From 66c3562ca10b598a647f95b837439530c038e2d5 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Wed, 26 Aug 2026 18:57:59 -0400 Subject: [PATCH 01/60] Add --report-jsonl to capture raw per-test outcomes for the dashboard pytest --report-jsonl PATH appends one JSON line per test (nodeid, phase, outcome, wasxfail, duration, user_properties, concise crash message) from a pytest_runtest_logreport hook. Only the xdist controller writes: workers forward their TestReports, so the guard on PYTEST_XDIST_WORKER prevents duplicate lines without any file locking. The two Google Sheet test functions now record category, source, source_url, query_id and query_label via record_property, so the dashboard gets that metadata structurally instead of regexing failure messages. Co-Authored-By: Claude Fable 5 --- tests/conftest.py | 57 +++++++++++++++++++++ tests/nameres/test_nameres_from_gsheet.py | 10 +++- tests/nodenorm/test_nodenorm_from_gsheet.py | 10 +++- 3 files changed, 75 insertions(+), 2 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index 0fbc4ed..c131668 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2,6 +2,7 @@ # conftest.py - pytest configuration settings # import glob +import json import logging import os import os.path @@ -62,7 +63,19 @@ def unlink_if_exists(path) -> None: logging.getLogger(__name__).warning("Could not delete cached file %s: %s", path, e) +# Open file handle for --report-jsonl, or None. Controller-only: xdist workers +# forward their TestReports (including user_properties and wasxfail) to the +# controller, where pytest_runtest_logreport fires again, so only the controller +# needs to write. +_report_file = None + + def pytest_configure(config): + global _report_file + report_path = config.getoption('--report-jsonl') + if report_path and not os.environ.get('PYTEST_XDIST_WORKER'): + _report_file = open(report_path, 'a', encoding='utf-8') + # Delete the Google Sheet CSV cache at the start of each run so tests always # use a fresh download. Only the controller does this — xdist workers skip it # so they can share the cache file written by the controller. @@ -78,6 +91,42 @@ def pytest_configure(config): unlink_if_exists(GITHUB_ISSUES_CACHE_FILE) +def pytest_runtest_logreport(report): + """ + When --report-jsonl is set, write one JSON line per test phase: every 'call' + report, plus setup/teardown reports that did not pass (setup skips and + errors). Raw pytest facts only — classification into + passed/failed/xfailed/xpassed/skipped/error happens in + src.babel_validation.tools.generate_report, where it is unit-testable. + + longrepr may contain untrusted text (issue bodies, sheet cells, service + responses); it is truncated here and repr-escaped by the report generator + before it is displayed anywhere. + """ + if _report_file is None: + return + if report.when != 'call' and report.outcome == 'passed': + return + # Prefer the one-line crash message ("AssertionError: ...") over the full + # traceback with source and locals; skips have a (path, line, reason) tuple + # longrepr with no reprcrash, for which str() is already the short form. + msg = None + if report.longrepr is not None: + crash = getattr(report.longrepr, 'reprcrash', None) + msg = crash.message if crash is not None else str(report.longrepr) + record = { + "id": report.nodeid, + "when": report.when, + "outcome": report.outcome, + "wasxfail": hasattr(report, 'wasxfail'), + "duration": round(report.duration, 3), + "props": dict(report.user_properties or []), + "msg": msg[:2000] if msg else None, + } + _report_file.write(json.dumps(record) + "\n") + _report_file.flush() + + def pytest_addoption(parser): # The target environment(s) to target. parser.addoption( @@ -100,6 +149,14 @@ def pytest_addoption(parser): help="The categories of tests to exclude." ) + # Write one JSON line per test outcome, for the dashboard report generator. + parser.addoption( + '--report-jsonl', + default=None, + help="Append raw per-test outcome records (JSONL) to this file, for " + "src.babel_validation.tools.generate_report." + ) + # Only test particular GitHub issues. parser.addoption( '--issue', diff --git a/tests/nameres/test_nameres_from_gsheet.py b/tests/nameres/test_nameres_from_gsheet.py index 1b9403f..7494955 100644 --- a/tests/nameres/test_nameres_from_gsheet.py +++ b/tests/nameres/test_nameres_from_gsheet.py @@ -33,11 +33,19 @@ def pytest_generate_tests(metafunc): ) -def test_label(target_info, test_row, test_category): +def test_label(target_info, test_row, test_category, record_property): nameres_url = target_info['NameResURL'] limit = target_info['NameResLimit'] nameres_xfail_if_in_top = int(target_info['NameResXFailIfInTop']) + # Structured metadata for the dashboard report (--report-jsonl); forwarded + # to the controller by xdist as user_properties. + record_property("category", test_row.Category) + record_property("source", test_row.Source) + record_property("source_url", test_row.SourceURL) + record_property("query_id", test_row.QueryID) + record_property("query_label", test_row.QueryLabel) + category = test_row.Category if not test_category(category): pytest.skip(f"Skipping category {category} because of the category filter.") diff --git a/tests/nodenorm/test_nodenorm_from_gsheet.py b/tests/nodenorm/test_nodenorm_from_gsheet.py index 057e8a7..136712c 100644 --- a/tests/nodenorm/test_nodenorm_from_gsheet.py +++ b/tests/nodenorm/test_nodenorm_from_gsheet.py @@ -30,9 +30,17 @@ def pytest_generate_tests(metafunc): ) -def test_normalization(target_info, test_row, test_category): +def test_normalization(target_info, test_row, test_category, record_property): nodenorm_url = target_info['NodeNormURL'] + # Structured metadata for the dashboard report (--report-jsonl); forwarded + # to the controller by xdist as user_properties. + record_property("category", test_row.Category) + record_property("source", test_row.Source) + record_property("source_url", test_row.SourceURL) + record_property("query_id", test_row.QueryID) + record_property("query_label", test_row.QueryLabel) + category = test_row.Category if not test_category(category): pytest.skip(f"Skipping category {category} because of the category filter.") From d3f055212136f1b56a580abc908caec1cb846909 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Wed, 26 Aug 2026 18:57:59 -0400 Subject: [PATCH 02/60] Generate the dashboard report.json and history.jsonl from raw outcomes src.babel_validation.tools.generate_report aggregates the --report-jsonl records per test (worst outcome wins across phases and subtests), classifies them into passed/failed/xfailed/xpassed/skipped/error (strict XPASS included), splits the target out of parametrize ids (either end, longest name first so ci-es beats ci), and merges in each target's NodeNorm/NameRes /status. report.json is published on a public website and everything feeding it is untrusted, so this module is the choke point: text is repr-escaped and truncated, issue ids and source URLs only become links when they match the targets.ini Repositories allowlist, /status responses pass a key whitelist, and blocklist test details are withheld entirely. Co-Authored-By: Claude Fable 5 --- src/babel_validation/tools/__init__.py | 0 src/babel_validation/tools/generate_report.py | 501 ++++++++++++++++++ tests/unit/__init__.py | 0 tests/unit/test_generate_report.py | 344 ++++++++++++ 4 files changed, 845 insertions(+) create mode 100644 src/babel_validation/tools/__init__.py create mode 100644 src/babel_validation/tools/generate_report.py create mode 100644 tests/unit/__init__.py create mode 100644 tests/unit/test_generate_report.py diff --git a/src/babel_validation/tools/__init__.py b/src/babel_validation/tools/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/babel_validation/tools/generate_report.py b/src/babel_validation/tools/generate_report.py new file mode 100644 index 0000000..e588d29 --- /dev/null +++ b/src/babel_validation/tools/generate_report.py @@ -0,0 +1,501 @@ +# +# generate_report.py - build the dashboard report from raw pytest outcomes. +# +# Reads the JSONL files written by `pytest --report-jsonl` (see tests/conftest.py), +# fetches each target's NodeNorm/NameRes /status endpoint, and writes: +# - report.json: the full latest-run report the dashboard renders +# - history.jsonl: an append-only one-line-per-run summary for trends +# +# Everything in the raw records is untrusted (issue bodies, sheet cells, service +# responses end up in test IDs, properties and failure messages), and report.json +# is published on a public website. So this module is the choke point: all text +# is escaped and truncated here, links are only emitted from validated parts +# (allowlisted org/repo#N issue IDs, allowlisted source URLs), /status responses +# pass through a key whitelist, and blocklist test details are redacted entirely. +# +# Run as: +# uv run python -m src.babel_validation.tools.generate_report \ +# --raw-dir raw --targets-ini tests/targets.ini \ +# --history-in old_history.jsonl --out-dir website/public/data + +import argparse +import configparser +import datetime +import json +import logging +import os +import re +import sys +from pathlib import Path + +import requests + +logger = logging.getLogger(__name__) + +# Neither Google Sheet may be referenced in the output: the report must not +# contain the test-case sheet's ID or any link to it (casual observers of the +# public website should not find the sheet), and the blocklist sheet is not +# referenced anywhere in this module at all. + +STATUS_TIMEOUT_SECONDS = 30 +MAX_MESSAGE_CHARS = 500 + +# Worst outcome wins when a nodeid has several records (phases, subtests). +OUTCOME_SEVERITY = { + "passed": 0, + "skipped": 1, + "xfailed": 2, + "xpassed": 3, + "failed": 4, + "error": 5, +} + +# Outcomes whose messages are worth publishing; passed/xfailed/skipped messages +# are noise and would bloat report.json. +OUTCOMES_WITH_MESSAGES = {"failed", "xpassed", "error"} + + +def sanitize(text, max_chars=MAX_MESSAGE_CHARS): + """ + Truncate untrusted text and escape every non-printable character (ANSI + escapes, C0/C1 controls, bidi overrides, zero-width characters) the way + repr() would, keeping newlines and tabs readable. Escaping rather than + stripping keeps hostile content visible instead of silently vanishing. + """ + if text is None: + return None + text = str(text) + if len(text) > max_chars: + text = text[:max_chars] + "…[truncated]" + return "".join( + ch if ch.isprintable() or ch in "\n\t" else repr(ch)[1:-1] for ch in text + ) + + +def classify_record(record): + """Map one raw JSONL record to a dashboard outcome.""" + when = record.get("when") + outcome = record.get("outcome") + wasxfail = record.get("wasxfail", False) + msg = record.get("msg") or "" + + if when in ("setup", "teardown"): + return "error" if outcome == "failed" else "skipped" + if outcome == "failed": + # A strict xfail that passed is reported as failed with this prefix. + if msg.startswith("[XPASS(strict)]"): + return "xpassed" + return "failed" + if outcome == "skipped": + return "xfailed" if wasxfail else "skipped" + if outcome == "passed": + return "xpassed" if wasxfail else "passed" + logger.warning("Unknown outcome %r in record for %r", outcome, record.get("id")) + return "error" + + +def read_targets(targets_ini_path): + """Return (target names without localhost, repository allowlist, config).""" + config = configparser.ConfigParser() + config.read(targets_ini_path, encoding="utf8") + targets = [section for section in config.sections() if section != "localhost"] + allowlist = [ + repo.strip().lower() + for repo in config.defaults().get("repositories", "").splitlines() + if repo.strip() + ] + return targets, allowlist, config + + +def split_target(param_id, targets): + """ + Split a parametrize id like 'ci-es-test_row:row=42' or 'test_row:row=42-ci-es' + into (target, rest). The target's position depends on which + pytest_generate_tests hook parametrized first, which has changed across + pytest versions — so accept it at either end. Target names can contain + hyphens ('ci-es'), so match known names longest-first instead of splitting + on a hyphen. + """ + for target in sorted(targets, key=len, reverse=True): + if param_id == target: + return target, "" + if param_id.startswith(target + "-"): + return target, param_id[len(target) + 1 :] + if param_id.endswith("-" + target): + return target, param_id[: -(len(target) + 1)] + return None, param_id + + +def parse_nodeid(nodeid, targets): + """ + Return (result_key, target, rest) for a nodeid. The result key is the + nodeid with the target stripped from its parametrize id, so the same test + run against different targets shares a key. Tests without a target (unit + tests, environment tests) or with an unrecognized target land in the '?' + bucket rather than crashing the report. + """ + match = re.match(r"^(.*?)\[(.*)\]$", nodeid) + if not match: + return nodeid, "?", "" + base, param_id = match.groups() + target, rest = split_target(param_id, targets) + if target is None: + logger.warning("Could not find a target in node ID %r", nodeid) + return nodeid, "?", param_id + key = f"{base}[{rest}]" if rest else base + return key, target, rest + + +# Issue ids must look like org/repo#N *and* be in the checked-in allowlist +# before we build a github.com link from them. +ISSUE_ID_RE = re.compile(r"^([A-Za-z0-9_.-]+/[A-Za-z0-9_.-]+)#([0-9]+)$") + + +def validate_issue_id(issue_id, allowlist): + """Return the validated 'org/repo#N' or None.""" + match = ISSUE_ID_RE.match(issue_id or "") + if not match: + return None + if match.group(1).lower() not in allowlist: + return None + return issue_id + + +def validate_source_url(source_url, allowlist): + """ + Return source_url only if it is a GitHub URL within an allowlisted + org/repo; otherwise None. SourceURL is free text from the Google Sheet. + """ + if not source_url or not source_url.startswith("https://github.com/"): + return None + parts = source_url[len("https://github.com/") :].split("/") + if len(parts) < 2: + return None + if f"{parts[0]}/{parts[1]}".lower() not in allowlist: + return None + return source_url + + +def _trimmed_int(value): + try: + return int(value) + except (TypeError, ValueError): + return None + + +def _trimmed_float(value): + try: + return round(float(value), 2) + except (TypeError, ValueError): + return None + + +def trim_status(raw): + """ + Whitelist the fields of a NodeNorm or NameRes /status response. The + response is untrusted service output: unknown keys are dropped, numbers are + coerced, strings are escaped and truncated, and babel_version_url is kept + only if it points into the NCATSTranslator GitHub org. + """ + if not isinstance(raw, dict): + return {"error": "InvalidStatus"} + trimmed = {} + if "status" in raw: + trimmed["status"] = sanitize(raw["status"], 50) + if "babel_version" in raw: + trimmed["babel_version"] = sanitize(raw["babel_version"], 50) + url = raw.get("babel_version_url") + if isinstance(url, str) and url.lower().startswith( + "https://github.com/ncatstranslator/" + ): + trimmed["babel_version_url"] = sanitize(url, 200) + biolink = raw.get("biolink_model") + if isinstance(biolink, dict) and "tag" in biolink: + trimmed["biolink_version"] = sanitize(biolink["tag"], 100) + + databases = raw.get("databases") + if isinstance(databases, dict): + trimmed_dbs = {} + for name, db in list(databases.items())[:20]: + if not isinstance(db, dict): + continue + entry = {} + count = _trimmed_int(db.get("count")) + if count is not None: + entry["count"] = count + if "used_memory_rss_human" in db: + entry["used_memory_rss_human"] = sanitize( + db["used_memory_rss_human"], 20 + ) + trimmed_dbs[sanitize(name, 50)] = entry + trimmed["databases"] = trimmed_dbs + + # NameRes-only fields. + if "nameres_version" in raw: + trimmed["nameres_version"] = sanitize(raw["nameres_version"], 50) + queries = raw.get("recent_queries") + if isinstance(queries, dict): + latencies = { + out_key: _trimmed_float(queries.get(in_key)) + for out_key, in_key in [ + ("mean_ms", "mean_time_ms"), + ("p50_ms", "p50_ms"), + ("p95_ms", "p95_ms"), + ("p99_ms", "p99_ms"), + ] + } + trimmed["recent_queries"] = { + key: value for key, value in latencies.items() if value is not None + } + solr = raw.get("solr") + if isinstance(solr, dict): + trimmed_solr = {} + num_docs = _trimmed_int(solr.get("numDocs")) + if num_docs is not None: + trimmed_solr["numDocs"] = num_docs + if "size" in solr: + trimmed_solr["size"] = sanitize(solr["size"], 20) + trimmed["solr"] = trimmed_solr + return trimmed + + +def fetch_status(base_url): + """GET {base_url}status and whitelist it. Errors become just a type name — + no message text, since it could echo the URL or response body.""" + try: + response = requests.get( + base_url.rstrip("/") + "/status", timeout=STATUS_TIMEOUT_SECONDS + ) + response.raise_for_status() + return trim_status(response.json()) + except Exception as e: + logger.warning("Could not fetch status from %r: %s", base_url, type(e).__name__) + return {"error": type(e).__name__} + + +def read_raw_records(raw_dir): + """Read every *.jsonl file in raw_dir. Bad lines are logged and skipped — + one corrupt line must not sink the whole report.""" + records = [] + for path in sorted(Path(raw_dir).glob("*.jsonl")): + with open(path, encoding="utf-8") as f: + for line_number, line in enumerate(f, start=1): + line = line.strip() + if not line: + continue + try: + record = json.loads(line) + if not isinstance(record, dict) or "id" not in record: + raise ValueError("not a record object") + records.append(record) + except (json.JSONDecodeError, ValueError) as e: + logger.warning("Skipping bad line %s:%d: %s", path, line_number, e) + return records + + +def build_results(records, targets, allowlist): + """ + Aggregate raw records into the report's results dict, plus per-target + outcome counts and whether the GitHub issue tests produced any results. + """ + # (key, target) -> list of records + by_test = {} + for record in records: + key, target, rest = parse_nodeid(record["id"], targets) + by_test.setdefault((key, target, rest), []).append(record) + + results = {} + counts = { + target: {outcome: 0 for outcome in OUTCOME_SEVERITY} + for target in list(targets) + ["?"] + } + github_issues_ran = False + + for (key, target, rest), test_records in by_test.items(): + outcome = max( + (classify_record(r) for r in test_records), + key=lambda o: OUTCOME_SEVERITY[o], + ) + counts[target][outcome] += 1 + + result = results.setdefault(key, {"outcomes": {}}) + cell = {"o": outcome} + # Blocklist messages are withheld unconditionally, before any cell is + # built — the blocklist sheet may not be public, and the messages + # interpolate its entries. + if outcome in OUTCOMES_WITH_MESSAGES and "test_blocklist.py" not in key: + messages = [r["msg"] for r in test_records if r.get("msg")] + if messages: + cell["msg"] = sanitize("\n---\n".join(messages)) + result["outcomes"][target] = cell + + if "kind" not in result: + _annotate_result(result, key, rest, test_records, allowlist) + if key.startswith("github_issues/"): + github_issues_ran = True + + return results, counts, github_issues_ran + + +def _annotate_result(result, key, rest, test_records, allowlist): + """Attach kind and validated metadata/link parts to one result.""" + if "test_blocklist.py" in key: + # The blocklist sheet may not be public: no metadata, no links. + # Messages are already withheld in build_results. + result["kind"] = "blocklist" + return + + if key.startswith("github_issues/"): + issue = validate_issue_id(rest, allowlist) + if issue: + result["kind"] = "issue" + result["issue"] = issue + return + result["kind"] = "other" + return + + row_match = re.search(r":row=([0-9]+)$", rest) + if "_from_gsheet.py" in key and row_match: + result["kind"] = "gsheet" + result["row"] = int(row_match.group(1)) + props = {} + for record in test_records: + props.update(record.get("props") or {}) + for prop in ("category", "source", "query_id", "query_label"): + if props.get(prop): + result[prop] = sanitize(props[prop], 200) + source_url = validate_source_url(props.get("source_url"), allowlist) + if source_url: + result["source_url"] = source_url + return + + result["kind"] = "other" + + +def build_report(results, counts, github_issues_ran, targets, allowlist, config): + now = datetime.datetime.now(datetime.timezone.utc) + target_sections = {} + for target in targets: + section = config[target] + nodenorm_url = section.get("NodeNormURL") + nameres_url = section.get("NameResURL") + target_counts = counts[target] + total = sum(target_counts.values()) + target_sections[target] = { + "nodenorm_url": nodenorm_url, + "nameres_url": nameres_url, + "nodenorm_status": fetch_status(nodenorm_url), + "nameres_status": fetch_status(nameres_url), + "counts": target_counts, + "unreachable": total == 0 or target_counts["error"] == total, + } + report = { + "generated_at": now.isoformat(timespec="seconds"), + "run": { + "github_run_id": os.environ.get("GITHUB_RUN_ID"), + "git_sha": os.environ.get("GITHUB_SHA"), + }, + "repos_allowlist": allowlist, + "github_issues_ran": github_issues_ran, + "targets": target_sections, + "results": results, + } + # Tests without a recognizable target only appear if something ran them. + if any(counts["?"].values()): + report["unattributed_counts"] = counts["?"] + return report + + +def build_history_line(report): + """The compact per-run summary appended to history.jsonl.""" + line = { + "date": report["generated_at"][:10], + "run_id": report["run"]["github_run_id"], + "targets": {}, + } + for target, section in report["targets"].items(): + nodenorm_status = section["nodenorm_status"] + nameres_status = section["nameres_status"] + eq_db = nodenorm_status.get("databases", {}).get("eq_id_to_id_db", {}) + solr = nameres_status.get("solr", {}) + line["targets"][target] = { + "babel_version": nodenorm_status.get("babel_version"), + "nameres_version": nameres_status.get("nameres_version"), + "biolink_version": nodenorm_status.get("biolink_version"), + "nn_eq_records": eq_db.get("count"), + "solr_docs": solr.get("numDocs"), + "solr_size": solr.get("size"), + "p95_ms": nameres_status.get("recent_queries", {}).get("p95_ms"), + "counts": section["counts"], + } + return line + + +def append_history(history_in_path, history_line): + """Return the new history.jsonl content: prior lines verbatim (bad lines + dropped so the file can never poison future runs), new line appended.""" + lines = [] + if history_in_path and os.path.isfile(history_in_path): + with open(history_in_path, encoding="utf-8") as f: + for line in f: + line = line.strip() + if not line: + continue + try: + json.loads(line) + except json.JSONDecodeError: + logger.warning("Dropping bad history line: %.80r", line) + continue + lines.append(line) + lines.append(json.dumps(history_line)) + return "\n".join(lines) + "\n" + + +def main(argv=None): + logging.basicConfig(level=logging.INFO) + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument( + "--raw-dir", + required=True, + help="Directory of *.jsonl files from pytest --report-jsonl", + ) + parser.add_argument( + "--targets-ini", required=True, help="Path to tests/targets.ini" + ) + parser.add_argument( + "--history-in", + default=None, + help="Previous history.jsonl to append to (may be missing)", + ) + parser.add_argument( + "--out-dir", + required=True, + help="Directory to write report.json and history.jsonl into", + ) + args = parser.parse_args(argv) + + targets, allowlist, config = read_targets(args.targets_ini) + records = read_raw_records(args.raw_dir) + logger.info("Read %d raw records for targets %s", len(records), targets) + results, counts, github_issues_ran = build_results(records, targets, allowlist) + report = build_report( + results, counts, github_issues_ran, targets, allowlist, config + ) + + out_dir = Path(args.out_dir) + out_dir.mkdir(parents=True, exist_ok=True) + with open(out_dir / "report.json", "w", encoding="utf-8") as f: + json.dump(report, f, separators=(",", ":")) + with open(out_dir / "history.jsonl", "w", encoding="utf-8") as f: + f.write(append_history(args.history_in, build_history_line(report))) + logger.info( + "Wrote %s (%d results) and %s", + out_dir / "report.json", + len(results), + out_dir / "history.jsonl", + ) + return 0 + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/tests/unit/__init__.py b/tests/unit/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/unit/test_generate_report.py b/tests/unit/test_generate_report.py new file mode 100644 index 0000000..158e847 --- /dev/null +++ b/tests/unit/test_generate_report.py @@ -0,0 +1,344 @@ +"""Unit tests for the dashboard report generator. No network: everything is fed +literal JSONL records and hostile inline payloads.""" + +import configparser +import inspect +import json + +import pytest + +from src.babel_validation.tools import generate_report +from src.babel_validation.tools.generate_report import ( + append_history, + build_results, + classify_record, + parse_nodeid, + sanitize, + split_target, + trim_status, + validate_issue_id, + validate_source_url, +) + +pytestmark = pytest.mark.unit + +TARGETS = ["prod", "test", "ci", "ci-es", "dev", "exp"] +ALLOWLIST = ["ncatstranslator/babel", "translatorsri/babel-validation"] + + +def _record( + nodeid, outcome="passed", when="call", wasxfail=False, msg=None, props=None +): + return { + "id": nodeid, + "when": when, + "outcome": outcome, + "wasxfail": wasxfail, + "duration": 0.1, + "props": props or {}, + "msg": msg, + } + + +class TestTargetExtraction: + def test_hyphenated_target_matches_longest_first(self): + assert split_target("ci-es-foo:row=1", TARGETS) == ("ci-es", "foo:row=1") + assert split_target("ci-foo", TARGETS) == ("ci", "foo") + + def test_target_as_suffix(self): + # Current pytest puts the module-level parametrize first, target last. + assert split_target("test_label:row=251-prod", TARGETS) == ( + "prod", + "test_label:row=251", + ) + assert split_target("test_label:row=251-ci-es", TARGETS) == ( + "ci-es", + "test_label:row=251", + ) + + def test_unknown_target(self): + assert split_target("staging-foo", TARGETS) == (None, "staging-foo") + + def test_parse_nodeid_strips_target_from_key(self): + key, target, rest = parse_nodeid( + "nodenorm/test_nodenorm_from_gsheet.py::test_normalization" + "[dev-test_nodenorm_from_gsheet.test_row:row=131]", + TARGETS, + ) + assert target == "dev" + assert rest == "test_nodenorm_from_gsheet.test_row:row=131" + assert key == ( + "nodenorm/test_nodenorm_from_gsheet.py::test_normalization" + "[test_nodenorm_from_gsheet.test_row:row=131]" + ) + + def test_parse_nodeid_without_params_goes_to_unknown_bucket(self): + key, target, rest = parse_nodeid("tests/test_cache_dir.py::test_mode", TARGETS) + assert (key, target) == ("tests/test_cache_dir.py::test_mode", "?") + + def test_parse_nodeid_unknown_target_does_not_crash(self): + key, target, rest = parse_nodeid("x.py::t[staging-row=1]", TARGETS) + assert target == "?" + assert key == "x.py::t[staging-row=1]" + + +class TestClassification: + @pytest.mark.parametrize( + "outcome,when,wasxfail,msg,expected", + [ + ("passed", "call", False, None, "passed"), + ("failed", "call", False, "AssertionError: nope", "failed"), + ("skipped", "call", True, "reason", "xfailed"), + ("passed", "call", True, None, "xpassed"), # imperative pytest.xfail + ("failed", "call", False, "[XPASS(strict)] issue is open", "xpassed"), + ("skipped", "setup", False, "category filter", "skipped"), + ("failed", "setup", False, "fixture blew up", "error"), + ("failed", "teardown", False, "cleanup blew up", "error"), + ], + ) + def test_single_record(self, outcome, when, wasxfail, msg, expected): + record = _record("x.py::t[dev-p]", outcome, when, wasxfail, msg) + assert classify_record(record) == expected + + def test_subtest_aggregation_worst_wins_and_messages_join(self): + nodeid = "github_issues/test_github_issues.py::test_github_issue[dev-NCATSTranslator/Babel#12]" + records = [ + _record(nodeid, "passed"), + _record(nodeid, "failed", msg="subtest one failed"), + _record(nodeid, "passed"), + ] + results, counts, ran = build_results(records, TARGETS, ALLOWLIST) + key = "github_issues/test_github_issues.py::test_github_issue[NCATSTranslator/Babel#12]" + assert results[key]["outcomes"]["dev"]["o"] == "failed" + assert "subtest one failed" in results[key]["outcomes"]["dev"]["msg"] + assert counts["dev"]["failed"] == 1 + assert sum(counts["dev"].values()) == 1 # aggregated, not three tests + assert ran is True + + +class TestLinkValidation: + def test_issue_id_allowlisted(self): + assert ( + validate_issue_id("NCATSTranslator/Babel#12", ALLOWLIST) + == "NCATSTranslator/Babel#12" + ) + + @pytest.mark.parametrize( + "issue_id", + [ + "evil/repo#1", + "NCATSTranslator/Babel#notanumber", + "NCATSTranslator/Babel/extra#1", + "../etc#1", + "", + None, + ], + ) + def test_issue_id_rejected(self, issue_id): + assert validate_issue_id(issue_id, ALLOWLIST) is None + + def test_source_url_allowlisted(self): + url = "https://github.com/NCATSTranslator/Babel/issues/12" + assert validate_source_url(url, ALLOWLIST) == url + + @pytest.mark.parametrize( + "url", + [ + "https://github.com.evil.example/NCATSTranslator/Babel/issues/12", + "https://github.com/evil/repo/issues/1", + "https://github.com/NCATSTranslator", + "http://github.com/NCATSTranslator/Babel/issues/12", + "javascript:alert(1)", + "", + None, + ], + ) + def test_source_url_rejected(self, url): + assert validate_source_url(url, ALLOWLIST) is None + + +class TestResultAnnotation: + def test_gsheet_row_and_props(self): + nodeid = ( + "nodenorm/test_nodenorm_from_gsheet.py::test_normalization" + "[dev-test_nodenorm_from_gsheet.test_row:row=131]" + ) + records = [ + _record( + nodeid, + "failed", + msg="AssertionError: wrong id", + props={ + "category": "Diseases", + "source": "hetio", + "source_url": "https://github.com/NCATSTranslator/Babel/issues/12", + "query_id": "MONDO:0005148", + "query_label": "type 2 diabetes", + }, + ) + ] + results, _, _ = build_results(records, TARGETS, ALLOWLIST) + (result,) = results.values() + assert result["kind"] == "gsheet" + assert result["row"] == 131 + assert result["category"] == "Diseases" + assert result["query_id"] == "MONDO:0005148" + assert ( + result["source_url"] == "https://github.com/NCATSTranslator/Babel/issues/12" + ) + + def test_gsheet_bad_source_url_omitted(self): + nodeid = "nameres/test_nameres_from_gsheet.py::test_label[prod-x:row=5]" + records = [ + _record( + nodeid, "failed", msg="m", props={"source_url": "https://evil.example/"} + ) + ] + results, _, _ = build_results(records, TARGETS, ALLOWLIST) + (result,) = results.values() + assert "source_url" not in result + + def test_issue_not_in_allowlist_becomes_other_without_link(self): + nodeid = ( + "github_issues/test_github_issues.py::test_github_issue[dev-evil/repo#1]" + ) + results, _, ran = build_results([_record(nodeid, "passed")], TARGETS, ALLOWLIST) + (result,) = results.values() + assert result["kind"] == "other" + assert "issue" not in result + assert ran is True # the suite ran even if the id was rejected + + def test_no_issue_records_means_not_ran(self): + records = [_record("nodenorm/test_x.py::t[dev-p]", "passed")] + _, _, ran = build_results(records, TARGETS, ALLOWLIST) + assert ran is False + + def test_blocklist_redacted_for_every_target(self): + base = "nameres/test_blocklist.py::test_blocklist_entry" + records = [ + _record(f"{base}[dev-blocklist_entry0]", "failed", msg="secret entry text"), + _record( + f"{base}[prod-blocklist_entry0]", "failed", msg="secret entry text" + ), + ] + results, _, _ = build_results(records, TARGETS, ALLOWLIST) + (result,) = results.values() + assert result["kind"] == "blocklist" + assert "secret" not in json.dumps(results) + for cell in result["outcomes"].values(): + assert "msg" not in cell + + +class TestNoSheetLeak: + def test_report_never_contains_the_sheet_id_or_a_sheet_link(self, monkeypatch): + # The public report must not let casual observers find the Google Sheet. + from src.babel_validation.sources.google_sheets.google_sheet_test_cases import ( + GoogleSheetTestCases, + ) + + sheet_id = ( + inspect.signature(GoogleSheetTestCases.__init__) + .parameters["google_sheet_id"] + .default + ) + monkeypatch.setattr( + generate_report, "fetch_status", lambda url: {"status": "ok"} + ) + records = [ + _record( + "nodenorm/test_nodenorm_from_gsheet.py::test_normalization[dev-x:row=42]", + "failed", + msg="boom", + props={"category": "Diseases", "query_id": "MONDO:1"}, + ) + ] + results, counts, ran = build_results(records, TARGETS, ALLOWLIST) + config = configparser.ConfigParser() + config.read_string( + "[dev]\nNodeNormURL = https://nn.example/\nNameResURL = https://nr.example/\n" + ) + report = generate_report.build_report( + results, counts, ran, ["dev"], ALLOWLIST, config + ) + dumped = json.dumps(report) + assert sheet_id not in dumped + assert "docs.google.com" not in dumped + + +class TestSanitize: + def test_truncates(self): + assert sanitize("a" * 1000).startswith("a" * 500) + assert sanitize("a" * 1000).endswith("[truncated]") + + def test_escapes_ansi_and_controls(self): + hostile = "red \x1b[31malert\x07 ‮done" + cleaned = sanitize(hostile) + assert "\x1b" not in cleaned and "\x07" not in cleaned and "‮" not in cleaned + assert "\\x1b" in cleaned # escaped, visibly, not silently stripped + + def test_keeps_newlines_and_tabs(self): + assert sanitize("a\nb\tc") == "a\nb\tc" + + def test_none(self): + assert sanitize(None) is None + + +class TestTrimStatus: + def test_hostile_payload(self): + hostile = { + "status": "ok\x1b[2Jcleared", + "babel_version": "x" * 5000, + "babel_version_url": "https://evil.example/NCATSTranslator/", + "biolink_model": {"tag": "v4", "download_url": "https://evil.example/"}, + "databases": { + "eq_id_to_id_db": { + "count": "12345", + "used_memory_rss_human": "9G" * 50, + }, + "weird": "not a dict", + }, + "recent_queries": {"mean_time_ms": "NaNish", "p95_ms": "12.5"}, + "solr": {"numDocs": 7, "size": "1 GB", "jvm": {"secrets": True}}, + "extra_key": {"anything": "dropped"}, + } + trimmed = trim_status(hostile) + assert "extra_key" not in trimmed + assert "babel_version_url" not in trimmed # not the NCATSTranslator org + assert "\x1b" not in trimmed["status"] + assert len(trimmed["babel_version"]) < 100 + assert trimmed["databases"]["eq_id_to_id_db"]["count"] == 12345 + assert ( + len(trimmed["databases"]["eq_id_to_id_db"]["used_memory_rss_human"]) <= 32 + ) + assert "weird" not in trimmed["databases"] + assert trimmed["recent_queries"] == {"p95_ms": 12.5} + assert trimmed["solr"] == {"numDocs": 7, "size": "1 GB"} + assert trimmed["biolink_version"] == "v4" + + def test_valid_babel_version_url_kept(self): + trimmed = trim_status( + {"babel_version_url": "https://github.com/ncatstranslator/Babel/blob/x.md"} + ) + assert trimmed["babel_version_url"].startswith("https://github.com/") + + def test_not_a_dict(self): + assert trim_status(["nope"]) == {"error": "InvalidStatus"} + + +class TestHistory: + def test_append_keeps_old_lines_verbatim(self, tmp_path): + old = tmp_path / "history.jsonl" + line1 = json.dumps({"date": "2026-08-24", "targets": {}}) + line2 = json.dumps({"date": "2026-08-25", "targets": {}}) + old.write_text(f"{line1}\n{line2}\nnot json\n", encoding="utf-8") + new_line = {"date": "2026-08-26", "targets": {}} + content = append_history(str(old), new_line) + lines = content.strip().split("\n") + assert lines[0] == line1 + assert lines[1] == line2 + assert json.loads(lines[2]) == new_line + assert len(lines) == 3 # the bad line is dropped + + def test_missing_history_file(self): + content = append_history("/nonexistent/history.jsonl", {"date": "2026-08-26"}) + assert content == json.dumps({"date": "2026-08-26"}) + "\n" From 9605a26c9c762ed462dadc721dc5cbe2b53f99f7 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Wed, 26 Aug 2026 19:12:12 -0400 Subject: [PATCH 03/60] Replace the website's superseded tools with a test-report dashboard The Prefix Comparator has moved into Babel (NCATSTranslator/Babel#889) and Autocomplete is moving into Babel Explorer (TranslatorSRI/babel-explorer#7), so both pages are gone, along with the never-deployed website-vue3-vite app that duplicated the Google Sheet test logic in the browser. The Astro site now renders data/report.json and data/history.jsonl (produced by generate_report): per-environment status cards (Babel/NameRes versions, database sizes, NameRes p95 latency, outcome counts), a tests-by-environment matrix defaulting to 'interesting only' rows (failing, unexpectedly passing, or differing across environments) with links out to the Google Sheet row, the GitHub issue, direct NodeNorm/NameRes queries and Babel Explorer, and a trends page listing one summary row per daily run. All report text is rendered via {{ }} interpolation only, and links are constructed from generator-validated parts, since the report is derived from untrusted input. Dependencies used only by the deleted tools are dropped. Co-Authored-By: Claude Fable 5 --- website-vue3-vite/.eslintrc.cjs | 23 - website-vue3-vite/.gitignore | 28 - website-vue3-vite/.prettierrc.json | 1 - website-vue3-vite/.vscode/extensions.json | 3 - website-vue3-vite/README.md | 48 - website-vue3-vite/cypress.config.js | 8 - website-vue3-vite/cypress/e2e/example.cy.js | 8 - website-vue3-vite/cypress/e2e/jsconfig.json | 8 - .../cypress/fixtures/example.json | 5 - website-vue3-vite/cypress/support/commands.js | 25 - website-vue3-vite/cypress/support/e2e.js | 20 - website-vue3-vite/index.html | 13 - website-vue3-vite/package-lock.json | 8209 ----------------- website-vue3-vite/package.json | 39 - website-vue3-vite/public/favicon.ico | Bin 4286 -> 0 bytes website-vue3-vite/src/App.vue | 8 - website-vue3-vite/src/assets/base.css | 75 - website-vue3-vite/src/assets/logo.svg | 1 - website-vue3-vite/src/assets/main.css | 6 - .../src/components/HelloWorld.vue | 43 - .../src/components/TestResult.vue | 101 - .../src/components/TextWithURLs.vue | 28 - 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website/package-lock.json | 3081 +------ website/package.json | 6 - .../prefix_report-2024oct24.json | 1388 --- .../prefix_report-dev-2025jan23.json | 1428 --- website/src/components/Autocomplete.vue | 254 - website/src/components/Card.astro | 61 - website/src/components/Dashboard.vue | 332 + website/src/components/PrefixComparator.vue | 350 - website/src/components/Trends.vue | 94 + website/src/components/bootstrap/BCard.vue | 20 - website/src/env.d.ts | 8 + website/src/pages/autocomplete/index.astro | 34 - website/src/pages/index.astro | 39 +- .../src/pages/prefix-comparator/index.astro | 18 - website/src/pages/trends/index.astro | 16 + 59 files changed, 586 insertions(+), 16921 deletions(-) delete mode 100644 website-vue3-vite/.eslintrc.cjs delete mode 100644 website-vue3-vite/.gitignore delete mode 100644 website-vue3-vite/.prettierrc.json delete mode 100644 website-vue3-vite/.vscode/extensions.json delete mode 100644 website-vue3-vite/README.md delete mode 100644 website-vue3-vite/cypress.config.js delete mode 100644 website-vue3-vite/cypress/e2e/example.cy.js delete mode 100644 website-vue3-vite/cypress/e2e/jsconfig.json delete mode 100644 website-vue3-vite/cypress/fixtures/example.json delete mode 100644 website-vue3-vite/cypress/support/commands.js delete mode 100644 website-vue3-vite/cypress/support/e2e.js delete mode 100644 website-vue3-vite/index.html delete mode 100644 website-vue3-vite/package-lock.json delete mode 100644 website-vue3-vite/package.json delete mode 100644 website-vue3-vite/public/favicon.ico delete mode 100644 website-vue3-vite/src/App.vue delete mode 100644 website-vue3-vite/src/assets/base.css delete mode 100644 website-vue3-vite/src/assets/logo.svg delete mode 100644 website-vue3-vite/src/assets/main.css delete mode 100644 website-vue3-vite/src/components/HelloWorld.vue delete mode 100644 website-vue3-vite/src/components/TestResult.vue delete mode 100644 website-vue3-vite/src/components/TextWithURLs.vue delete mode 100644 website-vue3-vite/src/components/TheWelcome.vue delete mode 100644 website-vue3-vite/src/components/WelcomeItem.vue delete mode 100644 website-vue3-vite/src/components/__tests__/HelloWorld.spec.js delete mode 100644 website-vue3-vite/src/components/icons/IconCommunity.vue delete mode 100644 website-vue3-vite/src/components/icons/IconDocumentation.vue delete mode 100644 website-vue3-vite/src/components/icons/IconEcosystem.vue delete mode 100644 website-vue3-vite/src/components/icons/IconSupport.vue delete mode 100644 website-vue3-vite/src/components/icons/IconTooling.vue delete mode 100644 website-vue3-vite/src/main.js delete mode 100644 website-vue3-vite/src/models/NameResTest.js delete mode 100644 website-vue3-vite/src/models/NodeNormTest.js delete mode 100644 website-vue3-vite/src/models/Test.js delete mode 100644 website-vue3-vite/src/models/TestResult.js delete mode 100644 website-vue3-vite/src/models/helpers.js delete mode 100644 website-vue3-vite/src/router/index.js delete mode 100644 website-vue3-vite/src/views/AboutView.vue delete mode 100644 website-vue3-vite/src/views/Autocomplete.vue delete mode 100644 website-vue3-vite/src/views/AutocompleteBulkValidator.vue delete mode 100644 website-vue3-vite/src/views/HomeView.vue delete mode 100644 website-vue3-vite/src/views/NameResValidator.vue delete mode 100644 website-vue3-vite/src/views/NodeNormValidator.vue delete mode 100644 website-vue3-vite/vite.config.js delete mode 100644 website/public/prefix_reports/prefix_report-2024oct24.json delete mode 100644 website/public/prefix_reports/prefix_report-dev-2025jan23.json delete mode 100644 website/src/components/Autocomplete.vue delete mode 100644 website/src/components/Card.astro create mode 100644 website/src/components/Dashboard.vue delete mode 100644 website/src/components/PrefixComparator.vue create mode 100644 website/src/components/Trends.vue delete mode 100644 website/src/components/bootstrap/BCard.vue delete mode 100644 website/src/pages/autocomplete/index.astro delete mode 100644 website/src/pages/prefix-comparator/index.astro create mode 100644 website/src/pages/trends/index.astro diff --git a/website-vue3-vite/.eslintrc.cjs b/website-vue3-vite/.eslintrc.cjs deleted file mode 100644 index b9d9d6a..0000000 --- a/website-vue3-vite/.eslintrc.cjs +++ /dev/null @@ -1,23 +0,0 @@ -/* eslint-env node */ -require("@rushstack/eslint-patch/modern-module-resolution"); - -module.exports = { - root: true, - env: { - node: true, - }, - extends: [ - "plugin:vue/vue3-essential", - "eslint:recommended", - "@vue/eslint-config-prettier", - ], - overrides: [ - { - files: ["cypress/e2e/**.{cy,spec}.{js,ts,jsx,tsx}"], - extends: ["plugin:cypress/recommended"], - }, - ], - parserOptions: { - ecmaVersion: "latest", - }, -}; diff --git a/website-vue3-vite/.gitignore b/website-vue3-vite/.gitignore deleted file mode 100644 index 38adffa..0000000 --- a/website-vue3-vite/.gitignore +++ /dev/null @@ -1,28 +0,0 @@ -# Logs -logs -*.log -npm-debug.log* -yarn-debug.log* -yarn-error.log* -pnpm-debug.log* -lerna-debug.log* - -node_modules -.DS_Store -dist -dist-ssr -coverage -*.local - -/cypress/videos/ -/cypress/screenshots/ - -# Editor directories and files -.vscode/* -!.vscode/extensions.json -.idea -*.suo -*.ntvs* -*.njsproj -*.sln -*.sw? diff --git a/website-vue3-vite/.prettierrc.json b/website-vue3-vite/.prettierrc.json deleted file mode 100644 index 9e26dfe..0000000 --- a/website-vue3-vite/.prettierrc.json +++ /dev/null @@ -1 +0,0 @@ -{} \ No newline at end of file diff --git a/website-vue3-vite/.vscode/extensions.json b/website-vue3-vite/.vscode/extensions.json deleted file mode 100644 index c0a6e5a..0000000 --- a/website-vue3-vite/.vscode/extensions.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "recommendations": ["Vue.volar", "Vue.vscode-typescript-vue-plugin"] -} diff --git a/website-vue3-vite/README.md b/website-vue3-vite/README.md deleted file mode 100644 index 7ad1d77..0000000 --- a/website-vue3-vite/README.md +++ /dev/null @@ -1,48 +0,0 @@ -# website - -This template should help get you started developing with Vue 3 in Vite. - -## Recommended IDE Setup - -[VSCode](https://code.visualstudio.com/) + [Volar](https://marketplace.visualstudio.com/items?itemName=Vue.volar) (and disable Vetur) + [TypeScript Vue Plugin (Volar)](https://marketplace.visualstudio.com/items?itemName=Vue.vscode-typescript-vue-plugin). - -## Customize configuration - -See [Vite Configuration Reference](https://vitejs.dev/config/). - -## Project Setup - -```sh -npm install -``` - -### Compile and Hot-Reload for Development - -```sh -npm run dev -``` - -### Compile and Minify for Production - -```sh -npm run build -``` - -### Run Unit Tests with [Vitest](https://vitest.dev/) - -```sh -npm run test:unit -``` - -### Run End-to-End Tests with [Cypress](https://www.cypress.io/) - -```sh -npm run build -npm run test:e2e # or `npm run test:e2e:ci` for headless testing -``` - -### Lint with [ESLint](https://eslint.org/) - -```sh -npm run lint -``` diff --git a/website-vue3-vite/cypress.config.js b/website-vue3-vite/cypress.config.js deleted file mode 100644 index 5957bf7..0000000 --- a/website-vue3-vite/cypress.config.js +++ /dev/null @@ -1,8 +0,0 @@ -const { defineConfig } = require("cypress"); - -module.exports = defineConfig({ - e2e: { - specPattern: "cypress/e2e/**/*.{cy,spec}.{js,jsx,ts,tsx}", - baseUrl: "http://localhost:4173", - }, -}); diff --git a/website-vue3-vite/cypress/e2e/example.cy.js b/website-vue3-vite/cypress/e2e/example.cy.js deleted file mode 100644 index 3130c00..0000000 --- a/website-vue3-vite/cypress/e2e/example.cy.js +++ /dev/null @@ -1,8 +0,0 @@ -// https://docs.cypress.io/api/introduction/api.html - -describe("My First Test", () => { - it("visits the app root url", () => { - cy.visit("/"); - cy.contains("h1", "You did it!"); - }); -}); diff --git a/website-vue3-vite/cypress/e2e/jsconfig.json b/website-vue3-vite/cypress/e2e/jsconfig.json deleted file mode 100644 index c790a70..0000000 --- a/website-vue3-vite/cypress/e2e/jsconfig.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "compilerOptions": { - "target": "es5", - "lib": ["es5", "dom"], - "types": ["cypress"] - }, - "include": ["./**/*", "../support/**/*"] -} diff --git a/website-vue3-vite/cypress/fixtures/example.json b/website-vue3-vite/cypress/fixtures/example.json deleted file mode 100644 index 02e4254..0000000 --- a/website-vue3-vite/cypress/fixtures/example.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "name": "Using fixtures to represent data", - "email": "hello@cypress.io", - "body": "Fixtures are a great way to mock data for responses to routes" -} diff --git a/website-vue3-vite/cypress/support/commands.js b/website-vue3-vite/cypress/support/commands.js deleted file mode 100644 index 119ab03..0000000 --- a/website-vue3-vite/cypress/support/commands.js +++ /dev/null @@ -1,25 +0,0 @@ -// *********************************************** -// This example commands.js shows you how to -// create various custom commands and overwrite -// existing commands. -// -// For more comprehensive examples of custom -// commands please read more here: -// https://on.cypress.io/custom-commands -// *********************************************** -// -// -// -- This is a parent command -- -// Cypress.Commands.add('login', (email, password) => { ... }) -// -// -// -- This is a child command -- -// Cypress.Commands.add('drag', { prevSubject: 'element'}, (subject, options) => { ... }) -// -// -// -- This is a dual command -- -// Cypress.Commands.add('dismiss', { prevSubject: 'optional'}, (subject, options) => { ... }) -// -// -// -- This will overwrite an existing command -- -// Cypress.Commands.overwrite('visit', (originalFn, url, options) => { ... }) diff --git a/website-vue3-vite/cypress/support/e2e.js b/website-vue3-vite/cypress/support/e2e.js deleted file mode 100644 index d076cec..0000000 --- a/website-vue3-vite/cypress/support/e2e.js +++ /dev/null @@ -1,20 +0,0 @@ -// *********************************************************** -// This example support/index.js is processed and -// loaded automatically before your test files. -// -// This is a great place to put global configuration and -// behavior that modifies Cypress. -// -// You can change the location of this file or turn off -// automatically serving support files with the -// 'supportFile' configuration option. -// -// You can read more here: -// https://on.cypress.io/configuration -// *********************************************************** - -// Import commands.js using ES2015 syntax: -import "./commands"; - -// Alternatively you can use CommonJS syntax: -// require('./commands') diff --git a/website-vue3-vite/index.html b/website-vue3-vite/index.html deleted file mode 100644 index ff54253..0000000 --- a/website-vue3-vite/index.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - Babel Validation - - -
- - - diff --git a/website-vue3-vite/package-lock.json b/website-vue3-vite/package-lock.json deleted file mode 100644 index c280acf..0000000 --- a/website-vue3-vite/package-lock.json +++ /dev/null @@ -1,8209 +0,0 @@ -{ - "name": "website", - "version": "0.0.0", - "lockfileVersion": 2, - "requires": true, - "packages": { - "": { - "name": "website", - "version": "0.0.0", - "dependencies": { - "@popperjs/core": "^2.11.6", - "bootstrap": "^5.2.1", - "bootstrap-vue-3": "^0.3.2", - "bottleneck": "^2.19.5", - "csv-stringify": "^6.4.4", - "file-saver": "^2.0.5", - "papaparse": "^5.3.2", - "vue": "^3.2.38", - "vue-router": "^4.1.5" - }, - "devDependencies": { - "@rushstack/eslint-patch": "^1.1.4", - "@vitejs/plugin-vue": "^3.0.3", - "@vue/eslint-config-prettier": "^7.0.0", - "@vue/test-utils": "^2.0.2", - "cypress": "^10.7.0", - "eslint": "^8.22.0", - "eslint-plugin-cypress": "^2.12.1", - "eslint-plugin-vue": "^9.3.0", - "jsdom": "^20.0.0", - "prettier": "^2.7.1", - "start-server-and-test": "^1.14.0", - 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"test:e2e:ci": "start-server-and-test preview http://localhost:4173/ 'cypress run --e2e'", - "lint": "eslint . --ext .vue,.js,.jsx,.cjs,.mjs --fix --ignore-path .gitignore" - }, - "dependencies": { - "@popperjs/core": "^2.11.6", - "bootstrap": "^5.2.1", - "bootstrap-vue-3": "^0.3.2", - "bottleneck": "^2.19.5", - "csv-stringify": "^6.4.4", - "file-saver": "^2.0.5", - "papaparse": "^5.3.2", - "vue": "^3.2.38", - "vue-router": "^4.1.5" - }, - "devDependencies": { - "@rushstack/eslint-patch": "^1.1.4", - "@vitejs/plugin-vue": "^3.0.3", - "@vue/eslint-config-prettier": "^7.0.0", - "@vue/test-utils": "^2.0.2", - "cypress": "^10.7.0", - "eslint": "^8.22.0", - "eslint-plugin-cypress": "^2.12.1", - "eslint-plugin-vue": "^9.3.0", - "jsdom": "^20.0.0", - "prettier": "^2.7.1", - "start-server-and-test": "^1.14.0", - "vite": "^3.0.9", - "vitest": "^0.23.0" - } -} diff --git a/website-vue3-vite/public/favicon.ico b/website-vue3-vite/public/favicon.ico deleted file mode 100644 index df36fcfb72584e00488330b560ebcf34a41c64c2..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4286 zcmds*O-Phc6o&64GDVCEQHxsW(p4>LW*W<827=Unuo8sGpRux(DN@jWP-e29Wl%wj zY84_aq9}^Am9-cWTD5GGEo#+5Fi2wX_P*bo+xO!)p*7B;iKlbFd(U~_d(U?#hLj56 zPhFkj-|A6~Qk#@g^#D^U0XT1cu=c-vu1+SElX9NR;kzAUV(q0|dl0|%h|dI$%VICy zJnu2^L*Te9JrJMGh%-P79CL0}dq92RGU6gI{v2~|)p}sG5x0U*z<8U;Ij*hB9z?ei z@g6Xq-pDoPl=MANPiR7%172VA%r)kevtV-_5H*QJKFmd;8yA$98zCxBZYXTNZ#QFk2(TX0;Y2dt&WitL#$96|gJY=3xX zpCoi|YNzgO3R`f@IiEeSmKrPSf#h#Qd<$%Ej^RIeeYfsxhPMOG`S`Pz8q``=511zm zAm)MX5AV^5xIWPyEu7u>qYs?pn$I4nL9J!=K=SGlKLXpE<5x+2cDTXq?brj?n6sp= zphe9;_JHf40^9~}9i08r{XM$7HB!`{Ys~TK0kx<}ZQng`UPvH*11|q7&l9?@FQz;8 zx!=3<4seY*%=OlbCbcae?5^V_}*K>Uo6ZWV8mTyE^B=DKy7-sdLYkR5Z?paTgK-zyIkKjIcpyO z{+uIt&YSa_$QnN_@t~L014dyK(fOOo+W*MIxbA6Ndgr=Y!f#Tokqv}n<7-9qfHkc3 z=>a|HWqcX8fzQCT=dqVbogRq!-S>H%yA{1w#2Pn;=e>JiEj7Hl;zdt-2f+j2%DeVD zsW0Ab)ZK@0cIW%W7z}H{&~yGhn~D;aiP4=;m-HCo`BEI+Kd6 z={Xwx{TKxD#iCLfl2vQGDitKtN>z|-AdCN|$jTFDg0m3O`WLD4_s#$S diff --git a/website-vue3-vite/src/App.vue b/website-vue3-vite/src/App.vue deleted file mode 100644 index 879d575..0000000 --- a/website-vue3-vite/src/App.vue +++ /dev/null @@ -1,8 +0,0 @@ - - - diff --git a/website-vue3-vite/src/assets/base.css b/website-vue3-vite/src/assets/base.css deleted file mode 100644 index f799d69..0000000 --- a/website-vue3-vite/src/assets/base.css +++ /dev/null @@ -1,75 +0,0 @@ -/* color palette from */ -:root { - --vt-c-white: #ffffff; - --vt-c-white-soft: #f8f8f8; - --vt-c-white-mute: #f2f2f2; - - --vt-c-black: #181818; - --vt-c-black-soft: #222222; - --vt-c-black-mute: #282828; - - --vt-c-indigo: #2c3e50; - - --vt-c-divider-light-1: rgba(60, 60, 60, 0.29); - --vt-c-divider-light-2: rgba(60, 60, 60, 0.12); - --vt-c-divider-dark-1: rgba(84, 84, 84, 0.65); - --vt-c-divider-dark-2: rgba(84, 84, 84, 0.48); - - --vt-c-text-light-1: var(--vt-c-indigo); - --vt-c-text-light-2: rgba(60, 60, 60, 0.66); - --vt-c-text-dark-1: var(--vt-c-white); - --vt-c-text-dark-2: rgba(235, 235, 235, 0.64); -} - -/* semantic color variables for this project */ -:root { - --color-background: var(--vt-c-white); - --color-background-soft: var(--vt-c-white-soft); - --color-background-mute: var(--vt-c-white-mute); - - --color-border: var(--vt-c-divider-light-2); - --color-border-hover: var(--vt-c-divider-light-1); - - --color-heading: var(--vt-c-text-light-1); - --color-text: var(--vt-c-text-light-1); - - --section-gap: 160px; -} - -/* -@media (prefers-color-scheme: dark) { - :root { - --color-background: var(--vt-c-black); - --color-background-soft: var(--vt-c-black-soft); - --color-background-mute: var(--vt-c-black-mute); - - --color-border: var(--vt-c-divider-dark-2); - --color-border-hover: var(--vt-c-divider-dark-1); - - --color-heading: var(--vt-c-text-dark-1); - --color-text: var(--vt-c-text-dark-2); - } -}*/ - -*, -*::before, -*::after { - box-sizing: border-box; - margin: 0; - position: relative; - font-weight: normal; -} - -body { - min-height: 100vh; - color: var(--color-text); - background: var(--color-background); - transition: color 0.5s, background-color 0.5s; - line-height: 1.6; - font-family: Inter, -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, - Cantarell, 'Fira Sans', 'Droid Sans', 'Helvetica Neue', sans-serif; - font-size: 15px; - text-rendering: optimizeLegibility; - -webkit-font-smoothing: antialiased; - -moz-osx-font-smoothing: grayscale; -} diff --git a/website-vue3-vite/src/assets/logo.svg b/website-vue3-vite/src/assets/logo.svg deleted file mode 100644 index bc826fe..0000000 --- a/website-vue3-vite/src/assets/logo.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/website-vue3-vite/src/assets/main.css b/website-vue3-vite/src/assets/main.css deleted file mode 100644 index e7d9b5f..0000000 --- a/website-vue3-vite/src/assets/main.css +++ /dev/null @@ -1,6 +0,0 @@ -@import "./base.css"; - -body { - margin: 2em; -} - diff --git a/website-vue3-vite/src/components/HelloWorld.vue b/website-vue3-vite/src/components/HelloWorld.vue deleted file mode 100644 index bd5f292..0000000 --- a/website-vue3-vite/src/components/HelloWorld.vue +++ /dev/null @@ -1,43 +0,0 @@ - - - - - diff --git a/website-vue3-vite/src/components/TestResult.vue b/website-vue3-vite/src/components/TestResult.vue deleted file mode 100644 index e7ea000..0000000 --- a/website-vue3-vite/src/components/TestResult.vue +++ /dev/null @@ -1,101 +0,0 @@ - - - - - \ No newline at end of file diff --git a/website-vue3-vite/src/components/TextWithURLs.vue b/website-vue3-vite/src/components/TextWithURLs.vue deleted file mode 100644 index 022ff90..0000000 --- a/website-vue3-vite/src/components/TextWithURLs.vue +++ /dev/null @@ -1,28 +0,0 @@ - - - - - \ No newline at end of file diff --git a/website-vue3-vite/src/components/TheWelcome.vue b/website-vue3-vite/src/components/TheWelcome.vue deleted file mode 100644 index 962413b..0000000 --- a/website-vue3-vite/src/components/TheWelcome.vue +++ /dev/null @@ -1,121 +0,0 @@ - - - diff --git a/website-vue3-vite/src/components/WelcomeItem.vue b/website-vue3-vite/src/components/WelcomeItem.vue deleted file mode 100644 index 6cff194..0000000 --- a/website-vue3-vite/src/components/WelcomeItem.vue +++ /dev/null @@ -1,86 +0,0 @@ - - - diff --git a/website-vue3-vite/src/components/__tests__/HelloWorld.spec.js b/website-vue3-vite/src/components/__tests__/HelloWorld.spec.js deleted file mode 100644 index da11e2e..0000000 --- a/website-vue3-vite/src/components/__tests__/HelloWorld.spec.js +++ /dev/null @@ -1,11 +0,0 @@ -import { describe, it, expect } from "vitest"; - -import { mount } from "@vue/test-utils"; -import HelloWorld from "../HelloWorld.vue"; - -describe("HelloWorld", () => { - it("renders properly", () => { - const wrapper = mount(HelloWorld, { props: { msg: "Hello Vitest" } }); - expect(wrapper.text()).toContain("Hello Vitest"); - }); -}); diff --git a/website-vue3-vite/src/components/icons/IconCommunity.vue b/website-vue3-vite/src/components/icons/IconCommunity.vue deleted file mode 100644 index ea8ddef..0000000 --- a/website-vue3-vite/src/components/icons/IconCommunity.vue +++ /dev/null @@ -1,12 +0,0 @@ - diff --git a/website-vue3-vite/src/components/icons/IconDocumentation.vue b/website-vue3-vite/src/components/icons/IconDocumentation.vue deleted file mode 100644 index 63a8534..0000000 --- a/website-vue3-vite/src/components/icons/IconDocumentation.vue +++ /dev/null @@ -1,12 +0,0 @@ - diff --git a/website-vue3-vite/src/components/icons/IconEcosystem.vue b/website-vue3-vite/src/components/icons/IconEcosystem.vue deleted file mode 100644 index 385a202..0000000 --- a/website-vue3-vite/src/components/icons/IconEcosystem.vue +++ /dev/null @@ -1,12 +0,0 @@ - diff --git a/website-vue3-vite/src/components/icons/IconSupport.vue b/website-vue3-vite/src/components/icons/IconSupport.vue deleted file mode 100644 index 7db961e..0000000 --- a/website-vue3-vite/src/components/icons/IconSupport.vue +++ /dev/null @@ -1,12 +0,0 @@ - diff --git a/website-vue3-vite/src/components/icons/IconTooling.vue b/website-vue3-vite/src/components/icons/IconTooling.vue deleted file mode 100644 index 660598d..0000000 --- a/website-vue3-vite/src/components/icons/IconTooling.vue +++ /dev/null @@ -1,19 +0,0 @@ - - diff --git a/website-vue3-vite/src/main.js b/website-vue3-vite/src/main.js deleted file mode 100644 index 9aa2e24..0000000 --- a/website-vue3-vite/src/main.js +++ /dev/null @@ -1,16 +0,0 @@ -import { createApp } from "vue"; -import App from "./App.vue"; -import router from "./router"; - -import BootstrapVue3 from 'bootstrap-vue-3' -import 'bootstrap/dist/css/bootstrap.css' -import 'bootstrap-vue-3/dist/bootstrap-vue-3.css' - -import "./assets/main.css"; - -const app = createApp(App); - -app.use(router); -app.use(BootstrapVue3); - -app.mount("#app"); diff --git a/website-vue3-vite/src/models/NameResTest.js b/website-vue3-vite/src/models/NameResTest.js deleted file mode 100644 index f245a98..0000000 --- a/website-vue3-vite/src/models/NameResTest.js +++ /dev/null @@ -1,277 +0,0 @@ -import {TestResult} from "@/models/TestResult"; -import {getURLForCURIE} from "@/models/helpers"; -import {Test} from "@/models/Test"; - -// Helper functions -/** - * This function generates tests for the previous NameRes format. - * - * We mainly need this to compare the outputs as we implement the new NameRes format, - * so this needs to be a quick-and-dirty implementation, which will eventually be phased out. - */ -function convertPrevNameResFormatToCurrent(response) { - // result is a dictionary, but when we iterate over it, we should get it in the same order as the input keys. - return Object.entries(response).map(([key, value]) => { - return { - curie: key, - synonyms: value.sort((a, b) => a.length - b.length), - }; - }); -} - -// A helper function that returns a Promise that evaluates to a JSON result object. -// TODO: cache this. -export function lookupNameRes(nameResEndpoint, query, expectedID="", limit=10, includePrefixes=[], excludePrefixes=[]) { - const url = new URL(nameResEndpoint + '/lookup'); - url.search = new URLSearchParams({ - 'string': query, - 'limit': limit, - 'only_prefixes': includePrefixes, - 'exclude_prefixes': excludePrefixes, - }) - - const request = new Request(url); - - return fetch(request).then(response => { - if (!response.ok) return TestResult.failure("Could not submit request to NameRes /lookup", 'text', response.statusText); - return response.json() - .catch(err => { - return TestResult.failure(`NameRes /lookup returned a non-JSON result: ${err}`, 'text', response); - }) - .then(responseJson => { - // There are two possible formats that could be returned. If this is the old format, the results - // will be a dictionary; if the new format, this will be a list. - let results; - if (Array.isArray(responseJson)) { - results = responseJson; - } else if(typeof responseJson === 'object') { - results = convertPrevNameResFormatToCurrent(responseJson); - } else { - return TestResult.failure(`NameRes /lookup returned an unexpected response`, 'json', responseJson); - } - - // Is the expectedID in the results? - if (!expectedID) { - return TestResult.success(`NameRes /lookup returned ${results.length} results, no expected ID`, 'NameRes', results); - } - if (results.length < 1) { - return TestResult.failure(`NameRes /lookup returned NO results`, 'NameRes', results); - } - - const topID = results[0]['curie']; - if (topID === expectedID) { - return TestResult.success(`NameRes /lookup returned ${results.length} results with expected ID ${expectedID} at top`, 'NameRes', results); - } - - const resultIDs = results.map(r => r['curie']); - if (resultIDs.includes(expectedID)) { - return TestResult.success(`NameRes /lookup returned ${results.length} results with expected ID ${expectedID} at position ${resultIDs.indexOf(expectedID) + 1}`, 'NameRes', results); - } - - return TestResult.failure(`NameRes /lookup returned ${results.length} results but missed expected ID ${expectedID}`, 'NameRes', results); - }); - }); -} - -/** - * Represents a single NameRes test in our test suite. This is constructed in some way (currently, from a row in a spreadsheet) - * and includes within it a closure that includes the test itself. The test can be executed by passing it an endpoint to - * test, and it returns a TestResult representing the result. - */ -export class NameResTest extends Test { - /** - * Convert a single row into zero or more tests. - */ - static convertRowToTests(row, limit=10) { - const source = row['Source']; - const source_url = row['Source URL']; - - // Define some standard test types. - function createCheckIDTest(id) { - return new NodeNormTest(`Check for ID ${id}`, { - [id]: getURLForCURIE(id) - }, source, source_url, function(nodeNormEndpoint) { - // Check to see if NodeNorm know about this ID. - // We have a success! Since the identifier was returned, this test is now passed. - return lookupNameRes(nodeNormEndpoint, id); - }); - } - - /** - * Check whether this identifier is of a particular Biolink class. - * Include a class in the format '!biolink:className' to pass only if this className is NOT present. - */ - function createBiolinkClassTest(id, biolinkClass) { - return new NodeNormTest(`Check that ID ${id} has Biolink class ${biolinkClass}`, { - [id]: getURLForCURIE(id) - }, source, source_url, function(nodeNormEndpoint) { - // Check to see if NodeNorm know about this ID. - // We have a success! Since the identifier was returned, this test is now passed. - return lookupNameRes(nodeNormEndpoint, id) - .then(result => { - // Continue propagating errors. - if (!result.status) return result; - - // We have a success if query_id was found at all. - // But to pass this test, we need to check that biolinkClass - // is one of the Biolink classes of this identifier. - const json = result.result; - const biolinkClasses = new Set(json['type'] || []); - - if (biolinkClass.startsWith('!')) { - const invertedBiolinkClass = biolinkClass.substring(1); - if (biolinkClasses.has(invertedBiolinkClass)) { - return TestResult.failure(`ID ${id} should not have Biolink class ${invertedBiolinkClass} but does`, 'NodeNorm', json); - } else { - return TestResult.success(`ID ${id} does not have Biolink class ${invertedBiolinkClass} as expected`, 'NodeNorm', json); - } - } else { - if (biolinkClasses.has(biolinkClass)) { - return TestResult.success(`ID ${id} has Biolink class ${biolinkClass}`, 'NodeNorm', json); - } else { - return TestResult.failure(`ID ${id} does not have Biolink class ${biolinkClass}`, 'NodeNorm', json); - } - } - }) - }); - } - - function createPreferredIdTest(query_id, preferred_id) { - return new NodeNormTest(`Check ID ${query_id} has preferred ID ${preferred_id}`, { - [query_id]: getURLForCURIE(query_id), - [preferred_id]: getURLForCURIE(preferred_id), - }, source, source_url, function(nodeNormEndpoint) { - return lookupNameRes(nodeNormEndpoint, query_id) - .then(result => { - // Continue propagating errors. - if (!result.status) return result; - - // We have a success if query_id was found at all. - // But to pass this test, we need to check that the - // preferred_id is specifically the preferred ID in - // the returned cluster. - const json = result.result; - const equiv_ids = getEquivalentIDs(json); - - if (json['id']['identifier'] === preferred_id && equiv_ids.has(query_id)) { - return TestResult.success(`Query ID ${query_id} has preferred ID ${preferred_id}`, 'NodeNorm', json); - } else { - return TestResult.failure(`Query ID ${query_id} has preferred ID ${json['id']['identifier']}, not ${preferred_id}`, 'NodeNorm', json); - } - }); - }); - } - - function createClusterTogetherTest(id1, id2) { - return new NodeNormTest(`Check ID ${id1} and ID ${id2} cluster together`, { - [id1]: getURLForCURIE(id1), - [id2]: getURLForCURIE(id2), - }, source, source_url,function(nodeNormEndpoint) { - return lookupNameRes(nodeNormEndpoint, id1) - .then(result => { - // Continue propagating errors. - if (!result.status) return result; - - // We have a success if id1 was found at all. - // But to pass this test, we need to check that the - // id2 is one of the equivalent identifiers. - const json = result.result; - const equiv_ids = getEquivalentIDs(json); - const preferred_id = json.id.identifier; - - if (equiv_ids.has(id1) && equiv_ids.has(id2)) { - return TestResult.success(`ID ${id1} and ID ${id2} are both equivalent to ${preferred_id}.`, 'NodeNorm', json); - } else { - return TestResult.failure(`ID ${id1} is equivalent to ${preferred_id} but ID ${id2} is not.`, 'NodeNorm', json); - } - }); - }); - } - - // Do we have a preferred ID? - let expectedID = ''; - if ('Preferred ID' in row) { - expectedID = row['Preferred ID']; - } - - // Are there prefixes to include or exclude? - const prefixes = (row['Prefixes'] ? row['Prefixes'] : "").split('|'); - const includePrefixes = []; - const excludePrefixes = []; - prefixes.forEach(prefix => { - if (!prefix) return; - if (prefix.startsWith('^')) { - excludePrefixes.push(prefix.substring(1)); - } else { - includePrefixes.push(prefix); - } - }) - - // Look for tests in this row. - const tests = []; - if('Query Label' in row) { // || 'Preferred label' in row) { - const query_label = row['Query Label']; - - if (query_label !== '') { - // To begin with, let's just return the results as-is. - tests.push(new NameResTest(`Lookup "${query_label}"`, {}, source, source_url, (nameResURL) => { - return lookupNameRes(nameResURL, query_label, expectedID, limit, includePrefixes, excludePrefixes); - })); - } - - const preferred_label = row['Preferred Label']; - if (preferred_label !== '') { - // To begin with, let's just return the results as-is. - tests.push(new NameResTest(`Lookup "${preferred_label}"`, {}, source, source_url, (nameResURL) => { - return lookupNameRes(nameResURL, preferred_label, expectedID, limit, includePrefixes, excludePrefixes); - })); - } - - - const additional_labels = row['Additional Labels'].split('|'); - additional_labels.forEach(additional_label => { - if (!additional_label) return; - - // To begin with, let's just return the results as-is. - tests.push(new NameResTest(`Lookup "${additional_label}"`, {}, source, source_url, (nameResURL) => { - return lookupNameRes(nameResURL, additional_label, expectedID, limit, includePrefixes, excludePrefixes); - })); - }); - - } else { - tests.push(TestResult.failure(`Could not understand row`, 'json', row)); - } - - return tests; - - /* - tests.push(createCheckIDTest(query_id)); - if(row['Preferred ID']) { - const preferred_id = row['Preferred ID']; - tests.push(createCheckIDTest(preferred_id)); - tests.push(createPreferredIdTest(query_id, preferred_id)); - - if(row['Additional IDs']) { - const additional_ids = row['Additional IDs'].split(/\s*\|\s* /); - - additional_ids.forEach(additional_id => { - tests.push(createPreferredIdTest(additional_id, preferred_id)); - tests.push(createClusterTogetherTest(additional_id, query_id)); - }); - } - } else if(row['Additional IDs']) { - const additional_ids = row['Additional IDs'].split(/\s*\|\s* /); - - additional_ids.forEach(additional_id => { - tests.push(createClusterTogetherTest(additional_id, query_id)); - }); - } - - if(row['Biolink classes']) { - const biolink_classes = row['Biolink classes'].split(/\s*\|\s* /); - biolink_classes.forEach(biolink_class => { - tests.push(createBiolinkClassTest(query_id, biolink_class)); - }); - } */ - } -} \ No newline at end of file diff --git a/website-vue3-vite/src/models/NodeNormTest.js b/website-vue3-vite/src/models/NodeNormTest.js deleted file mode 100644 index 5bc4bb0..0000000 --- a/website-vue3-vite/src/models/NodeNormTest.js +++ /dev/null @@ -1,201 +0,0 @@ -import {TestResult} from "@/models/TestResult"; -import {getURLForCURIE} from "@/models/helpers"; -import {Test} from "@/models/Test"; - -// Helper functions -function getEquivalentIDs(result) { - return new Set((result['equivalent_identifiers'] || []).map(r => r.identifier)) -} - -/** - * Represents a single test in our test suite. This is constructed in some way (currently, from a row in a spreadsheet) - * and includes within it a closure that includes the test itself. The test can be executed by passing it an endpoint to - * test, and it returns a TestResult representing the result. - */ -export class NodeNormTest extends Test { - /** - * Convert a single row into zero or more tests. - */ - static convertRowToTests(row) { - const source = row['Source']; - const source_url = row['Source URL']; - - // A helper function that returns a Promise that evaluates to a JSON result object. - // TODO: cache this. - function getNormalizedNodes(nodeNormEndpoint, id) { - const url = nodeNormEndpoint + "/get_normalized_nodes?curie=" + encodeURIComponent(id); - // console.log("Querying", url); - return fetch(url).then(response => { - if (!response.ok) return TestResult.failure("Could not get_normalized_nodes", 'text', response.statusText); - return response.json() - .catch(err => { - return TestResult.failure(`NodeNorm /get_normalized_nodes returned a non-JSON result: ${err}`, 'text', response); - }) - .then(results => { - // console.log("Results:", results); - if (!results) return TestResult.failure(`get_normalized_nodes returned invalid response`, 'text', response); - const result = results[id]; - // console.log("Result:", result); - if (!result) return TestResult.failure(`get_normalized_nodes returned no response for ${id}`, 'json', results); - const equiv_ids = getEquivalentIDs(result); - // console.log("Equiv IDs:", equiv_ids); - if (!equiv_ids.has(id)) { - return TestResult.failure(`ID ${id} could not be found`, 'NodeNorm', result); - } else { - let preferred_label_text = ""; - if (result['id']) { - const preferred_id = result.id['identifier']; - const preferred_label = result.id['label']; - if (id === preferred_id) { - preferred_label_text = ` (\"${preferred_label}\")`; - } else { - preferred_label_text = ` (${preferred_id} "${preferred_label}\")`; - } - } - return TestResult.success(`Found ID ${id}${preferred_label_text}`, "NodeNorm", result); - } - }); - }); - } - - // Define some standard test types. - /** Check whether this identifier is present in this NodeNorm instance. */ - function createCheckIDTest(id) { - return new NodeNormTest(`Check for ID ${id}`, { - [id]: getURLForCURIE(id) - }, source, source_url, function(nodeNormEndpoint) { - // Check to see if NodeNorm know about this ID. - // We have a success! Since the identifier was returned, this test is now passed. - return getNormalizedNodes(nodeNormEndpoint, id); - }); - } - - /** - * Check whether this identifier is of a particular Biolink class. - * Include a class in the format '!biolink:className' to pass only if this className is NOT present. - */ - function createBiolinkClassTest(id, biolinkClass) { - return new NodeNormTest(`Check that ID ${id} has Biolink class ${biolinkClass}`, { - [id]: getURLForCURIE(id) - }, source, source_url, function(nodeNormEndpoint) { - // Check to see if NodeNorm know about this ID. - // We have a success! Since the identifier was returned, this test is now passed. - return getNormalizedNodes(nodeNormEndpoint, id) - .then(result => { - // Continue propagating errors. - if (!result.status) return result; - - // We have a success if query_id was found at all. - // But to pass this test, we need to check that biolinkClass - // is one of the Biolink classes of this identifier. - const json = result.result; - const biolinkClasses = new Set(json['type'] || []); - - if (biolinkClass.startsWith('!')) { - const invertedBiolinkClass = biolinkClass.substring(1); - if (biolinkClasses.has(invertedBiolinkClass)) { - return TestResult.failure(`ID ${id} should not have Biolink class ${invertedBiolinkClass} but does`, 'NodeNorm', json); - } else { - return TestResult.success(`ID ${id} does not have Biolink class ${invertedBiolinkClass} as expected`, 'NodeNorm', json); - } - } else { - if (biolinkClasses.has(biolinkClass)) { - return TestResult.success(`ID ${id} has Biolink class ${biolinkClass}`, 'NodeNorm', json); - } else { - return TestResult.failure(`ID ${id} does not have Biolink class ${biolinkClass}`, 'NodeNorm', json); - } - } - }) - }); - } - - function createPreferredIdTest(query_id, preferred_id) { - return new NodeNormTest(`Check ID ${query_id} has preferred ID ${preferred_id}`, { - [query_id]: getURLForCURIE(query_id), - [preferred_id]: getURLForCURIE(preferred_id), - }, source, source_url, function(nodeNormEndpoint) { - return getNormalizedNodes(nodeNormEndpoint, query_id) - .then(result => { - // Continue propagating errors. - if (!result.status) return result; - - // We have a success if query_id was found at all. - // But to pass this test, we need to check that the - // preferred_id is specifically the preferred ID in - // the returned cluster. - const json = result.result; - const equiv_ids = getEquivalentIDs(json); - - if (json['id']['identifier'] === preferred_id && equiv_ids.has(query_id)) { - return TestResult.success(`Query ID ${query_id} has preferred ID ${preferred_id}`, 'NodeNorm', json); - } else { - return TestResult.failure(`Query ID ${query_id} has preferred ID ${json['id']['identifier']}, not ${preferred_id}`, 'NodeNorm', json); - } - }); - }); - } - - function createClusterTogetherTest(id1, id2) { - return new NodeNormTest(`Check ID ${id1} and ID ${id2} cluster together`, { - [id1]: getURLForCURIE(id1), - [id2]: getURLForCURIE(id2), - }, source, source_url,function(nodeNormEndpoint) { - return getNormalizedNodes(nodeNormEndpoint, id1) - .then(result => { - // Continue propagating errors. - if (!result.status) return result; - - // We have a success if id1 was found at all. - // But to pass this test, we need to check that the - // id2 is one of the equivalent identifiers. - const json = result.result; - const equiv_ids = getEquivalentIDs(json); - const preferred_id = json.id.identifier; - - if (equiv_ids.has(id1) && equiv_ids.has(id2)) { - return TestResult.success(`ID ${id1} and ID ${id2} are both equivalent to ${preferred_id}.`, 'NodeNorm', json); - } else { - return TestResult.failure(`ID ${id1} is equivalent to ${preferred_id} but ID ${id2} is not.`, 'NodeNorm', json); - } - }); - }); - } - - // Look for tests in this row. - const tests = []; - if(row['Query ID']) { - const query_id = row['Query ID']; - - tests.push(createCheckIDTest(query_id)); - if(row['Preferred ID']) { - const preferred_id = row['Preferred ID']; - tests.push(createCheckIDTest(preferred_id)); - tests.push(createPreferredIdTest(query_id, preferred_id)); - - if(row['Additional IDs']) { - const additional_ids = row['Additional IDs'].split(/\s*\|\s*/); - - additional_ids.forEach(additional_id => { - tests.push(createPreferredIdTest(additional_id, preferred_id)); - tests.push(createClusterTogetherTest(additional_id, query_id)); - }); - } - } else if(row['Additional IDs']) { - const additional_ids = row['Additional IDs'].split(/\s*\|\s*/); - - additional_ids.forEach(additional_id => { - tests.push(createClusterTogetherTest(additional_id, query_id)); - }); - } - - if(row['Biolink Classes']) { - const biolink_classes = row['Biolink Classes'].split(/\s*\|\s*/); - biolink_classes.forEach(biolink_class => { - tests.push(createBiolinkClassTest(query_id, biolink_class)); - }); - } - } - - return tests; - } -} \ No newline at end of file diff --git a/website-vue3-vite/src/models/Test.js b/website-vue3-vite/src/models/Test.js deleted file mode 100644 index 3533309..0000000 --- a/website-vue3-vite/src/models/Test.js +++ /dev/null @@ -1,16 +0,0 @@ -import {TestResult} from "@/models/TestResult"; - -export class Test { - /** - * Each test has a description, source, source_url and - */ - constructor(description, urls = {}, source = null, source_url = null, test = function (endpoint) { - return Promise.resolve(TestResult.failure(`Not implemented (${endpoint})`)); - }) { - this.description = description; - this.urls = urls; - this.source = source; - this.source_url = source_url; - this.test = test; - } -} \ No newline at end of file diff --git a/website-vue3-vite/src/models/TestResult.js b/website-vue3-vite/src/models/TestResult.js deleted file mode 100644 index 31cd141..0000000 --- a/website-vue3-vite/src/models/TestResult.js +++ /dev/null @@ -1,22 +0,0 @@ -/** - * A class representing the result of a test. - */ -export class TestResult { - /** Construct a TestResult based largely on a JSON result from . */ - constructor(status, message, resultType = "null", result = {}) { - this.status = status; - this.message = message; - this.resultType = resultType; - this.result = result; - } - - /** Create a TestResult for a success. */ - static success(message, resultType = "unknown", result = null) { - return new TestResult(true, message, resultType, result); - } - - /** Create a TestResult for a failure. */ - static failure(message, resultType = "unknown", result = null) { - return new TestResult(false, message, resultType, result); - } -} \ No newline at end of file diff --git a/website-vue3-vite/src/models/helpers.js b/website-vue3-vite/src/models/helpers.js deleted file mode 100644 index d0ba2ab..0000000 --- a/website-vue3-vite/src/models/helpers.js +++ /dev/null @@ -1,20 +0,0 @@ -export function getURLForCURIE(curie) { - const iri_stems = { - 'UMLS': 'https://uts.nlm.nih.gov/uts/umls/concept/', - } - - const curie_split = (curie.toUpperCase().split(':') || ['']) - const curie_prefix = curie_split[0]; - if (new Set('HTTP', 'HTTPS', 'URN').has(curie_prefix)) { - // Looks like a URI! Leave it unchanged. - return curie; - } - - if (iri_stems[curie_prefix] && curie_split.length > 1) { - return iri_stems[curie_prefix] + curie.substring(curie.indexOf(':') + 1); - } - - // Default to bioregistry.io lookup - return 'http://bioregistry.io/' + encodeURIComponent(curie); - // return 'https://google.com/search?q=' + encodeURIComponent(curie); -} \ No newline at end of file diff --git a/website-vue3-vite/src/router/index.js b/website-vue3-vite/src/router/index.js deleted file mode 100644 index dd52573..0000000 --- a/website-vue3-vite/src/router/index.js +++ /dev/null @@ -1,48 +0,0 @@ -import { createRouter, createWebHistory } from "vue-router"; -import HomeView from "@/views/HomeView.vue"; -import NodeNormValidator from "@/views/NodeNormValidator.vue"; -import NameResValidator from "@/views/NameResValidator.vue"; -import Autocomplete from "@/views/Autocomplete.vue"; -import AutocompleteBulkValidator from "@/views/AutocompleteBulkValidator.vue"; - -const router = createRouter({ - history: createWebHistory(import.meta.env.BASE_URL), - base: import.meta.env.BASE_URL, - routes: [ - { - path: "/", - name: "home", - component: () => import("../views/HomeView.vue"), - }, - { - path: "/nodenorm/", - name: "Node Normalization Validator", - component: () => import("../views/NodeNormValidator.vue"), - }, - { - path: "/nameres/", - name: "Name Resolver Validator", - component: () => import("../views/NameResValidator.vue"), - }, - { - path: "/autocomplete/", - name: "Autocomplete", - component: Autocomplete, - }, - { - path: "/autocomplete-bulk/", - name: "Autocomplete Bulk Validator", - component: AutocompleteBulkValidator, - }, - { - path: "/about/", - name: "about", - // route level code-splitting - // this generates a separate chunk (About.[hash].js) for this route - // which is lazy-loaded when the route is visited. - component: () => import("../views/AboutView.vue"), - }, - ], -}); - -export default router; diff --git a/website-vue3-vite/src/views/AboutView.vue b/website-vue3-vite/src/views/AboutView.vue deleted file mode 100644 index 756ad2a..0000000 --- a/website-vue3-vite/src/views/AboutView.vue +++ /dev/null @@ -1,15 +0,0 @@ - - - diff --git a/website-vue3-vite/src/views/Autocomplete.vue b/website-vue3-vite/src/views/Autocomplete.vue deleted file mode 100644 index b72cb74..0000000 --- a/website-vue3-vite/src/views/Autocomplete.vue +++ /dev/null @@ -1,256 +0,0 @@ - - - \ No newline at end of file diff --git a/website-vue3-vite/src/views/AutocompleteBulkValidator.vue b/website-vue3-vite/src/views/AutocompleteBulkValidator.vue deleted file mode 100644 index d697935..0000000 --- a/website-vue3-vite/src/views/AutocompleteBulkValidator.vue +++ /dev/null @@ -1,213 +0,0 @@ - - - diff --git a/website-vue3-vite/src/views/HomeView.vue b/website-vue3-vite/src/views/HomeView.vue deleted file mode 100644 index 7802064..0000000 --- a/website-vue3-vite/src/views/HomeView.vue +++ /dev/null @@ -1,25 +0,0 @@ - - - \ No newline at end of file diff --git a/website-vue3-vite/src/views/NameResValidator.vue b/website-vue3-vite/src/views/NameResValidator.vue deleted file mode 100644 index c53d626..0000000 --- a/website-vue3-vite/src/views/NameResValidator.vue +++ /dev/null @@ -1,136 +0,0 @@ - - - diff --git a/website-vue3-vite/src/views/NodeNormValidator.vue b/website-vue3-vite/src/views/NodeNormValidator.vue deleted file mode 100644 index cd44fdc..0000000 --- a/website-vue3-vite/src/views/NodeNormValidator.vue +++ /dev/null @@ -1,133 +0,0 @@ - - - diff --git a/website-vue3-vite/vite.config.js b/website-vue3-vite/vite.config.js deleted file mode 100644 index ad6f51f..0000000 --- a/website-vue3-vite/vite.config.js +++ /dev/null @@ -1,15 +0,0 @@ -import { fileURLToPath, URL } from "node:url"; - -import { defineConfig } from "vite"; -import vue from "@vitejs/plugin-vue"; - -// https://vitejs.dev/config/ -export default defineConfig({ - plugins: [vue()], - base: "/babel-validation/", - resolve: { - alias: { - "@": fileURLToPath(new URL("./src", import.meta.url)), - }, - }, -}); diff --git a/website/package-lock.json b/website/package-lock.json index 60e1098..753aa36 100644 --- a/website/package-lock.json +++ b/website/package-lock.json @@ -10,14 +10,8 @@ "dependencies": { "@astrojs/check": "^0.4.1", "@astrojs/vue": "^4.0.8", - "@popperjs/core": "^2.11.8", - "@types/bootstrap": "^5.2.10", "astro": "^4.1.1", - "astro-bootstrap": "^0.6.2", "bootstrap": "^5.3.2", - "csv-stringify": "^6.4.5", - "file-saver": "^2.0.5", - "lodash": "^4.17.21", "typescript": "^5.3.3", "vue": "^3.4.8" } @@ -183,14 +177,6 @@ "vue": "^3.2.30" } }, - "node_modules/@astrojs/webapi": { - "version": "2.2.0", - "resolved": "https://registry.npmjs.org/@astrojs/webapi/-/webapi-2.2.0.tgz", - "integrity": "sha512-mHAOApWyjqSe5AQMOUD9rsZJqbMQqe3Wosb1a40JV6Okvyxj1G6GTlthwYadWCymq/lbgwh0PLiY8Fr4eFxtuQ==", - "dependencies": { - "undici": "^5.22.0" - } - }, "node_modules/@babel/code-frame": { "version": "7.23.5", "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.23.5.tgz", @@ -661,7 +647,6 @@ "resolved": "https://registry.npmjs.org/@emnapi/runtime/-/runtime-0.44.0.tgz", "integrity": "sha512-ZX/etZEZw8DR7zAB1eVQT40lNo0jeqpb6dCgOvctB6FIQ5PoXfMuNY8+ayQfu8tNQbAB8gQWSSJupR8NxeiZXw==", "optional": true, - "peer": true, "dependencies": { "tslib": "^2.4.0" } @@ -1011,14 +996,6 @@ "node": ">=12" } }, - "node_modules/@fastify/busboy": { - "version": "2.1.0", - "resolved": "https://registry.npmjs.org/@fastify/busboy/-/busboy-2.1.0.tgz", - "integrity": "sha512-+KpH+QxZU7O4675t3mnkQKcZZg56u+K/Ct2K+N2AZYNVK8kyeo/bI18tI8aPm3tvNNRyTWfj6s5tnGNlcbQRsA==", - "engines": { - "node": ">=14" - } - }, "node_modules/@img/sharp-darwin-arm64": { "version": "0.33.1", "resolved": "https://registry.npmjs.org/@img/sharp-darwin-arm64/-/sharp-darwin-arm64-0.33.1.tgz", @@ -1030,7 +1007,6 @@ "os": [ "darwin" ], - "peer": true, "engines": { "glibc": ">=2.26", "node": "^18.17.0 || ^20.3.0 || >=21.0.0", @@ -1056,7 +1032,6 @@ "os": [ "darwin" ], - "peer": true, "engines": { "glibc": ">=2.26", "node": "^18.17.0 || ^20.3.0 || >=21.0.0", @@ -1082,7 +1057,6 @@ "os": [ "darwin" ], - "peer": true, "engines": { "macos": ">=11", "npm": ">=9.6.5", @@ -1104,7 +1078,6 @@ "os": [ "darwin" ], - "peer": true, "engines": { "macos": ">=10.13", "npm": ">=9.6.5", @@ -1126,7 +1099,6 @@ "os": [ "linux" ], - "peer": true, "engines": { "glibc": ">=2.28", "npm": ">=9.6.5", @@ -1148,7 +1120,6 @@ "os": [ "linux" ], - 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"curie_distinct_count": 25959, - "filenames": { - "Disease": 25959 - } - }, - "MP": { - "clique_distinct_count": 34, - "curie_count": 35, - "curie_distinct_count": 35, - "filenames": { - "Disease": 4, - "PhenotypicFeature": 31 - } - }, - "NCBIGene": { - "clique_distinct_count": 58008124, - "curie_count": 58008124, - "curie_distinct_count": 58008124, - "filenames": { - "Gene": 58008124 - } - }, - "NCBITaxon": { - "clique_distinct_count": 2615615, - "curie_count": 2615615, - "curie_distinct_count": 2615615, - "filenames": { - "OrganismTaxon": 2615615 - } - }, - "NCIT": { - "clique_distinct_count": 56459, - "curie_count": 57315, - "curie_distinct_count": 57258, - "filenames": { - "AnatomicalEntity": 4189, - "Cell": 2498, - "CellularComponent": 1457, - "Disease": 25976, - "GrossAnatomicalStructure": 2079, - "PhenotypicFeature": 21116 - } - }, - "OMIM": { - "clique_distinct_count": 27622, - "curie_count": 27645, - "curie_distinct_count": 27591, - "filenames": { - "Disease": 10133, - "Gene": 17512 - } - }, - "OMIM.PS": { - "clique_distinct_count": 565, - "curie_count": 565, - "curie_distinct_count": 565, - "filenames": { - "Disease": 565 - } - }, - "PANTHER.FAMILY": { - "clique_distinct_count": 26139, - "curie_count": 26139, - "curie_distinct_count": 26139, - "filenames": { - "GeneFamily": 26139 - } - }, - "PANTHER.PATHWAY": { - "clique_distinct_count": 175, - "curie_count": 175, - "curie_distinct_count": 175, - "filenames": { - "Pathway": 175 - } - }, - "PMC": { - "clique_distinct_count": 9801554, - "curie_count": 9802826, - "curie_distinct_count": 9802826, - "filenames": { - "Publication": 9802826 - } - }, - "PMID": { - "clique_distinct_count": 38230457, - "curie_count": 38230457, - "curie_distinct_count": 38230457, - "filenames": { - "Publication": 38230457 - } - }, - "PR": { - "clique_distinct_count": 251765, - "curie_count": 251765, - "curie_distinct_count": 251765, - "filenames": { - "Protein": 251765 - } - }, - "PUBCHEM.COMPOUND": { - "clique_distinct_count": 119360258, - "curie_count": 119360505, - "curie_distinct_count": 119360505, - "filenames": { - "ChemicalEntity": 41553, - "ChemicalMixture": 1, - "MolecularMixture": 10654979, - "SmallMolecule": 108663972 - } - }, - "REACT": { - "clique_distinct_count": 110308, - "curie_count": 110308, - "curie_distinct_count": 110308, - "filenames": { - "BiologicalProcess": 12, - "MolecularActivity": 87992, - "Pathway": 22304 - } - }, - "RGD": { - "clique_distinct_count": 91426, - "curie_count": 91426, - "curie_distinct_count": 91426, - "filenames": { - "Gene": 91426 - } - }, - "RHEA": { - "clique_distinct_count": 68524, - "curie_count": 68524, - "curie_distinct_count": 68524, - "filenames": { - "MolecularActivity": 68524 - } - }, - "RXCUI": { - "clique_distinct_count": 124063, - "curie_count": 124160, - "curie_distinct_count": 124160, - "filenames": { - "ChemicalEntity": 13216, - "Drug": 102206, - "MolecularMixture": 4497, - "SmallMolecule": 4241 - } - }, - "SGD": { - "clique_distinct_count": 7167, - "curie_count": 7167, - "curie_distinct_count": 7167, - "filenames": { - "Gene": 7167 - } - }, - "SMPDB": { - "clique_distinct_count": 30248, - "curie_count": 30248, - "curie_distinct_count": 30248, - "filenames": { - "Pathway": 30248 - } - }, - "SNOMEDCT": { - "clique_distinct_count": 141610, - "curie_count": 146401, - "curie_distinct_count": 146394, - "filenames": { - "Cell": 882, - "CellularComponent": 539, - "Disease": 97525, - "PhenotypicFeature": 47455 - } - }, - "TCDB": { - "clique_distinct_count": 22, - "curie_count": 22, - "curie_distinct_count": 22, - "filenames": { - "MolecularActivity": 22 - } - }, - "UBERON": { - "clique_distinct_count": 14496, - "curie_count": 14496, - "curie_distinct_count": 14496, - "filenames": { - "AnatomicalEntity": 4080, - "Cell": 3, - "CellularComponent": 8, - "GrossAnatomicalStructure": 10405 - } - }, - "UMLS": { - "clique_distinct_count": 3410195, - "curie_count": 3455457, - "curie_distinct_count": 3387680, - "filenames": { - "AnatomicalEntity": 139946, - "BiologicalProcess": 42213, - "Cell": 6342, - "CellularComponent": 8373, - "ChemicalEntity": 285668, - "ChemicalMixture": 6, - "ComplexMolecularMixture": 101, - "Disease": 351524, - "Drug": 256367, - "Gene": 46870, - "GrossAnatomicalStructure": 2376, - "MolecularActivity": 27100, - "MolecularMixture": 6915, - "OrganismTaxon": 769694, - "PhenotypicFeature": 363932, - "Polypeptide": 191, - "Protein": 165683, - "SmallMolecule": 74807, - "umls": 907349 - } - }, - "UNII": { - "clique_distinct_count": 134272, - "curie_count": 134411, - "curie_distinct_count": 134411, - "filenames": { - "ChemicalEntity": 53148, - "ChemicalMixture": 1, - "MolecularMixture": 14531, - "SmallMolecule": 66731 - } - }, - "UniProtKB": { - "clique_distinct_count": 254326154, - "curie_count": 254326154, - "curie_distinct_count": 254326154, - "filenames": { - "Protein": 254326154 - } - }, - "WBbt": { - "clique_distinct_count": 17, - "curie_count": 18, - "curie_distinct_count": 18, - "filenames": { - "AnatomicalEntity": 18 - } - }, - "WormBase": { - "clique_distinct_count": 48777, - "curie_count": 48777, - "curie_distinct_count": 48777, - "filenames": { - "Gene": 48777 - } - }, - "ZFA": { - "clique_distinct_count": 606, - "curie_count": 607, - "curie_distinct_count": 607, - "filenames": { - "AnatomicalEntity": 607 - } - }, - "ZFIN": { - "clique_distinct_count": 38079, - "curie_count": 38079, - "curie_distinct_count": 38079, - "filenames": { - "Gene": 38079 - } - }, - "dictyBase": { - "clique_distinct_count": 13892, - "curie_count": 13892, - "curie_distinct_count": 13892, - "filenames": { - "Gene": 13892 - } - }, - "doi": { - "clique_distinct_count": 29310262, - "curie_count": 29313924, - "curie_distinct_count": 29313924, - "filenames": { - "Publication": 29313924 - } - }, - "icd11": { - "clique_distinct_count": 5, - "curie_count": 5, - "curie_distinct_count": 5, - "filenames": { - "Disease": 5 - } - }, - "icd11.foundation": { - "clique_distinct_count": 3999, - "curie_count": 4032, - "curie_distinct_count": 4032, - "filenames": { - "Disease": 4032 - } - }, - "medgen": { - "clique_distinct_count": 20959, - "curie_count": 20969, - "curie_distinct_count": 20969, - "filenames": { - "Disease": 20969 - } - }, - "orphanet": { - "clique_distinct_count": 10953, - "curie_count": 10991, - "curie_distinct_count": 10991, - "filenames": { - "Disease": 10991 - } - } - }, - "count_cliques": 481727857, - "count_curies": 675768955 -} diff --git a/website/src/components/Autocomplete.vue b/website/src/components/Autocomplete.vue deleted file mode 100644 index 39b0df9..0000000 --- a/website/src/components/Autocomplete.vue +++ /dev/null @@ -1,254 +0,0 @@ - - - \ No newline at end of file diff --git a/website/src/components/Card.astro b/website/src/components/Card.astro deleted file mode 100644 index bd6d597..0000000 --- a/website/src/components/Card.astro +++ /dev/null @@ -1,61 +0,0 @@ ---- -interface Props { - title: string; - body: string; - href: string; -} - -const { href, title, body } = Astro.props; ---- - -
  • - -

    - {title} - → -

    -

    - {body} -

    -     -
    • - diff --git a/website/src/components/Dashboard.vue b/website/src/components/Dashboard.vue new file mode 100644 index 0000000..dc7f95e --- /dev/null +++ b/website/src/components/Dashboard.vue @@ -0,0 +1,332 @@ + + + + + + diff --git a/website/src/components/PrefixComparator.vue b/website/src/components/PrefixComparator.vue deleted file mode 100644 index 078d0ae..0000000 --- a/website/src/components/PrefixComparator.vue +++ /dev/null @@ -1,350 +0,0 @@ - - - - - diff --git a/website/src/components/Trends.vue b/website/src/components/Trends.vue new file mode 100644 index 0000000..1bc4400 --- /dev/null +++ b/website/src/components/Trends.vue @@ -0,0 +1,94 @@ + + + + diff --git a/website/src/components/bootstrap/BCard.vue b/website/src/components/bootstrap/BCard.vue deleted file mode 100644 index e9b19c0..0000000 --- a/website/src/components/bootstrap/BCard.vue +++ /dev/null @@ -1,20 +0,0 @@ - - - - - \ No newline at end of file diff --git a/website/src/env.d.ts b/website/src/env.d.ts index f964fe0..0cef870 100644 --- a/website/src/env.d.ts +++ b/website/src/env.d.ts @@ -1 +1,9 @@ /// + +// Let `astro check` (TypeScript) see Vue single-file components as default +// exports; the Vue integration handles the actual compilation. +declare module '*.vue' { + import type { DefineComponent } from 'vue'; + const component: DefineComponent, Record, unknown>; + export default component; +} diff --git a/website/src/pages/autocomplete/index.astro b/website/src/pages/autocomplete/index.astro deleted file mode 100644 index d2d9f59..0000000 --- a/website/src/pages/autocomplete/index.astro +++ /dev/null @@ -1,34 +0,0 @@ ---- -import Layout from '../../layouts/Layout.astro'; -import Autocomplete from '../../components/Autocomplete.vue'; ---- - -
    - Return to front page - -

    Autocomplete

    -

    - This implements a simple autocomplete in front of NameRes, allowing NameRes instances - to be tested in a manner similar to that used by the Translator UI. The main advantages - of this view are: -

    - -
      -
    • The ability to switch between different NameRes instances.
      • -
    • Try different flags and settings.
      • -
    - - - - -
    -     \ No newline at end of file diff --git a/website/src/pages/index.astro b/website/src/pages/index.astro index 48c2a5f..c542316 100644 --- a/website/src/pages/index.astro +++ b/website/src/pages/index.astro @@ -1,37 +1,22 @@ --- import Layout from '../layouts/Layout.astro'; +import Dashboard from '../components/Dashboard.vue'; --- - +

    Babel Validation

    -

    - Babel is the program that generates the datasets of - interrelated identifiers that underlies Node Normalization - and Name Resolution. This website is intended to - provide allows JavaScript-based tests to be executed against different instances of these tools. +

    + Babel generates the datasets of + interrelated identifiers behind Node Normalization + and Name Resolution. This dashboard shows the + results of running the babel-validation test + suite daily against every deployment environment. Because test expectations are pinned to the environment where + a new Babel version lands first, environments are not expected to all be green — the point is to see + which issues are visible in which environment. See also the + run history.

    -

    Individual queries

    - - - +
    - - diff --git a/website/src/pages/prefix-comparator/index.astro b/website/src/pages/prefix-comparator/index.astro deleted file mode 100644 index e3065b8..0000000 --- a/website/src/pages/prefix-comparator/index.astro +++ /dev/null @@ -1,18 +0,0 @@ ---- -import Layout from '../../layouts/Layout.astro'; -import PrefixComparator from '../../components/PrefixComparator.vue'; ---- - -
    - Return to front page - -

    Prefix Comparator

    -

    - Babel produces a prefix report that tells you how many CURIE prefixes are found underneath each - clique leader prefix. This tool allows you to compare two prefix reports to quickly understand - how two Babel outputs differ. -

    - - -
    -     diff --git a/website/src/pages/trends/index.astro b/website/src/pages/trends/index.astro new file mode 100644 index 0000000..48df7e0 --- /dev/null +++ b/website/src/pages/trends/index.astro @@ -0,0 +1,16 @@ +--- +import Layout from '../../layouts/Layout.astro'; +import Trends from '../../components/Trends.vue'; +--- + + +
    +

    Run history

    +

    + One row per daily validation run: Babel and NameRes versions, database sizes, NameRes p95 latency and test + counts for each environment. Back to the latest results. +

    + + +
    +     From fe29aa0cbd4d17955e0e83d8cacfda1a3fd5ebb3 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Wed, 26 Aug 2026 19:12:18 -0400 Subject: [PATCH 04/60] Regenerate and deploy the dashboard daily instead of on releases MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The new dashboard.yaml workflow (daily cron plus workflow_dispatch) runs the full test suite against every target in targets.ini except localhost — one sequential pytest run per target, capped at 45 minutes each so a hung environment cannot sink the job, with a nonzero exit treated as normal since the report is the artifact — then generates report.json/history.jsonl and deploys the built site to gh-pages. The previous run's history is fetched from the live site, because the deploy action force-pushes gh-pages as a single commit. The release-triggered deploy workflow is gone: it would publish a site with stale or missing data, and workflow_dispatch covers manual redeploys. README.md and CLAUDE.md now describe the dashboard, its generation flow, and the untrusted-input rules its generator and Vue components must follow. Co-Authored-By: Claude Fable 5 --- .github/workflows/dashboard.yaml | 76 +++++++++++++++++++ .../workflows/deploy-website-to-gh-pages.yaml | 29 ------- CLAUDE.md | 51 +++++++++---- README.md | 38 ++++++---- 4 files changed, 137 insertions(+), 57 deletions(-) create mode 100644 .github/workflows/dashboard.yaml delete mode 100644 .github/workflows/deploy-website-to-gh-pages.yaml diff --git a/.github/workflows/dashboard.yaml b/.github/workflows/dashboard.yaml new file mode 100644 index 0000000..6b0a32f --- /dev/null +++ b/.github/workflows/dashboard.yaml @@ -0,0 +1,76 @@ +# Runs the full validation suite against every environment daily, then builds +# and deploys the dashboard website to GitHub Pages. +name: Test dashboard + +on: + schedule: + - cron: '30 6 * * *' + workflow_dispatch: + +permissions: + contents: write # the deploy action pushes to the gh-pages branch + issues: read # the GitHub issue tests read this repo's issues + +concurrency: dashboard-deploy + +jobs: + test-and-deploy: + runs-on: ubuntu-latest + timeout-minutes: 350 + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v6 + + - name: Run the test suite against every target + env: + GITHUB_TOKEN: ${{ github.token }} + # A nonzero pytest exit (failing tests) is normal here: the report is + # the artifact. `timeout 45m` caps the damage from a hung or down + # environment, whose per-test timeouts would otherwise add up. + # ponytail: sequential loop; split into a matrix job with artifact + # merging if total runtime ever approaches the 6h job limit. + run: | + mkdir -p raw + for t in prod test ci ci-es dev exp; do + timeout 45m uv run pytest --target "$t" -n 8 \ + --report-jsonl "raw/$t.jsonl" || echo "target $t exited $?" + done + + - name: Fetch the previous run history + # The published file is the source of truth: the deploy action + # force-pushes gh-pages as a single commit, so the branch is not an + # append log. The Pages CDN caches for ~10 minutes, so a manual + # dispatch right after a deploy could drop one history line — fine at + # a daily cadence. + run: | + curl -fsSL -o old_history.jsonl \ + https://translatorsri.github.io/babel-validation/data/history.jsonl \ + || : > old_history.jsonl + + - name: Generate the report + run: | + uv run python -m src.babel_validation.tools.generate_report \ + --raw-dir raw --targets-ini tests/targets.ini \ + --history-in old_history.jsonl --out-dir website/public/data + + - name: Build the website + working-directory: website + run: | + npm ci + npm run build + touch dist/.nojekyll + + - name: Deploy to GitHub Pages + uses: JamesIves/github-pages-deploy-action@v4 + with: + folder: website/dist + + - name: Upload raw outcomes for debugging + if: always() + uses: actions/upload-artifact@v4 + with: + name: raw-jsonl + path: raw/ + retention-days: 14 diff --git a/.github/workflows/deploy-website-to-gh-pages.yaml b/.github/workflows/deploy-website-to-gh-pages.yaml deleted file mode 100644 index 61a9e16..0000000 --- a/.github/workflows/deploy-website-to-gh-pages.yaml +++ /dev/null @@ -1,29 +0,0 @@ -name: Publish Astro site in `website` to GitHub Pages -on: - release: - types: [released] -permissions: - contents: write -jobs: - build-and-deploy: - concurrency: ci-${{ github.ref }} # Recommended if you intend to make multiple deployments in quick succession. - runs-on: ubuntu-latest - steps: - - name: Checkout 🛎️ - uses: actions/checkout@v3 - - - name: Install and Build 🔧 - working-directory: website - run: | - npm ci - npm run build - - - name: Create a `.nojekyll` file. - run: | - touch website/dist/.nojekyll - - - - name: Deploy 🚀 - uses: JamesIves/github-pages-deploy-action@v4 - with: - folder: website/dist # The folder the action should deploy. diff --git a/CLAUDE.md b/CLAUDE.md index bf1739c..03610eb 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -33,20 +33,16 @@ Note that the repository is *not* currently black-clean — `black --check tests ~30 files it would reformat. Running `black` across the tree would bury a real change in unrelated churn, so format only the files you touch, or match the surrounding style. -### Vue Website (website-vue3-vite/) +### Dashboard Website (website/) ```bash -cd website-vue3-vite && npm install && npm run dev # Dev server -npm run build # Production build -npm run lint # ESLint + auto-fix -npm run test:unit # Vitest unit tests +cd website && npm install && npm run dev # Dev server at localhost:4321/babel-validation/ +npm run build # astro check + production build ``` -### Astro Documentation Site (website/) - -```bash -cd website && npm install && npm run dev # Dev server at localhost:4321 -``` +The dashboard fetches `data/report.json` and `data/history.jsonl`, which are gitignored; +generate them first with `pytest --report-jsonl` plus +`uv run python -m src.babel_validation.tools.generate_report` (see README). ## Architecture @@ -65,7 +61,9 @@ The core of this project. Tests validate NodeNorm and NameRes services across mu **Target system:** `tests/targets.ini` defines endpoints for each environment (dev, prod, test, ci, exp, localhost). Tests use `target_info` fixture to get URLs. The `conftest.py` parametrizes tests across targets via `--target` CLI option; default is `dev`. -**Google Sheet integration:** ~2000+ test cases are pulled from a [shared Google Sheet](https://docs.google.com/spreadsheets/d/11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no/). `src/babel_validation/sources/google_sheets/google_sheet_test_cases.py` fetches and parses these into `TestRow` dataclasses. Rows marked as not expected to pass are wrapped with `pytest.mark.xfail(strict=True)`. Tests are parametrized by row, with IDs like `gsheet:row=42`. +**Google Sheet integration:** ~2000+ test cases are pulled from a shared Google Sheet (its ID is +the `google_sheet_id` default in `src/babel_validation/sources/google_sheets/google_sheet_test_cases.py`), +which fetches and parses these into `TestRow` dataclasses. Rows marked as not expected to pass are wrapped with `pytest.mark.xfail(strict=True)`. Tests are parametrized by row, with IDs like `gsheet:row=42`. **Category filtering:** Google Sheet rows have a Category column. The `test_category` fixture (from conftest.py) returns a callable that tests use to `pytest.skip()` rows not matching `--category`/`--category-exclude` filters. @@ -74,10 +72,15 @@ The core of this project. Tests validate NodeNorm and NameRes services across mu - `tests/nameres/` — NameRes tests (label lookup, autocomplete, Biolink type filtering, blocklist, taxon_specific flag) - `tests/nodenorm/by_issue/` — Per-issue regression tests for NodeNorm (hand-written) -### Web Applications +### Dashboard Website -- **`website-vue3-vite/`** — Active Vue 3 + Vite app that fetches test cases from the same Google Sheet and runs them against multiple endpoints in the browser -- **`website/`** — Newer Astro-based site deployed to GitHub Pages with prefix comparator and autocomplete tools +- **`website/`** — Astro + Vue site deployed to GitHub Pages + (https://translatorsri.github.io/babel-validation/). Renders `report.json` (per-target + `/status` cards plus a tests-by-environment matrix) and `history.jsonl` (one summary line + per run). Regenerated daily by `.github/workflows/dashboard.yaml`: pytest per target with + `--report-jsonl` (a `pytest_runtest_logreport` hook in `tests/conftest.py`), then + `src/babel_validation/tools/generate_report.py` aggregates the raw outcomes, fetches each + target's `/status`, and writes both data files into `website/public/data/`. - **`scala-validation/`** — Legacy, unmaintained ## Untrusted Input @@ -125,6 +128,26 @@ allowlist *before* the call, or the value reaches the GitHub API as a URL path. truncated part of it. The same goes for missing credentials: the GitHub issue tests *skip* without a token, so a green run may have tested nothing. +**The dashboard publishes untrusted text on a public website.** +`src/babel_validation/tools/generate_report.py` is the choke point between the raw pytest +outcomes and `report.json`: it repr-escapes and truncates all text, passes `/status` +responses through a key whitelist, only emits issue ids and source URLs that match the +`targets.ini` `Repositories` allowlist, and withholds blocklist test details entirely (that +sheet may not be public — do not add `ids=` to the blocklist parametrize or link to it). +The Vue components must render report values with `{{ }}` interpolation only — never +`v-html` — and construct links from validated parts (allowlisted `org/repo#N`, +`targets.ini` URLs), never verbatim from report text. + +**Never leak the Google Sheet ID or the GitHub token.** The report, the website, and any +new Git commit must not contain the test-case sheet's ID or a link to either sheet — casual +observers of the public site must not be able to find them. Refer to it as the "Babel +Validation Google Sheet"; sheet *content* (row numbers, queried/expected CURIEs and labels, +category, source — often a GitHub issue link) is fine to publish once it passes the +generator's validation. The sheet ID necessarily lives in +`google_sheet_test_cases.py`, but must not be copied anywhere else. The sheet is expected +to be fully replaced by the GitHub issue system over the next few months, at which point it +can be removed from this repo entirely. + **Caches belong in `cache_dir()`** (`src/babel_validation/core/__init__.py`), a 0700 directory under the user's home — never a fixed name in the shared temp directory. On a CI runner or a shared machine anyone can pre-create such a file, and the issue cache decides what a later run diff --git a/README.md b/README.md index 8c11850..9a26c4c 100644 --- a/README.md +++ b/README.md @@ -9,8 +9,10 @@ underlying data used for the Translator ## PyTest The best tests in this repository are Python tests stored in the [`./tests`](./tests/) folder. -This includes both unit tests as well as "Google Sheet"-based tests, which uses -a [shared Google Sheet](https://docs.google.com/spreadsheets/d/11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no/edit?gid=0#gid=0) containing facts that we can use to test a NodeNorm instance. +This includes both unit tests as well as "Google Sheet"-based tests, which use the shared +Babel Validation Google Sheet containing facts that we can use to test a NodeNorm instance +(its ID is the `google_sheet_id` default in +`src/babel_validation/sources/google_sheets/google_sheet_test_cases.py`). To run these tests, you need to [install `uv`](https://docs.astral.sh/uv/getting-started/installation/). You can then use `uv` to run the tests. The file [`tests/targets.ini`](./tests/targets.ini) allows you to @@ -126,22 +128,30 @@ $ curl -s -H "Authorization: Bearer $GITHUB_TOKEN" https://api.github.com/rate_l The Jupyter Notebook in `log-analysis/` contains some basic analysis of the logs from NodeNorm (and, someday, NameRes) instances. -## The Babel Validator Vue Application +## The dashboard website -The easiest way to validate Babel results on NodeNorm is by running the -Vue app. +The Astro site in `website/` is deployed to https://translatorsri.github.io/babel-validation/. +It shows the results of running this test suite against every environment in +`tests/targets.ini`, alongside each environment's `/status` information (Babel version, +database sizes, NameRes latency). Because test expectations are pinned to the environment +where a new Babel version lands first, environments are not expected to all be green — the +dashboard's purpose is to show *which* issues are visible in *which* environment. -```shell -$ cd website-vue3-vite -$ npm install -$ npm run dev -``` +The `.github/workflows/dashboard.yaml` workflow regenerates and deploys it daily (or on +manual dispatch): it runs pytest per target with `--report-jsonl`, turns the raw outcomes +and `/status` responses into `report.json` and `history.jsonl` with +`src.babel_validation.tools.generate_report`, and publishes the built site to the +`gh-pages` branch. -This will start a local web application and report the URL for accessing it. This website -retrieves tests from [a Google Sheet document](https://docs.google.com/spreadsheets/d/11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no/edit?usp=sharing) -and displays their results across multiple NodeNorm (and, someday, NameRes) endpoints. +To regenerate it locally against a couple of environments: -A new website is in development at `website/` and is currently deployed to https://translatorsri.github.io/babel-validation/. +```shell +$ uv run pytest tests/nodenorm/test_nodenorm_from_gsheet.py tests/nameres/test_nameres_from_gsheet.py \ + --target dev --target prod -n 8 --report-jsonl raw/local.jsonl +$ uv run python -m src.babel_validation.tools.generate_report --raw-dir raw \ + --targets-ini tests/targets.ini --out-dir website/public/data +$ cd website && npm install && npm run dev +``` ## The Babel Validator in Scala From 714447de733f0f46eb69e28c60153f73f4a21ce1 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 27 Aug 2026 01:39:25 -0400 Subject: [PATCH 05/60] Read the Google Sheet ID from BABEL_VALIDATION_SHEET_ID instead of checking it in The sheet is shared as 'anyone with the link' because the CSV export is fetched unauthenticated, so the ID is the capability that grants access. GoogleSheetTestCases() now resolves it from the BABEL_VALIDATION_SHEET_ID environment variable (loaded from .env locally; a repository secret of the same name in the dashboard workflow), fails loudly when it is missing, and rejects values that do not look like a sheet ID before they reach a URL. Its __str__ no longer embeds the ID, since that string is interpolated into assertion messages the dashboard publishes. Once the sheet is re-shared under a new ID, the old ID in the public Git history stops working. The leak-guard unit test now plants a fake ID in the environment and checks the generator cannot surface it in report.json. Co-Authored-By: Claude Fable 5 --- .github/workflows/dashboard.yaml | 3 + CLAUDE.md | 25 ++--- README.md | 7 +- .../google_sheets/google_sheet_test_cases.py | 92 +++++++++++++------ tests/unit/test_generate_report.py | 14 +-- tests/unit/test_google_sheet_id.py | 34 +++++++ 6 files changed, 125 insertions(+), 50 deletions(-) create mode 100644 tests/unit/test_google_sheet_id.py diff --git a/.github/workflows/dashboard.yaml b/.github/workflows/dashboard.yaml index 6b0a32f..aed3867 100644 --- a/.github/workflows/dashboard.yaml +++ b/.github/workflows/dashboard.yaml @@ -26,6 +26,9 @@ jobs: - name: Run the test suite against every target env: GITHUB_TOKEN: ${{ github.token }} + # The Babel Validation Google Sheet ID is a secret: it must never be + # checked in or appear in anything this workflow publishes. + BABEL_VALIDATION_SHEET_ID: ${{ secrets.BABEL_VALIDATION_SHEET_ID }} # A nonzero pytest exit (failing tests) is normal here: the report is # the artifact. `timeout 45m` caps the damage from a hung or down # environment, whose per-test timeouts would otherwise add up. diff --git a/CLAUDE.md b/CLAUDE.md index 03610eb..9b64f5a 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -61,9 +61,11 @@ The core of this project. Tests validate NodeNorm and NameRes services across mu **Target system:** `tests/targets.ini` defines endpoints for each environment (dev, prod, test, ci, exp, localhost). Tests use `target_info` fixture to get URLs. The `conftest.py` parametrizes tests across targets via `--target` CLI option; default is `dev`. -**Google Sheet integration:** ~2000+ test cases are pulled from a shared Google Sheet (its ID is -the `google_sheet_id` default in `src/babel_validation/sources/google_sheets/google_sheet_test_cases.py`), -which fetches and parses these into `TestRow` dataclasses. Rows marked as not expected to pass are wrapped with `pytest.mark.xfail(strict=True)`. Tests are parametrized by row, with IDs like `gsheet:row=42`. +**Google Sheet integration:** ~2000+ test cases are pulled from the shared Babel Validation +Google Sheet. Its ID comes from the `BABEL_VALIDATION_SHEET_ID` environment variable (`.env` +locally, a repository secret in Actions) and is deliberately not checked in. +`src/babel_validation/sources/google_sheets/google_sheet_test_cases.py` fetches and parses +the rows into `TestRow` dataclasses. Rows marked as not expected to pass are wrapped with `pytest.mark.xfail(strict=True)`. Tests are parametrized by row, with IDs like `gsheet:row=42`. **Category filtering:** Google Sheet rows have a Category column. The `test_category` fixture (from conftest.py) returns a callable that tests use to `pytest.skip()` rows not matching `--category`/`--category-exclude` filters. @@ -139,14 +141,15 @@ The Vue components must render report values with `{{ }}` interpolation only — `targets.ini` URLs), never verbatim from report text. **Never leak the Google Sheet ID or the GitHub token.** The report, the website, and any -new Git commit must not contain the test-case sheet's ID or a link to either sheet — casual -observers of the public site must not be able to find them. Refer to it as the "Babel -Validation Google Sheet"; sheet *content* (row numbers, queried/expected CURIEs and labels, -category, source — often a GitHub issue link) is fine to publish once it passes the -generator's validation. The sheet ID necessarily lives in -`google_sheet_test_cases.py`, but must not be copied anywhere else. The sheet is expected -to be fully replaced by the GitHub issue system over the next few months, at which point it -can be removed from this repo entirely. +Git commit must not contain the test-case sheet's ID or a link to either sheet — casual +observers of the public site must not be able to find them, and the ID is the capability +that grants access (the sheet is shared as "anyone with the link", because the CSV fetch is +unauthenticated). It lives only in the `BABEL_VALIDATION_SHEET_ID` environment variable +(`.env` locally — gitignored — and a repository secret in Actions). Refer to it as the +"Babel Validation Google Sheet"; sheet *content* (row numbers, queried/expected CURIEs and +labels, category, source — often a GitHub issue link) is fine to publish once it passes the +generator's validation. The sheet is expected to be fully replaced by the GitHub issue +system over the next few months, at which point it can be removed from this repo entirely. **Caches belong in `cache_dir()`** (`src/babel_validation/core/__init__.py`), a 0700 directory under the user's home — never a fixed name in the shared temp directory. On a CI runner or a diff --git a/README.md b/README.md index 9a26c4c..128c206 100644 --- a/README.md +++ b/README.md @@ -10,9 +10,10 @@ underlying data used for the Translator The best tests in this repository are Python tests stored in the [`./tests`](./tests/) folder. This includes both unit tests as well as "Google Sheet"-based tests, which use the shared -Babel Validation Google Sheet containing facts that we can use to test a NodeNorm instance -(its ID is the `google_sheet_id` default in -`src/babel_validation/sources/google_sheets/google_sheet_test_cases.py`). +Babel Validation Google Sheet containing facts that we can use to test a NodeNorm instance. +The sheet's ID is deliberately not checked in: set `BABEL_VALIDATION_SHEET_ID` in `.env` +(ask a maintainer for the ID; in GitHub Actions it comes from a repository secret of the +same name). To run these tests, you need to [install `uv`](https://docs.astral.sh/uv/getting-started/installation/). You can then use `uv` to run the tests. The file [`tests/targets.ini`](./tests/targets.ini) allows you to diff --git a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py index d144aae..a5050fb 100644 --- a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py +++ b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py @@ -1,14 +1,21 @@ -# We store Babel test cases in Google Sheets at -# https://docs.google.com/spreadsheets/d/11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no/edit?usp=sharing +# We store Babel test cases in the Babel Validation Google Sheet. +# +# The sheet ID is deliberately not checked in: it is the capability that grants +# access to the sheet, so it lives in the BABEL_VALIDATION_SHEET_ID environment +# variable (via .env locally, a repository secret in GitHub Actions) and must +# never appear in the code, the Git history, or anything we publish. # # This library contains classes and methods for accessing those test cases. import csv import hashlib import io +import os +import re import time from collections import Counter from pathlib import Path +import dotenv import pytest import requests from _pytest.mark import ParameterSet @@ -24,17 +31,35 @@ class GoogleSheetTestCases: """ def __str__(self): - return f"Google Sheet Test Cases ({len(self.rows)} test cases from {self.google_sheet_id})" + # No sheet ID here: this string ends up in assertion messages and pytest + # output, which the dashboard publishes. + return f"Google Sheet Test Cases ({len(self.rows)} test cases)" - def __init__(self, google_sheet_id="11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no", cache_ttl_seconds: int = 3600): - """ Create a Google Sheet test case. + def __init__(self, google_sheet_id=None, cache_ttl_seconds: int = 3600): + """Create a Google Sheet test case. - :param google_sheet_id: The Google Sheet identifier to download test cases from. + :param google_sheet_id: The Google Sheet identifier to download test cases from. Defaults to + the BABEL_VALIDATION_SHEET_ID environment variable (loaded from .env if present). :param cache_ttl_seconds: How long a cached download stays valid. pytest deletes the cache at the start of every run (see tests/conftest.py), so this TTL mainly protects other consumers (e.g. csv-to-babeltests) from reading stale data forever. """ + if google_sheet_id is None: + dotenv.load_dotenv() + google_sheet_id = os.environ.get("BABEL_VALIDATION_SHEET_ID") + if not google_sheet_id: + raise RuntimeError( + "No Google Sheet ID: set BABEL_VALIDATION_SHEET_ID (e.g. in .env) to the " + "ID of the Babel Validation Google Sheet." + ) + # The ID goes into a URL path, so refuse anything that does not look like + # one (this also catches quoting mistakes in .env). + if not re.fullmatch(r"[A-Za-z0-9_-]{20,}", google_sheet_id): + raise RuntimeError( + "BABEL_VALIDATION_SHEET_ID does not look like a Google Sheet ID." + ) + self.google_sheet_id = google_sheet_id sheet_hash = hashlib.md5(google_sheet_id.encode()).hexdigest() @@ -42,7 +67,10 @@ def __init__(self, google_sheet_id="11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no lock_file = cache_file.with_suffix(".lock") with FileLock(lock_file): - if cache_file.exists() and time.time() - cache_file.stat().st_mtime < cache_ttl_seconds: + if ( + cache_file.exists() + and time.time() - cache_file.stat().st_mtime < cache_ttl_seconds + ): self.csv_content = cache_file.read_text(encoding="utf-8") else: csv_url = f"https://docs.google.com/spreadsheets/d/{google_sheet_id}/gviz/tq?tqx=out:csv&sheet=Tests" @@ -57,7 +85,12 @@ def __init__(self, google_sheet_id="11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no for row in reader: self.rows.append(row) - def test_rows(self, test_id_prefix: str, test_nodenorm: bool = False, test_nameres: bool = False) -> list[ParameterSet]: + def test_rows( + self, + test_id_prefix: str, + test_nodenorm: bool = False, + test_nameres: bool = False, + ) -> list[ParameterSet]: """ self.rows is the raw list of rows we got back from the Google Sheets. This method transforms that into a list of TestRows. @@ -66,6 +99,7 @@ def test_rows(self, test_id_prefix: str, test_nodenorm: bool = False, test_namer :return: A list of TestRows for the rows in this file. """ + def has_nonempty_value(d: dict): return not all(not s for s in d.values()) @@ -83,30 +117,36 @@ def has_nonempty_value(d: dict): if tr.ExpectPassInNodeNorm: trows.append(pytest.param(tr, id=row_id)) else: - trows.append(pytest.param( - tr, - marks=pytest.mark.xfail( - reason=f"Test row {row_count} is marked as not expected to pass NodeNorm in the " - f"Google Sheet: {tr}", - strict=True), - id=row_id - )) + trows.append( + pytest.param( + tr, + marks=pytest.mark.xfail( + reason=f"Test row {row_count} is marked as not expected to pass NodeNorm in the " + f"Google Sheet: {tr}", + strict=True, + ), + id=row_id, + ) + ) if test_nameres: if tr.ExpectPassInNameRes: trows.append(pytest.param(tr, id=row_id)) else: - trows.append(pytest.param( - tr, - marks=pytest.mark.xfail( - reason=f"Test row {row_count} is marked as not expected to pass NameRes in the " - f"Google Sheet: {tr}", - strict=True), - id=row_id - )) + trows.append( + pytest.param( + tr, + marks=pytest.mark.xfail( + reason=f"Test row {row_count} is marked as not expected to pass NameRes in the " + f"Google Sheet: {tr}", + strict=True, + ), + id=row_id, + ) + ) return trows def categories(self): - """ Return a dict of all the categories of tests available with their counts. """ - return Counter(map(lambda t: t.get('Category', ''), self.rows)) + """Return a dict of all the categories of tests available with their counts.""" + return Counter(map(lambda t: t.get("Category", ""), self.rows)) diff --git a/tests/unit/test_generate_report.py b/tests/unit/test_generate_report.py index 158e847..bac3145 100644 --- a/tests/unit/test_generate_report.py +++ b/tests/unit/test_generate_report.py @@ -2,7 +2,6 @@ literal JSONL records and hostile inline payloads.""" import configparser -import inspect import json import pytest @@ -232,15 +231,10 @@ def test_blocklist_redacted_for_every_target(self): class TestNoSheetLeak: def test_report_never_contains_the_sheet_id_or_a_sheet_link(self, monkeypatch): # The public report must not let casual observers find the Google Sheet. - from src.babel_validation.sources.google_sheets.google_sheet_test_cases import ( - GoogleSheetTestCases, - ) - - sheet_id = ( - inspect.signature(GoogleSheetTestCases.__init__) - .parameters["google_sheet_id"] - .default - ) + # The generator must not read the sheet ID at all, so plant a fake one in + # the environment and check it cannot surface in the output. + sheet_id = "FAKE-SHEET-ID-FOR-LEAK-TEST-0123456789" + monkeypatch.setenv("BABEL_VALIDATION_SHEET_ID", sheet_id) monkeypatch.setattr( generate_report, "fetch_status", lambda url: {"status": "ok"} ) diff --git a/tests/unit/test_google_sheet_id.py b/tests/unit/test_google_sheet_id.py new file mode 100644 index 0000000..d5562e2 --- /dev/null +++ b/tests/unit/test_google_sheet_id.py @@ -0,0 +1,34 @@ +"""The Google Sheet ID is a secret capability: it comes only from the +BABEL_VALIDATION_SHEET_ID environment variable, and a missing or implausible +value must fail loudly rather than fetch something unexpected.""" + +import pytest + +from src.babel_validation.sources.google_sheets.google_sheet_test_cases import ( + GoogleSheetTestCases, +) + +pytestmark = pytest.mark.unit + + +def test_missing_sheet_id_fails_loudly(monkeypatch): + # Set-but-empty, not deleted: dotenv.load_dotenv() will not override a key + # already in os.environ, so this defeats any ID in the developer's .env. + monkeypatch.setenv("BABEL_VALIDATION_SHEET_ID", "") + with pytest.raises(RuntimeError, match="BABEL_VALIDATION_SHEET_ID"): + GoogleSheetTestCases() + + +@pytest.mark.parametrize( + "bad_id", + [ + "too-short", + '"quoted-sheet-id-from-a-dotenv-mistake"', + "has spaces in the sheet id somewhere", + "path/traversal/attempt-0123456789abcdef", + ], +) +def test_implausible_sheet_id_is_rejected(monkeypatch, bad_id): + monkeypatch.setenv("BABEL_VALIDATION_SHEET_ID", bad_id) + with pytest.raises(RuntimeError, match="does not look like"): + GoogleSheetTestCases() From f22b9263351374daa468b6ec7fb01a1bf9a2aca0 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 27 Aug 2026 01:46:06 -0400 Subject: [PATCH 06/60] Read the blocklist sheet ID from the environment too The blocklist sheet logs Red Team offensive terms, so its ID is even more of a secret than the test-case sheet's. Both sheets now resolve their IDs through a shared resolve_sheet_id() helper: the environment variable (BABEL_VALIDATION_SHEET_ID / BABEL_VALIDATION_BLOCKLIST_SHEET_ID, loaded from .env locally, repository secrets in the dashboard workflow), failing loudly on a missing or implausible value. Co-Authored-By: Claude Fable 5 --- .github/workflows/dashboard.yaml | 5 +-- CLAUDE.md | 8 +++-- .../sources/google_sheets/__init__.py | 31 +++++++++++++++++++ .../sources/google_sheets/blocklist.py | 25 +++++++++------ .../google_sheets/google_sheet_test_cases.py | 19 ++---------- tests/unit/test_google_sheet_id.py | 27 +++++++++++----- 6 files changed, 76 insertions(+), 39 deletions(-) diff --git a/.github/workflows/dashboard.yaml b/.github/workflows/dashboard.yaml index aed3867..cf7321e 100644 --- a/.github/workflows/dashboard.yaml +++ b/.github/workflows/dashboard.yaml @@ -26,9 +26,10 @@ jobs: - name: Run the test suite against every target env: GITHUB_TOKEN: ${{ github.token }} - # The Babel Validation Google Sheet ID is a secret: it must never be - # checked in or appear in anything this workflow publishes. + # The Google Sheet IDs are secrets: they must never be checked in or + # appear in anything this workflow publishes. BABEL_VALIDATION_SHEET_ID: ${{ secrets.BABEL_VALIDATION_SHEET_ID }} + BABEL_VALIDATION_BLOCKLIST_SHEET_ID: ${{ secrets.BABEL_VALIDATION_BLOCKLIST_SHEET_ID }} # A nonzero pytest exit (failing tests) is normal here: the report is # the artifact. `timeout 45m` caps the damage from a hung or down # environment, whose per-test timeouts would otherwise add up. diff --git a/CLAUDE.md b/CLAUDE.md index 9b64f5a..aa88394 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -143,9 +143,11 @@ The Vue components must render report values with `{{ }}` interpolation only — **Never leak the Google Sheet ID or the GitHub token.** The report, the website, and any Git commit must not contain the test-case sheet's ID or a link to either sheet — casual observers of the public site must not be able to find them, and the ID is the capability -that grants access (the sheet is shared as "anyone with the link", because the CSV fetch is -unauthenticated). It lives only in the `BABEL_VALIDATION_SHEET_ID` environment variable -(`.env` locally — gitignored — and a repository secret in Actions). Refer to it as the +that grants access (the sheets are shared as "anyone with the link", because the CSV fetch +is unauthenticated). The IDs live only in the `BABEL_VALIDATION_SHEET_ID` and +`BABEL_VALIDATION_BLOCKLIST_SHEET_ID` environment variables (`.env` locally — gitignored — +and repository secrets in Actions), resolved through +`src/babel_validation/sources/google_sheets/resolve_sheet_id()`. Refer to it as the "Babel Validation Google Sheet"; sheet *content* (row numbers, queried/expected CURIEs and labels, category, source — often a GitHub issue link) is fine to publish once it passes the generator's validation. The sheet is expected to be fully replaced by the GitHub issue diff --git a/src/babel_validation/sources/google_sheets/__init__.py b/src/babel_validation/sources/google_sheets/__init__.py index e69de29..7045ef0 100644 --- a/src/babel_validation/sources/google_sheets/__init__.py +++ b/src/babel_validation/sources/google_sheets/__init__.py @@ -0,0 +1,31 @@ +# Google Sheet IDs are deliberately not checked in: for an unauthenticated CSV +# export the ID is the capability that grants access, so each sheet's ID lives +# in an environment variable (via .env locally, a repository secret in GitHub +# Actions) and must never appear in the code, the Git history, or anything we +# publish. +import os +import re + +import dotenv + +_SHEET_ID_RE = re.compile(r"[A-Za-z0-9_-]{20,}") + + +def resolve_sheet_id(env_var, sheet_id=None): + """ + Return a validated Google Sheet ID: the one passed in, or the value of the + named environment variable (loading .env first). A missing or implausible + value fails loudly — the ID goes into a URL path, and the format check also + catches quoting mistakes in .env. + """ + if sheet_id is None: + dotenv.load_dotenv() + sheet_id = os.environ.get(env_var) + if not sheet_id: + raise RuntimeError( + f"No Google Sheet ID: set {env_var} (e.g. in .env). " + "Ask a maintainer for the ID." + ) + if not _SHEET_ID_RE.fullmatch(sheet_id): + raise RuntimeError(f"{env_var} does not look like a Google Sheet ID.") + return sheet_id diff --git a/src/babel_validation/sources/google_sheets/blocklist.py b/src/babel_validation/sources/google_sheets/blocklist.py index 686bda1..1472662 100644 --- a/src/babel_validation/sources/google_sheets/blocklist.py +++ b/src/babel_validation/sources/google_sheets/blocklist.py @@ -5,6 +5,8 @@ import requests +from . import resolve_sheet_id + # The Translator Blocklist is stored in a private GitHub repository; however, # we are currently using a spreadsheet to manage "Red Team" exercises where @@ -16,6 +18,7 @@ class BlocklistEntry: """ A single Blocklist entry. """ + Query: Optional[str] = None CURIE: Optional[str] = None Blocked: Optional[str] = None @@ -26,8 +29,8 @@ class BlocklistEntry: Comment: Optional[str] = None def is_blocked(self): - """ Is this term supposed to be blocked? """ - if self.Blocked is not None and self.Blocked == 'y': + """Is this term supposed to be blocked?""" + if self.Blocked is not None and self.Blocked == "y": return True return False @@ -40,14 +43,14 @@ def from_gsheet_dict(row): """ return BlocklistEntry( - Query=row.get('String (optional)', None), - CURIE=row.get('CURIE (optional)', None), - Blocked=row['Blocked?'], - Status=row['Status (Feb 21, 2024)'], - Issue=row['Blocklist issue'], + Query=row.get("String (optional)", None), + CURIE=row.get("CURIE (optional)", None), + Blocked=row["Blocked?"], + Status=row["Status (Feb 21, 2024)"], + Issue=row["Blocklist issue"], TreatsOnly=row['Block for "treats" only?'], - Submitter=row['Submitter'], - Comment=row['Comment (optional)'], + Submitter=row["Submitter"], + Comment=row["Comment (optional)"], ) @@ -57,7 +60,9 @@ def load_blocklist_from_gsheet(): :return: A list of BlocklistEntry. """ - google_sheet_id = '1UR2eplHBvFRwaSIVOhlB44wpfNPY1z7AVzUkqzDqIWA' + # This sheet logs "Red Team" offensive terms, so its ID is doubly a secret: + # it comes only from the environment and must never be checked in. + google_sheet_id = resolve_sheet_id("BABEL_VALIDATION_BLOCKLIST_SHEET_ID") csv_url = f"https://docs.google.com/spreadsheets/d/{google_sheet_id}/gviz/tq?tqx=out:csv&sheet=Tests" response = requests.get(csv_url, timeout=10) diff --git a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py index a5050fb..c02733a 100644 --- a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py +++ b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py @@ -9,18 +9,16 @@ import csv import hashlib import io -import os -import re import time from collections import Counter from pathlib import Path -import dotenv import pytest import requests from _pytest.mark import ParameterSet from filelock import FileLock +from . import resolve_sheet_id from ...core import cache_dir from ...core.testrow import TestRow @@ -45,20 +43,7 @@ def __init__(self, google_sheet_id=None, cache_ttl_seconds: int = 3600): (e.g. csv-to-babeltests) from reading stale data forever. """ - if google_sheet_id is None: - dotenv.load_dotenv() - google_sheet_id = os.environ.get("BABEL_VALIDATION_SHEET_ID") - if not google_sheet_id: - raise RuntimeError( - "No Google Sheet ID: set BABEL_VALIDATION_SHEET_ID (e.g. in .env) to the " - "ID of the Babel Validation Google Sheet." - ) - # The ID goes into a URL path, so refuse anything that does not look like - # one (this also catches quoting mistakes in .env). - if not re.fullmatch(r"[A-Za-z0-9_-]{20,}", google_sheet_id): - raise RuntimeError( - "BABEL_VALIDATION_SHEET_ID does not look like a Google Sheet ID." - ) + google_sheet_id = resolve_sheet_id("BABEL_VALIDATION_SHEET_ID", google_sheet_id) self.google_sheet_id = google_sheet_id diff --git a/tests/unit/test_google_sheet_id.py b/tests/unit/test_google_sheet_id.py index d5562e2..2c3071b 100644 --- a/tests/unit/test_google_sheet_id.py +++ b/tests/unit/test_google_sheet_id.py @@ -1,22 +1,26 @@ -"""The Google Sheet ID is a secret capability: it comes only from the -BABEL_VALIDATION_SHEET_ID environment variable, and a missing or implausible -value must fail loudly rather than fetch something unexpected.""" +"""Google Sheet IDs are secret capabilities: they come only from environment +variables, and a missing or implausible value must fail loudly rather than +fetch something unexpected.""" import pytest +from src.babel_validation.sources.google_sheets import resolve_sheet_id from src.babel_validation.sources.google_sheets.google_sheet_test_cases import ( GoogleSheetTestCases, ) pytestmark = pytest.mark.unit +ENV_VARS = ["BABEL_VALIDATION_SHEET_ID", "BABEL_VALIDATION_BLOCKLIST_SHEET_ID"] -def test_missing_sheet_id_fails_loudly(monkeypatch): + +@pytest.mark.parametrize("env_var", ENV_VARS) +def test_missing_sheet_id_fails_loudly(monkeypatch, env_var): # Set-but-empty, not deleted: dotenv.load_dotenv() will not override a key # already in os.environ, so this defeats any ID in the developer's .env. - monkeypatch.setenv("BABEL_VALIDATION_SHEET_ID", "") - with pytest.raises(RuntimeError, match="BABEL_VALIDATION_SHEET_ID"): - GoogleSheetTestCases() + monkeypatch.setenv(env_var, "") + with pytest.raises(RuntimeError, match=env_var): + resolve_sheet_id(env_var) @pytest.mark.parametrize( @@ -31,4 +35,13 @@ def test_missing_sheet_id_fails_loudly(monkeypatch): def test_implausible_sheet_id_is_rejected(monkeypatch, bad_id): monkeypatch.setenv("BABEL_VALIDATION_SHEET_ID", bad_id) with pytest.raises(RuntimeError, match="does not look like"): + resolve_sheet_id("BABEL_VALIDATION_SHEET_ID") + # An explicit argument gets the same format check. + with pytest.raises(RuntimeError, match="does not look like"): + resolve_sheet_id("BABEL_VALIDATION_SHEET_ID", bad_id) + + +def test_google_sheet_test_cases_uses_the_env_var(monkeypatch): + monkeypatch.setenv("BABEL_VALIDATION_SHEET_ID", "") + with pytest.raises(RuntimeError, match="BABEL_VALIDATION_SHEET_ID"): GoogleSheetTestCases() From 725aaca6de307f2d5deb5c727063462c09337fe9 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 27 Aug 2026 02:11:25 -0400 Subject: [PATCH 07/60] Redesign the dashboard: status table in deployment order, filter panel, pagination, shareable links MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The per-environment status cards become one transposed table with environments as columns in deployment order (exp, dev, ci, ci-es, test, prod) and one row per status value, so a version working its way towards prod reads left to right and the odd environment out is highlighted (table-warning on cells that differ from the majority). Test-outcome counts follow as rows in the same table, and adding a status row is now one entry in STATUS_ROWS. The results matrix and the trends page use the same column order. The always-visible 'interesting only' checkbox — one accidental click away from rendering thousands of rows — moves into a collapsible Filters panel alongside text search, test-source and has-outcome filters, and the matrix is paginated (100 rows per page by default, selectable) instead of rendered in full. Filter state, page, and the expanded test live in the URL query string, so the address bar always reproduces the current view; a 'Copy link to this view' button copies it, and a shared link to a test hidden by the current filters pins that test at the top rather than showing nothing. Query parameters are untrusted input: they feed only string filters and key lookups, never markup or fetch targets. Co-Authored-By: Claude Fable 5 --- website/src/components/Dashboard.vue | 424 +++++++++++++++++++++------ website/src/components/Trends.vue | 4 +- 2 files changed, 344 insertions(+), 84 deletions(-) diff --git a/website/src/components/Dashboard.vue b/website/src/components/Dashboard.vue index dc7f95e..dba0b9d 100644 --- a/website/src/components/Dashboard.vue +++ b/website/src/components/Dashboard.vue @@ -1,16 +1,20 @@ @@ -202,76 +412,100 @@ export default { environments may have been unreachable during the run. -
    -
    -
    -
    - {{ target }} - - - Babel {{ report.targets[target].nodenorm_status.babel_version }} +

    Environments

    +
    + + + + + + + + + + + + + + + + + +
    + {{ target }} + no results +
    {{ statusRow.label }} + + {{ statusValue(statusRow, target) }} - - - - -
    -
    - NodeNorm status: {{ report.targets[target].nodenorm_status.error }} -
    -
    - NodeNorm: {{ formatCount(report.targets[target].nodenorm_status.databases?.eq_id_to_id_db?.count) }} identifiers - - -
    -
    - NameRes status: {{ report.targets[target].nameres_status.error }} -
    -
    - NameRes - - {{ formatCount(report.targets[target].nameres_status.solr?.numDocs) }} documents - - -
    -
    - -
    -
    - + +
    {{ outcome }} tests + + {{ formatCount(report.targets[target].counts[outcome]) }} + + — +
    +
    + +
    +

    Test results

    +
    + + {{ formatCount(filteredRows.length) }} of {{ formatCount(totalResults) }} results + +
    -
    -
    - - +
    +
    +
    + + +
    + + +
    +
    +
    +
    Test source
    +
    + + +
    +
    +
    +
    Has outcome (in any environment)
    +
    + + +
    +
    +
    + +
    + Could not access the clipboard — copy the address bar instead; it + carries the same filters. +
    + +
    -
    - +
    @@ -318,6 +552,25 @@ export default {
    Test

    No test results match the current filters.

    +
    @@ -329,4 +582,9 @@ export default { padding: 0.5rem; margin-bottom: 0; } +.results-matrix thead th { + position: sticky; + top: 0; + background: var(--bs-body-bg, #fff); +} diff --git a/website/src/components/Trends.vue b/website/src/components/Trends.vue index 1bc4400..edf9aa7 100644 --- a/website/src/components/Trends.vue +++ b/website/src/components/Trends.vue @@ -4,6 +4,8 @@ history file is derived from untrusted service responses. --> diff --git a/website/src/layouts/Layout.astro b/website/src/layouts/Layout.astro index 351d028..b546814 100644 --- a/website/src/layouts/Layout.astro +++ b/website/src/layouts/Layout.astro @@ -1,34 +1,81 @@ --- -// Load properties +// The one layout: page shell, navigation, footer, and the theme boot script. +// +// Content sits in cards on --bs-body-bg, over a --bs-body-tertiary page. That +// tint difference is the whole visual hierarchy; keep new sections in cards. +import 'bootstrap/dist/css/bootstrap.css'; +import '../styles/theme.css'; +import NavBar from '../components/NavBar.astro'; + interface Props { - title: string; - description: string; + title: string; + description: string; + active?: 'dashboard' | 'results' | 'history'; } -const { title, description } = Astro.props; +const { title, description, active } = Astro.props; +const base = import.meta.env.BASE_URL; -// Load Bootstrap -import 'bootstrap/dist/css/bootstrap.css' +const footerLinks = [ + { label: 'babel-validation', href: 'https://github.com/TranslatorSRI/babel-validation' }, + { label: 'Babel', href: 'https://github.com/NCATSTranslator/Babel' }, + { label: 'Babel Explorer', href: 'https://translatorsri.github.io/babel-explorer/' }, + { label: 'NodeNorm', href: 'https://github.com/NCATSTranslator/NodeNormalization' }, + { label: 'NodeNorm API', href: 'https://nodenorm.transltr.io/docs' }, + { label: 'NameRes', href: 'https://github.com/NCATSTranslator/NameResolution' }, + { label: 'NameRes API', href: 'https://name-lookup.transltr.io/docs' }, +]; --- - - - - - - - - {title} - - -
    - -
    - + + + + + + + + {title} + + + + + +
    + +
    + +     + - diff --git a/website/src/pages/index.astro b/website/src/pages/index.astro index c542316..446efad 100644 --- a/website/src/pages/index.astro +++ b/website/src/pages/index.astro @@ -3,20 +3,33 @@ import Layout from '../layouts/Layout.astro'; import Dashboard from '../components/Dashboard.vue'; --- - -
    -

    Babel Validation

    -

    - Babel generates the datasets of - interrelated identifiers behind Node Normalization - and Name Resolution. This dashboard shows the - results of running the babel-validation test - suite daily against every deployment environment. Because test expectations are pinned to the environment where - a new Babel version lands first, environments are not expected to all be green — the point is to see - which issues are visible in which environment. See also the - run history. -

    + +

    Babel Validation

    - -
    +
    +
    +

    + Babel generates the datasets of + interrelated identifiers behind Node Normalization + and Name Resolution. This + dashboard shows the results of running the + babel-validation test suite + daily against every deployment environment. Because test expectations are pinned to the + environment where a new Babel version lands first, environments are not expected to all be + green — the point is to see which issues are visible in which environment. +

    +
    +
    + +
    +
    + +
    +
    diff --git a/website/src/pages/trends/index.astro b/website/src/pages/trends/index.astro index 6b4945f..b5a2128 100644 --- a/website/src/pages/trends/index.astro +++ b/website/src/pages/trends/index.astro @@ -3,14 +3,20 @@ import Layout from '../../layouts/Layout.astro'; import Trends from '../../components/Trends.vue'; --- - -
    -

    Run history

    -

    - One row per daily validation run: Babel and NameRes versions, database sizes, NameRes p95 latency and test - counts for each environment. Back to the latest results. -

    + +

    Run history

    - -
    +
    +
    + One row per daily validation run: Babel and NameRes versions, database sizes, NameRes p95 + latency and test counts for each environment. +
    +
    + +
    +
    diff --git a/website/src/styles/theme.css b/website/src/styles/theme.css new file mode 100644 index 0000000..8bf0be7 --- /dev/null +++ b/website/src/styles/theme.css @@ -0,0 +1,118 @@ +/* + theme.css - the site's entire custom stylesheet, imported only by Layout.astro. + Everything else is stock Bootstrap 5.3: the look comes from a tinted page + behind cards on the body background, a dark navbar, and a denser table. + + Bootstrap's semantic variables (--bs-body-bg, --bs-border-color, the + *-subtle/*-emphasis pairs) all flip under data-bs-theme, so anything defined + in terms of them is dark-mode-correct for free. Hardcoded colours are not: + do not introduce any. +*/ + +:root { + /* Height of the sticky filter bar, measured at runtime by FilterBar.vue. + The results table header sticks directly beneath it. */ + --filterbar-h: 0px; +} + +body { + /* A deep link to a test must not land underneath the sticky filter bar. */ + scroll-padding-top: calc(var(--filterbar-h) + 1rem); +} + +/* --- Chrome ------------------------------------------------------------- */ + +.navbar-brand { + font-weight: 600; + letter-spacing: -0.01em; +} + +.site-footer { + border-top: 1px solid var(--bs-border-color); + font-size: 0.875rem; +} + +/* --- Surfaces ----------------------------------------------------------- */ + +/* Cards carry the content; the page tint behind them is what separates one + section from the next. Keep the header tint - it is the contrast that makes + a filter bar or a table heading findable. */ +.card { + --bs-card-border-color: var(--bs-border-color-translucent); +} + +.card-header { + font-weight: 600; +} + +/* --- Tables ------------------------------------------------------------- */ + +.table-dense { + font-size: 0.875rem; +} + +.table-dense > :not(caption) > * > * { + padding: 0.3rem 0.5rem; +} + +/* A sticky needs its own background: table cells are transparent by + default, so rows would show through as they scroll under it. + + Both sticky layers break silently if any ancestor gets `overflow: auto` - + which is exactly what .table-responsive sets. Do not wrap these tables in + one; drop columns at narrow widths instead. */ +.sticky-head thead th { + position: sticky; + top: var(--filterbar-h); + z-index: 2; + background: var(--bs-body-bg); +} + +/* --- Test outcomes ------------------------------------------------------ */ + +/* Only failures and errors are saturated. Everything else is a subtle pair, so + a screen of results reads as "mostly fine, these two are not" rather than as + a wall of colour. The subtle/emphasis pairs flip under data-bs-theme; the + solid text-bg-* helpers do not, which is why they are not used here. */ +.outcome { + display: inline-block; + min-width: 3.25rem; + text-align: center; + font-variant-numeric: tabular-nums; +} + +.outcome-passed { + background: var(--bs-success-bg-subtle); + color: var(--bs-success-text-emphasis); +} + +.outcome-xfailed, +.outcome-skipped { + background: var(--bs-secondary-bg-subtle); + color: var(--bs-secondary-text-emphasis); +} + +.outcome-xpassed { + background: var(--bs-warning-bg-subtle); + color: var(--bs-warning-text-emphasis); +} + +.outcome-failed { + background: var(--bs-danger); + color: #fff; +} + +.outcome-error { + background: var(--bs-dark); + color: #fff; +} + +/* --- Failure detail ----------------------------------------------------- */ + +.failure-message { + white-space: pre-wrap; + word-break: break-word; + background: var(--bs-tertiary-bg); + padding: 0.5rem; + margin-bottom: 0; +} From 40a6c1391b73d0daa6f5eaea8e4214eaad17cc31 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 27 Aug 2026 18:34:48 -0400 Subject: [PATCH 22/60] Move the report's non-rendering logic into src/reportData.js MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Dashboard.vue was 604 lines because it held everything: the status-row spec, the row labels, the interestingness predicate, the link builders and the fetch, alongside the markup. Splitting the page in two means two components need all of that, so it moves out first, on its own, with no behaviour change — the six tests pass untouched. The link builders move byte for byte. Their regexes and their encodeURIComponent calls are the security boundary between untrusted report text and a URL, so the file says so where someone might otherwise tidy them. Co-Authored-By: Claude Opus 5 --- website/src/components/Dashboard.vue | 164 ++++------------------ website/src/components/Trends.vue | 13 +- website/src/reportData.js | 198 +++++++++++++++++++++++++++ 3 files changed, 229 insertions(+), 146 deletions(-) create mode 100644 website/src/reportData.js diff --git a/website/src/components/Dashboard.vue b/website/src/components/Dashboard.vue index a86c43b..ee7c1b2 100644 --- a/website/src/components/Dashboard.vue +++ b/website/src/components/Dashboard.vue @@ -13,72 +13,26 @@ and key lookups, never markup or fetch targets. --> - - - - diff --git a/website/src/components/FilterBar.vue b/website/src/components/FilterBar.vue new file mode 100644 index 0000000..f4fb2f8 --- /dev/null +++ b/website/src/components/FilterBar.vue @@ -0,0 +1,178 @@ + + + + diff --git a/website/src/components/NavBar.astro b/website/src/components/NavBar.astro index 2804a72..fcba2c1 100644 --- a/website/src/components/NavBar.astro +++ b/website/src/components/NavBar.astro @@ -12,10 +12,10 @@ interface Props { const { active } = Astro.props; const base = import.meta.env.BASE_URL; -// Only pages that exist: Results arrives when the dashboard splits in two, and // History is still served from /trends/ until that page is rewritten. const pages = [ { id: 'dashboard', label: 'Dashboard', href: base }, + { id: 'results', label: 'Results', href: `${base}results/` }, { id: 'history', label: 'History', href: `${base}trends/` }, ]; diff --git a/website/src/components/Overview.vue b/website/src/components/Overview.vue new file mode 100644 index 0000000..0381336 --- /dev/null +++ b/website/src/components/Overview.vue @@ -0,0 +1,167 @@ + + + + diff --git a/website/src/components/Results.vue b/website/src/components/Results.vue new file mode 100644 index 0000000..df8cc47 --- /dev/null +++ b/website/src/components/Results.vue @@ -0,0 +1,406 @@ + + + + diff --git a/website/src/components/StatusMatrix.vue b/website/src/components/StatusMatrix.vue new file mode 100644 index 0000000..b54087e --- /dev/null +++ b/website/src/components/StatusMatrix.vue @@ -0,0 +1,163 @@ + + + + diff --git a/website/src/pages/index.astro b/website/src/pages/index.astro index 446efad..e8a6af0 100644 --- a/website/src/pages/index.astro +++ b/website/src/pages/index.astro @@ -1,6 +1,6 @@ --- import Layout from '../layouts/Layout.astro'; -import Dashboard from '../components/Dashboard.vue'; +import Overview from '../components/Overview.vue'; --- -

    Babel Validation

    +

    Babel Validation

    +

    + Babel generates the datasets of + interrelated identifiers behind Node Normalization and Name Resolution. This + dashboard runs the babel-validation test suite daily against every deployment environment. Because test expectations are pinned to + the environment where a new Babel version lands first, environments are not expected to all be + green — the point is to see which issues are visible in which environment. +

    -
    -
    -

    - Babel generates the datasets of - interrelated identifiers behind Node Normalization - and Name Resolution. This - dashboard shows the results of running the - babel-validation test suite - daily against every deployment environment. Because test expectations are pinned to the - environment where a new Babel version lands first, environments are not expected to all be - green — the point is to see which issues are visible in which environment. -

    -
    -
    - -
    -
    - -
    -
    +     diff --git a/website/src/pages/results/index.astro b/website/src/pages/results/index.astro new file mode 100644 index 0000000..28a546f --- /dev/null +++ b/website/src/pages/results/index.astro @@ -0,0 +1,14 @@ +--- +import Layout from '../../layouts/Layout.astro'; +import Results from '../../components/Results.vue'; +--- + + +

    Test results

    + + +     diff --git a/website/src/styles/theme.css b/website/src/styles/theme.css index 8bf0be7..b47593d 100644 --- a/website/src/styles/theme.css +++ b/website/src/styles/theme.css @@ -68,6 +68,19 @@ body { background: var(--bs-body-bg); } +/* The controls above the results table stay put while it scrolls, and the + table header sticks directly beneath them - hence --filterbar-h, which + FilterBar.vue measures because the bar wraps at narrow widths. Sticky + elements need an opaque background of their own or rows show through. */ +.filter-bar { + position: sticky; + top: 0; + z-index: 3; + background: var(--bs-body-bg); + border-bottom: 1px solid var(--bs-border-color); + margin-bottom: 1rem; +} + /* --- Test outcomes ------------------------------------------------------ */ /* Only failures and errors are saturated. Everything else is a subtle pair, so diff --git a/website/test/reportData.test.js b/website/test/reportData.test.js new file mode 100644 index 0000000..f0f7bf1 --- /dev/null +++ b/website/test/reportData.test.js @@ -0,0 +1,45 @@ +// The link builders turn untrusted report text into URLs, so they are the one +// piece of reportData.js worth testing directly. +import { describe, it, expect } from 'vitest'; +import { explorerLink, isInteresting, issueLink, rowLabel, runLink } from '../src/reportData.js'; + +describe('link builders', () => { + it('only links an issue id shaped like org/repo#N', () => { + expect(issueLink({ issue: 'NCATSTranslator/Babel#71' })).toBe( + 'https://github.com/NCATSTranslator/Babel/issues/71' + ); + for (const issue of ['evil/repo#1);drop', '../../etc#1', 'no-slash#1', 'a/b#x', undefined]) { + expect(issueLink({ issue })).toBeNull(); + } + }); + + it('encodes query values into the Explorer link', () => { + const link = explorerLink('nodenorm/t.py::x', { query_id: 'FOO:1&a#b', outcomes: { dev: {} } }, [ + 'dev', + ]); + expect(link).toContain('curie=FOO%3A1%26a%23b'); + expect(link).not.toContain('#b'); + }); + + it('only links a numeric run id', () => { + expect(runLink('123')).toContain('/actions/runs/123'); + expect(runLink('1 2')).toBeNull(); + expect(runLink(undefined)).toBeNull(); + }); +}); + +describe('row classification', () => { + it('counts disagreement between environments as interesting', () => { + expect(isInteresting({ outcomes: { dev: { o: 'passed' }, prod: { o: 'passed' } } })).toBe(false); + expect(isInteresting({ outcomes: { dev: { o: 'passed' }, prod: { o: 'xfailed' } } })).toBe(true); + expect(isInteresting({ outcomes: { dev: { o: 'failed' } } })).toBe(true); + }); + + it('never labels a blocklist row with its content', () => { + const label = rowLabel('nameres/test_blocklist.py::test[entry47]', { + kind: 'blocklist', + query_label: 'a blocked term', + }); + expect(label).toBe('blocklist entry (details withheld)'); + }); +}); diff --git a/website/test/dashboard.test.js b/website/test/results.test.js similarity index 58% rename from website/test/dashboard.test.js rename to website/test/results.test.js index afbbc68..655dbfa 100644 --- a/website/test/dashboard.test.js +++ b/website/test/results.test.js @@ -1,9 +1,9 @@ -// Regression tests for the dashboard's client-side logic. Everything here was -// a real bug: shared links that lost their page, and a query parameter that -// reached Object.prototype. +// Regression tests for the results page's client-side logic. Everything in the +// first block was a real bug: shared links that lost their page, and a query +// parameter that reached Object.prototype. import { describe, it, expect, beforeEach, vi } from 'vitest'; import { mount, flushPromises } from '@vue/test-utils'; -import Dashboard from '../src/components/Dashboard.vue'; +import Results from '../src/components/Results.vue'; import Trends from '../src/components/Trends.vue'; const TARGETS = ['dev', 'prod']; @@ -27,6 +27,7 @@ function report(rowCount = 60) { kind: 'gsheet', row: i, category: i % 2 ? 'Diseases' : 'Genes', + source: i % 3 ? 'Reported in an issue' : 'TAQA', outcomes: { dev: { o: 'failed' }, prod: { o: 'passed' } }, }; } @@ -44,12 +45,12 @@ function report(rowCount = 60) { async function mountAt(query, data = report()) { window.history.replaceState(null, '', query); global.fetch = vi.fn().mockResolvedValue({ ok: true, json: async () => data }); - const wrapper = mount(Dashboard, { props: { dataUrl: '/data/report.json' } }); + const wrapper = mount(Results, { props: { dataUrl: '/data/report.json' } }); await flushPromises(); return wrapper; } -describe('Dashboard URL state', () => { +describe('Results URL state', () => { beforeEach(() => { window.history.replaceState(null, '', '/'); }); @@ -102,3 +103,49 @@ describe('Trends', () => { expect(wrapper.text()).toContain('d'); }); }); + +describe('Results filters', () => { + it('round-trips the category, source and environment filters through the URL', async () => { + const wrapper = await mountAt('/?cat=Diseases&src=TAQA&env=dev&has=failed'); + expect(wrapper.vm.filters.cat).toBe('Diseases'); + expect(wrapper.vm.filters.src).toBe('TAQA'); + expect(wrapper.vm.filters.env).toBe('dev'); + wrapper.vm.filters.q = 'row'; + await flushPromises(); + const params = new URLSearchParams(window.location.search); + expect([params.get('cat'), params.get('src'), params.get('env')]).toEqual([ + 'Diseases', + 'TAQA', + 'dev', + ]); + }); + + it('applies the outcome filter to the chosen environment only', async () => { + const wrapper = await mountAt('/?env=prod&has=failed'); + // Every row passes in prod and fails in dev, so nothing matches. + expect(wrapper.vm.filteredRows).toHaveLength(0); + wrapper.vm.filters.env = 'dev'; + await flushPromises(); + expect(wrapper.vm.filteredRows.length).toBeGreaterThan(0); + }); + + it('withholds every detail of a blocklist row, whatever the report carries', async () => { + const key = 'nameres/test_blocklist.py::test_check_blocklist_entry[blocklist_entry47]'; + const data = report(2); + // A generator regression that started emitting these must not leak them here. + data.results[key] = { + kind: 'blocklist', + query_id: 'SECRET:12345', + query_label: 'a blocked term', + issue: 'NCATSTranslator/Babel#71', + source: 'the blocklist sheet', + outcomes: { dev: { o: 'failed', msg: 'blocked term SECRET:12345 was returned' } }, + }; + const wrapper = await mountAt(`/?all=1&test=${encodeURIComponent(key)}`, data); + const text = wrapper.text(); + expect(text).toContain('blocklist entry (details withheld)'); + for (const secret of ['SECRET:12345', 'a blocked term', 'Babel#71', 'the blocklist sheet']) { + expect(text).not.toContain(secret); + } + }); +}); diff --git a/website/test/statusMatrix.test.js b/website/test/statusMatrix.test.js new file mode 100644 index 0000000..fd57674 --- /dev/null +++ b/website/test/statusMatrix.test.js @@ -0,0 +1,60 @@ +// The odd-one-out shading is the whole point of showing environments side by +// side, and it had no test before the redesign split it into its own component. +import { describe, it, expect } from 'vitest'; +import { mount } from '@vue/test-utils'; +import StatusMatrix from '../src/components/StatusMatrix.vue'; + +const TARGETS = ['exp', 'dev', 'prod']; + +function target(babel, extra = {}) { + return { + nodenorm_status: { status: 'running', babel_version: babel, databases: {}, ...extra.nodenorm }, + nameres_status: { status: 'running', ...extra.nameres }, + counts: { passed: 1, failed: 0, xfailed: 0, xpassed: 0, skipped: 0, error: 0 }, + unreachable: false, + }; +} + +function mountWith(targets) { + return mount(StatusMatrix, { + props: { report: { targets }, targetNames: Object.keys(targets) }, + }); +} + +function babelRow(wrapper) { + const row = wrapper + .findAll('tbody tr') + .find((tr) => tr.find('th').text() === 'Babel version'); + return row.findAll('td').map((td) => td.classes().join(' ')); +} + +describe('StatusMatrix', () => { + it('shades only the environment that disagrees', () => { + const wrapper = mountWith({ + exp: target('2025oct1'), + dev: target('2025sep1'), + prod: target('2025sep1'), + }); + const [exp, dev, prod] = babelRow(wrapper); + expect(exp).toContain('table-warning'); + expect(dev).not.toContain('table-warning'); + expect(prod).not.toContain('table-warning'); + }); + + it('shades nothing when every environment agrees', () => { + const wrapper = mountWith(Object.fromEntries(TARGETS.map((t) => [t, target('2025sep1')]))); + expect(babelRow(wrapper).join(' ')).not.toContain('table-warning'); + }); + + it('marks a status error as danger, not as a minority value', () => { + const wrapper = mountWith({ + exp: target('2025sep1'), + dev: target('2025sep1'), + prod: target('2025sep1', { nodenorm: { error: 'ConnectionError', status: undefined } }), + }); + const row = wrapper + .findAll('tbody tr') + .find((tr) => tr.find('th').text() === 'NodeNorm status'); + expect(row.findAll('td')[2].classes()).toContain('table-danger'); + }); +}); From 8e25f2ecfaec0ebb3eb88161ed1c6d58eef5bf34 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 27 Aug 2026 18:41:50 -0400 Subject: [PATCH 24/60] Group failures by the shape they make across the pipeline MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Of the 526 tests worth looking at in the current report, 518 behave differently in different environments — and they do it in a handful of recurring ways. 147 tests pass everywhere but prod; 100 fail in ci-es and prod alone; 68 are expected failures that prod passes. Those are three findings about three Babel versions, not 315 unrelated failures, but the matrix showed them as 315 rows. The dashboard now groups the interesting tests by their outcome across every environment, in promotion order, and lists the most common patterns with a link into the results page. The pattern is a short string, one character per environment — "pppppF" is "passes everywhere except prod" — which makes it small enough for a URL and, because the alphabet is closed, checkable on the way back in. Co-Authored-By: Claude Opus 5 --- website/src/components/DriftPanel.vue | 97 +++++++++++++++++++++++++++ website/src/components/FilterBar.vue | 10 +++ website/src/components/Overview.vue | 9 ++- website/src/components/Results.vue | 10 +++ website/src/components/Trends.vue | 90 ------------------------- website/src/pages/trends/index.astro | 22 ------ website/src/reportData.js | 20 ++++++ website/test/driftPanel.test.js | 45 +++++++++++++ website/test/results.test.js | 32 +++++---- 9 files changed, 208 insertions(+), 127 deletions(-) create mode 100644 website/src/components/DriftPanel.vue delete mode 100644 website/src/components/Trends.vue delete mode 100644 website/src/pages/trends/index.astro create mode 100644 website/test/driftPanel.test.js diff --git a/website/src/components/DriftPanel.vue b/website/src/components/DriftPanel.vue new file mode 100644 index 0000000..0a6581a --- /dev/null +++ b/website/src/components/DriftPanel.vue @@ -0,0 +1,97 @@ + + + + diff --git a/website/src/components/FilterBar.vue b/website/src/components/FilterBar.vue index f4fb2f8..aa5672e 100644 --- a/website/src/components/FilterBar.vue +++ b/website/src/components/FilterBar.vue @@ -154,6 +154,16 @@ export default {
    + +
    {{ shown.toLocaleString('en-US') }} of {{ total.toLocaleString('en-US') }} diff --git a/website/src/components/Overview.vue b/website/src/components/Overview.vue index 0381336..ad476d6 100644 --- a/website/src/components/Overview.vue +++ b/website/src/components/Overview.vue @@ -10,11 +10,12 @@ --> - - diff --git a/website/src/pages/trends/index.astro b/website/src/pages/trends/index.astro deleted file mode 100644 index b5a2128..0000000 --- a/website/src/pages/trends/index.astro +++ /dev/null @@ -1,22 +0,0 @@ ---- -import Layout from '../../layouts/Layout.astro'; -import Trends from '../../components/Trends.vue'; ---- - - -

    Run history

    - -
    -
    - One row per daily validation run: Babel and NameRes versions, database sizes, NameRes p95 - latency and test counts for each environment. -
    -
    - -
    -
    -     diff --git a/website/src/reportData.js b/website/src/reportData.js index 7267d7f..4ae2552 100644 --- a/website/src/reportData.js +++ b/website/src/reportData.js @@ -43,6 +43,26 @@ export const OUTCOME_LABELS = { error: 'ERR', }; +// One character per outcome, so a row's behaviour across every environment fits +// in a short string: "pppppF" is "passes everywhere except prod". Compact +// enough for a URL, and the alphabet is closed, so ?sig= can be validated. +export const OUTCOME_CODES = { + passed: 'p', + failed: 'F', + xfailed: 'x', + xpassed: 'X', + skipped: 's', + error: 'E', +}; + +export const SIGNATURE_PATTERN = /^[pFxXsE-]{1,32}$/; + +export function signature(result, targetNames) { + return targetNames + .map((target) => OUTCOME_CODES[result.outcomes[target]?.o] ?? '-') + .join(''); +} + // Rendering thousands of all-passing rows at once freezes the browser, so the // matrix is paginated. The default page size is large enough that the // interesting rows normally fit on one page. diff --git a/website/test/driftPanel.test.js b/website/test/driftPanel.test.js new file mode 100644 index 0000000..f4ec1c9 --- /dev/null +++ b/website/test/driftPanel.test.js @@ -0,0 +1,45 @@ +// The drift panel is the redesign's one piece of new logic: it groups tests by +// how they behave along the pipeline, so 147 rows read as one finding. +import { describe, it, expect } from 'vitest'; +import { mount } from '@vue/test-utils'; +import DriftPanel from '../src/components/DriftPanel.vue'; +import { signature } from '../src/reportData.js'; + +const TARGETS = ['exp', 'dev', 'prod']; + +function row(exp, dev, prod) { + return { kind: 'gsheet', outcomes: { exp: { o: exp }, dev: { o: dev }, prod: { o: prod } } }; +} + +const RESULTS = { + a: row('passed', 'passed', 'failed'), + b: row('passed', 'passed', 'failed'), + c: row('passed', 'passed', 'failed'), + d: row('passed', 'failed', 'failed'), + e: row('passed', 'passed', 'passed'), // uninteresting: excluded +}; + +describe('signature', () => { + it('reads one character per environment, in deployment order', () => { + expect(signature(RESULTS.a, TARGETS)).toBe('ppF'); + expect(signature({ outcomes: { dev: { o: 'xpassed' } } }, TARGETS)).toBe('-X-'); + }); +}); + +describe('DriftPanel', () => { + const wrapper = mount(DriftPanel, { + props: { results: RESULTS, targetNames: TARGETS, resultsUrl: '/results/' }, + }); + + it('groups interesting rows by pattern, most common first', () => { + expect(wrapper.vm.patterns.map((p) => [p.sig, p.count])).toEqual([ + ['ppF', 3], + ['pFF', 1], + ]); + expect(wrapper.vm.totalPatterns).toBe(2); + }); + + it('links each pattern into the results page', () => { + expect(wrapper.find('tbody a').attributes('href')).toBe('/results/?sig=ppF'); + }); +}); diff --git a/website/test/results.test.js b/website/test/results.test.js index 655dbfa..f82775f 100644 --- a/website/test/results.test.js +++ b/website/test/results.test.js @@ -4,7 +4,6 @@ import { describe, it, expect, beforeEach, vi } from 'vitest'; import { mount, flushPromises } from '@vue/test-utils'; import Results from '../src/components/Results.vue'; -import Trends from '../src/components/Trends.vue'; const TARGETS = ['dev', 'prod']; @@ -91,19 +90,6 @@ describe('Results URL state', () => { }); }); -describe('Trends', () => { - it('drops history lines that are not run objects', async () => { - global.fetch = vi.fn().mockResolvedValue({ - ok: true, - text: async () => ['null', '123', JSON.stringify({ date: 'd', targets: {} }), ''].join('\n'), - }); - const wrapper = mount(Trends, { props: { dataUrl: '/data/history.jsonl' } }); - await flushPromises(); - expect(wrapper.vm.runs).toHaveLength(1); - expect(wrapper.text()).toContain('d'); - }); -}); - describe('Results filters', () => { it('round-trips the category, source and environment filters through the URL', async () => { const wrapper = await mountAt('/?cat=Diseases&src=TAQA&env=dev&has=failed'); @@ -149,3 +135,21 @@ describe('Results filters', () => { } }); }); + +describe('Results pattern filter', () => { + it('shows only the rows matching a ?sig= pattern, and rejects a malformed one', async () => { + const data = report(4); + data.results['nodenorm/x.py::t[odd]'] = { + kind: 'gsheet', + row: 999, + category: 'Genes', + outcomes: { dev: { o: 'failed' }, prod: { o: 'failed' } }, + }; + let wrapper = await mountAt('/?sig=FF', data); + expect(wrapper.vm.filteredRows.map((r) => r.key)).toEqual(['nodenorm/x.py::t[odd]']); + + wrapper = await mountAt('/?sig= + + diff --git a/website/src/components/NavBar.astro b/website/src/components/NavBar.astro index fcba2c1..eff979c 100644 --- a/website/src/components/NavBar.astro +++ b/website/src/components/NavBar.astro @@ -12,11 +12,10 @@ interface Props { const { active } = Astro.props; const base = import.meta.env.BASE_URL; -// History is still served from /trends/ until that page is rewritten. const pages = [ { id: 'dashboard', label: 'Dashboard', href: base }, { id: 'results', label: 'Results', href: `${base}results/` }, - { id: 'history', label: 'History', href: `${base}trends/` }, + { id: 'history', label: 'History', href: `${base}history/` }, ]; const external = [ diff --git a/website/src/pages/history/index.astro b/website/src/pages/history/index.astro new file mode 100644 index 0000000..1197b19 --- /dev/null +++ b/website/src/pages/history/index.astro @@ -0,0 +1,18 @@ +--- +import Layout from '../../layouts/Layout.astro'; +import History from '../../components/History.vue'; +--- + + +

    Run history

    +

    + One row per daily validation run: Babel and NameRes versions, database sizes, NameRes p95 + latency and test counts for each environment. +

    + + +     diff --git a/website/test/history.test.js b/website/test/history.test.js new file mode 100644 index 0000000..4b96384 --- /dev/null +++ b/website/test/history.test.js @@ -0,0 +1,57 @@ +// The history page has to survive a partial or malformed history file: it is +// rebuilt from the previously published one on every run. +import { describe, it, expect, vi } from 'vitest'; +import { mount, flushPromises } from '@vue/test-utils'; +import History from '../src/components/History.vue'; + +function run(date, babel, failed) { + return JSON.stringify({ + date, + targets: { dev: { babel_version: babel, counts: { failed, passed: 10 } } }, + }); +} + +async function mountWith(lines) { + global.fetch = vi.fn().mockResolvedValue({ ok: true, text: async () => lines.join('\n') }); + const wrapper = mount(History, { props: { dataUrl: '/data/history.jsonl' } }); + await flushPromises(); + return wrapper; +} + +describe('History', () => { + it('drops history lines that are not run objects', async () => { + global.fetch = vi.fn().mockResolvedValue({ + ok: true, + text: async () => ['null', '123', JSON.stringify({ date: 'd', targets: {} }), ''].join('\n'), + }); + const wrapper = mount(History, { props: { dataUrl: '/data/history.jsonl' } }); + await flushPromises(); + expect(wrapper.vm.runs).toHaveLength(1); + expect(wrapper.text()).toContain('d'); + }); +}); + + +describe('what changed since the previous run', () => { + it('reports version moves and count deltas, newest run against the one before', async () => { + const wrapper = await mountWith([ + run('2026-08-26', '2025sep1', 12), + run('2026-08-27', '2025oct1', 20), + ]); + expect(wrapper.vm.changes).toEqual([ + { target: 'dev', label: 'babel version', from: '2025sep1', to: '2025oct1' }, + { target: 'dev', label: 'failed', delta: 8, to: '20' }, + ]); + expect(wrapper.text()).toContain('+8'); + }); + + it('says so when nothing moved, and shows nothing with only one run', async () => { + let wrapper = await mountWith([run('2026-08-26', '2025sep1', 12), run('2026-08-27', '2025sep1', 12)]); + expect(wrapper.vm.changes).toEqual([]); + expect(wrapper.text()).toContain('Nothing changed'); + + wrapper = await mountWith([run('2026-08-27', '2025sep1', 12)]); + expect(wrapper.vm.changes).toEqual([]); + expect(wrapper.text()).not.toContain('Nothing changed'); + }); +}); From 4e5c2735f79f16653a8afb441f91235ca1757a28 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 27 Aug 2026 18:47:14 -0400 Subject: [PATCH 26/60] Shade only the status rows where environments should agree MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Screenshots of the redesign against the live report showed the fix this needed: NodeNorm record counts, Solr index sizes and p95 latencies differ between environments by nature, so highlighting the minority value turned almost every cell amber and taught the reader to ignore the colour. Only the rows that mean something when they disagree — the Babel, Biolink and NameRes versions, and the two service statuses — are compared now. The environment cards also move from a flex row to a six-column grid. Flex sized them by content, so at 1440px they wrapped four and two, and the pipeline stopped reading left to right halfway through. Co-Authored-By: Claude Opus 5 --- CLAUDE.md | 10 +++++++--- README.md | 3 ++- website/src/components/Overview.vue | 16 ++++++++++------ website/src/components/StatusMatrix.vue | 2 ++ website/src/reportData.js | 20 ++++++++++++++++++-- 5 files changed, 39 insertions(+), 12 deletions(-) diff --git a/CLAUDE.md b/CLAUDE.md index 966b708..f2a6fb7 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -90,9 +90,13 @@ the rows into `TestRow` dataclasses. Rows marked as not expected to pass are wra ### Dashboard Website - **`website/`** — Astro + Vue site deployed to GitHub Pages - (https://translatorsri.github.io/babel-validation/). Renders `report.json` (per-target - `/status` cards plus a tests-by-environment matrix) and `history.jsonl` (one summary line - per run). Regenerated daily by `.github/workflows/dashboard.yaml`: pytest per target with + (https://translatorsri.github.io/babel-validation/). Three pages under one `Layout.astro` + shell (nav bar, cards on a tinted page, `data-bs-theme` dark mode, all custom CSS in + `src/styles/theme.css`): `/` renders the environment cards, the promotion-drift panel and + the `/status` matrix from `report.json`; `/results/` renders the tests-by-environment + matrix behind a sticky filter bar; `/history/` renders `history.jsonl` plus a diff against + the previous run. Everything about the report that is not markup — link builders, labels, + the interestingness predicate — lives in `src/reportData.js`. Regenerated daily by `.github/workflows/dashboard.yaml`: pytest per target with `--report-jsonl` (a `pytest_runtest_logreport` hook in `tests/conftest.py`), then `src/babel_validation/tools/generate_report.py` aggregates the raw outcomes, fetches each target's `/status`, and writes both data files into `website/public/data/`. diff --git a/README.md b/README.md index 637f8a8..3ce6de9 100644 --- a/README.md +++ b/README.md @@ -144,7 +144,8 @@ and `/status` responses into `report.json` and `history.jsonl` with `src.babel_validation.tools.generate_report`, and publishes the built site to the `gh-pages` branch. -The Vue components' client-side logic (URL round-tripping, filtering, pagination) has vitest +The Vue components' client-side logic (URL round-tripping, filtering, pagination, the +odd-one-out shading, the drift grouping, and the withholding of blocklist detail) has vitest tests in `website/test/`, run by `npm test` and by the Tests workflow. To work on the site against the data the live dashboard is showing, download the published diff --git a/website/src/components/Overview.vue b/website/src/components/Overview.vue index ad476d6..0c9c0a3 100644 --- a/website/src/components/Overview.vue +++ b/website/src/components/Overview.vue @@ -107,11 +107,15 @@ export default { unreachable during the run.
    - -
    -
    - +
    this.statusValue(statusRow, t)); diff --git a/website/src/reportData.js b/website/src/reportData.js index 4ae2552..2feecb7 100644 --- a/website/src/reportData.js +++ b/website/src/reportData.js @@ -76,17 +76,28 @@ export function formatCount(value) { // One row per /status value; adding a row here is all it takes to show a new // one. `value` receives one entry of report.targets; null renders as an em // dash. `href` may return a generator-validated URL to link the value to. +// +// `compare` marks the rows where environments are *supposed* to agree, and so +// where a minority value is a finding. Record counts, index sizes and latencies +// differ between environments by nature; shading them made every row amber and +// taught the reader to ignore the colour. export const STATUS_ROWS = [ { label: 'Babel version', value: (t) => t.nodenorm_status.babel_version, href: (t) => t.nodenorm_status.babel_version_url, + compare: true, + }, + { + label: 'Biolink model', + value: (t) => t.nodenorm_status.biolink_version, + compare: true, }, - { label: 'Biolink model', value: (t) => t.nodenorm_status.biolink_version }, { label: 'NodeNorm status', value: (t) => t.nodenorm_status.error ?? t.nodenorm_status.status, danger: (t) => Boolean(t.nodenorm_status.error), + compare: true, }, { label: 'NodeNorm records', @@ -100,8 +111,13 @@ export const STATUS_ROWS = [ label: 'NameRes status', value: (t) => t.nameres_status.error ?? t.nameres_status.status, danger: (t) => Boolean(t.nameres_status.error), + compare: true, + }, + { + label: 'NameRes version', + value: (t) => t.nameres_status.nameres_version, + compare: true, }, - { label: 'NameRes version', value: (t) => t.nameres_status.nameres_version }, { label: 'Solr documents', value: (t) => formatCount(t.nameres_status.solr?.numDocs), From 203860e78deb9c867c8b5b59e7fce04177ec9a78 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 27 Aug 2026 18:58:55 -0400 Subject: [PATCH 27/60] Run the dashboard workflow from this branch instead of #118's MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit workflow_dispatch only works once the file is on the default branch, so a pre-merge run has to trigger on push. #118 carried that trigger and is now kept only for reference, so it moves here — the redesign is what needs deploying for review. Only one branch should have it at a time: each run takes about four hours and force-pushes gh-pages. Remove it before merging, as #118 did. Co-Authored-By: Claude Opus 5 --- .github/workflows/dashboard.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/dashboard.yaml b/.github/workflows/dashboard.yaml index a5966bd..cff8f76 100644 --- a/.github/workflows/dashboard.yaml +++ b/.github/workflows/dashboard.yaml @@ -6,6 +6,13 @@ on: schedule: - cron: '30 6 * * *' workflow_dispatch: + # Temporary, remove before merge: workflow_dispatch only works once this file + # is on the default branch, so pre-merge runs of the redesign trigger on push. + # Development moved here from #118, which carried the same trigger on its own + # branch; only one branch should have it at a time, since each run takes about + # four hours and force-pushes gh-pages. + push: + branches: [redesign-dashboard] permissions: contents: write # the deploy action pushes to the gh-pages branch From 4f3c9b9d67bbeb4ad0b30c2d6fc123c657bb97b4 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 27 Aug 2026 19:00:38 -0400 Subject: [PATCH 28/60] Regenerate package-lock.json so npm ci can install it MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit CI installs with `npm ci`, which refuses a lockfile that does not match package.json — and the lock left by the incremental installs that added vitest and upgraded Bootstrap was missing esbuild's platform packages for every OS but this one, so the new website-tests job could not start. Regenerated from scratch (72 @esbuild/* entries now present) and verified with npm ci, npm test and npm run build locally rather than on the runner. Co-Authored-By: Claude Opus 5 --- website/package-lock.json | 9485 +++++++++++++++++++++---------------- 1 file changed, 5421 insertions(+), 4064 deletions(-) diff --git a/website/package-lock.json b/website/package-lock.json index 6c725f9..b2121ef 100644 --- a/website/package-lock.json +++ b/website/package-lock.json @@ -22,22 +22,20 @@ "vitest": "^4.1.11" } }, - "node_modules/@ampproject/remapping": { - "version": "2.2.1", - "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.1.tgz", - "integrity": "sha512-lFMjJTrFL3j7L9yBxwYfCq2k6qqwHyzuUl/XBnif78PWTJYyL/dfowQHWE3sp6U6ZzqWiiIZnpTMO96zhkjwtg==", - "dependencies": { - "@jridgewell/gen-mapping": "^0.3.0", - "@jridgewell/trace-mapping": "^0.3.9" - }, - "engines": { - "node": ">=6.0.0" + "node_modules/@antfu/utils": { + "version": "0.7.10", + "resolved": "https://registry.npmjs.org/@antfu/utils/-/utils-0.7.10.tgz", + "integrity": 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"MIT", "dependencies": { "cliui": "^8.0.1", "escalade": "^3.1.1", @@ -8237,6 +9556,7 @@ "version": "21.1.1", "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-21.1.1.tgz", "integrity": "sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw==", + "license": "ISC", "engines": { "node": ">=12" } @@ -8245,6 +9565,7 @@ "version": "5.0.1", "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz", "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ==", + "license": "MIT", "engines": { "node": ">=8" } @@ -8252,12 +9573,14 @@ "node_modules/yargs/node_modules/emoji-regex": { "version": "8.0.0", "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz", - "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==" + "integrity": 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"sha512-iC+8Io04lddc+mVqQ9AZ7OQ2MrUKGN+oIQyq1vemgt46jwCwLfhq7/pwnBnNXXXZb8VTVLKwp9EDkx+ryxIWmg==", + "version": "3.25.76", + "resolved": "https://registry.npmjs.org/zod/-/zod-3.25.76.tgz", + "integrity": "sha512-gzUt/qt81nXsFGKIFcC3YnfEAx5NkunCfnDlvuBSSFS02bcXu4Lmea0AFIUwbLWxWPx3d9p8S5QoaujKcNQxcQ==", + "license": "MIT", "funding": { "url": "https://github.com/sponsors/colinhacks" } }, + "node_modules/zod-to-json-schema": { + "version": "3.25.2", + "resolved": "https://registry.npmjs.org/zod-to-json-schema/-/zod-to-json-schema-3.25.2.tgz", + "integrity": "sha512-O/PgfnpT1xKSDeQYSCfRI5Gy3hPf91mKVDuYLUHZJMiDFptvP41MSnWofm8dnCm0256ZNfZIM7DSzuSMAFnjHA==", + "license": "ISC", + "peerDependencies": { + "zod": "^3.25.28 || ^4" + } + }, + "node_modules/zod-to-ts": { + "version": "1.2.0", + "resolved": "https://registry.npmjs.org/zod-to-ts/-/zod-to-ts-1.2.0.tgz", + "integrity": "sha512-x30XE43V+InwGpvTySRNz9kB7qFU8DlyEy7BsSTCHPH1R0QasMmHWZDCzYm6bVXtj/9NNJAZF3jW8rzFvH5OFA==", + "peerDependencies": { + "typescript": "^4.9.4 || ^5.0.2", + "zod": "^3" + } + }, "node_modules/zwitch": { "version": "2.0.4", "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz", "integrity": "sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==", + "license": "MIT", "funding": { "type": "github", "url": "https://github.com/sponsors/wooorm" From 2a2e8956e53dad817717d29c1a7d5374c9a93c7f Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 27 Aug 2026 19:02:16 -0400 Subject: [PATCH 29/60] Build the website on Node 24 in CI, matching the lockfile's npm MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit npm 11 writes platform-specific packages into package-lock.json without `optional: true`, and npm 10 — the version bundled with the Node 20 the test job asked for, and with whatever the dashboard job inherited from the runner — refuses to install it: EBADPLATFORM on an Android build of lightningcss. Both jobs now pin Node 24. The dashboard job had no setup-node at all, so it would have failed at `npm ci` in its build step, four hours into the run and after every test had been paid for. Co-Authored-By: Claude Opus 5 --- .github/workflows/dashboard.yaml | 9 +++++++++ .github/workflows/tests.yaml | 6 +++++- 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/.github/workflows/dashboard.yaml b/.github/workflows/dashboard.yaml index cff8f76..3f9a8f6 100644 --- a/.github/workflows/dashboard.yaml +++ b/.github/workflows/dashboard.yaml @@ -69,6 +69,15 @@ jobs: --raw-dir raw --targets-ini tests/targets.ini \ --history-in old_history.jsonl --out-dir website/public/data + # Node 24 for npm 11 — see the note in tests.yaml. Without this the job + # gets the runner's default Node and fails at npm ci, four hours into the + # run, after every test has already been paid for. + - uses: actions/setup-node@v4 + with: + node-version: 24 + cache: npm + cache-dependency-path: website/package-lock.json + - name: Build the website working-directory: website run: | diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index f5bf34a..e3a5c90 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -41,9 +41,13 @@ jobs: steps: - uses: actions/checkout@v4 + # Node 24 for npm 11: the lockfile npm 11 writes omits `optional: true` on + # platform-specific packages, and npm 10 then refuses to install it + # (EBADPLATFORM on lightningcss-android-arm64). Keep this in step with the + # same block in dashboard.yaml. - uses: actions/setup-node@v4 with: - node-version: 20 + node-version: 24 cache: npm cache-dependency-path: website/package-lock.json From a099561a2bcf7e9584479d55360b79213cc54285 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 27 Aug 2026 19:12:08 -0400 Subject: [PATCH 30/60] Cover the overview page and the filter chips, and note the npm ci trap MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The redesign's two least-tested pieces were the landing page's links — which is all that page does, point at the right corner of the results table — and the filter chips, whose toggle state lives in the child component. Both are now tested: deployment ordering of the cards, the env/has links they build, the unreachable and unattributed cases, the issue-tests warning, chip toggling through to the query string, and Reset emptying every filter and the URL together. CLAUDE.md gains the two things this session cost real time to learn: that npm ci is much stricter than the npm install used locally and must be run before trusting a dependency change, with both workflows pinned to Node 24 for the lockfile npm 11 writes; and that a facet is as public as a cell, so anything aggregating over results has to exclude blocklist rows. env.d.ts picks up the .astro/types.d.ts reference that astro sync writes. Co-Authored-By: Claude Opus 5 --- CLAUDE.md | 13 +++++- website/src/env.d.ts | 1 + website/test/overview.test.js | 74 +++++++++++++++++++++++++++++++++++ website/test/results.test.js | 38 ++++++++++++++++++ 4 files changed, 125 insertions(+), 1 deletion(-) create mode 100644 website/test/overview.test.js diff --git a/CLAUDE.md b/CLAUDE.md index f2a6fb7..4a04d12 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -53,6 +53,14 @@ quickest way to get real data for frontend work. To make them from scratch inste `pytest --report-jsonl` plus `uv run python -m src.babel_validation.tools.generate_report` (see README). +CI installs with `npm ci`, which is far stricter than the `npm install` you run locally: it +refuses a lockfile that does not match `package.json`, and it fails on platform-specific +packages that npm 11 writes into the lock without `optional: true` when the runner's npm is +10 (`EBADPLATFORM` on an Android build of lightningcss). Both workflows therefore pin +`node-version: 24`. After changing any dependency, run `npm ci` locally — not just +`npm test` — or the failure surfaces only on the runner, and in `dashboard.yaml` it surfaces +four hours in, at the build step, after every test has been paid for. + Beware: the root `.gitignore`'s Python-template `lib/` pattern matches *any* directory named `lib`, including under `website/src/` — a file there builds locally but never reaches CI. Check `git status` shows new frontend files as tracked. @@ -155,7 +163,10 @@ responses through a key whitelist, only emits issue ids and source URLs that mat sheet may not be public — do not add `ids=` to the blocklist parametrize or link to it). The Vue components must render report values with `{{ }}` interpolation only — never `v-html` — and construct links from validated parts (allowlisted `org/repo#N`, -`targets.ini` URLs), never verbatim from report text. +`targets.ini` URLs), never verbatim from report text. A facet is as public as a cell: the +filter bar's category and source dropdowns are built from report values, so they exclude +blocklist rows exactly as the table does. Anything that aggregates over `results` needs the +same check. **Never leak the Google Sheet ID or the GitHub token.** The report, the website, and any Git commit must not contain the test-case sheet's ID or a link to either sheet — casual diff --git a/website/src/env.d.ts b/website/src/env.d.ts index 0cef870..980dd11 100644 --- a/website/src/env.d.ts +++ b/website/src/env.d.ts @@ -1,3 +1,4 @@ +/// /// // Let `astro check` (TypeScript) see Vue single-file components as default diff --git a/website/test/overview.test.js b/website/test/overview.test.js new file mode 100644 index 0000000..f5054e8 --- /dev/null +++ b/website/test/overview.test.js @@ -0,0 +1,74 @@ +// The landing page's job is to point at the right corner of the results table, +// so the links it builds are the part worth testing. +import { describe, it, expect, vi } from 'vitest'; +import { mount, flushPromises } from '@vue/test-utils'; +import Overview from '../src/components/Overview.vue'; + +function target(counts, extra = {}) { + return { + nodenorm_status: { status: 'running', babel_version: '2025sep1', databases: {} }, + nameres_status: { status: 'running' }, + counts: { passed: 0, failed: 0, xfailed: 0, xpassed: 0, skipped: 0, error: 0, ...counts }, + unreachable: false, + ...extra, + }; +} + +const REPORT = { + generated_at: '2026-08-27T15:53:57+00:00', + run: { github_run_id: '33088526759', git_sha: '80f750a1502c288532369f3a6bbbeb233d8ddd51' }, + github_issues_ran: true, + unattributed_counts: { passed: 1, failed: 0 }, + targets: { + prod: target({ failed: 326, xpassed: 73, passed: 327 }), + dev: target({ failed: 79, xpassed: 7, passed: 567 }), + exp: target({ failed: 20 }, { unreachable: true }), + }, + results: { + a: { kind: 'gsheet', outcomes: { dev: { o: 'passed' }, prod: { o: 'failed' } } }, + b: { kind: 'gsheet', outcomes: { dev: { o: 'passed' }, prod: { o: 'passed' } } }, + }, +}; + +async function mountOverview(report = REPORT) { + global.fetch = vi.fn().mockResolvedValue({ ok: true, json: async () => report }); + const wrapper = mount(Overview, { + props: { dataUrl: '/data/report.json', resultsUrl: '/babel-validation/results/' }, + }); + await flushPromises(); + return wrapper; +} + +describe('Overview', () => { + it('orders the environment cards by deployment, not by report order', async () => { + const wrapper = await mountOverview(); + const names = wrapper.findAll('.col .card-body > .d-flex > .fw-semibold').map((el) => el.text()); + expect(names).toEqual(['exp', 'dev', 'prod']); + }); + + it('links each count into the results page, filtered to that environment', async () => { + const wrapper = await mountOverview(); + const hrefs = wrapper.findAll('a').map((a) => a.attributes('href')); + expect(hrefs).toContain('/babel-validation/results/?env=prod&has=failed'); + expect(hrefs).toContain('/babel-validation/results/?env=dev&has=xpassed'); + }); + + it('says an unreachable environment has no results instead of showing zeroes', async () => { + const wrapper = await mountOverview(); + const exp = wrapper.findAll('.col')[0]; + expect(exp.text()).toContain('no results'); + expect(exp.text()).not.toContain('0 failed'); + }); + + it('surfaces results that no environment claimed', async () => { + const wrapper = await mountOverview(); + expect(wrapper.text()).toContain('could not be attributed'); + const quiet = await mountOverview({ ...REPORT, unattributed_counts: { passed: 0 } }); + expect(quiet.text()).not.toContain('could not be attributed'); + }); + + it('warns when the GitHub issue tests did not run at all', async () => { + const wrapper = await mountOverview({ ...REPORT, github_issues_ran: false }); + expect(wrapper.text()).toContain('A green board proves nothing about them'); + }); +}); diff --git a/website/test/results.test.js b/website/test/results.test.js index f82775f..6707c75 100644 --- a/website/test/results.test.js +++ b/website/test/results.test.js @@ -153,3 +153,41 @@ describe('Results pattern filter', () => { expect(wrapper.vm.filteredRows.length).toBeGreaterThan(1); }); }); + +describe('FilterBar', () => { + it('toggles an outcome chip on and off, and shows it in the URL', async () => { + const wrapper = await mountAt('/'); + const chip = wrapper + .findAll('button') + .find((button) => button.text() === 'failed'); + await chip.trigger('click'); + await flushPromises(); + expect(wrapper.vm.filters.has).toEqual(['failed']); + expect(chip.classes()).toContain('btn-secondary'); + expect(chip.attributes('aria-pressed')).toBe('true'); + expect(window.location.search).toContain('has=failed'); + + await chip.trigger('click'); + await flushPromises(); + expect(wrapper.vm.filters.has).toEqual([]); + expect(window.location.search).not.toContain('has='); + }); + + it('clears every filter at once, and empties the query string with them', async () => { + const wrapper = await mountAt('/?all=1&q=row&kinds=gsheet&cat=Genes&env=dev&page=2'); + const reset = wrapper.findAll('button').find((button) => button.text() === 'Reset'); + await reset.trigger('click'); + await flushPromises(); + expect(wrapper.vm.filters).toEqual({ + interestingOnly: true, + q: '', + kinds: [], + has: [], + cat: '', + src: '', + env: '', + sig: '', + }); + expect(window.location.search).toBe(''); + }); +}); From 133cdfcce68530b63e5493c0718afdc7ea1596fe Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 31 Aug 2026 09:37:37 -0400 Subject: [PATCH 31/60] Keep the address bar on /results/, and share only pages that exist MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit history.replaceState resolves a *relative* URL against the document base, not the current path, and Layout.astro emits . So the first filter change on /babel-validation/results/ wrote `?q=...`, which resolved to /babel-validation/?q=... — the Dashboard, which ignores every one of these parameters. Copy link reads window.location.href, so a shared or reloaded link came back to the wrong page with no results. The empty-filter branch was already safe because it used the absolute window.location.pathname; now both do. Also clamp the page before writing it. ?page=9999 on a three-page result set renders page 3, but kept writing page=9999 into the URL, so Copy link shared a page that does not exist. The vitest suite mounts at / with no , so it cannot reproduce the rebasing directly; the test asserts the shape that makes it impossible instead. The page test expands a row rather than editing a filter — a filter edit resets the page to 1, which hides the bug. Co-Authored-By: Claude Opus 5 --- website/src/components/Results.vue | 12 +++++++++- website/test/results.test.js | 37 ++++++++++++++++++++++++++++++ 2 files changed, 48 insertions(+), 1 deletion(-) diff --git a/website/src/components/Results.vue b/website/src/components/Results.vue index 211270a..cf7675d 100644 --- a/website/src/components/Results.vue +++ b/website/src/components/Results.vue @@ -241,6 +241,11 @@ export default { if (PAGE_SIZES.includes(pageSize)) this.pageSize = pageSize; }, writeUrl() { + // Clamp before writing: ?page=9999 on a three-page result set renders page + // 3, and the link we put in the address bar has to say 3 too. Safe here + // because writeUrl only runs after urlReady, i.e. after a user edit, by + // which time the report has loaded and pageCount is real. + if (this.page !== this.currentPage) this.page = this.currentPage; const params = new URLSearchParams(); if (!this.filters.interestingOnly) params.set('all', '1'); if (this.filters.q.trim()) params.set('q', this.filters.q.trim()); @@ -254,7 +259,12 @@ export default { if (this.pageSize !== DEFAULT_PAGE_SIZE) params.set('ps', String(this.pageSize)); if (this.expandedKey) params.set('test', this.expandedKey); const query = params.toString(); - window.history.replaceState(null, '', query ? `?${query}` : window.location.pathname); + // Always absolute. replaceState resolves a relative URL against the + // *document base*, and Layout.astro emits , + // so a bare `?q=...` here rewrites the address bar from /results/ to the + // Dashboard — which ignores every one of these parameters, so a reloaded + // or copied link comes back empty. + window.history.replaceState(null, '', `${window.location.pathname}${query ? `?${query}` : ''}`); }, resetFilters() { this.filters = emptyFilters(); diff --git a/website/test/results.test.js b/website/test/results.test.js index 6707c75..4448d2f 100644 --- a/website/test/results.test.js +++ b/website/test/results.test.js @@ -191,3 +191,40 @@ describe('FilterBar', () => { expect(window.location.search).toBe(''); }); }); + +// Layout.astro emits , and history.replaceState +// resolves a *relative* URL against the document base rather than the current +// path — so `?q=...` silently moved the address bar from /results/ to the +// Dashboard, which ignores every one of these parameters. jsdom has no , +// so the only thing that catches a regression is the shape of the URL we pass. +describe('the URL written back to the address bar', () => { + it('is absolute, so it cannot be re-based onto another page', async () => { + const wrapper = await mountAt('/results/'); + const replaceState = vi.spyOn(window.history, 'replaceState'); + + await wrapper.find('input[type="search"]').setValue('row=3'); + await flushPromises(); + + expect(replaceState).toHaveBeenCalled(); + for (const [, , url] of replaceState.mock.calls) { + expect(url.startsWith('/results/')).toBe(true); + } + replaceState.mockRestore(); + }); + + it('never shares a page number the results do not have', async () => { + const wrapper = await mountAt('/results/?all=1&page=9999'); + expect(wrapper.vm.page).toBe(9999); + expect(wrapper.vm.pageCount).toBeLessThan(9999); + + // Expanding a row rewrites the URL without touching the page — unlike a + // filter edit, which resets it to 1 and would hide the bug being tested. + await wrapper.findAll('tbody tr[role="button"]')[0].trigger('click'); + await flushPromises(); + + expect(window.location.search).toContain('test='); + expect(window.location.search).not.toContain('page=9999'); + expect(wrapper.vm.page).toBe(wrapper.vm.pageCount); + }); +}); + From 696ca8f5ec067797192566aa6598921f15cdd6c5 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 31 Aug 2026 09:37:37 -0400 Subject: [PATCH 32/60] Drop only the unparseable line from the run history, not the whole file MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit fetchHistory mapped JSON.parse over every line, so one truncated line — a partial CDN response, a deploy interrupted mid-write — rejected the promise and the page showed "Could not load the run history" instead of the runs that parsed perfectly well. The file header and the test file both already claimed the page survives a partial history. The existing test only fed valid JSON that wasn't an object (null, 123), which the .filter() after the map already handled — so the guard that had a test was the one that wasn't needed. The new test feeds a genuinely truncated line. Co-Authored-By: Claude Opus 5 --- website/src/reportData.js | 11 ++++++++++- website/test/history.test.js | 17 +++++++++++++++++ 2 files changed, 27 insertions(+), 1 deletion(-) diff --git a/website/src/reportData.js b/website/src/reportData.js index 2feecb7..a3ad99c 100644 --- a/website/src/reportData.js +++ b/website/src/reportData.js @@ -147,7 +147,16 @@ export async function fetchHistory(url) { return text .split('\n') .filter((line) => line.trim()) - .map((line) => JSON.parse(line)) + .map((line) => { + // Per line, not over the whole file: a truncated last line — a partial + // CDN response, a deploy interrupted mid-write — must cost one run, not + // the entire page. + try { + return JSON.parse(line); + } catch { + return null; + } + }) .filter((run) => run && typeof run === 'object') .reverse(); } diff --git a/website/test/history.test.js b/website/test/history.test.js index 4b96384..3760068 100644 --- a/website/test/history.test.js +++ b/website/test/history.test.js @@ -55,3 +55,20 @@ describe('what changed since the previous run', () => { expect(wrapper.text()).not.toContain('Nothing changed'); }); }); + +describe('a malformed history file', () => { + it('drops only the unparseable line, not every run in the file', async () => { + // A deploy interrupted mid-write, or a partial CDN response, leaves a + // truncated last line. JSON.parse over the whole file threw, and the page + // showed "Could not load the run history" instead of the runs it had. + const wrapper = await mountWith([ + run('2026-08-26', '2025sep1', 12), + '{"date": "2026-08-27", "targets": {"dev": {"babel_ver', + ]); + + expect(wrapper.vm.loadError).toBe(null); + expect(wrapper.vm.runs).toHaveLength(1); + expect(wrapper.text()).toContain('2026-08-26'); + }); +}); + From 37994c377239fb20676d41730ab4411d9654063f Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 31 Aug 2026 09:37:37 -0400 Subject: [PATCH 33/60] Shade nothing when environments have no majority value MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit sort((a, b) => b[1] - a[1])[0] picks a winner even when the split is even, so which half of the row got shaded amber depended on Map insertion order. Three environments on the new Babel version and three on the old is not a fault to highlight — it is exactly what a promotion halfway through looks like. Co-Authored-By: Claude Opus 5 --- website/src/components/StatusMatrix.vue | 8 +++++++- website/test/statusMatrix.test.js | 19 +++++++++++++++++++ 2 files changed, 26 insertions(+), 1 deletion(-) diff --git a/website/src/components/StatusMatrix.vue b/website/src/components/StatusMatrix.vue index dfc124c..33b42ff 100644 --- a/website/src/components/StatusMatrix.vue +++ b/website/src/components/StatusMatrix.vue @@ -69,7 +69,13 @@ export default { for (const value of values) { if (value != null) tally.set(value, (tally.get(value) ?? 0) + 1); } - const majority = [...tally.entries()].sort((a, b) => b[1] - a[1])[0][0]; + const ranked = [...tally.entries()].sort((a, b) => b[1] - a[1]); + // A tie has no odd one out. Three environments on the new Babel version + // and three on the old is exactly what mid-promotion looks like, and + // picking a winner by Map insertion order would shade half the row amber + // to say nothing. + if (ranked.length > 1 && ranked[0][1] === ranked[1][1]) return ''; + const majority = ranked[0][0]; return this.statusValue(statusRow, target) === majority ? '' : 'table-warning'; }, database(target, name) { diff --git a/website/test/statusMatrix.test.js b/website/test/statusMatrix.test.js index fd57674..daf3edf 100644 --- a/website/test/statusMatrix.test.js +++ b/website/test/statusMatrix.test.js @@ -58,3 +58,22 @@ describe('StatusMatrix', () => { expect(row.findAll('td')[2].classes()).toContain('table-danger'); }); }); + +describe('an even split', () => { + it('shades nothing when no value has a majority', () => { + // Half the environments on the new Babel version and half on the old is + // what mid-promotion looks like. Picking a "majority" by Map insertion + // order would shade three of six amber to say nothing at all. + const wrapper = mountWith({ + exp: target('2025oct1'), + dev: target('2025oct1'), + ci: target('2025oct1'), + test: target('2025sep1'), + prod: target('2025sep1'), + staging: target('2025sep1'), + }); + + expect(babelRow(wrapper).join(' ')).not.toContain('table-warning'); + }); +}); + From d5a91574d51a787fc806c1f884985a3c135501d3 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 31 Aug 2026 09:37:38 -0400 Subject: [PATCH 34/60] Set scroll-padding-top on the root element, where it has an effect MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The viewport takes its scroll padding from the root element; the rule was on body, where it does nothing, so the stated goal — a deep link to a test not landing underneath the sticky filter bar — was not being met. Nothing exercises it yet, since rows carry no id anchors, but the comment claimed a behaviour the code did not have. Co-Authored-By: Claude Opus 5 --- website/src/styles/theme.css | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/website/src/styles/theme.css b/website/src/styles/theme.css index b47593d..858e57f 100644 --- a/website/src/styles/theme.css +++ b/website/src/styles/theme.css @@ -15,8 +15,10 @@ --filterbar-h: 0px; } -body { - /* A deep link to a test must not land underneath the sticky filter bar. */ +html { + /* A deep link to a test must not land underneath the sticky filter bar. The + viewport takes its scroll padding from the root element; setting this on + body does nothing at all. */ scroll-padding-top: calc(var(--filterbar-h) + 1rem); } From 7f384857c5ff1e7281a44e906e8b97f56d175bcb Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 31 Aug 2026 09:37:48 -0400 Subject: [PATCH 35/60] Drop the test-redis target now that NodeNorm Redis in Test is switched off MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit nodenorm.test.transltr.io was turned off on 2026-08-31, so [test-redis] pointed at nothing. Test now matches CI: NodeNorm ES against the Solr-backed NameRes, with NameRes ES deliberately absent because it is being validated in CI first. It also could not have worked here. The report generator takes every section in targets.ini except localhost, but the dashboard workflow runs a hardcoded list of six targets — so test-redis arrived with no records at all: a seventh environment permanently flagged unreachable, a standing alert on the Dashboard, an always-empty column in every ?sig= signature (which silently invalidates shared links), and, being absent from DEPLOYMENT_ORDER, a sort position after prod that made Overview read "reaches exp first and test-redis last". The two lists should not be able to disagree in the first place. Left as-is for now because the fix belongs with the workflow's structure, not with this removal. Co-Authored-By: Claude Opus 5 --- tests/targets.ini | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/tests/targets.ini b/tests/targets.ini index 1d60533..6c9c5c3 100644 --- a/tests/targets.ini +++ b/tests/targets.ini @@ -46,22 +46,17 @@ Repositories = NodeNormURL = https://nodenorm.transltr.io/ NameResURL = https://name-lookup.transltr.io/ -# NodeNorm ES is now up in Test; the Redis-backed https://nodenorm.test.transltr.io/ -# is still there if it needs testing too. NameRes here is still the Solr-backed -# name-lookup. +# Test matches CI: NodeNorm ES against the Solr-backed NameRes. The Redis-backed +# nodenorm.test.transltr.io was turned off on 2026-08-31, so there is no Redis +# NodeNorm here to compare against — dev, exp and prod still run one. NameRes ES +# is deliberately absent: it is being validated in CI ([ci-es]) before it goes +# any further. [test] NodeNormURL = https://nodenorm-es.test.transltr.io/ NodeNormBackend = elasticsearch NodeNormOpenAPIPath = webapp/openapi.json NameResURL = https://name-lookup.test.transltr.io/ -# The same environment, against the Redis-backed NodeNorm that is still deployed -# there. [test] moved to nodenorm-es, and this keeps the other flavour reachable so -# the two can be compared rather than one replacing the other in our coverage. -[test-redis] -NodeNormURL = https://nodenorm.test.transltr.io/ -NameResURL = https://name-lookup.test.transltr.io/ - # nodenorm-es has completely replaced the Redis-backed nodenorm.ci. [ci] NodeNormURL = https://nodenorm-es.ci.transltr.io/ From 42bc4a5159efd01a62da8e26ee13c9319de975ee Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 31 Aug 2026 09:37:48 -0400 Subject: [PATCH 36/60] Correct the dashboard workflow's own estimate of how long it takes MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The comment said "about four hours", which is the worst case implied by six targets at `timeout 45m` each, not anything that has happened. The last ten runs took 19-36 minutes, of which 25m48s in the most recent was the test loop and about 30 seconds was everything else — checkout, report generation, the website build and the deploy. Co-Authored-By: Claude Opus 5 --- .github/workflows/dashboard.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/dashboard.yaml b/.github/workflows/dashboard.yaml index 3f9a8f6..83593fc 100644 --- a/.github/workflows/dashboard.yaml +++ b/.github/workflows/dashboard.yaml @@ -9,8 +9,8 @@ on: # Temporary, remove before merge: workflow_dispatch only works once this file # is on the default branch, so pre-merge runs of the redesign trigger on push. # Development moved here from #118, which carried the same trigger on its own - # branch; only one branch should have it at a time, since each run takes about - # four hours and force-pushes gh-pages. + # branch; only one branch should have it at a time, since each run takes + # 20-35 minutes and force-pushes gh-pages. push: branches: [redesign-dashboard] From 184eec75098776488156da83e9deae820fe4e777 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 31 Aug 2026 15:36:00 -0400 Subject: [PATCH 37/60] Take the workflow's target list from targets.ini, not a second copy of it MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The loop ran a hardcoded `prod test ci ci-es dev exp` while generate_report's read_targets() takes every section in targets.ini except localhost. Two lists, free to disagree — and they did: adding [test-redis] put it in every table on the site as a permanently unreachable environment, sorted after prod because DEPLOYMENT_ORDER had never heard of it, and as an always-empty column in every ?sig= signature, which silently invalidates shared links. Now the loop asks read_targets() what exists, so a new section is either run or absent from both, never in one and not the other. Verified by parsing the YAML and running the step's script with pytest stubbed: same six targets. Co-Authored-By: Claude Opus 5 --- .github/workflows/dashboard.yaml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/dashboard.yaml b/.github/workflows/dashboard.yaml index 83593fc..1520d10 100644 --- a/.github/workflows/dashboard.yaml +++ b/.github/workflows/dashboard.yaml @@ -47,7 +47,15 @@ jobs: # know --target/--report-jsonl, and every worker dies at argparse. run: | mkdir -p raw - for t in prod test ci ci-es dev exp; do + # Ask the report generator which targets exist rather than keeping a + # second list here. The two silently disagreed once already: adding + # [test-redis] to targets.ini put it in every table on the site — as a + # permanently unreachable environment, sorted after prod, and as an + # always-empty column in every ?sig= signature — because read_targets + # takes every section but localhost while this loop did not run it. + targets=$(uv run python -c "from src.babel_validation.tools.generate_report import read_targets; print(' '.join(read_targets('tests/targets.ini')[0]))") + echo "Running against: $targets" + for t in $targets; do timeout 45m uv run pytest tests --target "$t" -n 8 -m "not unit" \ --report-jsonl "raw/$t.jsonl" || echo "target $t exited $?" done From d15eb45bc7b1055fb4f2427c3696835cfad9c986 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 31 Aug 2026 15:36:00 -0400 Subject: [PATCH 38/60] Label a sheet row by its number alone when it has nothing else A Google Sheet row with neither query_label nor query_id rendered as "row 53:", a colon trailing into blank space. The row number is the whole label in that case. Also records, at fetchReport, that report.json needs no sessionStorage memo: GitHub Pages serves it with `cache-control: max-age=600` (measured 2026-08-31), so navigating between the Dashboard and Results inside ten minutes is served from the browser cache and never reaches the network. The note is there so the next person to notice the 1.8 MB fetch re-measures instead of assuming. Co-Authored-By: Claude Opus 5 --- website/src/reportData.js | 10 +++++++++- website/test/reportData.test.js | 15 +++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) diff --git a/website/src/reportData.js b/website/src/reportData.js index a3ad99c..1e6dc11 100644 --- a/website/src/reportData.js +++ b/website/src/reportData.js @@ -134,6 +134,11 @@ export const STATUS_ROWS = [ // --- Loading ------------------------------------------------------------- +// Fetched whole on both pages: report.json is ~1.8 MB. No sessionStorage memo, +// because there is nothing to fix — GitHub Pages serves it with +// `cache-control: max-age=600` (measured 2026-08-31), so a navigation between +// the Dashboard and Results inside ten minutes is served from the browser cache +// and never reaches the network. Re-measure before adding one. export async function fetchReport(url) { const response = await fetch(url); if (!response.ok) throw new Error(`HTTP ${response.status}`); @@ -175,7 +180,10 @@ export function isInteresting(result) { export function rowLabel(key, result) { if (result.kind === 'gsheet') { - return `row ${result.row}: ${result.query_label || result.query_id || ''}`; + // A sheet row can carry neither a label nor an ID, and rendered as "row 53:" + // trailing off into nothing. The row number is the whole label in that case. + const label = result.query_label || result.query_id; + return label ? `row ${result.row}: ${label}` : `row ${result.row}`; } if (result.kind === 'issue') return result.issue; if (result.kind === 'blocklist') return 'blocklist entry (details withheld)'; diff --git a/website/test/reportData.test.js b/website/test/reportData.test.js index f0f7bf1..2f6d018 100644 --- a/website/test/reportData.test.js +++ b/website/test/reportData.test.js @@ -43,3 +43,18 @@ describe('row classification', () => { expect(label).toBe('blocklist entry (details withheld)'); }); }); + +describe('row labels', () => { + it('labels a sheet row by its number when it has neither a label nor an id', () => { + expect(rowLabel('k', { kind: 'gsheet', row: 53 })).toBe('row 53'); + expect(rowLabel('k', { kind: 'gsheet', row: 53, query_label: '' })).toBe('row 53'); + }); + + it('still puts the label after the row number when there is one', () => { + expect(rowLabel('k', { kind: 'gsheet', row: 53, query_label: 'MONDO:1' })).toBe( + 'row 53: MONDO:1' + ); + expect(rowLabel('k', { kind: 'gsheet', row: 7, query_id: 'CHEBI:2' })).toBe('row 7: CHEBI:2'); + }); +}); + From 2fd3fff688e73afc83e0984b1339bb5f3a835d2b Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 31 Aug 2026 15:36:00 -0400 Subject: [PATCH 39/60] Replace the Astro starter README with one about this site website/README.md was still "Astro Starter Kit: Basics", down to the StackBlitz badges and the astronaut emoji. It now covers what the three pages answer, that the site renders two generated files rather than querying anything itself, how to get real data locally, the commands, and the constraints that are not obvious from the code: everything rendered is untrusted input, so {{ }} only and no v-html; links are built from validated parts; blocklist rows withhold their detail; and the Google Sheet IDs are secrets that must never appear. Co-Authored-By: Claude Opus 5 --- website/README.md | 90 +++++++++++++++++++++++++++-------------------- 1 file changed, 52 insertions(+), 38 deletions(-) diff --git a/website/README.md b/website/README.md index 1db3fb3..f667f12 100644 --- a/website/README.md +++ b/website/README.md @@ -1,54 +1,68 @@ -# Astro Starter Kit: Basics +# Babel Validation dashboard -```sh -npm create astro@latest -- --template basics -``` +The site published at . It shows the result of +running this repository's validation suite against every NodeNorm and NameRes deployment, once a +day, so that a failure can be read against where it sits in the promotion pipeline: a test that +fails in prod but passes everywhere else is a different problem from one that fails everywhere. + +Astro for the pages and the build, Vue islands for the parts that filter and sort, Bootstrap 5.3 +with a small theme layer in `src/styles/theme.css`. + +## Pages -[![Open in StackBlitz](https://developer.stackblitz.com/img/open_in_stackblitz.svg)](https://stackblitz.com/github/withastro/astro/tree/latest/examples/basics) -[![Open with CodeSandbox](https://assets.codesandbox.io/github/button-edit-lime.svg)](https://codesandbox.io/p/sandbox/github/withastro/astro/tree/latest/examples/basics) -[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/withastro/astro?devcontainer_path=.devcontainer/basics/devcontainer.json) +| Page | What it answers | +| --- | --- | +| `/` | Is anything wrong right now? Run banner, per-environment cards, promotion-drift patterns, and the environment detail matrix. | +| `/results/` | Which tests, exactly? The full matrix behind a sticky filter bar, filterable by outcome, category, source and environment, with the filter state in the URL so a view can be shared. | +| `/history/` | What changed since yesterday? A diff against the previous run, then one row per run. | -> 🧑‍🚀 **Seasoned astronaut?** Delete this file. Have fun! +## Where the data comes from -![just-the-basics](https://github.com/withastro/astro/assets/2244813/a0a5533c-a856-4198-8470-2d67b1d7c554) +Nothing here queries NodeNorm or NameRes. The site renders two files that +`.github/workflows/dashboard.yaml` regenerates daily and publishes to `gh-pages` alongside it: -## 🚀 Project Structure +- **`data/report.json`** — one entry per test, with an outcome per environment, plus each + deployment's `/status`. Written by `src/babel_validation/tools/generate_report.py` from the JSONL + that `pytest --report-jsonl` emits. +- **`data/history.jsonl`** — one summary line per run, appended to the previously published file. -Inside of your Astro project, you'll see the following folders and files: +To work against real data locally, download the published report into `public/data/`: -```text -/ -├── public/ -│ └── favicon.svg -├── src/ -│ ├── components/ -│ │ └── Card.astro -│ ├── layouts/ -│ │ └── Layout.astro -│ └── pages/ -│ └── index.astro -└── package.json +```sh +mkdir -p public/data +curl -o public/data/report.json https://translatorsri.github.io/babel-validation/data/report.json +curl -o public/data/history.jsonl https://translatorsri.github.io/babel-validation/data/history.jsonl ``` -Astro looks for `.astro` or `.md` files in the `src/pages/` directory. Each page is exposed as a route based on its file name. +Or generate your own from a test run — see `generate_report.py`'s header for the invocation. + +## Commands -There's nothing special about `src/components/`, but that's where we like to put any Astro/React/Vue/Svelte/Preact components. +```sh +npm install # or `npm ci` against the lockfile, which is what CI uses +npm run dev # dev server at localhost:4321 +npm run build # production build into dist/ +npm test # vitest +``` -Any static assets, like images, can be placed in the `public/` directory. +CI runs `npm ci` and `npm test` on Node 24, matching the lockfile's npm version. -## 🧞 Commands +## Working on it -All commands are run from the root of the project, from a terminal: +**Everything in the report is untrusted input.** It is built from GitHub issue bodies, Google Sheet +cells and service responses, none of which anyone reviewed. The generator validates and escapes it +server-side, but this site must also: -| Command | Action | -| :------------------------ | :----------------------------------------------- | -| `npm install` | Installs dependencies | -| `npm run dev` | Starts local dev server at `localhost:4321` | -| `npm run build` | Build your production site to `./dist/` | -| `npm run preview` | Preview your build locally, before deploying | -| `npm run astro ...` | Run CLI commands like `astro add`, `astro check` | -| `npm run astro -- --help` | Get help using the Astro CLI | +- render report values as text through `{{ }}` only — there is no `v-html` anywhere, and adding one + is how this site would start executing what an issue author wrote; +- build links from validated parts, as `reportData.js` does, never from report text verbatim; +- keep blocklist rows withholding their detail, in the expanded-row markup as well as the label; +- never show a Google Sheet ID or a link to one of the sheets. They are repository secrets. -## 👀 Want to learn more? +`src/reportData.js` holds everything about `report.json` that isn't rendering — fetching, labels, +the "interesting" predicate, the link builders — and is the right place for logic that would +otherwise be duplicated across two components. It is deliberately not in a `lib/` directory: the +root `.gitignore`'s Python-template `lib/` pattern silently swallows any directory of that name. -Feel free to check [our documentation](https://docs.astro.build) or jump into our [Discord server](https://astro.build/chat). +`src/deploymentOrder.js` fixes the left-to-right order of every table. Environments read in +promotion order, so a value that differs from its left neighbour is a change on its way through. From 77971a1284e8cadea5e24f92bef289d9a1b97d21 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 31 Aug 2026 16:13:11 -0400 Subject: [PATCH 40/60] Record the two traps this round cost time on A unit test with no `pytestmark = pytest.mark.unit` is silently deselected by CI's only pytest job, so the file looks like a passing suite while testing nothing. #112 had six tests in that state, and nothing said so. And the site is served under , which is why a relative URL handed to history.replaceState rewrites the address bar to a different page. The trap is that no test can catch it: vitest mounts components at / with no , so the relative form works there and fails only in production. That belongs next to the note about how the components are tested, not only in the one comment beside the call. Also drops the manual curl block added to website/README.md earlier today, which duplicated the `npm run fetch-data` script that already exists. Co-Authored-By: Claude Opus 5 --- CLAUDE.md | 4 ++++ website/README.md | 19 ++++++++++--------- 2 files changed, 14 insertions(+), 9 deletions(-) diff --git a/CLAUDE.md b/CLAUDE.md index a64faad..ca38c02 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -227,4 +227,8 @@ When writing new tests: `'1e-06'` and the validator reports `'1e-06' is not of type 'number'` against JSON that is perfectly valid. The spurious error is also first, so it masks the real one further down the document. +- **A new unit test needs `pytestmark = pytest.mark.unit`, or CI never runs it.** The only pytest + job in `tests.yaml` is `pytest -m unit`, so an unmarked file is silently deselected — it looks + like a passing suite while testing nothing. This is not hypothetical: `test_milestones_page.py` + in #112 had six tests that had never run. - Import shared classes from `src.babel_validation.*` (e.g. `from src.babel_validation.services.nodenorm import CachedNodeNorm`) diff --git a/website/README.md b/website/README.md index f667f12..d6447dc 100644 --- a/website/README.md +++ b/website/README.md @@ -26,15 +26,9 @@ Nothing here queries NodeNorm or NameRes. The site renders two files that that `pytest --report-jsonl` emits. - **`data/history.jsonl`** — one summary line per run, appended to the previously published file. -To work against real data locally, download the published report into `public/data/`: - -```sh -mkdir -p public/data -curl -o public/data/report.json https://translatorsri.github.io/babel-validation/data/report.json -curl -o public/data/history.jsonl https://translatorsri.github.io/babel-validation/data/history.jsonl -``` - -Or generate your own from a test run — see `generate_report.py`'s header for the invocation. +To work against real data locally, `npm run fetch-data` downloads the published copies into +`public/data/`, which is gitignored. Or generate your own from a test run — see +`generate_report.py`'s header for the invocation. ## Commands @@ -64,5 +58,12 @@ the "interesting" predicate, the link builders — and is the right place for lo otherwise be duplicated across two components. It is deliberately not in a `lib/` directory: the root `.gitignore`'s Python-template `lib/` pattern silently swallows any directory of that name. +**The site is served under ``, and vitest is not.** A relative URL +passed to `history.pushState`/`replaceState` resolves against the *document base*, not the current +path, so `replaceState(null, '', '?q=1')` on `/results/` silently rewrites the address bar to the +site root — a different page, which ignores the parameters. Always build these from +`window.location.pathname`. No test can catch it: the suite mounts components at `/` with no +`` element, so the relative form works there and fails only in production. + `src/deploymentOrder.js` fixes the left-to-right order of every table. Environments read in promotion order, so a value that differs from its left neighbour is a change on its way through. From 689ad6169c6e809c164803c2d4e26a6d3974228c Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 31 Aug 2026 16:13:11 -0400 Subject: [PATCH 41/60] Pin read_targets, now that the workflow's run loop comes from it MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit read_targets had no tests. It decides which environments the report contains, and as of the dashboard workflow taking its loop from it, which environments are run at all — so the localhost exclusion and the section order are load-bearing in a way they were not when the workflow carried its own list. Four tests: every section but localhost, order preserved as the file gives it, the repository allowlist lowercased and blank-stripped, and the checked-in targets.ini yielding a non-empty list without localhost in it. Dropping the localhost exclusion fails them. Co-Authored-By: Claude Opus 5 --- tests/unit/test_generate_report.py | 49 ++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/tests/unit/test_generate_report.py b/tests/unit/test_generate_report.py index 050410d..6d2e602 100644 --- a/tests/unit/test_generate_report.py +++ b/tests/unit/test_generate_report.py @@ -14,6 +14,7 @@ fetch_status, parse_nodeid, read_raw_records, + read_targets, sanitize, split_target, trim_status, @@ -438,3 +439,51 @@ def test_history_line_without_targets_is_dropped(self, tmp_path): def test_missing_url_does_not_reach_the_network(self): assert fetch_status(None) == {"error": "NoURL"} + + +# read_targets is the single source of truth for which environments exist: as of +# the dashboard workflow taking its loop from it, a section it returns is one that +# gets run, and one it drops is never mentioned again. When those two disagreed, +# the extra target reached the site as a permanently unreachable column. +class TestReadTargets: + def _ini(self, tmp_path, text): + path = tmp_path / "targets.ini" + path.write_text(text, encoding="utf8") + return path + + def test_it_returns_every_section_except_localhost(self, tmp_path): + path = self._ini( + tmp_path, + "[DEFAULT]\nRepositories =\n org/one\n\n" + "[prod]\nNodeNormURL = https://prod.example/\n\n" + "[test-redis]\nNodeNormURL = https://redis.example/\n\n" + "[localhost]\nNodeNormURL = http://localhost:2434/\n", + ) + + targets, allowlist, _ = read_targets(path) + + assert targets == ["prod", "test-redis"] + assert allowlist == ["org/one"] + + def test_it_keeps_the_order_the_file_gives(self, tmp_path): + # The site sorts by DEPLOYMENT_ORDER, but the workflow runs them in this + # order, and a report is easier to read against the file it came from. + path = self._ini(tmp_path, "".join(f"[{name}]\nNodeNormURL = https://{name}.example/\n\n" + for name in ("exp", "dev", "ci", "prod"))) + + assert read_targets(path)[0] == ["exp", "dev", "ci", "prod"] + + def test_the_repository_allowlist_is_lowercased_and_stripped(self, tmp_path): + path = self._ini( + tmp_path, + "[DEFAULT]\nRepositories =\n NCATSTranslator/Babel\n \n TranslatorSRI/Babel-Explorer\n\n" + "[prod]\nNodeNormURL = https://prod.example/\n", + ) + + assert read_targets(path)[1] == ["ncatstranslator/babel", "translatorsri/babel-explorer"] + + def test_the_checked_in_targets_ini_has_no_localhost_and_is_not_empty(self): + targets, _, _ = read_targets("tests/targets.ini") + + assert "localhost" not in targets + assert targets, "the workflow builds its run loop from this list" From 521c4611d521808390a85f86c2cea9a50794f08e Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 31 Aug 2026 16:44:34 -0400 Subject: [PATCH 42/60] Say so when an environment is missing from the promotion order MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit DEPLOYMENT_ORDER is the last hardcoded list of environments on the site: the workflow and generate_report both read targets.ini now, but promotion order is a semantic fact about the pipeline that no config file states, so it cannot be derived from one and has to stay written down. What it should not do is fail quietly. An unrecognised target sorted last, which is indistinguishable from "this is the end of the pipeline" — and the sentence above the cards then read "reaches exp first and last", asserting something nobody had said. The Dashboard now names the environments the order does not know, and builds that sentence only from the ones it does. Co-Authored-By: Claude Opus 5 --- website/src/components/Overview.vue | 18 ++++++++++++++--- website/src/deploymentOrder.js | 10 ++++++++++ website/test/overview.test.js | 31 +++++++++++++++++++++++++++++ 3 files changed, 56 insertions(+), 3 deletions(-) diff --git a/website/src/components/Overview.vue b/website/src/components/Overview.vue index 0c9c0a3..f99927a 100644 --- a/website/src/components/Overview.vue +++ b/website/src/components/Overview.vue @@ -9,7 +9,7 @@ built with URLSearchParams rather than string concatenation. -->