Description

Story: https://breedinginsight.atlassian.net/browse/BI-1689

There were 2 bugs causing the "Complete count" (a.k.a. finished count) to be less than the "Total count" on the jobs page:

1. The first bug was at the end of the BrAPIDAOUtil.post method where it was updating the finished count to be listResult.size(). The problem was that listResult contains all the BrAPI objects created during that call to post, but the finished count needs to account for BrAPI objects created during previous calls to post. I fixed this by using the local variable finished which is initially set to the current finished count (thus accounting for previous calls to post) and then incremented after each BrAPI call.
2. The object counts that are generated when a file is parsed, e.g. by GermplasmProcessor.getStatisticsMap, count related objects (e.g. pedigree for germplasm). These related objects are not POSTed separately to the BrAPI service, so there isn't a generic way to keep track of them, they would need to be tracked differently for each BrAPI object type. An expedient solution was to update the finished count to account for these related objects at the end of the ProcessorManager.postBrapiData method (Line 118). There is already logic to make sure the expected number of primary BrAPI objects matches the number created in BrAPIDAOUtil.post (Lines 322-324).

Checklist:

• I have performed a self-review of my own code
• I have tested my code and ensured it meets the acceptance criteria of the story
• I have tested that my code works with both the brapi-java-server and BreedBase
• I have create/modified unit tests to cover this change
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to documentation
• I have run TAF: https://github.com/Breeding-Insight/taf/actions/runs/4982646479 (2nd run succeeded)