search

cianfrocco-lab / COSMIC-CryoEM-Gateway

Web platform for analyzing cryo-EM data on Comet cluster at San Diego Supercomputer Center
http://cosmic-cryoem.org
GNU General Public License v3.0
9 stars 1 forks source link

Github permissions error on cosmic2dev server github repo #262

Closed mcianfrocco closed 4 years ago

mcianfrocco commented 4 years ago

Hi @kenneth59715 -

I'm trying to check in a new tool into our github repo from dev, but I'm getting a permissions issue with Github: 

(gatewayVE)[cosmic2-gw@cosmic2dev gateway_config]$ git pull error: insufficient permission for adding an object to repository database .git/objects fatal: git write-tree failed to write a tree

Do you know how to fix this? It seems like a chown permissions issue and I'm not sure exactly how to fix it. 

I found this help page: https://ducfilan.wordpress.com/2017/09/26/git-pull-error-error-insufficient-permission-for-adding-an-object-to-repository-database-gitobjects/

Mike

kenneth59715 commented 4 years ago

Interesting! What command did you run and as which github user? I usually git push from dev to github...

Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Thursday, September 3, 2020 8:17 PM, Michael A. Cianfrocco notifications@github.com wrote:

Hi @kenneth59715 -

I'm trying to check in a new tool into our github repo from dev, but I'm getting a permissions issue with Github:

(gatewayVE)[cosmic2-gw@cosmic2dev gateway_config]$ git pull error: insufficient permission for adding an object to repository database .git/objects fatal: git write-tree failed to write a tree

Do you know how to fix this? It seems like a chown permissions issue and I'm not sure exactly how to fix it.

I found this help page: https://ducfilan.wordpress.com/2017/09/26/git-pull-error-error-insufficient-permission-for-adding-an-object-to-repository-database-gitobjects/

Mike

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or unsubscribe.

mcianfrocco commented 4 years ago

logged in as cosmic2-gw and using my account name mcianfrocco

mcianfrocco commented 4 years ago

It looks like there should be a .git folder which is missing from the github directory portal-R41.14/gateway_config

kenneth59715 commented 4 years ago

I'll try the push as my github user.

Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Friday, September 4, 2020 8:02 AM, Michael A. Cianfrocco notifications@github.com wrote:

logged in as cosmic2-gw and using my account name mcianfrocco

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or unsubscribe.

kenneth59715 commented 4 years ago

I think gateway_config is a symlink to /projects/cosmic2/kennethtest/dev/41.14/COSMIC-CryoEM-Gateway/gateway_config so the relevant .git is /projects/cosmic2/kennethtest/dev/41.14/COSMIC-CryoEM-Gateway/.git

Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Friday, September 4, 2020 8:03 AM, Michael A. Cianfrocco notifications@github.com wrote:

It looks like there should be a .git folder which is missing from the github directory portal-R41.14/gateway_config

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or unsubscribe.

kenneth59715 commented 4 years ago

There are a number of directories with no group-write in

/projects/cosmic2/kennethtest/dev/41.14/COSMIC-CryoEM-Gateway/.git/objects

I think these are owned by mona. Probably need to add group write to these.

Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Friday, September 4, 2020 8:08 AM, Kenneth808 kenneth808@protonmail.com wrote:

I think gateway_config is a symlink to /projects/cosmic2/kennethtest/dev/41.14/COSMIC-CryoEM-Gateway/gateway_config so the relevant .git is /projects/cosmic2/kennethtest/dev/41.14/COSMIC-CryoEM-Gateway/.git

Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Friday, September 4, 2020 8:03 AM, Michael A. Cianfrocco notifications@github.com wrote:

It looks like there should be a .git folder which is missing from the github directory portal-R41.14/gateway_config

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or unsubscribe.

mcianfrocco commented 4 years ago

Can you do that or does Mona have to do that?

On Fri, Sep 4, 2020 at 11:15 AM kenneth59715 notifications@github.com wrote:

There are a number of directories with no group-write in

/projects/cosmic2/kennethtest/dev/41.14/COSMIC-CryoEM-Gateway/.git/objects

I think these are owned by mona. Probably need to add group write to these.

Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Friday, September 4, 2020 8:08 AM, Kenneth808 < kenneth808@protonmail.com> wrote:

I think gateway_config is a symlink to

/projects/cosmic2/kennethtest/dev/41.14/COSMIC-CryoEM-Gateway/gateway_config so the relevant .git is /projects/cosmic2/kennethtest/dev/41.14/COSMIC-CryoEM-Gateway/.git

Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Friday, September 4, 2020 8:03 AM, Michael A. Cianfrocco < notifications@github.com> wrote:

It looks like there should be a .git folder which is missing from the github directory portal-R41.14/gateway_config

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cianfrocco-lab/COSMIC-CryoEM-Gateway/issues/262#issuecomment-687212369, or unsubscribe https://github.com/notifications/unsubscribe-auth/AALFRFN3MHVJ5UFI3MGZZN3SEEAAXANCNFSM4QW27Q5A .

kenneth59715 commented 4 years ago

Okay, try it now. I did a mv and cp -ipr back, so the dirs should be writable.

Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Friday, September 4, 2020 8:16 AM, Michael A. Cianfrocco notifications@github.com wrote:

Can you do that or does Mona have to do that?

On Fri, Sep 4, 2020 at 11:15 AM kenneth59715 notifications@github.com wrote:

There are a number of directories with no group-write in

/projects/cosmic2/kennethtest/dev/41.14/COSMIC-CryoEM-Gateway/.git/objects

I think these are owned by mona. Probably need to add group write to these.

Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Friday, September 4, 2020 8:08 AM, Kenneth808 < kenneth808@protonmail.com> wrote:

I think gateway_config is a symlink to

/projects/cosmic2/kennethtest/dev/41.14/COSMIC-CryoEM-Gateway/gateway_config so the relevant .git is /projects/cosmic2/kennethtest/dev/41.14/COSMIC-CryoEM-Gateway/.git

Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Friday, September 4, 2020 8:03 AM, Michael A. Cianfrocco < notifications@github.com> wrote:

It looks like there should be a .git folder which is missing from the github directory portal-R41.14/gateway_config

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cianfrocco-lab/COSMIC-CryoEM-Gateway/issues/262#issuecomment-687212369, or unsubscribe https://github.com/notifications/unsubscribe-auth/AALFRFN3MHVJ5UFI3MGZZN3SEEAAXANCNFSM4QW27Q5A .

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or unsubscribe.

mcianfrocco commented 4 years ago

Fixed! Thanks!