Merge branch 'main' into topic-release

Author: RLIndia

packer-rg.json

@@ -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"],

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

@@ -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/img-builder-config.json

@@ -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/make-ami-list-json.sh

@@ -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)) )'

scripts/fixdocdb.sh

@@ -70,7 +70,7 @@ echo "Downloading new dump file..."
 # fi
 aws s3 cp s3://${S3_SOURCE}/dump.zip "$RG_SRC"
 echo "Extracting seed data from dump file."
-unzip "$RG_SRC/dump.zip" -d "$RG_SRC"
+unzip "$RG_SRC/dump.zip" -o -d "$RG_SRC"
 if [ ! "$(ls -A $RG_SRC/dump)" ]; then
 	echo "Error: No files found in dump folder. Your database cannot be seeded."
 else

scripts/import-seed-db.sh

@@ -0,0 +1,71 @@
+#!/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
+if [ $# -gt 0 ]; then
+	mydbname=$1
+fi
+
+if [ $# -gt 1 ]; then
+	mycollection=$2
+fi
+[ -z "$RG_HOME" ] && RG_HOME='/opt/deploy/sp2'
+echo "RG_HOME=$RG_HOME"
+[ -z "$RG_SRC" ] && RG_SRC='/home/ubuntu'
+echo "RG_SRC=$RG_SRC"
+myinput=$(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
+if [ "$mycollection" == "ALL" ]; then
+        echo "Importing all 3 collections into $mydocdburl"
+        mongoimport --host "$mydocdburl:27017" --ssl \
+                --sslCAFile "$RG_HOME/config/rds-combined-ca-bundle.pem" \
+                --username "$mydbuser" --password "$mydbuserpwd" \
+                --db "${mydbname}" --collection=studies \
+                "$RG_SRC/dump/studies.json"
+        mongoimport --host "$mydocdburl:27017" --ssl \
+                --sslCAFile "$RG_HOME/config/rds-combined-ca-bundle.pem" \
+                --username "$mydbuser" --password "$mydbuserpwd" \
+                --db "${mydbname}" --collection=standardcatalogitems\
+                "$RG_SRC/dump/standardcatalogitems.json"
+        mongoimport --host "$mydocdburl:27017" --ssl \
+                --sslCAFile "$RG_HOME/config/rds-combined-ca-bundle.pem" \
+                --username "$mydbuser" --password "$mydbuserpwd" \
+                --db "${mydbname}" --collection=configs\
+                "$RG_SRC/dump/configs.json"
+else
+        # trunk-ignore(shellcheck/SC2060)
+        mycollection=$(echo "$mycollection" | tr [:upper:] [:lower:])
+        if [ "$mycollection" != "studies" ] && [ "$mycollection" != "standardcatalogitems" ] && [ "$mycollection" != "configs" ]; then
+                echo "Unknown collection $mycollection" && exit 1
+        fi
+        mongoimport --host "$mydocdburl:27017" --ssl \
+                --sslCAFile "$RG_HOME/config/rds-combined-ca-bundle.pem" \
+                --username "$mydbuser" --password "$mydbuserpwd" \
+                --db "${mydbname}" --collection=$mycollection \
+                "$RG_SRC/dump/$mycollection.json"
+fi

updatescripts.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 # Download the latest scripts
-version='0.1.3'
+version='0.1.4'
 echo "updatescripts.sh version: $version"
 [ -z "$RG_HOME" ] && RG_HOME='/opt/deploy/sp2'
 echo "RG_HOME=$RG_HOME"
@@ -64,6 +64,11 @@ if [ ! -f /usr/local/sbin/updatessmpaths.sh ] || [ $RG_SRC/scripts/updatessmpath
 	echo "Found newer version of updatessmpaths.sh. Updating"
 	cp $RG_SRC/scripts/updatessmpaths.sh /usr/local/sbin/
 fi
-grep -i 'version=' /usr/local/sbin/fix*.sh /usr/local/sbin/start_server.sh
+if [ ! -f /usr/local/sbin/import-seed-db.sh ] || [ $RG_SRC/scripts/import-seed-db.sh -nt /usr/local/sbin/import-seed-db.sh ]; then
+	echo "Found newer version of import-seed-db.sh. Updating"
+	cp $RG_SRC/scripts/import-seed-db.sh /usr/local/sbin/
+fi
+
+grep -i 'version=' /usr/local/sbin/fix*.sh /usr/local/sbin/start_server.sh /usr/local/sbin/import-seed-db.sh /usr/local/sbin/updatessmpaths.sh
 rm -rf $RG_SRC/scripts
 echo "Done updating scripts"