Add jupyter,search profiles to avoid default start

.github/workflows/docker_compose_test.yaml

@@ -59,4 +59,4 @@ jobs:
       - name: Test docker-compose.yaml
         run: |-
           export BE_VERSION=${{ matrix.BE_VERSION }}
-          docker compose up --wait --wait-timeout 300
+          docker compose --profile '*' up --wait --wait-timeout 300

README.md

@@ -1,6 +1,6 @@
 # SciCat
 
-Files for running SciCat with docker-compose.
+Files for running SciCat with docker compose.
 
 ## Tags
 
@@ -18,19 +18,34 @@ Note: older versions might not contain certain functionality (e.g. archival mock
    ```
 2. Run with the following command inside the directory
    ```sh
-   docker-compose up -d
+   docker compose up -d
    ```
 
 ## Default setup
 
-By running `docker-compose up -d` these steps take place:
-1. a [mongodb**](./services/mongodb/) container is created with some intial data.
-2. the SciCat [backend v4*](./services/backendv4/) container is created and connected to (1).
-3. the SciCat [frontend**](./services/frontend/) container is created and connected to (2).
-4. the SciCat [PaN searchapi](./services/searchapi/) container is created and connected to (2).
-5. a reverse [proxy](./services/proxy) container is created and routes traffic to (2), (3) and (4) through localhost subdomains, in the form: `http://${service}.localhost` (for the ones of need). The frontend is available at simply `http://localhost`.
+By running `docker compose up -d` these steps take place:
+1. a [mongodb](./services/mongodb/) container is created with some initial data.
+2. the SciCat [backend v4](./services/backendv4/) container is created and connected to (1).
+3. the SciCat [frontend](./services/frontend/) container is created and connected to (2).
+4. a reverse [proxy](./services/proxy) container is created and routes traffic to (2) and (3) through localhost subdomains, in the form: `http://${service}.localhost` (for the ones in need). The frontend is available at simply `http://localhost`.
 
-Here below we show the dependencies (if `B` depends on `A`, then we visualize as `A --> B`):
+## Enable extra services
+
+By using [docker compose profiles](https://docs.docker.com/compose/profiles/), some extra services can be enabled, in addition to the default ones. To enable any, run `docker compose --profile <PROFILE> up -d`, or export the `COMPOSE_PROFILES` env variable as described [either](https://docs.docker.com/compose/environment-variables/envvars-precedence/). If needed, the user can specify more than one profile in the CLI by using the flag as `--profile <PROFILE1> --profile <PROFILE1>`. 
+
+The available profiles and additional services are:
+
+| Profile      | Service           |
+| ------------ | ----------------- |
+| analysis     | jupyter           |
+| search       | searchapi         |
+| '*'          | jupyter,searchapi |
+
+In addition to optionally setting the profile(s), the user can still select the service(s) to run as described [here](#select-the-services) and the [BE_VERSION](#select-the-be-version-to-use) to use.
+
+## Dependencies
+
+Here below we show the dependencies, including the ones of the [extra services](#enable-extra-services) (if `B` depends on `A`, then we visualize it as `A --> B`):
 
 ```mermaid
 graph TD
@@ -54,71 +69,70 @@ We flag with `*` the services which have extra internal dependencies, which are
 
 ## Select the BE version to use
 
-The user can select what backend version to use, by setting the `BE_VERSION` environment variable (either `v3` or `v4`), [either](https://docs.docker.com/compose/environment-variables/envvars-precedence/) setting it in the shell or changing the [.env](./.env#L1) file. If this variable is blank, the system will default to `v4`. The services with `**` have a dependency on the `BE_VERSION` value. 
+The user can select what backend version to use, by setting the `BE_VERSION` environment variable (either `v3` or `v4`), [either](https://docs.docker.com/compose/environment-variables/envvars-precedence/) setting it in the shell or changing the [.env](./.env#L1) file. If this variable is blank, the system will default to `v4`.
 
 For example, by running: 
 
 ```sh
 export BE_VERSION=v3
-docker-compose up -d
+docker compose up -d
 ```
 
-Service (2) of the [default setup](README.md#default-setup) is replaced with the [v3* service](./services/backendv3/) and then steps from (1) to (5) are run. 
+Service (2) of the [default setup](README.md#default-setup) is replaced with the [v3* service](./services/backendv3/) and then steps from (1) to (4) are run. 
 
 For any value of `BE_VERSION`, the `backend` is available at `http://backend.localhost`.
 
 After optionally setting the `BE_VERSION`, one can still select the services to run as described [here](README.md#select-the-services).
 
 ## Select the services
 
-The user can selectively decide the containers to spin up and the dependencies will be resolved accordingly. The available services are in the [services](./services/) folder and called consistently.
+The user can selectively decide the containers to spin up and the dependencies will be resolved accordingly. The available services are in the [services](./services/) folder and are called consistently.
 
 For example, one could decide to only run the `backend` by running (be aware that this will not run the `proxy`, so the service will not be available at `backend.localhost`):
 
 ```sh
-docker-compose up -d backend
+docker compose up -d backend
 ```
 
-(or a list of services, for example, with the proxy `docker-compose up -d backend proxy`)
+(or a list of services, for example, with the proxy `docker compose up -d backend proxy`)
 
 This will run, from the [previous section](#default-setup), (1) and (2) but skip the rest.
 
 Accordingly,
 ```sh
-docker-compose up -d frontend
+docker compose up -d frontend
 ```
 
-Will run, from the [previous section](#default-setup), (1), (2) and (3) but skip (4) and (5).
+Will run, from the [previous section](#default-setup), (1), (2) and (4) but skip (5).
 
 And 
 
 ```sh
-docker-compose up -d searchapi
+docker compose --profile search up -d searchapi
 ```
 
-Will run, from the [previous section](#default-setup), (1), (2) and (4) but skip (3) and (5).
-
+Will run, from the [previous section](#default-setup), (1) and (2), skip (3) and (4), and add the `searchapi` service.
 
 ## Custom configure a service
 
-Every service folder (inside the [services](./services/) parent directory) contains its configuration and some instructions, at least for the non third-party containers.
+Every service folder (inside the [services](./services/) parent directory) contains its configuration and some instructions, at least for the non-third-party containers.
 
 For example, to configure the [frontend](./services/frontend/), the user can change any file in the [frontend config](./services/frontend/config/) folder, for which instructions are available in the [README](./services/frontend/README.md) file.
 
-After any configuration change, `docker-compose up -d` must be rerun, to allow loading the changes.
+After any configuration change, `docker compose up -d` must be rerun, to allow loading the changes.
 
 ## Add a new service
 
 To add a new service (see the [backend v4](./services/backendv4/) for an extensive example):
 1. create a dedicated folder in the [services](./services/) one
 2. name it as the service
 3. create the `docker-compose.yaml` file with the required dependencies (if any)
-4. eventually include any service in (3) which is specific to the service and not shared across the global setup
-5. eventually add the condition on the backend version (e.g. [here](./services/frontend/docker-compose.yaml#L14))
-6. eventually create a `config` folder if it requires configuration
-7. eventually add a `README.md` file in the service
-8. include the reference to (3) to the global [docker-compose include list](docker-compose.yaml#L2)
-9. eventually update the main [README.md](README.md)
+4. eventually, include any service in (3) which is specific to the service and not shared across the global setup
+5. eventually, add the condition on the backend version (e.g. [here](./services/frontend/docker-compose.yaml#L14))
+6. eventually, create a `config` folder if it requires configuration
+7. eventually, add a `README.md` file in the service
+8. include the reference to (3) to the global [docker compose include list](docker-compose.yaml#L2)
+9. eventually, update the main [README.md](README.md)
 
 ## General use of SciCat
 

services/jupyter/docker-compose.yaml

@@ -11,3 +11,5 @@ services:
       - ./config/notebooks:/home/jovyan/notebooks
     env_file:
       - config/.env
+    profiles:
+      - analysis

services/searchapi/docker-compose.yaml

@@ -7,3 +7,5 @@ services:
       - traefik.http.routers.searchapi.rule=Host(`searchapi.localhost`)
     env_file:
       - ./config/.env
+    profiles:
+      - search