From 77deb53503d7192cf1edc99c23664647f15225ef Mon Sep 17 00:00:00 2001
From: dpwrussell <douglas_russell@hms.harvard.edu>
Date: Mon, 24 Jul 2017 12:30:16 -0400
Subject: [PATCH 1/3] Restore database from file location

---
 60-database.sh | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/60-database.sh b/60-database.sh
index 076c153a..bfe1ccaf 100755
--- a/60-database.sh
+++ b/60-database.sh
@@ -39,7 +39,12 @@ psql -w -h "$DBHOST" -U "$DBUSER" "$DBNAME" -c \
     "select * from dbpatch" 2> /dev/null && {
     echo "Upgrading database"
     $omego db upgrade --serverdir=OMERO.server
-} || {
-    echo "Initialising database"
-    $omego db init --rootpass "$ROOTPASS" --serverdir=OMERO.server
-}
+    } || {
+        if [ -f "/sql/db.sql" ]; then
+            echo "Restoring database"
+            $omego db init --omerosql "/sql/db.sql" --serverdir=OMERO.server
+        else
+            echo "Initialising database"
+            $omego db init --rootpass "$ROOTPASS" --serverdir=OMERO.server
+        fi
+    }

From 0b0ebbdac833383472b0758a4a36588ca202eb96 Mon Sep 17 00:00:00 2001
From: dpwrussell <douglas_russell@hms.harvard.edu>
Date: Wed, 26 Jul 2017 15:50:59 -0400
Subject: [PATCH 2/3] Make sql file location a bit more logical and in a
 directory owned by omero-server

---
 60-database.sh | 4 ++--
 Dockerfile     | 3 +++
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/60-database.sh b/60-database.sh
index bfe1ccaf..79b445f1 100755
--- a/60-database.sh
+++ b/60-database.sh
@@ -40,9 +40,9 @@ psql -w -h "$DBHOST" -U "$DBUSER" "$DBNAME" -c \
     echo "Upgrading database"
     $omego db upgrade --serverdir=OMERO.server
     } || {
-        if [ -f "/sql/db.sql" ]; then
+        if [ -f "/opt/omero/sql/db.sql" ]; then
             echo "Restoring database"
-            $omego db init --omerosql "/sql/db.sql" --serverdir=OMERO.server
+            $omego db init --omerosql "/opt/omero/sql/db.sql" --serverdir=OMERO.server
         else
             echo "Initialising database"
             $omego db init --rootpass "$ROOTPASS" --serverdir=OMERO.server
diff --git a/Dockerfile b/Dockerfile
index fc884cf4..936df3e0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -19,6 +19,9 @@ RUN curl -L -o /usr/local/bin/dumb-init \
 ADD entrypoint.sh /usr/local/bin/
 ADD 50-config.py 60-database.sh 99-run.sh /startup/
 
+RUN mkdir -p /opt/omero/sql && \
+    chown omero-server:omero-server /opt/omero/sql
+
 USER omero-server
 
 EXPOSE 4063 4064

From 219a7a86530241e06e073de94c6ebaf82a9283d8 Mon Sep 17 00:00:00 2001
From: jmoore <josh@glencoesoftware.com>
Date: Thu, 8 Feb 2018 07:31:07 +0000
Subject: [PATCH 3/3] Override omero.db.name (fix #16)

omego assumes that the DBHOSE and DBNAME are set via
bin/omero config. DBNAME was previously *not* set to
prevent an accidental upgrade of a database. Here we
set DBNAME only if the database has not been created
elsewhere.
---
 60-database.sh | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/60-database.sh b/60-database.sh
index 076c153a..d4909e63 100755
--- a/60-database.sh
+++ b/60-database.sh
@@ -16,8 +16,19 @@ else
     DBHOST=db
     $omero config set omero.db.host "$DBHOST"
 fi
+
+CONFIG_omero_db_name=${CONFIG_omero_db_name:-}
+if [ -n "$CONFIG_omero_db_name" ]; then
+    DBNAME="$CONFIG_omero_db_name"
+    DBNAME_src=env
+else
+    # Delay setting in config until *after*
+    # the upgrade is attempted.
+    DBNAME=omero
+    DBNAME_src=default
+fi
+
 DBUSER="${CONFIG_omero_db_user:-omero}"
-DBNAME="${CONFIG_omero_db_name:-omero}"
 DBPASS="${CONFIG_omero_db_pass:-omero}"
 ROOTPASS="${ROOTPASS:-omero}"
 
@@ -40,6 +51,9 @@ psql -w -h "$DBHOST" -U "$DBUSER" "$DBNAME" -c \
     echo "Upgrading database"
     $omego db upgrade --serverdir=OMERO.server
 } || {
+    if [ "$DBNAME_src" = default ]; then
+        $omero config set omero.db.name "$DBNAME"
+    fi
     echo "Initialising database"
     $omego db init --rootpass "$ROOTPASS" --serverdir=OMERO.server
 }