Sensormap is a project to assist in fieldwork for the Soil Biogeochemistry Laboratory at EPFL. The project is a fullstack application to handle soil samples and profiles in the field, as well as processing tools to handle instrument data.
This repository contains the frontend application for the project, and consists of the following external repositories:
-
sensormap-bff - The Backend-for-Frontend (BFF) to proxy requests between Keycloak and the SOIL-API.
-
soil-api - The REST API for SOIL related projects (including this one).
The changelog can be found in the CHANGELOG file. For backend changes, refer to their respective repositories.
The application is built with the following libraries and frameworks:
There is a docker-compose file to start the application in development mode. To start the application:
- Clone the repositories above into the folder beneath this one, as to have the following structure:
.
├── sensormap-bff
├── sensormap-ui
└── soil-apimkdir -p ./sensormap
cd ./sensormap
git clone http://github.com/LabSOIL/sensormap-bff
git clone http://github.com/LabSOIL/sensormap-ui
git clone http://github.com/LabSOIL/soil-api- Setup a Keycloak instance with a realm and client suitable for development
for both the UI and the BFF independently, and then in this
sensormap-uirepository, create a.envfile with the Keycloak configuration similar to below:
KEYCLOAK_CLIENT_ID=sensormap-frontend-local
KEYCLOAK_BFF_ID=sensormap-frontend-local-bff
KEYCLOAK_BFF_SECRET=<BFF_CLIENT_SECRET>
KEYCLOAK_REALM=SOIL
KEYCLOAK_URL=https://<KEYCLOAK_ROOT_URL/Note: Make sure the user you will be using has the realm role 'admin'.
- Start the application from within this repository (sensormap-ui) with the following command (this will build the images and start the containers):
docker-compose up --build- In the default configuration, the application will be available at
http://soil:88. Therefore, you will need to add the following line to your/etc/hostsfile:
echo -e "127.0.0.1\tsoil" | sudo tee -a /etc/hostsIf this is undesired, the hostname can be changed in the docker-compose.yml
file.
- The application should now be available at
http://soil:88. Login with your Keycloak credentials and you should be able to access the application.
The application is designed to be intuitive and easy to use. The main features are:
- Projects: Create projects to group elements of the other components together. For example, areas, plots, samples, and soil profiles.
- Areas: These are the regions in which plots and samples are taken.
- Plots: Create plots within areas to represent the location of samples, sensors and transects.
- Samples: Represent soil samples taken from plots, and their characteristics, including chemical composition, and texture.
- Sensors: Relate to sensors placed in the field that collect data related to a plot.
- Soil Profiles: Represent the vertical distribution of soil properties in a plot.
- Soil Types: Define the soil types that can be assigned to soil profiles.
- Transects: Represent a relationship of several plots in a line.
- GNSS: Allows the uploading of handheld GPX waypoint data to enable the creation of plots and soil profiles from field locations.
- Instrument Processing: Tools to process instrument data in the lab that may relate to samples taken from the field.
The main view of the application is the projects view. Here you can see all the projects for the lab that have been created.
Clicking on a project will take you to the project view, where you can see a list of areas. The project allows other components to be consolidated together, and defines the colour its assets are represented in associated components, such as in map views.
The areas view allows you to see all of the areas in the field on a map. Areas represent the regions in which plots, sensors, soil profiles and samples are defined.
Clicking on an area will take you to the area view, where you can see a list of plots, sensors, soil profiles and samples associated with the area on a map. The region is represented by a polygon on the map, dynamically generated as the convex hull of the plots in the area.
You can visualise a summary of the components by clicking on them, and move through to their respective record views.
The plots view allows you to see all of the plots in the field on a map. Plots represent the location of samples, can have sensors associated with them, and can be part of transects.
An image of a plot can be uploaded to represent the location in the field, and the associated samples can be viewed and navigated to on the left
The samples view shows the data collected from each sample, including the texture, chemical composition, and other properties. A sample is defined by its depth, where A, B, and C generally represent the soil at different depths. You can navigate to the other samples at the top left of the page.
The instrument processing view allows you to upload instrument data files to
process them into the database. The workflow replicates the
InstrumentProcessing.ipynb notebook available in the
lab-codes repository.
The workflow allows you to upload a file from a supported instrument, and process it into the database. The processed data can be baseline filtered interactively, and samples can be integrated and spliced out of the data, and finally exported.
This project was developed by Evan Thomas and the Soil Biogeochemistry Laboratory at EPFL.
The images used in this README are for illustrative purposes and have been created for the purpose of demonstration and testing.
This project is licensed under the MIT License - see the LICENSE file for details.