Fixed bug related to statuses sometimes containing notes

Parser/extraction_lib.py

@@ -3,6 +3,7 @@ from copy import copy
 from datetime import datetime
 import psycopg2
 from bs4 import BeautifulSoup
+import argparse
 #import textprocessing as tp #cuz tp is important
 #requires Python 3.10
 
@@ -163,13 +164,16 @@ def extract_study_statuses(study_status_form, version_a,version_b):
 
             case ["Overall Status:" as row_label, old,new]:
                 print("row matched: {}".format(row_label)) if VERBOSE else ""
-                version_a._overall_status = optional_strip(old.text)
-                version_b._overall_status = optional_strip(new.text)
+                #split out any notes such as "Suspended [reason for suspenstion ]"
+                version_a._overall_status = optional_strip(old.text.split("[")[0])
+                #split out any notes such as "Suspended [reason for suspenstion ]"
+                version_b._overall_status = optional_strip(new.text.split("[")[0])
                 #FIX: There is an issue with NCT00789633 where the overall status includes information as to why it was suspended.
 
             case _ as row_label:
                 print("row not matched: {}".format(row_label)) if VERBOSE else ""
 
+
 def extract_study_design(study_status_form, version_a,version_b):
     """
     This extracts data from a study_status form and returns one or two 
@@ -377,9 +381,33 @@ def get_data_from_versions(nct_id,html, version_a_int, version_b_int):
 
 
 if __name__ == "__main__":
-    VERBOSE = True 
+    argParser = argparse.ArgumentParser()
+
+    # Adding diagnostic printing
+    argParser.add_argument(
+            "-V"
+            ,"--verbose"
+            , help="Display a lot of of diagnostic information"
+            , action='store_true'
+            )
+
+    # host
+    argParser.add_argument(
+            "--host"
+            , help="Change hostname"
+            )
+
+
+    args = argParser.parse_args()
+    VERBOSE = args.verbose 
+
+    if args.host:
+        host=args.host
+    else:
+        host="localhost"
+
 
-    with psycopg2.connect(dbname="aact_db", user="root", password="root",host="will-office") as db_connection:
+    with psycopg2.connect(dbname="aact_db", user="root", password="root",host=host) as db_connection:
         #pull the requests from the db
         with db_connection.cursor() as curse:
             sql = """

justfile

@@ -81,5 +81,13 @@ select-trials:
 download-trial-histories:
     cd history_downloader && python ./downloader.py
 
+#Check if you can connect to the db
 test-db-connection:
     cd history_downloader && python db_connection.py
+
+#Parse previously downloaded histories into tables.
+parse-trial-histories:
+    cd Parser && python extraction_lib.py
+
+#Download and install 
+get-histories: download-trial-histories parse-trial-histories