how to import study into dockerized cbioportal with keycloak

[aghil hooshmand]

hi ,

Dose anyone have experience with importing new study to local deodorized cbioportal+dockerized keycloak as authentication system.

I think keycloack dont let me to access portal and importing new study. when I want to import new study I got this error :

LookupError: No portal information found at http://cbioportal:8080

[John Reber]

Hi Aghil

 

To import a study into cbioportal that has authentication, you need to dump the portal info via:

 

export PORTAL_HOME=<cbioportal_configuration_folder> ./dumpPortalInfo.pl /SOMEDIRECTORY/my_portal_info_folder/

 

then when importing add the “-p” switch during the import process:

 

                -p /SOMEDIRECTORY/my_portal_info_folder/

 

John

------

John Reber
Systems Development Manager

Philadelphia, PA 19107
John....@jefferson.edu
KimmelCancerCenter.org

 

 

From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of aghil hooshmand <aghil.h...@gmail.com>
Date: Tuesday, October 17, 2023 at 06:59
To: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: [cbioportal] how to import study into dockerized cbioportal with keycloak

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[Didier Croes]

Hello,

After fighting a lot I succeded to make cbioportal work with keycloak.

Now I more or less followed the instructions you gave :

I did:

docker exec -it cbioportal-container bash

cd /cbioportal/core/src/main/scripts/

./dumpPortalInfo.pl /portalinfodump/

then

metaImport.py -p /portalinfodump -s /study/lgg_ucsf_2014/ -o

the importation went to the end . last line:

 13:48:54.981 [main] INFO  o.s.c.s.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - Bean 'businessDataSource' of type [org.mskcc.cbio.portal.dao.JdbcDataSource] is not eligible for getting processed by all BeanPostProcessors (

for example: not eligible for auto-proxying)
13:48:54.988 [main] INFO  o.s.c.s.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - Bean 'org.springframework.beans.factory.config.MethodInvokingFactoryBean#0' of type [org.springframework.beans.factory.config.MethodInvokingFa
ctoryBean] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
13:48:55.022 [main] INFO  o.s.c.s.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - Bean 'appConfig' of type [org.cbioportal.service.util.AppConfig$$EnhancerBySpringCGLIB$$4c13d16c] is not eligible for getting processed by all
BeanPostProcessors (for example: not eligible for auto-proxying)
13:48:57.209 [main] INFO  o.c.persistence.CacheEnabledConfig - Cache is enabled: false
Recaching...
Finished recaching...
13:48:59.209 [main] INFO  o.m.cbio.portal.util.ServerDetector - Detected server null
Updating study status to :  'AVAILABLE' for study: lgg_ucsf_2014
Done.
Total time:  6488 ms

I restarted : docker compose restart cbioportal

but study appeared on the overview page of cbioportal

There was a warning during the import but It went to the end

13:48:05.967 [main] WARN  o.a.commons.dbcp2.ObjectNameWrapper - Failed to complete JMX registration for org.cbioportal:DataSource=cbioportal
javax.management.InstanceAlreadyExistsException: org.cbioportal:DataSource=cbioportal

What did I miss?

Kind regards

[John Reber]

Hi Aghil

I’m not a java, but they look like warnings, that may or not be ignored.  If you click on the study are you able to access it?

 

John

------

John Reber
Systems Development Manager

Philadelphia, PA 19107
John....@jefferson.edu
KimmelCancerCenter.org

 

 

From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of Didier Croes <didier...@gmail.com>

Date: Wednesday, October 18, 2023 at 10:31
To: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>

Subject: Re: [cbioportal] how to import study into dockerized cbioportal with keycloak

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WARNING:  External Email - This email originated outside of Jefferson. DO NOT CLICK links or attachments unless you recognize the sender and are expecting the email. Click the "Report Message" button on your Outlook toolbar to alert IS&T.

 

Hello,

 

 

From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of aghil hooshmand <aghil.h...@gmail.com>
Date: Tuesday, October 17, 2023 at 06:59
To: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: [cbioportal] how to import study into dockerized cbioportal with keycloak

You don't often get email from aghil.h...@gmail.com. Learn why this is important

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hi ,

Dose anyone have experience with importing new study to local deodorized cbioportal+dockerized keycloak as authentication system.

I think keycloack dont let me to access portal and importing new study. when I want to import new study I got this error :

 

LookupError: No portal information found at http://cbioportal:8080

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The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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[aghil hooshmand]

Hi john,

yes, I could to import study after duming portal info at the directory. I did this commands :

first:

docker-compose run -v "[your local portal info directory]:/portalinfo" -w  [path of scripts(may be core/src/main/scripts)] [name of your portal app] ./dumpPortalInfo.pl /portalinfo

then run command for importing study:

 docker-compose run  -v "/portalinfo:/portalinfo" cbioportal metaImport.py -p /portalinfo -s /study/lgg_ucsf_2014/ -o

after importing study again i got error and I have to insert email in user table. Albeight for other users it didnt need to import. its may be need to insert at least one of user in keycloak into user. Its not logical but for me it has worked

[Didier Croes]

OOOH I did a mistake in the first message. The dataset does NOT appear in the datasets list.....

Kind regards

Didier

[Didier Croes]

Thanks for your reply.

I cannot click on it, it does not appear at all in the datasets list.

Kind regards

Didier

[Didier Croes]

Found it:

this was : saml.custom.userservice.class=org.cbioportal.security.spring.authentication.saml.SAMLUserDetailsServiceImpl

and it should be:
saml.custom.userservice.class=org.cbioportal.security.spring.authentication.keycloak.SAMLUserDetailsServiceImpl

now it works

Have a nice day