[GITFLOW]merging 'release-1.87.0' into 'master'

.github/dependabot.yml

@@ -34,6 +34,8 @@ updates:
       - dependency-name: org.eclipse.microprofile.config:microprofile-config-api
       - dependency-name: org.glassfish:javax.el
       - dependency-name: org.glassfish.corba:glassfish-corba-omgapi
+      - dependency-name: org.glassfish.hk2:*
+      - dependency-name: org.glassfish.hk2.*:*
       - dependency-name: org.glassfish.jaxb:*
       - dependency-name: org.glassfish.jersey*:jersey-*
       - dependency-name: org.glassfish.soteria:javax.security.enterprise

.github/workflows/ci.yml

@@ -97,7 +97,7 @@ jobs:
         uses: github/codeql-action/analyze@v2
 
       - name: Run Trivy vulnerability scanner in repo mode
-        uses: aquasecurity/trivy-action@0.9.2
+        uses: aquasecurity/trivy-action@0.11.2
         with:
           scan-type: 'fs'
           ignore-unfixed: true

.github/workflows/github_pages.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout development
-        uses: actions/checkout@v1
+        uses: actions/checkout@v3
       - name: Copy files
         run: |
           cp README.md docs/index.md

.github/workflows/linter.yml

@@ -46,7 +46,7 @@ jobs:
       # Run Linter against code base #
       ################################
       - name: Lint Code Base
-        uses: github/super-linter/slim@v4
+        uses: github/super-linter/slim@v5
         env:
           DEFAULT_BRANCH: development
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -25,6 +25,7 @@ deploy
 /sormas-app/java_pid21052.hprof
 bin
 /sormas-base/setup/setup.log
+/sormas-base/setup/keycloak/keycloak_setup.log
 
 # Exclude maven wrapper
 !/.mvn/wrapper/maven-wrapper.jar

docs/CONTRIBUTING.md

@@ -22,6 +22,7 @@ This allows us to consider and process your contribution as quickly and smoothly
 * [Development Workflow](#development-workflow)
   * [Versioning](#versioning)
   * [Branches](#branches)
+  * [Dependency Management](#dependency-management)
 
 ## Submitting an Issue
 
@@ -226,3 +227,26 @@ Once the new version is merged to `master`/`master-<version`, the `release-`/`ho
 
 These kind of branches are manually created and maintained by developers who work on an issue. Such branches are used to create pull requests or to review the changes before merged into a permanent or supporting branch.
 * **feature-1234_short_description**: Any branch that is supposed to contribute to `development` or a `hotfix` branch.
+
+### Dependency Management
+
+Dependencies are managed in Maven POM files. For most dependencies the version is defined in [sormas-base/pom.xml](sormas-base/pom.xml). \
+[sormas-app](../sormas-app/app/build.gradle) and [sormas-e2e-tests](../sormas-e2e-tests/build.gradle) use Gradle instead.
+
+#### Automatic updates
+
+**Process**: At the beginning of each iteration, look over all [dependency update PRs](https://github.com/SORMAS-Foundation/SORMAS-Project/pulls?q=is%3Apr+is%3Aopen+label%3Adependencies) created by dependabot and process them according to the following rules:
+1. Always use "Rebase and merge" instead of creating a merge commit! If needed use the comment `@dependabot rebase` to rebase the PR to the latest development commit.
+2. If all CI checks are successful, minor and micro version updates can be merged
+3. For major version updates read the changelog to understand implications and possible migration steps of the update. \
+  Decide on you own wheter it is necessary to manually test the PR before merging.
+4. If CI checks are negative or migration steps are needed, decide whether the update is important enough to justify the effort of additional work. \
+If the PR is not needed, you can use `@dependabot ignore this major version` or `@dependabot ignore this minor version`.
+
+#### Payara
+All required dependencies provided by the Payara application server are set to "provided" in maven and may only be updated in combination with an update of the Payara version. \
+These dependencies have been added to the dependabot ignore list, so no dependency update PR is automatically created.
+
+#### Keycloak
+The Keycloak version in SORMAS-Project only defines the version of the Keycloak admin client library. When a new version of Keycloak is available this should be updated after the [Keycloak version is SORMAS-Docker](https://github.com/SORMAS-Foundation/SORMAS-Docker/blob/devops/keycloak/Dockerfile) has been updated. \
+This can be tested locally by building the updated Keycloak docker image and then using it in a  [container](https://github.com/SORMAS-Foundation/SORMAS-Project/tree/development/sormas-base/setup/keycloak) together with a local Payara instance.

docs/SERVER_SETUP.md

@@ -88,7 +88,7 @@ Unzip the archive, copy/upload its contents to **/root/deploy/sormas/$(date +%F)
 
 ```bash
 sudo su
-mkdir /root/deploy/sormas
+mkdir -p /root/deploy/sormas
 cd /root/deploy/sormas
 SORMAS_VERSION=1.y.z
 wget https://github.com/sormas-foundation/SORMAS-Project/releases/download/v${SORMAS_VERSION}/sormas_${SORMAS_VERSION}.zip

sormas-api/pom.xml

@@ -2,7 +2,7 @@
 	<parent>
 		<groupId>de.symeda.sormas</groupId>
 		<artifactId>sormas-base</artifactId>
-		<version>1.86.0</version>
+		<version>1.87.0</version>
 		<relativePath>../sormas-base</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

sormas-api/src/main/java/de/symeda/sormas/api/CountryHelper.java

@@ -24,6 +24,7 @@ public final class CountryHelper {
 	public static final String COUNTRY_CODE_GERMANY = "de";
 	public static final String COUNTRY_CODE_FRANCE = "fr";
 	public static final String COUNTRY_CODE_SWITZERLAND = "ch";
+	public static final String COUNTRY_CODE_LUXEMBOURG = "lu";
 
 	public static boolean isCountry(String countryLocale, String country) {
 		// If the country locale is complete (e.g. de-DE), check the last (country) part; 

sormas-api/src/main/java/de/symeda/sormas/api/DeletableFacade.java

@@ -1,12 +1,18 @@
 package de.symeda.sormas.api;
 
+import java.util.List;
+
 import de.symeda.sormas.api.common.DeletionDetails;
 
 public interface DeletableFacade {
 
 	void delete(String uuid, DeletionDetails deletionDetails);
 
+    List<String> delete(List<String> uuids, DeletionDetails deletionDetails);
+
 	void restore(String uuid);
 
+	List<String> restore(List<String> uuids);
+
 	boolean isDeleted(String uuid);
 }

sormas-api/src/main/java/de/symeda/sormas/api/PermanentlyDeletableFacade.java

@@ -0,0 +1,10 @@
+package de.symeda.sormas.api;
+
+import java.util.List;
+
+public interface PermanentlyDeletableFacade {
+
+	void delete(String uuid);
+
+	void delete(List<String> uuids);
+}

sormas-api/src/main/java/de/symeda/sormas/api/caze/CaseBulkEditData.java

@@ -42,8 +42,9 @@ public class CaseBulkEditData extends EntityDto {
 	private static final long serialVersionUID = -4670022133882295863L;
 
 	public static final String DISEASE = "disease";
-	public static final String DISEASE_VARIANT = "diseaseVariant";
 	public static final String DISEASE_DETAILS = "diseaseDetails";
+	public static final String DISEASE_VARIANT = "diseaseVariant";
+	public static final String DISEASE_VARIANT_DETAILS = "diseaseVariantDetails";
 	public static final String PLAGUE_TYPE = "plagueType";
 	public static final String DENGUE_FEVER_TYPE = "dengueFeverType";
 	public static final String RABIES_TYPE = "rabiesType";
@@ -60,9 +61,11 @@ public class CaseBulkEditData extends EntityDto {
 	public static final String DONT_SHARE_WITH_REPORTING_TOOL = "dontShareWithReportingTool";
 
 	private Disease disease;
-	private DiseaseVariant diseaseVariant;
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_DEFAULT, message = Validations.textTooLong)
 	private String diseaseDetails;
+	private DiseaseVariant diseaseVariant;
+	@Size(max = FieldConstraints.CHARACTER_LIMIT_DEFAULT, message = Validations.textTooLong)
+	private String diseaseVariantDetails;
 	private PlagueType plagueType;
 	private DengueFeverType dengueFeverType;
 	private RabiesType rabiesType;
@@ -87,6 +90,14 @@ public void setDisease(Disease disease) {
 		this.disease = disease;
 	}
 
+	public String getDiseaseDetails() {
+		return diseaseDetails;
+	}
+
+	public void setDiseaseDetails(String diseaseDetails) {
+		this.diseaseDetails = diseaseDetails;
+	}
+
 	public DiseaseVariant getDiseaseVariant() {
 		return diseaseVariant;
 	}
@@ -95,12 +106,12 @@ public void setDiseaseVariant(DiseaseVariant diseaseVariant) {
 		this.diseaseVariant = diseaseVariant;
 	}
 
-	public String getDiseaseDetails() {
-		return diseaseDetails;
+	public String getDiseaseVariantDetails() {
+		return diseaseVariantDetails;
 	}
 
-	public void setDiseaseDetails(String diseaseDetails) {
-		this.diseaseDetails = diseaseDetails;
+	public void setDiseaseVariantDetails(String diseaseVariantDetails) {
+		this.diseaseVariantDetails = diseaseVariantDetails;
 	}
 
 	public PlagueType getPlagueType() {

sormas-api/src/main/java/de/symeda/sormas/api/caze/CaseFacade.java

@@ -124,8 +124,6 @@ Long countCasesForMap(
 
 	List<CaseDataDto> getAllCasesOfPerson(String personUuid);
 
-	List<String> deleteCases(List<String> caseUuids, DeletionDetails deletionDetails);
-
 	void deleteWithContacts(String caseUuid, DeletionDetails deletionDetails);
 
 	Date getOldestCaseOnsetDate();
@@ -182,6 +180,7 @@ Integer saveBulkCase(
 		List<String> caseUuidList,
 		@Valid CaseBulkEditData updatedCaseBulkEditData,
 		boolean diseaseChange,
+		boolean diseaseVariantChange,
 		boolean classificationChange,
 		boolean investigationStatusChange,
 		boolean outcomeChange,
@@ -191,6 +190,7 @@ Integer saveBulkEditWithFacilities(
 		List<String> caseUuidList,
 		@Valid CaseBulkEditData updatedCaseBulkEditData,
 		boolean diseaseChange,
+		boolean diseaseVariantChange,
 		boolean classificationChange,
 		boolean investigationStatusChange,
 		boolean outcomeChange,

sormas-api/src/main/java/de/symeda/sormas/api/contact/ContactFacade.java

@@ -33,7 +33,6 @@
 import de.symeda.sormas.api.MergeFacade;
 import de.symeda.sormas.api.caze.CaseReferenceDto;
 import de.symeda.sormas.api.caze.CoreAndPersonDto;
-import de.symeda.sormas.api.common.DeletionDetails;
 import de.symeda.sormas.api.common.Page;
 import de.symeda.sormas.api.dashboard.DashboardContactDto;
 import de.symeda.sormas.api.externaldata.ExternalDataDto;
@@ -61,8 +60,6 @@ public interface ContactFacade extends CoreFacade<ContactDto, ContactIndexDto, C
 
 	List<MapContactDto> getContactsForMap(RegionReferenceDto regionRef, DistrictReferenceDto districtRef, Disease disease, Date from, Date to);
 
-	List<String> deleteContacts(List<String> contactUuids, DeletionDetails deletionDetails);
-
 	FollowUpPeriodDto getCalculatedFollowUpUntilDate(ContactDto contactDto, boolean ignoreOverwrite);
 
 	List<ContactListEntryDto> getEntriesList(String personUuid, Integer first, Integer max);

sormas-api/src/main/java/de/symeda/sormas/api/customizableenum/CustomizableEnumFacade.java

@@ -63,6 +63,19 @@ public interface CustomizableEnumFacade {
 	 */
 	<T extends CustomizableEnum> T getEnumValue(CustomizableEnumType type, String value, Disease disease) throws CustomEnumNotFoundException;
 
+	/**
+	 * Checks if the specified enum value exists for the specified type and disease.
+	 * 
+	 * @param type
+	 *            The type for which to retrieve the enum value
+	 * @param value
+	 *            The values to search for
+	 * @param disease
+	 *            The disease for which to retrieve the enum values. If null, all enum values that are disease-independent are retrieved
+	 * @return true if the enum value exists
+	 */
+	boolean existsEnumValue(CustomizableEnumType type, String value, Disease disease);
+
 	/**
 	 * Retrieves the cached contents of all enum value instances of the specified type. The results are already
 	 * internationalized based on the user's language, or the server language as a fallback. If the enum values for the

sormas-api/src/main/java/de/symeda/sormas/api/environment/EnvironmentFacade.java

@@ -1,14 +1,10 @@
 package de.symeda.sormas.api.environment;
 
-import java.util.Date;
-import java.util.List;
-
 import javax.ejb.Remote;
 
 import de.symeda.sormas.api.CoreFacade;
 
 @Remote
 public interface EnvironmentFacade extends CoreFacade<EnvironmentDto, EnvironmentIndexDto, EnvironmentReferenceDto, EnvironmentCriteria> {
 
-	List<EnvironmentDto> getAllEnvironmentsAfter(Date date);
 }

sormas-api/src/main/java/de/symeda/sormas/api/event/EventFacade.java

@@ -28,7 +28,6 @@
 
 import de.symeda.sormas.api.CoreFacade;
 import de.symeda.sormas.api.caze.CaseDataDto;
-import de.symeda.sormas.api.common.DeletionDetails;
 import de.symeda.sormas.api.common.Page;
 import de.symeda.sormas.api.externaldata.ExternalDataDto;
 import de.symeda.sormas.api.externaldata.ExternalDataUpdateException;
@@ -46,8 +45,6 @@ public interface EventFacade extends CoreFacade<EventDto, EventIndexDto, EventRe
 
 	List<EventDto> getAllByCase(CaseDataDto caseDataDto);
 
-	List<String> deleteEvents(List<String> eventUuids, DeletionDetails deletionDetails);
-
 	Page<EventIndexDto> getIndexPage(@NotNull EventCriteria eventCriteria, Integer offset, Integer size, List<SortProperty> sortProperties);
 
 	List<EventExportDto> getExportList(EventCriteria eventCriteria, Collection<String> selectedRows, Integer first, Integer max);

sormas-api/src/main/java/de/symeda/sormas/api/event/EventGroupFacade.java

@@ -18,6 +18,7 @@
 package de.symeda.sormas.api.event;
 
 import java.util.List;
+import java.util.Set;
 
 import javax.ejb.Remote;
 import javax.validation.Valid;
@@ -58,7 +59,7 @@ Page<EventGroupIndexDto> getIndexPage(
 
 	void linkEventsToGroup(List<EventReferenceDto> eventReferences, EventGroupReferenceDto eventGroupReference);
 
-	void linkEventsToGroups(List<EventReferenceDto> eventReferences, List<EventGroupReferenceDto> eventGroupReferences);
+	void linkEventsToGroups(List<String> eventUuids, List<String> eventGroupReferences);
 
 	void unlinkEventGroup(EventReferenceDto eventReference, EventGroupReferenceDto eventGroupReference);
 
@@ -72,5 +73,7 @@ Page<EventGroupIndexDto> getIndexPage(
 
 	void notifyEventAddedToEventGroup(EventGroupReferenceDto eventGroupReference, List<EventReferenceDto> eventReferences);
 
+	void notifyEventAddedToEventGroup(String eventGroupUuid, Set<String> eventUuids);
+
 	void notifyEventRemovedFromEventGroup(EventGroupReferenceDto eventGroupReference, List<EventReferenceDto> eventReferences);
 }

sormas-api/src/main/java/de/symeda/sormas/api/externalmessage/ExternalMessageDto.java

@@ -21,6 +21,7 @@
 
 import javax.validation.constraints.Size;
 
+import de.symeda.sormas.api.CountryHelper;
 import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.audit.AuditIncludeProperty;
 import de.symeda.sormas.api.audit.AuditedClass;
@@ -29,6 +30,7 @@
 import de.symeda.sormas.api.externalmessage.labmessage.SampleReportDto;
 import de.symeda.sormas.api.feature.FeatureType;
 import de.symeda.sormas.api.i18n.Validations;
+import de.symeda.sormas.api.infrastructure.country.CountryReferenceDto;
 import de.symeda.sormas.api.person.PhoneNumberType;
 import de.symeda.sormas.api.person.PresentCondition;
 import de.symeda.sormas.api.person.Sex;
@@ -37,6 +39,7 @@
 import de.symeda.sormas.api.utils.DataHelper;
 import de.symeda.sormas.api.utils.DependingOnFeatureType;
 import de.symeda.sormas.api.utils.FieldConstraints;
+import de.symeda.sormas.api.utils.HideForCountriesExcept;
 
 @AuditedClass
 @DependingOnFeatureType(featureType = FeatureType.EXTERNAL_MESSAGES)
@@ -69,7 +72,7 @@ public class ExternalMessageDto extends SormasToSormasShareableDto {
 	public static final String PERSON_EMAIL = "personEmail";
 	public static final String PERSON_STREET = "personStreet";
 	public static final String PERSON_HOUSE_NUMBER = "personHouseNumber";
-	public static final String PERSON_COUNTRY_ISO_CODE = "personCountryIsoCode";
+	public static final String PERSON_COUNTRY = "personCountry";
 	public static final String EXTERNAL_MESSAGE_DETAILS = "externalMessageDetails";
 	public static final String PROCESSED = "processed";
 	public static final String REPORT_ID = "reportId";
@@ -100,8 +103,10 @@ public class ExternalMessageDto extends SormasToSormasShareableDto {
 	private String personFirstName;
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_SMALL, message = Validations.textTooLong)
 	private String personLastName;
+	@HideForCountriesExcept(countries = CountryHelper.COUNTRY_CODE_LUXEMBOURG)
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_DEFAULT, message = Validations.textTooLong)
 	private String personExternalId;
+	@HideForCountriesExcept(countries = CountryHelper.COUNTRY_CODE_LUXEMBOURG)
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_SMALL, message = Validations.textTooLong)
 	private String personNationalHealthId;
 	private Sex personSex;
@@ -117,10 +122,11 @@ public class ExternalMessageDto extends SormasToSormasShareableDto {
 	private String personStreet;
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_SMALL, message = Validations.textTooLong)
 	private String personHouseNumber;
-	@Size(max = FieldConstraints.CHARACTER_LIMIT_SMALL, message = Validations.textTooLong)
-	private String personCountryIsoCode;
+	@HideForCountriesExcept(countries = CountryHelper.COUNTRY_CODE_LUXEMBOURG)
+	private CountryReferenceDto personCountry;
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_SMALL, message = Validations.textTooLong)
 	private String personPhone;
+	@HideForCountriesExcept(countries = CountryHelper.COUNTRY_CODE_LUXEMBOURG)
 	private PhoneNumberType personPhoneNumberType;
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_SMALL, message = Validations.textTooLong)
 	private String personEmail;
@@ -329,12 +335,12 @@ public void setPersonHouseNumber(String personHouseNumber) {
 		this.personHouseNumber = personHouseNumber;
 	}
 
-	public String getPersonCountryIsoCode() {
-		return personCountryIsoCode;
+	public CountryReferenceDto getPersonCountry() {
+		return personCountry;
 	}
 
-	public void setPersonCountryIsoCode(String personCountryIsoCode) {
-		this.personCountryIsoCode = personCountryIsoCode;
+	public void setPersonCountry(CountryReferenceDto personCountry) {
+		this.personCountry = personCountry;
 	}
 
 	public String getPersonPhone() {