a51a9e2eec975f01419e03107d70c74dfe5e0766 hiram Tue Apr 28 14:35:28 2026 -0700 different response messages for liftRequest vs. assembly request refs #31811 diff --git src/hg/utils/otto/userRequests/ottoRequest.py src/hg/utils/otto/userRequests/ottoRequest.py index e29b9bc9d87..2df6933c138 100755 --- src/hg/utils/otto/userRequests/ottoRequest.py +++ src/hg/utils/otto/userRequests/ottoRequest.py @@ -2,101 +2,174 @@ """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] """ import argparse 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', +} + 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.""" + """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] 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 = line.split('\t') + 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] 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 sendMail(toAddr, subject, body, fromAddr=None): +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.""" + 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 @@ -106,79 +179,84 @@ 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() 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') - notifyEmail = conf.get('chainFileRequestEmail') - if not notifyEmail: - sys.exit("Error: chainFileRequestEmail not defined in config") - # 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: - subject = f"ottoRequest #{req['id']}: {req['requestType']} pending" - body = ( - f"##################################################\n" - f"Pending {req['requestType']} request #{req['id']}\n" - f"\n" - f" From: {req['fromDb']}\n" - f" To: {req['toDb']}\n" - f" Email: {req['email']}\n" - f" Comment: {req['comment']}\n" - f" Time: {req['requestTime']}\n" - f"##################################################\n" - f"testing ottoRequest watch cron job\n" - f"##################################################\n" - ) - if sendMail(notifyEmail, subject, body, fromAddr=notifyEmail): -# print(f"Notified {notifyEmail} about request #{req['id']}") - hgsqlUpdate(dbName, - f"UPDATE {table} SET status = 1" - f" WHERE id = {req['id']}") - else: - print(f"Failed to notify about request #{req['id']}", + 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 - # send acknowledgment to the requesting user userEmail = req.get('email', '') - if userEmail: - userSubject = (f"UCSC Genome Browser: your {req['requestType']}" + 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") - userBody = ( - f"Your request for chain/liftOver files has been received\n" - f"and is being processed.\n" + 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" Type: {req['requestType']}\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"You will receive another email when your files are ready.\n" + f"Will advise when this alignment is available in the genome browser.\n" f"\n" - f"- UCSC Genome Browser\n" + f"-- UCSC Genome Browser\n" ) - if not sendMail(userEmail, userSubject, userBody, - fromAddr=notifyEmail): - print(f"Warning: failed to send acknowledgment to" - f" {userEmail} for request #{req['id']}", + 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()