USER VISIBLE CHANGES
(v 1.17.18) Added has_avworkspace function to check for the existence of
an AnVIL workspace environment.
(v 1.17.10) Internal functions now use AnVILGCP for gcloud utilities.
(v 1.17.8) Functions that use gcloud utilities are deprecated and will be
moved to AnVILGCP. See help(package = "AnVIL") for a complete list.
Documentation pages have a *-deprecated suffix.
(v 1.17.3) Added Terra Data Repository (TDR) service as TDR(). See service
at https://data.terra.bio.
(v 1.17.1) Gen3 services, avworkflow*_configuration() functions, install(),
repository(), and repositories() have been removed.
(v 1.17.1) Defunct repository_stats function in favor of
BiocPkgTools::repositoryStats (@LiNk-NY)
BUG FIXES AND MINOR IMPROVEMENTS
(v 1.17.20) Use lifeCycle from BiocBaseUtils to mark functions as
deprecated or defunct.
(v 1.17.19) Increase robustness of gcloud_exists by testing gcloud
with the version command.
(v 1.17.18) Remove mentions of AnVIL::install from the vignette.
(v 1.17.13) Update to changes in rapiclient and use native pipe operator.
(v 1.17.7) Do not evaluate vignette chunks if gcloud_exists() is FALSE
(v 1.17.6) Update Dockstore API file, version, and URL
(v 1.17.2) Use application/json as default Content-Type.
USER VISIBLE CHANGES
(v 1.15.10) Validate API versions against hardcoded variables; produce warning when discordant (@LiNk-NY, #101).
(v 1.15.8) Add gcloud_storage() and gcloud_storage_buckets() to
create and manage Google Cloud Storage buckets (@LiNk-NY, #72).
Gen3 services, avworkflow*_configuration() functions, install(),
repository(), and repositories() are defunct.
(v 1.15.5) Catch avtable_import_status() errors in the response object.
(v 1.15.1) Update vignette with examples for avworkflow_info() (@mtmorgan,
@yubocheng).
BUG FIXES AND MINOR IMPROVEMENTS
(v 1.15.11) Update Dockstore API file, version, and URL
(v 1.15.9) Use assertions from BiocBaseUtils
(v 1.15.7) Use URLencode for table in avtable and direct request to
Rawls endpoint (@LiNk-NY, #98)
(v 1.15.6) Update the Dockstore API reference URL and use
api_referenc_url instead of API file (@LiNk-NY).
NEW FEATURES
(v 1.13.1) Add paged support for large tables in avtable_import()
and avtable_import_set().
(v 1.13.2) Only show avtable_paged() and avtable_import*()
progress bar in interactive() sessions
(v 1.13.4) Report messages when avtable_import_status()
contains one. https://github.com/Bioconductor/AnVIL/issues/79
(v 1.13.3) Use 'op' when .avworkflow_response() calls avstop_for_status(). https://github.com/Bioconductor/AnVIL/issues/80
(v 1.13.7) Check requester pays for destination URIs when using
gsutil_cp (@smgogarten, #82)
USER VISIBLE CHANGES
(v 1.13.8) Update documentation on updating workflow configurations. (@amstilp, #84)
(v 1.13.11) Added workflowId to avworkflow_files() and
avworkflow_localize() to allow for filtering by workflow
(@yubocheng, #90).
USER VISIBLE CHANGES
(v 1.11.2) update workflow file discovery to use API, rather than 'scraping' google bucket. https://github.com/Bioconductor/AnVIL/issues/69
(v 1.11.3) Gen3 services deprecated
(v 1.11.5) Add na = to handle NA encoding in avtable() /
avtable_import(). Changes default behavior.
https://github.com/Bioconductor/AnVIL/issues/75
BUG FIXES
name, to allow
for spaces. https://github.com/Bioconductor/AnVIL/issues/67NEW FEATURES
(v 1.9.1) add drs_access_url() to returned signed https:// URLs
from drs:// URIs. Enhance drs_cp().
(v 1.9.4) add auto_unbox= argument to Service class, allowing
other developers flexibility in unboxing values passed to REST
APIs.
(v 1.9.7) add developer facilities for tracking API changes in Rawls, Terra, and Leonardo services
USER VISIBLE CHANGES
(v 1.9.2) Deprecate AnVIL::install() & friends in favor of BiocManager::install(), which now knows about container binary repositories.
(v 1.9.8) Update Rawls, Terra, and Leonardo services. Changed endpoints include:
## Rawls
$removed
[1] admin_delete_refresh_token admin_statistics_get
[3] refreshToken refreshTokenDate
$updated
[1] listUserBillingAccounts createWorkspace getTags
[4] clone entity_type_metadata get_entity
[7] entityQuery createSubmission validateSubmission
## Terra
$removed
[1] userTrial listImportPFBJobs importPFBStatus
$updated
[1] deleteBillingProject billingAccounts
[3] createWorkspace cloneWorkspace
[5] entityQuery flexibleImportEntities
[7] importEntities createSubmission
[9] validateSubmission browserDownloadEntitiesTSV
[11] setProfile
## Leonardo
$removed
[1] batchNodepoolCreate
$updated
[1] listApp listAppByProject deleteApp
[4] createApp listDisks listDisksByProject
[7] createDisk updateRuntime createRuntime
[10] setCookie proxyClusterJupyter proxyClusterJupyterLab
[13] proxyClusterRStudio
(v 1.9.9) add 'gadgets' (simple graphical interfaces) to key
functions, avworkspace_gadget(), avtable_gadget(),
avworkflow_gadget(). Also browse_workspace() for opening a terra
workspace in the browser.
BUG FIXES
(v 1.9.3 / 1.8.2) avworkflow_localize() looks for submissionId
files correctly.
(v 1.9.5 / 1.8.3) drs_stat() works when accessUrl is included in
response.
(v 1.9.6 / 1.8.5) gsutil_cp() and gsutil_rsync() use
normalizePath() on source and destination arguments to avoid
creating directories in unexpected locations when provided with
paths containing ~, . or ...
(v 19.10 / v 1.8.6) gcloud_account("<new account>") did not
invalidate cached access tokens.
https://github.com/Bioconductor/AnVIL/issues/66
(v 1.9.11 / v 1.8.7) avoid changing status of 'Done' workflows to 'Aborted' https://github.com/Bioconductor/AnVIL/issues/64
(v 1.9.11 / v 1.8.7) allow 'NULL' for entity arguments of avworkflow_run() https://github.com/Bioconductor/AnVIL/issues/65
NEW FEATURES
(v 1.7.4) add avworkflow_configuration_*() functions for
manipulating workflow configurations, and a vignette describing use.
(v 1.7.5) add avdata_import() to import 'REFERENCE DATA' and
'OTHER DATA' tables.
(v 1.7.9) export repository_stats() to summarize binary package
availability.
USER VISIBLE CHANGES
(v 1.7.4) Deprecate avworkflow_configuration(),
avworkflow_import_configuration().
(v 1.7.4) Update Dockstore md5sum.
(v 1.7.5) avdata() is re-implemented to more faithfully report
only 'REFERENCE DATA' and 'OTHER DATA' workspace attributes;
previously, other attributes such as the description and tags (from
the workspace landing page) were also reported.
BUG FIXES
(v 1.7.4) avworkflow_files() and avworkflow_localize() do not
fail when the workflow has produced no files.
(v 1.7.6) improve handling of authentication token for gcloud utilities.
(v 1.8.2) avworkflow_localize() looks for submissionId files
correctly.
(v 1.8.3) drs_stat() works when accessUrl is included in
response.
BUG FIXES
BUG FIXES
NEW FEATURES
(v. 1.5.5) add repository() to return the binary repository
location, if available.
(v. 1.5.7) drs_stat() and drs_cp() support signed URLs
USER VISIBLE CHANGES
(v. 1.5.2) drs_stat() uses multiple cores (on non-Windows) to enhance
performance
(v. 1.5.6) install() delegates to BiocManager::install(),
providing more flexibility (e.g., installing from GitHub) and
robustness.
(v. 1.5.7) drs_stat() returns fields more selectively.
BUG FIXES
NEW FEATURES
(v 1.3.1) support Rawls() service (more fine-grained implementation
/ extension of the 'Terra()' orchestration API).
(v 1.3.2) introduce avworkspace_*() functions for viewing and updating
workflow configurations.
(v 1.3.3) introduce avnotebooks_() functions for managing notebooks
on workspaces and runtimes.
(v 1.3.11) introduce avtable_paged() for page-wise access to tables
(v 1.3.14) introduce avworkspace_clone() for cloning existing
workspaces.
(v 1.3.21) avworkspaces() returns a tibble of available workspaces.
(v 1.3.24) gsutil_rsync() supports a regular expresion exclude =
to exclude files from synchronization.
(v 1.3.24) avworkflow_localize() copies workflow control and / or
output files to the local disk.
USER VISIBLE CHANGES
(v 1.3.1) service functions have signatures like fun(x, ..., .__body__ = list(y)), where x is a argument for the 'URL' of the
RESTful interface, and y is an argument for the 'BODY' of POST and
similar requests. The ... provide backward compatibility, and is
used to populate elements of .__body__; the full interface is
required when URL and BODY have identically named arguments.
(v 1.3.10, 1.3.11) return 'entity' column with name 'table_id',
rather than 'name'.
(v 1.3.22) localize() / delocalize() warn when dry = TRUE, so that
lack of localization is more apparent.
(v 1.3.24) gsutil_stat() returns a tibble summaring bucket status,
rather than character().
(v 1.3.30) Add Referer: header to all Leonardo requests
BUG FIXES
(v 1.3.6) when .__body__ consists of 1 argument, it is represented
as an unnamed set.
(v 1.3.7) allow positional matching for .__body__ arguments
(v. 1.2.1 / 1.3.31) drs_stat() returns a single record per URL when multiple hashes available.
NEW FEATURES
(v 1.1.3) introduce .deprecated flag in operations() / tags(); don't include
deprecated APIs by default; warn on use of deprecated APIs.
(v 1.1.4) add repositories() to return binary (if available),
Bioconductor, and CRAN repository paths.
(v 1.1.6) provide md5sum as check on service version.
(v 1.1.9) add avfiles_*() for managing workspace bucket files.
(v 1.1.15) add avtable_import_set() to create subsets of tables,
following the Terra data model.
(v 1.1.16) add avruntimes(), avworkspace_jobs() to query for runtimes
and jobs associated with the active billing account.
(v 1.1.17) add avdisks() to query for persistent disks associate
with the active billing account.
(v 1.1.21) add avworkflow_*() for interacting with workflow jobs
and outputs.
BUG FIXES
(v 1.0.1) collapse 'produces' vectors to scalars, for httr::accept()
(v 1.0.3) access correct binary repository, more robustly
USER VISIBLE CHANGES
listRuntimes() and friends
(listClusters() deprecated)av, gcloud, gsutil type functions added to interface with AnVIL
and the cloudleonardo, terra, dockstore and gen3* APIsleonardo, terra, dockstore and gen3* symbols not defined; users must
create these themselves, e.g., `leonardo <-
Added a NEWS.md file to track changes to the package.