Feature/2309/workflow entryname hosted and apps

[Richard-Hansen]

Ticket: https://ucsc-cgl.atlassian.net/browse/DOCK-633

Fixing previous issues regarding handling HOSTED tools and workflows and DOCKSTORE_YML workflows.
Added integration tests.

Changes were very small, hiding whitespace will help.

[codecov]

Codecov Report

Base: 69.57% // Head: 69.57% // Decreases project coverage by -0.01% ⚠️

Coverage data is based on head (e7e6b6f) compared to base (0633024).
Patch coverage: 80.85% of modified lines in pull request are covered.

Additional details and impacted files

@@              Coverage Diff              @@
##             develop      #52      +/-   ##
=============================================
- Coverage      69.57%   69.57%   -0.01%     
- Complexity      1049     1065      +16     
=============================================
  Files             47       47              
  Lines           6041     6050       +9     
  Branches         792      796       +4     
=============================================
+ Hits            4203     4209       +6     
  Misses          1510     1510              
- Partials         328      331       +3     

Flag	Coverage Δ
bitbuckettests	9.93% <4.25%> (+0.01%)	⬆️
confidentialtooltests	54.79% <53.19%> (+0.26%)	⬆️
confidentialworkflowtests	27.76% <34.04%> (-0.06%)	⬇️
nonconfidentialtests	32.41% <4.25%> (-0.05%)	⬇️
singularitytests	16.69% <4.25%> (+<0.01%)	⬆️
unittests	8.38% <4.25%> (+0.02%)	⬆️

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

Impacted Files	Coverage Δ
.../java/io/dockstore/client/cli/ArgumentUtility.java	84.52% <ø> (ø)
...io/dockstore/client/cli/nested/WorkflowClient.java	70.93% <78.94%> (-0.39%)	⬇️
...ava/io/dockstore/client/cli/nested/ToolClient.java	72.64% <82.14%> (+0.01%)	⬆️
...in/java/io/github/collaboratory/wdl/WDLClient.java	79.20% <0.00%> (-1.00%)	⬇️
.../src/main/java/io/dockstore/client/cli/Client.java	50.00% <0.00%> (-0.25%)	⬇️
...ckstore/client/cli/nested/AbstractEntryClient.java	74.85% <0.00%> (+0.39%)	⬆️

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[lgtm-com]

This pull request introduces 2 alerts and fixes 2 when merging ba43a63 into 1f9fa14 - view on LGTM.com

new alerts:

• 2 for Dereferenced variable may be null

fixed alerts:

• 2 for Dereferenced variable may be null

[lgtm-com]

This pull request introduces 2 alerts and fixes 2 when merging 016d17a into 1f9fa14 - view on LGTM.com

new alerts:

• 2 for Dereferenced variable may be null

fixed alerts:

• 2 for Dereferenced variable may be null

[Richard-Hansen]

Looks like there are some unexpected TravisCI errors, I'll remove reviewers until after fixing them.

Sorry for the email clutter.

[lgtm-com]

This pull request fixes 2 alerts when merging bdf225d into c92896b - view on LGTM.com

fixed alerts:

• 2 for Dereferenced variable may be null

[sonarcloud]

SonarCloud Quality Gate failed.   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
11 Code Smells

No Coverage information
2.5% Duplication

[sonarcloud]

SonarCloud Quality Gate failed.   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
1 Code Smell

5.6% Coverage
2.5% Duplication

[lgtm-com]

This pull request fixes 2 alerts when merging 33cce74 into 64911f5 - view on LGTM.com

fixed alerts:

• 2 for Dereferenced variable may be null

[sonarcloud]

SonarCloud Quality Gate failed.   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
1 Code Smell

77.4% Coverage
0.0% Duplication

[denis-yuen]

FYI, this was mostly about trying out the various changes to the build, webservice (cache, rate limit behaviour)