Project

General

Profile

Actions
Copy link

Bug #4275

open

sinedon querying to leginondb instead of appiondb

Added by Neil Voss over 8 years ago. Updated over 8 years ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Start date:
07/01/2016
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:

Description

  File "/tank/software/myami-3.2/appion/bin/makestack2.py", line 1142, in postLoopFunctions
    apStackMeanPlot.makeStackMeanPlot(stackid)
  File "/tank/software/myami-3.2/appion/appionlib/apStackMeanPlot.py", line 53, in makeStackMeanPlot
    partdatas = sinedon.directq.complexMysqlQuery('appiondata',sqlcmd)
  File "/tank/software/myami-3.2/sinedon/directq.py", line 24, in complexMysqlQuery
    results = cur.selectall(query)
  File "/tank/software/myami-3.2/sinedon/sqldb.py", line 44, in selectall
    self.c.execute(strSQL, param)
  File "/usr/lib/python2.7/dist-packages/MySQLdb/cursors.py", line 174, in execute
    self.errorhandler(self, exc, value)
  File "/usr/lib/python2.7/dist-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler
    raise errorclass, errorvalue
_mysql_exceptions.ProgrammingError: (1146, "Table 'leginondb.ApStackParticleData' doesn't exist")

Note it says <b>'leginondb.ApStackParticleData'</b>

I checked the code and had it print the info:

sqlcmd = "SELECT " + \
 "particleNumber, mean, stdev " + \
 "FROM ApStackParticleData " + \
 "WHERE `REF|ApStackData|stack` = %i"%(stackid)
print sinedon.getConfig('appiondata')
partdatas = sinedon.directq.complexMysqlQuery(newdbname, sqlcmd)

{'passwd': 'xxxx', 'host': '127.0.0.1', 'db': 'ap9', 'user': 'usr_object'}
connecting

any ideas? this is the northwestern install using myami 3.2 under debian 8.

Actions
Copy link
 #1

Updated by Neil Voss over 8 years ago

works using same server with myami 3.1

Actions
Copy link
 #2

Updated by Neil Voss over 8 years ago

  • Description updated (diff)
Actions
Copy link
 #3

Updated by Neil Voss over 8 years ago

  • Description updated (diff)
Actions
Copy link
 #4

Updated by Anchi Cheng over 8 years ago

Mayve the sql connection cursor got set to leginondb during force insert of ApStackParticleData some how that was not in the older version.

Can you try if adding something like this to sinedon directq.py getConnection function will help ?

dbname = param['db']
connections[modulename[.dbConnection.select_db(dbname)
return connections[modulename]
Actions
Copy link
 #5

Updated by Neil Voss over 8 years ago

I was not sure how to implement the commands you have above, but I did this for a test case:

Appion v3.2

module load appion #v3.2
python
import sinedon
import sinedon.directq
from appionlib import apProject
newdbname = apProject.getAppionDBFromProjectId(1)
sinedon.setConfig('appiondata', db=newdbname)
sinedon.getConfig('appiondata')
sqlcmd = "SELECT particleNumber FROM ApStackParticleData LIMIT 10;" 
results = sinedon.directq.complexMysqlQuery('appiondata',sqlcmd)

output:

>>> import sinedon
>>> import sinedon.directq
>>> from appionlib import apProject
>>> newdbname = apProject.getAppionDBFromProjectId(1)
>>> sinedon.setConfig('appiondata', db=newdbname)
{'passwd': 'xxxxx', 'host': '127.0.0.1', 'db': 'ap1', 'user': 'usr_object'}
>>> sinedon.getConfig('appiondata')
{'passwd': 'xxxxx', 'host': '127.0.0.1', 'db': 'ap1', 'user': 'usr_object'}
>>> sqlcmd = "SELECT particleNumber FROM ApStackParticleData LIMIT 10;" 
>>> results = sinedon.directq.complexMysqlQuery('appiondata',sqlcmd)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/tank/software/myami-3.2/sinedon/directq.py", line 24, in complexMysqlQuery
    results = cur.selectall(query)
  File "/tank/software/myami-3.2/sinedon/sqldb.py", line 44, in selectall
    self.c.execute(strSQL, param)
  File "/usr/lib/python2.7/dist-packages/MySQLdb/cursors.py", line 174, in execute
    self.errorhandler(self, exc, value)
  File "/usr/lib/python2.7/dist-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler
    raise errorclass, errorvalue
_mysql_exceptions.ProgrammingError: (1146, "Table 'leginondb.ApStackParticleData' doesn't exist")

Appion 3.1 (also works with beta and trunk)

module load appion-3.1 #v3.1
python
import sinedon
import sinedon.directq
from appionlib import apProject
newdbname = apProject.getAppionDBFromProjectId(1)
sinedon.setConfig('appiondata', db=newdbname)
sinedon.getConfig('appiondata')
sqlcmd = "SELECT particleNumber FROM ApStackParticleData LIMIT 10;" 
results = sinedon.directq.complexMysqlQuery('appiondata',sqlcmd)

output:

Python 2.7.9 (default, Mar  1 2015, 12:57:24) 
[GCC 4.9.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sinedon
>>> import sinedon.directq
>>> from appionlib import apProject
>>> newdbname = apProject.getAppionDBFromProjectId(1)
>>> sinedon.setConfig('appiondata', db=newdbname)
{'passwd': 'xxxx', 'host': '127.0.0.1', 'db': 'ap1', 'user': 'usr_object'}
>>> sinedon.getConfig('appiondata')
{'passwd': 'xxxx', 'host': '127.0.0.1', 'db': 'ap1', 'user': 'usr_object'}
>>> sqlcmd = "SELECT particleNumber FROM ApStackParticleData LIMIT 10;" 
>>> results = sinedon.directq.complexMysqlQuery('appiondata',sqlcmd)
connecting

I am not sure what makes Appion v3.2 so special as to fail, whereas 3.1, beta, and trunk all work.

Actions
Copy link

Also available in: Atom PDF