Report currently running Apptainer in platform reproducibility table

[slager]

• adds an apptainer entry to the platform reproducibilty table in get_session_info(). This is currently supported when:

1. launching a container from the command line, e.g., with apptainer exec mysif.sif R
2. launching an Rstudio Apptainer via Open OnDemand with a scicomp-built R/bioconductor image
3. launching an Rstudio Apptainer via Open OnDemand with a custom SIF image

• also refactors the platform table section of the git_session_info() function to be more maintainable, using a key-value system rather than a series of small data.frames.

Closes #152

Suggested tests for reviewer(s):

1. test with command line apptainer exec

<ssh rhino>
<grabnode>
module load Apptainer
apptainer exec /home/dslager/shared/test_image.sif R -q -e "VISCfunctions::get_session_info()[[1]]"

2. test with scicomp-built Rstudio server on OOD (does not have PR commit of VISCfunctions pre-installed)

https://openondemand.fredhutch.org/pun/sys/dashboard/batch_connect/sys/ood_rstudio_server_apptainer/session_contexts/new

Make sure "Custom Apptainer .sif file" field is blank

• Launch
• Connect to Rstudio Server

remotes::install_github('FredHutch/VISCfunctions', ref = '08229d3') # install PR commit for testing
VISCfunctions::get_session_info()[[1]]
remotes::install_github('FredHutch/VISCfunctions') # revert to `main`

3. test with custom-built sif image, has preinstalled VISCfunctions at ref = '08229d3'

https://openondemand.fredhutch.org/pun/sys/dashboard/batch_connect/sys/ood_rstudio_server_apptainer/session_contexts/new

Make sure "Custom Apptainer .sif file" field has /home/dslager/shared/test_image.sif

• Launch
• Connect to Rstudio Server

VISCfunctions::get_session_info()[[1]]

[slager]

Hi @valduran18, any chance you can test? Suggested test setup is above, or you could try it on one of your ICS reports.

[valduran18]

hi Dave! I tried following your suggested tests but couldn't your test image. I think the permissions might have changed for your test folder.

I did test it on the command line, using the FH image, and then on OD using the same FH image:

[slager]

Hi @valduran18, I added a permission to my test image; are you able to test that now?

It looks like it's reporting the cache path for your command line test. Can you describe what you did before the screenshot to get that output? I'd like to fix it to not report the cache.

[valduran18]

Hi @valduran18, I added a permission to my test image; are you able to test that now?

It looks like it's reporting the cache path for your command line test. Can you describe what you did before the screenshot to get that output? I'd like to fix it to not report the cache.

I'm able to test it in the command line, but I'm still not able to access it through OD.

command line output:

vduran@gizmoj5:~$ apptainer exec /home/dslager/shared/test_image.sif R -q -e "VISCfunctions::get_session_info()[[1]]"
> VISCfunctions::get_session_info()[[1]]
        name                               value
1   nodename                             gizmoj5
2  apptainer /home/dslager/shared/test_image.sif
3    version        R version 4.4.2 (2024-10-31)
4         os                  Ubuntu 24.04.1 LTS
5     system                   x86_64, linux-gnu
6         ui                                 X11
7   language                              en_US:
8    collate                         en_US.UTF-8
9      ctype                         en_US.UTF-8
10        tz                             Etc/UTC
11      date                          2026-07-22
12    pandoc             3.6.3 @ /usr/bin/pandoc
13    quarto      1.5.57 @ /usr/local/bin/quarto
14  filename              No Input File Detected
15  location                        /home/vduran
16      user                              vduran

for the cache output, I used the FH container:

vduran@gizmoj5:~$ apptainer exec https://sif-registry.fredhutch.org/bioconductor_docker_RELEASE_3_20.sif R -q -e "VISCfunctions::get_session_info()[[1]]"
> VISCfunctions::get_session_info()[[1]]
        name
1   nodename
2  apptainer
3    version
4         os
5     system
6         ui
7   language
8    collate
9      ctype
10        tz
11      date
12    pandoc
13  filename
14  location
15      user
                                                                                                value
1                                                                                             gizmoj5
2  /home/vduran/.apptainer/cache/net/9e44ef05d1da69e02b7260a707a9395d12365f8b51068342c899985a87a65bd3
3                                                                        R version 4.4.2 (2024-10-31)
4                                                                                  Ubuntu 24.04.1 LTS
5                                                                                   x86_64, linux-gnu
6                                                                                                 X11
7                                                                                              en_US:
8                                                                                         en_US.UTF-8
9                                                                                         en_US.UTF-8
10                                                                                            Etc/UTC
11                                                                                         2026-07-22
12                                                                              3.6 @ /usr/bin/pandoc
13                                                                             No Input File Detected
14                                                                                       /home/vduran
15                                                                                             vduran

[slager]

Hi @valduran18 can you try testing it again with my test image? I had a typo in the test image path above, the correct path should be /home/dslager/shared/test_image.sif.