<img src="assets/biokeeper_logo.png" width="3%"> Biokeeper

Citizen science biosample annotation tool

<table align='center'> <t0> <td><img src="assets/pic4.svg" height=100></td> <td><img src="assets/pic3.svg" height=100></td> <td><img src="assets/pic5.svg" height=100></td> <td><img src="assets/pic6.svg" height=100></td> <td><img src="assets/pic1.svg" height=100></td> <td><img src="assets/pic7.svg" height=100></td> <td><img src="assets/pic8.svg" height=100></td> </tr> </table>

For users

Project structure

Repositories

The Biokeeper project file structure organized into several submodules for ease of development several logical parts of the project. Currently they are:

biokeeper # this repo, contains common docker-compose.yml to start all the server-side services
├── biokeeper-admin    # admin web page
├── biokeeper-auth     # users authentication service
├── biokeeper-backend  # core server-side application logic
├── biokeeper-frontend # React Native cross-platform app
└── biokeeper-mq       # RabbitMQ message broker

Microservice architecture

<img src="assets/biokeeper_architecture_diagram.svg" width=70% height=400>

Start of work

First you need to clone this repo with all the submodues:

git clone --recurse-submodules git@github.com:phlaster/biokeeper.git
cd biokeeper

Then make sure you put relevant JWT public and private keys into jwt_keys/ directory and feel free to run:

docker-compose build
docker-compose up

For developers

Setting up GIT

To work on this or any child repo you need:

1. Set up your git credentials (where USERNAME is your user name):

   git config --global user.name "USERNAME"
   git config --global user.email USERNAME@users.noreply.github.com
   

2. In GitHub web UI FORK CHOSEN REPO.

3. Clone the repo to your local machine:

   git clone git@github.com:USERNAME/REPONAME.git
   cd REPONAME
   

4. Explicitly set upstream:

   git remote add upstream git@github.com:phlaster/REPONAME.git
   

5. Check that everything is as expected:

   git remote -v
   

   You should see something like:

   origin	git@github.com:USERNAME/REPONAME.git (fetch)
   origin	git@github.com:USERNAME/REPONAME.git (push)
   upstream	git@github.com:phlaster/REPONAME.git (fetch)
   upstream	git@github.com:phlaster/REPONAME.git (push)
   

6. Fetch updates from upstream repo:

   git fetch upstream
   

7. Merge updates with the branch of your choice:

   git checkout master
   git merge upstream/master
   # OR
   git checkout dev
   git merge upstream/dev
   

8. Then after work is done push changes into your personal repo:

   git push origin master
   # OR
   git push origin dev
   

Contributors

<table> <tr> <td align="center" style="word-wrap: break-word; width: 150.0; height: 150.0"> <a href=https://github.com/Mityamops> <img src=https://avatars.githubusercontent.com/u/125828608?v=4 width="100;" style="border-radius:50%;align-items:center;justify-content:center;overflow:hidden;padding-top:10px" alt=Mityamops/> <br /> <sub style="font-size:14px"><b>Mityamops</b></sub> </a> </td> <td align="center" style="word-wrap: break-word; width: 150.0; height: 150.0"> <a href=https://github.com/Momochka> <img src=https://avatars.githubusercontent.com/u/125281818?v=4 width="100;" style="border-radius:50%;align-items:center;justify-content:center;overflow:hidden;padding-top:10px" alt=Momochka/> <br /> <sub style="font-size:14px"><b>Momochka</b></sub> </a> </td> <td align="center" style="word-wrap: break-word; width: 150.0; height: 150.0"> <a href=https://github.com/kiriklzz> <img src=https://avatars.githubusercontent.com/u/112094641?v=4 width="100;" style="border-radius:50%;align-items:center;justify-content:center;overflow:hidden;padding-top:10px" alt=kiriklzz/> <br /> <sub style="font-size:14px"><b>kiriklzz</b></sub> </a> </td> <td align="center" style="word-wrap: break-word; width: 150.0; height: 150.0"> <a href=https://github.com/Rimk4> <img src=https://avatars.githubusercontent.com/u/82030462?v=4 width="100;" style="border-radius:50%;align-items:center;justify-content:center;overflow:hidden;padding-top:10px" alt=Rimk4/> <br /> <sub style="font-size:14px"><b>Rimk4</b></sub> </a> </td> </tr> <tr> <td align="center" style="word-wrap: break-word; width: 150.0; height: 150.0"> <a href=https://github.com/catfield123> <img src=https://avatars.githubusercontent.com/u/38911774?v=4 width="100;" style="border-radius:50%;align-items:center;justify-content:center;overflow:hidden;padding-top:10px" alt=catfield123/> <br /> <sub style="font-size:14px"><b>catfield123</b></sub> </a> </td> <td align="center" style="word-wrap: break-word; width: 150.0; height: 150.0"> <a href=https://github.com/d3biruwan> <img src=https://avatars.githubusercontent.com/u/91975865?v=4 width="100;" style="border-radius:50%;align-items:center;justify-content:center;overflow:hidden;padding-top:10px" alt=d3biruwan/> <br /> <sub style="font-size:14px"><b>d3biruwan</b></sub> </a> </td> <td align="center" style="word-wrap: break-word; width: 150.0; height: 150.0"> <a href=https://github.com/Lo-Lap> <img src=https://avatars.githubusercontent.com/u/116972772?v=4 width="100;" style="border-radius:50%;align-items:center;justify-content:center;overflow:hidden;padding-top:10px" alt=Lo-Lap/> <br /> <sub style="font-size:14px"><b>Lo-Lap</b></sub> </a> </td> <td align="center" style="word-wrap: break-word; width: 150.0; height: 150.0"> <a href=https://github.com/phlaster> <img src=https://avatars.githubusercontent.com/u/125278254?v=4 width="100;" style="border-radius:50%;align-items:center;justify-content:center;overflow:hidden;padding-top:10px" alt=phlaster/> <br /> <sub style="font-size:14px"><b>phlaster</b></sub> </a> </td> </tr> </table>