EC-Lab and BT-Lab Email Notification System

This python script is designed to run headless on a Windows machine running EC-Lab or BT-Lab software from Bio-logic. It watches for .mpl (log) files to be deleted by the programme and uses information in the file name to send an email to the owner of the experiment that their experiment is complete.

Project Architecture and Examples

This system is designed to work with a specific data architecture. For example:

.
└── Data
    ├── Alvin
    │   ├── SampleA1
    │   │   ├── Test1.mpr
    │   │   ├── Test2.mpr
    │   │   ├── Test3.mpl	#This is the log file
    │   │   └── Test3.mpr
    │   └── SampleA2
    │       └── Test1.mpr
    ├── Simon
    │   └── Sample-S1
    │       └── Test1.mpr
    └── Theodore
        └── Sample-T1
            └── Test1.mpr

Each user (Alvin, Simon and Theodore) have their own separate data folder with their data inside. Once Alvins Test3 finishes, bio-logic software deletes the .mpl file (see below for more info). Once the file is deleted, DirectoryWatcher.py takes the filename as a string, in this case ./Data/Alvin/SampleA1/Test3.mpl.

It then tries to match an id in user_info.py to the string of the filename. Here is an example user_info.py file:

user_info.py This file must be created before running

# Users go here as tuples. The ordering is 'name', 'email', 'id1', 'id2' .... There is no limit to the number of ids
users = (
    ('Alvin', '[email protected]', 'Alvin', 'alvin', 'ALVIN'),
    ('Simon', '[email protected]', 'Simon', 'simon', 'SIMON'),
    ('Theodore', '[email protected]', 'Theodore', 'theodore', 'THEODORE')
)
# Pretty print the users by running python `users_info.py`
if __name__ == "__main__":
    for user in users:
        print ('{0}\t{1:16}\t{2}'.format(user[0], user[1], user[2:]))

In this case, Alvin is contained in the string ./Data/Alvin/SampleA1/Test3.mpl, so an email notification would be sent to [email protected].

Installation

Clone this git repo to a location of your choice, install the requirements, and create the user_info.py (see above) file.

git clone [email protected]:CabanaLab/ElectrochemNotification.git
cd ./ElectrochemNotification
pip install -r requirements.txt
touch ./EmailWhenDone/user_info.py
touch ./EmailWhenDone/localsettings.py

localsettings.py This file must be created before running

#localsettings

## Moderator Information
moderator = ''							#Your moderators name
moderator_email = ''					#Moderators email address (for error reporting)

## Email Client Information
server_email = ''						#the email address you wish to send notifications from (works with gmail)
username = ''							#email username
password = ''							#email password

## Ignore List - Ignores a filename if any of theses strings are contained in it.
ignore_list = [
    'strings',
    'that',
    'should',
    'be',
    'ignored'
]

Running the client headless

On a windows machine, the script can be run headless from the command line using:

pythonw DirectoryWatcher.py /directory/to/Data

This file can also be run on Linux as a systemd service by creating a service file.

Running tests

cd ./EmailWhenDone
python3 -m unittest tests/tests.py

Does my installation of BT-Lab/EC-Lab delete .mpl files when the experiment is complete?

You can check whether your version of EC-Lab or BT-Lab is deleting .mpl files by going to Tools > Options > General tab and checking LOG files (*.mpl) automatic erasing on stop