Merge pull request #119 from RLOpenCatalyst/topic-release

Newbuild 1.14.0 updates

Author: ravigurram8

config/config.json

@@ -200,6 +200,8 @@
     "endTime": "21:10:00"
   },
   "cronJobForEodSync" : "*/60 * * * *",
+  "cronJobForSync" : "00 08 * * *",
+  "cronJobForEodPIReport": "00 10 * * *",
   "sampleCSVForUser": "users.csv",
   "sampleCSVBucketRegion": "REPLACE_WITH_REGION",
   "sessionMaxAge" : 900000

config/mongo-config.json

@@ -1,14 +1,15 @@
 {
         "db_ssl_enable": "REPLACE_WITH_TRUE_FALSE",
         "db_auth_enable": "REPLACE_WITH_TRUE_FALSE",
-	"db_documentdb_enable": "REPLACE_WITH_TRUE_FALSE",
+	    "db_documentdb_enable": "REPLACE_WITH_TRUE_FALSE",
         "db_ssl_config": {
             "CAFile": "rds-combined-ca-bundle.pem",
             "PEMFile": "REPLACE_WITH_PEM_FILE_NAME"
         },
         "db_auth_config": {
             "username": "app",
             "password": "App123",
+            "secretName": "REPLACE_WITH_secretarn",
             "authenticateDb":"admin"
         }
 

config/settings-config.json

@@ -84,10 +84,6 @@
           {
             "action": "Unshare",
             "imageUrl": "../../assets/images/unshare@2x.png"
-          },
-          {
-            "action": "Upload",
-            "imageUrl": "../../assets/images/cloud-computing@2x.png"
           }
         ]
       },
@@ -793,7 +789,7 @@
         ],
         "action": []
       },
-      "external": {
+      "internal": {
         "connect":[
           {
             "menu": "Explore",
@@ -804,7 +800,12 @@
             "imageUrl": "../../assets/images/link@2x.png"
           }
         ],
-        "action":[]
+        "action":[
+          {
+            "action": "Edit",
+            "imageUrl": "../../assets/images/editStudy.png"
+          }
+        ]
       },
       "Personal": {
         "connect": [
@@ -880,7 +881,7 @@
       },
       {
         "key": "studyType",
-        "value": "external"
+        "value": "internal"
       },
       {
         "key": "studyType",

deploy.sh

@@ -246,6 +246,7 @@ aws s3 cp "$localhome"/config.tar.gz s3://"$bucketname"
 rm -f config.tar.gz
 
 echo "Copying script files to new bucket"
+sed -i "s/secret_name/RL-RG-$runid-$env/g"  "$localhome"/scripts/connect-db.sh  
 tar -czf scripts.tar.gz scripts/*
 tar -tf scripts.tar.gz
 aws s3 cp "$localhome"/scripts.tar.gz s3://"$bucketname"
@@ -337,10 +338,10 @@ function create_cognito_pool() {
 function create_doc_db() {
 	echo "Creating new stack $1"
 	aws cloudformation deploy --template-file "$localhome"/rg_document_db.yml --stack-name "$1" \
-		--parameter-overrides MasterUser="$appuser" MasterPassword="$appuserpassword" \
+		--parameter-overrides DocDBSecretName="RL-RG-$runid-$env" VpceSecurityGroupName="RGVE-SG-$runid" \
 		DBClusterName="RGCluster-$runid" DBInstanceName="RGInstance-$runid" DBInstanceClass="db.t3.medium" \
 		Subnet1="$subnet1id" Subnet2="$subnet2id" Subnet3="$subnet3id" VPC="$vpcid" \
-		SecurityGroupName="RGDB-SG-$runid" DocDBSubnetGroupName="RGDBSubnet-$runid"
+		SecurityGroupName="RGDB-SG-$runid" DocDBSubnetGroupName="RGDBSubnet-$runid" --capabilities CAPABILITY_IAM CAPABILITY_NAMED_IAM CAPABILITY_AUTO_EXPAND
 	echo "Waiting for stack $1 to finish deploying..."
 	aws cloudformation wait stack-create-complete --stack-name "$1"
 }
@@ -355,6 +356,7 @@ function create_image_builder() {
 
 }
 
+
 function create_main_stack() {
 	echo "Creating new stack $1"
 	#update the AMI id in the RGMainStack CFT
@@ -366,14 +368,14 @@ function create_main_stack() {
 	echo "UserPool ClientId: $userpoolclient_id"
 	echo "BucketName $bucketname"
 	echo "RG URL: $rgurl"
-	if [ -n "$appuserpassword" ]; then
+	if [ -n "$secpassword" ]; then
 		echo "UserPassword is not a blank string"
 	fi
 	if [ -n "$adminpassword" ]; then
 		echo "AdminPassword is not a blank string"
 	fi
 	echo "VPC Id: $vpcid"
-	echo "subnet1id: subnet1id"
+	echo "subnet1id: $subnet1id"
 	echo "Key Pair: $keypairname"
 	echo "TGARN: $tgarn"
 	echo "DocDBURL: $docdburl"
@@ -382,7 +384,7 @@ function create_main_stack() {
 	aws cloudformation deploy --template-file "$localhome"/rg_main_stack.yml \
 		--stack-name "$mainstackname" \
 		--parameter-overrides CFTBucketName="$bucketname" RGUrl="$rgurl"\
-		UserPassword="$appuserpassword" AdminPassword="$adminpassword" \
+		UserPassword="$secpassword" AdminPassword="$adminpassword" \
 		VPC="$vpcid" Subnet1="$subnet1id" KeyName1="$keypairname" TGARN="$tgarn" \
 		DocumentDBInstanceURL="$docdburl" Environment="$env" BaseAccountPolicyName="RG-Portal-Base-Account-Policy-$env-$runid" \
 		--capabilities CAPABILITY_NAMED_IAM
@@ -506,12 +508,14 @@ ac_name=$(aws sts get-caller-identity --query "Account" --output text)
 r53_domain_name="${rgurl//http[s]*:\/\//}"
 jqcmd='.HostedZones[] | select(.Name=='"\"${r53_domain_name}.\""')|.Id'
 hosted_zone=$(aws route53 list-hosted-zones-by-name --dns-name "$r53_domain_name" | jq -r "$jqcmd" | sed -e 's#\/hostedzone\/##')
+secretdb_arn=$(aws secretsmanager get-secret-value --secret-id RL-RG-$runid-$env | jq --raw-output .ARN) 
 echo "Creating configs locally"
 export RG_ENV="$env"
 ./makeconfigs.sh "$userpool_id" "$userpoolclient_id"  "$bucketname" "$appuser" "$appuserpassword" \
-            "$runid" "$rgurl" "$region" "ROLE_NAME" "$ac_name" "$hosted_zone"
+            "$runid" "$rgurl" "$region" "ROLE_NAME" "$ac_name" "$hosted_zone" "$secretdb_arn"
 echo "Uploading configs to $bucketname"
 aws s3 cp "$localhome"/config.tar.gz s3://"$bucketname"
+secpassword=$(aws secretsmanager get-secret-value --secret-id RL-RG-$runid-$env  --version-stage AWSCURRENT | jq --raw-output .SecretString| jq -r ."password")
 #===============================================================================================================
 #Creating Main stack
 echo "Deploying main stack (roles, ec2 instance etc.)"

docker-compose.yml

@@ -18,7 +18,7 @@ services:
       - sp2net
 
   cc-3102:
-    image: 045938549113.dkr.ecr.us-east-2.amazonaws.com/researchportal:_fd_1.13.2_b1352
+    image: 045938549113.dkr.ecr.us-east-2.amazonaws.com/researchportal:_fd_1.14.0_b1444
     secrets:
       - source: sp2prod-config.json
         target: /rlc/cc/server/app/config/config.json
@@ -42,7 +42,7 @@ services:
     command: /bin/bash start.sh
 
   scheduler-3102:
-    image: 045938549113.dkr.ecr.us-east-2.amazonaws.com/researchportal:_fd_1.13.2_b1352
+    image: 045938549113.dkr.ecr.us-east-2.amazonaws.com/researchportal:_fd_1.14.0_b1444
     secrets:
       - source: sp2prod-config.json
         target: /rlc/cc/server/app/config/config.json
@@ -62,7 +62,7 @@ services:
     command: node ./app/scheduler/app.js
 
   notificationsink:
-    image: 045938549113.dkr.ecr.us-east-2.amazonaws.com/notificationsink:1.13.2_b3
+    image: 045938549113.dkr.ecr.us-east-2.amazonaws.com/notificationsink:1.14.0_b3
     secrets:
       - source: sp2prod-config.json
         target: /opt/app/config/config.json

dump/configs.json

@@ -345,7 +345,8 @@
         "ownCatalogWithTagLink" : "https://researchgateway.readthedocs.io/en/latest/",
         "isProductDailyCostMigration_v1_13_0_Required" : true,
         "projectStorage" : "https://researchgateway.readthedocs.io/en/latest/GettingStarted.html#project-storage"
-    }
+    },
+    "studySelectionCount" : 2
   },
   {
     "_id" : { 
@@ -394,5 +395,18 @@
         "pipeline_git_url": "https://github.com/gatk-workflows/gatk4-basic-joint-genotyping.git"
       }
     ]
-  }
+  },
+  {
+        "key" : "study",
+        "message" : "This config help us to configure the external studies in the product launch form",
+        "value" : {
+                "productList" : [
+                        "ec2",
+                        "rstudio",
+                        "nextflow",
+                        "cromwell"
+                ]
+        },
+        "studySelectionCount" : 4
+}
 ]

makeconfigs.sh

@@ -2,7 +2,7 @@
 version="0.1.0"
 echo "Making configs locally...(makeconfigs.sh v$version)"
 # Ensure right number of params
-if [ $# -lt 11 ]; then
+if [ $# -lt 12 ]; then
 	echo 'At least 11 parameters are required!'
 	echo '  Param 1: AWS Cognito User Pool id'
 	echo '  Param 2: AWS Cognito client id'
@@ -19,6 +19,7 @@ if [ $# -lt 11 ]; then
 	echo '            same account to which Research Gateway is to be deployed'
 	echo '  Param 11: Hosted Zone Id in Route53 to be used for enabling SSL'
     echo '            in projects'
+	echo '  Param 12: AWS secret ARN'
 	exit 1
 fi
 
@@ -31,6 +32,7 @@ myrunid=$6
 myurl=$7
 region=$8
 role_name=$9
+secret_arn=${12}
 RG_HOME=$(mktemp -d -t "config.$myrunid.XXX")
 echo "RG_HOME=$RG_HOME"
 RG_SRC=$(pwd)
@@ -106,6 +108,7 @@ jq -r ".db_ssl_enable=true" "$mytemp/mongo-config.json" |
 	jq -r ".db_documentdb_enable=true" |
 	jq -r ".db_auth_config.username=\"$myappuser\"" |
 	jq -r ".db_auth_config.password=\"$myapppwd\"" |
+	jq -r ".db_auth_config.secretName=\"$secret_arn\"" |
 	jq -r '.db_auth_config.authenticateDb="admin"' >"${RG_HOME}/config/mongo-config.json"
 
 echo "Modifying notification-config.json"
@@ -122,6 +125,7 @@ jq -r ".db_ssl_enable=true" "$mytemp/mongo-config.json" |
 	jq -r '.db_ssl_config.PEMFile="mongodb.pem"' |
 	jq -r ".db_auth_config.username=\"$myappuser\"" |
 	jq -r ".db_auth_config.password=\"$myapppwd\"" |
+	jq -r ".db_auth_config.secretName=\"$secret_arn\"" |
 	jq -r '.db_auth_config.authenticateDb="admin"' >"${RG_HOME}/config/mongo-config.json"
 tar -C "$RG_HOME" -czf config.tar.gz "config"/*
 tar -tf config.tar.gz

provisioners/provision-ecr.sh

@@ -1,5 +1,5 @@
 #!/bin/bash -xe
 sudo docker login -u AWS -p $(aws ecr get-login-password --region us-east-2) 045938549113.dkr.ecr.us-east-2.amazonaws.com
-sudo docker pull 045938549113.dkr.ecr.us-east-2.amazonaws.com/researchportal:_fd_1.13.2_b1352
+sudo docker pull 045938549113.dkr.ecr.us-east-2.amazonaws.com/researchportal:_fd_1.14.0_b1444
 sudo docker pull 045938549113.dkr.ecr.us-east-2.amazonaws.com/nginx:latest
-sudo docker pull 045938549113.dkr.ecr.us-east-2.amazonaws.com/notificationsink:1.13.2_b3
+sudo docker pull 045938549113.dkr.ecr.us-east-2.amazonaws.com/notificationsink:1.14.0_b3