracks render time for saved sessions. Each variant " + "is a user/sessionName reference." + ), formatter_class=argparse.RawDescriptionHelpFormatter, ) here = os.path.dirname(os.path.abspath(__file__)) p.add_argument( "--config", default=os.path.join(here, "cases.yaml"), help="YAML config file (default: cases.yaml next to script)", ) p.add_argument( "--cases", default=None, help="Comma-separated list of case ids to run (default: all)", ) p.add_argument( "--server-override", default=None, - help="Override every variant's `server` with this server name from defaults.servers", + help="Override every case's server with this server name from defaults.servers", ) p.add_argument( "--iterations", type=int, default=None, help="Override defaults.iterations", ) p.add_argument( "--warmup", type=int, default=None, help="Override defaults.warmup", ) p.add_argument( "--out", @@ -97,135 +103,117 @@ def load_config(path): with open(path) as f: cfg = yaml.safe_load(f) if "cases" not in cfg or not cfg["cases"]: sys.exit(f"{path}: no `cases` defined") cfg.setdefault("defaults", {}) cfg["defaults"].setdefault("iterations", 5) cfg["defaults"].setdefault("warmup", 1) cfg["defaults"].setdefault("timeout", 60) cfg["defaults"].setdefault("servers", {}) return cfg -def resolve_variant(variant, defaults, server_override): - """Merge defaults into a variant and resolve its server hostname.""" - merged = {} - for k in ("db", "hubUrl", "track", "extraCgi"): - if k in defaults: - merged[k] = defaults[k] - merged.update(variant) - server_key = server_override or merged.get("server") +def parse_session(s): + """Split 'user/sessionName' (or '/s/user/name'). Returns (user, name).""" + if not isinstance(s, str): + raise ValueError(f"variant must be a 'user/sessionName' string, got: {s!r}") + s = s.strip() + if s.startswith("/s/"): + s = s[3:] + if "/" not in s: + raise ValueError(f"variant must contain '/': {s!r}") + user, name = s.split("/", 1) + if not user or not name: + raise ValueError(f"empty user or session name in: {s!r}") + return user, name + + +def resolve_server(case, defaults, server_override): + server_key = server_override or case.get("server") if not server_key: - raise ValueError(f"variant has no server: {variant}") + raise ValueError(f"case '{case.get('id')}' has no server") servers = defaults.get("servers", {}) if server_key not in servers: raise ValueError( f"server '{server_key}' not in defaults.servers ({list(servers)})" ) - merged["serverKey"] = server_key - merged["serverUrl"] = servers[server_key].rstrip("/") - return merged + return server_key, servers[server_key].rstrip("/") + +def build_url(server_url, user, session_name): + """Build an hgTracks URL that loads a saved session at its saved position. -def build_url(variant, position): - """Build an hgTracks URL that isolates one named track at a given position.""" - if "track" not in variant or "db" not in variant: - raise ValueError(f"variant missing track/db: {variant}") + The position is NOT overridden via URL: a native session and its + quickLifted counterpart sit on different assemblies, so identical + chr:start-end ranges would not be biologically equivalent. Whatever + region the session was saved at is what gets rendered. + """ params = [ - ("db", variant["db"]), - ("position", position), - ("hideTracks", "1"), - (variant["track"], "full"), + ("hgS_doOtherUser", "submit"), + ("hgS_otherUserName", user), + ("hgS_otherUserSessionName", session_name), ("hgt.trackImgOnly", "1"), - ("hgt.reset", "1"), ("measureTiming", "1"), ] - if variant.get("hubUrl"): - params.append(("hubUrl", variant["hubUrl"])) - extra = variant.get("extraCgi") or {} - for k, v in extra.items(): - params.append((k, str(v))) - return f"{variant['serverUrl']}/cgi-bin/hgTracks?{urlencode(params)}" + return f"{server_url}/cgi-bin/hgTracks?{urlencode(params)}" -def parse_track_timing(html, want_track): - """ - Pull per-track load/draw/total ms out of the trackTiming span. - - The HTML emits the track's shortLabel, not the trackDb track name we use - in the URL. So we try (a) exact/case-insensitive match against the label - first; (b) if that misses AND there's exactly one data row across all - spans (the expected case when hideTracks=1 isolates a single track), we - return that row. Otherwise we return None so the caller can log - `no-track-timing` and the user can fix the case. - - Returns (load_ms, draw_ms, total_ms) or (None, None, None). - """ +def parse_track_timing_rows(html): + """Return a list of (shortLabel, load_ms, draw_ms, total_ms) rows.""" if not html: - return None, None, None - spans = TRACK_TIMING_SPAN_RE.findall(html) - if not spans: - return None, None, None - - rows = [] # (label, load, draw, total) - for span in spans: + return [] + rows = [] + for span in TRACK_TIMING_SPAN_RE.findall(html): text = span.replace(" ", " ") for raw in text.split("<br />"): raw = raw.strip() # Drop the inner red <idiv> "average for all windows" rows. if "<idiv" in raw or "</idiv" in raw: continue if not raw or raw.startswith("track,"): continue m = TRACK_TIMING_ROW_RE.match(raw) if not m: continue label, load, draw, total = m.groups() rows.append((label.strip(), int(load), int(draw), int(total))) - - if not rows: - return None, None, None - - for label, load, draw, total in rows: - if label == want_track or label.lower() == want_track.lower(): - return load, draw, total - - if len(rows) == 1: - # Single track rendered (the hideTracks=1 case); the shortLabel didn't - # match the trackDb name but there's no ambiguity. - _, load, draw, total = rows[0] - return load, draw, total - - return None, None, None + return rows def parse_phase_timings(html): """Pull all <span class='timing'>label: NNN millis</span> entries.""" if not html: return {} out = {} for m in TIMING_SPAN_RE.finditer(html): label = m.group(1).strip() - # Strip HTML tags that sometimes sneak into labels (e.g. format strings) + # Strip HTML tags that sneak into labels (e.g. format strings) label = re.sub(r"<[^>]+>", "", label).strip() out[label] = int(m.group(2)) return out +def parse_overall_total(html): + """Return the 'Overall total time' value from the footer timing span, + or None if not found.""" + phases = parse_phase_timings(html) + return phases.get(OVERALL_TIMING_LABEL) + + def detect_block(html): """Return a short error reason if the response indicates bot-block / error.""" if html is None: return "no-response" lower = html.lower() if "you've been blocked" in lower or "you have been blocked" in lower: return "bot-blocked" if "<title>error" in lower or "errabort" in lower: return "errabort" return None def run_request(session, url, timeout): """Fetch a URL once. Return (http_ms, status_code, html, error).""" start = time.monotonic() @@ -242,31 +230,30 @@ def median_or_none(xs): xs = [x for x in xs if x is not None] if not xs: return None return int(statistics.median(xs)) def p90(xs): xs = sorted(x for x in xs if x is not None) if not xs: return None if len(xs) == 1: return xs[0] - # Nearest-rank p90 k = max(0, int(round(0.9 * (len(xs) - 1)))) return xs[k] def fmt_ms(v): return "-" if v is None else str(v) def main(): args = parse_args() cfg = load_config(args.config) defaults = cfg["defaults"] iterations = args.iterations if args.iterations is not None else defaults["iterations"] warmup = args.warmup if args.warmup is not None else defaults["warmup"] @@ -283,228 +270,222 @@ if missing: sys.exit(f"unknown case id(s): {sorted(missing)}") if not cases: sys.exit("no cases selected") timestamp = datetime.now().strftime("%Y%m%d-%H%M%S") out_dir = args.out or os.path.join(os.path.dirname(os.path.abspath(__file__)), "results", timestamp) os.makedirs(out_dir, exist_ok=True) results_path = os.path.join(out_dir, "results.tsv") summary_path = os.path.join(out_dir, "summary.tsv") print(f"writing results to {out_dir}", file=sys.stderr) results_fields = [ - "case", "variant", "server", "db", "track", - "position_label", "position", "iteration", - "http_ms", "load_ms", "draw_ms", "total_ms", + "case", "variant", "server", "user", "session", "iteration", + "http_ms", "load_ms_sum", "draw_ms_sum", "n_tracks", "total_ms", "status_code", "error", ] - summary_fields = [ - "case", "position_label", "position", "metric", - ] - # Collect rows in memory for the summary pass. all_rows = [] with open(results_path, "w", newline="") as rf: writer = csv.DictWriter(rf, fieldnames=results_fields, delimiter="\t") writer.writeheader() for case in cases: cid = case["id"] description = case.get("description", "") print(f"\n=== {cid}: {description}", file=sys.stderr) - positions = case.get("positions") or [] - if not positions: - print(f" skipped: no positions", file=sys.stderr) + + try: + server_key, server_url = resolve_server(case, defaults, args.server_override) + except ValueError as e: + print(f" {e}", file=sys.stderr) continue + variants = case.get("variants") or {} if not variants: print(f" skipped: no variants", file=sys.stderr) continue - # Fresh session per case to mint a new hgsid and avoid cart pollution - # across cases. + # Fresh session per case to keep an independent hgsid lineage. session = requests.Session() session.headers.update({"User-Agent": "quickLiftBench/1.0"}) for vname, vraw in variants.items(): try: - variant = resolve_variant(vraw, defaults, args.server_override) + user, session_name = parse_session(vraw) except ValueError as e: print(f" variant {vname}: {e}", file=sys.stderr) continue - for pos in positions: - plabel = pos["label"] if isinstance(pos, dict) else "default" - pvalue = pos["value"] if isinstance(pos, dict) else pos - url = build_url(variant, pvalue) + url = build_url(server_url, user, session_name) if args.verbose: print(f" URL: {url}", file=sys.stderr) - # Warmup - discard for _ in range(warmup): run_request(session, url, timeout) for it in range(1, iterations + 1): http_ms, code, html, err = run_request(session, url, timeout) block = detect_block(html) if not err else None if block and not err: err = block - load_ms = draw_ms = total_ms = None + + load_sum = draw_sum = total_ms = None + n_tracks = None if html and not err: - load_ms, draw_ms, total_ms = parse_track_timing( - html, variant["track"] - ) - if load_ms is None: - err = "no-track-timing" + rows = parse_track_timing_rows(html) + n_tracks = len(rows) + if rows: + load_sum = sum(r[1] for r in rows) + draw_sum = sum(r[2] for r in rows) + total_ms = parse_overall_total(html) + if total_ms is None and not rows: + err = "no-timing" + row = { "case": cid, "variant": vname, - "server": variant["serverKey"], - "db": variant["db"], - "track": variant["track"], - "position_label": plabel, - "position": pvalue, + "server": server_key, + "user": user, + "session": session_name, "iteration": it, "http_ms": http_ms, - "load_ms": load_ms, - "draw_ms": draw_ms, - "total_ms": total_ms, + "load_ms_sum": load_sum if load_sum is not None else "", + "draw_ms_sum": draw_sum if draw_sum is not None else "", + "n_tracks": n_tracks if n_tracks is not None else "", + "total_ms": total_ms if total_ms is not None else "", "status_code": code if code is not None else "", "error": err or "", } writer.writerow(row) rf.flush() all_rows.append(row) if args.verbose: print( - f" {vname:8s} {plabel:8s} it={it} " + f" {vname:8s} it={it} " f"http={fmt_ms(http_ms)} " - f"load={fmt_ms(load_ms)} draw={fmt_ms(draw_ms)} " + f"load_sum={fmt_ms(load_sum)} draw_sum={fmt_ms(draw_sum)} " + f"tracks={fmt_ms(n_tracks)} " f"total={fmt_ms(total_ms)} {err or ''}", file=sys.stderr, ) write_summary(cases, all_rows, summary_path) print(f"\nresults: {results_path}", file=sys.stderr) print(f"summary: {summary_path}", file=sys.stderr) +def _to_int(v): + if v == "" or v is None: + return None + return int(v) + + def write_summary(cases, rows, path): """ - Per (case, position): for each variant compute median + p90 of - (http_ms, load_ms, draw_ms, total_ms). Then for each compare-pair, emit - median ratios. + Per (case, variant): compute median + p90 of (http_ms, load_ms_sum, + draw_ms_sum, total_ms). Then for each compare-pair, emit median ratios. """ - by_case_pos_var = {} + by_case_var = {} for r in rows: - key = (r["case"], r["position_label"], r["position"]) - by_case_pos_var.setdefault(key, {}).setdefault(r["variant"], []).append(r) + by_case_var.setdefault(r["case"], {}).setdefault(r["variant"], []).append(r) fields = [ - "case", "position_label", "position", "variant", + "case", "variant", "n", "n_ok", "http_median", "http_p90", - "load_median", "load_p90", - "draw_median", "draw_p90", + "load_sum_median", "load_sum_p90", + "draw_sum_median", "draw_sum_p90", "total_median", "total_p90", ] pair_fields = [ - "case", "position_label", "position", + "case", "left_variant", "right_variant", "left_total_median", "right_total_median", - "ratio_total", "ratio_load", "ratio_draw", "ratio_http", + "ratio_total", "ratio_load_sum", "ratio_draw_sum", "ratio_http", ] - summary_lines = [] # for stdout pretty-print + summary_lines = [] with open(path, "w", newline="") as f: w_v = csv.DictWriter(f, fieldnames=fields, delimiter="\t") w_v.writeheader() - per_variant_stats = {} # (case, plabel, pvalue, variant) -> dict of medians + per_variant_stats = {} - for (cid, plabel, pvalue), variants in sorted(by_case_pos_var.items()): + for cid, variants in sorted(by_case_var.items()): for vname, vrows in sorted(variants.items()): ok = [r for r in vrows if not r["error"]] - http = [r["http_ms"] for r in ok] - load = [r["load_ms"] for r in ok] - draw = [r["draw_ms"] for r in ok] - total = [r["total_ms"] for r in ok] + http = [_to_int(r["http_ms"]) for r in ok] + load = [_to_int(r["load_ms_sum"]) for r in ok] + draw = [_to_int(r["draw_ms_sum"]) for r in ok] + total = [_to_int(r["total_ms"]) for r in ok] stats = { "case": cid, - "position_label": plabel, - "position": pvalue, "variant": vname, "n": len(vrows), "n_ok": len(ok), "http_median": median_or_none(http), "http_p90": p90(http), - "load_median": median_or_none(load), - "load_p90": p90(load), - "draw_median": median_or_none(draw), - "draw_p90": p90(draw), + "load_sum_median": median_or_none(load), + "load_sum_p90": p90(load), + "draw_sum_median": median_or_none(draw), + "draw_sum_p90": p90(draw), "total_median": median_or_none(total), "total_p90": p90(total), } w_v.writerow({k: ("" if v is None else v) for k, v in stats.items()}) - per_variant_stats[(cid, plabel, pvalue, vname)] = stats + per_variant_stats[(cid, vname)] = stats f.write("\n# Pairwise comparisons (right/left ratio of medians)\n") w_p = csv.DictWriter(f, fieldnames=pair_fields, delimiter="\t") w_p.writeheader() for case in cases: cid = case["id"] pairs = case.get("compare") variants = list((case.get("variants") or {}).keys()) if not pairs: - # default: compare every other variant against the first if len(variants) < 2: continue pairs = [[variants[0], v] for v in variants[1:]] - positions = case.get("positions") or [] - for pos in positions: - plabel = pos["label"] if isinstance(pos, dict) else "default" - pvalue = pos["value"] if isinstance(pos, dict) else pos for left, right in pairs: - ls = per_variant_stats.get((cid, plabel, pvalue, left)) - rs = per_variant_stats.get((cid, plabel, pvalue, right)) + ls = per_variant_stats.get((cid, left)) + rs = per_variant_stats.get((cid, right)) if not ls or not rs: continue row = { "case": cid, - "position_label": plabel, - "position": pvalue, "left_variant": left, "right_variant": right, "left_total_median": ls["total_median"] if ls["total_median"] is not None else "", "right_total_median": rs["total_median"] if rs["total_median"] is not None else "", "ratio_total": ratio(rs["total_median"], ls["total_median"]), - "ratio_load": ratio(rs["load_median"], ls["load_median"]), - "ratio_draw": ratio(rs["draw_median"], ls["draw_median"]), + "ratio_load_sum": ratio(rs["load_sum_median"], ls["load_sum_median"]), + "ratio_draw_sum": ratio(rs["draw_sum_median"], ls["draw_sum_median"]), "ratio_http": ratio(rs["http_median"], ls["http_median"]), } w_p.writerow(row) summary_lines.append( - f" {cid:30s} {plabel:8s} {left}->{right} " + f" {cid:30s} {left}->{right} " f"total {ls['total_median']}->{rs['total_median']} ms " f"ratio={row['ratio_total']}" ) if summary_lines: - print("\nPairwise summary (lifted/native ratio of total render time):", + print("\nPairwise summary (right/left ratio of overall total render time):", file=sys.stderr) for line in summary_lines: print(line, file=sys.stderr) def ratio(num, denom): if num is None or denom is None or denom == 0: return "" return f"{num / denom:.2f}" if __name__ == "__main__": main()