Merge pull request #659 from NUM-Forschungsdatenplattform/release/1.22.0

Merge release branch '1.22.0'

.config/intellij-codestyle.xml

@@ -0,0 +1,168 @@
+<code_scheme name="NUM-Codestyle" version="1">
+  <option name="OTHER_INDENT_OPTIONS">
+    <value>
+      <option name="INDENT_SIZE" value="2" />
+      <option name="CONTINUATION_INDENT_SIZE" value="4" />
+      <option name="TAB_SIZE" value="2" />
+      <option name="USE_TAB_CHARACTER" value="false" />
+      <option name="SMART_TABS" value="false" />
+      <option name="LABEL_INDENT_SIZE" value="0" />
+      <option name="LABEL_INDENT_ABSOLUTE" value="false" />
+      <option name="USE_RELATIVE_INDENTS" value="false" />
+    </value>
+  </option>
+  <option name="INSERT_INNER_CLASS_IMPORTS" value="true" />
+  <option name="CLASS_COUNT_TO_USE_IMPORT_ON_DEMAND" value="100" />
+  <option name="NAMES_COUNT_TO_USE_IMPORT_ON_DEMAND" value="100" />
+  <option name="PACKAGES_TO_USE_IMPORT_ON_DEMAND">
+    <value />
+  </option>
+  <option name="IMPORT_LAYOUT_TABLE">
+    <value>
+      <package name="org.highmed" withSubpackages="true" static="false" />
+      <emptyLine />
+      <package name="" withSubpackages="true" static="false" />
+      <emptyLine />
+      <package name="java" withSubpackages="true" static="false" />
+      <package name="javax" withSubpackages="true" static="false" />
+      <emptyLine />
+      <package name="static org.highmed" withSubpackages="true" static="false" />
+      <emptyLine />
+      <package name="" withSubpackages="true" static="true" />
+    </value>
+  </option>
+  <option name="RIGHT_MARGIN" value="150" />
+  <option name="JD_ALIGN_PARAM_COMMENTS" value="false" />
+  <option name="JD_ALIGN_EXCEPTION_COMMENTS" value="false" />
+  <option name="JD_P_AT_EMPTY_LINES" value="false" />
+  <option name="JD_KEEP_EMPTY_PARAMETER" value="false" />
+  <option name="JD_KEEP_EMPTY_EXCEPTION" value="false" />
+  <option name="JD_KEEP_EMPTY_RETURN" value="false" />
+  <option name="JD_INDENT_ON_CONTINUATION" value="true" />
+  <option name="KEEP_CONTROL_STATEMENT_IN_ONE_LINE" value="false" />
+  <option name="KEEP_BLANK_LINES_BEFORE_RBRACE" value="0" />
+  <option name="KEEP_BLANK_LINES_IN_CODE" value="1" />
+  <option name="BLANK_LINES_AFTER_CLASS_HEADER" value="0" />
+  <option name="ALIGN_MULTILINE_PARAMETERS" value="false" />
+  <option name="ALIGN_MULTILINE_FOR" value="false" />
+  <option name="CALL_PARAMETERS_WRAP" value="1" />
+  <option name="METHOD_PARAMETERS_WRAP" value="1" />
+  <option name="EXTENDS_LIST_WRAP" value="1" />
+  <option name="THROWS_KEYWORD_WRAP" value="1" />
+  <option name="METHOD_CALL_CHAIN_WRAP" value="1" />
+  <option name="BINARY_OPERATION_WRAP" value="1" />
+  <option name="BINARY_OPERATION_SIGN_ON_NEXT_LINE" value="true" />
+  <option name="TERNARY_OPERATION_WRAP" value="1" />
+  <option name="TERNARY_OPERATION_SIGNS_ON_NEXT_LINE" value="true" />
+  <option name="FOR_STATEMENT_WRAP" value="1" />
+  <option name="ARRAY_INITIALIZER_WRAP" value="1" />
+  <option name="WRAP_COMMENTS" value="true" />
+  <option name="IF_BRACE_FORCE" value="3" />
+  <option name="DOWHILE_BRACE_FORCE" value="3" />
+  <option name="WHILE_BRACE_FORCE" value="3" />
+  <option name="FOR_BRACE_FORCE" value="3" />
+  <option name="SPACE_BEFORE_ARRAY_INITIALIZER_LBRACE" value="true" />
+  <XML>
+    <option name="XML_ALIGN_ATTRIBUTES" value="false" />
+    <option name="XML_LEGACY_SETTINGS_IMPORTED" value="true" />
+    <option name="XML_SPACE_INSIDE_EMPTY_TAG" value="true" />
+  </XML>
+  <codeStyleSettings language="JAVA">
+    <option name="KEEP_FIRST_COLUMN_COMMENT" value="false" />
+    <option name="KEEP_CONTROL_STATEMENT_IN_ONE_LINE" value="false" />
+    <option name="KEEP_BLANK_LINES_IN_CODE" value="1" />
+    <option name="KEEP_BLANK_LINES_BETWEEN_PACKAGE_DECLARATION_AND_HEADER" value="0" />
+    <option name="BLANK_LINES_AFTER_CLASS_HEADER" value="1" />
+    <option name="ALIGN_MULTILINE_CHAINED_METHODS" value="false" />
+    <option name="ALIGN_MULTILINE_PARAMETERS" value="false" />
+    <option name="ALIGN_MULTILINE_FOR" value="false" />
+    <option name="CALL_PARAMETERS_WRAP" value="1" />
+    <option name="CALL_PARAMETERS_LPAREN_ON_NEXT_LINE" value="true" />
+    <option name="METHOD_PARAMETERS_WRAP" value="1" />
+    <option name="EXTENDS_LIST_WRAP" value="1" />
+    <option name="THROWS_KEYWORD_WRAP" value="1" />
+    <option name="METHOD_CALL_CHAIN_WRAP" value="1" />
+    <option name="BINARY_OPERATION_WRAP" value="1" />
+    <option name="BINARY_OPERATION_SIGN_ON_NEXT_LINE" value="true" />
+    <option name="TERNARY_OPERATION_WRAP" value="1" />
+    <option name="TERNARY_OPERATION_SIGNS_ON_NEXT_LINE" value="true" />
+    <option name="FOR_STATEMENT_WRAP" value="1" />
+    <option name="ARRAY_INITIALIZER_WRAP" value="1" />
+    <option name="WRAP_COMMENTS" value="true" />
+    <option name="IF_BRACE_FORCE" value="3" />
+    <option name="DOWHILE_BRACE_FORCE" value="3" />
+    <option name="WHILE_BRACE_FORCE" value="3" />
+    <option name="FOR_BRACE_FORCE" value="3" />
+    <option name="ENUM_CONSTANTS_WRAP" value="2" />
+    <option name="WRAP_ON_TYPING" value="0" />
+    <option name="PARENT_SETTINGS_INSTALLED" value="true" />
+    <indentOptions>
+      <option name="INDENT_SIZE" value="2" />
+      <option name="CONTINUATION_INDENT_SIZE" value="4" />
+      <option name="TAB_SIZE" value="2" />
+    </indentOptions>
+  </codeStyleSettings>
+  <codeStyleSettings language="JSON">
+    <indentOptions>
+      <option name="CONTINUATION_INDENT_SIZE" value="4" />
+      <option name="TAB_SIZE" value="2" />
+    </indentOptions>
+  </codeStyleSettings>
+  <codeStyleSettings language="XML">
+    <indentOptions>
+      <option name="INDENT_SIZE" value="2" />
+      <option name="CONTINUATION_INDENT_SIZE" value="2" />
+      <option name="TAB_SIZE" value="2" />
+    </indentOptions>
+    <arrangement>
+      <rules>
+        <section>
+          <rule>
+            <match>
+              <AND>
+                <NAME>xmlns:.*</NAME>
+                <XML_ATTRIBUTE />
+                <XML_NAMESPACE>^$</XML_NAMESPACE>
+              </AND>
+            </match>
+            <order>BY_NAME</order>
+          </rule>
+        </section>
+        <section>
+          <rule>
+            <match>
+              <AND>
+                <NAME>style</NAME>
+                <XML_ATTRIBUTE />
+                <XML_NAMESPACE>^$</XML_NAMESPACE>
+              </AND>
+            </match>
+          </rule>
+        </section>
+        <section>
+          <rule>
+            <match>
+              <AND>
+                <NAME>.*</NAME>
+                <XML_ATTRIBUTE />
+                <XML_NAMESPACE>^$</XML_NAMESPACE>
+              </AND>
+            </match>
+            <order>BY_NAME</order>
+          </rule>
+        </section>
+        <section>
+          <rule>
+            <match>
+              <AND>
+                <NAME>.*</NAME>
+                <XML_NAMESPACE>.*</XML_NAMESPACE>
+              </AND>
+            </match>
+            <order>BY_NAME</order>
+          </rule>
+        </section>
+      </rules>
+    </arrangement>
+  </codeStyleSettings>
+</code_scheme>

.github/workflows/build-for-development.yml

@@ -5,7 +5,7 @@ on:
     branches: [ 'feature/**' ]  
   pull_request:
     branches: [ develop, main ]
-    types: [ opened, ready_for_review]
+    types: [ opened, ready_for_review ]
   pull_request_target:
     branches: [ develop, main ]
     types: [ closed ]
@@ -24,6 +24,8 @@ jobs:
           java-version: '17'
           distribution: 'temurin'
           cache: 'maven'
+      - name: Run Checkstyle
+        run: mvn validate
       - name: Run unit tests
         run: mvn clean test
       - name: Run integration tests

README.md

@@ -1,26 +1,57 @@
 # Num-portal
+The num-portal repository includes the backend for the Routine Data Platform (RDP). 
 
 ## Building and running locally
+To get the backend running first a postgres instance needs to be running.
 
-1. Postgres should be up and running, instructions below
+To start a local instance of PostgreSQL:
+
+```
+docker run --name postgres -e POSTGRES_PASSWORD=postgres -d -p 5432:5432 postgres
+```
+Then you can start the project with the setting for the application-local.yml:
 
 In the root folder of the project, open cmd and run:
 
 1. Build app: `mvn clean install`
 2. Run: `spring_profiles_active=local mvn spring-boot:run`
 
-## Database 
+After that you can visit the swagger website: 
 
-Start a local instance of PostgreSQL: 
+### Swagger 
 
-```
-docker run --name postgres -e POSTGRES_PASSWORD=postgres -d -p 5432:5432 postgres
-```
+http://localhost:8090/swagger-ui/index.html
 
-## Swagger
+## Contributing
 
-http://localhost:8090/swagger-ui/index.html
+Pull requests are welcome.
+For major changes, please open an issue first to discuss what you would like to change.
+After that and the approval of HiGHmed e.V. ([email protected]) you can add the code in a Branch. 
+1. Create a branch named 'feature/name-of-branch' because of pipeline requirements
+2. Check you code with our provided [checkstyle](/.config/checkstyle.xml)
+3. Update the previously tests
+4. PRs can only be merged once the [build_for_development pipeline](/.github/workflows/build-for-development.yml) has been successfully completed
 
+### Checkstyle 
+
+To integrate checkstyle in your IDE (IntelliJ) you need the checkstyle-plugin. 
+And for intelliJ we include a [intellij-codestyle.xml](/.config/intellij-codestyle.xml) file
+
+#### IntelliJ Steps
+
+1. Add the file in Settings -> Editor -> Code Style -> Java 
+2. For the checkstyle-plugin you can add the file [checkstyle](/.config/checkstyle.xml) under Settings -> Tools -> Checkstyle -> Configuration File
+
+### Feature 
+
+Within the backend, controllers that are defined as Featurable can be activated and deactivated.
+
+Example: 
+
+```
+(@ConditionalOnProperty(value = “feature.search-by-manager”, havingValue = “true”) 
+```
+They are defined within the application.yml. This configuration is then picked up in the frontend and deactivated features are not displayed there.
 
 ## License
 

local-env/docker-compose.yaml

@@ -14,7 +14,7 @@ services:
     volumes:
       - ./keycloak.conf:/opt/keycloak/conf/keycloak.conf
     ports:
-      - 8180:8080
+      - "8180:8080"
     networks:
       - num-portal
     depends_on:
@@ -23,7 +23,7 @@ services:
     image: postgres:16.2
     restart: always
     ports:
-      - 5432:5432
+      - "5432:5432"
     networks:
       - num-portal
     environment:
@@ -35,7 +35,7 @@ services:
     image: dpage/pgadmin4:8.9
     restart: always
     ports:
-      - 8888:80
+      - "8888:80"
     networks:
       - num-portal
     environment:
@@ -48,7 +48,7 @@ services:
   ehrbase:
     image: ehrbase/ehrbase:2.5.0
     ports:
-      - 8080:8080
+      - "8080:8080"
     networks:
       - num-portal
     env_file:
@@ -62,10 +62,21 @@ services:
       DB_PASS: ${DB_PASS}
     depends_on:
       - postgres
+  clamav:
+    image: clamav/clamav:1.3.2
+    container_name: clamav
+    ports:
+      - "3310:3310"
+    volumes:
+      - clamav-db:/var/lib/clamav
+    environment:
+      - CLAMD_CONF_FILE=/etc/clamav/clamd.conf
+      - FRESHCLAM_CONF_FILE=/etc/clamav/freshclam.conf
 
 volumes:
   pgdata:
   pgadmin-data:
+  clamav-db:
 networks:
   num-portal:
     driver: bridge