Merge pull request #10 from helxplatform/redis-schema-fix

Redis schema fix

PLATER/requirements.txt

@@ -7,6 +7,6 @@ uvicorn
 httpx
 redis==4.1.2
 reasoner-transpiler==1.7.1
-bmt==0.8.2
+bmt==1.1.3
 git+https://github.com/TranslatorSRI/reasoner-pydantic@v1.1.2.1#egg=reasoner-pydantic
 git+https://github.com/patrickkwang/fastapi#egg=fastapi

PLATER/services/util/drivers/redis_driver.py

@@ -51,8 +51,8 @@ def decode_if_byte(value):
             return value.decode('utf-8')
         except:
             return value
-
-    async def run(self, query, **kwargs):
+        
+    def run_graph_query(self, query, **kwargs):
         query_timeout = kwargs.get('query_timeout', None)
         results = self.redis_graph.query(query, read_only=True, timeout= query_timeout)
         headers = list(map(lambda x: RedisDriver.decode_if_byte(x[1]), results.header))
@@ -75,9 +75,12 @@ async def run(self, query, **kwargs):
             response.append(new_row)
         return self.format_cypher_result((headers, response))
 
+
+    async def run(self, query, **kwargs):
+        return self.run_graph_query(query, **kwargs)
+
     def run_sync(self, cypher_query):
-        results = self.sync_redis_client.execute_command('GRAPH.RO_QUERY', self.graph_name, cypher_query)
-        return RedisDriver.format_cypher_result(results)
+        return self.run_graph_query(cypher_query)
 
     @staticmethod
     def convert_to_dict(response: dict) -> list:

PLATER/services/util/graph_adapter.py

@@ -129,8 +129,8 @@ def search(self, query, indexes, fields=None, options={
             result = self.driver.run_sync(query)
             hits = self.convert_to_dict(result)
             for hit in hits:
-                hit["labels"] = dict(hit["node"])["labels"]
-                hit["node"] = dict(dict(hit["node"])["properties"])
+                hit["labels"] = dict(hit["node"])["category"]
+                hit["node"] = dict(dict(hit["node"]))
                 hit["score"] = float(hit["score"])
             hits.sort(key=lambda hit: hit["score"], reverse=True)
             return {
@@ -164,13 +164,15 @@ def get_schema(self, force_update=False):
                     # Since there are some nodes in data currently just one label ['biolink:NamedThing']
                     # This filter is to avoid that scenario.
                     # @TODO need to remove this filter when data build avoids adding nodes with single ['biolink:NamedThing'] labels.
-                    filter_named_thing = lambda x: filter(lambda y: y != 'biolink:NamedThing', x)
+                    filter_named_thing = lambda x: filter(lambda y: y != 'biolink.NamedThing', x)
+                    format_to_old_type = lambda y: [x.replace('biolink.', 'biolink:') for x in y]
                     # For redis convert these to arrays
                     source_labels = [triplet['source_labels']] if isinstance(triplet['source_labels'], str) else triplet['source_labels']
                     target_labels = [triplet['target_labels']] if isinstance(triplet['target_labels'], str) else triplet['target_labels']
-                    source_labels, predicate, target_labels = self.find_biolink_leaves(filter_named_thing(source_labels)), \
-                                                              triplet['predicate'], \
-                                                              self.find_biolink_leaves(filter_named_thing(target_labels))
+                    source_labels, predicate, target_labels = self.find_biolink_leaves(format_to_old_type(filter_named_thing(source_labels))), \
+                                                              triplet['predicate'].replace('biolink.', 'biolink:'), \
+                                                              self.find_biolink_leaves(format_to_old_type(filter_named_thing(target_labels)))
+
 
                     for source_label in source_labels:
                         for target_label in target_labels:

setup.py

@@ -10,7 +10,7 @@
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
-version = "2.0.2"
+version = "3.0.2"
 
 class PublishClass(Command):
     description = "Publish the package"