Model querying, loading local ontology in memory

[ssssarah]

DKE-1239

• Added sparql method to Model archetype.
• Added get_context_prefix_vocab abstract method to Model archetype: the reason for this is that when rewriting sparql queries, you need to use the context. However, BlueBrainNexus (the store) cannot simply just use a Context object, because it is merging the metadata context's document with the data context's document, and keeping data context's vocab, and the data context's prefixes. As a result, if you want to use the SparqlQueryBuilder (to do sparql queries, which is what we're trying to enable), you need to implement this function that returns prefixes, a context document (as a dict) and prefixes.
• Moved the transformation of Context into a dict from the ReadOnlyStore to the Context class: formatting the Context is no longer just a ReadOnlyStore's concern, but a Model may need to as well. In any case, it's the manipulation of a Context, so it makes sense for it to live there.
• get_model and get_store accessors in KnowledgeGraphForge
• RdfModelService : _build_shapes_map method to implement: it returns the shapes into a Graph, a dictionary indicating the source the shape originates from, and a dictionary that says which class is constrained by which shape. By centralizing it in the same method (which was not the case before), it enables knowing which file contained which schema (for the implementation in RdfModelServiceFromDirectory)
• RdfModelServiceFromDirectory : formerly named DirectoryService, get_shape_source can now be implemented (formerly named schema_source_id) due to the change in RdfModelService base class
• specializations.stores.service : bug with the context cache not being used fixed

[ssssarah]

This is the parameter ontology, I assume a dummy ontology file would be more appropriate

[crisely09]

Yes, you could keep just a part of the file, not all of it

[ssssarah]

I've made the file shorter

[MFSY]

The actual return type is Shape.

[ssssarah]

_shapes_graph is a ShapesGraphWrapper, and the lookup_shape_from_node method is overridden, and the shape is being wrapped in a ShapeWrapper, no?

[codecov-commenter]

Codecov Report

Attention: 69 lines in your changes are missing coverage. Please review.

Comparison is base (2e616cd) 74.36% compared to head (e05ca33) 74.45%.

Files	Patch %	Lines
...zations/models/rdf/rdf_model_service_from_store.py	23.33%	23 Missing ⚠️
kgforge/specializations/stores/nexus/service.py	50.00%	12 Missing ⚠️
...ge/specializations/models/rdf/rdf_model_service.py	72.22%	10 Missing ⚠️
kgforge/core/commons/es_query_builder.py	28.57%	5 Missing ⚠️
kgforge/specializations/stores/bluebrain_nexus.py	63.63%	4 Missing ⚠️
kgforge/specializations/models/rdf_model.py	86.36%	3 Missing ⚠️
kgforge/core/archetypes/model.py	89.47%	2 Missing ⚠️
kgforge/core/archetypes/store.py	71.42%	2 Missing ⚠️
kgforge/core/forge.py	50.00%	2 Missing ⚠️
kgforge/specializations/models/demo_model.py	60.00%	2 Missing ⚠️
... and 3 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #351      +/-   ##
==========================================
+ Coverage   74.36%   74.45%   +0.08%     
==========================================
  Files         100      101       +1     
  Lines        6315     6376      +61     
==========================================
+ Hits         4696     4747      +51     
- Misses       1619     1629      +10     

Flag	Coverage Δ
unittests	74.45% <72.50%> (+0.08%)	⬆️

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[ssssarah]

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