Pybis: mounting error

Data Management
1

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
2

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.

3

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,
Thiago

4

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