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Graph validation test revisions #100

Merged
merged 33 commits into from
Apr 3, 2024
Merged

Graph validation test revisions #100

merged 33 commits into from
Apr 3, 2024

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RichardBruskiewich
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The major release changes relate to adapting the reasoner-validator to the new (2023-24) Translator testing infrastructure:

  • Two higher levels of indexing are added to the message catalog of the ValidationReporter: indexing by target (endpoint url) and indexing by test identifier.
  • Support for "Skipped Tests" added to the codes.yaml and code base
  • The ValidationReporter 'prefix' field converted into a 'default_target' field and accessor methods provided, with a new basic unit test
  • OpenTelemetry features in API disabled for the time being, pending future update

@RichardBruskiewich
add ValidationReporter prefix attribute accessor methods (beyond the …
88fd4fd 
…constructor)
@RichardBruskiewich
Support for "Skipped Tests" added to the codes.yaml and code base; ac…
e124d56 
…cessors for the ValidationReporter 'prefix' field added, with a basic unit test
@RichardBruskiewich
Tweaked Markdown docs for 'skipped' category
994b65b
@RichardBruskiewich
Cleaned up some loose ends relating to the new 'skipped' category of …
159ce4f 
…messages; added a unit test to suit
@RichardBruskiewich
comment tweak
4daddfb
@RichardBruskiewich
Starting design refactor into two higher levels of indexing added to …
55ab612 
…the message catalog of the **ValidationReporter**
@RichardBruskiewich
Another incomplete iteration of refactoring message structure to incl…
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…ude test and target level indexing
@RichardBruskiewich
interim iteration (with deliberate syntax error... )
6a9f5ac
@RichardBruskiewich
Refactored 'add_messages' to consumer a full "MESSAGES_BY_TARGET" blo…
1602eae 
…b of messages, indexed by target and test, ...not just a single core info.. etc. block
@RichardBruskiewich
First quick attempt to fix the report dump to take new target/test in…
7eec91a 
…dexing into account.
@RichardBruskiewich
CHANGELOG updated with more details of new release
9910dcc
@RichardBruskiewich
poetry update bumping up package release to 4.0.0
0aa8f55
@RichardBruskiewich
First iteration to repair unit tests to reflect release 4.0.0 code re…
b5f9a5e 
…visions
@RichardBruskiewich
Iterative debugging of code, especially in 'add_messages()
b5997e8
@RichardBruskiewich
apply 'default_test' and 'default_target' more uniformly across all V…
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…alidationReporter (sub)classes
@RichardBruskiewich
Cleaned up report dump
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@RichardBruskiewich
Update default biolink to 4.1.4 (earlier versions now problematic in …
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…parsing - something changed in tab parsing...)
@RichardBruskiewich
Remove target string from report header (rather, embed 'target' insid…
0e195ff 
…e the report)
@RichardBruskiewich
Another iteration repairing unit tests (and fixing associated code)
adb9762
@RichardBruskiewich
Substantial implementation (untested) of get_all_messages_of_type() t…
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…o aggregate all messages of a given type from all test and target contexts of a ValidationReporter.
@RichardBruskiewich
Roughing in unit tests relating to test_get_all_messages_of_type() an…
2a675e0 
…d supporting functions
@RichardBruskiewich
Elaborating unit tests for various message component 'merge' methods;…
a28e5eb 
… fixing code (if and as necessary) along the way
@RichardBruskiewich
Troubleshooting the "test_validation_report.test_messages" unit test
ee874e5
@RichardBruskiewich
ditto
21d69bb
@RichardBruskiewich
ValidationReporter dump() fixed and cleaned up a bit; all unit tests …
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…now pass?
@RichardBruskiewich
testing the api and docker (compose) implementation; updating docs sl…
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…ightly, to reflect the latest changes
@RichardBruskiewich
Adding in 1.5-beta as a TRAPI release - however, this breaks a number…
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… of TRAPI related tests, so we need to put this on a development branch for now
@RichardBruskiewich
Remove TRAPI 1.5 references in this branch - leaving them on another …
6e7a7c6 
…branch; unit tests all pass now
@RichardBruskiewich
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RichardBruskiewich commented Mar 27, 2024 •
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Hi all, the new failing checks don't have much to do with the PR itself but rather, with my clumsy updating of the PR branch to see the latest TRAPI. I'll try to roll back these changes to remove the CI errors....Fixed!

@RichardBruskiewich RichardBruskiewich merged commit 114e5de into master Apr 3, 2024
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@RichardBruskiewich RichardBruskiewich deleted the graph-validation-test-revisions branch April 3, 2024 01:01
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@kennethmorton kennethmorton Awaiting requested review from kennethmorton

@sierra-moxon sierra-moxon Awaiting requested review from sierra-moxon

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