[MSNoise] Error after install
Healy, David
d.healy at abdn.ac.uk
Thu Oct 7 10:58:19 UTC 2021
Still no success.
I uninstalled everything, msnoise and MySQL.
Re-installed MySQL 8.0.18, server and workbench; did the setup steps; looks ok.
Setup a new Anaconda environment for msnoise; reinstalled the packages. Tried to run 'msnoise test', 'msnoise bugreport' and 'msnoise db init'. Same errors for all of the me.
Is MSNoise compatible with Python 3.8?
Cheers,
Dave
David Healy [he/him]
School of Geosciences
Meston Walk
University of Aberdeen
Aberdeen AB24 3UE
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On 07/10/2021, 09:15, "msnoise-bounces at mailman-as.oma.be on behalf of Thomas Lecocq" <msnoise-bounces at mailman-as.oma.be on behalf of Thomas.Lecocq at seismology.be> wrote:
CAUTION: External email. Ensure this message is from a trusted source before clicking links/attachments. If you are concerned forward this email to spam at abdn.ac.uk
Hi,
if you "msnoise db init" in the project folder, it'll create the tables
for you
thomas
Le 07/10/2021 à 10:14, Healy, David a écrit :
> OK thanks.
>
> After setting up the default/basic 'msnoise' database in MySQL, do *I* need to build a table called 'config'? or is that automatic?
>
> Cheers,
> Dave
>
> David Healy [he/him]
> School of Geosciences
> Meston Walk
> University of Aberdeen
> Aberdeen AB24 3UE
>
> My working day may not be your working day. Please do not feel obliged to reply to this e-mail outside of your normal working hours.
>
> Publications: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.google.com%2Fcitations%3Fhl%3Den%26user%3Dug9DnVoAAAAJ&data=04%7C01%7Cd.healy%40abdn.ac.uk%7Cb396c90da8ff4a55bdba08d9896aa891%7C8c2b19ad5f9c49d490773ec3cfc52b3f%7C0%7C0%7C637691913460390120%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=O8pdCBpJ5IjTXAf8nt76QtqYYhkoLok5zuBS0HRzDhg%3D&reserved=0
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>
>
> On 06/10/2021, 13:40, "msnoise-bounces at mailman-as.oma.be on behalf of Thomas Lecocq" <msnoise-bounces at mailman-as.oma.be on behalf of Thomas.Lecocq at seismology.be> wrote:
>
> [You don't often get email from thomas.lecocq at seismology.be. Learn why this is important at http://aka.ms/LearnAboutSenderIdentification.]
>
> CAUTION: External email. Ensure this message is from a trusted source before clicking links/attachments. If you are concerned forward this email to spam at abdn.ac.uk
>
>
> Hey Dave,
>
> it seems there are lots of issues with some recent codebase changes in
> dependencies, leading to crazy errors in the test suite.
>
> You should go ahead and try making a small project folder, and running
> the workflow,
>
> Let me know how it goes,
>
> Thomas
>
> Le 06/10/2021 à 14:32, Healy, David a écrit :
> > Hello
> >
> > I’m trying to install MSNoise, but keep getting unintelligible (to me) errors when running msnoise test:
> > *****
> > Traceback (most recent call last):
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1276, in _execute_context
> > self.dialect.do_execute(
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute
> > cursor.execute(statement, parameters)
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/cursors.py", line 148, in execute
> > result = self._query(query)
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/cursors.py", line 310, in _query
> > conn.query(q)
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/connections.py", line 548, in query
> > self._affected_rows = self._read_query_result(unbuffered=unbuffered)
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/connections.py", line 775, in _read_query_result
> > result.read()
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/connections.py", line 1156, in read
> > first_packet = self.connection._read_packet()
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/connections.py", line 725, in _read_packet
> > packet.raise_for_error()
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/protocol.py", line 221, in raise_for_error
> > err.raise_mysql_exception(self._data)
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/err.py", line 143, in raise_mysql_exception
> > raise errorclass(errno, errval)
> > pymysql.err.ProgrammingError: (1146, "Table 'msnoise.config' doesn't exist")
> >
> > The above exception was the direct cause of the following exception:
> >
> > Traceback (most recent call last):
> > File "/opt/anaconda3/bin/msnoise", line 5, in <module>
> > from msnoise.scripts.msnoise import run
> > File "/opt/anaconda3/lib/python3.8/site-packages/msnoise/scripts/msnoise.py", line 1183, in <module>
> > plugins = get_config(db, "plugins")
> > File "/opt/anaconda3/lib/python3.8/site-packages/msnoise/api.py", line 215, in get_config
> > config = session.query(table).filter(table.name == name).first()
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 3429, in first
> > ret = list(self[0:1])
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 3203, in __getitem__
> > return list(res)
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 3535, in __iter__
> > return self._execute_and_instances(context)
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 3560, in _execute_and_instances
> > result = conn.execute(querycontext.statement, self._params)
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1011, in execute
> > return meth(self, multiparams, params)
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 298, in _execute_on_connection
> > return connection._execute_clauseelement(self, multiparams, params)
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1124, in _execute_clauseelement
> > ret = self._execute_context(
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1316, in _execute_context
> > self._handle_dbapi_exception(
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1510, in _handle_dbapi_exception
> > util.raise_(
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
> > raise exception
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1276, in _execute_context
> > self.dialect.do_execute(
> > File "/opt/anaconda3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute
> > cursor.execute(statement, parameters)
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/cursors.py", line 148, in execute
> > result = self._query(query)
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/cursors.py", line 310, in _query
> > conn.query(q)
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/connections.py", line 548, in query
> > self._affected_rows = self._read_query_result(unbuffered=unbuffered)
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/connections.py", line 775, in _read_query_result
> > result.read()
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/connections.py", line 1156, in read
> > first_packet = self.connection._read_packet()
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/connections.py", line 725, in _read_packet
> > packet.raise_for_error()
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/protocol.py", line 221, in raise_for_error
> > err.raise_mysql_exception(self._data)
> > File "/opt/anaconda3/lib/python3.8/site-packages/pymysql/err.py", line 143, in raise_mysql_exception
> > raise errorclass(errno, errval)
> > sqlalchemy.exc.ProgrammingError: (pymysql.err.ProgrammingError) (1146, "Table 'msnoise.config' doesn't exist")
> > [SQL: SELECT config.name AS config_name, config.value AS config_value
> > FROM config
> > WHERE config.name = %(name_1)s
> > LIMIT %(param_1)s]
> > [parameters: {'name_1': 'plugins', 'param_1': 1}]
> > (Background on this error at: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsqlalche.me%2Fe%2F13%2Ff405&data=04%7C01%7Cd.healy%40abdn.ac.uk%7Cb396c90da8ff4a55bdba08d9896aa891%7C8c2b19ad5f9c49d490773ec3cfc52b3f%7C0%7C0%7C637691913460400112%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Ke3LZSqZ7SO4yncpg0r7b6rCWFMQNnFYOkXITWlxCL0%3D&reserved=0)
> > *****
> >
> > I’ve got all the required Python packages, MySQLServer and Workbench versions 8.0.18 (compatible with my macOS Mojave 10.14.6). Local database and user are set-up.
> >
> > Any ideas?
> >
> > Thanks,
> > Dave
> >
> > David Healy [he/him]
> > School of Geosciences
> > Meston Walk
> > University of Aberdeen
> > Aberdeen AB24 3UE
> >
> > My working day may not be your working day. Please do not feel obliged to reply to this e-mail outside of your normal working hours.
> >
> > Publications: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.google.com%2Fcitations%3Fhl%3Den%26user%3Dug9DnVoAAAAJ&data=04%7C01%7Cd.healy%40abdn.ac.uk%7Cb396c90da8ff4a55bdba08d9896aa891%7C8c2b19ad5f9c49d490773ec3cfc52b3f%7C0%7C0%7C637691913460400112%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=kFpoq0LbNb7aO1bjV2MQX2IJZCy6bPJ6RPdm5JXFz3E%3D&reserved=0
> > Software: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.fracturedrockphysics.com%2Fsoftware.html&data=04%7C01%7Cd.healy%40abdn.ac.uk%7Cb396c90da8ff4a55bdba08d9896aa891%7C8c2b19ad5f9c49d490773ec3cfc52b3f%7C0%7C0%7C637691913460400112%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=A3%2F8WemtQLoU75RcSpHALJ87C6%2Fqr8%2BXFFPWEqzFJ0A%3D&reserved=0
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> >
> >
> >
> > The University of Aberdeen is a charity registered in Scotland, No SC013683.
> > Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
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> >
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>
>
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
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