Normalize

README.md

@@ -13,3 +13,6 @@ Initially, design considerations will be discussed and voted on. Eventually, the
 # Workflow Runner
 The following repo will, after you stand it up, provide an endpoint to which you can post workflows and registered ARAs will execute the operations they have implemented.
 https://github.com/NCATSTranslator/workflow-runner
+
+# New Operations
+Creation of a new operation involves generation of the operation definition in the `operations` directory, then rebuilding the docs with `docs/build/generate_docs.py` and the schema with `schema/build/generate_schema.py`

docs/index.md

@@ -19,6 +19,7 @@
 - [filter_results_top_n](./filter_results_top_n.md)
 - [lookup](./lookup.md)
 - [lookup_and_score](./lookup_and_score.md)
+- [normalize_nodes](./normalize_nodes.md)
 - [overlay](./overlay.md)
 - [overlay_compute_jaccard](./overlay_compute_jaccard.md)
 - [overlay_compute_ngd](./overlay_compute_ngd.md)

docs/normalize_nodes.md

@@ -0,0 +1,30 @@
+# normalize nodes
+
+This operation updates the identifiers on qgraph and kgraph nodes to their preferred identifiers, and adds equivalent identifiers in a property for knodes.  When two kgraph nodes normalize to the same  preferred identifier, the two knodes are merged.  The new node contain the union of the properties of the two original nodes.  All edges attached to either of the two original nodes are now subsequently attached to the new merged knode.  Qnodes are not merged, so that the structure of the query can be preserved.   The updates to kgraph node identifiers also necessitates the updating of result node bindings.
+
+### examples
+
+- [input](../examples/normalize_nodes/messages/01_prenormalized_message.json), [output](../examples/)
+- [input](../examples/), [output](../examples/normalize_nodes/messages/02_postnormalized_message.json)
+
+### input requirements
+
+None
+
+### output guarantees
+
+None
+
+### allowed changes
+
+- modify qnodes
+- modify knodes
+- remove knodes
+- modify kedges
+- modify node bindings
+
+### parameters
+
+```yaml
+{}
+```

examples/normalize_nodes/messages/01_prenormalized_message.json

@@ -0,0 +1,170 @@
+{
+  "message": {
+    "query_graph": {
+      "nodes": {
+        "n1": {
+          "ids": ["HGNC:11603"],
+          "categories": [
+            "biolink:Gene"
+          ]
+        },
+        "n2": {
+          "ids": ["NCBIGene:9496"],
+          "categories": [
+            "biolink:Gene"
+          ]
+        },
+        "n3": {
+          "ids": ["MONDO:0005002"],
+          "categories": [
+            "biolink:Disease"
+          ]
+        },
+        "n4": {
+          "ids": ["DOID:3083"],
+          "categories": [
+            "biolink:Disease"
+          ]
+        },
+        "n5": {
+          "categories": [
+            "biolink:Disease"
+          ]
+        }
+      },
+      "edges": {
+        "e1": {
+          "subject": "n1",
+          "object": "n3"
+        },
+        "e2": {
+          "subject": "n2",
+          "object": "n4",
+          "predicates": ["biolink:related_to"]
+        },
+        "e3": {
+          "subject": "n1",
+          "object": "n5"
+        }
+      }
+    },
+    "knowledge_graph": {
+      "nodes": {
+        "HGNC:11603": {
+          "name": "TBX4",
+          "categories": [
+            "biolink:Gene"
+          ]
+        },
+        "NCBIGene:9496": {
+          "name": "T-box transcription factor 4",
+          "categories": [
+            "biolink:Gene"
+          ]
+        },
+        "MONDO:0005002": {
+          "name": "chronic obstructive pulmonary disease",
+          "categories": [
+            "biolink:Disease"
+          ]
+        },
+        "DOID:3083": {
+          "name": "chronic obstructive pulmonary disease",
+          "categories": [
+            "biolink:Disease"
+          ]
+        },
+        "UMLS:CN202575": {
+          "name": "heritable pulmonary arterial hypertension",
+          "categories": [
+            "biolink:Disease"
+          ]
+        }
+      },
+      "edges": {
+        "a8575c4e-61a6-428a-bf09-fcb3e8d1644d": {
+          "subject": "HGNC:11603",
+          "object": "MONDO:0005002",
+          "predicate": "biolink:related_to"
+        },
+        "2d38345a-e9bf-4943-accb-dccba351dd04": {
+          "subject": "NCBIGene:9496",
+          "object": "DOID:3083",
+          "predicate": "biolink:related_to"
+        },
+        "044a7916-fba9-4b4f-ae48-f0815b0b222d": {
+          "subject": "HGNC:11603",
+          "object": "UMLS:CN202575",
+          "predicate": "biolink:related_to"
+        }
+      }
+    },
+    "results": [
+      {
+        "node_bindings": {
+          "n1": [
+            {
+              "id": "HGNC:11603"
+            }
+          ],
+          "n3": [
+            {
+              "id": "MONDO:0005002"
+            }
+          ]
+        },
+        "edge_bindings": {
+          "e1": [
+            {
+              "id": "a8575c4e-61a6-428a-bf09-fcb3e8d1644d"
+            }
+          ]
+        }
+      },
+      {
+        "node_bindings": {
+          "n2": [
+            {
+              "id": "NCBIGene:9496"
+            }
+          ],
+          "n4": [
+            {
+              "id": "DOID:3083"
+            }
+          ]
+        },
+        "edge_bindings": {
+          "e2": [
+            {
+              "id": "2d38345a-e9bf-4943-accb-dccba351dd04"
+            }
+          ]
+        }
+      },
+      {
+        "node_bindings": {
+          "n1": [
+            {
+              "id": "HGNC:11603"
+            }
+          ],
+          "n5": [
+            {
+              "id": "UMLS:CN202575"
+            }
+          ]
+        },
+        "edge_bindings": {
+          "e3": [
+            {
+              "id": "044a7916-fba9-4b4f-ae48-f0815b0b222d"
+            }
+          ]
+        }
+      }
+    ]
+  },
+  "logs": null,
+  "status": null
+}