cBioPortal database connection issue

[Muralidharan, Aditya Trilok]

Hi,

 

I am getting the below error message on the landing page of the local instance of cBioPortal. It would be great if you could help in this regard so that I can leverage the functionality provided by cBioPortal.

Oops! An error occurred while trying to connect to the database. This could happen if the database does not contain any cancer studies.

 

 

Looking forward to hear from you. Thank you so much.

 

 

With Regards,

Adi

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[Pieter Lukasse]

Hi Adi,

can you share the steps have you followed to load a test study into your own db? 

Thanks,

Pieter

[Muralidharan, Aditya Trilok]

Hi Pieter,

 

As a follow-up to the previous email – on trying to import the study using metaImport script, I am getting the following message on the console:

 

Cannot create PoolableConnectionFactory (Access denied for user 'cbio_user'@'5CG7021714.roswellpark.org' (using password: YES))

 

I am not sure if it is because I have permission issues that is impeding successful connection! I would be delighted to hear from you.

 

 

Thanks & Regards,

Adi

[Muralidharan, Aditya Trilok]

Hi Pieter,

 

I changed MySQL port no associated with cbioportal to 3307 as I was having some issues with default port 3306. I used MySQL workbench on my Windows machine to import the database schema cgds.sql. The import was successful and I am able to see the tables on the workbench.

 

I used a username of cbio_user and set my password. MySQL server is up and running as well. But I am getting the mentioned error message in the landing page. Similarly, when I try to import studies using metaImport.py, I am getting CommunicationException: Communications Link failure thereby the import of study is failing.

 

I believe these two issues are related. I can also attach you a copy of portal.properties if that might help.

 

With Regards,

Adi

 

From: Pieter Lukasse [mailto:pie...@thehyve.nl]
Sent: Thursday, August 10, 2017 12:47 PM
To: cBioPortal for Cancer Genomics Discussion Group
Cc: Muralidharan, Aditya Trilok
Subject: Re: cBioPortal database connection issue

 

Hi Adi,

[Pieter Lukasse]

Hi Adi,

when changing mysql connection details, you will have to do this in 2 places:

- portal.properties

- context.xml: see https://github.com/cBioPortal/cbioportal/blob/master/docs/Deploying.md#set-up-the-database-connection-pool

Have you done this last one?

Thanks,

Pieter