20 Sep
2016
20 Sep
'16
6:29 p.m.
The problem was actually in PyTables... I reinstalled it with apt-get and it did not
work...then i checked with anaconda. it was not installed there, so i installed it, and
now it works.
Next problem is, as i saw the same, as Emily had last month... was it resolved?
i try to stack and i get:
Lets STACK !
2016-09-20 18:21:23 [DEBUG] Starting the ref stack
[]
2016-09-20 18:21:24 [DEBUG] Processing SL_CEY:SL_JAVS-ZZ-2
Traceback (most recent call last):
File "/home/blaz/miniconda2/bin/msnoise", line 11, in <module>
sys.exit(run())
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/msnoise/scripts/msnoise.py",
line 614, in run
cli(obj={})
File "/home/blaz/miniconda2/lib/python2.7/site-packages/click/core.py", line
716, in __call__
return self.main(*args, **kwargs)
File "/home/blaz/miniconda2/lib/python2.7/site-packages/click/core.py", line
696, in main
rv = self.invoke(ctx)
File "/home/blaz/miniconda2/lib/python2.7/site-packages/click/core.py", line
1060, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/blaz/miniconda2/lib/python2.7/site-packages/click/core.py", line
889, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/blaz/miniconda2/lib/python2.7/site-packages/click/core.py", line
534, in invoke
return callback(*args, **kwargs)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/msnoise/scripts/msnoise.py",
line 301, in stack
main('ref', interval)
File "/home/blaz/miniconda2/lib/python2.7/site-packages/msnoise/s04stack.py",
line 203, in main
updated_days = updated_days_for_dates(db, start, end, pair.replace('_',
'.'), jobtype='CC',
interval=datetime.timedelta(days=interval),returndays=True)
File "/home/blaz/miniconda2/lib/python2.7/site-packages/msnoise/api.py", line
1189, in updated_days_for_dates
days = session.query(Job).filter(Job.pair == pair).filter(Job.day >=
date1).filter(Job.day <= date2).filter(Job.jobtype == jobtype).filter(Job.lastmod >=
lastmod).group_by(Job.day).order_by(Job.day).all()
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/sqlalchemy/orm/query.py",
line 2613, in all
return list(self)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/sqlalchemy/orm/query.py",
line 2761, in __iter__
return self._execute_and_instances(context)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/sqlalchemy/orm/query.py",
line 2776, in _execute_and_instances
result = conn.execute(querycontext.statement, self._params)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 914, in execute
return meth(self, multiparams, params)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/sqlalchemy/sql/elements.py",
line 323, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1010, in _execute_clauseelement
compiled_sql, distilled_params
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1146, in _execute_context
context)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1341, in _handle_dbapi_exception
exc_info
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/sqlalchemy/util/compat.py",
line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1139, in _execute_context
context)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/sqlalchemy/engine/default.py",
line 450, in do_execute
cursor.execute(statement, parameters)
File "/home/blaz/miniconda2/lib/python2.7/site-packages/pymysql/cursors.py",
line 166, in execute
result = self._query(query)
File "/home/blaz/miniconda2/lib/python2.7/site-packages/pymysql/cursors.py",
line 322, in _query
conn.query(q)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/pymysql/connections.py", line
835, in query
self._affected_rows = self._read_query_result(unbuffered=unbuffered)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/pymysql/connections.py", line
1019, in _read_query_result
result.read()
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/pymysql/connections.py", line
1302, in read
first_packet = self.connection._read_packet()
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/pymysql/connections.py", line
981, in _read_packet
packet.check_error()
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/pymysql/connections.py", line
393, in check_error
err.raise_mysql_exception(self._data)
File "/home/blaz/miniconda2/lib/python2.7/site-packages/pymysql/err.py", line
107, in raise_mysql_exception
raise errorclass(errno, errval)
sqlalchemy.exc.InternalError: (pymysql.err.InternalError) (1055, u"Expression #1 of
SELECT list is not in GROUP BY clause and contains nonaggregated column
'msnoise.jobs.ref' which is not functionally dependent on columns in GROUP BY
clause; this is incompatible with sql_mode=only_full_group_by") [SQL: u'SELECT
jobs.ref AS jobs_ref, jobs.day AS jobs_day, jobs.pair AS jobs_pair, jobs.jobtype AS
jobs_jobtype, jobs.flag AS jobs_flag, jobs.lastmod AS jobs_lastmod \nFROM jobs \nWHERE
jobs.pair = %(pair_1)s AND jobs.day >= %(day_1)s AND jobs.day <= %(day_2)s AND
jobs.jobtype = %(jobtype_1)s AND jobs.lastmod >= %(lastmod_1)s GROUP BY jobs.day ORDER
BY jobs.day'] [parameters: {u'day_2': datetime.date(2016, 9, 20),
u'lastmod_1': datetime.datetime(2016, 9, 19, 18, 21, 24, 191369),
u'day_1': datetime.date(1970, 1, 1), u'jobtype_1': 'CC',
u'pair_1': 'SL.CEY:SL.JAVS'}]
So, as you mentioned, i added sql_mode=TRADITIONAL line in my.cnf, and the same as for
Emily,
sudo service mysql restart did not work. i added [mysql] in front of the line that i
added, and now restart works, but I get the same error as before when calling
msnoise stack -r -m
any idea? or should i install older version of mysql?
thanks
________________________________
From: msnoise-bounces(a)mailman-as.oma.be <msnoise-bounces(a)mailman-as.oma.be> on
behalf of Thomas Lecocq <Thomas.Lecocq(a)seismology.be>
Sent: Tuesday, September 20, 2016 5:10:46 PM
To: msnoise(a)mailman-as.oma.be
Subject: Re: [MSNoise] Station list
Hi,
you probably checked "keep all" parameter. it's really not properly
tested. just avoid it for the moment.
Thomas
On 20/09/2016 15:50, VICIC BLAZ [PHD0900016] wrote:
Sorry, but there is another problem...
i ran:
msnoise -t 2 scan_archive --init
msnoise new_jobs
without problems.
then i tried with
msnoise -t 4 compute_cc
it starts to work, but after some time it produces this error:
...
2016-09-20 16:42:18 [DEBUG] Azimuth=258.9
Process Process-1:
Traceback (most recent call last):
File "/home/blaz/miniconda2/lib/python2.7/multiprocessing/process.py", line
258, in _bootstrap
self.run()
File "/home/blaz/miniconda2/lib/python2.7/multiprocessing/process.py", line
114, in run
self._target(*self._args, **self._kwargs)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/msnoise/s03compute_cc.py",
line 683, in main
export_allcorr(db, ccfid, allcorr[ccfid])
File "/home/blaz/miniconda2/lib/python2.7/site-packages/msnoise/api.py",
line 825, in export_allcorr
df.to_hdf(os.path.join(path, date+'.h5'), 'data')
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/pandas/core/generic.py", line
1101, in to_hdf
return pytables.to_hdf(path_or_buf, key, self, **kwargs)
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/pandas/io/pytables.py", line
259, in to_hdf
complib=complib) as store:
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/pandas/io/pytables.py", line
389, in __init__
'importing'.format(ex=str(ex)))
ImportError: HDFStore requires PyTables, "No module named tables" problem
importing
I tried reinstalling PyTables without luck.
Thanks!
________________________________
From: msnoise-bounces(a)mailman-as.oma.be <msnoise-bounces(a)mailman-as.oma.be> on
behalf of VICIC BLAZ [PHD0900016] <BLAZ.VICIC(a)phd.units.it>
Sent: Tuesday, September 20, 2016 3:43:22 PM
To: msnoise(a)mailman-as.oma.be
Subject: Re: [MSNoise] Station list
Thanks, it works now.
Blaž
________________________________
From: msnoise-bounces(a)mailman-as.oma.be <msnoise-bounces(a)mailman-as.oma.be> on
behalf of Thomas Lecocq <Thomas.Lecocq(a)seismology.be>
Sent: Tuesday, September 20, 2016 3:01:07 PM
To: msnoise(a)mailman-as.oma.be
Subject: Re: [MSNoise] Station list
Hi,
You have to import data_structure too :
from msnoise.data_structures import data_structure
otherwise it'll fail (your custom.py file is not valid, fails at import).
Thomas
On 20/09/2016 12:59, VICIC BLAZ [PHD0900016] wrote:
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Thank you.
Which brings me to the 2nd question...
I tried to populate with this command, but of course it is not working...
What I tried:
in the folder
msnoise/data I have put a miniseed file of one station of one day.
Name of the miniseed is in the format:
STA.NET.CHAN.YEAR.DAY
as data_folder in settings I have set this folder.
in the data_structures.py I added this line:
data_structure['SEI'] = "STA.NET.CHAN.YEAR.DAY"
i created a custom.py script:
from obspy import read
data_structure['SEI'] = "STA.NET.CHAN.YEAR.DAY"
def populate():
st = read("*")
st.merge()
stations = []
for tr in st:
sta = str(tr.stats.station)
net = str(tr.stats.network)
stations.append(str("%s_%s") % (net, sta))
return stations
So,now i have main folder with sub folder data, where I have miniseed file. in the main
folder I put custom.py and db.ini and, if I understand right, run msnoise populate from
here. In the browser I set data_folder to where my miniseed is and data_structure as SEI.
When i run the populate command, i get error:
()
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http://mailman-as.oma.be/mailman/listinfo/msnoise > Populating the Station table
()
Can't parse the archive for format SEI !
trying to import local parser (should return a station list)
()
No file named custom.py in the /home/blaz/Documents/msnoise folder
(custom.py IS in /home/blaz/Documents/msnoise)
I hope I was clear enough.
Thanks!
________________________________
From: msnoise-bounces(a)mailman-as.oma.be <msnoise-bounces(a)mailman-as.oma.be> on
behalf of Thomas Lecocq <Thomas.Lecocq(a)seismology.be>
Sent: Tuesday, September 20, 2016 12:56:56 PM
To: msnoise(a)mailman-as.oma.be
Subject: Re: [MSNoise] Station list
Hi,
Yes, this bug was recently reported by another user and I haven't had
time to fix it.
The best way to add the station currently is to use the "msnoise
populate" command.
Cheers,
Thomas
On 20/09/2016 11:51, VICIC BLAZ [PHD0900016] wrote:
Dear all
I would like to try to use msnoise. I installed it on Ubuntu 16.04, and as far as I know,
everything was installed as planed.
Now, I open msnoise admin and try to manually add stations in the browser. I set NET,
STA, X, Y, ALT, COORD and click save. When I do that, I get a lot of errors:
*
File "/home/blaz/miniconda2/lib/python2.7/site-packages/flask/app.py", line
2000, in __call__
return self.wsgi_app(environ, start_response)
*
File "/home/blaz/miniconda2/lib/python2.7/site-packages/flask/app.py", line
1991, in wsgi_app
response = self.make_response(self.handle_exception(e))
*
File "/home/blaz/miniconda2/lib/python2.7/site-packages/flask/app.py", line
1567, in handle_exception
reraise(exc_type, exc_value, tb)
*
File "/home/blaz/miniconda2/lib/python2.7/site-packages/flask/app.py", line
1988, in wsgi_app
response = self.full_dispatch_request()
*
File "/home/blaz/miniconda2/lib/python2.7/site-packages/flask/app.py", line
1641, in full_dispatch_request
rv = self.handle_user_exception(e)
*
File "/home/blaz/miniconda2/lib/python2.7/site-packages/flask/app.py", line
1544, in handle_user_exception
reraise(exc_type, exc_value, tb)
*
File "/home/blaz/miniconda2/lib/python2.7/site-packages/flask/app.py", line
1639, in full_dispatch_request
rv = self.dispatch_request()
*
File "/home/blaz/miniconda2/lib/python2.7/site-packages/flask/app.py", line
1625, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
*
File "/home/blaz/miniconda2/lib/python2.7/site-packages/flask_admin/base.py",
line 69, in inner
return self._run_view(f, *args, **kwargs)
*
File "/home/blaz/miniconda2/lib/python2.7/site-packages/flask_admin/base.py",
line 368, in _run_view
return fn(self, *args, **kwargs)
*
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/flask_admin/model/base.py",
line 1920, in create_view
model = self.create_model(form)
*
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/flask_admin/contrib/sqla/view.py",
line 1028, in create_model
if not self.handle_view_exception(ex):
*
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/flask_admin/contrib/sqla/view.py",
line 1011, in handle_view_exception
return super(ModelView, self).handle_view_exception(exc)
*
File
"/home/blaz/miniconda2/lib/python2.7/site-packages/flask_admin/contrib/sqla/view.py",
line 1022, in create_model
model = self.model()
TypeError: __init__() takes exactly 9 arguments (1 given)
What am I doing wrong?
Thanks,
Blaz
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