Description

Story: https://breedinginsight.atlassian.net/browse/BI-1900

We parse Excel and CSV files into tablesaw Tables. For Excel files, we use Apache POI to parse, do some validation, and then build a Table. For CSV files, we were using tablesaw to read the CSV into a Table directly. While tablesaw does return descriptive error messages, it doesn't give us as fine-grained control over parsing and exception handling as we want. To solve this, I made changes to FileUtil::parseTableFromCsv to

• read the InputStream into a String,
• parse the string with apache.commons.CSVParser and do validation, which enables us to return descriptive error messages that we control to the user, and
• finally build a Table from the String.

Testing

Note: this only applies to Germplasm and Experiment & Observation uploads, Ontology uses a different code path (for now).

New feature:

Try uploading Excel and CSV files with duplicate column names, make sure the error message shown to the user is descriptive.

Regression

Try uploading Excel and CSV files with required column names missing, any other data issues you can think of, and make sure the error message shown to the user is descriptive.

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/6422962193