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Allow any port to be used by connection but default to 5432 #176

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Merged
christabone merged 2 commits into from
Feb 20, 2026
Merged

Allow any port to be used by connection but default to 5432 #176

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2db3716
Allow any port to be used by connection but default to 5432
ianlongden Feb 20, 2026
c3c586e
Merge branch 'master' into any_port
ianlongden Feb 20, 2026
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5 changes: 3 additions & 2 deletions harvdev_utils/psycopg_functions/establish_db_connection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,20 +14,21 @@
log = logging.getLogger(__name__)


def establish_db_connection(database_host, database, username, password):
def establish_db_connection(database_host, database, username, password, port=5432):
"""Establish a connection to some postgres db.

Args:
arg1 (str): The "database_host" (server).
arg2 (str): The "database" name.
arg3 (str): The "username".
arg4 (str): The postgres "password".
arg5 (int): The "port" (default 5432).

Returns:
psycopg2.extensions.connection: A psycopg2 database connection object.

"""
conn_string = "host={} dbname={} user={} password='{}'".format(database_host, database, username, password)
conn_string = "host={} dbname={} user={} password='{}' port={}".format(database_host, database, username, password, port)
db_connection = psycopg2.connect(conn_string)
conn_description = 'Made connection to database {} on db_host {}.'.format(database, database_host)

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5 changes: 4 additions & 1 deletion harvdev_utils/psycopg_functions/set_up_db_reading.py
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Expand Up @@ -52,6 +52,7 @@ def set_up_db_reading(report_label):
database = config['default']['Database']
username = config['default']['User']
password = config['default']['PGPassword']
port = config['default'].get('Port', '5432')
database_release = config['default']['Release']
epicycle = config['default']['Epicycle']
assembly = config['default']['Assembly']
Expand All @@ -73,6 +74,7 @@ def set_up_db_reading(report_label):
input_dir = '/src/input/'
log_dir = '/src/logs/'
# Optional variables:
port = os.environ.get('PORT', '5432')
epicycle = os.environ.get('EPICYCLE', 'unspecified')
assembly = os.environ.get('ASSEMBLY', 'R6')
annotation_release = os.environ.get('ANNOTATIONRELEASE', 'unspecified')
Expand Down Expand Up @@ -103,6 +105,7 @@ def set_up_db_reading(report_label):
set_up_dict['testing'] = args.testing

# Output filename
formatter = logging.Formatter('%(asctime)s : %(levelname)s : %(filename)s : Line No %(lineno)d : %(message)s')
alliance = args.alliance
if alliance is True:
set_up_dict['output_filename'] = output_dir + 'FB_' + alliance_schema + '_' + report_label + '.json'
Expand All @@ -128,7 +131,7 @@ def set_up_db_reading(report_label):
set_up_dict['log'] = logging.getLogger(__name__)

# Establish database connection.
set_up_dict['conn'], conn_description = establish_db_connection(server, database, username, password)
set_up_dict['conn'], conn_description = establish_db_connection(server, database, username, password, port)

# Official timestamp for this script.
set_up_dict['the_time'] = strict_rfc3339.now_to_rfc3339_localoffset()
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