fetch pubmed file from /gn-meta/lit

2 files changed, 7 insertions, 7 deletions

diff --git a/gn3/api/llm.py b/gn3/api/llm.py
index e857365..661d055 100644
--- a/gn3/api/llm.py
+++ b/gn3/api/llm.py
@@ -45,7 +45,7 @@ def gnqa():
     try:
         auth_token = current_app.config.get("FAHAMU_AUTH_TOKEN")
         task_id, answer, refs = get_gnqa(
-            query, auth_token, current_app.config.get("TMPDIR", "/tmp"))
+            query, auth_token, current_app.config.get("DATA_DIR"))
 
         response = {
             "task_id": task_id,
@@ -77,10 +77,10 @@ def rating(task_id):
                                               results.get("answer"),
                                               results.get("weight", 0))
 
-            logging.debug("the user id %s", str(user_id))
             # get base name for sqlite
             llm_path = os.path.join(os.path.dirname(
                 current_app.config["AUTH_DB"]), "llm.db")
+            logging.info("lmdb path is %s",llm_path)
             with db.connection(llm_path) as conn:
                 cursor = conn.cursor()
                 create_table = """CREATE TABLE IF NOT EXISTS Rating(
diff --git a/gn3/llms/process.py b/gn3/llms/process.py
index b29d4c9..468f86a 100644
--- a/gn3/llms/process.py
+++ b/gn3/llms/process.py
@@ -71,26 +71,26 @@ def rate_document(task_id, doc_id, rating, auth_token):
 
 def load_file(filename, dir_path):
     """function to open and load json file"""
-    file_path = os.path.join(dir_path, f"/{filename}")
+    file_path = os.path.join(dir_path, f"{filename}")
     if not os.path.isfile(file_path):
         raise FileNotFoundError(f"{filename} was not found or is a directory")
     with open(file_path, "rb") as file_handler:
         return json.load(file_handler)
 
 
-def fetch_pubmed(references, file_name, tmp_dir=""):
+def fetch_pubmed(references, file_name, data_dir=""):
     """method to fetch and populate references with pubmed"""
 
     try:
-        pubmed = load_file(file_name, tmp_dir)
+        pubmed = load_file(file_name, os.path.join(data_dir, "gn-meta/lit"))
         for reference in references:
             if pubmed.get(reference["doc_id"]):
                 reference["pubmed"] = pubmed.get(reference["doc_id"])
         return references
 
     except FileNotFoundError:
-        logging.debug("failed to find pubmed_path for %s/%s",
-                      tmp_dir, file_name)
+        logging.error("failed to find pubmed_path for %s/%s",
+                      data_dir, file_name)
         return references