Project

General

Profile

Actions

Bug #1299

open

leginondata versus leginon.leginondata

Added by Anchi Cheng over 13 years ago. Updated about 11 years ago.

Status:
Assigned
Priority:
Normal
Assignee:
Category:
-
Target version:
-
Start date:
05/12/2011
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.1.0
Show in known bugs:
No
Workaround:

Description

From Scott Stagg:

Second I always get the exception below even with the myami-2.1 release. Do I have something wrong with my database?

Traceback (most recent call last): File "/usr/local/myami_dev/appion/bin/tomoaligner.py", line 488, in ? app.close() File "/usr/local/myami_dev/appion/appionlib/appionScript.py", line 325, in close clustdata = self.getClusterJobData() File "/usr/local/myami_dev/appion/appionlib/appionScript.py", line 183, in getClusterJobData clustdatas = clustq.query() File "/usr/local/myami_dev/sinedon/data.py", line 395, in query results = db.query(self, **kwargs) File "/usr/local/myami_dev/sinedon/dbdatakeeper.py", line 85, in query result = self._query(*args, **kwargs) File "/usr/local/myami_dev/sinedon/dbdatakeeper.py", line 108, in query myresult = result.fetchall() File "/usr/local/myami_dev/sinedon/sqldict.py", line 561, in fetchall cursorresult = self._format(subfetch, qikey) File "/usr/local/myami_dev/sinedon/sqldict.py", line 656, in _format newdata.friendly_update(r) File "/usr/local/myami_dev/sinedon/data.py", line 430, in friendly_update super(Data, self).friendly_update(other) File "/usr/local/myami_dev/sinedon/newdict.py", line 88, in friendly_update self[key] = other[key] File "/usr/local/myami_dev/sinedon/data.py", line 504, in setitem super(Data, self)._setitem__(key, value) File "/usr/local/myami_dev/sinedon/newdict.py", line 79, in setitem value = validator(value) File "/usr/local/myami_dev/sinedon/data.py", line 320, in validator raise ValueError('need instance of %s, got %s instead' % (cls, value.dataclass)) ValueError: need instance of <class 'leginon.leginondata.SessionData'>, got <class 'leginondata.SessionData'> instead Exception exceptions.ValueError: <exceptions.ValueError instance at 0x1b1f1758> in <bound method protomoAligner.__del__ of <__main__.protomoAligner object at 0x1b2ae0d0>> ignored


Files

ApAppionJobData.tiff (26.1 KB) ApAppionJobData.tiff Anchi Cheng, 05/12/2011 05:22 PM
Actions #1

Updated by Anchi Cheng over 13 years ago

Scott,

Does this happen to other appion job or just tomoaligner? Which python version do you use?

We did change the way packages are arranged when we migrated to myami, but not all scripts are using the new import syntex. Yours seem to be more sensitive to the inconsistency. Maybe Jim has an explanation.

Actions #2

Updated by Scott Stagg over 13 years ago

This only happens with tomoaligner. I am using python2.4 on this machine.

Actions #3

Updated by Anchi Cheng over 13 years ago

Scott,

Jim and I looked at it for a bit. One possibility is that somehow your system has an

import leginon.leginondata

and some other module has

from leginon import leginondata

somehow sinedon reconize them as different.

We found only apBeamTilt.py in appionlib is doing the second case, and changed it in r15636

However, since we don't have the problem here, we don't know if it helps. Could you check your local development to see if you have some of these?

The other idea is that may be your apAppionJobData field names are not quite right. Here is our screenshot.

Actions #4

Updated by Anchi Cheng over 13 years ago

  • Assignee changed from Jim Pulokas to Scott Stagg
Actions #5

Updated by Scott Stagg over 13 years ago

I'm still having the error after svn updating. I checked my ApAppionJobData table, and it looks the same as yours. I searched for any instances of "from leginon import leginondata" , and I get the following:

[sstagg@athena myami_dev]$ grep -r 'from leginon import leginondata' *appion/bin/contourpickerTubeCircleTextFileGenerator.py:from leginon import leginondataappion/bin/contourpickerTextFileGenerator.py:from leginon import leginondata
appion/bin/contourpicker.py:from leginon import leginondata
appion/bin/.svn/text-base/contourpickerTubeCircleTextFileGenerator.py.svn-base:from leginon import leginondata
appion/bin/.svn/text-base/contourpickerTextFileGenerator.py.svn-base:from leginon import leginondata
appion/bin/.svn/text-base/contourpicker.py.svn-base:from leginon import leginondata
leginon/alignmentmanager.py:from leginon import leginondata
leginon/.svn/text-base/alignmentmanager.py.svn-base:from leginon import leginondata

Is there anything else I should try?

Actions #6

Updated by Jim Pulokas over 13 years ago

Hi Scott,
Is this causing the whole thing to fail, or does it just ignore the exception and everything else seems ok?
Jim

Actions #7

Updated by Jim Pulokas over 13 years ago

  • Assignee changed from Scott Stagg to Jim Pulokas
Actions #8

Updated by Scott Stagg over 13 years ago

It happens at the very end after everything seems to be complete, but the program doesn't exit; it spits out the exception. Perhaps it doesn't finish telling the database that it is finished running?

Actions #9

Updated by Jim Pulokas about 11 years ago

  • Assignee changed from Jim Pulokas to Anchi Cheng

unknown status, two year old issue

Actions

Also available in: Atom PDF