Workspaces on AnVIL Azure are a way to organize and manage data and analysis resources. Workspaces are created by users and can be shared with other users.
The avworkspaces() function lists the workspaces
available to the current user.
Workspaces on AnVIL are managed resources and do not provide a lot of
freedom to work across workspaces. The AnVILAz package
mainly provides functions to work with workspaces within the same
namespace.
There may be some workspaces that still operate using the Google
Cloud Platform (GCP) and these workspaces are not accessible through the
AnVILAz package though they may be listed in
avworkspaces(). We refer users to AnVILGCP for
working with GCP-based workspaces.
The avworkspace() function returns the name of the
current workspace provided that it is set.
The avworkspace() function can be used to set the
current workspace.
Typically this is not necessary as these values can be gathered from the AnVIL Azure environment.
The avworkspace_clone() function clones a workspace.
avworkspace_clone(
namespace = "my-namespace",
name = "my-workspace",
to_namespace = "my-new-namespace",
to_name = "my-workspace-clone"
)
avworkspaces()Note that currently, the createdBy field is not
populated with the user’s information. This is a known issue and will be
addressed in a future release.
To delete a workspace, it is recommended to use the AnVIL Azure interface.
Notebooks are a way to interact with the data and analysis resources
in a workspace. The avnotebooks() function lists the
notebooks available in the current workspace.
Typically, notebooks are kept on the Azure Blob Storage (ABS)
Container in a analyses/ folder.
The avnotebooks_localize() function downloads a notebook
to the local filesystem. By default, it will download all the notebooks
located in the analyses/ folder to a matching
analyses local folder. Note that this is a convenience
function for avcopy file transfer operations.
On the other hand, the avnotebooks_delocalize() function
uploads all the notebooks within the given directory (by default, the
current directory) to the Azure Blob Storage Container. It places them
in the analyses/ folder on the ABS Container.
The avworkflows_jobs() function reports the status of
the current workflows within the workspace.
It provides a tibble with workflow information such as the
run_set_id, run_set_name,
submission_timestamp, error_count,
run_count, state, etc.
sessionInfo()
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] AnVILAz_1.1.0 BiocStyle_2.33.1
##
## loaded via a namespace (and not attached):
## [1] vctrs_0.6.5 httr_1.4.7 cli_3.6.3
## [4] knitr_1.48 rlang_1.1.4 xfun_0.48
## [7] jsonlite_1.8.9 glue_1.8.0 rjsoncons_1.3.1.9100
## [10] buildtools_1.0.0 htmltools_0.5.8.1 maketools_1.3.1
## [13] BiocBaseUtils_1.7.3 sys_3.4.3 sass_0.4.9
## [16] fansi_1.0.6 rappdirs_0.3.3 rmarkdown_2.28
## [19] tibble_3.2.1 evaluate_1.0.1 jquerylib_0.1.4
## [22] fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4
## [25] httr2_1.0.5 BiocManager_1.30.25 compiler_4.4.1
## [28] pkgconfig_2.0.3 digest_0.6.37 R6_2.5.1
## [31] utf8_1.2.4 pillar_1.9.0 magrittr_2.0.3
## [34] bslib_0.8.0 tools_4.4.1 AnVILBase_0.99.32
## [37] cachem_1.1.0