1. AnVIL
  2. NEWS.md
Raw Blame Patch Log History
# AnVIL 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) # AnVIL 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 # AnVIL 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> # AnVIL 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. # AnVIL 1.6.7 / 1.7.13 BUG FIXES - Correct gcloud_project() when user environment variable set. https://github.com/Bioconductor/AnVIL/pull/52 # AnVIL 1.6.6 BUG FIXES - Correct gsutil_pipe() argument mis-match, see https://support.bioconductor.org/p/9141780/ # AnVIL 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. # AnVIL 1.4.1 BUG FIXES - Only install binary packages on Bioconductor docker images # AnVIL 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. # AnVIL 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. # AnVIL 1.0.x 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) # AnVIL 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 # AnVIL 0.0.20 - Support untagged swagger # AnVIL 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.