Merge pull request #344 from nanglo123/add_dkg_resource

Add resources to dkg

docker/Dockerfile

@@ -31,7 +31,7 @@ RUN wget -O /sw/nodes.tsv.gz https://askem-mira.s3.amazonaws.com/dkg/$domain/bui
 
 # Python packages
 RUN python -m pip install --upgrade pip && \
-    python -m pip install git+https://github.com/gyorilab/mira.git@main#egg=mira[web,uvicorn,dkg-client] && \
+    python -m pip install git+https://github.com/gyorilab/mira.git@main#egg=mira[web,uvicorn,dkg-client,dkg-construct] && \
     python -m pip uninstall -y flask_bootstrap && \
     python -m pip uninstall -y bootstrap_flask && \
     python -m pip install bootstrap_flask && \

mira/dkg/api.py

@@ -2,7 +2,7 @@
 
 import itertools as itt
 import os
-from typing import Any, List, Mapping, Optional, Union, Dict
+from typing import Any, List, Mapping, Optional, Union
 
 import pydantic
 from fastapi import APIRouter, Body, HTTPException, Path, Query, Request
@@ -13,6 +13,7 @@
 
 from mira.dkg.client import AskemEntity, Entity, Relation
 from mira.dkg.utils import DKG_REFINER_RELS
+from mira.dkg.construct import add_resource_to_dkg
 
 __all__ = [
     "api_blueprint",
@@ -360,6 +361,37 @@ def add_relations(
             request.app.state.client.add_relation(relation)
 
 
+    @api_blueprint.post(
+        "/add_resources",
+        response_model=None,
+        tags=["relations"],
+    )
+    def add_resources(
+        request: Request,
+        resource_prefix_list: List[str] = Body(
+            ...,
+            description="A of resources to add to the DKG",
+            title="Resource Prefixes",
+            example=["probonto", "wikidata", "eiffel", "geonames", "ncit",
+                     "nbcbitaxon"],
+        )
+    ):
+        """From a list of resource prefixes, add a list of nodes and edges
+        extract from each resource to the DKG"""
+        for resource_prefix in resource_prefix_list:
+            # nodes and edges will be a list of dicts
+            nodes, edges = add_resource_to_dkg(resource_prefix.lower())
+            # node_info and edge_info are dictionaries that will be
+            # unpacked when creating instances of entities and relations
+            entities = [Entity(**node_info) for node_info in nodes]
+            relations = [Relation(**edge_info) for edge_info in edges]
+
+            for entity in entities:
+                request.app.state.client.add_node(entity)
+            for relation in relations:
+                request.app.state.client.add_relation(relation)
+
+
 class IsOntChildResult(BaseModel):
     """Result of a query to /is_ontological_child"""
 

mira/dkg/client.py

@@ -170,6 +170,7 @@ def from_data(cls, data):
         -------
         A MIRA entity
         """
+
         if isinstance(data, neo4j.graph.Node):
             data = dict(data.items())
         properties = defaultdict(list)
@@ -185,6 +186,8 @@ def from_data(cls, data):
         ):
             synonyms.append(Synonym(value=value, type=type))
         xrefs = []
+
+
         for curie, type in zip(
             data.pop("xrefs", []),
             data.pop("xref_types", []),
@@ -343,29 +346,70 @@ def add_node(self, entity):
         entity:
             The node object that will be added to the DKG
         """
-        curie = entity.id
+        xrefs, xref_types = [], []
+        synonyms, synonym_types = [], []
+        property_predicates, property_values = [], []
+        for xref in entity.xrefs:
+            xrefs.append(xref.id)
+            xref_types.append(xref.type)
+        for synonym in entity.synonyms:
+            synonyms.append(synonym.value)
+            synonym_types.append(synonym.type)
+        for property_predicate, property_value_list in entity.properties.items():
+            property_predicates.append(property_predicate)
+            property_values.extend(property_value_list)
+
+        _id = entity.id
         name = entity.name
         type = entity.type
         obsolete = entity.obsolete
         description = entity.description
-        synonyms = entity.synonyms
         alts = entity.alts
-        xrefs = entity.xrefs
         labels = entity.labels
 
         create_source_node_query = (
-            f"MERGE (n {{curie: '{curie}', "
-            f"name: '{name}', "
-            f"type: '{type}', "
-            f"obsolete: {obsolete}, "
-            f"description: '{description}', "
-            f"synonyms: {synonyms}, "
-            f"alts: {alts}, "
-            f"xrefs: {xrefs}, "
-            f"labels: {labels} }} )"
+            "MERGE (n {id: $id, "
+            "type: $type, "
+            "obsolete: $obsolete"
         )
 
-        self.create_tx(create_source_node_query)
+        if name:
+            create_source_node_query += ", name: $name"
+        if description:
+            create_source_node_query += ", description: $description"
+        if alts:
+            create_source_node_query += ", alts: $alts"
+        if labels:
+            create_source_node_query += ", labels: $labels"
+        if xrefs:
+            create_source_node_query += ", xrefs: $xrefs"
+            create_source_node_query += ", xref_types: $xref_types"
+        if synonyms:
+            create_source_node_query += ", synonyms: $synonyms"
+            create_source_node_query += ", synonym_types: $synonym_types"
+        if property_predicates:
+            create_source_node_query += ", property_predicates: $property_predicates"
+            create_source_node_query += ", property_values: $property_values"
+
+        create_source_node_query += "})"
+
+        query_parameters = {
+            "id": _id,
+            "name": name,
+            "type": type,
+            "obsolete": obsolete,
+            "description": description,
+            "synonyms": synonyms,
+            "synonym_types": synonym_types,
+            "alts": alts,
+            "xrefs": xrefs,
+            "xref_types": xref_types,
+            "labels": labels,
+            "property_predicates": property_predicates,
+            "property_values": property_values
+        }
+
+        self.create_tx(create_source_node_query, **query_parameters)
 
     def add_relation(self, relation):
         """Add a relation to the DKG
@@ -384,8 +428,8 @@ def add_relation(self, relation):
         graph = relation.graph
 
         create_relation_query = (
-            f"MATCH (source_node {{curie: '{source_curie}'}}), "
-            f"(target_node {{curie: '{target_curie}'}}) "
+            f"MATCH (source_node {{id: '{source_curie}'}}), "
+            f"(target_node {{id: '{target_curie}'}}) "
             f"MERGE (source_node)-[rel:{type}]->(target_node)"
             f"SET rel.pred = '{pred}'"
             f"SET rel.source = '{source}'"
@@ -395,7 +439,6 @@ def add_relation(self, relation):
 
         self.create_tx(create_relation_query)
 
-
     def create_single_property_node_index(
         self,
         index_name: str,