Merge pull request #21 from greenjune-ship-it/12-display-ed50-and-ed5…

…0-thermal-threshold

12 display ed50, release v0.1.1

.gitignore

@@ -9,4 +9,5 @@ django_app/staticfiles/
 pg_dump.sql
 backup.pgdump
 
-.~*
+.~*
+/django_app/users/management/commands/user_data.json

README.md

@@ -31,39 +31,57 @@ CONTACT_EMAIL_ADDRESS=''
 
 ### Deploy
 
-From backup:
+#### Up the project from scratch
 
 ```commandline
-bash deploy.sh
+docker compose up -d
+
 ```
 
-Up the project from scratch:
+#### Create superuser
 
 ```commandline
-sudo docker compose up -d
-
+docker compose exec django-app python manage.py createsuperuser
 ```
 
-Collect static files:
+You can also prepare your `user_data.json` and populate your database automatically:
 
 ```commandline
-sudo docker compose exec django-app python manage.py collectstatic --noinput
-```
+[
+    {"username": "user1", "password": "password123", "first_name": "John", "last_name": "Doe", "email": "[email protected]"},
+    {"username": "user2", "password": "password456", "first_name": "Jane", "last_name": "Smith", "email: "[email protected]"},
+    {"username": "admin", "password": "adminpassword", "first_name": "Admin", "last_name": "User", "email": "[email protected]"}
+]
 
-Create superuser:
+```
+And then run custom django-admin command:
 
 ```commandline
-sudo docker compose exec django-app python manage.py createsuperuser
+docker compose exec django-app python manage.py create_users path/to/user_data.json
 ```
+Don't forget to replace the path to your `user_data.json` file.
+
+#### Populate the database 
 
-Populate the database (let's say my superuser is `adm_iakovyu1`:
+Let's say my superuser is `adm_iakovyu1`.
+
+For complete datasets:
 
 ```commandline
-sudo docker compose exec django-app python populate_db.py \
-    --owner iakovyu1 \
+docker compose exec django-app python populate_db.py \
+    --owner adm_iakovyu1 \
     --csv_path static/datasheets/cbass_84.csv
 ```
 
+For incomplete datasets, use `--no-pam` argument:
+
+```commandline
+docker compose exec django-app python populate_db.py \
+    --owner adm_iakovyu1 \
+    --csv_path static/datasheets/redsea_gradient_study.csv \
+    --no-pam
+```
+
 ## Database Backups
 
 Create a database backup:

deploy.sh

@@ -1,18 +1,10 @@
 #!/bin/bash
 
-source .env
-
 docker compose up -d
 
-docker compose pause django-app
-
-docker compose cp backup.pgdump database:backup.pgdump
-
-echo "Drop the database and restore from backup"
-
-docker compose exec database \
-  pg_restore --clean --dbname $DB_NAME -U $DB_USER backup.pgdump
+docker compose exec django-app python manage.py create_users user_data.json
 
-echo "Done!"
+docker compose exec django-app python manage.py populate_db --owner voolsch1 --csv_path static/datasheets/cbass_84.csv
+docker compose exec django-app python manage.py populate_db --owner voolsch1 --csv_path static/datasheets/redsea_gradient_study.csv --no-pam
 
-docker compose unpause django-app
+docker compose exec django-app python manage.py link_biosamples

django_app/api/serializers.py

@@ -1,5 +1,5 @@
+from projects.models import BioSample, Colony, Observation, Project
 from rest_framework import serializers
-from projects.models import BioSample, Colony, Observation
 
 
 class BioSampleSerializer(serializers.ModelSerializer):
@@ -9,12 +9,26 @@ class Meta:
 
 
 class ColonySerializer(serializers.ModelSerializer):
+    projects = serializers.SerializerMethodField()
+
+    def get_projects(self, obj):
+        # Get the related projects for the colony's biosamples
+        biosamples = obj.biosamples.all()
+        projects = Project.objects.filter(biosamples__in=biosamples).distinct()
+        # Assuming you want to serialize projects' names
+        return [project.name for project in projects]
+
     class Meta:
         model = Colony
-        fields = '__all__'
-
+        fields = ['id', 'name', 'species', 'country', 'latitude', 'longitude', 'ed50_value', 'projects']
 
 class ObservationSerializer(serializers.ModelSerializer):
     class Meta:
         model = Observation
         fields = '__all__'
+
+
+class ProjectSerializer(serializers.ModelSerializer):
+    class Meta:
+        model = Project
+        fields = ['id', 'name', 'description']

django_app/api/urls.py

@@ -1,7 +1,7 @@
 # api/urls.py
 from django.urls import path, include
 from api.views import CheckAuthenticationApiView, UserCartApiView
-from api.views import BioSamplesApiView, ColoniesApiView, ObservationsApiView
+from api.views import BioSamplesApiView, ColoniesApiView, ObservationsApiView, ProjectsApiView
 
 urlpatterns = [
     path('auth/', include([
@@ -12,6 +12,7 @@
     path('public/', include([
         path('biosamples/', BioSamplesApiView.as_view()),
         path('colonies/', ColoniesApiView.as_view()),
-        path('observations/', ObservationsApiView.as_view())
+        path('observations/', ObservationsApiView.as_view()),
+        path('projects/', ProjectsApiView.as_view())
     ]))
 ]

django_app/api/views.py

@@ -1,13 +1,13 @@
 # api/views.py
+from api.serializers import BioSampleSerializer, ColonySerializer, \
+    ObservationSerializer, ProjectSerializer
+# Apps imports
+from projects.models import BioSample, Colony, Observation, Project, UserCart
 from rest_framework import generics, status
 from rest_framework.authentication import SessionAuthentication
 from rest_framework.permissions import IsAuthenticated
 from rest_framework.response import Response
 from rest_framework.views import APIView
-# Apps imports
-from projects.models import BioSample, Colony, Observation, UserCart
-from api.serializers import BioSampleSerializer, ColonySerializer, \
-    ObservationSerializer
 
 
 class CheckAuthenticationApiView(APIView):
@@ -21,6 +21,17 @@ def get(self, request):
             'username': request.user.username})
 
 
+class ProjectsApiView(APIView):
+    """
+    This endpoint allows users to retrieve a list of available Projects.
+    """
+
+    def get(self, request):
+        projects = Project.objects.all()
+        serializer = ProjectSerializer(projects, many=True)
+        return Response(serializer.data, status=status.HTTP_200_OK)
+
+
 class BioSamplesApiView(APIView):
     """
     This endpoint allows users to retrieve a list of BioSamples.

django_app/django_app/settings.py

@@ -35,6 +35,7 @@
     # Installed pip packages
     'bootstrap5',
     'corsheaders',
+    'django_extensions',
     'leaflet',
     'rest_framework',
     # Custom apps