Installation

Requirement

Install python3 and pip using Miniconda

Note

Below is an example for Ubuntu 20.04

apt-get update
apt-get install wget locales git -y

echo "export LC_ALL=C" >> ~/.bashrc
echo 'export LANGUAGE="en_US.UTF-8"' >> ~/.bashrc

cd ~/Downloads
wget https://repo.anaconda.com/miniconda/Miniconda3-py38_4.10.3-Linux-x86_64.sh
bash Miniconda3-py38_4.10.3-Linux-x86_64.sh

source ~/.bashrc

AMP-SCZ Lochness

Install AMP-SCZ Lochness and AMP-SCZ Yaxil using pip.

pip install ampscz-lochness

Note

For the most recent AMP-SCZ lochness verion for debugging, it might be better off to pull most recent commits directly from github.

git clone https://github.com/AMP-SCZ/lochness
cd lochness
pip install -r requirements.txt

echo "export PYTHONPATH=${PYTHONPATH}:lochness" >> ~/.bashrc  # add path
echo "export PATH=${PATH}:lochness/scripts" >> ~/.bashrc  # add path
source ~/.bashrc

After pip installation, the scripts below should be available from your console.

sync.py -h
lochness_create_template.py -h
crypt.py -h

Amazon Web Service (AWS) commandline tool

AMP-SCZ can also push the downloaded data to Amazon Web Service (AWS) s3 bukcet. To use this functionality, AWS commandline tool needs be installed and configured. Install awscli using apt-get

sudo apt-get install awscli

Note

If you do not have sudo privileges, you can also download awscli excutables here.

Then configure AWS CLI with your AWS credentials for the s3 bucket.

aws configure

AWS Access Key ID [None]: AKIAIOSFODNN7EXAMPLE
AWS Secret Access Key [None]: wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY
Default region name [None]: us-east
Default output format [None]: json

Your s3 bucket should be available from your shell environment.

$ aws s3 ls YourBucketName

mailx for sending out emails

Lochness can send out email updates. This requires mailx installed in the data aggregation server. In the current version sync.py is configured to use mailx as the default mechanism, but Google SMTP server can also be used when sync.py is slightly tweaked.

Note

To use Google SMTP server, change the two lines send_out_daily_updates(Lochness) to send_out_daily_updates(Lochness, mailx=False)

In order to use Google SMTP in sending out the emails, you need to create a google account and set the Less secure app access under the “Account settings” to “ON”.

Installation complete!