Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Modifying setup_script.sh #172

Open
wants to merge 3 commits into
base: develop
Choose a base branch
from
Open

Modifying setup_script.sh #172

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
0833ae8
Modifying setup_script.sh
SanjanaSogimatt Mar 24, 2024
abc98e0
Changing mongo to mongosh
SanjanaSogimatt Mar 24, 2024
60340e3
updating setup script again
SanjanaSogimatt Mar 26, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
208 changes: 62 additions & 146 deletions setup_script.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,210 +1,126 @@
#!/bin/bash

###
## ensure that required params are passed into script
###
if [ -n "$1" ]; then
HOST=$1
else
echo "[ database ] : name not passed, set to default value (127.0.0.1)"
HOST="127.0.0.1"
fi

###
## specify which database to operate on, if not specified, set default to camic
###
if [ -n "$2" ]; then
DB_NAME=$2
echo "[ database ] : name set as ${DB_NAME}"
else
echo "[ database ] : name not passed, set to default value (camic)"
DB_NAME="camic"
fi

###
## check if the system has required services installed
###
if ! command -v "mongo" &>/dev/null; then
echo "mongo could not be found on path. Please ensure that mongo is installed and is on PATH"
exit
fi

if ! command -v "node" &>/dev/null; then
echo "node could not be found on path. Please ensure that node is installed and is on PATH"
exit
fi

###
# check for the existence of required files in the Distro and camicroscope repository
###
echo "Checking for required files"

#if [[ ! -d ../Distro/db ]]
#then echo "../Distro/db does not exist"
# exit
#fi

if [[ ! -d ../Distro/config ]]
then echo "../Distro/config does not exist"
exit
fi

if [[ ! -d ../Distro/jwt_keys ]]
then echo "../Distro/jwt_keys does not exist"
exit
fi

if [[ ! -d ../caMicroscope ]]
then echo "../caMicroscope does not exist"
exit
fi
# Ensure required params are passed into the script
HOST="${1:-127.0.0.1}"
DB_NAME="${2:-camic}"

# Function to check if a command exists
check_command() {
if ! command -v "$1" &>/dev/null; then
echo "$1 could not be found on path. Please ensure that $1 is installed and is on PATH"
exit 1
fi
}

# Check for required commands
check_command "mongod"
check_command "node"
check_command "wget"

# Function to check if a directory exists
check_directory() {
if [ ! -d "$1" ]; then
echo "$1 does not exist"
exit 1
fi
}

# Check for required directories
check_directory "../Distro/config"
check_directory "../Distro/jwt_keys"
check_directory "../caMicroscope"

echo "Required files exist."

echo "Copying files..."

#if [[ ! -d ../data ]]
#then
# mkdir ../data
# cp -r ../Distro/db ../data/
#fi

if [[ ! -d ../config ]]
then
mkdir ../config
cp -r ../Distro/config ../config/
fi

if [[ ! -d ./static ]]
then
mkdir ./static
cp ../Distro/config/login.html ./static/login.html
fi
# Copy required files
mkdir -p ../config
cp -r ../Distro/config/* ../config/

if [[ ! -d ./keys/jwt_keys ]]
then
cp -r ../Distro/jwt_keys ./keys/
fi
mkdir -p ./static
cp ../Distro/config/login.html ./static/login.html

if [[ ! -f ./contentSecurityPolicy.json ]]
then
cp ../Distro/config/contentSecurityPolicy.json ./contentSecurityPolicy.json
fi
mkdir -p ./keys/jwt_keys
cp -r ../Distro/jwt_keys/* ./keys/jwt_keys/

if [[ ! -f ./static/additional_links.json ]]
then
cp ../Distro/config/additional_links.json ./static/additional_links.json
fi
cp ../Distro/config/contentSecurityPolicy.json ./contentSecurityPolicy.json
cp ../Distro/config/additional_links.json ./static/additional_links.json

if [[ ! -d ./camicroscope ]]
then
cp -r ../caMicroscope ./camicroscope
fi
cp -r ../caMicroscope/* ./camicroscope

echo "Copying files complete!"




###
## try connecting to mongodb instance
###
until mongo --host "${HOST}" --eval "print(\"Connected!\")" >/dev/null; do
# Try connecting to mongoDB instance
until mongosh --host "$HOST" --eval "print(\"Connected!\")" >/dev/null; do
sleep 2
done
echo "[ database ] : connection established"

###
## check if database exists
###
QUERY="db.getMongo().getDBNames().indexOf(\"${DB_NAME}\")"
COMMAND="mongo ${HOST} --eval '${QUERY}' --quiet"
if [ $(mongo ${HOST} --eval ${QUERY} --quiet) -lt 0 ]; then
echo "[ database ] : does not exist"
# Check if database exists
if ! mongosh "$HOST" --eval "db.getMongo().getDBNames().indexOf(\"$DB_NAME\")" --quiet; then
echo "[ database ] : $DB_NAME does not exist"
exit 1
else
echo "[ database ] : database named ${DB_NAME} found"
echo "[ database ] : database named $DB_NAME found"
fi

###
## ask developer if they wish to seed the database
###
# Ask user if they wish to seed the database
read -p "[ resource ] : Do you wish to initialize the database with indexes and configs? (y/n) : " yn
case $yn in
[Yy]*)
###
## Download the files from github and save to local directory
###
echo "[ resource ] : downloading seeding files"

# resource targets
# Resource URLs
RESOURCE_IDX="https://raw.githubusercontent.com/camicroscope/Distro/master/config/mongo_idx.js"
RESOURCE_COLLECTION="https://raw.githubusercontent.com/camicroscope/Distro/master/config/mongo_collections.js"
RESOURCE_DEFAULT_DATA="https://raw.githubusercontent.com/camicroscope/Distro/master/config/default_data.js"

# get data from resource targets
wget -q RESOURCE_IDX -O .seeder.idx.js
wget -q RESOURCE_DEFAULT_DATA -O .seeder.default.js
wget -q RESOURCE_COLLECTION -O .seeder.collection.js
# Download files
wget -q "$RESOURCE_IDX" -O .seeder.idx.js
wget -q "$RESOURCE_DEFAULT_DATA" -O .seeder.default.js
wget -q "$RESOURCE_COLLECTION" -O .seeder.collection.js

echo "[ resource ] : clearing old configurations"
echo "[ resource ] : seeding collections"
mongo --quiet --host $HOST $DB_NAME .seeder.collection.js
mongosh --quiet --host "$HOST" "$DB_NAME" .seeder.collection.js
echo "[ resource ] : seeding indexes"
mongo --quiet --host $HOST $DB_NAME .seeder.idx.js
mongosh --quiet --host "$HOST" "$DB_NAME" .seeder.idx.js
echo "[ resource ] : seeding configurations"
mongo --quiet --host $HOST $DB_NAME .seeder.default.js
mongosh --quiet --host "$HOST" "$DB_NAME" .seeder.default.js

###
## ask the user if they want to remove the seeding files
###
# Ask the user if they want to remove the seeding files
read -p "[ resource ] : Do you wish to keep the seeding files generated ? (y/n) :" yn
case $yn in
[Yy]*) echo "[ resource ] : The seeder files are present in current directory with name : .seeder.*.js" ;;
[Yy]*) echo "[ resource ] : The seeder files are present in the current directory with names: .seeder.*.js" ;;
[Nn]*) rm .seeder.* ;;
*) echo "[ resource ] : Please answer y/n." ;;
esac
;;
### seeder file cleanup ends here

[Nn]*) echo "[ resource ] : database initialization skipped" ;;
*) echo "[ resource ] : skipped" ;;
esac
### seeder prompt ends here

###
## load the default routes.json file if it does not exist in the file system
###
if [ -f "routes.json" ]; then
echo "[ routes ] : routes.json file already exists"
else
# Additional setup
if [ ! -f "routes.json" ]; then
cp routes.json.example routes.json
echo "[ routes ] : routes.json file generated from routes.json.example"
fi

if [ -f "keys/key" ] && [ -f "keys/key.pub" ]; then
echo "[ keys ] : public and private keys already exist"
else
if [ ! -f "keys/key" ] && [ ! -f "keys/key.pub" ]; then
bash ./keys/make_key.sh
echo "[ routes ] : routes.json file generated from routes.json.example"
echo "[ keys ] : public and private keys generated"
fi

###
## install the packages if not done already
###
if [ ! -d "node_modules" ]; then
echo "[ modules ] : packages not installed, running : npm install"
npm install
else
echo "[ modules ] : packages directory already exist, to reinstall, delete the node_modules folder and run npm install"
echo "[ modules ] : packages directory already exists. To reinstall, delete the node_modules folder and run npm install"
fi

###
## initialize the environment variable configs
###
if [ ! -f ".env" ]; then
echo "[ env ] : .env file not found"
cp .env.example .env
echo "[ env ] : .env file generated from .env.example"
else
echo "[ env ] : .env file already exists"
fi
Expand Down