It seems that the recently dx uploaded files does not show up on /mnt/project until I re-start the whole Jupyter Lab VM

• 

  Ondrej Klempir DNAnexus Team

  • 13 June 2022 13:45

  Yes, I have the same understanding.

   

  The filesystem mounted with dxfuse is "static" and does not update automatically. Therefore, it is a "reflection" of the project at the time when the JupyterLab app (and dxfuse in it) was started.

   

  In order to "refresh" the data, the project needs to be "unmounted" and "mounted" back again. This can be done with the following commands:

   

  $ umount /mnt

  $ mkdir -p /mnt

  $ /home/dnanexus/dxfuse -readOnly /mnt /home/dnanexus/.dxfuse_manifest.json

   

  0
• 

  Former User of DNAx Community_13

  • 05 August 2022 23:35

  @Ondrej Klempir? that solution didn't work for me, please see the attached image. Am I missing something?

   

  

  0
• 

  Ondrej Klempir DNAnexus Team

  • 19 August 2022 12:12

  If manifest.json is not present on the path, I would try to create one:

   

  # Create a manifest file for dxfuse

  echo "{

       \"files\" : [],

       \"directories\" : [

          {

           \"proj_id\" : \"$DX_PROJECT_CONTEXT_ID\",

           \"folder\" : \"/\",

           \"dirname\" : \"/project\"

          }

       ]

     }" > .dxfuse_manifest.json

  0
• 

  Former User of DNAx Community_57

  • 04 November 2022 14:38

  Hi,

   

  This answer is very helpful. I was wondering if anything similar is possible in RStudio. When I try to run `umount /mnt` in the terminal, I get:

   

  "umount: /mnt: umount failed: Operation not permitted."

  0
• 

  Alexandra Lee DNAnexus Team

  • 07 November 2022 19:53

  Hi Rosemary,

   

  Unfortunately it appears that `umount` doesn't work in the terminal in RStudio, as you've found. Thank you for bringing this to our attention - we will make a note of this and work to address this in the future.

   

  For now, one possible work around is to use the terminal in the JupyterLab workstation where you can also use an R notebook.

   

   

  0
• 

  Former User of DNAx Community_57

  • 08 November 2022 08:18

  Thanks!

  0
• 

  Dan Gealow

  • Edited 02 December 2024 17:08

  It's now possible to refresh the mount in a Posit/Rstudio session with the following commands (h/t Hoang on email support):

  # Set the parameters:
  FUSE_MOUNT="/mnt"
  MANIFEST_FILE="/home/dnanexus/.dxfuse_manifest.json"
  
  # Unmount the project:
  sudo umount $FUSE_MOUNT
  
  # Restart dxfuse:
  sudo -E /home/dnanexus/dxfuse -readOnly $FUSE_MOUNT $MANIFEST_FILE

  or if you want a one-liner:

  sudo umount /mnt; sudo -E /home/dnanexus/dxfuse -readOnly /mnt /home/dnanexus/.dxfuse_manifest.json

  (Make sure you're not currently in the `/mnt` directory when you try to unmount it.)

  1

Please sign in to leave a comment.