elabftw Documentation
Release 1.1.5
Nicolas CARPi
July 25, 2015
Contents
1
Install on GNU/Linux
1.1 Prerequisites . .
1.2 Getting the files .
1.3 SQL part . . . .
1.4 Final step . . . .
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1
1
1
2
4
2
Install in a docker container
5
3
Install in a drop
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4
Install on Mac OS X
4.1 Install XAMPP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.2 Setup a database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.3 Final step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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5
Common errors
5.1 Add the secret key . . . . . . . . . . . . . . . . . . . . . . . . . .
5.2 Failed creating uploads/ directory . . . . . . . . . . . . . . . . . .
5.3 Extension is not loaded . . . . . . . . . . . . . . . . . . . . . . . .
5.4 I can’t upload a file bigger than 2 Mb . . . . . . . . . . . . . . . .
5.5 I can’t export my (numerous) experiments in zip, I get an error 500
5.6 No thumbnails on the uploaded images . . . . . . . . . . . . . . .
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12
Post install
6.1 Setting up email . . . . . . . . . . . . . . . . . . . . .
6.2 Setting up the teams . . . . . . . . . . . . . . . . . . .
6.3 Setting up timestamping . . . . . . . . . . . . . . . . .
6.4 Using other languages . . . . . . . . . . . . . . . . . .
6.5 Setting up backup . . . . . . . . . . . . . . . . . . . .
6.6 Allowing more memory to php . . . . . . . . . . . . .
6.7 Making sure that the uploads folder cannot be accessed
6.8 Updating . . . . . . . . . . . . . . . . . . . . . . . . .
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7
How to backup
7.1 Backup SQL database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.2 Making it automatic using cron . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.3 How to restore a backup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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8
How to update
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i
8.1
8.2
9
If you installed it with git . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
If you installed it from a .zip or .tar.gz archive . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Frequently asked questions
9.1 Is it totally free ? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9.2 But how is it better than something I can buy ? . . . . . . . . . . . . . . . . . . . . . . . .
9.3 What about patents and intellectual property ? . . . . . . . . . . . . . . . . . . . . . . . .
9.4 Why use eLabFTW ? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9.5 Is this system stable ? Can I trust my data with it ? . . . . . . . . . . . . . . . . . . . . . .
9.6 Is the data encrypted ? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9.7 Is eLabFTW still maintained ? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9.8 Will I be able to import my plasmids/antibodies/whatever in the database from a Excel file ?
9.9 Can I try it before I install it ? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9.10 But what about the others ELN out there ? . . . . . . . . . . . . . . . . . . . . . . . . . .
9.11 What about compliance to standards ? . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9.12 What are the technical specifications ? . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10 Features
10.1 General . . . . . . .
10.2 Experiments . . . .
10.3 Database . . . . . .
10.4 Security . . . . . . .
10.5 Intellectual property
10.6 User experience . .
10.7 Planned features . .
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11 Manual
29
12 Contributing
12.1 What can you do to help this project ?
12.2 Translating . . . . . . . . . . . . . .
12.3 Contributing to the code . . . . . . .
12.4 Reminders . . . . . . . . . . . . . .
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13 Thanks
14 Changelog
14.1 Version 1.1.5 . . .
14.2 Version 1.1.4-p3 .
14.3 Version 1.1.4-p2 .
14.4 Version 1.1.4-p1 .
14.5 Version 1.1.4 . . .
14.6 Version 1.1.3 . . .
14.7 Version 1.1.2-p1 .
14.8 Version 1.1.2 . . .
14.9 Version 1.1.1 . . .
14.10 Version 1.1.0 . . .
14.11 Version 1.0.0 . . .
14.12 Version 1.0.0-beta
14.13 Version 1.0.0-alpha
14.14 Version 0.12.6 . .
14.15 Version 0.12.5 . .
14.16 Version 0.12.4 . .
14.17 Version 0.12.0 . .
14.18 Version 0.11.0 . .
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37
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14.19
14.20
14.21
14.22
14.23
14.24
14.25
14.26
14.27
14.28
14.29
14.30
14.31
14.32
14.33
14.34
14.35
14.36
14.37
14.38
14.39
14.40
14.41
14.42
14.43
14.44
14.45
14.46
14.47
14.48
Version 0.10.2 . . . .
Version 0.10.1 . . . .
Version 0.10.0 . . . .
Version 0.9.5 . . . . .
Version 0.9.4.2 . . . .
Version 0.9.4.1 . . . .
Version 0.9.4 . . . . .
Version 0.9.3 . . . . .
Version 0.9.2 . . . . .
Version 0.9.1 . . . . .
Version 0.9 . . . . . .
Version 0.8.2 . . . . .
Version 0.8.1 . . . . .
Version 0.8 . . . . . .
Version 0.7.3.2 . . . .
Version 0.7 . . . . . .
Version 0.6 . . . . . .
Version 0.5.8 and 0.5.9
Version 0.5.7 . . . . .
Version 0.5.6 . . . . .
Version 0.5.5 . . . . .
Version 0.5.4 . . . . .
Version 0.5.3 . . . . .
Version 0.5.2 . . . . .
Version 0.5.1 . . . . .
Version 0.5 . . . . . .
Version 0.4 . . . . . .
Version 0.3 . . . . . .
Version 0.2 . . . . . .
Version 0.1 . . . . . .
15 License
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iii
iv
CHAPTER 1
Install on GNU/Linux
1.1 Prerequisites
Please refer to your distribution’s documentation to install :
• A webserver (like nginx, Apache, lighttpd or cherokee)
• PHP version > 5.5
• MySQL version > 5.5
• Git
Tip: If you don’t know how to do that, have a look at installing eLabFTW on a drop.
Note: I wouldn’t recommend HHVM because Gettext support is not here yet (see this issue).
1.2 Getting the files
The first part is to get the files composing eLabFTW on your server.
1
elabftw Documentation, Release 1.1.5
1.2.1 Option 1 : Using git
Connect to your server with SSH:
$ ssh user@12.34.56.78
cd to the public directory where you want eLabFTW to be installed (can be /var/www, ~/public_html, or any folder
you’d like, as long as the webserver is configured properly, in doubt use /var/www)
$ cd /var/www
# make the directory writable by your user (if it's not already the case)
$ sudo chown `whoami`:`whoami` .
Note the . at the end that means current folder.
Get latest stable version via git:
$ git clone --depth 1 https://github.com/elabftw/elabftw.git
(this will create a folder elabftw) The –depth 1 option is to avoid downloading the whole history.
Tip: If you cannot connect, it’s probably the proxy setting missing; try one of these two commands:
$ export https_proxy="proxy.example.com:3128"
$ git config --global http.proxy http://proxy.example.com:8080
1.2.2 Option 2 : Download archive
Download the latest release from this page as a zip archive or a tarball.
Copy it to your server with FTP or SCP, or directly wget it from the server.
1.3 SQL part
The second part is putting the database in place.
1.3.1 Option 1 : Command line way
# first we connect to mysql
$ mysql -u root -p
# we create the database (note the ; at the end !)
mysql> create database elabftw;
# we create the user that will connect to the database.
mysql> grant usage on *.* to elabftw@localhost identified by 'YOUR_PASSWORD';
# we give all rights to this user on this database
mysql> grant all privileges on elabftw.* to elabftw@localhost;
mysql> exit
You will be asked for the password you put after identified by three lines above.
2
Chapter 1. Install on GNU/Linux
elabftw Documentation, Release 1.1.5
1.3.2 Option 2 : Graphical way with phpmyadmin
You need to install the package phpmyadmin if it’s not already done.
Note: It is not recommended to have phpmyadmin installed on a production server (for security reasons).
$ sudo apt-get install phpmyadmin
Now you will connect to the phpmyadmin panel from your browser on your computer. Type the IP address of the
server followed by /phpmyadmin.
Example : https://12.34.56.78/phpmyadmin
Login with the root user on PhpMyAdmin panel (use the password you setup for mysql root user).
Create a user elabftw with all rights on the database elabftw.
Now click the Users tab and click:
Do like this:
1.3. SQL part
3
elabftw Documentation, Release 1.1.5
1.4 Final step
Finally, point your browser to the install folder (install/) and read onscreen instructions.
For example: https://12.34.56.78/elabftw/install
Please report bugs on github.
~Thank you for using eLabFTW :)
4
Chapter 1. Install on GNU/Linux
CHAPTER 2
Install in a docker container
Warning: This is experimental!
If you know Docker already and want to use a dockerized elabftw, please see this repo.
More infos coming soon.
5
elabftw Documentation, Release 1.1.5
6
Chapter 2. Install in a docker container
CHAPTER 3
Install in a drop
A drop is a cheap server, and you install elabftw on it with one command: everything is automagic!
The following actions will be performed :
• install of nginx (web server)
• install of mariadb (sql server)
• install of elabftw
• get everything up and running
Warning: This script will work for a fresh drop. If you already have a server running, you should consider a
normal install instead.
• Create an account on DigitalOcean
• Create a droplet with Ubuntu 14.04 x64 (works also with 14.10, but not with 12.04.5)
• Open a terminal and SSH to your droplet. The IP address can be found in the digitalocean website:
ssh root@12.34.56.78
Note: The root password is in your mailbox. It will not echo when you type it, it’s normal, don’t panic.
• Go inside a tmux session:
tmux
• Enter the following command:
wget -qO- https://get.elabftw.net|sh
7
elabftw Documentation, Release 1.1.5
Danger: Don’t get into the habit of executing unknown scripts as root without reading them first!
Hint: To follow the install progress, open a new pane with Ctrl-b, release and press %. Then enter tail -f
elabftw.log
• Read what is displayed at the end.
ENJOY! :D
8
Chapter 3. Install in a drop
CHAPTER 4
Install on Mac OS X
This guide assumes you want to install eLabFTW locally for your personnal use (not shared with other team members).
As eLabFTW is designed with a client <=> server architecture in mind, we’ll need to install a server on your computer.
Don’t worry though, it’s easy :)
4.1 Install XAMPP
Download XAMPP for OS X. Take the greatest version number (second link).
Now that it’s downloaded, double click it and open the installer. You can untick the XAMPP Developer Files and
Learn more about Bitnami checkboxes.
Once it’s installed, you let it start XAMPP. On the application manager (/Applications/XAMPP/manager-osx.app):
• Go to the tab ‘’‘Manage Servers’‘’
• Select MySQL Database
• Click Start
Test that everything is working by going to https://localhost. You should see a warning that the certificate is not signed
and cannot be trusted, which is normal.
Download the latest release and extract its content to /Applications/XAMPP/htdocs/elabftw.
Now we need to fix the permissions. Open the terminal and type:
cd /Applications/XAMPP/htdocs/elabftw
mkdir -p uploads/tmp
chmod -R 777 .
4.2 Setup a database
With XAMPP comes phpmyadmin. We will use this interface to do this part easily.
• Go to https://localhost/phpmyadmin
• Click on the Databases tab
• Create a database named elabftw
9
elabftw Documentation, Release 1.1.5
4.3 Final step
Browse to : https://localhost/elabftw/install and follow onscreen instructions.
Hint: There is no password for the mysql user root. So put root as mysql username and no password.
Note: Remember to keep your installation backuped and updated ;)
10
Chapter 4. Install on Mac OS X
CHAPTER 5
Common errors
5.1 Add the secret key
Starting from version 1.1.2 there is a secret key present in the config file. If you have restrictive permissions on it, the
webserver won’t be able to add it when you run the update.php script. To fix this issue, the simplest way is to:
chmod a+w config.php
Then run the /update.php script again. And bring back good permissions afterwards:
chmod 400 config.php
You might need to use sudo to achieve these commands.
5.2 Failed creating uploads/ directory
If eLabFTW couldn’t create an uploads/ folder, that’s because the httpd user (www-data on Debian/Ubuntu) didn’t
have the necessary rights. To fix it you need to:
1. Find what is the user/group of the web server. There is a good chance that it is www-data. But it might also be
something else. To check it you can try something like:
ps -ef | grep nginx
OR
ps -ef | grep apache
OR
ps -ef | grep httpd
What you want will be in the first column. Possible values are infinite, but it is generally www-data, http, httpdusr, or
things like that.
Now that you know the user/group of the webserver, you can do that (example is shown with www-data, but adapt to
your need):
cd /path/to/elabftw
mkdir -p uploads/{export,tmp}
chown -R www-data:www-data uploads
chmod -R 755 .
chmod 644 config.php
The last line is to keep your config file secure. It might fail because the file is not there yet. Finish the install and do it
after then.
11
elabftw Documentation, Release 1.1.5
If you have problems updating (git pull is failing because of permissions), read more about GNU/Linux permissions
and groups. For instance, you can add your user to the www-data group:
usermod -a -G www-data `whoami`
5.3 Extension is not loaded
Install everything needed by elabftw:
sudo apt-get install php5-openssl php5-gd php5-gettext php5-curl
Now reload the Apache server:
sudo service apache2 reload
5.4 I can’t upload a file bigger than 2 Mb
Edit the file php.ini and change the value of upload_max_filesize to something bigger, example:
upload_max_filesize = 128M
Warning: Don’t forget to remove the ; at the beginning of the line !
5.5 I can’t export my (numerous) experiments in zip, I get an error 500
This is because the script might take too long to execute and php is cutting it. To solve this, edit the file
/etc/php5/apache2/php.ini and increase the value of max_execution_time and max_input_time. Then restart your
server:
sudo service apache2 restart
5.6 No thumbnails on the uploaded images
That’s because the gd extension of php isn’t activated (deactivated by default on ArchLinux server) You need to
uncomment ;extension=gd.so in /etc/php.ini and install the package php-gd.
12
Chapter 5. Common errors
CHAPTER 6
Post install
6.1 Setting up email
By default, eLabFTW will try to use the local MTA aka Sendmail. However, it is recommended to use an authenticated
SMTP account to avoid the emails going to the spam folders of recipients. That is, unless your MTA is perfectly
configured (with DKIM and SPF).
Go to the Sysadmin panel (elabftw/sysconfig.php) and add the requested infos.
If you don’t know what to do, register a new account on Mandrill or Mailgun. These services will give you a free
SMTP account. :)
6.2 Setting up the teams
The Sysadmin panel (elabftw/sysconfig.php) allows you to add another team to your install.
6.3 Setting up timestamping
eLabFTW provides an easy way to do Trusted Timestamping for your experiments, so you can have strong legal value
for your lab notebook.
By default, it is setup to use pki.dfn.de as TSA (TimeStampingAuthority). It is free for researchers. The only problem,
is that they don’t have ETSI certification for this service (although their PKI infrastructure is certified ETSI TS 102
042).
So if you need a stronger certification, you should go with a commercial solution providing an RFC 3161 way of
timestamping documents. We recommend Universign.eu, as they are one of the most serious and recognized TSA out
there, but feel free to use the one you prefer.
Remember: no data is sent to the TSA (TimeStampingAuthority), only the hash of the data is sent, so no information
can leak!
6.4 Using other languages
eLabFTW uses gettext <https://en.wikipedia.org/wiki/Gettext> to translate text. This means that you need to have the
associated locales on the server. To see what locale you have:
13
elabftw Documentation, Release 1.1.5
locale -a
To add a locale, edit the file /etc/locale.gen and uncomment (remove the #) the locales you want. If you don’t find this
file you can try directly the command:
locale-gen fr_FR.UTF-8
Replace with the locale you want, of course. See here to see a list of languages (and locales) supported by eLabFTW.
Then do:
sudo locale-gen
And reload the webserver.
6.5 Setting up backup
See the backup page.
6.6 Allowing more memory to php
By default the amount of memory a script (page loading) can take is quite low compared to how much memory any
modern computer has. It is a good idea to increase this value in order to prevent future errors (when you try to export
a lot of experiments for instance).
Edit the file /etc/php/php.ini or any file called php.ini somewhere on your filesystem. Try sudo updatedb;locate php.ini.
For XAMPP install, it is in the config folder of XAMPP. Now that you have located the file and opened it in a text
editor, search for memory_limit and increase it to what you wish. Official documentation on memory_limit.
6.7 Making sure that the uploads folder cannot be accessed
Just visit /uploads/ (add this at the end of the URL) and see if you see the files there (or at least the tmp folder). If you
see a white page, all is good. If not, either configure Apache to AllowOverride All (so the .htaccess will work), or put
an empty index.php file in the folder.
6.8 Updating
It is important to keep your install up to date with the latest bug fixes and new features.
See instructions on updating eLabFTW on How to update.
Watch the repository to receive an email on new updates.
14
Chapter 6. Post install
CHAPTER 7
How to backup
This page shows you how to backup an existing elabftw installation.
There is basically two things to backup : the SQL database, and the elabftw folder (with your config file and your
uploaded files).
7.1 Backup SQL database
You’ll want to have a little script that do the backup automatically. Here is the script I’m using, adapt it to your needs:
#!/bin/sh
# backup.sh - Backup eLabFTW installation
# ------------# Get clean date (make sure your version of
y=`date --rfc-3339=date |awk -F '-' '{print
m=`date --rfc-3339=date |awk -F '-' '{print
d=`date --rfc-3339=date |awk -F '-' '{print
date=$y$m$d
date supports this option)
$1}'|cut -c3-4`
$2}'`
$3}'`
# elab sql backup
###################
# make a dump of the database in elabftw.sql file
mysqldump -u elabftw -p'PUT_YOUR_SQL_PASSWORD_HERE' elabftw > elabftw.sql
# copy this file somewhere else using ssh (scp)
scp -q elabftw.sql user@192.168.0.3:.backups/sql/elabftw-$date.sql
# move the file to a local backup dir
mv elabftw.sql /home/pi/.backups/sql/elabftw-$date.sql
# www files backup
###################
# make a tarball of www
tar czf www.tar.gz -C /var/ www
# copy the tarball to somewhere else using ssh (scp)
scp -q www.tar.gz user@192.168.0.3:.backups/www/www-$date.tar.gz && rm www.tar.gz
If you don’t remember your SQL password, look in the file elabftw/config.php!
15
elabftw Documentation, Release 1.1.5
7.2 Making it automatic using cron
A good backup is automatic.
If you’re under a GNU/Linux system, try:
export EDITOR=nano ; crontab -e
This will open a file.
Add this line at the bottom:
00 04 * * * sh /path/to/script.sh
This will run the script everyday at 4 am.
7.3 How to restore a backup
Get a fresh elabftw folder, make the required directories, copy the config file:
git clone --depth 1 https://github.com/elabftw/elabftw
mkdir -p elabftw/uploads/{tmp}
chmod -R 777 elabftw/uploads
cp -r /path/to/backup/uploads elabftw/
cp /path/to/backup/config.php elabftw/
Now import your SQL database back
16
Chapter 7. How to backup
elabftw Documentation, Release 1.1.5
You can use phpmyadmin, create a new database and import your .sql backup, or use the command line:
mysql -uroot -p elabftw < /path/to/backup/elabftw.sql
Stay safe ;)
7.3. How to restore a backup
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CHAPTER 8
How to update
8.1 If you installed it with git
To update, cd in the elabftw folder and do:
$ git pull
Once the new files are here, you need to update the database : visit /update.php in your browser, logged in as a
sysadmin.
8.2 If you installed it from a .zip or .tar.gz archive
1. Get the latest archive
2. Unpack it on your server, overwriting all the files.
3. Visit /update.php in your browser, logged in as a sysadmin.
That’s it :)
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CHAPTER 9
Frequently asked questions
9.1 Is it totally free ?
YES. eLabFTW is free software, so it is totally free of charge and always will be. Read more about the free software
philosophy.
9.2 But how is it better than something I can buy ?
The difference is huge. Because eLabFTW is not only free (as in beer), but it is free (as in speech). This means that
you can have a look at the code (and improve it) and you can also redistribute the code with your improvements.
But more importantly, you cannot trust your data with something that acts like a black box. What if the data you
upload on the server of a company can be read by someone else ? With eLabFTW, you install it on your own server,
and you are the master of your data at all time.
9.3 What about patents and intellectual property ?
eLabFTW allows rock solid timestamping of your experiments, you can timestamp a pdf export with any TimeStamping Authority allowing RFC 3161 timestamping.
The timestamp system is integrated to eLabFTW and you are just one click away from having a legally certified
experiment :)
9.4 Why use eLabFTW ?
• It’s free and open source software
• It improves the value of your experiments by allowing you to keep a good track of it
• It makes searching your data as easy as a google search
• Everything can be organized in your lab
• It makes it easy to share information between co-workers or collaborators
• It is simple to install and to keep up to date
• It works for Windows, Mac OS X, Linux, BSD, Solaris, _etc. . .
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• Protected access with login/password (password is very securely stored as salted SHA-512 sum
• It can be used by multiple users at the same time
• It can be used by multiple teams
• You can have templates for experiments you do often
• You can export an experiment as a PDF
• You can timestamp an experiment so it is legally strong
• You can export one or several experiments as a ZIP archive
• You can duplicate experiments in one click
• There is advanced search capabilities
• The tagging system allows you to keep track of family of experiments
• Experiments can have color coded statuses (that you can edit at will)
• You can link an experiment with an item from the database to retrieve in a click the plasmid/sirna/antibody/chemical you used
• And it works the other way around, you can find all experiments done with a particular item from the database !
• There is a locking mechanism preventing further edition
• You can prevent users from deleting experiments
• You can comment on an experiment (if it’s not your experiment)
• You can import your old database stored in an excel file
• and much more. . .
9.5 Is this system stable ? Can I trust my data with it ?
It’s still in beta, but you can already start using it. New features are added very often and they don’t break what exists
already. However, having an automated backup strategy is mandatory in order to be sure nothing will be lost.
Being able to do backups is yet another advantage over paper (you can’t backup paper !).
9.6 Is the data encrypted ?
The MySQL database can be installed on a encrypted drive. And backup can be encrypted, too. But this has to be
done by your system admininstrator.
Also, as you need an account to access the data, no external individual can see your data !
Finally, eLabFTW works fully in HTTPS for added security.
9.7 Is eLabFTW still maintained ?
As of July 25, 2015 I’m still actively working on it. Improvements are coming in a steady flow. There are good
chances that I will continue to do so for a few years. In the unlikely event I’m not able to work on it anymore, anyone
can continue the work, as the source code is available and well commented.
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9.8 Will I be able to import my plasmids/antibodies/whatever in the
database from a Excel file ?
Yes, in the admin panel, click on the Import CSV link and follow the instructions.
9.9 Can I try it before I install it ?
Sure, there is a demo online here : eLabFTW live DEMO Login with username : demo and password demo
9.10 But what about the others ELN out there ?
First I’ll only speak about the others free and open source lab notebook. Because there is no point in comparing free
and privative software, as it’s not the same philosophy at all !
• Labtrove : labtrove is a glorified Wordpress plugin. Unfortunately, I didn’t manage to install it so I can’t really
talk about it... Also, it wasn’t updated since 2011 so it probably won’t work with latest versions of Wordpress.
• Indigo : It’s for chemists only and it’s in Java :/
• Electronic laboratory notebook on sourceforge : Looks like it was made in 1999, poorly written, only client (no
server), java.
• MediaWiki : although it’s very nice to have a wiki in your team, this is not designed to be an electronic lab
notebook. So you should definitely have a wiki, but don’t use it to store your experiments !
• Mylabbook : based on Drupal. So you need to have all the Drupal stuff around. I used Drupal in the past, it’s
way too complicated !
• Labbook : A perl based software, still stuck in 1999 and virtually impossible to install/use.
• Cynote : I cannot manage to download it !
9.11 What about compliance to standards ?
eLabFTW tries to comply to the following standards :
• Code of Federal Regulations Title 21, paragraph 11
• FERPA
• HIPAA
• FISMA
9.12 What are the technical specifications ?
eLabFTW is a server software that should be installed on a server.
Requirements for the server :
• PHP version > 5.5
• MySQL version > 5.5
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• HTTPS enabled
• PHP extensions openssl, gd, hash and zip activated
The operating system of the server can be any, but GNU/Linux or FreeBSD is recommended for obvious reasons. The
server software can be any (nginx, apache, cherokee, lighttpd, . . . ).
Requirements for the client : - Any operating system with any browser (latest version). Internet Explorer is not
recommended for obvious reasons.
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CHAPTER 10
Features
10.1 General
• free (as in speech)
• free (as in beer)
• multi-plateform (server or client)
• web based (no install necessary on client)
• multiple teams
• quick search + advanced search
• git deployement
10.2 Experiments
• custom status
• visibility setting
• rich wysiwyg editor
• insert images into text
• upload multiple files
• duplicate experiments
• export as pdf
• export as zip archive
• general default experiment template
• user templates
• export/import user templates to files
• lock the experiment
• tags
• join any type of file
• attached mol files will display the molecule in the thumbnail
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• link with database items
• molecule drawer (optional)
10.3 Database
• import from spreadsheet files
• export/import zip archives
• import items from Excel file
• custom type of items with templates
• same features as experiments
• rating system
• see all experiments linked with this item
• molecule drawer (optional)
10.4 Security
• HTTPS
• formkeys
• anti bruteforce system
• log system
• secure storage of password (sha512)
• secure password reset mechanism
• option for new account admin validation
10.5 Intellectual property
• timestamping of experiments (pdf export)
• RFC 3161 compliant Trusted Timestamping
• allow or not users to delete experiments
• revisions system to see history
• attached files are md5summed and thus timestamped with the experiment
10.6 User experience
• lovely design (by Manon Potier)
• internationalization (several languages available)
• optimized code/assets for speed and correctness
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• customizable keyboard shortcuts
• option for displaying a warning on editor tab close
• display preferences
• custom link in menu
• statistics
• tagcloud
• TODOlist
10.7 Planned features
• a lot
10.7. Planned features
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CHAPTER 11
Manual
This guide assumes you already have a working installation of eLabFTW on a server. If you are looking for installation
instructions, go here.
The first person to register an account will be ‘Sysadmin’ and will have access to the ‘sysconfig’ page. The first person
to register an account in a Team will be ‘Admin’ of this team and have access to the ‘Admin panel’ page.
1. Creating an account
New users need to register an account on the register page, accessible from the login page. They need to choose a team
from the list. By default, newly created accounts are disabled. The admin of the team needs to validate them by going
into the admin panel and activate new users.
2. Creating an experiment
Once logged in, you can create an experiment by pressing ‘c’ or clicking the «Create experiment» button. You will be
presented with an «edition» page (you can see ‘mode=edit’ in the URL; the two other modes being ‘view’ and ‘show’).
You can also load a template. Go to your user panel to edit your templates. You can export them as .elabftw.tpl files,
and import them, too!
2.1 Tags
The first field is the tags, that you can use to group experiments (think folders). All experiments with the same tag will
be accessible by clicking this tag. To validate a tag, press Enter. It is saved automatically. The number of tags is not
limited. Click on a tag to remove it (in edit mode).
2.2 Date
The date is today’s date by default, in the format YYYYMMDD. You can edit it as you wish. The real creation
date/time is stored in the database in another column.
2.3 Visibility
By default, all experiments can be viewed by other team members. If you wish to restrict viewing of a particular
experiment, set this to ‘Only me’.
2.4 Status
This useful feature lets you set the ‘status’ of an experiment. By default you can have : - Running (selected upon
creation) - Need to be redone - Success - Fail
These status can be modified completely by the admin in the admin panel. 2.5 Title
The title of your experiment. A duplicated experiment will have a «I» character appended to the title upon creation.
2.6 Experiment (body)
This is where you describe your experiment and write your results. It is a rich text editor where you can have formatting, tables, colors, images, links, etc. . . To insert an image in this field, first upload it by dragging it in the ‘Attach
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files’ block. Then you will see a new block appear just below, with a thumbnail of the file, its name and size. Right
click on the image and select «Copy link location». Next, click on the «Insert/edit image» button in the toolbar of the
rich text editor (third button before the last). Paste it. Press OK. That’s it, you have an image inside your main text.
2.7 Linked items
This field allows you to link an item from the database. Just begin to type the name of what you want to link and you
will see an autocompletion list appear. Select the one you want and press Enter. The number of links is not limited.
2.8 Attach a file
You can click this region to open a file browser, or drag-and-drop a file inside. The file size limit is 5 Mo, and there is
no limit on file type. If you upload an image, a thumbnail will be created. There is no limit on the number of files you
can attach to an experiment.
When you are done, click the button.
You are now in view mode.
3. View mode of experiment
In the view mode, several actions are accessible under the date.
3.1 Edit
Go back to edit mode. You can also click the main text.
3.2 Duplicate
Duplicating an experiment allows you to create a new item with the same Title, tags, body and links, but with today’s
date and a running status. Uploaded files are not duplicated. A «I» character will be added to the title to denote that it
is a replicate. 3.3 Make a pdf
Clicking this will create a pdf from your experiment. The generated pdf will contain all the information related to the
experiment.
3.4 Lock
Once locked, an experiment cannot be modified anymore. Unless you unlock it. If it is locked by someone with
locking powers (the PI), you will not be able to unlock it. Once locked, a new action appears :
3.5 Timestamp
A locked experiment can be timestamped. Once timestamped it cannot be edited anymore.
What happens when you timestamp an experiment :
• a pdf is generated
• a sha256 sum of this pdf is generated
• this data is sent to the Time Stamping Authority (TSA)
• they timestamp it
• we get a token back
More info here : https://en.wikipedia.org/wiki/Trusted_timestamping eLabFTW uses RFC 3161 for timestamping. So
any TSA providing a RFC 3161 compatible way of timestamping will work.
3.7 elabid
In the bottom right part of the experiment, you can see something like : «Unique elabid : 20150526e72646c3ecf59b4f72147a52707629150bca0f91». This number is unique to each experiment. You can use it to reference an experiment with an external database.
3.8 Comments
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People can leave comments on experiments. They cannot edit your experiment, but they can leave a comment. The
owner of the experiment will receive an email if someone comment their experiment.
4. Database
Same as experiments for a lot of things, except there is no status, but a rating system (little stars). You can store any
type of items inside, the admin can edit the available types of items.
In view mode, click the link icon to show all experiments linked with this item. 5. Admin Panel
The admin panel allows the admin of a team to edit : - status - type of items - template for experiment (what is in the
body upon experiment creation) - users - the link in the menu - timestamping credentials (if you don’t/can’t use the
global ones provided by the sysadmin)
From there, you can also import a .csv (save an Excel file as .csv) into the database.
6. Sysconfig
The sysconfig page is only available to the sysadmin user(s). From there, you can configure : - the teams (add or edit)
- the default language - activate or not the debug mode - proxy settings - some security configs - email config
To configure emails, I would recommend to setup an account with Mandrill.com, they provide free SMTP access and
it works very well.
7. Miscellaneous
You can export experiments in .zip. If the experiment was timestamped you will find in the archive the timestamped
pdf and the corresponding .asn1 token. You can export and import items from the database (it can be several items).
Press ‘t’ to have a TODO list.
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CHAPTER 12
Contributing
12.1 What can you do to help this project ?
• Have a look at the current issues
• Translate it
• Talk about it to your colleagues, spread the word!
• Open GitHub issues to discuss bugs or suggest features
• Star it on GitHub
12.2 Translating
Do you know several languages? Are you willing to help localize eLabFTW? You’re in the right place.
Languages 100% translated:
• British English : en_GB.UTF8
• Catalan : ca_ES.UTF8
• German : de_DE.UTF8
• French : fr_FR.UTF8
• Italian : it_IT.UTF8
• Spanish : es_ES.UTF8
• Brazilian Portuguese : pt_BR.UTF8
• Simplified Chinese : zh_CN.UTF8
How to translate ?
• Join the project on poeditor.com
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• Select elabftw
• Add a language (or select an existing one)
• Start translating
• Ignore things like <strong>, <br>, %s, %d and keep the ponctuation like it was!
Then email me the result, or send a pull request.
12.3 Contributing to the code
• before doing a pull request, open an issue so we can discuss about it (unless it is obvious that your code should
be merged ;).
• base your PR on the next branch, which is the development branch; master being the release branch.
• most of the code is procedural, but a progressive transition to object oriented code is on the way.
• classes should be in inc/classes with namespace ElabftwElabftw
• a new class will be loaded automagically thanks to the use of PSR-4 with composer
• for i18n, we use gettext
• if you change a string in gettext _(‘they look like this’), change it also in a .po file (generally the french one) and
generate a .mo file (with poedit)
• same if you add a string shown to the user, it needs to be gettexted
• if you make a change to the SQL stucture, you need to put it in update.php and also install/elabftw.sql
• the update.php script is sequential. So add a block of code before the END comment. Make a check to see if
you need to alter something, and if yes, do it.
• most of the functions are in inc/functions.php
• you can use the constant ELAB_ROOT (which ends with a /) to have a full path
• comment your code wisely
• your code must follow the PSR standards
• add a plugin to your editor to show trailing whitespaces in red
• add a plugin to your editor to show PSR-1 errors
• remove BOM
12.4 Reminders
• update of SwiftMailer and mPDF is done with composer update
• update of the js components is done with bower update
• after update of tinymce, lang files need to be downloaded again, and the ones without proper name (ca instead
of ca_ES) need to be edited (change first line to ca_ES)
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CHAPTER 13
Thanks
A big thanks to early alpha testers and everyone who contributed through their ideas or suggestions to this project.
The people that helped with internationalization:
• pt-BR : Carlos Kikuti
• zh-CN : Suyoung Wang
• it-IT : Maddalena Nano, Paolo Maiuri
• es-ES : Elena, Arnau Montagud, Amaya Blesa Siemann, Jesus
• de-DE : Marko Storch, Timo Betz, Christian Wunder, Doug Morse
eLabFTW uses open source code from others. A big thanks to them for making their code available !
• jQuery
• jQuery UI
• Jeditable
• Star Rating
• Complexify
• Fancybox
• Keymaster
• TinyMCE
• Cornify
• Google Chart Tools
• mPDF
• Swiftmailer
• Raphael
• Colorwheel
• File upload
• ChemDoodle
• FileSaver.js
• tinymce-mention
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Other resources
• Icons
• LeDjamRadio for non stop music during the coding sessions
• Vim
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CHAPTER 14
Changelog
14.1 Version 1.1.5
• move doc to reStructeredText
• fix ‘Error getting latest version from server’
• new registered users will get the server lang as lang
• tag list on search page is now filtered by selected user
• add autocompletion to experiments (start with # to get item list) (fix #65)
• improve zip import now also imports attached files to an item (fix #21)
• remove MANIFEST file from zip archives
• remove .export.txt file from zip archives
• add .elabftw.json file in zip archives (to allow easy reimport)
• various code improvements
14.2 Version 1.1.4-p3
• fix bug on install page
14.3 Version 1.1.4-p2
• fix INSTALLED_VERSION constant so it displays correctly if an update is available in sysconfig
14.4 Version 1.1.4-p1
• fix bug in zip/csv generation
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14.5 Version 1.1.4
• fix bug in search page showing tags of other teams
• fix bug in search page returning items from other teams
• add ordering options to items types, status and templates (try sorting them!)
• add possibility to export experiments templates to a file (.elabftw.tpl)
• add possibility to import a template from a .elabftw.tpl file
• add possibility to import .elabftw.zip archives in the database
• switch to pki.dfn.de as default timestamper (it is free)
• revamp the timestamping class
• timestamping is properly validated
• add pagebreak tag in editor
• max file upload size is now based on system configuration (thx @jcapellman)
• move creation/duplication functions to Create() class
• timestamped pdf is now in the exported zip along with the .asn1 token
• removed check for update button in footer
• check for latest version on sysconfig page
• various little improvements and bug fixes
• update tinymce to 4.1.10
• update jquery to 2.1.4
• update SwiftMailer to 5.4.1
14.6 Version 1.1.3
• add new way to send emails (thanks to @Athemis)
• add new visibility setting (organization)
• add user guide in doc/ folder
• fix bug on experiment duplication
• display version in sysconfig page
• update pt-BR translation (thanks Kikuti)
• code cleaning
14.7 Version 1.1.2-p1
• fix css layout
• fix german translation (thanks Athemis)
• update JS components (bower update)
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• update PHP components (composer update)
• use PSR-4 for autoloading classes
14.8 Version 1.1.2
• add RFC 3161 compatible trusted timestamping (#100)
• add filtering options (#15)
• add encryption for passwords of SMTP and Timestamp stored in the SQL database (#129)
• add a check for curl extension at install (#141)
• add hidden field to prevent bot registration (#84)
• fix team_id not added on db tag add
• fix no experiments/db item showing if there is no tags
• update mpdf library
• update swiftmailer library
14.9 Version 1.1.1
• add a CONTRIBUTING file to help contributors
• add tag in search (#63)
• fix a bug where images where not added to timestamp pdf (#131)
• fix a bug in SQL install file (only impacts new installs)
14.10 Version 1.1.0
• multiple file upload now possible
• add ChemDoodle on Team page
• add a bash script in install folder to help beginners
• fix a bug where the top right search bar was not searching at the good place if the lang was not english
• add a log view for the sysadmin
• various little improvements in code
• fix a CSS bug with Chemdoodle
• fix a bug where a file was not properly deleted from system
14.11 Version 1.0.0
• no changes from beta
14.8. Version 1.1.2
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14.12 Version 1.0.0-beta
• changelog is now in markdown
• move some files in doc/ folder
• improve download.php code
• add deps to composer.json
14.13 Version 1.0.0-alpha
• different folder structure
14.14 Version 0.12.6
• better docker/haproxy integration
• show counter of unvalidated users to admin
14.15 Version 0.12.5
• add possibility to update via the web
14.16 Version 0.12.4
• add languages : Catalan, Spanish, German and Italian
• easier install on docker
• fix a bug where wrong admin was informed of new user
14.17 Version 0.12.0
• new todolist
• 1 step less for install
• internationalization (only English, Brazilian, Chinese and French at the moment)
• use of gettext for i18n
• the font is now loaded locally
• use bootstrap for css disposition
• fix some issues reported by users
• a lot of other things
• like really a lot of little stuff
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14.18 Version 0.11.0
• So many things. . .
14.19 Version 0.10.2
• Add a possibility for timestamping a pdf export of an experiment
• Removed old update.php content
• Add md5sum to uploaded files
• Display md5sum of attached files in the pdf
14.20 Version 0.10.1
• Fix a bug in authentification
• Error logs make their apparition in the database
• l33t theme is no more
• Removed the github ssl cert (was not used anyway)
• Move files around (js dependencies in js/)
• Better bower integration
14.21 Version 0.10.0
• Support of several teams on the same install
• Fixed a bug in the search page
• Added groups for better permissions control
• Add MANIFEST file in zip archive
• Add lock info in pdf
• Minor bugs fixing and improvements
• A lot of other things
14.22 Version 0.9.5
• Use of bower to keep track of dependencies
• HTML5 video and audio can now be added
• Add a user preference to ask before leaving an edit page
• Add CSV file to ZIP exports
• Add a revision system (to be able to see old versions of an experiment)
14.18. Version 0.11.0
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• Add body to CSV export
14.23 Version 0.9.4.2
• Add import CSV page
• Add general template for experiments
• Add linked items and comments on PDF
• Easier install on Mac and Windows
• Add linked items list to pdf and list of attached files
• Add links button in editor
• Add image button in editor
• Add URL in CSV export
• Show the lock on database item
• Removed the html from zip export
• Fix div blocks not passing the filter and losing formatting (thx David !)
• Fix a bug with lock/unlock of items
• Fix a bug in zip generation
14.24 Version 0.9.4.1
• Status are now fully editable
• Bugfixes and cosmetic improvements
14.25 Version 0.9.4
• Security improvements against CSRF
• Config is now stored in the database and editable on admin page
• Add detection of login attempts, and configurable ban time and number of tries
• You can only unlock a lock experiment if you are the locker.
• Only a user with locking rights can lock an experiment of someone else.
• You can now forbid users to delete an experiment with a setting in the conf file
• You can add comments on experiments
• Date is now YYYYMMDD
• Email setup is no more mandatory on install
• Updated some js libraries
• Add a ‘Saved’ notification upon saving with the Save button of TinyMCE
• Clearer code
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14.26 Version 0.9.3
• Add item type to folder of zip export
• Add useragent on github API request (checkforupdates)
• Add items locks
• Bugfixes and improvements
14.27 Version 0.9.2
• mpdf replaced html2pdf for pdf creation
• the check for updates button is fixed
• the minimum password size is now 8 characters
• HTTPS is now the only way to use eLabFTW
• install is now easier
• various bugfixes and improvements
14.28 Version 0.9.1
• Possibility to limit the visibility of an experiment to yourself only
14.29 Version 0.9
• Newer versions of JQuery and JQuery UI
• config.ini is now config.php
• Cosmetic changes
• Ctrl-Shift-D will add the date in the editor
• Possibility to search experiments owned by a unique user
• Conformation to coding standard PSR-2
14.30 Version 0.8.2
• Added check for updates button
• TinyMCE 4
• Editor’save button saves date, title and body
14.26. Version 0.9.3
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14.31 Version 0.8.1
• Admin can reset password
• You can search in everyone’s experiments if you want
14.32 Version 0.8
• You can upload big files now
• Better register form
• Fix in html zip export
• Better name of zip files when there is only one experiment
• Bug fixes and improvements
14.33 Version 0.7.3.2
• Apparition of the view arrow to fix the tab opening behavior
• Clicking a tag will now make a search in the tags only
• No more root user, admin user is made on install
• Force https
• Fix bugs
• Upgrade the mail library (swift)
• Documentation for backup
14.34 Version 0.7
• Multiple bugfixes
• Real search page
• Possiblity to export in zip or spreadsheet
• Thumbnails are clickable
• Better pdf generation
• Better html generation
• Install is now easier
14.35 Version 0.6
• Swith repo from gitorious to github (because it has wiki, bug tracker, and bigger community)
• Items in DB can now be everything, and you can edit them
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• Improvement on reset password strategy
• eLabID is a unique ID bound to each experiment (useful for tracking raw data)
• Star ratings are shown on DB show mode
• You can lock for edition an experiment
• Autosave every second on edit
• Improvements in .zip creation
• Multiple bugfixes
• Show linked experiments to a database item
14.36 Version 0.5.8 and 0.5.9
• I don’t really care about version numbers, I do it for fun.
14.37 Version 0.5.7
• Database
• Publish button
• TinyMCE for editing the body (text formatting)
• Better info boxes
• Better presentation of UCP
• Better search
14.38 Version 0.5.6
• Various bugfixes
14.39 Version 0.5.5
• Calendar on date
• Autocomplete on tags
• Ajax for tags
14.40 Version 0.5.4
• Added modification «history» on protocols
• Added dates on labmeeting and journal clubs uploads
14.36. Version 0.5.8 and 0.5.9
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14.41 Version 0.5.3
• Added templates for experiments
• You can now upload past journal clubs, labmeetings
• Added robots.txt file
14.42 Version 0.5.2
• TODO list accessible via a keyboard shortcut (‘t’ by default)
• Better profile
• Better TEAM page
14.43 Version 0.5.1
• No more Scriptaculous/Prototype, only jQuery
• TODO list added
• Images are now in themes folders
• Various FTW titles
• Git repo @ gitorious
14.44 Version 0.5
• UCP
• Themes
• Keyboard Shortcuts
• View modes
• Admin Panel
• Profile
• Send zip by email
• Better Tagcloud
• Can attach protocol to experiment
• User need validation after registration
• Unique config.ini file
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14.45 Version 0.4
• Tagcloud
• Recover password
• Make zip archive
• Editable file comments
14.46 Version 0.3
• Tags on a separate table
• Make pdf
• Statistics
• Comment on attached files
• Quick tagsearch
14.47 Version 0.2
• Search page
• Password storage using salted SHA-512
• Attaching files
14.48 Version 0.1
• Register / Login
• Show / view / edit / duplicate :: experiments / protocols
14.45. Version 0.4
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48
Chapter 14. Changelog
CHAPTER 15
License
GNU AFFERO GENERAL PUBLIC LICENSE Version 3, 19 November 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone is permitted to copy and distribute
verbatim copies of this license document, but changing it is not allowed.
Preamble
The GNU Affero General Public License is a free, copyleft license for software and other kinds of works, specifically
designed to ensure cooperation with the community in the case of network server software.
The licenses for most software and other practical works are designed to take away your freedom to share and change
the works. By contrast, our General Public Licenses are intended to guarantee your freedom to share and change all
versions of a program–to make sure it remains free software for all its users.
When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed
to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that
you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free
programs, and that you know you can do these things.
Developers that use our General Public Licenses protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License which gives you legal permission to copy, distribute and/or modify the software.
A secondary benefit of defending all users’ freedom is that improvements made in alternate versions of the program, if
they receive widespread use, become available for other developers to incorporate. Many developers of free software
are heartened and encouraged by the resulting cooperation. However, in the case of software used on network servers,
this result may fail to come about. The GNU General Public License permits making a modified version and letting
the public access it on a server without ever releasing its source code to the public.
The GNU Affero General Public License is designed specifically to ensure that, in such cases, the modified source
code becomes available to the community. It requires the operator of a network server to provide the source code of
the modified version running there to the users of that server. Therefore, public use of a modified version, on a publicly
accessible server, gives the public access to the source code of the modified version.
An older license, called the Affero General Public License and published by Affero, was designed to accomplish
similar goals. This is a different license, not a version of the Affero GPL, but Affero has released a new version of the
Affero GPL which permits relicensing under this license.
The precise terms and conditions for copying, distribution and modification follow.
TERMS AND CONDITIONS
0. Definitions.
“This License” refers to version 3 of the GNU Affero General Public License.
“Copyright” also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.
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elabftw Documentation, Release 1.1.5
“The Program” refers to any copyrightable work licensed under this License. Each licensee is addressed as “you”.
“Licensees” and “recipients” may be individuals or organizations.
To “modify” a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission,
other than the making of an exact copy. The resulting work is called a “modified version” of the earlier work or a work
“based on” the earlier work.
A “covered work” means either the unmodified Program or a work based on the Program.
To “propagate” a work means to do anything with it that, without permission, would make you directly or secondarily
liable for infringement under applicable copyright law, except executing it on a computer or modifying a private copy.
Propagation includes copying, distribution (with or without modification), making available to the public, and in some
countries other activities as well.
To “convey” a work means any kind of propagation that enables other parties to make or receive copies. Mere interaction with a user through a computer network, with no transfer of a copy, is not conveying.
An interactive user interface displays “Appropriate Legal Notices” to the extent that it includes a convenient and
prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no
warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under
this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such
as a menu, a prominent item in the list meets this criterion.
1. Source Code.
The “source code” for a work means the preferred form of the work for making modifications to it. “Object code”
means any non-source form of a work.
A “Standard Interface” means an interface that either is an official standard defined by a recognized standards body,
or, in the case of interfaces specified for a particular programming language, one that is widely used among developers
working in that language.
The “System Libraries” of an executable work include anything, other than the work as a whole, that (a) is included in
the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only
to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A “Major Component”, in this context, means a major essential
component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work
runs, or a compiler used to produce the work, or an object code interpreter used to run it.
The “Corresponding Source” for a work in object code form means all the source code needed to generate, install,
and (for an executable work) run the object code and to modify the work, including scripts to control those activities. However, it does not include the work’s System Libraries, or general-purpose tools or generally available free
programs which are used unmodified in performing those activities but which are not part of the work. For example,
Corresponding Source includes interface definition files associated with source files for the work, and the source code
for shared libraries and dynamically linked subprograms that the work is specifically designed to require, such as by
intimate data communication or control flow between those subprograms and other parts of the work.
The Corresponding Source need not include anything that users can regenerate automatically from other parts of the
Corresponding Source.
The Corresponding Source for a work in source code form is that same work.
2. Basic Permissions.
All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided
the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program.
The output from running a covered work is covered by this License only if the output, given its content, constitutes a
covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law.
You may make, run and propagate covered works that you do not convey, without conditions so long as your license
otherwise remains in force. You may convey covered works to others for the sole purpose of having them make
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modifications exclusively for you, or provide you with facilities for running those works, provided that you comply
with the terms of this License in conveying all material for which you do not control copyright. Those thus making or
running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms
that prohibit them from making any copies of your copyrighted material outside their relationship with you.
Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not
allowed; section 10 makes it unnecessary.
3. Protecting Users’ Legal Rights From Anti-Circumvention Law.
No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling
obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting
or restricting circumvention of such measures.
When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to
the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and
you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work’s
users, your or third parties’ legal rights to forbid circumvention of technological measures.
4. Conveying Verbatim Copies.
You may convey verbatim copies of the Program’s source code as you receive it, in any medium, provided that you
conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating
that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices
of the absence of any warranty; and give all recipients a copy of this License along with the Program.
You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection
for a fee.
5. Conveying Modified Source Versions.
You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of
source code under the terms of section 4, provided that you also meet all of these conditions:
a) The work must carry prominent notices stating that you modified it, and giving a relevant date.
b) The work must carry prominent notices stating that it is released under this License and any conditions added under
section 7. This requirement modifies the requirement in section 4 to “keep intact all notices”.
c) You must license the entire work, as a whole, under this License to anyone who comes into possession of a copy.
This License will therefore apply, along with any applicable section 7 additional terms, to the whole of the work, and
all its parts, regardless of how they are packaged. This License gives no permission to license the work in any other
way, but it does not invalidate such permission if you have separately received it.
d) If the work has interactive user interfaces, each must display Appropriate Legal Notices; however, if the Program
has interactive interfaces that do not display Appropriate Legal Notices, your work need not make them do so.
A compilation of a covered work with other separate and independent works, which are not by their nature extensions
of the covered work, and which are not combined with it such as to form a larger program, in or on a volume of a
storage or distribution medium, is called an “aggregate” if the compilation and its resulting copyright are not used
to limit the access or legal rights of the compilation’s users beyond what the individual works permit. Inclusion of a
covered work in an aggregate does not cause this License to apply to the other parts of the aggregate.
6. Conveying Non-Source Forms.
You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey
the machine-readable Corresponding Source under the terms of this License, in one of these ways:
a) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange.
b) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by a written offer, valid for at least three years and valid for as long as you offer spare parts or customer support
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elabftw Documentation, Release 1.1.5
for that product model, to give anyone who possesses the object code either (1) a copy of the Corresponding Source
for all the software in the product that is covered by this License, on a durable physical medium customarily used for
software interchange, for a price no more than your reasonable cost of physically performing this conveying of source,
or (2) access to copy the Corresponding Source from a network server at no charge.
c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source.
This alternative is allowed only occasionally and noncommercially, and only if you received the object code with such
an offer, in accord with subsection 6b.
d) Convey the object code by offering access from a designated place (gratis or for a charge), and offer equivalent
access to the Corresponding Source in the same way through the same place at no further charge. You need not require
recipients to copy the Corresponding Source along with the object code. If the place to copy the object code is a
network server, the Corresponding Source may be on a different server (operated by you or a third party) that supports
equivalent copying facilities, provided you maintain clear directions next to the object code saying where to find the
Corresponding Source. Regardless of what server hosts the Corresponding Source, you remain obligated to ensure
that it is available for as long as needed to satisfy these requirements.
e) Convey the object code using peer-to-peer transmission, provided you inform other peers where the object code and
Corresponding Source of the work are being offered to the general public at no charge under subsection 6d.
A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System
Library, need not be included in conveying the object code work.
A “User Product” is either (1) a “consumer product”, which means any tangible personal property which is normally
used for personal, family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling.
In determining whether a product is a consumer product, doubtful cases shall be resolved in favor of coverage. For
a particular product received by a particular user, “normally used” refers to a typical or common use of that class
of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or
expects or is expected to use, the product. A product is a consumer product regardless of whether the product has
substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use
of the product.
“Installation Information” for a User Product means any methods, procedures, authorization keys, or other information
required to install and execute modified versions of a covered work in that User Product from a modified version of its
Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object
code is in no case prevented or interfered with solely because modification has been made.
If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the
conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to
the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding
Source conveyed under this section must be accompanied by the Installation Information. But this requirement does
not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for
example, the work has been installed in ROM).
The requirement to provide Installation Information does not include a requirement to continue to provide support
service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product
in which it has been modified or installed. Access to a network may be denied when the modification itself materially
and adversely affects the operation of the network or violates the rules and protocols for communication across the
network.
Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format
that is publicly documented (and with an implementation available to the public in source code form), and must require
no special password or key for unpacking, reading or copying.
7. Additional Terms.
“Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more
of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they
were included in this License, to the extent that they are valid under applicable law. If additional permissions apply
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only to part of the Program, that part may be used separately under those permissions, but the entire Program remains
governed by this License without regard to the additional permissions.
When you convey a copy of a covered work, you may at your option remove any additional permissions from that
copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases
when you modify the work.) You may place additional permissions on material, added by you to a covered work, for
which you have or can give appropriate copyright permission.
Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized
by the copyright holders of that material) supplement the terms of this License with terms:
a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or
b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or
c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be
marked in reasonable ways as different from the original version; or
d) Limiting the use for publicity purposes of names of licensors or authors of the material; or
e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or
f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual
assumptions directly impose on those licensors and authors.
All other non-permissive additional terms are considered “further restrictions” within the meaning of section 10. If
the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with
a term that is a further restriction, you may remove that term. If a license document contains a further restriction but
permits relicensing or conveying under this License, you may add to a covered work material governed by the terms
of that license document, provided that the further restriction does not survive such relicensing or conveying.
If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement
of the additional terms that apply to those files, or a notice indicating where to find the applicable terms.
Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as
exceptions; the above requirements apply either way.
8. Termination.
You may not propagate or modify a covered work except as expressly provided under this License. Any attempt
otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including
any patent licenses granted under the third paragraph of section 11).
However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a)
provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently,
if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.
Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you
of the violation by some reasonable means, this is the first time you have received notice of violation of this License
(for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.
Termination of your rights under this section does not terminate the licenses of parties who have received copies or
rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not
qualify to receive new licenses for the same material under section 10.
9. Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation
of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise
does not require acceptance. However, nothing other than this License grants you permission to propagate or modify
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elabftw Documentation, Release 1.1.5
any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or
propagating a covered work, you indicate your acceptance of this License to do so.
10. Automatic Licensing of Downstream Recipients.
Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run,
modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third
parties with this License.
An “entity transaction” is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction,
each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party’s
predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding
Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For
example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License,
and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim
is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.
11. Patents.
A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the
Program is based. The work thus licensed is called the contributor’s “contributor version”.
A contributor’s “essential patent claims” are all patent claims owned or controlled by the contributor, whether already
acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using,
or selling its contributor version, but do not include claims that would be infringed only as a consequence of further
modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent
sublicenses in a manner consistent with the requirements of this License.
Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor’s essential
patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its
contributor version.
In the following three paragraphs, a “patent license” is any express agreement or commitment, however denominated,
not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To “grant” such a patent license to a party means to make such an agreement or commitment not to enforce a
patent against the party.
If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is
not available for anyone to copy, free of charge and under the terms of this License, through a publicly available
network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so
available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange,
in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients.
“Knowingly relying” means you have actual knowledge that, but for the patent license, your conveying the covered
work in a country, or your recipient’s use of the covered work in a country, would infringe one or more identifiable
patents in that country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring
conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing
them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is
automatically extended to all recipients of the covered work and works based on it.
A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of,
or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License.
You may not convey a covered work if you are a party to an arrangement with a third party that is in the business
of distributing software, under which you make payment to the third party based on the extent of your activity of
conveying the work, and under which the third party grants, to any of the parties who would receive the covered work
from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies
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made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the
covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.
12. No Surrender of Others’ Freedom.
If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of
this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to
satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence
you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further
conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
13. Remote Network Interaction; Use with the GNU General Public License.
Notwithstanding any other provision of this License, if you modify the Program, your modified version must prominently offer all users interacting with it remotely through a computer network (if your version supports such interaction) an opportunity to receive the Corresponding Source of your version by providing access to the Corresponding
Source from a network server at no charge, through some standard or customary means of facilitating copying of
software. This Corresponding Source shall include the Corresponding Source for any work covered by version 3 of
the GNU General Public License that is incorporated pursuant to the following paragraph.
Notwithstanding any other provision of this License, you have permission to link or combine any covered work with
a work licensed under version 3 of the GNU General Public License into a single combined work, and to convey the
resulting work. The terms of this License will continue to apply to the part which is the covered work, but the work
with which it is combined will remain governed by version 3 of the GNU General Public License.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of the GNU Affero General Public License
from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address
new problems or concerns.
Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the
GNU Affero General Public License “or any later version” applies to it, you have the option of following the terms and
conditions either of that numbered version or of any later version published by the Free Software Foundation. If the
Program does not specify a version number of the GNU Affero General Public License, you may choose any version
ever published by the Free Software Foundation.
If the Program specifies that a proxy can decide which future versions of the GNU Affero General Public License can
be used, that proxy’s public statement of acceptance of a version permanently authorizes you to choose that version
for the Program.
Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR
IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME
THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE
OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE
WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF
THE POSSIBILITY OF SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according
to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil
liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the
Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve
this is to make it free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to
most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to
where the full notice is found.
<one line to give the program’s name and a brief idea of what it does.> Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General
Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any
later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero
General Public License for more details.
You should have received a copy of the GNU Affero General Public License along with this program. If not, see
<http://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If your software can interact with users remotely through a computer network, you should also make sure that it
provides a way for users to get its source. For example, if your program is a web application, its interface could
display a “Source” link that leads users to an archive of the code. There are many ways you could offer source, and
different solutions will be better for different programs; see section 13 for the specific requirements.
You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer”
for the program, if necessary. For more information on this, and how to apply and follow the GNU AGPL, see
<http://www.gnu.org/licenses/>.
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Index
R
RFC
RFC 3161, 13, 21, 26, 39
57