You were right... i found the solution:

If someone else will have this problem.

On Ubuntu 16.04 u need to add this at the end of my.cnf file:


[mysqld]
sql_mode="TRADITIONAL,NO_AUTO_CREATE_USER"



________________________________
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 8:08:11 PM
To: msnoise@mailman-as.oma.be
Subject: Re: [MSNoise] Station list

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

Reply via email to