Merge branch 'dev' into prod

DEPLOYING.md

@@ -12,6 +12,10 @@ Below are the steps to perform a production deploy.
 
 ## Instructions
 
+1. Create MongoDB Docker volumes:
+    ```bash
+    docker volume create --name=modulector_postgres_data
+    ```
 1. Make a copy of `docker-compose_dist.yml` with the name `docker-compose.yml`.
 1. Set the environment variables that are empty with data. They are listed below by category:
     - Django:
@@ -29,7 +33,7 @@ Below are the steps to perform a production deploy.
         - `POSTGRES_PASSWORD` : Database username's password. By default the docker image uses `modulector`.
         - `POSTGRES_PORT` : Database server listen port. By default the docker image uses `5432`.
         - `POSTGRES_DB` : Database name to be used. By default the docker image uses `modulector`.
-    - Healthchecks and alerts:
+    - Health-checks and alerts:
         - `HEALTH_URL` : indicates the url that will be requested on Docker healthchecks. By default it is http://localhost:8000/drugs/. The healthcheck makes a GET request on it. Any HTTP code value greatear or equals than 400 is considered an error.
         - `HEALTH_ALERT_URL` : if you want to receive an alert when healthchecks failed, you can set this variable to a webhook endpoint that will receive a POST request and a JSON body with the field **content** that contains the fail message.
 1. Go back to the project's root folder and run the following commands:
@@ -39,6 +43,7 @@ Below are the steps to perform a production deploy.
     - [Docker Swarm](https://docs.docker.com/engine/swarm/):
         - Start: `docker stack deploy --compose-file docker-compose.yml modulector`
         - Stop: `docker stack rm modulector`
+1. Import all the data following the instructions detailed in the [Import section](#import).
 1. (Optional) Create a super user to access to the admin panel (`<URL>/admin`).
     1. Enter the running container: `docker container exec -it <backend_container_name> bash`. The name is usually `modulector_web_1` but you can check it with `docker container ps`.
     1. Run: `python3 manage.py createsuperuser`
@@ -125,25 +130,20 @@ That command will create a compressed file with the database dump inside.
 You can use set Modulector DB in three ways.
 
 
-### Using official Docker image (recommended)
+### Importing an existing database dump (recommended)
 
-You can just use the [modulector-db][modulector-db-docker] and avoid all kind of importations steps. This is the default setting in `docker-compose_dist.yml`.
-
-
-### Importing an existing database dump
-
-1. Comment the service in your `docker-compose.yml` that uses the `omicsdatascience/modulector-db` image.
+1. Check that the service in your `docker-compose.yml` that uses the `omicsdatascience/modulector-db` image is commented and uncomment the service that uses `postgres` image.
 1. Start up a PostgreSQL service. You can use the same service listed in the `docker-compose.dev.yml` file. 
-1. **Optional but recommended (You can omit these steps if it's the first time you are deploying Modulector)**: due to major changes, it's probably that an import thrown several errors when importing. To prevent that you could do the following steps before doing the importation:
-    1. Drop all the tables from the DB:
-        1. Log into docker container: `docker container exec -it [name of the DB container] bash`
-        1. Log into Postgres: `psql -U [username]`
-        1. (**Danger, will drop all the data**) Remove the `modulector` database: `DROP DATABASE modulector;`
-        1.  Create an empty database: `CREATE DATABASE modulector;`
+1. **Optional but recommended (you can omit these steps if it's the first time you are deploying Modulector)**: due to major changes, it's probably that an import thrown several errors when importing. To prevent that you could do the following steps before doing the importation:
+    1. Drop all the tables from the DB: `docker exec -i [name of the DB container] psql modulector -U modulector -c "DROP DATABASE modulector"`
+    1. Create an empty database: `docker exec -i [name of the DB container] psql modulector -U modulector -c "CREATE DATABASE modulector"`
 1. Download `.sql.gz` from [Modulector releases pages](https://github.com/omics-datascience/modulector/releases) or use your own export file.
-1. Restore the db: `zcat modulector.sql.gz | docker exec -i [name of the DB container] psql modulector -U modulector`
+1. Restore the db: `zcat modulector.sql.gz | docker exec -i [name of the DB container] psql modulector -U modulector`. This command will restore the database using a compressed dump as source, **keep in mind that could take several minutes to finish the process**.
+
+
+### Using official Docker image
 
-That command will restore the database using a compressed dump as source.
+You can just use the [modulector-db][modulector-db-docker] and avoid all kind of importations steps. This is the default setting in `docker-compose_dist.yml`. This is a good method if you want to avoid having to set the database from scratch. But keep in mind that **initialization times can take many minutes, so it is NOT recommended for use in production**, in the latter case it is recommended to use the method described above.
 
 
 ### Regenerating the data manually

docker-compose_dist.yml

@@ -1,18 +1,39 @@
 version: '3'
 
 services:
-    # PostgreSQL
+    # PostgreSQL (empty DB)
     db_modulector:
-      image: omicsdatascience/modulector-db:2.0.0
-      # Uncomment this to add your custom config
-      # volumes:
-      #     - ./config/postgres/postgres.conf:/etc/postgresql/postgresql.conf
+        image: postgres:16
+        restart: always
+        ports:
+            - '5433:5432'
+        # Uncomment this to add your custom config
+        # command: postgres -c 'config_file=/etc/postgresql/postgresql.conf'
+        environment:
+            # IMPORTANT: these three params must be the same than POSTGRES_USERNAME, POSTGRES_PASSWORD, POSTGRES_DB
+            # below in 'web' service respectively
+            POSTGRES_USER: 'modulector'
+            POSTGRES_PASSWORD: 'modulector'
+            POSTGRES_DB: 'modulector'
+        volumes:
+            - postgres_data:/var/lib/postgresql/data/
+            # Uncomment this to add your custom config
+            # - ./config/postgres/postgres.conf:/etc/postgresql/postgresql.conf
+
+    # Uncomment this if you want to use the DB image (start with a filled DB the startup time is very slow)
+    #PostgreSQL
+    #db_modulector:
+    #    image: omicsdatascience/modulector-db:2.0.0
+    #    # Uncomment this to add your custom config
+    #    volumes:
+    #       #    - ./config/postgres/postgres.conf:/etc/postgresql/postgresql.conf
 
     # Django Proxy Server
     nginx_modulector:
         image: nginx:1.23.3
+        restart: always
         ports:
-            - "80:8000"
+            - '80:8000'
         volumes:
             - ./config/nginx/conf.d:/etc/nginx/conf.d
         depends_on:
@@ -21,6 +42,7 @@ services:
     # Django Backend Server
     web_modulector:
         image: omicsdatascience/modulector:2.0.3
+        restart: always
         depends_on:
             - db_modulector
         environment:
@@ -32,3 +54,8 @@ services:
             # Hosts separated by comma ('http://', 'https://' prefixes are mandatory)
             # Example: CSRF_TRUSTED_ORIGINS: 'http://127.0.0.1', 'http://127.0.0.1,https://127.0.0.1:8000', etc
             CSRF_TRUSTED_ORIGINS: ''
+
+volumes:
+    postgres_data:
+        external:
+            name: 'modulector_postgres_data'