Referenced data can not be found
Added by Anonymous over 19 years ago
Dear Denis, Jim and Christian,
thanks again for a very good week in your lab. After the "Biophysical", and one week of teaching I have started here now.
I put my hands on a Tecnai G2 Spirit (newest tecnai FEI got) installed everything, connected the two computers, and on day 3 (today) I am finally stuck: (There were many problems with the connection (I have to use a PPP connection ...), and I had to re-hardwire all the IP addresses .... and there maybe something went wrong. But where ?
Problem 1: Leginon client on the EM computer: It comes up with the two windows, however, it only has the menu items:
File -> Exit
Settings -> Logging
Application is missing .... why, what else needs to be installed, OR is there a link to Problem 2:
Problem 2: On the labtop everything was fine at first (start-leginon.py, windows came up, Apache server, ...., even after changing all the IP addresses). Then I tried to make an entry for the new microscope in the database admin tool. During that process I somehow doubled the Tecnai data set, and deleted one copy again (it was the original one .... sorry). At the same time it happens that now I have a new database (mysql) with 6 new tables which have not been there before .... (Before there was only dbemdata and test (without anything).
And, last but not least, now after start-leginon.py I get an error message - instead of the Leginon window:
Unable to start Leginon: Referenced data can not be found: DataReference(1111479404), class:<class 'data.InstrumentData">, dmid:None, dbid:3
HOW TO RECOVER ?? It looks to me, as if I have deleted some information or I have linked leginon to the wrong database ?? Yes, No ???? Should I simply delete the new database ? If yes, how ? What have I done wrong to make this new database appear / to delete the correct link / information ?
Thanks for your help !!!!!
All the best
Rasmus
Replies (1)
Re: Leginon problem in Frankfurt mail_1 - Added by Jim Pulokas over 19 years ago
Rasmus R. Schroeder wrote:
Problem 1: Leginon client on the EM computer: It comes up with the two windows, however, it only has the menu items:
File -> Exit
Settings -> Logging
Application is missing .... why, what else needs to be installed, OR is there a link to Problem 2:
The reason for not having an application menu is because the Leginon Client can not start an application. It is only there as a slave to the main Leginon program running somewhere else, which starts the application. If you want to start an application directly on the tecnai computer without involving another computer, just start the main leginon program on the tecnai instead of the leginon client.
Problem 2: On the labtop everything was fine at first (start-leginon.py, windows came up, Apache server, ...., even after changing all the IP addresses). Then I tried to make an entry for the new microscope in the database admin tool. During that process I somehow doubled the Tecnai data set, and deleted one copy again (it was the original one .... sorry). At the same time it happens that now I have a new database (mysql) with 6 new tables which have not been there before .... (Before there was only dbemdata and test (without anything).
And, last but not least, now after start-leginon.py I get an error message - instead of the Leginon window:
Unable to start Leginon: Referenced data can not be found: DataReference(1111479404), class:<class 'data.InstrumentData">, dmid:None, dbid:3
HOW TO RECOVER ?? It looks to me, as if I have deleted some information or I have linked leginon to the wrong database ?? Yes, No ???? Should I simply delete the new database ? If yes, how ? What have I done wrong to make this new database appear / to delete the correct link / information ?
It does sound like something has been deleted from the database (probably some instrument data), and something that is still in there (probably some SessionData) is still referencing that deleted instrument. You could try to clean it up manually by finding sessions with invalid references to instruments that don't exist, and delete them. But it is a core philosophy of Leginon that nothing ever gets deleted from the database (to prevent broken references, to prevent deleting something importand by accident, and because the database takes up so little space anyway). The easier solution might be to just create a new database. Then edit your leginon.cfg on both the laptop and the tecnai to reference this new database. Then you are starting over from scratch (create users, groups, instruments). You can delete the old database if you want to, but it is not necessary since leginon.cfg will only refer to the new one.
Let us know if this helps you get going
Jim