From cc5e1c699cd93293d4322f0eb8f6adea587266ae Mon Sep 17 00:00:00 2001 From: Dmytro Trotsko Date: Tue, 27 Jun 2023 00:11:18 +0300 Subject: [PATCH] Resolved conflicts --- src/acquisition/cdcp/cdc_dropbox_receiver.py | 4 +--- src/acquisition/cdcp/cdc_extract.py | 2 +- src/acquisition/cdcp/cdc_upload.py | 2 +- src/acquisition/ecdc/ecdc_db_update.py | 4 ++-- src/acquisition/ght/ght_update.py | 3 +-- src/acquisition/kcdc/kcdc_update.py | 2 +- src/acquisition/nidss/taiwan_update.py | 2 +- src/acquisition/paho/paho_db_update.py | 8 ++++---- src/acquisition/quidel/quidel_update.py | 4 ++-- src/acquisition/twtr/twitter_update.py | 2 +- src/acquisition/wiki/wiki_extract.py | 2 +- src/acquisition/wiki/wiki_update.py | 2 +- 12 files changed, 17 insertions(+), 20 deletions(-) diff --git a/src/acquisition/cdcp/cdc_dropbox_receiver.py b/src/acquisition/cdcp/cdc_dropbox_receiver.py index 4fa20368e..1e9062c7d 100644 --- a/src/acquisition/cdcp/cdc_dropbox_receiver.py +++ b/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)") diff --git a/src/acquisition/cdcp/cdc_extract.py b/src/acquisition/cdcp/cdc_extract.py index 0d38e0bcc..adedc25ce 100644 --- a/src/acquisition/cdcp/cdc_extract.py +++ b/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 diff --git a/src/acquisition/cdcp/cdc_upload.py b/src/acquisition/cdcp/cdc_upload.py index 0e191267b..94fe69c04 100644 --- a/src/acquisition/cdcp/cdc_upload.py +++ b/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` diff --git a/src/acquisition/ecdc/ecdc_db_update.py b/src/acquisition/ecdc/ecdc_db_update.py index 84423c376..4483f26da 100644 --- a/src/acquisition/ecdc/ecdc_db_update.py +++ b/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() diff --git a/src/acquisition/ght/ght_update.py b/src/acquisition/ght/ght_update.py index 9e8d48d1d..7d7a5a65f 100644 --- a/src/acquisition/ght/ght_update.py +++ b/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(): diff --git a/src/acquisition/kcdc/kcdc_update.py b/src/acquisition/kcdc/kcdc_update.py index 713b21f00..5fe8f27a2 100644 --- a/src/acquisition/kcdc/kcdc_update.py +++ b/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( diff --git a/src/acquisition/nidss/taiwan_update.py b/src/acquisition/nidss/taiwan_update.py index 30d458481..2bbeba6eb 100644 --- a/src/acquisition/nidss/taiwan_update.py +++ b/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])}") diff --git a/src/acquisition/paho/paho_db_update.py b/src/acquisition/paho/paho_db_update.py index b351d3ff2..4792d4967 100644 --- a/src/acquisition/paho/paho_db_update.py +++ b/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() diff --git a/src/acquisition/quidel/quidel_update.py b/src/acquisition/quidel/quidel_update.py index 563cea898..3f8cacf11 100644 --- a/src/acquisition/quidel/quidel_update.py +++ b/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(): diff --git a/src/acquisition/twtr/twitter_update.py b/src/acquisition/twtr/twitter_update.py index 80a023f19..6385375bb 100644 --- a/src/acquisition/twtr/twitter_update.py +++ b/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(): diff --git a/src/acquisition/wiki/wiki_extract.py b/src/acquisition/wiki/wiki_extract.py index 718a64c20..8da272284 100644 --- a/src/acquisition/wiki/wiki_extract.py +++ b/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 diff --git a/src/acquisition/wiki/wiki_update.py b/src/acquisition/wiki/wiki_update.py index a9f240629..eb396e870 100644 --- a/src/acquisition/wiki/wiki_update.py +++ b/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