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Update, alphabetize AbstractEntryClient prints #180

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merged 2 commits into from
Aug 17, 2022

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aofarrel
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@aofarrel aofarrel commented Aug 15, 2022

Updates dockstore x --help output.

  • Arguments are now listed in alphabetical order
  • Previously undocumented nfl argument is now included, but only when x=workflow
  • WDL argument no longer incorrectly implies it's attached to a Docker image (seems to be a holdover from WDL tools being the norm)

Haven't run with unit tests yet hence draft. I've decided not to wrestle homebrew into installing an outdated version of jdk to get past maven-enforcer-plugin:3.0.0:enforce so I'm going to disobey what this repo asks me to do and open this PR anyway. Sorry.

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CircleCI is a docker pull timeout; if the issue my lacking of creds it may be need to be rerun by someone else.

@aofarrel aofarrel marked this pull request as ready for review August 15, 2022 20:29
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codecov bot commented Aug 15, 2022

Codecov Report

Merging #180 (7d042d7) into develop (fefc41f) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop     #180      +/-   ##
===========================================
+ Coverage    68.59%   68.60%   +0.01%     
===========================================
  Files           49       49              
  Lines         6008     6011       +3     
  Branches       791      792       +1     
===========================================
+ Hits          4121     4124       +3     
  Misses        1575     1575              
  Partials       312      312              
Flag Coverage Δ
bitbuckettests 9.89% <0.00%> (?)
confidentialtooltests 53.30% <100.00%> (+0.02%) ⬆️
confidentialworkflowtests 28.16% <0.00%> (-0.02%) ⬇️
nonconfidentialtests 32.47% <0.00%> (-0.02%) ⬇️
singularitytests 16.70% <0.00%> (-0.01%) ⬇️
unittests 8.04% <0.00%> (-0.01%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
...ckstore/client/cli/nested/AbstractEntryClient.java 74.30% <100.00%> (+0.07%) ⬆️

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I ran it and see this:

list : lists all the Workflows published by the user

nfl : returns the Nextflow Workflowdefintion for this entry
publish : publish/unpublish a Workflow in Dockstore

refresh : updates your list of Workflows stored on Dockstore or an individual Workflow

  1. Missing space before definition on the nfl line
  2. The nfl line doesn't have two blank lines around it like all the other lines do.

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sonarcloud bot commented Aug 16, 2022

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

0.0% 0.0% Coverage
0.0% 0.0% Duplication

@aofarrel aofarrel merged commit bc8ffbe into develop Aug 17, 2022
@aofarrel aofarrel deleted the feature/fix-help-args branch August 17, 2022 16:44
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3 participants