aws gateway in vhdcprod

What's Changed

• fix change pvc from test pvc to prod pvc by @UchicagoZchen138 in #67

Full Changelog: 1.2.3...1.2.4

aws gateway

What's Changed

• feat adding linter by @UchicagoZchen138 in #60
• fix networkpolicy issues with task and engine pods by @UchicagoZchen138 in #62
• [PXP-8989] feat: update Docker image to Go 1.17 by @m0nhawk in #61
• Feat/integrate aws gateway and indexd commonsfiles by @UchicagoZchen138 in #65
• Feat - get metadata for commons files by @kmhernan in #66

Full Changelog: 1.2.2...1.2.3

Workflow enhancements

What's Changed

• docs(readme): update mariner readme by @cterrazas2 in #48
• adding additional documentation for s3 sidecar by @UchicagoZchen138 in #49
• Feat/workflow db by @UchicagoZchen138 in #53
• adding travis.yml by @UchicagoZchen138 in #54
• fix initworkdir requirements by @UchicagoZchen138 in #55
• docs(readme): Remove redundant readme info by @UchicagoZchen138 in #57
• Feat/pre genesis wf by @UchicagoZchen138 in #59

Bug Fixes

• Initial work directory will now be initiated in the right place instead of root directory
• Numerous small changes related to making initial work directory more robust such as evaluation of expression for file and directories

Enhancements

• Automated unit tests are ran automatically as part of ci/cd
• Pre genesis workflow runs successfully

Full Changelog: 1.2.1...1.2.2

Workflow Refresh Token

Release Notes

For: uc-cdis/mariner

Notes since tag: 1.2.0

Notes to tag/commit: 1.2.1

Generated: 2021-04-06

Bug Fixes

• Checks for a refresh token before running a workflow via Workspace Token Service, fetching a new refresh token if expired.
  This prevents a workflow from failing and not fetching commons data if user never opens /workspace
  within the last 30 days. (#46)

ExpressionTools for Mariner

Release Notes

For: uc-cdis/mariner

Notes since tag: 1.1.1

Notes to tag/commit: 1.2.0

Generated: 2021-02-23

New Features

• Brought back ExpressionTools with EBS, this means ExpressionTools for any
  given workflow is now executed in its own task pod. Note, EBS was
  implemented in Mariner release
  1.1.0 (#45)
• Update Mariner codebase to use go modules (#44)
• Pin dependencies (#44)
• Remove vendor/ folder (#44)
• Update Docker to 1.15-buster (#44)

Deployment Changes

• ExpressionTools now dispatches as a K8s job outside of the MarinerEngine
  (#45)

Bug Fixes

• Change base image to our hosted base image (#42)

Expect "bearer" in the auth header

Release Notes

For: uc-cdis/mariner

Notes since tag: 1.1.0

Notes to tag/commit: 1.1.1

Generated: 2020-11-12

Improvements

• Expect "bearer" in the authorization header, and strip it to get the JWT
  (#41)

No Fuse

Retire Goofys (FUSE tool) in favor of EBS and S3 file transfer for read/write to the user-data-space/engine-workspace.

Known/Intended Immediate Use-Cases:

1. COVID-19 epi model run on all USA counties for the Chicagoland Pandemic Response Commons
2. Pilot GWAS Workflow for the VA

NOTE: ExpressionTools are not supported in this release - support for ExpressionTools will be re-implemented in a future release.

Deactivate Intermediate File Cleanup

Intermediate file cleanup routine is busted (deletes files it shouldn't);
In this release, Mariner doesn't delete / cleanup any intermediate files.

VA GWAS Pilot

Big race conditions fixed, improved case and error handling.

Done Flag Disconnect Patch

Fix error done flag disconnects as bytes are being written to it