PTV-1810 fix obj input 3

[briehl]

Description of PR purpose/changes

Actually go through the code to update how object inputs get matched here.

There's a few minor details and code styling yet to do on app_util.transform_param_value, but this is ready for GHA testing / review.

The goal, as mentioned elsewhere (#3320) is to update the transform_param_value function to effectively take any form of object input and transform it appropriately. Previously, it was implicitly assumed that input values were always object names, and transforms were only done when target_type_transform was present. Now, however, inputs can be of any format, and combinations of target_type_transform are used to infer what's required.

• target_type_transform not present = object name string output
• target_type_transform = "ref" or "unresolved-ref" = ws_name/obj_name format
• target_type_transform = "resolved-ref" or "upa" (not officially supported, but should be) = upa / path format

TODO:

• make sure ref paths work as expected, when expected
• clean up some minor code duplications
• double-check comments
• add release notes

Jira Ticket / Issue

Related Jira ticket: https://kbase-jira.atlassian.net/browse/PTV-1810

• Added the Jira Ticket to the title of the PR (e.g. DATAUP-69 Adds a PR template)

Testing Instructions

• Details for how to test the PR:

• Tests pass locally and in GitHub Actions
• Changes available by spinning up a local narrative and navigating to X to see Y

Dev Checklist:

• My code follows the guidelines at https://sites.google.com/lbl.gov/trussresources/home?authuser=0
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• (JavaScript) I have run Prettier and ESLint on changed code manually or with a git precommit hook
• (Python) I have run Black and Flake8 on changed Python code manually or with a git precommit hook
• Any dependent changes have been merged and published in downstream modules

Updating Version and Release Notes (if applicable)

• Version has been bumped for each release
• Release notes have been updated for each release (and during the merge of feature branches)

[codecov]

Codecov Report

Merging #3322 (d869e99) into develop (4580595) will increase coverage by 23.63%.
Report is 17 commits behind head on develop.
The diff coverage is 89.09%.

Additional details and impacted files

@@             Coverage Diff              @@
##           develop    #3322       +/-   ##
============================================
+ Coverage     5.62%   29.25%   +23.63%     
============================================
  Files          496      496               
  Lines        50486    50512       +26     
============================================
+ Hits          2841    14779    +11938     
+ Misses       47645    35733    -11912     

Files Changed	Coverage Δ
src/biokbase/narrative/app_util.py	82.93% <89.09%> (-1.29%)	⬇️

... and 326 files with indirect coverage changes

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[ialarmedalien]

🎉

[ialarmedalien]

I don't know if it'd be marginally more readable as

if transform_type in ["ref", "unresolved-ref"]:

Probably not enough to make it worth changing.

PR still in progress

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
6 Code Smells

No Coverage information
0.0% Duplication

[briehl]

These were put in place (I think) because the mocker was switching them around to the one true mock UPA.

Switching them back to the correct UPA seems to have fixed the tests.

[briehl]

Same thing as above. The mocked upas were bleeding over into the returned test data.

[briehl]

Adjusts the mock so if a test calls get_object_info3 with an N-step reference path, like:

{"objects": [{"ref": "ws1/obj1;ws2/obj2"}]}

It returns:

{
    "infos": standard mocked object info stuff,
    "paths": [["1/1/1", "2/2/2", ... "N-1/N-1/N-1", "18836/5/1"]] (the mocked upa)
}

Really, this should get factored into a pytest fixture and take expected ins and outs, but that's a bigger project.