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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
147 stars 43 forks source link

Can't connect to chanjo database #4648

Closed northwestwitch closed 1 month ago

northwestwitch commented 1 month ago 
2024-05-29 14:39:27,099 - [scout.server.app](http://scout.server.app/) - ERROR: Exception on /reports/report [POST] [in /venv/lib/python3.8/site-packages/flask/app.py:1414]
Traceback (most recent call last):
  File "/venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 2336, in _wrap_pool_connect
    return fn()
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 364, in connect
    return _ConnectionFairy._checkout(self)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 778, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 495, in checkout
    rec = pool._do_get()
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/impl.py", line 140, in _do_get
    self._dec_overflow()
  File "/venv/lib/python3.8/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
    compat.raise_(
  File "/venv/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
    raise exception
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/impl.py", line 137, in _do_get
    return self._create_connection()
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 309, in _create_connection
    return _ConnectionRecord(self)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 440, in __init__
    self.__connect(first_connect_check=True)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 661, in __connect
    pool.logger.debug("Error on connect(): %s", e)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
    compat.raise_(
  File "/venv/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
    raise exception
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 656, in __connect
    connection = pool._invoke_creator(self)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect
    return dialect.connect(*cargs, **cparams)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 508, in connect
    return self.dbapi.connect(*cargs, **cparams)
  File "/venv/lib/python3.8/site-packages/pymysql/connections.py", line 358, in __init__
    self.connect()
  File "/venv/lib/python3.8/site-packages/pymysql/connections.py", line 664, in connect
    self._request_authentication()
  File "/venv/lib/python3.8/site-packages/pymysql/connections.py", line 954, in _request_authentication
    auth_packet = self._read_packet()
  File "/venv/lib/python3.8/site-packages/pymysql/connections.py", line 772, in _read_packet
    packet.raise_for_error()
  File "/venv/lib/python3.8/site-packages/pymysql/protocol.py", line 221, in raise_for_error
    err.raise_mysql_exception(self._data)
  File "/venv/lib/python3.8/site-packages/pymysql/err.py", line 143, in raise_mysql_exception
    raise errorclass(errno, errval)
pymysql.err.OperationalError: (1045, "Access denied for user 'produser'@'[cg-services-prod.scilifelab.se](http://cg-services-prod.scilifelab.se/)' (using password: YES)")

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/venv/lib/python3.8/site-packages/flask/app.py", line 2190, in wsgi_app
    response = self.full_dispatch_request()
  File "/venv/lib/python3.8/site-packages/flask/app.py", line 1486, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/venv/lib/python3.8/site-packages/flask_cors/extension.py", line 178, in wrapped_function
    return cors_after_request(app.make_response(f(*args, **kwargs)))
  File "/venv/lib/python3.8/site-packages/flask/app.py", line 1484, in full_dispatch_request
    rv = self.dispatch_request()
  File "/venv/lib/python3.8/site-packages/flask/app.py", line 1469, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)
  File "/venv/lib/python3.8/site-packages/chanjo_report/server/blueprints/report/views.py", line 131, in report
    return render_template("report/report.html", **data)
  File "/venv/lib/python3.8/site-packages/flask/templating.py", line 151, in render_template
    return _render(app, template, context)
  File "/venv/lib/python3.8/site-packages/flask/templating.py", line 132, in _render
    rv = template.render(context)
  File "/venv/lib/python3.8/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/venv/lib/python3.8/site-packages/jinja2/environment.py", line 939, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/venv/lib/python3.8/site-packages/chanjo_report/server/blueprints/report/templates/report/report.html", line 252, in top-level template code
    {% if hidden %}
  File "/venv/lib/python3.8/site-packages/chanjo_report/server/blueprints/report/templates/report/layouts/base.html", line 36, in top-level template code
    {% block body %}
  File "/venv/lib/python3.8/site-packages/chanjo_report/server/blueprints/report/templates/report/layouts/base.html", line 51, in block 'body'
    {% block main %}{% endblock %}
  File "/venv/lib/python3.8/site-packages/chanjo_report/server/blueprints/report/templates/report/report.html", line 35, in block 'main'
    {{ overview_table(sex_rows) }}
  File "/venv/lib/python3.8/site-packages/jinja2/runtime.py", line 782, in _invoke
    rv = self._func(*arguments)
  File "/venv/lib/python3.8/site-packages/chanjo_report/server/blueprints/report/templates/report/report.html", line 73, in template
    {% for sample in sex_rows %}
  File "/venv/lib/python3.8/site-packages/chanjo_report/server/blueprints/report/utils.py", line 79, in samplesex_rows
    samples = itertools.groupby(sex_query, lambda row: row[0])
  File "/venv/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 3535, in __iter__
    return self._execute_and_instances(context)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 3556, in _execute_and_instances
    conn = self._get_bind_args(
  File "/venv/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 3571, in _get_bind_args
    return fn(
  File "/venv/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 3550, in _connection_from_session
    conn = self.session.connection(**kw)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1142, in connection
    return self._connection_for_bind(
  File "/venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1150, in _connection_for_bind
    return self.transaction._connection_for_bind(
  File "/venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 433, in _connection_for_bind
    conn = bind._contextual_connect()
  File "/venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 2302, in _contextual_connect
    self._wrap_pool_connect(self.pool.connect, None),
  File "/venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 2339, in _wrap_pool_connect
    Connection._handle_dbapi_exception_noconnection(
  File "/venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1583, in _handle_dbapi_exception_noconnection
    util.raise_(
  File "/venv/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
    raise exception
  File "/venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 2336, in _wrap_pool_connect
    return fn()
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 364, in connect
    return _ConnectionFairy._checkout(self)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 778, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 495, in checkout
    rec = pool._do_get()
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/impl.py", line 140, in _do_get
    self._dec_overflow()
  File "/venv/lib/python3.8/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
    compat.raise_(
  File "/venv/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
    raise exception
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/impl.py", line 137, in _do_get
    return self._create_connection()
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 309, in _create_connection
    return _ConnectionRecord(self)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 440, in __init__
    self.__connect(first_connect_check=True)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 661, in __connect
    pool.logger.debug("Error on connect(): %s", e)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
    compat.raise_(
  File "/venv/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
    raise exception
  File "/venv/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 656, in __connect
    connection = pool._invoke_creator(self)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect
    return dialect.connect(*cargs, **cparams)
  File "/venv/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 508, in connect
    return self.dbapi.connect(*cargs, **cparams)
  File "/venv/lib/python3.8/site-packages/pymysql/connections.py", line 358, in __init__
    self.connect()
  File "/venv/lib/python3.8/site-packages/pymysql/connections.py", line 664, in connect
    self._request_authentication()
  File "/venv/lib/python3.8/site-packages/pymysql/connections.py", line 954, in _request_authentication
    auth_packet = self._read_packet()
  File "/venv/lib/python3.8/site-packages/pymysql/connections.py", line 772, in _read_packet
    packet.raise_for_error()
  File "/venv/lib/python3.8/site-packages/pymysql/protocol.py", line 221, in raise_for_error
    err.raise_mysql_exception(self._data)
  File "/venv/lib/python3.8/site-packages/pymysql/err.py", line 143, in raise_mysql_exception
    raise errorclass(errno, errval)
sqlalchemy.exc.OperationalError: (pymysql.err.OperationalError) (1045, "Access denied for user 'produser'@'[cg-services-prod.scilifelab.se](http://cg-services-prod.scilifelab.se/)' (using password: YES)")
(Background on this error at: http://sqlalche.me/e/13/e3q8)
northwestwitch commented 1 month ago

That in turn causes this:

2024-05-29 14:39:29,067 - [scout.server.app](http://scout.server.app/) - ERROR: Exception on /cust002/F0058642/pdf_report [GET] [in /venv/lib/python3.8/site-packages/flask/app.py:1414]
Traceback (most recent call last):
  File "/venv/lib/python3.8/site-packages/flask/app.py", line 2190, in wsgi_app
    response = self.full_dispatch_request()
  File "/venv/lib/python3.8/site-packages/flask/app.py", line 1486, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/venv/lib/python3.8/site-packages/flask_cors/extension.py", line 178, in wrapped_function
    return cors_after_request(app.make_response(f(*args, **kwargs)))
  File "/venv/lib/python3.8/site-packages/flask/app.py", line 1484, in full_dispatch_request
    rv = self.dispatch_request()
  File "/venv/lib/python3.8/site-packages/flask/app.py", line 1469, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)
  File "/home/worker/app/scout/server/blueprints/cases/views.py", line 278, in pdf_case_report
    data["coverage_report"] = controllers.coverage_report_contents(
  File "/home/worker/app/scout/server/blueprints/cases/controllers.py", line 133, in coverage_report_contents
    html_body_content = resp.text.split("<body>")[1].split("</body>")[0]
IndexError: list index out of range
northwestwitch commented 1 month ago

This was caused by a change of the mysql password for the chanjo database. Restarting the scout prod service fixed the error. Closing this issue