From 1c9348dc7950fd4f5b2b22f7065e9a058fb5090d Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Fri, 14 Jun 2024 09:11:42 -0400
Subject: [PATCH] feat!: change default postgresql port to 5432 (#292)

* close #288
---
 docs/source/install.rst                   | 4 ++--
 docs/source/usage.rst                     | 2 +-
 src/cool_seq_tool/sources/uta_database.py | 2 +-
 src/cool_seq_tool/version.py              | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/docs/source/install.rst b/docs/source/install.rst
index c6c66977..547b7054 100644
--- a/docs/source/install.rst
+++ b/docs/source/install.rst
@@ -42,9 +42,9 @@ Cool-Seq-Tool requires an available instance of the Universal Transcript Archive
 
    export UTA_VERSION=uta_20210129b.pgd.gz  # most recent as of 2023/12/05
    curl -O https://dl.biocommons.org/uta/$UTA_VERSION
-   gzip -cdq ${UTA_VERSION} | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5433
+   gzip -cdq ${UTA_VERSION} | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5432
 
-By default, Cool-Seq-Tool expects to connect to the UTA database via a PostgreSQL connection served local on port 5433, under the PostgreSQL username ``uta_admin`` and the schema ``uta_20210129b``.
+By default, Cool-Seq-Tool expects to connect to the UTA database via a PostgreSQL connection served local on port 5432, under the PostgreSQL username ``uta_admin`` and the schema ``uta_20210129b``.
 
 Set up SeqRepo
 --------------
diff --git a/docs/source/usage.rst b/docs/source/usage.rst
index d717659a..1920a12c 100644
--- a/docs/source/usage.rst
+++ b/docs/source/usage.rst
@@ -101,7 +101,7 @@ Individual classes will accept arguments upon initialization to set parameters r
    * - ``SEQREPO_ROOT_DIR``
      - Path to SeqRepo directory (i.e. contains ``aliases.sqlite3`` database file, and ``sequences`` directory). Used by :py:class:`SeqRepoAccess <cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess`. If not defined, defaults to ``/usr/local/share/seqrepo/latest``.
    * - ``UTA_DB_URL``
-     - A `libpq connection string <https://www.postgresql.org/docs/current/libpq-connect.html#LIBPQ-CONNSTRING>`_, i.e. of the form ``postgresql://<user>:<password>@<host>:<port>/<database>/<schema>``, used by the :py:class:`cool_seq_tool.sources.uta_database.UtaDatabase` class. By default, it is set to ``postgresql://uta_admin:uta@localhost:5433/uta/uta_20210129b``.
+     - A `libpq connection string <https://www.postgresql.org/docs/current/libpq-connect.html#LIBPQ-CONNSTRING>`_, i.e. of the form ``postgresql://<user>:<password>@<host>:<port>/<database>/<schema>``, used by the :py:class:`cool_seq_tool.sources.uta_database.UtaDatabase` class. By default, it is set to ``postgresql://uta_admin:uta@localhost:5432/uta/uta_20210129b``.
    * - ``LIFTOVER_CHAIN_37_TO_38``
      - A path to a `chainfile <https://genome.ucsc.edu/goldenPath/help/chain.html>`_ for lifting from GRCh37 to GRCh38. Used by :py:class:`cool_seq_tool.sources.uta_database.UtaDatabase` as input to `agct <https://pypi.org/project/agct/>`_. If not provided, agct will fetch it automatically from UCSC.
    * - ``LIFTOVER_CHAIN_38_TO_37``
diff --git a/src/cool_seq_tool/sources/uta_database.py b/src/cool_seq_tool/sources/uta_database.py
index 4ff5e3de..2a622e05 100644
--- a/src/cool_seq_tool/sources/uta_database.py
+++ b/src/cool_seq_tool/sources/uta_database.py
@@ -24,7 +24,7 @@
 LIFTOVER_CHAIN_38_TO_37 = environ.get("LIFTOVER_CHAIN_38_TO_37")
 
 UTA_DB_URL = environ.get(
-    "UTA_DB_URL", "postgresql://uta_admin:uta@localhost:5433/uta/uta_20210129b"
+    "UTA_DB_URL", "postgresql://uta_admin:uta@localhost:5432/uta/uta_20210129b"
 )
 
 logger = logging.getLogger(__name__)
diff --git a/src/cool_seq_tool/version.py b/src/cool_seq_tool/version.py
index b8b2f532..0ffdb5fe 100644
--- a/src/cool_seq_tool/version.py
+++ b/src/cool_seq_tool/version.py
@@ -1,2 +1,2 @@
 """Define package version."""
-__version__ = "0.4.0-dev3"
+__version__ = "0.4.0-dev4"