Merge pull request #10 from bibbox/v8.2.RC2

V8.2.rc2
bibbox · Mar 2, 2022 · b0f45a5 · b0f45a5
2 parents ff383df + fc7702c
commit b0f45a5
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Showing 7 changed files with 35 additions and 90 deletions.
diff --git a/README.md b/README.md
@@ -30,14 +30,7 @@ The following steps must be executed:
   * MYSQL_ROOT_PASSWORD = password, only used within the docker container
   * MYSQL_DATABASE = name of the mysql database, typical *openspecimen*. The DB file is stored in the mounted volume
   * MYSQL_USER = name of the mysql user, typical *openspecimen*
-  * MYSQL_PASSWORD = mysql user password used in the setup of seeddms, for testing you can stay with `seeddms4bibbox`
-  * INSTITUTE_NAME = freely selectable by the user
-  * EMAIL_ADRESS = freely selectable by the user
-  * FIRST_NAME = freely selectable by the user
-  * LAST_NAME = freely selectable by the user
-  * LOGIN_NAME = freely selectable by the user
-  * PORT = 9000
-
+  * MYSQL_PASSWORD = mysql user password used for Openspecimen DB
 
 ------------------------------------------------------------------------------------------
 ## In case the installation process reccurently shows the following information message

diff --git a/appinfo.json b/appinfo.json
@@ -1,8 +1,8 @@
 {
-	"name": "OpenSpecimen v8.0.x",
+	"name": "OpenSpecimen v8.2.RC2",
 	"short_name": "OpenSpecimen",
-	"version": "v8.0.x",
-	"description": "OpenSpecimen Version 8.0.x",
+	"version": "v8.2.RC2",
+	"description": "OpenSpecimen Version 8.2.RC2",
 	"catalogue_url": "http://biobankapps.com/software/view?id=26",
 	"application_url": "https://openspecimen.atlassian.net/wiki/spaces/CAT/pages/1115878/End+User+Training",
 	"tags": ["Sample Management", "BIMS"],

diff --git a/configs/openspecimen/scripts/entrypoint.sh b/configs/openspecimen/scripts/entrypoint.sh
@@ -5,6 +5,8 @@ echo "Starting OpenSpecimen Application!"
 
 . defaultvar.sh
 
+sed -e "s/__DB_PW/$MYSQL_PASSWORD/g" -e "s/__DB_USER/$MYSQL_USER/g" /var/lib/tomcat9/conf/context.xml.template > /var/lib/tomcat9/conf/context.xml
+
 echo "Wait for DB server to be ready"
 /opt/scripts/waitforit.sh "${DATABASE_HOST}:${DATABASE_PORT}"
 

diff --git a/configs/openspecimen/scripts/sqlproperties.properties b/configs/openspecimen/scripts/sqlproperties.properties
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -15,7 +15,7 @@ services:
     environment:
       - MYSQL_ROOT_PASSWORD=openspecimen
       - MYSQL_DATABASE=openspecimen
-      - MYSQL_USER=openspecimen
+      - MYSQL_USER=FRANZ
       - MYSQL_PASSWORD=openspecimen
     volumes:
       - ./data/mysql:/var/lib/mysql
@@ -24,7 +24,7 @@ services:
       - SYS_NICE 
 
   local-openspecimen-web:
-    image: bibbox/openspecimen:v8-1-RC8
+    image: bibbox/openspecimen:v8-2-RC2
     container_name: local-openspecimen-web
     restart: unless-stopped
     networks:
@@ -37,11 +37,6 @@ services:
       - MYSQL_DATABASE=openspecimen
       - MYSQL_USER=openspecimen
       - MYSQL_PASSWORD=openspecimen
-      - INSTITUTE_NAME=BIBBOX_Demo_Biobank
-      - EMAIL_ADRESS="[email protected]"
-      - FIRST_NAME=admin
-      - LAST_NAME=Bibbox
-      - LOGIN_NAME=bibboxadmin  
     depends_on:
       - local-openspecimen-db
     volumes:

diff --git a/docker-compose.yml.template b/docker-compose.yml.template
@@ -13,16 +13,16 @@ services:
     networks:
       - bibbox-default-network
     environment:
-      - MYSQL_ROOT_PASSWORD=openspecimen
+      - MYSQL_ROOT_PASSWORD=thispasswordisneverusededoutsidethecontainer
       - MYSQL_DATABASE=openspecimen
-      - MYSQL_USER=openspecimen
-      - MYSQL_PASSWORD=openspecimen
+      - MYSQL_USER=§§MYSQL_DATABASE_USER
+      - MYSQL_PASSWORD=§§MYSQL_DATABASE_PASSWORD
     volumes:
       - ./data/mysql:/var/lib/mysql
       - ./configs/openspecimen/configs/openspecimen.cnf:/etc/mysql/conf.d/openspecimen.cnf:ro
 
   §§INSTANCE-openspecimen-web:
-    image: bibbox/openspecimen:v8-1-RC8
+    image: bibbox/openspecimen:v8-2-RC2
     container_name: §§INSTANCE-openspecimen-web
     restart: unless-stopped
     networks:
@@ -31,15 +31,10 @@ services:
       - §§INSTANCE-openspecimen-db:openspecimen-db
     environment:
       - DATABASE_HOST=openspecimen-db
-      - MYSQL_ROOT_PASSWORD=openspecimen
+      - MYSQL_ROOT_PASSWORD=thispasswordisneverusededoutsidethecontainer
       - MYSQL_DATABASE=openspecimen
-      - MYSQL_USER=openspecimen
-      - MYSQL_PASSWORD=openspecimen
-      - INSTITUTE_NAME=§§INSTITUTE_NAME
-      - EMAIL_ADRESS=§§EMAIL_ADRESS
-      - FIRST_NAME=§§FIRST_NAME
-      - LAST_NAME=§§LAST_NAME
-      - LOGIN_NAME=§§LOGIN_NAME
+      - MYSQL_USER=§§MYSQL_DATABASE_USER
+      - MYSQL_PASSWORD=§§MYSQL_DATABASE_PASSWORD
     proxy:
      TYPE: PRIMARY
      URLPREFIX: §§INSTANCE
@@ -51,5 +46,6 @@ services:
       - ./data/os-data:/var/lib/openspecimen/data
       - ./data/os-plugins:/var/lib/openspecimen/plugins
       - ./configs/openspecimen/ROOT:/var/lib/tomcat9/webapps/ROOT
+      - ./configs/openspecimen/scripts/entrypoint.sh:/opt/scripts/entrypoint.sh
     ports:
       - "9000:8080"
diff --git a/environment-parameters.json b/environment-parameters.json
@@ -1,48 +1,20 @@
 [
-   {
-      "id":"INSTITUTE_NAME",
-      "display_name":"OpenSpecimen Institute",
-      "type":"text",
-      "default_value":"BIBBOX Demo Biobank",
-      "description":"Institute name in OpenSpecimen for the first user.",
-      "min_length": "1",
-      "max_length": "128"
-   },
-   {
-      "id":"EMAIL_ADRESS",
-      "display_name":"email-adress",
-      "type":"text",
-      "default_value":"[email protected]",
-      "description":"email adress of the user",
-      "min_length": "1",
-      "max_length": "128"
-   },
-   {
-      "id":"FIRST_NAME",
-      "display_name":"First name",
-      "type":"text",
-      "default_value":"admin",
-      "description":"First Name of the User",
-      "min_length": "1",
-      "max_length": "128"
-   },
-   {
-      "id":"LAST_NAME",
-      "display_name":"Last name",
-      "type":"text",
-      "default_value":"Bibbox",
-      "description":"First Name of the User",
-      "min_length": "1",
-      "max_length": "128"
-   },
-   {
-      "id":"LOGIN_NAME",
-      "display_name":"Login Name",
-      "type":"text",
-      "default_value":"bibboxadmin",
-      "description":"Login Name of the User",
-      "min_length": "1",
-      "max_length": "128"
-   }
-
-]
+	{
+	   "id":"MYSQL_DATABASE_USER",
+	   "display_name":"Name of the mysql user",
+	   "type":"text",
+	   "default_value":"Default Value",
+	   "description":"The User of the DB created for OpenSpecimen",
+	   "min_length": "1",
+	   "max_length": "128"
+	},
+	{
+	   "id":"MYSQL_DATABASE_PASSWORD",
+	   "display_name":"Password of mySQL user",
+	   "type":"password",
+	   "default_value":"Default Value",
+	   "description":"The Password of the DB User created for OpenSpecimen",
+	   "min_length": "1",
+	   "max_length": "128"
+	}
+ ]