From 866285fcff0501eb5b972d63155a0e17d261f3b1 Mon Sep 17 00:00:00 2001
From: Avery Wang <averyjwang@gmail.com>
Date: Tue, 16 Jul 2024 08:11:21 -0700
Subject: [PATCH] new script for automating truststore update

---
 README.md            |  9 +++++++++
 update_truststore.sh | 37 +++++++++++++++++++++++++++++++++++++
 2 files changed, 46 insertions(+)
 create mode 100644 update_truststore.sh

diff --git a/README.md b/README.md
index 2aac9ae..5b84dce 100644
--- a/README.md
+++ b/README.md
@@ -62,6 +62,15 @@ keytool -import -noprompt \
     -storepass annotation-tools
 ```
 
+### Updating an existing trust store
+
+If an existing trust store is already available, the `update_truststore.sh` script can be used to update it with the latest certificate. The script requires `openssl` and `keytool` be installed on the machine; it will pull the latest certificate from `https://genie.genomenexus.org` and update it in the trust store. 
+
+The script can be run as follows:
+```
+sh update_truststore.sh <path to truststore> <truststore password>
+```
+
 ### Install Python packages
 
 You need to have python3 installed.
diff --git a/update_truststore.sh b/update_truststore.sh
new file mode 100644
index 0000000..7aef3ca
--- /dev/null
+++ b/update_truststore.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+
+GENIE_GENOMENEXUS_SITE="genie.genomenexus.org"
+GENOMENEXUS_SERVERNAME="www.genomenexus.org"
+
+truststore=$1
+truststore_password=$2
+
+if [ -z $truststore ] ; then
+	echo "Missing truststore, exiting..."
+	exit 1
+fi
+
+if [ -z $truststore_password ] ; then
+	echo "Missing truststore password, exiting..."
+	exit 1
+fi
+
+which openssl
+if [ $? -ne 0 ] ; then
+	echo "openssl needs to be installed. Exiting..."
+	exit 1
+fi
+
+which keytool
+if [ $? -ne 0 ] ; then
+	echo "keytool needs to be installed. Exiting..."
+	exit 1
+fi
+
+true | openssl s_client -connect $GENIE_GENOMENEXUS_SITE:443 -servername $GENOMENEXUS_SERVERNAME 2>/dev/null | openssl x509 > tmp.cert
+
+keytool -delete -noprompt -alias $GENIE_GENOMENEXUS_SITE -keystore $truststore -storepass $truststore_password
+keytool -import -noprompt -alias $GENIE_GENOMENEXUS_SITE -file tmp.cert -keystore $truststore -storepass $truststore_password
+rm tmp.cert
+
+echo "$truststore updated with newest cert from $GENOMENEXUS_SITE"