211c215c654c363993a9d480cbda679de0bbd7e9 hiram Fri May 1 13:59:15 2026 -0700 eliminating stderr information to avoid cron job noise refs #31811 diff --git src/hg/utils/otto/userRequests/ottoRequest.py src/hg/utils/otto/userRequests/ottoRequest.py index ebfb5dc8b68..75141e61783 100755 --- src/hg/utils/otto/userRequests/ottoRequest.py +++ src/hg/utils/otto/userRequests/ottoRequest.py @@ -1,292 +1,296 @@ #!/usr/bin/env python3 """ottoRequest.py - check ottoRequest table for pending requests and send email notification for each one found. Intended to run from cron. Reads the notification email address and table name from an hg.conf file. Uses hgsql for database access. Usage: ottoRequest.py [-c /path/to/hg.conf] Options: -c, --conf Path to hg.conf [default: /usr/local/apache/cgi-bin/hg.conf] + +cron entry in the otto user: +1,8,15,22,29,36,43,50,57 * * * * /hive/data/outside/otto/liftRequest/ottoRequest.py + """ import argparse import fcntl import os import re import subprocess import sys NOTIFY_FROM = 'genome-www@soe.ucsc.edu' BCC_BY_TYPE = { 'liftOver': 'chain-file-request-group@ucsc.edu', 'assembly': 'genark-request-group@ucsc.edu', } scriptDir = os.path.dirname(os.path.abspath(__file__)) lockPath = os.path.join(scriptDir, "ottoRequest.lock") def acquireSingletonLock(): """Ensure only one instance of this script runs at a time. Holds an exclusive flock on lockPath for the lifetime of the process; the kernel releases it on exit (including crash / kill -9), so no stale lock cleanup is needed. Returns the open file handle, which the caller must keep alive.""" # "a+" opens read+write without truncating (and creates if missing), # so a second instance that fails to lock doesn't wipe the running # instance's PID from the file before exiting. fh = open(lockPath, "a+") try: fcntl.flock(fh, fcntl.LOCK_EX | fcntl.LOCK_NB) except BlockingIOError: sys.exit(0) # we own the lock truncate and write our PID for information fh.seek(0) fh.truncate() fh.write("%d\n" % os.getpid()) fh.flush() return fh ### FYI: can also see the locking process via: lsof ottoRequest.lock def parseHgConf(path): """Return a dict of key=value pairs from an hg.conf file. Handles 'include' directives with paths relative to the directory of the file containing the include.""" conf = {} confDir = os.path.dirname(os.path.abspath(path)) try: with open(path) as fh: for line in fh: line = line.strip() if not line or line.startswith('#'): continue if line.startswith('include '): inclPath = line.split(None, 1)[1] if not os.path.isabs(inclPath): inclPath = os.path.join(confDir, inclPath) inclConf = parseHgConf(inclPath) conf.update(inclConf) continue if '=' in line: key, value = line.split('=', 1) conf[key.strip()] = value.strip() except FileNotFoundError: sys.exit(f"Error: config file not found: {path}") except PermissionError: sys.exit(f"Error: cannot read config file: {path}") return conf def unescapeMysql(s): """Reverse mysql -B batch-mode escaping: \\n -> newline, \\t -> tab, \\\\ -> backslash, \\0 -> NUL. Single pass so \\\\n stays a literal backslash followed by 'n'.""" out = [] i = 0 n = len(s) while i < n: if s[i] == '\\' and i + 1 < n: c = s[i+1] if c == 'n': out.append('\n') elif c == 't': out.append('\t') elif c == '\\': out.append('\\') elif c == '0': out.append('\0') else: out.append(s[i:i+2]) i += 2 else: out.append(s[i]) i += 1 return ''.join(out) def hgsqlQuery(db, sql): """Run a SQL query via hgsql and return rows as list of dicts. hgsql -B emits tabs/newlines/backslashes inside field values as literal \\t / \\n / \\\\ so each row stays on one line undo that on each field before returning.""" - cmd = ['hgsql', db, '-N', '-B', '-e', sql] + cmd = ['/cluster/bin/x86_64/hgsql', db, '-N', '-B', '-e', sql] result = subprocess.run(cmd, capture_output=True, text=True) if result.returncode != 0: sys.exit(f"hgsql error: {result.stderr.strip()}") rows = [] if not result.stdout.strip(): return rows for line in result.stdout.strip().split('\n'): fields = [unescapeMysql(f) for f in line.split('\t')] rows.append({ 'id': fields[0], 'requestType': fields[1], 'fromDb': fields[2], 'toDb': fields[3], 'email': fields[4], 'comment': fields[5], 'requestTime': fields[6], }) return rows def hgsqlUpdate(db, sql): """Run a SQL update/insert statement via hgsql.""" - cmd = ['hgsql', db, '-N', '-B', '-e', sql] + cmd = ['/cluster/bin/x86_64/hgsql', db, '-N', '-B', '-e', sql] result = subprocess.run(cmd, capture_output=True, text=True) if result.returncode != 0: print(f"hgsql update error: {result.stderr.strip()}", file=sys.stderr) return False return True def parseAssemblyComment(comment): """Assembly requests pack fields into the ottoRequest.comment column via hubApi/findGenome.c:apiAssemblyRequest: name: '<name>'[; betterName: '<bn>'][; comment: '<user comment>'] The user comment may itself contain newlines and apostrophes, so the inner quote pair is matched greedily up to the trailing closing quote. re.DOTALL lets '.' span newlines. Return (name, betterName, userComment).""" name = '' betterName = '' userComment = '' m = re.match(r"name: '([^']*)'(.*)$", comment, re.DOTALL) if not m: return name, betterName, comment name = m.group(1) rest = m.group(2) m2 = re.match(r"; betterName: '([^']*)'(.*)$", rest, re.DOTALL) if m2: betterName = m2.group(1) rest = m2.group(2) m3 = re.match(r"; comment: '(.*)'\s*$", rest, re.DOTALL) if m3: userComment = m3.group(1) else: userComment = rest.lstrip('; ') return name, betterName, userComment def sendMail(toAddr, subject, body, fromAddr=None, bccAddr=None): """Send email via /usr/sbin/sendmail. If fromAddr is provided it is used as the envelope sender (-f) and the From: header so that bounces return to that address. If bccAddr is provided, sendmail -t reads it from the header, delivers a copy, and strips the Bcc: line before transmission.""" headers = f"To: {toAddr}\nSubject: {subject}" if bccAddr: headers = f"Bcc: {bccAddr}\n{headers}" if fromAddr: headers = (f"From: {fromAddr}\n" f"Reply-To: {fromAddr}\n" f"Return-Path: {fromAddr}\n" f"{headers}") message = f"{headers}\n\n{body}\n" cmd = ['/usr/sbin/sendmail', '-t'] if fromAddr: cmd += ['-f', fromAddr] result = subprocess.run(cmd, input=message, capture_output=True, text=True) if result.returncode != 0: print(f"Warning: sendmail failed: {result.stderr.strip()}", file=sys.stderr) return False return True def main(): parser = argparse.ArgumentParser( description='Process pending ottoRequest entries.') parser.add_argument('-c', '--conf', default='/usr/local/apache/cgi-bin/hg.conf', help='Path to hg.conf [default: %(default)s]') args = parser.parse_args() # bind to a local so the FD stays open for the lifetime of main() _lock = acquireSingletonLock() # noqa: F841 conf = parseHgConf(args.conf) dbName = conf.get('central.db') if not dbName: sys.exit("Error: central.db not defined in config") table = conf.get('ottoTable', 'ottoRequest') # find pending requests sql = (f"SELECT id, requestType, fromDb, toDb, email, comment, " f"requestTime FROM {table} WHERE status = 0") pending = hgsqlQuery(dbName, sql) if not pending: return # nothing to do -- silent for cron for req in pending: reqType = req['requestType'] bccAddr = BCC_BY_TYPE.get(reqType) if not bccAddr: print(f"Warning: unknown requestType '{reqType}' for" f" request #{req['id']}, skipping", file=sys.stderr) continue userEmail = req.get('email', '') if not userEmail: print(f"Warning: no user email for request #{req['id']}," f" skipping", file=sys.stderr) continue subject = (f"UCSC Genome Browser: your {reqType}" f" request has been received") if reqType == 'assembly': name, betterName, userComment = parseAssemblyComment(req['comment']) body = ( f"Your assembly request has been received and is being\n" f"processed.\n" f"\n" f"name: '{name}'\n" f"email: '{userEmail}'\n" f"asmId: '{req['fromDb']}'\n" f"betterName: '{betterName}'\n" f"comment: '{userComment.rstrip()}'\n" f"date: '{req['requestTime']}'\n" f"\n" f"Will advise when this assembly is available in the genome browser.\n" f"\n" f"-- UCSC Genome Browser\n" ) else: body = ( f"Your alignment request has been received and is being\n" f"processed.\n" f"\n" f"Request details:\n" f" From: {req['fromDb']}\n" f" To: {req['toDb']}\n" f" Comment: {req['comment'].rstrip()}\n" f" Submitted: {req['requestTime']}\n" f"\n" f"Will advise when this alignment is available in the genome browser.\n" f"\n" f"-- UCSC Genome Browser\n" ) if sendMail(userEmail, subject, body, fromAddr=NOTIFY_FROM, bccAddr=bccAddr): hgsqlUpdate(dbName, f"UPDATE {table} SET status = 1" f" WHERE id = {req['id']}") else: print(f"Failed to send notification for request #{req['id']}", file=sys.stderr) if __name__ == '__main__': main()