[MSNoise] populate stations table with script
Phil Cummins
phil.cummins at anu.edu.au
Sat Apr 30 10:56:54 UTC 2016
Hi Thomas,
Yeah, that worked! Looks like I'm in business. I would like to know how
t do the instrument field also, but for the moment I will be dealing
with stations that all have the same response.
Many thanks!
- Phil
> Thomas Lecocq <mailto:Thomas.Lecocq at seismology.be>
> 30 April 2016 7:59 pm
> Hi,
>
>
> not sure without testing, but try passing float(st_inv[0].latitude)
> instead of the Latitude object...
>
>
> Thomas
>
>
>
>
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> Phil Cummins <mailto:phil.cummins at anu.edu.au>
> 30 April 2016 11:05 am
> Hi Thomas,
>
> Thanks for your reply. I am getting my station info from a seiscomp3
> fdsnws server, so the script I wrote to do this looks like:
>
> from msnoise.api import connect,get_stations,update_station
> from obspy.clients.fdsn.client import Client
>
> client = Client('http://compute2.rses.anu.edu.au:8080')
> stns_inv = client.get_stations(network='XU',station='JK*')[0]
> msn=connect()
> stns = get_stations(msn)
> for st in stns:
> st_inv = stns_inv.select(station=st.sta)
> if len(st_inv) == 0:
> print 'WARNING! Station %s not found in fdsnws' % st.sta
> continue
> print 'updating %s:lon=%g, lat=%g' %
> (st.sta,st_inv[0].longitude,st_inv[0].latitude)
>
> update_station(msn,'XU',st.sta,st_inv[0].longitude,st_inv[0].latitude,
> st_inv[0].elevation,coordinates='DEG')
> msn.commit()
>
> It produces the following output/error message, ending in
> "AttributeError: 'Latitude' object has no attribute 'translate' ". Any
> suggestions?
>
> - Phil
>
> updating JKA01:lon=106.872, lat=-6.1208
> Traceback (most recent call last):
>
> File "<ipython-input-93-fca1e24e504a>", line 1, in <module>
>
> runfile('/home/seis/pcummins/Indonesia/Jakarta/msnoise/update_stns.py', wdir='/home/seis/pcummins/Indonesia/Jakarta/msnoise')
>
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/spyderlib/widgets/externalshell/sitecustomize.py",
> line 699, in runfile
> execfile(filename, namespace)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/spyderlib/widgets/externalshell/sitecustomize.py",
> line 81, in execfile
> builtins.execfile(filename, *where)
>
> File "/home/seis/pcummins/Indonesia/Jakarta/msnoise/update_stns.py",
> line 22, in <module>
> st_inv[0].elevation,coordinates='DEG')
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/msnoise/api.py",
> line 380, in update_station
> session.commit()
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/session.py",
> line 801, in commit
> self.transaction.commit()
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/session.py",
> line 392, in commit
> self._prepare_impl()
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/session.py",
> line 372, in _prepare_impl
> self.session.flush()
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/session.py",
> line 2019, in flush
> self._flush(objects)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/session.py",
> line 2137, in _flush
> transaction.rollback(_capture_exception=True)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py",
> line 60, in __exit__
> compat.reraise(exc_type, exc_value, exc_tb)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/session.py",
> line 2101, in _flush
> flush_context.execute()
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py",
> line 373, in execute
> rec.execute(self)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py",
> line 532, in execute
> uow
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py",
> line 170, in save_obj
> mapper, table, update)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py",
> line 706, in _emit_update_statements
> execute(statement, multiparams)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
> line 914, in execute
> return meth(self, multiparams, params)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/sql/elements.py",
> line 323, in _execute_on_connection
> return connection._execute_clauseelement(self, multiparams, params)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
> line 1010, in _execute_clauseelement
> compiled_sql, distilled_params
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
> line 1146, in _execute_context
> context)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
> line 1344, in _handle_dbapi_exception
> util.reraise(*exc_info)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
> line 1139, in _execute_context
> context)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/sqlalchemy/engine/default.py",
> line 450, in do_execute
> cursor.execute(statement, parameters)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/pymysql/cursors.py",
> line 156, in execute
> query = self.mogrify(query, args)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/pymysql/cursors.py",
> line 135, in mogrify
> query = query % self._escape_args(args, conn)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/pymysql/cursors.py",
> line 115, in _escape_args
> return dict((key, conn.escape(val)) for (key, val) in args.items())
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/pymysql/cursors.py",
> line 115, in <genexpr>
> return dict((key, conn.escape(val)) for (key, val) in args.items())
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/pymysql/connections.py",
> line 781, in escape
> return escape_item(obj, self.charset, mapping=mapping)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/pymysql/converters.py",
> line 26, in escape_item
> val = encoder(val, mapping)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/pymysql/converters.py",
> line 109, in escape_unicode
> return u"'%s'" % _escape_unicode(value)
>
> File
> "/usr/local/anaconda2/lib/python2.7/site-packages/pymysql/converters.py",
> line 72, in _escape_unicode
> return value.translate(_escape_table)
>
> AttributeError: 'Latitude' object has no attribute 'translate'
>
>
>
>
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> MSNoise mailing list
> MSNoise at mailman-as.oma.be
> http://mailman-as.oma.be/mailman/listinfo/msnoise
> Thomas Lecocq <mailto:thomas.lecocq at oma.be>
> 26 April 2016 5:28 pm
> Hi Phil !
>
> Indeed, the populate step actually only lists the stations from the
> archive. No files are read at this point.
>
> Aurélien has written some updated populate code to read the metadata
> information from dataless or inventoryXML , but we still have to make
> it clean in order to make it available.
>
> Meanwhile:
>
> 1/ you can populate "normally"
> 2/ select - deselect the stations you want in the Station table (if
> you are using 1.4: in the Admin).
> 3/ write a small python script to interact with the API: use
> "connect", "get_stations" and "update_station" to update the existing
> fields.
>
> Let me know how it goes,
>
> Thomas
>
>
>
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> MSNoise mailing list
> MSNoise at mailman-as.oma.be
> http://mailman-as.oma.be/mailman/listinfo/msnoise
> Phil Cummins <mailto:phil.cummins at anu.edu.au>
> 26 April 2016 8:04 am
> Hi,
>
> I'm new to msnoise, and was unable to find a searchable archive for
> this list(?), apologies if the question has been asked before.
>
> I want to populate my station table, and msnoise has scanned my sds
> database and identified all the stations. However, it has only filled
> out the name fields, and I need at a minimum the locations, and would
> like to do the instruments as well.
>
> So I would like to find a way to populate the stations table using a
> python script. Presumably one would use pymysql? I have never used
> pymysql, and was wondering if maybe someone had such a script. If you
> do, could you please send it to me?
>
> (actually, I want to do it this way in any case, since in future my
> sds database will have more stations than I want to use with msnoise).
>
> Thanks,
>
> - Phil
>
>
--
Phil Cummins
Prof. Natural Hazards
Research School of Earth Sciences
Australian National University
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