add metadata parsing to batch sample import service

[JeffreyThiessen]

What does this PR do and why?

Describe in detail what your merge request does and why.

• additional headers on the spreadsheet for sample imports will be used as metadata.

Screenshots or screen recordings

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How to set up and validate locally

Numbered steps to set up and validate the change are strongly suggested.

1. seed your db
2. Start irida next with command line enabled
3. Sign into User3
4. navigate to http://localhost:3000/borrelia/borrelia-burgdorferi/outbreak-2024/-/samples
5. in the file test/fixtures/files/batch_sample_import_with_metadata_valid.csv, edit the project_puid values to match the project we are importing to.
6. run the following in the terminal to import new samples.

u = User.all[3];n = Project.all[0].namespace;

# replace this path with the path to your irida next git directory
filepath = '/home/CSCScience.ca/jthiessen/git/irida-next-core/test/fixtures/files/batch_sample_import_with_metadata_valid.csv'

blob = ActiveStorage::Blob.create_and_upload!(io: File.open(filepath), filename: 'batch_sample_import_with_metadata_valid.csv')

s = Samples::BatchFileImportService.new(n,u, blob.id, {sample_name_column: 'sample_name', project_puid_column: 'project_puid', sample_description_column: "description"} )

s.execute

7. You should see 2 new samples added to the project you are viewing, each with 2 metadata fields

PR acceptance checklist

This checklist encourages us to confirm any changes have been analyzed to reduce risks in quality, performance, reliability, security, and maintainability.

• I have evaluated the PR acceptance checklist for this PR.

[ksierks]

Worked as described. Also tried importing an existing sample & missing project_puid.

[deepsidhu85]

This is looking good but we need to update the activities being attached upon sample import with metadata. Currently it creates an activity for the sample creation and for the update of the sample metadata. We will probably want to pass in a param into the samples create service such as include_activity which we can set to false (the metadata update service already has this setup) and then in the batch sample import service we can create a single activity for the batch import of samples or samples with metadata.

[github-actions]

Code Metrics Report

Coverage	Test Execution Time
93.1%	11m17s

Code coverage of files in pull request scope (98.5%)

Files	Coverage
app/services/samples/batch_file_import_service.rb	98.5%

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Reported by octocov