NEWS.md

In Bioconductor/AnVIL: Bioconductor on the AnVIL compute environment

AnVIL 1.16.0

USER VISIBLE CHANGES

• (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

• (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)

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)

• (v 1.13.11) Added workflowId to avworkflow_files() and avworkflow_localize() to allow for filtering by workflow (@yubocheng, #90).

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.

Bioconductor/AnVIL documentation built on April 12, 2024, 6:41 p.m.