Merge remote-tracking branch 'upstream/topic-release' into topic-release

Author: AdityaSrikanth

docker-compose.yml

@@ -18,7 +18,7 @@ services:
       - sp2net
 
   cc-3102:
-    image: 045938549113.dkr.ecr.us-east-2.amazonaws.com/researchportal:_fd_1.9.1_b982
+    image: 045938549113.dkr.ecr.us-east-2.amazonaws.com/researchportal:_fd_1.9.2_b995
     secrets:
       - source: sp2prod-config.json
         target: /rlc/cc/server/app/config/config.json
@@ -43,7 +43,7 @@ services:
     command: /bin/bash start.sh 
 
   scheduler-3102:
-    image: 045938549113.dkr.ecr.us-east-2.amazonaws.com/researchportal:_fd_1.9.1_b982
+    image: 045938549113.dkr.ecr.us-east-2.amazonaws.com/researchportal:_fd_1.9.2_b995
     secrets:
       - source: sp2prod-config.json
         target: /rlc/cc/server/app/config/config.json

dump/studies.json

@@ -1,5 +1,6 @@
 #!/bin/bash
 # Verify that utilities we use in this script are installed on the machine
+# this is a test 
 echo "Verifying utilities are installed"
 apps=(jq aws)
 for program in "${apps[@]}"; do

mainonly.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+while IFS=$'\n' read -r c; do
+	if [ "$c" == "q" ]; then
+		echo "$c" >&2
+		exit 0
+	fi
+	echo "$c" | yq -o=json eval '.' "$c" |
+		jq -r '{
+            name: .Name,
+            description: .Description,
+            tags:.Tags,
+            resourceDetails:(
+                .Resources|map({
+                    description: .Description,
+                    arn: .ARN,
+                    region: .Region,
+                    type: (.Type|select(.=="S3 Bucket")| "s3")}
+                    )
+                ),
+            moreInformation: (.License+"\n"+.Documentation+"\n"+.Contact),
+            bookmarkedBy: [],
+            projectId: [],
+            levelOfSharing: 0,
+            sharedTo: [],
+            studyType: "Public",
+            __v: 0,
+            isDeleted: false,
+            repositoryName: "Registry of Open Data on AWS",
+            isShared: false,
+            isLinked: false
+        }'
+done | jq -s

makestudies.sh

@@ -80,6 +80,12 @@
         "source": "config",
         "destination": "{{user `RG_SRC`}}/config"
     },
+    {
+      "type": "shell",
+      "inline": [
+         "sudo apt install zip -y"
+        ]
+    },
     {
       "type": "shell",
       "environment_vars": ["RG_HOME=/opt/deploy/sp2","RG_SRC=/home/ubuntu"],

packer-rg.json

@@ -5,7 +5,7 @@ sudo yum update -y
 sudo yum install -y gcc-7.3.* gcc-gfortran-7.3.* gcc-c++-7.3.*
 sudo yum install -y java-1.8.0-openjdk-devel-1.8.0.*
 sudo yum install -y readline-devel-6.2 zlib-devel-1.2.* bzip2-devel-1.0.* xz-devel-5.2.* pcre-devel-8.32
-sudo yum install -y libcurl-devel-7.76.1 libpng-devel-1.5.* cairo-devel-1.15.* pango-devel-1.42.*
+sudo yum install -y libcurl-devel-7.79.* libpng-devel-1.5.* cairo-devel-1.15.* pango-devel-1.42.*
 sudo yum install -y xorg-x11-server-devel-1.20.* libX11-devel-1.6.* libXt-devel-1.1.*
 
 # Install R from source (https://docs.rstudio.com/resources/install-r-source/)

products/RStudio/machine-images/config/infra/provisioners/provision-rstudio.sh

@@ -1,12 +1,12 @@
 [
-    {
-        "product": "Nextflow Advanced",
-        "pipeline": "RL_RG_Nextflow_Advanced",
-        "path": "/RL/RG/StandardCatalog/nextflow-latest"
-    },
-    {
-        "product": "RStudio",
-        "pipeline": "RL_RG_RStudio",
-        "path": "/RL/RG/StandardCatalog/RStudio"
-    }
+  {
+    "product": "Nextflow Advanced",
+    "pipeline": "RL_RG_Nextflow_Advanced",
+    "path": "/RL/RG/StandardCatalog/nextflow-latest"
+  },
+  {
+    "product": "RStudio",
+    "pipeline": "RL_RG_RStudio",
+    "path": "/RL/RG/StandardCatalog/RStudio"
+  }
 ]

products/img-builder-config.json

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-jq -r '.Products | map( (.ami_id_list |= ( map_values(to_entries ) | flatten)) )'
+jq -r '.Products | map( (.ami_id_list |= ( map_values(to_entries ) | flatten)) )'

products/make-ami-list-json.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_1.9.1_b982
+sudo docker pull 045938549113.dkr.ecr.us-east-2.amazonaws.com/researchportal:_fd_1.9.2_b995
 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:1.9.0_b2

provisioners/provision-ecr.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+version="0.1.0"
+echo "Connecting to DB....(connect-db.sh v$version)"
+
+if [ "$1" == "-h" ]; then
+	echo "Usage: $(basename $0)"
+	exit 0
+fi
+
+[ -z "$RG_HOME" ] && RG_HOME='/opt/deploy/sp2'
+echo "RG_HOME=$RG_HOME"
+myinput=$(cat "$RG_HOME/config/mongo-config.json")
+if [ -z "$myinput" ]; then
+	echo "Could not find DB details file. Exiting"
+	exit 1
+fi
+
+mydbuser=$(jq -r '.db_auth_config.username' <<<"${myinput}")
+mydbuserpwd=$(jq -r '.db_auth_config.password' <<<"${myinput}")
+
+if [ -z "$mydbuser" ] || [ -z "$mydbuserpwd" ]; then
+	echo "Could not find DB details. Exiting"
+	exit 1
+fi
+
+if [ ! -f "$RG_HOME/docker-compose.yml" ]; then
+	echo "docker-compose.yml does not exist. Exiting"
+	exit 1
+fi
+mydocdburl=$(grep DB_HOST "$RG_HOME/docker-compose.yml" | head -1 | sed -e "s/.*DB_HOST=//")
+if [ -z "$mydocdburl" ]; then
+	echo "Could not find DB URL. Exiting"
+	exit 1
+fi
+
+mongo --ssl --host "$mydocdburl:27017" --sslCAFile "$RG_HOME/config/rds-combined-ca-bundle.pem" \
+	--username "$mydbuser" --password "$mydbuserpwd"