[BI-768] - Pedigree Importer

[ctucker3]

This will work with the brapi server, but needs to create a trial and study object before it will work with breedbase. There are some breedbase endpoints that need to be fixed before this will work with breedbase, see this card:

https://breedinginsight.atlassian.net/secure/RapidBoard.jspa?rapidView=1&projectKey=BI&modal=detail&selectedIssue=BI-782

This is a large PR, so it might not be possible to look through all of the code. Maybe look through it and get an understanding of what the flow is and if there is anything glaringly obvious?

There is a list of TODOs for improvements that I identified as I was working on it. You can see these in the PedigreeImportService.java file.

The class names could be cleaned up a little better to be more distinct to better represent the stages in the importer. I was planning on doing this after I got the pedigree importer fully working.

TODOS - Cards to create:

• All germplasm not being saved to brapi server on save. See if this is an issue with brapi server, or with the importer.
• API Documentation
• Tests
• Add enum drop down option for fields. (Ex. cross type in (BIPARENTAL, SELF, etc.)
• Make an @ImportIgnore annotation to be able to ignore certain fields in different imports
• Get import to work with Breedbase
• Check pagination result in search and grab all results if all weren't returned.
• Allow generic post method in BrAPIDAO to accept post size and use default if none specified.
• Handle date times in importer
• Implement search crosses in brapi systems (brapi java server and breedbase). Change pedigree importer to use search crosses.
• Allow use to choose whether to throw error if relationship isn't found
• Allow user to specify header row index
• Allow user to specify which excel sheet to use
• Add validations (missing mapping, blank value) and row level validations

[ctucker3]

A bunch of comments on renaming to try and make class purpose more clear from the name. There are a few different groups of classes:

1. Micronaut classes (controller, services, dao) -> Like we usually do.
2. Import Configurations (generates import configuration and provides the class to map to)
3. Mapping Classes (structs and managers to handle the mapping from file to import configs)
4. Import Classes (classes that work with import configurations to POST the data)

[nickpalladino]

What's the plan for tests and/or docs? I know I asked in an earlier iteration and it was being pushed.

[ctucker3]

What's the plan for tests and/or docs? I know I asked in an earlier iteration and it was being pushed.

I think a separate card for tests and a separate card for docs. I think docs should come first. I wanted to get everything approved before spending time on tests/docs since things might undergo big changes before approval.