Problem: When I run a gene expression query, I get a Java stack trace error regardless of whether the query or study is new or previously saved or deployed.

*Topic*: caIntegrator Usage

*Release*: caIntegrator 1.2 and above

*Date entered*: 03/30/2012

Solution

This error occurs in Linux when caIntegrator can not access study data, which by default is stored in the system temporary directory (/tmp). This could occur due to insufficient user privileges to read from the tmp directory, insufficient disk space to write to the tmp directory, or if the contents of the directory have been flushed during an application restartEvery time the application is restarted, the contents of this /tmp directory are flushed, so when the user attempts to run a query after the restart, the query will not be able to access the study data it needs, regardless of whether the query is new or if it was saved before the restart.

An example of the Java stack trace error is attached below as a plain text file:

JavaStackTrace.txt

The exact error message you get may vary slightly from the contents of the attached text file. Note that this error is not recorded in the server log; it is only displayed in the caIntegrator browser window after the query attempt fails.

The best solution to this problem is to change the study data storage location from the default /tmp directory to a permanent location on a drive where the user has administrative privileges and there is sufficient disk space. For instructions on how to change the study storage location, please refer to the KB article at https://wiki.nci.nih.gov/x/oZKNAg^{Image Removed}.

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