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IT-4004: Update notebook product to use Docker named volumes, change RStudio mount point, and update container versions #340

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merged 2 commits into from
Nov 14, 2024

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brucehoff
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Current R-Studio notebook loses user content placed in /home/rstudio (the home directory).

This PR changes the volume mount point from /home/rstudio/work subfolder to /home/rstudio.
It also changes from mounting a user folder to mounting a Docker "named volume". The reason for this
is so that the initial content of /home/rstudio is preserved (copied from the container to the host volume rather
than being masked by the empty host volume).

We update the versions of the notebook containers:

  • RStudio: To get fixes made for IT-4004
  • Jupyter: Bumping the Python version from 3.11 to 3.12

@brucehoff brucehoff requested review from a team as code owners November 14, 2024 00:30
@brucehoff brucehoff requested a review from xschildw November 14, 2024 00:30
env:
NETWORK_NAME:
'Fn::FindInMap': [GlobalVars, DockerNetworkName, Value]
NOTEBOOK_CONTAINER_NAME:
'Fn::FindInMap': [GlobalVars, NotebookContainerName, Value]
EC2_WORK_DIR:
'Fn::FindInMap': [NotebookTypeToInitParams, !Ref NotebookType, EC2WorkDir]
WORK_VOLUME_NAME:
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(Optional) I would suggest normalizing JUPYTER_WORK_DIR and RSTUDIO_WORK_DIR to just NOTEBOOK_WORK_DIR

@brucehoff brucehoff merged commit a9f7e0d into Sage-Bionetworks:master Nov 14, 2024
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2 participants