cbioportal Permission issue on Tomcat logs

[Bob Lanese]

I know this is more of a Unix Issue than cbioportal but advice would be helpful. The cbioportal commands (validate, import, ...) and data resides in a user directory I created. Whenever I import data into cbioportal via the ./metaimport.py command I always get the "java.io.FileNotFoundException: /usr/local/tomcat7/logs/public-portal.log (Permission denied)". Now, the import works fine, it just doesn't write to the the log file. Tomcat is owned by root in my case, but I changed the logs directory to be the same group (and writable) as my user that runs the cbioportal scripts. I believe when Tomcat creates a new logfile, its user and group are set to root. I am no a Unix permission expert I am afraid. What I am I doing wrong?

The setting for the directory is seen below where my group is called "cbioportal":
drwxrwxr-x 2 root cbioportal 8192 Dec 1 11:03 logs/

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Bob Lanese

Data Architect; Institute for Computational Biology and Case Comprehensive Cancer Center
6-102A Wolstein Research Building  / 2103 Cornell Rd. / Cleveland, OH USA 44106

P:  216.368.0252 / M: 216.346.4029

bob.l...@case.edu

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[cBioPortal for Cancer Genomics Discussion Group]

Hi Bob,

What are all the permissions of the folders upstream to that logs/ folder. That is:

/usr/

/local/

tomcat7/

logs/

And the file itself

public-portal.log 

The reason why I'm asking is that the user should be able to traverse the entire directory path, otherwise you will still get a permission denied error if one of those folders is not accessible by the user. 

Best wishes,

Ino

[Pieter Lukasse]

Have you tried changing your log4j  configuration to point to a folder where you have access rights? Maybe that helps ? 

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