Overhaul of filter transformers, mappers and response fields

[ml-evs]

This PR lays the groundwork for dealing with some outstanding issues:

1. Returning None for "unknown unknown" properties (e.g. _other_implementation_band_gap) (closes Missing optional fields are not returned as null when requested with response_fields #516) and the raising of errors for "known unknown" properties in filters (e.g. unprefixed_optimade_field) (closes Respect responses for unknown properties #263).
2. Abstraction of the aliasing code so that "Quantities" can be defined independent of the backend (closes Move aliasing code to base transformer #743).
3. Definition of provider fields via pydantic models so that they can be filtered appropriately
4. MongoDB $size: 1 queries match non-existent fields (closes mongomock $size queries match all non-array fields for {$size: 1}, even nulls #807) Removed, as this is actually a mongomock bug

It does so by:

• Moving aliasing code from individual transformers out to the base transformer, by making use of the Quantity classes defined for elasticsearch.
• Adding a ENTRY_RESOURCE_ATTRIBUTE_CLASS class attribute to the mappers, such that model schemas can be accessed.

Still to-do:

• Add passthrough for "other provider" fields so that querying for _exmpl2_band_gap does not fail for provider _exmpl1_.
• Emit warning if provider prefix is unknown and allow through if provider is registered with OPTIMADE
  • This is done via the providers submodule (rather than the get_providers) request. We could consider making this a configuration option instead.
• Handle unknown response_fields
  • Return any requested, missing field as None if present in response_fields
  • Raise an error if an unknown, unprefixed field is requested in response_fields (e.g. fractional_coordinates)
  • Emit a warning if a provider-specific field is requested that does not exist (e.g. _exmpl_test)
  • Passthrough other-provider-specific fields as if they were missing from the entry (i.e. replace them with null)

[codecov]

Codecov Report

Merging #797 (ec8318f) into master (0f11919) will decrease coverage by 0.00%.
The diff coverage is 96.52%.

❗ Current head ec8318f differs from pull request most recent head eb69f62. Consider uploading reports for the commit eb69f62 to get more accurate results

@@            Coverage Diff             @@
##           master     #797      +/-   ##
==========================================
- Coverage   92.68%   92.68%   -0.01%     
==========================================
  Files          68       68              
  Lines        3677     3759      +82     
==========================================
+ Hits         3408     3484      +76     
- Misses        269      275       +6     

Flag	Coverage Δ
project	92.68% <96.52%> (-0.01%)	⬇️
validator	92.68% <96.52%> (-0.01%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
optimade/validator/validator.py	82.49% <93.75%> (+0.34%)	⬆️
optimade/filtertransformers/elasticsearch.py	84.57% <94.59%> (+0.79%)	⬆️
optimade/server/mappers/entries.py	97.11% <95.34%> (-1.42%)	⬇️
optimade/filtertransformers/mongo.py	97.00% <96.42%> (-0.60%)	⬇️
optimade/filtertransformers/base_transformer.py	97.45% <96.82%> (-1.28%)	⬇️
optimade/filtertransformers/__init__.py	100.00% <100.00%> (ø)
optimade/server/entry_collections/elasticsearch.py	97.40% <100.00%> (-0.52%)	⬇️
...made/server/entry_collections/entry_collections.py	97.63% <100.00%> (+0.22%)	⬆️
optimade/server/mappers/links.py	100.00% <100.00%> (ø)
optimade/server/mappers/references.py	100.00% <100.00%> (ø)
... and 6 more

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[ml-evs]

• Handle unknown response_fields
  * Return any requested, missing field as None if present in response_fields
  * Raise an error if an unknown, unprefixed field is requested in response_fields (e.g. fractional_coordinates)
  * Emit a warning if a provider-specific field is requested that does not exist (e.g. _exmpl_test)
  * Passthrough other-provider-specific fields as if they were missing from the entry (i.e. replace them with null)

@CasperWA: this might be an over-interpretation of the spec. Looks like other implementations just return null for any requested response field, but above I have described (and implemented) something that more closely follows the recommendations on filters.

[markus1978]

I can only provide some more superficial comments. I think the biggest issues are

• the increased number of terms for the same thing (quantity, property, attribute, field). I know I contributed to that.
• I feel that the quantities related functionality belongs into the ResourceMapper classes.

[ml-evs]

Hi @JPBergsma, I have rebased your final suggestions into one commit eb69f62. Thanks again for the thorough review, it would be great to merge this with enough time to prepare tutorials for the workshop!

[JPBergsma]

I think you have handled all my comments, so I think you can merge it with the main branch.