minor adjustments to improve workflow

scripts/Icd10ConditionsMatching/Icd10ConditionsMatching/validation.py

@@ -90,6 +90,7 @@ def validate_trial(nct_id):
                 record_suggested_matches(db_conn, nct_id, condition, code)
                 return redirect(request.path)
             else:
+                record_suggested_matches(db_conn, nct_id, condition + "| Code not in GBD list", code)
                 return """
                 Entered `{}`, which is not in the list of available ICD-10 codes. <a href={}>Return to trial summary</a>
                 """.format(code.strip("-"),request.path), 422

scripts/Icd10ConditionsMatching/match_conditions_to_icd10.txt

@@ -1,16 +0,0 @@
-The purpose of this application is to provide an easy way to manually review the 
-proposed matches between trial conditions and proposed icd10 codes.
-
-Plan:
- - get list of proposed matches For each NCT_ID
-    - present appropriate information from trial
-        - nctid, descriptions, browse_conditions info (including mesh-ansestors)
-    - for each condition
-        - show proposed codes
-        - each code has a check box next to it.
-        - If there are no proposed codes, an entry box is made available.
-
-Design steps:
-
-Setup SQL queries and tables.
-Setup Flask App

scripts/drugtools/historical_nct_extractor.py

@@ -3,6 +3,7 @@ from copy import copy
 from datetime import datetime
 from bs4 import BeautifulSoup
 from drugtools.env_setup import ENV,postgres_conn
+from tqdm import tqdm
 #requires Python 3.10
 
 #### GLOBALS
@@ -391,7 +392,7 @@ def run():
             WHERE response_code = 200
             """
             curse.execute(sql)
-            for response in curse.fetchall():
+            for response in tqdm(curse.fetchall()):
                 nct_id, version_a, version_b, html = response
 
                 print(nct_id, version_a, version_b) if VERBOSE else ""