The Representational State Transfer Application Program Interface (REST) server can be used to retrieve tree information from Metadata Enhanced PhyloXML (MEP) files.
https://tools.cifr.ncsu.edu/rest
The basic login is ccrp / spring_retain. The tool will unzip a MEP file and provide a link the the REST page for this run id.
The decifr-rest server allows a user to share information about placements from T-BAS with other users via the web. The program is written to run in a Python 3 virtual environment. The default location of the virtual environment is set to /usr/local/pythonenvs. To change it edit the first line in the /usr/local/decifr-rest/decifr-rest.py script. Follow the commands below to create the virtual environment.
cd /usr/local
sudo su
mkdir pythonenvs
cd /usr/local/pythonenvs
python3 -m venv decifr-rest
source decifr-rest/bin/activate
pip install Flask
pip install lxml
Next install the server using git.
cd /usr/local
git clone https://github.com/ncsu-decifr/decifr-rest.git
To share the results of some placements, copy the MEP files created either on the public T-BAS site or with docker to a folder on your computer, and uncompress them by double-clicking if on Mac or Windows or using Linux command gunzip *. An example (6BLUBNSA.mep.gz) is included. Edit the line in /usr/local/decifr-rest/decifr-rest.py with app.config['TMP_FOLDER'] = "/tmp/rest" to the value of the directory with the MEP files.
cd /tmp
mkdir rest
cd /usr/local/decifr-rest
cp 6BLUBNSA.mep.gz /tmp/rest
cd /tmp/rest
gunzip *
cd /usr/local/decifr-rest
./decifr-rest.py
To run just type ./decifr-rest.py. This will start the REST server. Open your browser to localhost:8090/list and there are links to a runid for each MEP file. Click on a link to see more information about the run.
If you want to restrict access to pages with basic authentication you can edit the /usr/local/decifr-rest/decifr-rest.py file. Each function in the file has a line @requires_auth that is commented out. If you uncomment this line that page will be restricted. Edit the function check_auth to set the login credentials.
The server can serve files to the browser, the command line or programatically. To use wget to retrieve mep files with the correct extension and if password protected use this command.
wget --content-disposition --user admin --password secret localhost:8090/mep/<runid>
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