Merge pull request #107 from medizininformatik-initiative/84-redcap-d…

…eploy-variante-1-ip-redcap-from-redcap-plain-download 84 redcap deploy variante 1 ip redcap from redcap plain download
medizininformatik-initiative · Feb 21, 2024 · 5e79a96 · 5e79a96
2 parents 4b46dca + d8c1d56
commit 5e79a96
Show file tree

Hide file tree

Showing 5 changed files with 18 additions and 17 deletions.
diff --git a/Dockerfile_R b/Dockerfile_R
@@ -1,7 +1,7 @@
-# etlutils
-
 FROM rocker/r-ver:4.3.2
 
+# etlutils
+
 RUN apt-get update \
     && apt-get install -y libssl-dev libcurl4-openssl-dev libpq-dev
 
@@ -17,18 +17,16 @@ RUN R CMD INSTALL --preclean --no-multiarch --with-keep.source R-etlutils/etluti
 
 
 # kds2db
+
 COPY R-kds2db R-kds2db
 
 RUN R CMD build R-kds2db/kds2db
 
 RUN R CMD INSTALL --preclean --no-multiarch --with-keep.source R-kds2db/kds2db
 
-#COPY StartRetrieval.R /src/StartRetrieval.R
-
-#COPY kds2db_config.toml /src/kds2db_config.toml
-
 
 # db2frontend
+
 RUN apt-get install -y libsodium-dev
 
 RUN /rocker_scripts/bin/install2.r redcapAPI dplyr
@@ -39,9 +37,7 @@ RUN R CMD build R-db2frontend/db2frontend
 
 RUN R CMD INSTALL --preclean --no-multiarch --with-keep.source R-db2frontend/db2frontend
 
-#COPY StartDB2Frontend.R /src/StartDB2Frontend.R
-
-#COPY db2frontend_config.toml /src/db2frontend_config.toml
 
 # cleanup
+
 RUN apt-get autoremove && apt-get clean
diff --git a/REDCap-app/html/Readme.md b/REDCap-app/html/Readme.md
@@ -13,6 +13,15 @@ $username   = 'redcap'; 	//your_mysql_db_username
 $password   = 'password_for_redcap_user'; 	//your_mysql_db_password
 ```
 
+Passen Sie die Zugriffrechte für die folgenden Verzeichnisse an:
+REDCap-app/html/redcap/temp
+REDCap-app/html/redcap/modules
+REDCap-app/html/redcapdocs
+
+```
+chmod ugo+x REDCap-app/html/redcap/temp REDCap-app/html/redcap/modules REDCap-app/html/redcapdocs
+```
+
 Rufen Sie im Browser die Seite auf: http://127.0.0.1:8082/redcap/
 
 (Sollten Sie eine Fehlermeldung erhalten, rufen Sie im Browser die Install-Seite auf: http://127.0.0.1:8082/redcap/install.php)

diff --git a/REDCap-db/init/redcap.sql b/REDCap-db/init/redcap.sql
@@ -4183,7 +4183,7 @@ INSERT INTO redcap_config (field_name, value) VALUES
 ('file_repository_upload_max', ''),
 ('file_repository_enabled', '1'),
 ('temp_files_last_delete', now()),
-('edoc_path', ''),
+('edoc_path', '/var/www/html/redcapdocs'),
 ('enable_edit_survey_response', '1'),
 ('enable_plotting', '2'),
 ('enable_plotting_survey_results', '1'),

diff --git a/REDCap-db/mariadb.cnf b/REDCap-db/mariadb.cnf
@@ -22,5 +22,7 @@ max_allowed_packet=1G
 # Vorschläge für Cache Parameter (nicht aktiv)
 #query_cache_size = 256M
 #query_cache_limit = 64K
+optimizer_switch=rowid_filter=OFF
+
 # Import all .cnf files from configuration directory
 !includedir /etc/mysql/mariadb.conf.d/
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -26,8 +26,6 @@ services:
   # SQL Server for redcap
   redcap_db:
     image: mariadb:11
-    #container_name: ${COMPOSE_PROJECT_NAME}_mysql
-    #command: --default-authentication-plugin=mysql_native_password
     restart: unless-stopped
     env_file: ${PWD}/REDCap-db/.env-redcap-db
     secrets:
@@ -40,12 +38,12 @@ services:
       - redcap-db-data:/var/lib/mysql
       - ${PWD}/REDCap-db/init:/docker-entrypoint-initdb.d
       #- ./.my.cnf:/root/.my.cnf
+    #command: --default-authentication-plugin=mysql_native_password
 
   # Frontend (redcap)
   redcap:
     build: ./REDCap-app/build
     #user: "www-data:www-data"
-    #container_name: ${COMPOSE_PROJECT_NAME}_app
     depends_on:
       - redcap_db
     restart: unless-stopped
@@ -63,9 +61,7 @@ services:
 
   # Database (postgres) for medical safety (AMTS) information
   amts_db:
-    #image: postgres:15
     build: ./Postgres-amts_db/build
-    #container_name: pg_container
     restart: unless-stopped
         #    healthcheck:
     # test: [ "CMD-SHELL", "pg_isready -U postgres -d interpolar" ]
@@ -92,7 +88,6 @@ services:
   # Web-administration of amts_db (optional)
   pgadmin:
     image: dpage/pgadmin4:7.2
-    #container_name: pgadmin4_container
     restart: unless-stopped
     ports:
       - "127.0.0.1:8089:80"
@@ -117,7 +112,6 @@ services:
     working_dir: /src
     restart: "no"
     volumes:
-      #- ./R-kds2db:/src
       - ./R-kds2db/outputLocal:/src/R-kds2db/outputLocal
       - ./R-kds2db/outputGlobal:/src/R-kds2db/outputGlobal
       - ./R-kds2db/kds2db_config.toml:/src/R-kds2db/kds2db_config.toml