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. > > > Blaž > > ________________________________ > 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