Added debugging to edge endpoint

README.md

@@ -31,5 +31,8 @@ For webapps developed against a local deployment of this service, the `PYTHON_EN
 ## Redis server
 Start server: redis-server --dbfilename aragorn_cache.rdb --dir /home/joeyr/data/kg_summarizer
 
+## API Location
+https://kg-summarizer.apps.renci.org/docs
+
 ## Todo
 

kg_summarizer/server.py

@@ -3,9 +3,11 @@
 from starlette.middleware.base import BaseHTTPMiddleware
 from typing import Optional
 from pydantic import BaseModel
+import pathlib
 import logging
-import kg_summarizer.config as CFG
+import json
 
+import kg_summarizer.config as CFG
 from kg_summarizer.trapi import EdgeContainer
 from kg_summarizer.ai import generate_response
 from kg_summarizer.utils import LoggingUtil
@@ -39,12 +41,13 @@ class EdgeItem(BaseModel):
     parameters: Parameters
 
 
-KG_SUM_VERSION = "0.0.9"
+KG_SUM_VERSION = "0.0.10"
 
 # declare the application and populate some details
 app = FastAPI(
     title="Knowledge Graph Summarizer - A FastAPI UI/web service",
     version=KG_SUM_VERSION,
+    debug=True,
 )
 
 app.add_middleware(
@@ -84,7 +87,14 @@ async def summarize_abstract_handler(item: AbstractItem):
 
 @app.post("/summarize/edge")
 async def summarize_edge_handler(item: EdgeItem):
-    edge = EdgeContainer(item.edge)
+    if item.edge:
+        summary = ""
+        edge = EdgeContainer(item.edge)
+    else:
+        summary = f"{50*'*'}\nNo edge passed - loading example\n{50*'*'}\n"
+        p = pathlib.Path(__file__).parents[1].joinpath("data/edge_david_example.json")
+        with open(p) as f:
+            edge = EdgeContainer(json.load(f))
 
     spo_sentence = edge.format_spo_sentence()
 
@@ -95,12 +105,12 @@ async def summarize_edge_handler(item: EdgeItem):
         Summarize the following edge publication abstracts listed in the knowledge graph. Make sure the summary supports the statement '{spo_sentence}'. Only use information explicitly stated in the publication abstracts. I repeat, do not make up any information.
         """
 
-    if edge["edge"]["publications"] or edge["edge"]["sentences"]:
+    if edge.edge["publications"] or edge.edge["sentences"]:
         logger.info(f"GPT Prompt: {system_prompt}")
         logger.info(f"GPT Mode: {item.parameters.llm.gpt_model}")
         logger.info(f"GPT Temperature: {item.parameters.llm.temperature}")
         logger.info(f"GPT Input: {edge}")
-        summary = generate_response(
+        summary += generate_response(
             system_prompt,
             str(edge),
             item.parameters.llm.gpt_model,
@@ -110,7 +120,7 @@ async def summarize_edge_handler(item: EdgeItem):
         logger.info(
             "Edge contained no publications or sentences. Returning with standarized summary."
         )
-        summary = f"The edge '{spo_sentence}' contains no publications or supporting sentences for an LLM to summarize."
+        summary += f"The edge '{spo_sentence}' contains no publications or supporting sentences for an LLM to summarize."
 
     logger.info(f"Edge Summary: {summary}")
     return summary

kg_summarizer/trapi.py

@@ -160,6 +160,7 @@ class GraphContainer:
     response: dict
     verbose: bool = True
     result_idx: int = 0
+    fetch_pubs: bool = True
     graph_type: str = field(init=False)  # lookup or creative
     sorted_results: list = field(default_factory=list, init=False)
     result: dict = field(default_factory=dict, init=False)
@@ -191,7 +192,7 @@ def set_result(self, idx):
         self.result_idx = idx
         self.result = self.sorted_results[idx]
         self.get_node_info()
-        self.get_edge_info()
+        self.get_edge_info(fetch_pubs=self.fetch_pubs)
         self.vprint(f"Result: \n{self.result}\n")
 
     def vprint(self, msg):
@@ -241,9 +242,10 @@ def parse_node_attributes(attr_list_of_dicts, node_norm_name):
             node_attr_data["same_as"] = list(set(node_attr_data["same_as"]))
 
             # Fetch publications
-            node_attr_data["publications"] = get_publications(
-                node_attr_data["publications"]
-            )
+            if self.fetch_pubs:
+                node_attr_data["publications"] = get_publications(
+                    node_attr_data["publications"]
+                )
 
             return node_attr_data
 

setup.py

@@ -9,7 +9,7 @@
 
 setup(
     name="kg-summarizer",
-    version="0.0.9",
+    version="0.0.10",
     author="Joey Richardson",
     author_email="[email protected]",
     url="https://github.com/jrichardson97/kg-summarizer",