AnVILAz 1.0.0
library(AnVILAz)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.
avworkspaces()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.
avworkspace()The avworkspace() function can be used to set the current workspace.
avworkspace("my-namespace/my-workspace")
avworkspace()Typically this is not necessary as these values can be gathered from the AnVIL Azure environment.
The avworkspace_namespace() and avworkspace_name() functions return the
namespace and name of the current workspace.
avworkspace_namespace()avworkspace_name()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.
avnotebooks()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.
avnotebooks_localize(destination = "./analyses")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.
avnotebooks_delocalize(source = "./")The avworkflows_jobs() function reports the status of the current workflows
within the workspace.
avworkflows_jobs()It provides a tibble with workflow information such as the run_set_id,
run_set_name, submission_timestamp, error_count, run_count, state,
etc.
The avworkflows_jobs_inputs() function lists the inputs for a given workflow.
It returns a list of tibbles with the inputs for each workflow within the
current workspace.
avworkflows_jobs_inputs()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: /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB 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: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] AnVILAz_1.0.0 BiocStyle_2.34.0
##
## 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
## [10] htmltools_0.5.8.1 BiocBaseUtils_1.8.0 sass_0.4.9
## [13] fansi_1.0.6 rmarkdown_2.28 rappdirs_0.3.3
## [16] evaluate_1.0.1 jquerylib_0.1.4 tibble_3.2.1
## [19] fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4
## [22] httr2_1.0.5 bookdown_0.41 BiocManager_1.30.25
## [25] compiler_4.4.1 pkgconfig_2.0.3 digest_0.6.37
## [28] R6_2.5.1 utf8_1.2.4 pillar_1.9.0
## [31] magrittr_2.0.3 bslib_0.8.0 tools_4.4.1
## [34] AnVILBase_1.0.0 cachem_1.1.0