From 3a915435c50576bb450b395d0505eb642cbc416c Mon Sep 17 00:00:00 2001
From: Matthew Andres Moreno <mmore500.login+gpg@gmail.com>
Date: Fri, 16 Feb 2024 23:39:12 -0500
Subject: [PATCH 1/2] Prompt user for potentially-destructive init op

---
 scripts/init/make_init_data.cypher.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/scripts/init/make_init_data.cypher.sh b/scripts/init/make_init_data.cypher.sh
index 6598e56..fc2ca69 100755
--- a/scripts/init/make_init_data.cypher.sh
+++ b/scripts/init/make_init_data.cypher.sh
@@ -24,5 +24,11 @@ CALL apoc.cypher.runMany("MATCH(n) DETACH DELETE n;
 CREATE (:User {provider: 'google', id: '${USER_ID}', deprecated: false})-[:CONTAINS_DETAILS {from: datetime(), version: 1}]->(:UserDetails {role: 'admin'});", {});
 EOF
 
-#cat init_data.cypher | docker exec --interactive phylodb-neo4j sh -c "cypher-shell -u neo4j -p password"
+echo "Initialize phylodb-neo4j container with init_data.cypher?"
+echo "WARNING: Performs a potentially destructive full delete operation."
+read -p "Continue? (y/n):" user_input
 
+if [[ "$user_input" = y* ]]; then
+    echo "Initializing container with init_data.cypher..."
+    cat init_data.cypher | docker exec --interactive phylodb-neo4j sh -c "cypher-shell -u neo4j -p password"
+fi

From cee3aa9050dd6b0da9affe16cef9f076ae908689 Mon Sep 17 00:00:00 2001
From: Matthew Andres Moreno <mmore500.login+gpg@gmail.com>
Date: Sat, 17 Feb 2024 00:19:21 -0500
Subject: [PATCH 2/2] Add direct instructions for example

---
 README.md | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/README.md b/README.md
index 75518c1..9224ee1 100644
--- a/README.md
+++ b/README.md
@@ -85,6 +85,26 @@ The script [`example.sh`](scripts/example/example.sh) illustrates the API use ca
 It is important that a Google account is registered as admin, and that you have a valid token.
 Check the initialization step in the [`example.sh`](scripts/example/example.sh) script, and/or the [template for data initialization](scripts/init/init_data.cypher).
 
+To run the example,
+
+   export TOKEN="YOUR_TOKEN"
+   export USER_ID="YOUR_USER_ID"
+   git clone https://github.com/phyloviz/phyloDB.git phyloDB.git
+   cd phyloDB.git/
+   sed 's|#spring.data.neo4j.uri=bolt://phylodb-neo4j:7687|spring.data.neo4j.uri=bolt://phylodb-neo4j:7687|g' -i phylodb/bin/main/application.properties
+   sed 's|spring.data.neo4j.uri=bolt://localhost:7687|#spring.data.neo4j.uri=bolt://localhost:7687|g' -i phylodb/bin/main/application.properties
+   ./configure.sh
+   cd docker
+   ./build-docker.sh
+   ./start-docker.sh
+   cd ../scripts/example
+   echo y | ./example.sh
+
+To generate `YOUR_TOKEN`, access <https://developers.google.com/oauthplayground/>, sign in, and click 'Authorize
+APIs' with the custom scope `https://www.googleapis.com/auth/userinfo.email`.
+Click in 'Exchange authorization code for tokens' and use the provided 'Access token'.
+Use the account email associated with this token as `YOUR_USER_ID`.
+
 # More documentation
 The [Wiki](https://github.com/phyloviz/phyloDB/wiki) of this project documents several topics, namely archictecural views, deployment, authentication and API definition (usage).