Changes in version 1.16.0
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).
- Update namespace in vignette and examples (@kozo2, #54)
Changes in version 1.14.0
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).
Changes in version 1.12.0
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
- (v 1.11.1) consistently URLencode workspace and workflow name, to
allow for spaces. https://github.com/Bioconductor/AnVIL/issues/67
Changes in version 1.10.0
NEW 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
Changes in version 1.8.0
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.
Changes in version 1.7.13
BUG FIXES
- Correct gcloud_project() when user environment variable set.
https://github.com/Bioconductor/AnVIL/pull/52
Changes in version 1.6.6
BUG FIXES
- Correct gsutil_pipe() argument mis-match, see
https://support.bioconductor.org/p/9141780/
Changes in version 1.6.0
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.
Changes in version 1.4.1
BUG FIXES
- Only install binary packages on Bioconductor docker images
Changes in version 1.4.0
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.
Changes in version 1.2.0
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.
Changes in version 1.0
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
- (v 1.0.2) support updated Leonardo listRuntimes() and friends
(listClusters() deprecated)
Changes in version 1.0.0
- AnVIL is _finally on Bioconductor!
- Support OpenAPI Specification version 2 (aka Swagger 2.0)
- av, gcloud, gsutil type functions added to interface with AnVIL and
the cloud
- Support leonardo, terra, dockstore and gen3* APIs
Changes in version 0.0.20
- Support untagged swagger
Changes in version 0.0.17
- leonardo, 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.