From 6a6a4ebeb08379e77160924d0747d2fadc2e1a58 Mon Sep 17 00:00:00 2001
From: korikuzma <korikuzma@gmail.com>
Date: Fri, 19 Jan 2024 13:06:18 -0500
Subject: [PATCH 1/3] docs: update readme instructions for installing db dumps

* Add command to create anonymous user
* Update UTA version
---
 README.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index ef737ad..adcbbe3 100644
--- a/README.md
+++ b/README.md
@@ -243,11 +243,13 @@ the installation environment.*
     uta_admin are likely to ease installation.
 
         $ createuser -U postgres uta_admin
-        $ createdb -U postgres -O uta_admin uta 
+        $ createuser -U postgres anonymous
+        $ createdb -U postgres -O uta_admin uta
 
 3.  Restore the database.
 
-        $ gzip -cdq uta_20150827.pgd.gz | psql -U uta_admin -1 -v ON_ERROR_STOP=1 -d uta -Eae
+        $ uta_v=uta_20210129b
+        $ gzip -cdq $uta_v.pgd.gz | psql -U uta_admin -1 -v ON_ERROR_STOP=1 -d uta -Eae
 
 ## Developer Setup
 

From feedaa686faf9b003b3e7030b1b83f3d06100962 Mon Sep 17 00:00:00 2001
From: Brendan O'Donnell <1258849+b0d0nne11@users.noreply.github.com>
Date: Tue, 26 Mar 2024 11:40:36 -0400
Subject: [PATCH 2/3] Fix uta container search path (#256)

---
 misc/docker/load-uta.sh | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/misc/docker/load-uta.sh b/misc/docker/load-uta.sh
index 3c9105b..dd6f2bf 100755
--- a/misc/docker/load-uta.sh
+++ b/misc/docker/load-uta.sh
@@ -9,7 +9,7 @@
 
 # Overwrite pg_hba.conf, including whatever edits might have been made
 # by the postgres image
-cat <<EOF >"$PGDATA/pg_hba.conf" 
+cat <<EOF >"$PGDATA/pg_hba.conf"
 # allow the anonymous user to access uta without password
 # These lines must occur before more stringent authentication methods
 host   all   anonymous     0.0.0.0/0      trust
@@ -50,7 +50,7 @@ gzip -cdq < "${UTA_PGD_FN}" \
 
 gzip -cdq < "${UTA_PGD_FN}" \
     | perl -n \
-	   -e 'm/CREATE SCHEMA (uta_\d+)/ && print("ALTER DATABASE :DBNAME SET search_path=$1;\n");' \
+	   -e 'm/CREATE SCHEMA (uta_[\d\w]+)/ && print("ALTER DATABASE :DBNAME SET search_path=$1;\n");' \
 	   -e 'print if s/CREATE MATERIALIZED VIEW (.\S+) AS/REFRESH MATERIALIZED VIEW $1;/' \
     | psql -1e -U uta_admin -d uta -v ON_ERROR_STOP=1
 
@@ -58,16 +58,16 @@ gzip -cdq < "${UTA_PGD_FN}" \
 cat <<EOF
 =======================================================================
 =======================================================================
-== 
+==
 == $UTA_VERSION installed from
 == $UTA_PGD_URL
-== 
+==
 == You may now connect to uta like this:
-== 
+==
 == $  psql -h localhost -p <port> -U anonymous -d uta
-== 
+==
 == No password is required.
-== 
+==
 =======================================================================
 =======================================================================
 

From 53243eab2016c549eafc10b9306cd5fdd1ed6e92 Mon Sep 17 00:00:00 2001
From: Reece Hart <reece@biocommons.org>
Date: Mon, 8 Jul 2024 08:11:21 -0700
Subject: [PATCH 3/3] Update README.md

Fix small typo
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 5877cdc..70c7e92 100644
--- a/README.md
+++ b/README.md
@@ -10,7 +10,7 @@ aligning the same transcript to multiple references using multiple
 alignment methods. Specifically, it facilitates the following:
 
 -   Querying for multiple transcript sources through a single interface
--   Interpretating variants reported in literature against obsolete
+-   Interpreting variants reported in literature against obsolete
     transcript records
 -   Identifying regions where transcript and reference genome sequence
     assemblies disagree