BioWardrobe NG

Ubuntu

To build relocatable biowardrobe-ng.tar.gz that can be run with PM2 on Ubuntu 18.04 run the following command.

cd build-scripts
./pack_ubuntu.sh

To run relocatable biowardrobe-ng.tar.gz on clean Ubuntu 18.04 run the following commands.

curl -sL https://deb.nodesource.com/setup_12.x | sudo -E bash -
sudo apt-get install nodejs
mkdir ~/.npm-global
npm config set prefix '~/.npm-global'
export PATH=~/.npm-global/bin:$PATH
npm install -g pm2
cd ubuntu_post_build
tar xzf biowardrobe-ng.tar.gz
pm2 start ./configs/ecosystem.config.js

File with the default configuration biowardrobe_ng_default_settings.json

{
    "defaultLocations": {
        "systemRoot": "./biowardrobe_ng_oauth"
    },
    "networkSettings": {
        "proxy": "",
        "noProxy": ""
    },
    "mongoSettings": {
        "port": 27017,
        "collection": "biowardrobe_ng_oauth"
    },    
    "meteorSettings": {
        "name": "biowardrobe_ng",
        "base_url": "http://localhost:3069/",
        "port": 3069,
        "logLevel": "debug",
        "cors_package": true,
        "public":{
            "staleSessionInactivityTimeout": 300000,
            "staleSessionHeartbeatInterval": 120000,
            "staleSessionPurgeInterval": 60000,
            "staleSessionForceLogout": true,
            "staleSessionActivityEvents": "mousemove click keydown"
        }, 
        "accounts":{
            "sendVerificationEmail": false,
            "forbidClientAccountCreation": true,
            "loginExpirationInDays": 7
        },
        "SSL":{
            "key": "",
            "cert": "",
            "port": ""
        },
        "ldap": {},
        "oauth2server": {}
    }
}

After updating to the refactored version of BioWardrobe-NG the old services.scidapsatellite field in the users collection should be removed. Otherwise, users will get Service scidapsatellite already registered [403] error when trying to log in. To remove services.scidapsatellite do the following steps

1. Backup scidap database

   mongodump --archive --db scidap |7z a -si dump.7z

2. Run mongo shell and execute

   db.users.find({"services.scidapsatellite": { $exists: true }})
   db.users.updateMany({}, {$unset: {"services.scidapsatellite": ""}})
   db.users.find({"services.scidapsatellite": { $exists: true }})
   

3. If something went wrong, restore from backup

   7z e -so dump.7z |mongorestore --archive --drop