Pybis: mounting error

Dear community,

We have an internal “standard*” OpenBis installation at our department. We use PyBIS (version 1.33.1) to do most of our management, which is great. I would like to use pybis.mount() to transfer datasets and metadata. However, when I try to mount, I get a generic error: read: Connection reset by peer, which means the server is not accepting connections. Our DSS is running and seems to be working. I think I may be missing some configuration on how to set up this connection.

The mount is Linux to Linux, and the dependencies (sshfs and fuse) are installed.

  • By standard, I mean we have the following core-plugins: monitoring-support, dropbox-monitor, dataset-uploader, dataset-file-search, xls-import, search-store, openbis-sync, openbis-ng-ui, illumina-ngs, eln-lims, microscopy, shared, eln-lims-life-sciences

Hi Thiago,

the pyBIS mount method is merely a wrapper for the sshfs command:

sshfs username@hostname:path mountpoint -o port=2222 -o ssh_command=“ssh -oKexAlgorithms=+diffie-hellman-group1-sha1” -oauto_cache,reconnect -oStrictHostKeyChecking=no

I have not checked this method for a while, so maybe certain default parameters have changed in the meantime. If you can mount openBIS manually, you might change the parameters in your mount() method to achieve the same.

Dear Swen,
Thanks for the prompt response. I now understand how the mount method works. If I’ve got it right, we have to manually configure the ssh connection to the OpenBSD server, right?

All the best,

Hi Thiago,

yes, I would try out to get a mounting point first manually and then try to specify the params accordingly using pyBIS. Unfortunately the sshfs mount is not straight forward and quite a few things that can go wrong…

Best, Swen