mvn -DskipTests clean install error

[J Luo]

Hi Benjamin,

 

We need your help again.  I am in the process of trying again regarding the integration of cBioportal with Keycloak.  When we tried to run

 

mvn -DskipTests clean install

 

We have encountered the following error.

 

#############################################################

 

[INFO] Portal Web Layer ................................... FAILURE [  2.011 s]

[INFO] Portal Core ........................................ SKIPPED

[INFO] cBioPortal ......................................... SKIPPED

[INFO] Portal Scripts ..................................... SKIPPED

[INFO] ------------------------------------------------------------------------

[INFO] BUILD FAILURE

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 23.506 s

[INFO] Finished at: 2021-03-30T13:52:00+01:00

[INFO] Final Memory: 54M/224M

[INFO] ------------------------------------------------------------------------

[ERROR] Failed to execute goal on project web: Could not resolve dependencies for project org.mskcc.cbio:web:jar:3.4.21-4-g6f00070-dirty-SNAPSHOT: Could not transfer artifact org.mongodb:mongodb-driver-core:jar:4.0.5 from/to plugins-release (https://repo.spring.io/plugins-release): Not authorized , ReasonPhrase:Unauthorized. -> [Help 1]

org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal on project web: Could not resolve dependencies for project org.mskcc.cbio:web:jar:3.4.21-4-g6f00070-dirty-SNAPSHOT: Could not transfer artifact org.mongodb:mongodb-driver-core:jar:4.0.5 from/to plugins-release (https://repo.spring.io/plugins-release): Not authorized , ReasonPhrase:Unauthorized.

 

 

Their build process makes use of repo.spring.io to download plugins including the MongoDB driver, but Spring put a stop to using it this way back in January.

 

https://spring.io/blog/2020/10/29/notice-of-permissions-changes-to-repo-spring-io-fall-and-winter-2020

 

Just wondering if there is an alternative location for the plugins repository for the pom.xml.  Liam has checked the current one from the cbioportal GitHub repository and it still uses the same Spring repo that is now disallowed.

 

In /local/cbioportal/pom.xml we have seen that the 'Spring Plugins' repository is linked to https://repo.spring.io/plugins-release and it's this link that is now blocked.

 

Your help is very much appreciated.

 

Best Regards,

 

Jinli  and Liam Gretton
Systems Specialist

*************************************************************

Dr. Jinli Luo

Bioinformatics Analysis Support Hub (BASH)

College of Life Sciences

Room 210, Adrian Building

University Road

University of Leicester

Leicester, LE1 7RH, UK

 

t: +44 (0)116 252 3350

m: 07765005321
e:  jl...@le.ac.uk

w: https://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/bbash

[Karthik Kalletla]

Hi Jinli,

What version of portal are you using? I don't see any errors while building latest version or master code.

Could you try migrating to latest version if you are using an older one.

Thanks

Karthik

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[J Luo]

Hi karthik,

Sorry for the late reply.

The version number we used is : 3.4.21-4-g6f00070

Could you let me know what the latest version is?

Many thanks,

Jinli

[Ino de Bruijn]

Hi Jinli,

The latest version is v3.6.10:

https://github.com/cBioPortal/cbioportal/releases/tag/v3.6.10

Could you try that one and see if it solves your issue?

Thanks,

Ino

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[J Luo]

Many thank Ino.

I will try this and let you know the outcome.

Best Regards,

Jinli

[J Luo]

Hi Ino,

I have downloaded the new version v3.6.10.

Does it mean I need to install cBioportal from scratch.  I have looked the migration procedure  https://docs.cbioportal.org/3.-cbioportal-maintenance/updating-your-cbioportal-installation,  but this is for migration the database, is it correct?

Please advice,

Many thanks

Jinli

On Wednesday, April 7, 2021 at 6:55:18 PM UTC+1 Ino de Bruijn wrote:

[Ino de Bruijn]

Hi Jinli,

Looks like that documentation is slightly outdated. If you are using the docker compose setup, all you have to do is change the version on the image:

https://github.com/cBioPortal/cbioportal-docker-compose/blob/master/.env#L1

Migration should happen automatically in that case.

If you are not using docker then yes, following those steps would be necessary since you need to update the database as well in this case. You are migrating from 3.4.x to 3.6.y. Any time a migration is necessary, the middle number in the version gets bumped.

Hope that helps!

Best wishes,

Ino

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/fe1949ae-746b-40d7-82b9-7c5827b26641n%40googlegroups.com.

[J Luo]

Hi Ino,

Thank you very much for you reply.

We are not using docker.

If I understand correctly I need to update the cbioportal as well as the database.  What is the latest seed-database?  The one I used before is seed-cbioportal_hg19_v2.7.3.sql .  Is this still the correct one to use?

If I install from scratch, using the following command, it will pull the latest version of cbioportal, am I correct?

git clone https://github.com/cBioPortal/cbioportal.git

Best Regards,

Jinli

[J Luo]

Hi

I have followed the instruction to install the new cbioportal database from scratch.

But this time I have encountered a problem with importing the seed database see-cbioportal_hg19-v2.7.3.sql.

$ mysql --user=cbio_user --password=PASSWORD cbioportal < seed-cbioportal_hg19_v2.7.3.sql
ERROR 1054 (42S22) at line 275: Unknown column 'CYTOBAND' in 'field list'

We are installing cbioportal without docker.

I saw similar post related my problem as well.

https://groups.google.com/g/cbioportal/c/BU-aW8zNBwk/m/PDM8J0owBwAJ

I would be grateful if anyone could give me some advice.

Best Regards,

Jinli