Chemicals

.gitignore

@@ -119,7 +119,7 @@ ipython_config.py
 __pypackages__/
 
 # Environments
-.env
+*.env
 .env.development.local
 .env.test.local
 .env.production.local

README.md

@@ -7,7 +7,7 @@ Install prerequisites:
 or 
 - docker
 
-Setting up the .env file:
+Setting up the `.backend.env` file:
 
 ```python
 # .env
@@ -38,192 +38,32 @@ conda activate flask
 
 ### React
 
-In the frontend directory, run:
+In the `frontend/` directory, run:
 
 ````bash
 npm install
 ````
 
-## Setting up the PostgreSQL Database
-
-### Docker
+# Running the ELN instance
 
+### Backend
 ````bash
-docker compose -d --build
+docker compose up -d --build
 ````
-
-### Native
-
-In the terminal (backend/), initialize a postgres database by:
+or with a respective .env file:
 ````bash
-initdb -D database
+docker compose --env-file .backend.env up -d --build
 ````
 
-start the server modus/instance of postgres
-
-````bash
-pg_ctl -D database -l logfile start
-
-#waiting for server to start.... done
-#server started
-````
-
-create a non-superuser:
-
-````bash
-createuser --encrypted --pwprompt admin
-# asks for name and password
-````
-
-using this superuser, create inner database inside the base database
-
-````bash
-createdb --owner=admin flask_database
-````
-
-### Populating the Database
-
-Migrations to the database need to be applied by:
-```python
-python3 manage.py makemigrations
-python3 manage.py migrate
-```
-If you want to add entries to the database yourself, you need to create a superuser first:
-```python
-python3 manage.py createsuperuser
-```
-Otherwise, you can populate the database with example data (including superuser (email:'admin@admin.com', password:'admin'))
-```python
-python3 manage.py loaddata init.json
-```
-
-### Backing up the Database
-
-#### Via Django
-
-````bash
-python3 manage.py dumpdata --indent=2 > init.json
-````
-
-#### Using pg_dump
-
-See: [pg_dump manual](https://www.postgresql.org/docs/12/app-pgdump.html)
-
-````bash
-pg_dump -h [host] -U [option] -W -F [file_type] [database_name] > [backup_name]
-````
-
-for example:
-
-````bash
-pg_dump -h localhost -U admin -W -F t userinterface_db > ./init.tar
-````
-
-
-### Stop running the Postgres Instance
-
-#### Docker
+#### Stop running the Postgres Instance
 
 ````bash
 docker compose down
 ````
+### Frontend
 
-#### Native
+In `frontend/`, run:
 
-monitor whether a postgres instance/server is running or not
 ````bash
-ps aux | grep postgres
+npm start
 ````
-if no instance is running, you will see only one line as the answer to your query - which is from your grep search,
-ending with: grep --color=auto postgres
-(ignore this line)
-
-e.g. the output of `ps aux | grep postgres` was:
-````bash
-# username  2673  0.0  0.0  14760   512 pts/11   S+   07:34   0:00 grep --color=auto postgres
-# username 30550  0.0  0.0 179144 18996 ?        S    Jun13   0:01 /home/username/miniconda3/envs/django/bin/postgres -D mylocal_db
-# username 30552  0.0  0.0 179276  4756 ?        Ss   Jun13   0:00 postgres: checkpointer process   
-# username 30553  0.0  0.0 179144  5216 ?        Ss   Jun13   0:01 postgres: writer process   
-# username 30554  0.0  0.0 179144  8464 ?        Ss   Jun13   0:01 postgres: wal writer process   
-# username 30555  0.0  0.0 179700  5792 ?        Ss   Jun13   0:01 postgres: autovacuum launcher process   
-# username 30556  0.0  0.0  34228  3416 ?        Ss   Jun13   0:03 postgres: stats collector process  
-````
-
-if an instance of postgresql server is running, then several processes are running
-you can kill the server by the first number of the leading line!
-
-````bash
-kill <number>
-````
-
-
-# Getting Started with Create React App
-
-This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app).
-
-## Available Scripts
-
-In the project directory, you can run:
-
-### `npm start`
-
-Runs the app in the development mode.\
-Open [http://localhost:3000](http://localhost:3000) to view it in your browser.
-
-The page will reload when you make changes.\
-You may also see any lint errors in the console.
-
-### `npm test`
-
-Launches the test runner in the interactive watch mode.\
-See the section about [running tests](https://facebook.github.io/create-react-app/docs/running-tests) for more information.
-
-### `npm run build`
-
-Builds the app for production to the `build` folder.\
-It correctly bundles React in production mode and optimizes the build for the best performance.
-
-The build is minified and the filenames include the hashes.\
-Your app is ready to be deployed!
-
-See the section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information.
-
-### `npm run eject`
-
-**Note: this is a one-way operation. Once you `eject`, you can't go back!**
-
-If you aren't satisfied with the build tool and configuration choices, you can `eject` at any time. This command will remove the single build dependency from your project.
-
-Instead, it will copy all the configuration files and the transitive dependencies (webpack, Babel, ESLint, etc) right into your project so you have full control over them. All of the commands except `eject` will still work, but they will point to the copied scripts so you can tweak them. At this point you're on your own.
-
-You don't have to ever use `eject`. The curated feature set is suitable for small and middle deployments, and you shouldn't feel obligated to use this feature. However we understand that this tool wouldn't be useful if you couldn't customize it when you are ready for it.
-
-## Learn More
-
-You can learn more in the [Create React App documentation](https://facebook.github.io/create-react-app/docs/getting-started).
-
-To learn React, check out the [React documentation](https://reactjs.org/).
-
-### Code Splitting
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/code-splitting](https://facebook.github.io/create-react-app/docs/code-splitting)
-
-### Analyzing the Bundle Size
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size](https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size)
-
-### Making a Progressive Web App
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app](https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app)
-
-### Advanced Configuration
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/advanced-configuration](https://facebook.github.io/create-react-app/docs/advanced-configuration)
-
-### Deployment
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/deployment](https://facebook.github.io/create-react-app/docs/deployment)
-
-### `npm run build` fails to minify
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify](https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify)

backend/README.md

@@ -0,0 +1,97 @@
+## Setting up the PostgreSQL Database
+
+### Native
+
+In the terminal (backend/), initialize a postgres database by:
+````bash
+initdb -D database
+````
+
+start the server modus/instance of postgres
+
+````bash
+pg_ctl -D database -l logfile start
+
+#waiting for server to start.... done
+#server started
+````
+
+create a non-superuser:
+
+````bash
+createuser --encrypted --pwprompt admin
+# asks for name and password
+````
+
+using this superuser, create inner database inside the base database
+
+````bash
+createdb --owner=admin flask_database
+````
+
+### Populating the Database
+
+Migrations to the database need to be applied by:
+```python
+python3 manage.py makemigrations
+python3 manage.py migrate
+```
+If you want to add entries to the database yourself, you need to create a superuser first:
+```python
+python3 manage.py createsuperuser
+```
+Otherwise, you can populate the database with example data (including superuser (email:'admin@admin.com', password:'admin'))
+```python
+python3 manage.py loaddata init.json
+```
+
+### Backing up the Database
+
+#### Via Django
+
+````bash
+python3 manage.py dumpdata --indent=2 > init.json
+````
+
+#### Using pg_dump
+
+See: [pg_dump manual](https://www.postgresql.org/docs/12/app-pgdump.html)
+
+````bash
+pg_dump -h [host] -U [option] -W -F [file_type] [database_name] > [backup_name]
+````
+
+for example:
+
+````bash
+pg_dump -h localhost -U admin -W -F t userinterface_db > ./init.tar
+````
+
+
+### Stop running the Postgres Instance
+
+monitor whether a postgres instance/server is running or not
+````bash
+ps aux | grep postgres
+````
+if no instance is running, you will see only one line as the answer to your query - which is from your grep search,
+ending with: grep --color=auto postgres
+(ignore this line)
+
+e.g. the output of `ps aux | grep postgres` was:
+````bash
+# username  2673  0.0  0.0  14760   512 pts/11   S+   07:34   0:00 grep --color=auto postgres
+# username 30550  0.0  0.0 179144 18996 ?        S    Jun13   0:01 /home/username/miniconda3/envs/django/bin/postgres -D mylocal_db
+# username 30552  0.0  0.0 179276  4756 ?        Ss   Jun13   0:00 postgres: checkpointer process   
+# username 30553  0.0  0.0 179144  5216 ?        Ss   Jun13   0:01 postgres: writer process   
+# username 30554  0.0  0.0 179144  8464 ?        Ss   Jun13   0:01 postgres: wal writer process   
+# username 30555  0.0  0.0 179700  5792 ?        Ss   Jun13   0:01 postgres: autovacuum launcher process   
+# username 30556  0.0  0.0  34228  3416 ?        Ss   Jun13   0:03 postgres: stats collector process  
+````
+
+if an instance of postgresql server is running, then several processes are running
+you can kill the server by the first number of the leading line!
+
+````bash
+kill <number>
+````

backend/api/settings.py

@@ -11,9 +11,11 @@
 """
 
 from pathlib import Path
-from decouple import config, Csv
+from decouple import config, Csv  # Config, RepositoryEnv, Csv  #
 from datetime import timedelta
 
+# config = Config(RepositoryEnv(Path(Path(__file__).resolve().parent.parent.parent, ".backend.env")))
+
 # Build paths inside the project like this: BASE_DIR / 'subdir'.
 BASE_DIR = Path(__file__).resolve().parent.parent
 
@@ -46,7 +48,7 @@
     'rest_framework_simplejwt.token_blacklist',
     'corsheaders',
 
-    'phonenumber_field',
+    # 'phonenumber_field',
     # 'barcode_field'
     # 'django_rdkit',
 

backend/api/urls.py

@@ -16,7 +16,7 @@
 router.register(r'building', BuildingViewSet, basename='buildings')
 router.register(r'unit', UnitViewSet, basename='units')
 router.register(r'substance', SubstanceViewSet, basename='substances')
-router.register(r'component', ComponentViewSet, basename='containers')
+router.register(r'component', ComponentViewSet, basename='components')
 router.register(r'compound', CompoundViewSet, basename='compounds')
 router.register(r'container', ContainerViewSet, basename='containers')
 

backend/api/views.py

@@ -44,7 +44,7 @@ def list(self, request):
     def create(self, request):
         serializer = self.serializer_class(data=request.data)
         if serializer.is_valid():
-            # todo: problems with create user?
+            # todo: problems with create_user?!
             self.model.objects.create(**serializer.validated_data)
             return Response(serializer.validated_data, status=status.HTTP_201_CREATED)
         return Response(serializer.errors, status=status.HTTP_400_BAD_REQUEST)