Add mapping for multiple environments

[marySalvi]

Description

Please include a summary of the changes and the related issue. Please also include relevant motivation and context. List any dependencies that are required for this change.

Replace # (issue) below with a reference to the issue that this PR addresses, of the form #\d+. If merging this PR should close the issue, use Fixes or Closes. Then delete this paragraph.

Fixes # 1367

Type of change

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• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update I'm not sure

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration, if it is not simply make up-test && make test-run.

• Adjusted test fakes to represent multiple environments

Configuration Details: none

Definition of Done (DoD) Checklist:

A simple checklist of necessary activities that add verifiable/demonstrable value to the product by asserting the quality of a feature, not the functionality of that feature; the latter should be stated as acceptance criteria in the issue this PR closes. Not all activities in the PR template will be applicable to each feature since the definition of done is intended to be a comprehensive checklist. Consciously decide the applicability of value-added activities on a feature-by-feature basis.

• My code follows the style guidelines of this project (have you run black nmdc_runtime/?)
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation (in docs/ and in https://github.com/microbiomedata/NMDC_documentation/?)
• I have added tests that prove my fix is effective or that my feature works, incl. considering downstream usage (e.g. https://github.com/microbiomedata/notebook_hackathons) if applicable.
• New and existing unit and functional tests pass locally with my changes (make up-test && make test-run)

[mslarae13]

@marySalvi status update?

[marySalvi]

@mslarae13 We are meeting tomorrow to debug and get a working solution. I will post an updated ETA as soon as possible.

[dwinston]

issue here related to microbiomedata/submission-schema#186

[pkalita-lbl]

I think a lot of this is on the right track, but it seems to be missing a few pieces related to how the JGI and EMSL tabs are handled in conjunction with the multiple environments. If you want to go over this in more detail together just let me know.

[pkalita-lbl]

@marySalvi Sorry I sort of led you astray a bit with my initial feedback. After looking at this again the real key is not adding the analysis templates (the EMSL and JGI ones) into the enum, but rather to skip setting the env_package slot while traversing the keys containing that data. Then while processing an individual sample's data, the logic is to find the first (in reality only) object where env_package is set to identify the environmental data.

As to not have a bunch more back and forth on this I went ahead and expanded the test data to capture this use case and updated the translator logic.