[MSNoise] populate stations table with script

Sat Apr 30 01:05:12 UTC 2016

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'

Thomas Lecocq wrote:
> 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
>
> Le 26/04/2016 00:04, Phil Cummins a écrit :
>> 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
>>
>>
>
> _______________________________________________
> MSNoise mailing list
> MSNoise at mailman-as.oma.be
> http://mailman-as.oma.be/mailman/listinfo/msnoise