Pathways

Installation

Note: This installation guide assumes familiarity with command line on unix like systems. It is tailored toward macOS, as most of the developers on this project use macs. Windows and Linux installations will have the same dependecies, although installations may vary. Contact the lead backend developers with questions / concerns.

Clone the repository in the directory where you would like the application to live.

git clone https://github.coecis.cornell.edu/Pathways/PathwaysApp-Public

Global Installations

Install xmlsec, using brew if on mac (otherwise, google xmlsec install + your machine here)

brew install Libxmlsec1
brew install pkg-config

If you are unsure whether either of these packages is installed, run the following command to determine whether it has been installed or not.

brew install -v package-name

Create Virtual Environment (Done only once)

For Unix system users

Navigate to the react-app/api folder, and run:

If you don't have pip, run:

python get-pip.py

If you don't have virtualenv,

python3 -m pip install --user virtualenv

Create a new virtual environment:

python3 -m venv venv

Activate the virtual environment:

source venv/bin/activate

Install all of these packages, once you have activated your virtual environment.

pip install python-dotenv Flask-PyMongo nltk pandas scikit-learn numpy autocorrect python3-saml onelogin xmlsec argparse guppy3 redis scipy openpyxl

At this point, you python environment should be set up. If there are any issues during the installation process, contact the lead backend developer.

For Windows system users

Navigate to the react-app/api folder, and run:

If you don't have pip, run:

python get-pip.py

If you don't have virtualenv,

python -m pip install --user virtualenv

Create a new virtual environment, please click the create_venv_windows.cmd file

Activate the virtual environment:

api\venv\Scripts\activate.bat

Install all of these packages, once you have activated your virtual environment.

pip install python-dotenv Flask-PyMongo nltk pandas scikit-learn numpy autocorrect python3-saml onelogin xmlsec argparse guppy3 redis scipy openpyxl

At this point, you python environment should be set up. If there are any issues during the installation process, contact the lead backend developer.

Install and Set Up Database

This is the first step. Install mongoDB (default for mac is homebrew installation). If you are not using mac, refer to:

https://docs.mongodb.com/manual/installation/

brew tap mongodb/brew
brew install mongodb-community@4.4
brew install redis

Create a new folder from your home directory called ~/data/db.

Run the App

1. Launch Database

Navigate to the root folder of the repository and run ./start_mongo.sh. You should see a lot of text come up in the screen, meaning that the database is running. For testing and development purposes, keep this terminal window open as long as you want the database to run. If you know tmux, you can also run the database using a detachable tmux session so you don't have to keep the terminal window open.

./clear_mongo.sh is a script for removing all of the data from the database, and should only be used in testing and development setups.

clicks on start_redis.cmd to start redis server on windows, or run ./start_redis.sh in linux system.

stop_redis.cmd can shutdown redis server on windows and run ./stop_redis.sh on linux system do the same thing.

2. Launch Backend

Navigate to react-app/api and click generate_data.cmd file on windows, or run ./generate_data.sh on Mac. This will output the necessary .pickle files that the backend reads (this only needs to be done once, unless the csv files have been updated).

Navigate to Pathways/react-app in a separate terminal session and run npm start. This will start the backend server. If you are getting dependency not satisfied errors, activate the virtual environment (per above) and do pip install <insert-dependency-here>.

If you get errors when running npm start and the errors are not dependency errors, navigate to Pathways/api in a separate terminal session and run flask run

3. Launch Frontend

Navigate to Pathways/react-app in a separate terminal session and run npm start. This will start the frontend server. If you are getting dependencny not satisfied errors, do npm install insert-dependency-here in Pathways/react-app folder.

Troubleshooting

Activate the virtual environment (source venv/bin/activate on Mac or venv\Scripts\activate.bat from api folder) and do pip install insert-dependency-here.

Dependency not satisfied errors with react: do npm install insert-dependecy-here from Pathways/react-app folder to add dependencies not downloaded.

SSL: CERTIFICATE_VERIFY_FAILED error: see answers to this question: https://stackoverflow.com/questions/50236117/scraping-ssl-certificate-verify-failed-error-for-http-en-wikipedia-org

GarlGuo / Pathways