[MSNoise] Error after install
Thomas Lecocq
Thomas.Lecocq at seismology.be
Thu Oct 7 11:00:11 UTC 2021
Hi,
if your project is small, you might want to use sqlite, that will work
smooth.
There have been changes to Mysql since MySQL 5 which could be the culprit.
Alternatively, you could try the latest "dev" version available from github.
Yes, msnoise is py3.8 compatible.
Thomas
Le 07/10/2021 à 12:58, Healy, David a écrit :
> 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
>
> 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://scholar.google.com/citations?hl=en&user=ug9DnVoAAAAJ
> Software: http://www.fracturedrockphysics.com/software.html
> Home page: http://www.fracturedrockphysics.com/index.html
>
>
> 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
> > 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%7C637691913460390120%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=yyEVy2RKkJPXcEhNSXHD%2B8wrBEqzhAgg6YcMpjC7%2FIM%3D&reserved=0
> > Home page: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.fracturedrockphysics.com%2Findex.html&data=04%7C01%7Cd.healy%40abdn.ac.uk%7Cb396c90da8ff4a55bdba08d9896aa891%7C8c2b19ad5f9c49d490773ec3cfc52b3f%7C0%7C0%7C637691913460390120%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=9iC3i%2FxXVCI6nSie7EnENNnYKleYA5YNvjAA9tMcnj8%3D&reserved=0
> >
> >
> > 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.
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> >
> > The University of Aberdeen is a charity registered in Scotland, No SC013683.
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>
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