[MSNoise] populate stations table with script

Sat Apr 30 09:59:06 UTC 2016

Hi,

not sure without testing, but try passing float(st_inv[0].latitude) 
instead of the Latitude object...

Thomas

On 30/04/2016 03:05, Phil Cummins wrote:
> 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
>>>
>>>
>>
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