Remove all instances of cloneDeep()

[tokebe]

After investigation of the below query, it's become apparent that the use of cloneDeep in any function which is expected to be called many times in quick succession, or is expected to perform transformations on large objects, i.e. _createBTEEdges(), is more-or-less bound to cause performance issues (both in responsiveness and overall resource use).

It would probably be worthwhile to figure out how best to change the internal flow of data such that any current uses can be removed. Currently all uses are in qedge2bteedge.

The following query causes server crash due to out-of-memory exception while cloning:

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                     "ids": ["MONDO:0005359", "SNOMEDCT:197354009"],
                     "categories": ["biolink:DiseaseOrPhenotypicFeature"]
                },
                "n1": {
                    "categories": ["biolink:DiseaseOrPhenotypicFeature"]
                },
                "n2": {
                    "categories": ["biolink:Gene"]
                },
                "n3": {
                    "categories": ["biolink:Drug", "biolink:SmallMolecule"]
                }
            },
            "edges": {
                "e01": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": ["biolink:has_real_world_evidence_of_association_with"]
                },
                "e02": {
                    "subject": "n2",
                    "object": "n1",
                    "predicates": ["biolink:gene_associated_with_condition"]
                },
                "e03": {
                    "subject": "n3",
                    "object": "n2",
                    "predicates": ["biolink:affects", "biolink:interacts_with"]
                }
            }
        }
    },
    "submitter": "WorkflowBNotebook",
    "stream_progress": false,
    "query_options": {
        "kp_timeout": 1800
    }
}

[tokebe]

Tests show that removing cloneDeep improves memory usage, but does not prevent the above query from crashing BTE.

[colleenXu]

@tokebe @newgene Can this be closed or is this an ongoing task?

[tokebe]

This can be closed.