Resolved conflicts

src/acquisition/cdcp/cdc_dropbox_receiver.py

@@ -44,12 +44,10 @@ def get_timestamp_string():
 
 def trigger_further_processing():
     """Add CDCP processing scripts to the Automation run queue."""
-
     # connect
     u, p = secrets.db.auto
-    cnx = mysql.connector.connect(user=u, password=p, database="automation")
+    cnx = mysql.connector.connect(user=u, password=p, database="automation", host=secrets.db.host)
     cur = cnx.cursor()
-
     # add step "Process CDCP Data" to queue
     cur.execute("CALL automation.RunStep(46)")
 

src/acquisition/cdcp/cdc_extract.py

@@ -154,7 +154,7 @@ def extract(first_week=None, last_week=None, test_mode=False):
 
     # connect
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     cur = cnx.cursor()
 
     # weeks to update

src/acquisition/cdcp/cdc_upload.py

@@ -165,7 +165,7 @@
 def upload(test_mode):
     # connect
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     cur = cnx.cursor()
 
     # insert (or update) table `cdc`

src/acquisition/ecdc/ecdc_db_update.py

@@ -48,7 +48,7 @@
 
 def ensure_tables_exist():
     (u, p) = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     try:
         cursor = cnx.cursor()
         cursor.execute(
@@ -98,7 +98,7 @@ def update_from_file(issue, date, dir, test_mode=False):
     # Read ECDC data from CSVs and insert into (or update) the database.
     # database connection
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     rows1 = get_rows(cnx, "ecdc_ili")
     print(f"rows before: {int(rows1)}")
     insert = cnx.cursor()

src/acquisition/ght/ght_update.py

@@ -247,11 +247,10 @@
     "WY",
 ]
 
-
 def update(locations, terms, first=None, last=None, countries=["US"]):
     # connect to the database
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     cur = cnx.cursor()
 
     def get_num_rows():

src/acquisition/kcdc/kcdc_update.py

@@ -45,7 +45,7 @@
 
 def ensure_tables_exist():
     (u, p) = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     try:
         cursor = cnx.cursor()
         cursor.execute(

src/acquisition/nidss/taiwan_update.py

@@ -105,7 +105,7 @@ def update(test_mode=False):
 
     # Database connection
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     rows1 = get_rows(cnx)
     print(f"rows before (flu): {int(rows1[0])}")
     print(f"rows before (dengue): {int(rows1[1])}")

src/acquisition/paho/paho_db_update.py

@@ -66,7 +66,7 @@
 
 def ensure_tables_exist():
     (u, p) = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     try:
         cursor = cnx.cursor()
         cursor.execute(
@@ -168,8 +168,8 @@ def update_from_file(issue, date, filename, test_mode=False):
     # Current code ignores PAHO-given issue, is based on argument 'issue'
 
     # database connection
-    u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     rows1 = get_rows(cnx, "paho_dengue")
     print(f"rows before: {int(rows1)}")
     insert = cnx.cursor()
@@ -226,7 +226,7 @@ def update_from_file(issue, date, filename, test_mode=False):
         rows2 = rows1
     else:
         cnx.commit()
-        rows2 = get_rows(cnx)
+        rows2 = get_rows(cnx, "paho_dengue")
     print(f"rows after: {int(rows2)} (added {int(rows2 - rows1)})")
     cnx.close()
 

src/acquisition/quidel/quidel_update.py

@@ -58,13 +58,13 @@ def update(locations, first=None, last=None, force_update=False, load_email=True
     if not qd.need_update and not force_update:
         print("Data not updated, nothing needs change.")
         return
-
+    
     qd_data = qd.load_csv()
     qd_measurements = qd.prepare_measurements(qd_data, start_weekday=4)
     qd_ts = quidel.measurement_to_ts(qd_measurements, 7, startweek=first, endweek=last)
     # connect to the database
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     cur = cnx.cursor()
 
     def get_num_rows():

src/acquisition/twtr/twitter_update.py

@@ -62,7 +62,7 @@
 def run():
     # connect to the database
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     cur = cnx.cursor()
 
     def get_num_rows():

src/acquisition/wiki/wiki_extract.py

@@ -67,7 +67,7 @@ def get_timestamp(name):
 def run(job_limit=100):
     # connect to the database
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     cur = cnx.cursor()
 
     # # Some preparation for utf-8, and it is a temporary trick solution. The real solution should change those char set and collation encoding to utf8 permanently

src/acquisition/wiki/wiki_update.py

@@ -90,7 +90,7 @@ def get_manifest(year, month, optional=False):
 def run():
     # connect to the database
     u, p = secrets.db.epi
-    cnx = mysql.connector.connect(user=u, password=p, database="epidata")
+    cnx = mysql.connector.connect(user=u, password=p, database="epidata", host=secrets.db.host)
     cur = cnx.cursor()
 
     # get the most recent job in wiki_raw