Blaz,

The solution I gave worked for me. Ask you sysadmin or someone who knows about linux systems, it might be a different setting on different flavours of linux... It's not a MSNoise problem, I'll try to come up with a workaround later but for now I'm sure you'll find a solution.


Thomas


On 20/09/2016 17:29, VICIC BLAZ [PHD0900016] wrote:
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-boun...@mailman-as.oma.be <msnoise-boun...@mailman-as.oma.be> on behalf 
of Thomas Lecocq <thomas.lec...@seismology.be>
Sent: Tuesday, September 20, 2016 5:10:46 PM
To: msnoise@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-boun...@mailman-as.oma.be <msnoise-boun...@mailman-as.oma.be> on behalf 
of VICIC BLAZ [PHD0900016] <blaz.vi...@phd.units.it>
Sent: Tuesday, September 20, 2016 3:43:22 PM
To: msnoise@mailman-as.oma.be
Subject: Re: [MSNoise] Station list

Thanks, it works now.


Bla┼ż

________________________________
From: msnoise-boun...@mailman-as.oma.be <msnoise-boun...@mailman-as.oma.be> on behalf 
of Thomas Lecocq <thomas.lec...@seismology.be>
Sent: Tuesday, September 20, 2016 3:01:07 PM
To: msnoise@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:
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:


()
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-boun...@mailman-as.oma.be <msnoise-boun...@mailman-as.oma.be> on behalf 
of Thomas Lecocq <thomas.lec...@seismology.be>
Sent: Tuesday, September 20, 2016 12:56:56 PM
To: msnoise@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
_______________________________________________
MSNoise mailing list
MSNoise@mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise
_______________________________________________
MSNoise mailing list
MSNoise@mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise
_______________________________________________
MSNoise mailing list
MSNoise@mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise
_______________________________________________
MSNoise mailing list
MSNoise@mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise
_______________________________________________
MSNoise mailing list
MSNoise@mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise
_______________________________________________
MSNoise mailing list
MSNoise@mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise
_______________________________________________
MSNoise mailing list
MSNoise@mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise
_______________________________________________
MSNoise mailing list
MSNoise@mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise

_______________________________________________
MSNoise mailing list
MSNoise@mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise

Reply via email to