VPC and EC2 added to the deploy

README.md

@@ -1,17 +1,46 @@
 # VCH MRI Booking Rule Based System
-- To start this project, you will need an AWS account with CLI and [SAM setup](https://docs.aws.amazon.com/serverless-application-model/latest/developerguide/serverless-sam-cli-install.html), as well as the following prior to running the Cloudformation script: 
-1. S3 bucket to store Cloudformation
-2. An EC2 instance with postgreSQL installed (See instructions below)
-3. Security Groups for Lambdas to access the database: Enable PostgreSQL on Port 5432 Inbound on the EC2 instance security group for the Lambda Security Group
-4. VPC with Private and Public Subnets, an Internet Gateway, and an Elastic IP Address. See [https://docs.aws.amazon.com/vpc/latest/userguide/VPC_Internet_Gateway.html](https://docs.aws.amazon.com/vpc/latest/userguide/VPC_Internet_Gateway.html) for more details. 
-- You will need add the security group and subnet into the [template file](template.yaml)
-- To run the cloudformation code, use the following commands: 
+- To start this project, you will need an AWS account with CLI and [SAM setup](https://docs.aws.amazon.com/serverless-application-model/latest/developerguide/serverless-sam-cli-install.html) as well as SSM Session Manager installed to log into your EC2 instance with a private IP address.
+
+
+# Deployment
+
+## 1. S3 bucket to store Cloudformation
+
+```
+aws s3api create-bucket --bucket {YOUR-BUCKET-NAME} --create-bucket-configuration  --region {YOUR-REGION}
+```
+## 2. Create an aws ec2 keypair
+
+```
+aws ec2 create-key-pair --key-name {MY-KEY-PAIR-NAME} --query 'KeyMaterial' --output text > MY-KEY-PAIR-NAME.pem 
+``` 
+
+## 3. Run the cloudformation code, use the following commands: 
+
+```
+sam package --s3-bucket {YOUR-BUCKET-NAME} --output-template-file out.yaml
+```
+
+```
+sam deploy --template-file out.yaml --capabilities CAPABILITY_IAM CAPABILITY_AUTO_EXPAND --stack-name {STACK-NAME} --parameter-overrides KeyName={YOUR-KEYNAME} 
+```
+## 4. Get the Instance ID of the  EC2 instance :
+
+Replace YOUR-REGION and YOUR-PROFILE
+
+```
+aws ec2 describe-instances --region {YOUR-REGION} --profile {YOUR-PROFILE}  --filter Name=tag:Name,Values=MriPostgresDB --filter Name=instance-state-name,Values=running  --query 'Reservations[*].Instances[*].{Instance:InstanceId}'   --output table 
+```
+
+## 5. Login to the EC2 instance using the SSM client 
+
+Replace  YOUR-INSTANCE-ID with results from step 4. as well as YOUR-REGION nad YOUR-PROFILE
+
 ```
-sam package --s3-bucket <s3 bucket name> --output-template-file out.yaml
-sam deploy --template-file out.yaml --capabilities CAPABILITY_IAM CAPABILITY_AUTO_EXPAND --stack-name <stack name>
+aws ssm start-session --region {YOUR-REGION} --profile {YOUR-PROFILE}  --target {YOUR-INSTANCE-ID} 
 ```
 
-## Setup PostgreSQL in EC2
+## 6. Setup PostgreSQL in EC2
 - Follow [these instructions](https://installvirtual.com/install-postgresql-10-on-amazon-ec2/) to download postgres onto EC2
 - To update the configuration for remote access of postgres: 
 ```bash
@@ -73,4 +102,4 @@ aws ssm put-parameter --name /mri-phsa/ec2 --value <instance id> --type SecureSt
 - [Sample Result](/csv/mri_dataset_results_0828.xlsx): Form to P-Value Data (most recent)
 
 ### Further Recommendations 
-This is a proof of concept for VCH and PHSA done by UBC CIC in collaboration with AWS. The algorithm can be improved by modifying weights and adding more words to conjunctions and spellchecker. Furthermore, one can also begin to consider the impact of other metadata that is already being recorded such as height, weight and age for scheduling an MRI scan. 
+This is a proof of concept for VCH and PHSA done by UBC CIC in collaboration with AWS. The algorithm can be improved by modifying weights and adding more words to conjunctions and spellchecker. Furthermore, one can also begin to consider the impact of other metadata that is already being recorded such as height, weight and age for scheduling an MRI scan.