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AnVIL 1.18.0

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.

AnVIL 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)

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. #79

  • (v 1.13.3) Use 'op' when .avworkflow_response() calls avstop_for_status(). #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. #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. #75

BUG FIXES

  • (v 1.11.1) consistently URLencode workspace and workflow name, to allow for spaces. #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. #66

  • (v 1.9.11 / v 1.8.7) avoid changing status of 'Done' workflows to 'Aborted' #64

  • (v 1.9.11 / v 1.8.7) allow 'NULL' for entity arguments of avworkflow_run() #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. #52

AnVIL 1.6.6

BUG FIXES

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.