From e2edf1eb6b3e83cec4b042e4726d4ed634cbcd2f Mon Sep 17 00:00:00 2001
From: youainti <youainti@protonmail.com>
Date: Thu, 23 Mar 2023 16:08:08 -0700
Subject: [PATCH] created base of umls linking script

---
 scripts/umls_requests.py | 58 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 scripts/umls_requests.py

diff --git a/scripts/umls_requests.py b/scripts/umls_requests.py
new file mode 100644
index 0000000..8d3da9a
--- /dev/null
+++ b/scripts/umls_requests.py
@@ -0,0 +1,58 @@
+from dotenv import dotenv_values
+import requests
+import json
+from drugtools.env_setup import ENV,postgres_conn
+from psycopg2 import extras
+
+
+
+class Requestor():
+    def __init__(self,api_key):
+        self.key = api_key
+
+    def search(self,search_term,inputType="sourceUi", returnIdType="code", addnl_terms={}):
+        query_terms = {
+            "apiKey":self.key,
+            "sabs":"ICD10",
+            "string":search_term,
+            "returnIdType":returnIdType,
+            "inputType":inputType
+        } | addnl_terms
+        query = "https://uts-ws.nlm.nih.gov/rest/search/current/"
+
+        r = requests.get(query,params=query_terms)
+        print(r.url)
+        return r
+
+
+r = Requestor(ENV.get("UMLS_API_KEY"))
+print(json.dumps(r.search("leukemia").json(),indent=2))
+
+
+conditions_link = {}
+
+pconn =  postgres_conn()
+pcurse = pconn.cursor(cursor_factory=extras.DictCursor)
+sql = """
+select nct_id, downcase_mesh_term
+from ctgov.browse_conditions bc
+where 
+mesh_type = 'mesh-list'
+and 
+nct_id in (select distinct nct_id from history.trial_snapshots ts)
+order by nct_id
+;
+"""
+pcurse.execute(sql)
+rows = pcurse.fetchall()
+for row in rows:
+    nctid = row[0]
+    condition = row[1]
+    print(nctid,condition)
+
+    results = r.search(row[1]).json().get('result', Exception("No result entry in json")).get('results',Exception("No results entry in json"))
+    for entry in results:
+        print("\t", entry["ui"], entry["name"])
+
+
+