wiki:FAQ

FAQ

Exceptions and Errors

Jobs ending with an out of memory error

If jobs are ending with an out of memory error, the probable reason is that the Proteios SE server has not been configured to use more than the default memory allocated. The server administrator should then change the Tomcat memory settings, see: server administration

Error when importing search results

After upgrading to 2.13 there may be problems with searchdatabases due to a datatype change. In most versions of mysql the table is updated automatically when running the proteios update. If not:

Login to mysql and connect to the proteios database. Then issue the following command:
ALTER TABLE searchdatabases MODIFY number_of_residues LONG NULL

Error after login after upgrade to 2.8

After upgrading to 2.8 or later from 2.7 or earier, there may be a stack trace after log in when trying to list projects. With most versions of mysql this shouldn't happen, but if it does, the server administrator will have to use mysql command line client and connect to the Proteios database. Then perform the following commands:
UPDATE Projects SET closed=false;
UPDATE Projects SET project_type=0;
COMMIT;
Now the problem should be resolved. The reference for this update is ticket #587. The problem has been reported for: mysql 5.0.45 SUSE MySQL RPM

Error message instead of login screen

(Only concerning 2.0 or earlier)

After installation of Proteios 2.0 there is an error message: java.lang.NullPointerException

at org.proteios.action.Loader.addActions(Loader.java:81)...

The reason for this error is that the file path of the Apache Tomcat server contains space characters, which leads to problems when loading some files. It has been solved in the 2.1 version of Proteios. In the meantime there is a quick solution (Windows description):

  1. Move the proteios directory from webapps to c:\proteios2.
  2. Edit the tomcat/config/server.xml file so that appBase="c:/proteios2".
  3. Restart Tomcat

Not possible to add sample

(Resolved in 2.0 and later)

If an error message occurs when you try to add a sample, saying that it is not possible to insert the sample data into the database, it could be related to some old database constraints. This only applies to installations where the database has not been reinstalled after build 1978 (beta1 and before). The problem is related to some old not-null constrains that are not updated properly by Hibernate on database upgrade. In the (long) error message there is a complaint about the field normalized_volume being null. The simple solution is to upgrade to the newest version of Proteios, run the installation script and drop the database. But if you need to keep the database, the following will also do:

Login to mysql and connect to the proteios database. Then issue the following commands:
ALTER TABLE biomaterials MODIFY normalized_volume FLOAT NULL;
ALTER TABLE biomaterials MODIFY pixel_x_coord INT NULL;
ALTER TABLE biomaterials MODIFY pixel_y_coord INT NULL;
ALTER TABLE biomaterials MODIFY volume FLOAT NULL;
ALTER TABLE biomaterials MODIFY apparent_mass FLOAT NULL;
ALTER TABLE biomaterials MODIFY apparent_pi FLOAT NULL;
ALTER TABLE separationmethods MODIFY massStart INT NULL;
ALTER TABLE separationmethods MODIFY massEnd INT NULL;
ALTER TABLE separationmethods MODIFY percentAcrylamide INT NULL;
commit;

Last modified 7 years ago Last modified on Jun 11, 2010, 1:39:41 PM