Reshape SPARQL query writer

[samwaseda]

I would like to suggest a new way to deal with SPARQL queries: Use one-to-one conversion to a networkx.DiGraph. In particular, it has nodes consisting of subjects and objects, and the predicates are stored in the metadata. You can see this also in the construct in the code:

G = nx.DiGraph()
G.add_edge(subj, obj, predicate=pred)

Then nodes for which the output should be computed get the extra argument output=True in the metadata. All BNodes are translated into local variables, while URIRefs are treated as URIs.

The main reason why I'm suggesting this is because it makes extensions easier, i.e. if I have a more complicated query, where for example I would like to specify the units or user-defined URIs, I have the possibility to append the lines to a given graph.

For the usual kinetic energy example, the SPARQL text looks like this:

print(sw.get_query_text(comp.my_workflow.inputs.distance, comp.my_workflow.outputs.kinetic_energy))

Output:

SELECT ?http___pyiron_org_ontology_my_workflow_inputs_distance_data_value ?http___pyiron_org_ontology_my_workflow_get_kinetic_energy_0_outputs_output_data_value WHERE {
?http___pyiron_org_ontology_my_workflow_inputs_distance_data a <http://pyiron.org/ontology/my_workflow-inputs-distance_data> .
?http___pyiron_org_ontology_my_workflow_inputs_distance_data rdf:value ?http___pyiron_org_ontology_my_workflow_inputs_distance_data_value .
?http___pyiron_org_ontology_my_workflow_get_kinetic_energy_0_outputs_output_data a <http://pyiron.org/ontology/my_workflow-get_kinetic_energy_0-outputs-output_data> .
?http___pyiron_org_ontology_my_workflow_get_kinetic_energy_0_outputs_output_data rdf:value ?http___pyiron_org_ontology_my_workflow_get_kinetic_energy_0_outputs_output_data_value .
?http___pyiron_org_ontology_my_workflow_inputs_distance <http://purl.obolibrary.org/obo/OBI_0000293> ?http___pyiron_org_ontology_my_workflow_inputs_distance_data .
?http___pyiron_org_ontology_my_workflow <http://purl.obolibrary.org/obo/BFO_0000051> ?http___pyiron_org_ontology_my_workflow_inputs_distance .
?http___pyiron_org_ontology_my_workflow <http://purl.obolibrary.org/obo/BFO_0000051> ?http___pyiron_org_ontology_my_workflow_outputs_kinetic_energy .
?http___pyiron_org_ontology_my_workflow_outputs_kinetic_energy <http://purl.obolibrary.org/obo/OBI_0000299> ?http___pyiron_org_ontology_my_workflow_get_kinetic_energy_0_outputs_output_data .
}

[github-actions]

👈 Launch a binder notebook on branch pyiron/semantikon/query

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.30%. Comparing base (58eeb54) to head (2eecb0e).
⚠️ Report is 7 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #350      +/-   ##
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+ Coverage   97.28%   97.30%   +0.01%     
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  Files           9        9              
  Lines        1435     1445      +10     
==========================================
+ Hits         1396     1406      +10     
  Misses         39       39              

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