Gandalf filtering

workers/aragorn_pathfinder/worker.py

@@ -76,6 +76,17 @@ async def shadowfax(task, logger: logging.Logger):
         intermediate_categories = ["biolink:NamedThing"]
 
     # Create 3-hop query
+    gandalf_parameters = {
+        "min_information_content": message.get("parameters", {})
+        .get("gandalf_parameters", {})
+        .get("min_information_content", 69),
+        "max_node_degree": message.get("parameters", {})
+        .get("gandalf_parameters", {})
+        .get("max_node_degree", 5000),
+        "dehydrated": message.get("parameters", {})
+        .get("gandalf_parameters", {})
+        .get("dehydrated", True),
+    }
     threehop = {
         "message": {
             "query_graph": {
@@ -180,6 +191,7 @@ async def shadowfax(task, logger: logging.Logger):
                 },
             },
         },
+        "parameters": {"gandalf_parameters": gandalf_parameters},
     }
 
     callback_id = str(uuid.uuid4())[:8]

workers/gandalf/Dockerfile

@@ -21,6 +21,7 @@ COPY ./workers/gandalf/requirements.txt .
 RUN pip install -r requirements.txt
 
 # switch to the non-root user (nru). defined in the base image
+ENV PYSTOW_HOME=/tmp/pystow
 USER nru
 
 # Copy in files

workers/gandalf/requirements.txt

@@ -1,2 +1,2 @@
-gandalf-csr>=0.1.11
+gandalf-csr>=0.3.3
 

workers/gandalf/worker.py

@@ -74,7 +74,29 @@ def load_graph(path: str, fmt: str = "auto") -> CSRGraph:
 def gandalf_lookup(graph, bmt, in_message, task_logger: logging.Logger):
     """Run a Gandalf lookup for a single task."""
     task_logger.info("Starting Gandalf lookup")
-    return lookup(graph, in_message, bmt=bmt)
+    max_node_degree = (
+        in_message.get("parameters", {})
+        .get("gandalf_parameters", {})
+        .get("max_node_degree", None)
+    )
+    min_information_content = (
+        in_message.get("parameters", {})
+        .get("gandalf_parameters", {})
+        .get("min_information_content", None)
+    )
+    dehydrated = (
+        in_message.get("parameters", {})
+        .get("gandalf_parameters", {})
+        .get("dehydrated", False)
+    )
+    return lookup(
+        graph,
+        in_message,
+        bmt=bmt,
+        max_node_degree=max_node_degree,
+        min_information_content=min_information_content,
+        dehydrated=dehydrated,
+    )
 
 
 async def poll_for_tasks(graph: CSRGraph, bmt: Toolkit):

workers/gandalf_rehydrate/Dockerfile

@@ -21,6 +21,7 @@ COPY ./workers/gandalf_rehydrate/requirements.txt .
 RUN pip install -r requirements.txt
 
 # switch to the non-root user (nru). defined in the base image
+ENV PYSTOW_HOME=/tmp/pystow
 USER nru
 
 # Copy in files

workers/score_paths/Dockerfile

@@ -27,6 +27,7 @@ COPY ./workers/score_paths .
 RUN chmod -R 777 .
 
 # switch to the non-root user (nru). defined in the base image
+ENV PYSTOW_HOME=/tmp/pystow
 USER nru
 
 # Variables that can be overriden

workers/score_paths/worker.py

@@ -24,31 +24,6 @@
 tracer = setup_tracer(STREAM)
 
 
-def get_most_specific_category(categories, logger):
-    valid = []
-    for cat in categories:
-        element = bmt.get_element(cat)
-        if not element:
-            logger.error(f"Category {cat} doesn't exist.")
-            continue
-        valid.append(cat)
-
-    if not valid:
-        return None
-
-    most_specific = []
-    for cat in valid:
-        dominated = any(
-            cat in bmt.get_ancestors(other, reflexive=False)
-            for other in valid
-            if other != cat
-        )
-        if not dominated:
-            most_specific.append(cat)
-
-    return bmt.get_element(most_specific[0])
-
-
 def convert_path_to_sentence(source, target, path, knowledge_graph, logger):
 
     path_node_list = [source]
@@ -99,13 +74,10 @@ def convert_path_to_sentence(source, target, path, knowledge_graph, logger):
                         path_predicate_list[hop_num].add(inv)
         current_node = next_node
 
-    source_cat = get_most_specific_category(
-        knowledge_graph["nodes"][source]["categories"], logger
-    )
+    source_cat = knowledge_graph["nodes"][source]["categories"][0]
     if not source_cat:
         raise ValueError(f"Could not determine category for source node {source}.")
-
-    path_sentence = f"{knowledge_graph['nodes'][source]['name']} (a {source_cat.name}) "
+    path_sentence = f"{knowledge_graph['nodes'][source]['name']} (a {source_cat.removeprefix('biolink:')}) "
     first_hop = True
     for path_node, hop_predicates in zip(path_node_list[1:], path_predicate_list):
         hop_preds = list(hop_predicates)
@@ -122,14 +94,10 @@ def convert_path_to_sentence(source, target, path, knowledge_graph, logger):
             for hop_pred in hop_preds[:-1]:
                 path_sentence += f"{hop_pred} or "
             path_sentence += f"{hop_preds[-1]}]"
-        node_cat = get_most_specific_category(
-            knowledge_graph["nodes"][path_node]["categories"], logger
-        )
+        node_cat = knowledge_graph["nodes"][path_node]["categories"][0]
         if not node_cat:
             raise ValueError(f"Could not determine category for node {path_node}.")
-        path_sentence += (
-            f" {knowledge_graph['nodes'][path_node]['name']} (a {node_cat.name})"
-        )
+        path_sentence += f" {knowledge_graph['nodes'][path_node]['name']} (a {node_cat.removeprefix('biolink:')})"
 
     return path_sentence