Merge branch 'dev'

.github/workflows/deploy.yml

@@ -9,8 +9,8 @@ env:
   SSH_USER: lhendrix
   SSH_HOST: 51.68.188.78
   REGISTRY: ghcr.io
-  IMAGE_NAME: battmoteam/battmogui:latest
-  WORKDIR: battmogui
+  IMAGE_NAME: battmoteam/battmoapp:latest
+  WORKDIR: battmoapp
 
 jobs:
   publish:

README.md

@@ -1,95 +1,107 @@
-# BattMo - Graphical User Interface (GUI)
+# BattMoApp
 
 [![](./python/resources/images/battmo_logo.png)](https://github.com/BattMoTeam/BattMo.git)
 [![](https://zenodo.org/badge/410005581.svg)](https://zenodo.org/badge/latestdoi/410005581)
 
-The Battery Modelling Toolbox (**BattMo**) is a resource for continuum modelling of electrochemical devices in MATLAB and Julia. 
-It offers users a flexible framework for building fully coupled electrochemical-thermal simulations of electrochemical 
-devices using 1D, 2D, or 3D geometries. The original **BattMo** is implemented in MATLAB and builds on the open-source MATLAB 
+The Battery Modelling Toolbox (**BattMo**) is a resource for continuum modelling of electrochemical devices in MATLAB and Julia.
+It offers users a flexible framework for building fully coupled electrochemical-thermal simulations of electrochemical
+devices using 1D, 2D, or 3D geometries. The original **BattMo** is implemented in MATLAB and builds on the open-source MATLAB
 Reservoir Simulation Toolbox (MRST) developed at SINTEF. BattMo being rewritten in Julia and builds on the open source Julia framework for multiphysics simulators, Jutul.jl. This repository builds further upon BattMo.jl.
 
 Additional information about BattMo on the [BattMo repository](https://github.com/BattMoTeam/BattMo.git)
 
-The **BattMo GUI** is a web-based application build with **streamlit** which offers a user-friendly interface to 
-conduct an end to end simulation experience. Each physical quantity needed to define an experimental protocol can be 
-modified to suit the user's needs. The parameter set thus defined is then used to run the BattMo P2D model. 
+**BattMoApp** is a web-based application which offers a user-friendly interface to
+conduct an end to end simulation experience. Each physical quantity needed to define an experimental protocol can be
+modified to suit the user's needs. The parameter set thus defined is then used to run the BattMo P2D model.
+
+The application consists of a Web socket API build with **HTTP.jl** and configered to run BattMo simulations, and a graphical user interface build with **Streamlit**.
 
 ## Using the application
 
 The BattMo application can very easily be used on [app.batterymodel.com](http://app.batterymodel.com/). If you'd rather use the application offline, it can be installed using Docker. If you'd like to install for development, see the next section called 'Developer installation'. The BattMo GUI is available as a set of Docker images in the Github container registry and can be found among BattMoTeam's packages. In order to use it you have to install Docker and Docker Compose. See the [Docker website](https://www.docker.com/) for more information about Docker and how to install it. Assuming you have both Docker and Docker Compose installed on your machine:
 
-Open a bash terminal and pull the latest Docker images from the registry. For the streamlit image that represents the frontend:
+Open a bash terminal and pull the latest Docker images from the registry. For the Docker image that represents the GUI:
+
 ```<bash>
-docker pull ghcr.io/battmoteam/battmogui_streamlit:latest
+docker pull ghcr.io/battmoteam/battmoapp_gui:latest
 ```
-For the genie Docker image that serves as an api and runs the BattMo.jl package:
+
+For the Docker image that serves as a Web socket API and runs the BattMo.jl package:
+
 ```<bash>
-docker pull ghcr.io/battmoteam/battmogui_genie:latest
+docker pull ghcr.io/battmoteam/battmoapp_api:latest
 ```
+
 And for the production server Nginx:
+
 ```<bash>
 docker pull ghcr.io/battmoteam/battmogui_nginx:latest
 ```
+
 Run the images in containers by using a docker compose file. Create a docker-compose.yml file with the following content:
+
 ```<docker>
 version: "3.3"
 
 services:
 
-  genie:
-    image: ghcr.io/battmoteam/battmogui_genie:latest
-    build: ./genie
-    container_name: genie
+  api:
+    image: ghcr.io/battmoteam/battmoapp_api:latest
+    build:
+      context: ./api
+      dockerfile: Dockerfile
+      target: prod
+    container_name: api
     restart: always
     ports:
-      - "8000:8000"
-    volumes:
-      - ./genie:/home/genie/app
-    command: julia --project=. -e 'include("app/rest.jl")' --color=yes --depwarn=no --project=@. --sysimage="/home/sysimage.so" -q -i -- $$(dirname $$0)/../bootstrap.jl -s=true "$$@"
+      - "8081:8081"
+      - "8080:8080"
+    command: julia --project=. -e 'include("api.jl")' --color=yes --depwarn=no --project=@. --sysimage="pre-compilation/sysimage.so" -q -i -- $$(dirname $$0)/../bootstrap.jl -s=true "$$@"
 
   nginx:
-    image: ghcr.io/battmoteam/battmogui_nginx:latest
+    image: ghcr.io/battmoteam/battmoapp_nginx:latest
     build: ./nginx
     container_name: nginx
     restart: always
     ports:
       - "8001:8001"
       - "8002:8002"
-    volumes:
-      - ./nginx:/app
-
     depends_on:
-      - genie
-      - streamlit
- 
-  streamlit:
-    image: ghcr.io/battmoteam/battmogui_streamlit:latest
-    build: ./streamlit
-    container_name: streamlit
+      - api
+      - gui
+
+  gui:
+    image: ghcr.io/battmoteam/battmoapp_gui:latest
+    build: ./gui
+    container_name: gui
     restart: always
     ports:
-      - "8501:8501"
-    volumes:
-      - ./streamlit:/app
-    depends_on:
-      - genie
+      - "80:80"
+    command: streamlit run app.py --global.disableWidgetStateDuplicationWarning true --server.port=80
+```
+
+Now run the following command to build the containers:
 
-    command: streamlit run Introduction.py --global.disableWidgetStateDuplicationWarning true --server.port=8501
+```<bash>
+docker-compose build
 ```
+
 Now run the following command to start the containers:
+
 ```<bash>
 docker-compose up -d
 ```
 
-Now you can open your browser and go to 'localhost:8501' where the GUI should be visible and ready to use.
+Now you can open your browser and go to 'localhost:8501' where **BattMoApp** should be visible and ready to use.
 
 ## Developer installation
 
 If you'd like to install the BattMo application for development you need to have both Docker and Docker Compose installed on your computer. See the [Docker website](https://www.docker.com/) for more information about Docker and how to install it. Assuming you have both Docker and Docker Compose installed on your machine:
 
 Clone the repository:
+
 ```<git>
-git clone https://github.com/BattMoTeam/BattMo-gui.git
+git clone https://github.com/BattMoTeam/BattMoApp.git
 ```
 
 Now the only thing you have to do in order to run the application is to build the images and run the docker containers using Docker Compose. The building setup for the development environment can be found in the file 'docker-compose.yml'. To build the images, go into the BattMo-GUI directory in your terminal and run:
@@ -106,58 +118,56 @@ docker-compose up -d
 
 Now you can go to 'Localhost:8501' in your browser in order to visualize and use the web-application.
 
-After changing anything in the streamlit folder, in order to see the changes in the application you can run:
+After changing anything in the streamlit folder, in order to see the changes in the application you can rerun the webpage or run in your terminal:
 
 ```<bash>
-docker restart streamlit
+docker restart gui
 ```
 
 After changing anything in the genie folder, in order to see the changes in the application you can run:
 
 ```<bash>
-docker restart genie
+docker restart api
 ```
 
 When changing anything in the recources and database, or in the Julia system image building setup, make sure to rebuild the images again instead of only restarting certain containers.
 
 ## Development structure
 
-The **BattMo GUI** is build in python using **streamlit**. 
-- The *streamlit* directory contains the streamlit app code and a 
-database that stores the parameters used to define an experimental protocol (default values, metadata).
-- The *genie* directory contains the Julia backend code that uses the Genie framework to create a rest-api. This api enables data transfer between the **BattMo** package and the streamlit frontend and starts a simulation upon receiving input data from the streamlit frontend.
+**BattMoApp** consists or three main components:
+
+- The _gui_ directory contains the Python-based code for the streamlit GUI and a
+  database that stores the parameters used to define an experimental protocol (default values, metadata).
+- The _api_ directory contains the Julia-based code that uses the HTTP.jl to create a Web socket API. This API enables data transfer between the **BattMo** package and the streamlit GUI and starts a simulation upon receiving input data from the GUI.
 
 This streamlit app is a multipage app
 (cf [streamlit doc](https://docs.streamlit.io/library/get-started/multipage-apps/create-a-multipage-app)).
-The first page, and therefore the file to run to start the app, is *Introduction.py*. The other pages' start files
-are stored in the *pages* directory, as specified in the streamlit documentation. Here below is a brief description
+All the pages are stored in the _app_pages_ directory and are specified in the _app.py_ file which includes the general settings of the applications and needs to be executed in order to start the application. Here below is a brief description
 of each page.
 
-- **Introduction** : The starting page, gives an introduction to the app. It provides a description on BattMo, a nevigation to the other pages, and links to more information and documentation.
+- **Home** : The starting page, gives an introduction to the app. It provides a description on BattMo, a navigation to the other pages, and links to more information and documentation.
 
-- **Simulation** : Allows user to define all physical quantities needed to define the desired 
-experimental protocol. The parameters and metadata (units, IRIs, values from literature) are stored in a SQLite file
-called *BattMo_gui.db*. Once the physical quantities fit the user's need, one must **UPDATE** them using the corresponding
-widget, which will save the parameters in a json file called *battmo_input* (stored in the BattMoJulia directory). 
-The *battmo_input* file contains all the parameters' metadata; a second file called *battmo_formatted_input* is also
-created, it's the version used as input by the Julia code. After updating the parameters, the user can click on the **RUN** button to launch the simulation, based on the parameters saved in the *battmo_formatted_input* file.
+- **Simulation** : Allows user to define all physical quantities needed to define the desired
+  experimental protocol. The parameters and metadata (units, IRIs, values from literature) are stored in a SQLite file
+  called _BattMo_gui.db_ within the _database_ directory. The parameter values in the page are saved in a json file called _linked_data_input_ (stored in the BattMoJulia directory).
+  The _linked_data_input_ file contains all the parameters' metadata; a second file called _battmo_formatted_input_ is also
+  created, it's the version used as input by BattMo.jl. After changing the parameters, the user can click on the **RUN** button to launch the simulation, based on the parameters saved in the _battmo_formatted_input_ file.
 
-- **Results** : Plots the results of the last simulation run, using matplotlib.
+- **Results** : Plots the results of previous simulations using Plotly.
 
 - **Materials and models**: Provides more information on the models and materials that can be selected.
 
-
 ## Acknowledgements
 
 Contributors, in alphabetical order
 
--   Oscar Bolzinger, SINTEF Industry
--   Simon Clark, SINTEF Industry
--   Eibar Flores, SINTEF Industry
--   Lorena Hendrix, SINTEF Industry
+- Oscar Bolzinger, SINTEF Industry
+- Simon Clark, SINTEF Industry
+- Eibar Flores, SINTEF Industry
+- Lorena Hendrix, SINTEF Industry
 
 BattMo has received funding from the European Union's Horizon 2020
 innovation program under grant agreement numbers:
 
--   875527 HYDRA
--   957189 BIG-MAP
+- 875527 HYDRA
+- 957189 BIG-MAP

docker-compose-deploy.yml

@@ -3,7 +3,7 @@ version: "3.3"
 services:
 
   api:
-    image: ghcr.io/battmoteam/battmogui_api:latest
+    image: ghcr.io/battmoteam/battmoapp_api:latest
     build:
       context: ./api
       dockerfile: Dockerfile
@@ -16,7 +16,7 @@ services:
     command: julia --project=. -e 'include("api.jl")' --color=yes --depwarn=no --project=@. --sysimage="pre-compilation/sysimage.so" -q -i -- $$(dirname $$0)/../bootstrap.jl -s=true "$$@"
 
   nginx:
-    image: ghcr.io/battmoteam/battmogui_nginx:latest
+    image: ghcr.io/battmoteam/battmoapp_nginx:latest
     build: ./nginx
     container_name: nginx
     restart: always
@@ -28,7 +28,7 @@ services:
       - gui
 
   gui:
-    image: ghcr.io/battmoteam/battmogui_streamlit:latest
+    image: ghcr.io/battmoteam/battmoapp_gui:latest
     build: ./gui
     container_name: gui
     restart: always