From 66c3562ca10b598a647f95b837439530c038e2d5 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Wed, 26 Aug 2026 18:57:59 -0400 Subject: [PATCH 01/20] 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 02/20] 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 03/20] 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 04/20] 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 05/20] 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 06/20] 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 07/20] 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. -->