update readme

README.md

@@ -27,6 +27,7 @@ Yet another try to containerize [REDCap](https://www.project-redcap.org/) but wi
     - [Custom apache virtual host directives](#custom-apache-virtual-host-directives)
     - [Custom install SQL Script](#custom-install-sql-script)
     - [User provisioning files](#user-provisioning-files)
+    - [REDCap file repository](#redcap-file-repository)
   - [File Ownership](#file-ownership)
 
 # Disclaimer
@@ -54,14 +55,12 @@ This is our try, to containerize REDCap in a way, we can deploy a new instance,
 
 # Roadmap
 
-* Define user file repo directory in env var (investigate)
-* Testing if REDCap upgrades work with this setup
+* Testing if REDCap upgrades work with this setup (probably will)
 
 # Ideas
 
 * Project provisioning
 
-
 # Minimal example docker compose
 
 > We assume some basic knowledge about `docker` and `docker compose` and that it is installed
@@ -151,6 +150,16 @@ If the file is not provided, we will just pull a generic version it from the RED
 
 `/opt/redcap-docker/users` directory that will be scanned for user data to be provisioned. See [User provisioning](#user-provisioning) for more details.
 
+### REDCap file repository
+
+By the default the REDCap user uploaded filw will be saved into your document root dir `/var/www/html/edocs`. But as stated by the REDCap manual you may want to change that.  
+
+This is easy with this container image, Just set `RCCONF_edoc_path` (e.g. `RCCONF_edoc_path=/data`) to the path of your choice and mount this path via docker to your host system.  
+
+Have a look at the [docker compose example](examples/local_instance_custom_edocs) how it works in action.
+
+
+
 ## File Ownership
 
 If you are not happy with the file ownership UID/GID of the containers internal apache run user, have a look at [`WWW_DATA_UID`/`WWW_DATA_GID`](#www-data-user-and-group-id).

examples/local_instance_custom_edocs/README.md

@@ -0,0 +1,5 @@
+# Simple docker compose example
+
+This example show how to save user upload into a non apache folder
+
+Have a look at the docker-composes.yaml `volumes:` and environment variables at `environment:`

examples/local_instance_custom_edocs/docker-compose.yaml

@@ -0,0 +1,81 @@
+services:
+  redcap:
+    image: dzdde/redcap-docker
+    environment:
+      DB_PORT: 3306
+      DB_HOSTNAME: db
+      DB_NAME: redcap
+      DB_USERNAME: redcap
+      DB_PASSWORD: redcap123
+      # Do not reuse this example DB_SALT
+      DB_SALT: d369a86842347f7e3e40a3ec64b9f9d950bdfde05beba3a61da69bb1fb28dcea9152fbf723889181a9bd9a97f34b90faf17a
+      REDCAP_INSTALL_ENABLE: true
+      APPLY_RCCONF_VARIABLES: true
+
+      # Here we define where to store user uploaded files
+      RCCONF_edoc_path: /data
+
+      RCCONF_institution: "Weyland-Yutani Corporation"
+      RCCONF_homepage_contact: "Karl Bishop "
+      RCCONF_homepage_contact_email: "k.bishop@wyyu.earth"
+      RCCONF_project_contact_name: Colette Ferro
+      RCCONF_project_contact_email: c.ferro@wyyu.earth
+    restart: always
+    depends_on:
+          db:
+            condition: service_healthy
+    ports:
+      - "80:80"
+    volumes:
+      # We mount the upload repo to the local path ./data/user-files
+      - ./data/user-files:/data
+      - ./data/redcap:/var/www/html
+    logging:
+      options:
+        max-size: "10m"
+        max-file: "3"
+  db:
+    image: mysql:lts
+    restart: always
+    cap_add:
+      - SYS_NICE # CAP_SYS_NICE
+    volumes:
+      - ./data/db:/var/lib/mysql
+    ports:
+      - 3306:3306
+    environment:
+      - MYSQL_ROOT_PASSWORD=redcaproot123
+      - MYSQL_DATABASE=redcap
+      - MYSQL_USER=redcap
+      - MYSQL_PASSWORD=redcap123
+      - TZ=UTC
+    healthcheck:
+            test: "/usr/bin/mysql -u $$MYSQL_USER -p$$MYSQL_PASSWORD $$MYSQL_DATABASE --execute \"SHOW TABLES;\""
+            timeout: 3s
+            interval: 5s
+            retries: 4
+    command:
+      # Per REDCap Recommendations
+      - --max_allowed_packet=128M
+      # If you have a larger development database, you may want to increase this value:
+      # Default is 128MB (134217728) - I'm upping it to 512MB
+      - --innodb_buffer_pool_size=536870912
+      # 2x default
+      # sort_buffer_size=524288
+      - --sort_buffer_size=1024K
+      # Default
+      #read_rnd_buffer_size=262144
+      - --read_rnd_buffer_size=1024K
+      # By default we only accept connections from localhost but we want to allow connections from anywhere!
+      # bind-address=127.0.0.1
+      - --bind-address=0.0.0.0
+      # MAKE SEPARATE FILES PER TABLE
+      - --innodb_file_per_table=1
+      # Disabling symbolic-links is recommended to prevent assorted security risks
+      - --symbolic-links=0
+      # SLOW QUERY LOGGING
+      - --log_output=FILE
+      - --slow_query_log=0
+      - --slow_query_log_file=/var/log/mysql_slow.log
+      - --long_query_time=2.000
+      - --log-queries-not-using-indexes=0