Merge remote-tracking branch 'GitHub/main'

# Conflicts:
#	cytomine.template

configs/README.md

@@ -0,0 +1,75 @@
+# Configuration overrides folder
+For each service, you can override any file within the container.
+## File override
+Under this `configs/` folder, just recreate the folder structure of the file from the root filesystem path and place a file there.
+Example: override the `/etc/nginx/cors_params` of the `nginx` service.
+```
+configs
+└─ nginx                   <-- service name
+   └─ etc                  <-- /etc inside the container
+      └─ nginx
+         └─ cors_params    <-- file
+```
+
+## File templating
+Additionally, environment variables can be interpolated inside those files if they end with `.sample`.
+For instance, `/etc/nginx/nginx.conf.sample` of the `nginx` service   
+```conf
+...
+    server {
+        client_max_body_size 0;
+        listen       80;
+        server_name  $URLS_CORE;
+...        
+```
+Will become `/etc/nginx/nginx.conf` with `$URLS_CORE` replaced by `cytomine.local`
+```conf
+...
+    server {
+        client_max_body_size 0;
+        listen       80;
+        server_name  cytomine.local
+...        
+```
+# List of services and overrides examples
+Here is a list of what can be defined in the `configs/` folder.
+## core
+Example:
+```
+configs
+└─ core                    <-- service name
+   └─ app                  <-- /app inside the container
+      └─ logback.xml       <-- file
+```
+See here what can be overridden https://github.com/cytomine/Cytomine-core-spring/blob/main/README.md#override-configuration
+
+## nginx
+Example:
+```
+configs
+└─ nginx                   <-- service name
+   └─ etc                  <-- /etc inside the container
+      └─ nginx
+         └─ cors_params    <-- file
+```
+See here what can be overridden https://github.com/cytomine/Cytomine-nginx/tree/main/cm_configs_default
+
+## pims
+Example:
+```
+configs
+└─ pims                    <-- service name
+   └─ app                  <-- /app inside the container
+      └─ logging.xml       <-- file
+```
+See here what can be overridden https://github.com/cytomine/pims
+
+## web_ui
+Example:
+```
+configs
+└─ web_ui                              <-- service name
+   └─ app                              <-- /app inside the container
+      └─ configuration.json.sample     <-- file
+```
+See here what can be overridden https://github.com/cytomine/Cytomine-Web-UI

cytomine.template

@@ -1,5 +1,4 @@
-
-# -------------------------------------------------- # 
+# -------------------------------------------------- #
 # Update these to configure your instance
 global:
   urls:
@@ -36,13 +35,13 @@ global:
     constant:
       BIOFORMAT: cytomine/bioformat:v1.2.0
       CORE: cytomine/core:4.4.0
-      MONGO: mongo:4.4.18-focal
-      NGINX: cytomine/nginx:1.22.1-1.2.0
+      MONGO: cytomine/mongo:0.1.0
+      NGINX: cytomine/nginx:2.0.0
       PIMS_CACHE: redis:7.0.8
-      PIMS: cytomine/pims-ce-package:0.0.2
-      POSTGIS: cytomine/postgis:15-3.3-alpine-1.2.1
+      PIMS: cytomine/pims-ce-package:0.2.0
+      POSTGIS: cytomine/postgis:1.3.0
       RABBITMQ: rabbitmq:3.10
-      WEB_UI: cytomine/web_ui:2.6.1
+      WEB_UI: cytomine/web_ui:2.6.2
 
   internal_docker_urls: # must match respective container hostnames from compose file
     constant: 
@@ -113,6 +112,7 @@ global:
         DICOM=DICOM.
         MIRAX=MIRAX.
         ICC_PROFILE=ICC_PROFILE.
+        OME=OME.
 
 services:
   default: