The AnVILBase
package defines S4 generics for AnVIL
packages. The package is designed to be used in conjunction with either
AnVILGCP
or AnVILAz
packages. The
AnVILBase
package is not intended to be used as a
standalone package.
The AnVILBase
package defines S4 generics for the AnVIL
package. These include methods for copying, listing, removing, and
backing up files in the cloud. All generics in the package have methods
defined for ‘missing’ and ‘ANY’ signatures.
The AnVILBase
package is designed to support packages
that work with the AnVIL cloud platforms. Downstream packages expose
Google Cloud Platform (AnVILGCP) and the Azure Cloud Platform (AnVILAz)
application programming interfaces (APIs). To increase usability, the
AnVILBase
package attempts to deduce the user’s cloud
platform from environment variables. This is codified in the
cloud_platform
function:
Packages that use the AnVILBase
package can
conditionally run tests using the avplatform_namespace()
function. It will return either AnVILGCP
or
AnVILAz
depending on the cloud environment variables that
are set. If no environment variables are set, the function will return
""
.
## [1] ""
The following generics are defined in the AnVILBase
package:
avcopy()
: Copy a file to and from the cloudavlist()
: List files in the cloud storage locationavremove()
: Remove a file from the cloudavbackup()
: Backup files to the cloudavrestore()
: Restore files from the cloudavstorage()
: Get the storage address in the cloudThe following generics are defined in the AnVILBase
package for tables:
avtable
: Get a table by name from a workspaceavtables
: List tables in the workspace(s)avtable_import
: Upload a table to a workspaceavtable_import_set
: Create a set (grouped) table from
an existing tableavtable_delete
: Remove a table from a workspaceavtable_delete_values
: Delete values from a tableThe following generics are defined in the AnVILBase
package for workspaces:
avworkspace
: Set the active workspaceavworkspaces
: List current workspace(s) on AnVILavworkspace_name
: Get the workspace nameavworkspace_namespace
: Get the workspace namespaceNote that the AnVILBase
package also includes helper
functions that are used across AnVIL
cloud platforms. These
include functions mainly for working with the AnVIL
API
responses.
The following generics are defined in the AnVILBase
package for workflows:
avworkflow_jobs
: Get the execution status of a
workflowThe following generics are defined in the AnVILBase
package for notebooks:
avnotebooks
: List notebooks in the workspaceavnotebooks_localize
: Download notebooks from a cloud
to a workspaceavnotebooks_delocalize
: Upload notebooks from a
workspace to a cloud## R version 4.4.2 (2024-10-31)
## 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] AnVILBase_1.1.0 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] vctrs_0.6.5 httr_1.4.7 cli_3.6.3
## [4] knitr_1.49 rlang_1.1.4 xfun_0.49
## [7] jsonlite_1.8.9 glue_1.8.0 buildtools_1.0.0
## [10] htmltools_0.5.8.1 maketools_1.3.1 sys_3.4.3
## [13] sass_0.4.9 fansi_1.0.6 rmarkdown_2.29
## [16] rappdirs_0.3.3 tibble_3.2.1 evaluate_1.0.1
## [19] jquerylib_0.1.4 fastmap_1.2.0 yaml_2.3.10
## [22] lifecycle_1.0.4 httr2_1.0.7 BiocManager_1.30.25
## [25] compiler_4.4.2 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_4.4.2
## [34] cachem_1.1.0