DOCK-2170: Fix tools and DAG generation problem

[svonworl]

Description
This PR fixes some bugs in the CWL "tool list" and DAG generation code.

While testing the previous PR (#5063), Charles found a workflow for which the list of tools and DAG were generated incorrectly:
https://qa.dockstore.org/workflows/github.com/sevenbridges-openworkflows/Broad-Best-Practice-Data-pre-processing-CWL1.0-workflow-GATK-4.1.0.0/GATK_4_1_0_0_data_pre_processing_workflow:master?tab=info

The problem was that the workflow ID included slashes, which messed up the workflow step ID and dependency parsing algorithms. This PR changes the algorithms to be more robust.

Yes, that one function takes a ridiculous number of arguments, and now, it's even ridiculous-er, because I added an argument.
Alas, there's not an obviously-better alternative, unless we rewrite large chunks of the code (which we might if we ever implement multi-level DAG generation).

Review Instructions
Clone the repo of the above-mentioned workflow, register the cloned workflow, and confirm that the resulting list of tools and DAG are equivalent to those referenced by the original link.

Issue
https://ucsc-cgl.atlassian.net/browse/DOCK-2170
#4906

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[codecov]

Codecov Report

Base: 73.04% // Head: 73.00% // Decreases project coverage by -0.04% ⚠️

Coverage data is based on head (311d7d8) compared to base (4db3e99).
Patch coverage: 85.71% of modified lines in pull request are covered.

❗ Current head 311d7d8 differs from pull request most recent head 190ef62. Consider uploading reports for the commit 190ef62 to get more accurate results

Additional details and impacted files

@@              Coverage Diff              @@
##             develop    #5232      +/-   ##
=============================================
- Coverage      73.04%   73.00%   -0.05%     
+ Complexity      4358     4350       -8     
=============================================
  Files            287      287              
  Lines          16707    16704       -3     
  Branches        1835     1836       +1     
=============================================
- Hits           12204    12194      -10     
- Misses          3638     3642       +4     
- Partials         865      868       +3     

Flag	Coverage Δ
bitbuckettests	28.28% <0.00%> (+<0.01%)	⬆️
integrationtests	57.70% <64.28%> (-0.02%)	⬇️
languageparsingtests	10.87% <0.00%> (+<0.01%)	⬆️
toolintegrationtests	30.42% <0.00%> (-0.02%)	⬇️
unit-tests_and_non-confidential-tests	26.35% <50.00%> (-0.04%)	⬇️
workflowintegrationtests	40.40% <82.14%> (-0.06%)	⬇️

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

Impacted Files	Coverage Δ
.../io/dockstore/webservice/languages/CWLHandler.java	62.45% <85.71%> (-0.61%)	⬇️
...re/webservice/helpers/DockerRegistryAPIHelper.java	69.48% <0.00%> (-2.60%)	⬇️
...store/webservice/resources/DockerRepoResource.java	77.01% <0.00%> (-0.46%)	⬇️
.../java/io/openapi/api/impl/ToolsApiServiceImpl.java	70.28% <0.00%> (-0.45%)	⬇️
...ckstore/webservice/resources/WorkflowResource.java	71.07% <0.00%> (ø)
...main/java/io/swagger/api/impl/ToolsImplCommon.java	86.58% <0.00%> (+0.81%)	⬆️
...bservice/resources/AliasableResourceInterface.java	96.87% <0.00%> (+3.12%)	⬆️

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[denis-yuen]

Alas, there's not an obviously-better alternative, unless we rewrite large chunks of the code (which we might if we ever implement multi-level DAG generation).

Can you link to this, I think I'd like to read up on this and wonder if its a reference to a previous ticket/discussion

[svonworl]

Alas, there's not an obviously-better alternative, unless we rewrite large chunks of the code (which we might if we ever implement multi-level DAG generation).

Can you link to this, I think I'd like to read up on this and wonder if its a reference to a previous ticket/discussion

I would add a link, but I don't have one. :) The "not an obviously-better alternative" part is my software-engineering opinion, "multi-level DAG" is an idea for a DAG that renders the steps in the subworkflows (rather than represent each subworkflow as a single node, as we have historically).

[denis-yuen]

multi-level DAG generation

was mainly curious what this meant, thanks!

[coverbeck]

It would be nice to have a test for this so it doesn't break in the future.

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
2 Code Smells

88.1% Coverage
0.0% Duplication