database error
niharika toom
cbioportal-container exited with code 1
cbioportal-container | db.portal_db_name=cbioportal
cbioportal-container | db.password=somepassword
cbioportal-container | mysqladmin: [Warning] Using a password on the command line interface can be insecure.
'@'172.19.0.4' (using password: YES)3-03-29T23:08:42.905203Z 120 [Note] Access denied for user 'cbio_user'
Please help with this issue
Best regards,
Niharika Toom
de Bruijn, Ino
Hi Niharika,
Thanks for reaching out!
Can you elaborate on how you are running cbioportal docker compose. Are you using the exact setup here:
https://github.com/cBioPortal/cbioportal-docker-compose
Or are you connecting to a different mysql database?
Thanks!
Ino
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de Bruijn, Ino
Hi Niharika,
It looks like a particular table doesn’t exist according to the log you shared. I’m guessing something went wrong the first time you set up the database. Can you delete all the volumes and try again from the beginning:
docker-compose down -v
Then try to connect to the mysql database and check if you see the table there
Thanks!
Ino
From:
niharika toom <niharik...@gmail.com>
Date: Monday, April 3, 2023 at 3:05 PM
To: de Bruijn, Ino <debr...@mskcc.org>
Subject: [EXTERNAL] Re: [cbioportal] database error
Yes. I am using the same documentation. Below is the attachment of my error. I'm running all containers except the database container. I'm receiving database errors. Thank You, Niharika Toom On Mon, Apr 3, 2023 at 2: 35 PM de Bruijn,
Yes. I am using the same documentation.
Below is the attachment of my error. I'm running all containers except the database container. I'm receiving database errors.
Thank You,
Niharika Toom
de Bruijn, Ino
Can you share the logs you see when you start from scratch?
Could you also provide:
- The version of cBioPortal you are running (this is in the .env variable)
- The commit id of the cbioportal-docker compose repo
- Operating system
- Hardware specs
Thanks!
Ino
From:
niharika toom <niharik...@gmail.com>
Date: Monday, April 3, 2023 at 3:23 PM
To: de Bruijn, Ino <debr...@mskcc.org>
Subject: [EXTERNAL] Re: [cbioportal] database error
I did the same but I am getting the same error. Could you please help me with this? Thank you, Niharika Toom On Mon, Apr 3, 2023 at 3: 20 PM de Bruijn, Ino <debruiji@ mskcc. org> wrote: Hi Niharika, It looks like a particular table doesn’t
I did the same but I am getting the same error. Could you please help me with this?
Thank you,
Niharika Toom
de Bruijn, Ino
Hi Niharika,
To clarify: are you saying you were able to get the cBioPortal docker compose setup running now but you are having trouble to import studies?
Thanks so much!
Ino
From:
niharika toom <niharik...@gmail.com>
Date: Monday, April 3, 2023 at 3:38 PM
To: de Bruijn, Ino <debr...@mskcc.org>
Subject: [EXTERNAL] Re: [cbioportal] database error
May I know the issue of working on importing studies? https: //docs. cbioportal. org/deployment/docker/ Thank You, Niharika Toom On Mon, Apr 3, 2023 at 3: 32 PM niharika toom <niharikatoom09@ gmail. com> wrote: Hello Ino, Thank you for your
May I know the issue of working on importing studies?
Thank You,
Niharika Toom
On Mon, Apr 3, 2023 at 3:32 PM niharika toom <niharik...@gmail.com> wrote:
Hello Ino,
Thank you for your email. I switched from arm64 to arm64/v8, which does not work with my laptop. It is now loaded and ready to use the localhost.
Thank you
Niharika Toom
de Bruijn, Ino
Sounds good
What is the issue you see in the logs when importing?
Thanks!
Ino
From:
niharika toom <niharik...@gmail.com>
Date: Monday, April 3, 2023 at 3:49 PM
To: de Bruijn, Ino <debr...@mskcc.org>
Subject: [EXTERNAL] Re: [cbioportal] database error
Yes, Ino. Thank You, Niharika Toom On Mon, Apr 3, 2023 at 3: 47 PM de Bruijn, Ino <debruiji@ mskcc. org> wrote: Hi Niharika, To clarify: are you saying you were able to get the cBioPortal docker compose setup running now but you are having
Yes, Ino.
Thank You,
Niharika Toom
de Bruijn, Ino
Sent: Tuesday, April 4, 2023 4:59:50 PM