c-ruttkies / massbank-web

The web server application and directly connected components for a MassBank web server

Installation

There are two possibilities: Install MassBank in a virtual machine without major impact on the host computer or install it as "Dynamic Web Module" in eclipse for development(requires installation of local Apache httpd).

Virtual Machine Installation

The requirement is the "vagrant" system and Virtualbox. I used the latest vagrant (1.9.5) with Virtualbox 5.1 on Ubuntu 16.04. Please follow the instructions on https://www.vagrantup.com/docs/installation/ and https://www.virtualbox.org/wiki/Linux_Downloads. Note: 16.04 default vagrant(1.8.1) refuses to work correctly with 16.04 client boxes.

Install git on your system if not present. Check out the MassBank-web project(or fork on github first and clone from your own repository), which contains 1) The virtual machine initialization files Vagrantfile and bootstrap.sh and 2) the MassBank software to be installed inside the virtual machine.

After cloning the repo, create the virtual machine and fire it up in virtualbox. Once everything finished, you should have a running MassBank, so point your browser to http://192.168.35.18/MassBank/. You can also ssh into the virtual machine without password:

git clone https://github.com/MassBank/MassBank-web
cd MassBank-web 
vagrant up
vagrant ssh

Fedora 22 Workstation (!Not tested with latest MassBank!)

Install vagrant

sudo dnf install vagrant

According to this StackExchange post, Fedora is not using VirtualBox as a default provider. When geting the follwoing error:

The provider 'libvirt' could not be found, but was requested to
back the machine 'default'. Please use a provider that exists.

Execute the these two steps:

$ echo "export VAGRANT_DEFAULT_PROVIDER=virtualbox" >> ~/.zshr
$ source ~/.zshrc

The vagrant version from the repository (Version 1.7.2) does NOT support Virtualbox Version 5

Windows 7 64 bit (!Not tested for other Windows versions!)

Install Virtualbox for Windows https://www.virtualbox.org/wiki/Downloads

Install Vagrant for Windows https://www.vagrantup.com/downloads.html

Install Git for Windows https://git-scm.com/download/win

Clone the repo to your favorite folder

cmd
cd your_favorite_folder
git clone https://github.com/MassBank/MassBank-web

Install the Tortoise Git client if you don't feel comfortable with the command line tool https://tortoisegit.org/download/

Clone the repo by right mouse click and click to "Git clone" to your favorite folder Source: https://github.com/MassBank/MassBank-web

Start a commandline window and change to the folder with the repo:

cd your_favorite_folder\MassBank-web
run Setup_MassBank.bat

You will be asked for an username and the password to access the mbadmin environment Now the the virtual machine should be available in the Oracle VM VirtualBox manager

Type to connect to the VM

vagrant ssh

You may also use your favorite terminal software such as Putty. You will find the private key to connect to the VM under MassBank-web.vagrant\machines\default\virtualbox

Transfer to VMWare ESX cluster or VMWare workstation

Start the Oracle VM VirtualBox manager and export the appliance to the Open Virtualisation Format (ova file). Use the expert mode for individual settings (e.g. the name of the machine) and select the tickbox to create a manifest file. If the tickbox is checked, the integrity of the appliance will be checked during the import.

Import the ova file to your VMWare environment and change the settings if necessary using the console

Install in eclipse for development

There are three parts needed to have a working development environment:

1. MySQL database - we use a MariaDB docker container
2. Apache httpd
3. Local Apache tomcat in eclipse

Install MariaDB

Install and configure docker environment including docker-compose. Make sure that your system-user is in the group 'docker'. Create a mariadb data directory sudo mkdir /mariadb and issue docker-compose up -d in the root directory of this repo. Check with docker ps for massbank_mariadb. Check database with mysql -u bird -h 127.0.0.1 -p.

Install Apache httpd content

Install dependencies: apache2 libcgi-pm-perl build-essential libmysqlclient-dev libapache2-mod-jk libdbd-mysql-perl mariadb-client. Install apache httpd and make sure you have no old projects installed.

# copy Massbank-web content into folder '/var/www/'
sudo cp -rp modules/apache/error /var/www/
sudo cp -rp modules/apache/html /var/www/

# built Search.cgi and copy to '/var/www/html/MassBank/cgi-bin/'
(cd ./modules/Search.cgi/ ; make clean ; make ) 
sudo cp -p ./modules/Search.cgi/Search.cgi /var/www/html/MassBank/cgi-bin/
(cd ./modules/Search.cgi/ ; make clean)

# configure file system rights
sudo chown -R www-data:www-data /var/www/*
sudo chown -R $USER /var/www/html/MassBank/DB
sudo chown -R $USER /var/www/html/MassBank/massbank.conf

Configure apache httpd.

# write server-name to apache2.conf
sudo bash -c 'cat >> /etc/apache2/apache2.conf << EOF
ServerName localhost
EOF'

# enable apache sites and modules
sudo bash -c 'install -m 644 -o root -g root modules/apache/conf/010-a2site-massbank.conf /etc/apache2/sites-available
a2ensite 010-a2site-massbank
a2enmod rewrite
a2enmod authz_groupfile
a2enmod cgid
a2enmod jk'

# configure htpasswd for mbadmin
sudo htpasswd -b -c /etc/apache2/.htpasswd massbank bird2006

Restart server: sudo systemctl restart apache2.

Import project into Eclipse

Download and install the Eclipse IDE for Java EE Developers with "Maven Integration for Eclipse" and "Maven Integration for WTP" and extract it to your preferred folder. Start eclipse and import the clones github-project 'Massbank-web': File -> Import -> Existing Maven Project -> Select this repo for import. Download Apache Tomcat and extract it to your preferred folder. Then create a Tomcat server in eclipse. Please follow the instructions here and here. Edit '/var/www/html/MassBank/massbank.conf' and set <MiddleServer URL="http://localhost/MassBank/"/>. Run the MassBank-project on the Tomcat server and access MassBank at http://localhost/MassBank/.

PIWIK log analyser (https://piwik.org/)

The default MassBank server installation includes the PIWIK log analyser. Consider that user tracking has privacy issues. The default preset follows very strict rules according to http://piwik.org/docs/privacy/ and only the following usage data:

• Site from which the file was requested
• Name of the file
• Date and time of the request
• Volume of data transferred
• Access status (file transferred, file not found)
• Description of the type of web browser used
• IP address of the requesting computer shortened by the last six digits.

The creation of personal user profiles is therefore precluded.

customised piwik tracking code

The tracking code for piwik is specific for each site and configuration in order to fullfil your local legal and personal requirements! The tracking code for http://your_server_url/MassBank is called from /var/www/html/MassBank/script/Piwik.js. Make sure to replace the default code with your customised tracking code. Exclude the script tags. Make also sure that you customise your superuser if using the default bootstrap.sh!