DOCK-2323: Log source and destination paths for file provisioning #252

hyunnaye · Aug 4, 2023

Description
This PR allows file provisioning to display source and destination paths.

Review Instructions

Remove ~/.dockstore/libraries/
Run dockstore workflow launch --entry github.com/dockstore-testing/Metaphlan-WDL:master and see cromwell download with the source and destination path logged like below.

> dockstore workflow launch --entry github.com/dockstore-testing/Metaphlan-WDL:master 
WARNING: Docker is not running. If this workflow uses Docker, it will fail.
Saving https://github.com/broadinstitute/cromwell/releases/download/84/cromwell-84.jar to /home/nhyun/.dockstore/libraries/cromwell-84.jar
[##########################                        ] 53%

Issue
https://ucsc-cgl.atlassian.net/browse/DOCK-2323

Security
If there are any concerns that require extra attention from the security team, highlight them here.

Please make sure that you've checked the following before submitting your pull request. Thanks!

Check that you pass the basic style checks and unit tests by running ./mvnw clean install
If this PR is for a user-facing feature, create and link a documentation ticket for this feature (usually in the same milestone as the linked issue). Style points if you create a documentation PR directly and link that instead.

codecov · Aug 4, 2023

Codecov Report

Patch coverage: 66.66% and project coverage change: +1.66% 🎉

Comparison is base (ad4a2ea) 68.71% compared to head (7184278) 70.37%.

Additional details and impacted files

@@              Coverage Diff              @@
##             develop     #252      +/-   ##
=============================================
+ Coverage      68.71%   70.37%   +1.66%     
- Complexity      1010     1048      +38     
=============================================
  Files             47       47              
  Lines           6067     6070       +3     
  Branches         799      799              
=============================================
+ Hits            4169     4272     +103     
+ Misses          1556     1455     -101     
- Partials         342      343       +1

Flag	Coverage Δ
bitbuckettests	`9.83% <0.00%> (-0.01%)`	⬇️
confidentialtooltests	`55.66% <66.66%> (+3.99%)`	⬆️
confidentialworkflowtests	`30.52% <66.66%> (+0.01%)`	⬆️
nonconfidentialtests	`32.28% <66.66%> (+0.01%)`	⬆️
singularitytests	`16.58% <66.66%> (+0.02%)`	⬆️
unittests	`8.35% <66.66%> (+0.02%)`	⬆️