Materialize mongo alldocs collection

[dwinston]

Description

Fixes #543

Type of change

Please delete options that are not relevant.

• New feature (non-breaking change which adds functionality)
• This change requires a documentation update

How Has This Been Tested?

• Tested manually in local instance of dagster
  

• added test_materialize_all_docs()

Configuration Details: none

Checklist:

• 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)

[PeopleMakeCulture]

TODO:

• standardize alldocs vs all_docs usage
• update documentation in notebook
• consider refactoring notebook to use op.py code and utils

[sujaypatil96]

It looks like there are a couple of merge conflicts that need to be resolved on a couple of files in this PR, would you like to resolve them @PeopleMakeCulture, or should I do it? they seem fairly trivial so I'm happy to do it as well, do let me know.

[PeopleMakeCulture]

It looks like there are a couple of merge conflicts that need to be resolved on a couple of files in this PR, would you like to resolve them @PeopleMakeCulture, or should I do it? they seem fairly trivial so I'm happy to do it as well, do let me know.

@sujaypatil96 Hey sorry for the delayed response. I'm still catching up from covid last week. Could you go ahead and resolve the conflicts? Happy to take a look if there's anything confusing

[PeopleMakeCulture]

Dependency versions updated via: #585