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Setup instructions for formr

formr can run on Linux, Mac OS and Windows. However, we only have experience with Linux and therefore recommend a Linux environment. The installation instructions detailed below are for a Debian 9 Environment but can be modified accordingly for other platforms.

Virtual Machines

We recommend setting up OpenCPU in a separate virtual machine to the formr instance, mainly because their load requirements may differ, and because you may at some point want to add a load balancer to OpenCPU. It may also be advisable to separate out a database server for formr, but we will not go into this here. You should force all VMs to be accessible exclusively via https. Formr redirects to the SSL version automatically and you need to make sure formr accesses OpenCPU via https.

Install OpenCPU

Visit the OpenCPU repository and follow the installation instructions there on how to set up and configure OpenCPU.

#requires Ubuntu 16.04 (Xenial) or 18.04 (Bionic)
sudo add-apt-repository -y ppa:opencpu/opencpu-2.1
sudo apt-get update 
sudo apt-get upgrade

#install opencpu server
sudo apt-get install -y opencpu-server

OpenCPU will automatically start running as a system service. It will be available under the subfolder "ocpu" under the domain name for your VM. You will need to set this domain name up in the formr settings.

Now, you need to install a few packages. You'll need at least the formr package, which you can install by executing sudo -i R and then running devtools::install_github("rubenarslan/formr", upgrade_dependencies = FALSE).

Other packages you might wish to install: install.packages(c("codebook", "tidyverse", "pander")). For a longer list, see this usually up-to-date list of the stack maintained on our machine.

We next recommend editing the following configuration files:

Open /etc/opencpu/server.conf using e.g., sudo nano. Edit the key_length setting to be longer. We use 50, OpenCPU uses 13. We also set the following packages to "preload": ["stringr", "dplyr","knitr", "lubridate","formr", "rmarkdown"].

Open /etc/nginx/opencpu.d/ocpu.conf using e.g., sudo nano. Remove the first location block and replace it with

# OpenCPU API
location /ocpu {
        proxy_pass  http://ocpu/ocpu;
        include /etc/nginx/opencpu.d/cache.conf;
}

location ~* /ocpu/tmp/.+?/(messages|source|console|stdout|info|files/.+\.Rmd) {
        allow IP_ADDRESS_OF_YOUR_FORMR_VM;
        deny all;
        proxy_pass  http://ocpu;
        include /etc/nginx/opencpu.d/cache.conf;
}

Take care to ensure the IP_ADDRESS_OF_YOUR_FORMR_VM is accurate. This step ensures that the commands sent to OpenCPU are not readable by end users, which is important if you plan to send along secret API tokens (e.g., for text messaging services).

After packages are installed and configuration files edited, run sudo service apache2 restart and check that OpenCPU runs as expected.

Installing an instance of the formr website

These are the instructions to run a local or online copy of the formr.org distribution. It is much easier to install the R package if that's what you're looking for. Those who don't mind running on a frequently-updated server, we will probably also give you access to our hosted version at formr.org.

0. Requirements

The following requirements should be installed on the system you intend to install formr on:

  • Git (for installation)
  • PHP ≥ 7.2
    • composer
    • php-curl
    • php-fpm (often: php7.x-fpm e. g. php7.2-fpm)
    • php-mbstring (often: php7.x-mbstring e. g. php7.2-mbstring)
    • php-mysql
    • php-zip
    • php-xml
    • php-gd
    • php-intl
    • php-xml
    • pandoc (not needed in develop branch for libsodium23)
  • Apache >= 2.4
  • MySQL / MariaDB >= 5.6
  • Composer (for installing dependencies)
  • The Sodium crypto library (Libsodium)
    • The repository version of libsodium is currently incompatible to formR. Use these instructions to set it up.
    • The Branch develop supports libsodium23 v1.0.16 which is the default version on most current distributions.
  • Supervisor OPTIONAL. Though optional, we recommend using supervisor for sending out email notifications in queues and well as processing uni sessions.
  • smysqlin OPTIONAL (for managing database patches)

Paket list for copying:

sudo apt-get install git php apache2 mysql-server composer php-curl php-fpm php-mbstring php-mysql php-zip php-xml php-gd php-intl php-xml pandoc

Install libsodium now. See instructions above.

Apache needs the rewrite mod enabled:

    sudo a2enmod rewrite

And overrides need to be allowed for the virtual host. On a standard Ubuntu or Debian installation, insert the following block at the end of your default virtual host in /etc/apache2/sites-enabled/000-default.conf.

	<Directory /var/www/html>
		Options Indexes FollowSymlinks MultiViews
		AllowOverride All
		Order allow,deny
		allow from all

	</Directory>

Make sure apache2 and php7.x-fpm run.

1. Clone the Git repository and checkout the desired release (version)

The suggested file structure is as follows: Place formr.org's folder, e. g. /var/www, accessible for apache's user e. g. www-data and to create a symlink to the webroot.

You'll need Git (a version management software). After installing it, navigate to the folder where you want to place formr and run

    cd /var/www/
    git clone https://github.com/rubenarslan/formr.org.git #depending on the system you might need sudo for this

Create the symlink and fix access rights:

    ln -s /var/www/formr.org/webroot /var/www/html/formr 
    chown -R www-data:www-data /var/www/formr.org

You can also download the repository as a zip file, but trust me, use Git for this.

To see the existing releases of formr, go to https://github.com/rubenarslan/formr.org/releases. It is recommended to run a release of formr for easy update an maintenance. To run a release use the command

    git fetch --tags && git checkout <release> -b <release>

Suppose for example you want to run release v0.18.0 git fetch --tags && git checkout v0.18.0 -b v0.18.0

At this point you should have your formr files present in the installation directory. Go to the root of the installation directory and install the application dependencies by running

    composer install

 

2. Create an empty MySQL database

Login to mysql server with a user that has appropriate privileges and execute these commands to create the database

    CREATE DATABASE formr DEFAULT CHARACTER SET utf8 COLLATE utf8_unicode_ci;
    GRANT ALL PRIVILEGES ON formr.* TO formr@localhost IDENTIFIED BY 'EnterPassword';
    FLUSH PRIVILEGES;
    quit;

Import the initial required database structure

    mysql formr -uformr -pEnterPassword < /path/to/formr/sql/schema.sql

You'll need to apply patchsets 29 and 30 in sql/patches manually.

Optionally, you could use smysqlin to set up and manage patches to the formr mysql database. SQL patches are created with updates and found in the directory /path/to/formr/sql/patches. Any patch will be announced in the update release and you can either run this patch directly against your database or use smysqlin.

3. Configuration

Create the config folder
  • Duplicate (don't rename) the folder config-dist, name it config.
  • Edit the /path/to/formr/config/settings.php to configure the right values for the various config items. The comments in the config file should help you identify the meaning of the config items. Some common items you need to modify are
    • database connection parameters
    • the OpenCPU instance to you
    • the application timezone
    • email SMTP configuration
    • cron or deamon settings depending on how you want to process jobs in the background
Installing the formr cron and/or deamon

In other to process sessions in the background, you will have to setup the formr cron OR the formr deamon BUT NOT BOTH. The cronjob is necessary to send automated email reminders and the like.

  • To install the formr crontab in a linux system, uncomment the cron command you will like to use in /path/to/formr/config/formr_crontab and then create a symbolic link to install the formr crontab in the system's crontab configuration
    ln -s /path/to/formr/config/formr_crontab /etc/cron.d/formr
  • To use the formr queues (for email and unit session processing), you will need to install and setup Supervisor. formr comes with a programs supervisor config in /path/to/formr/config/supervisord.conf. Edit this file to suit your needs. This config can be added to supervisor's default config by creating a symbolic link as follows or moving the config file to supervisor's default config directory
    ln -s /path/to/formr/config/supervisord.conf /etc/supervisor/conf.d/formr.conf
Configure smysqlin for installing db patches

If you decided to use smysqlin to manage your database patches. The you could setup a formr configuration for smysqlin using the file in /path/to/formr/config/formr.ini. Modify it accordingly and add it to the smysql in configuration by copying file or creating a symbolic link

    ln -s /path/to/formr/config/formr.ini /etc/smysqlin/formr.ini
Set paths and permissions

The followings folders (and their sub-folders) have to be writable: /tmp and /webroot/assets/tmp. You may need to modify the .htaccess files to suit your needs. See config item define_root to specify installation path, url and test mode.

4. Done

You should be able to see your installation up and running by visiting the configured URL.

Problems rolling out?

  • check .htaccess config, commonly there are problems which can be fixed by appropriately setting RewriteBase
  • is /tmp writable?
  • define_root has a hardcoded path at the time.
  • internal server errors: check permissions (tmp), case-sensitive paths, .htaccess path trouble
  • contact us
  • If your layout seems broken, disable developer mode in the settings.php
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