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@KimberleyChong
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@KimberleyChong KimberleyChong commented Feb 23, 2023

Description
Spin off ticket from DOCK-2300 (UI Relying on Beta TRS) this ticket switches from using TRS 2.0.0-beta.2 API to TRS 2.0.0 in the CLI. Appears to only be used in the serverMetadata() function, like in the UI, switched from using the /api/ga4gh/v2/metadata call to /ga4gh/trs/v2/service-info.

Output from --server-metadata before:

{
  "apiVersion": "2.0.0",
  "country": "CAN",
  "friendlyName": "Dockstore",
  "version": "1.13.1"
}
Dockstore server: https://dockstore.org/api

Output from --server-metadata after:

{
  "contactUrl": "https://discuss.dockstore.org/t/opening-helpdesk-tickets/1506",
  "createdAt": "Jul 1, 2020, 8:00:00 PM",
  "description": "Dockstore is an implementation of the GA4GH Tool Registry API which is a standard for listing and describing available tools (both stand-alone, Docker-based tools as well as workflows in CWL, WDL, Nextflow, or Galaxy)",
  "documentationUrl": "https://docs.dockstore.org",
  "environment": "prod",
  "id": "1",
  "name": "Dockstore",
  "organization": {
    "name": "Dockstore",
    "url": "https://dockstore.org"
  },
  "type": {
    "artifact": "TRS",
    "group": "org.ga4gh",
    "version": "2.0.1"
  },
  "updatedAt": "Feb 3, 2023, 3:20:42 PM",
  "version": "1.13.1"
}
Dockstore server: https://dockstore.org/api

Review Instructions

Issue
SEAB-5206

Security
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@sonarqubecloud
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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

100.0% 100.0% Coverage
0.0% 0.0% Duplication

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codecov bot commented Feb 23, 2023

Codecov Report

Base: 69.46% // Head: 69.59% // Increases project coverage by +0.12% 🎉

Coverage data is based on head (d0e705f) compared to base (8e49041).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files
@@              Coverage Diff              @@
##             develop     #226      +/-   ##
=============================================
+ Coverage      69.46%   69.59%   +0.12%     
- Complexity      1043     1061      +18     
=============================================
  Files             47       47              
  Lines           6062     6061       -1     
  Branches         801      801              
=============================================
+ Hits            4211     4218       +7     
  Misses          1511     1511              
+ Partials         340      332       -8     
Flag Coverage Δ
bitbuckettests 9.89% <0.00%> (-0.02%) ⬇️
confidentialtooltests 54.62% <100.00%> (+0.22%) ⬆️
confidentialworkflowtests 27.80% <0.00%> (+0.10%) ⬆️
nonconfidentialtests 32.51% <0.00%> (+0.02%) ⬆️
singularitytests 16.64% <0.00%> (-0.02%) ⬇️
unittests 8.34% <0.00%> (-0.02%) ⬇️

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

Impacted Files Coverage Δ
.../src/main/java/io/dockstore/client/cli/Client.java 49.87% <100.00%> (+0.12%) ⬆️
...ava/io/dockstore/client/cli/nested/ToolClient.java 72.25% <0.00%> (-0.40%) ⬇️
...in/java/io/github/collaboratory/cwl/CWLClient.java 80.24% <0.00%> (-0.18%) ⬇️
...ckstore/client/cli/nested/AbstractEntryClient.java 74.75% <0.00%> (+0.29%) ⬆️
...ockstore/client/cli/nested/BaseLanguageClient.java 58.43% <0.00%> (+0.60%) ⬆️
...io/dockstore/client/cli/nested/WorkflowClient.java 71.53% <0.00%> (+0.75%) ⬆️
...in/java/io/github/collaboratory/wdl/WDLClient.java 78.76% <0.00%> (+0.88%) ⬆️
.../collaboratory/cwl/cwlrunner/CWLRunnerFactory.java 53.33% <0.00%> (+6.66%) ⬆️

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@KimberleyChong KimberleyChong self-assigned this Feb 23, 2023
@KimberleyChong KimberleyChong marked this pull request as ready for review February 23, 2023 20:46
try {
final Metadata metadata = ga4ghApi.metadataGet();
final TRSService serviceinfo = ga4ghv20Api.getServiceInfo();
final Gson gson = io.cwl.avro.CWL.getTypeSafeCWLToolDocument();
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This is an interesting way to do it, getting a CWL-specific Gson for non-CWL, but was like that and no need to change. :)

@KimberleyChong KimberleyChong merged commit 600049a into develop Feb 24, 2023
@KimberleyChong KimberleyChong deleted the SEAB-5206/beta-trs-api branch February 24, 2023 21:25
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