The JBioFramework Web Application is a more efficient method of performing 1-Dimensional through the use of a browser and file selection in the format of FASTA files. This document will contain information regarding Download and Installation, Usage for Development, and Testing Usage for the application.
Dr. Paul Craig received his B.S. in Chemistry from Oral Roberts University in 1979, and his Ph.D. in Biological Chemistry from The University of Michigan in 1985. Following a post-doc at Henry Ford Hospital (biophysical chemistry of blood clotting; 1985-1988), he spent five years as an analytical biochemistry at BioQuant, Inc., in Ann Arbor, Michigan before joining RIT in 1993.
git clone https://github.com/AmrMualla/RITSimulationofProteinSimulations.gitWindows:
cd RITSimulationofProteinSimulations\py -m pip install -r requirements.txtmacOS or Linux:
cd RITSimulationofProteinSimulations/pip install -r requirements.txt- Python 3.7 or higher
- Node.js 20.11.0 or higher
- React 18.2.0 or higher
Navigate to the top level directory by typing in the command line
Windows:
cd RITSimulationofProteinSimulations\macOS or Linux:
cd RITSimulationofProteinSimulations/Launch the API server by typing in the command line:
uvicorn server:app --reloadNavigate to the jbio-web-app subdirectory by typing in the command line
Windows:
cd frontend\jbio-web-app\macOS or Linux:
cd frontend/jbio-web-app/Launch the application by typing in the command line:
npm startA browser will open with the URL: http://localhost:3000/
Press the 1D Electrophoresis button on the left.
Follow the instructions listed beneath the simulation to load the desired FASTA files and begin the simulation:
This guide will be going over the basics of the Jest tests created in this project, including how to install Jest, create a basic Jest class, and the standards followed creating the existing Jest tests. Jest was a great choice for the team because of the choice to use Node.js and React. Jest synergizes very well with both of these and makes it easy to use.
Installation for Jest is simple with the help of a package manager. Since we are using Node.js with npm as the package manager, installation is as easy as pasting:
npm install --save-dev jestonce you navigate to
Windows:
..\RITSimulationofProteinSimulations\frontend\jbio-web-appmacOS or Linux:
~/RITSimulationofProteinSimulations/frontend/jbio-web-appTo do so, open the terminal, which is usually found under the View tab in most IDEs, and select the Terminal button. It will open up the terminal in the default directory. Then navigate to the desired directory by typing
Windows:
cd frontend\jbio-web-appmacOS or Linux:
cd frontend/jbio-web-appThis should put you in the correct directory, so typing
npm install --save-dev jestin the terminal will install Jest for you and have everything ready to go.
Once the installation is complete, typing
npm testwill bring up the watch usage buttons which you can use to run the tests. If there is every an error saying:
npm test is not recognizedtype:
npm installagain to update the package. Then you should see this:
awill run all the test suites.
f will run all the failed tests.
p will let you chose a test suite to test by typing its name.
t will let you chose a specific test to test by typing its name.
q will end the session.
After running a test, it will tell you how many test suites and tests have passed and if they failed, where and why they did. Heres an example output:
If on Windows, the Jest tests are stored in
.\\RITSimulationofProteinSimulations\frontend\jbio-web-app\src\components\__tests__If on macOS or Linux, the Jest tests are stored in
~/RITSimulationofProteinSimulations/frontend/jbio-web-app/src/components/__tests__Currently, there is a test class for each frontend component in the project. They all vary depending on the component but all have a similar format that should be used when creating more tests. For starters, these imports are needed for jest tests:
These are pretty standard imports, the first line doesn’t change, it imports React which is what is used for the web app. The second line is the same format, but you will add in methods you use in your tests. Some examples would be
render, fireEvent, screen, and various others. Adding more methods would look like this:
Now for creating tests, the default test will look like this:
You can replace the 'Test name' with whatever you want to name the test. Ensure that it is detailed for ease of viewing which test is being run.
Navigate to the top level directory by typing in the command line
Windows:
cd .\RITSimulationofProteinSimulations\
py -m unittest backend.Electro1DTests.ProteinTestmacOS or Linux:
cd ~/RITSimulationofProteinSimulations/
python3 -m unittest backend.Electro1DTests.ProteinTestOR
Some IDEs have a built-in run function for files that can be executed. If you wish to do this, navigate to the ProteinTest.py or any other test file and click the run button.
Analyze results from the tests being run and modify the test or method being tested if failed.
- TODO
- Fall 2023 to Spring 2024:
- Coach:
- Developers: