[GITFLOW]merging 'release-1.89.0' into 'master'

docs/EXTERNAL_MESSAGES_ADAPTER.md

@@ -13,9 +13,6 @@ A minimal maven project structure for an external message adapter module is show
     |   |   |   |   |-- MyExternalMessageFacadeEjb.java
     |   |   |-- resources
     |   |   |   |-- version.txt
-    |   |   |-- webapp
-    |   |   |   |-- META-INF
-    |   |   |   |   |-- context.xml
     |   |-- test
     |   |   |-- java
     |   |   |   |-- my.project
@@ -90,14 +87,6 @@ Example:
 ${project.name} ${project.version}
 ```
 
-### context.xml
-This xml is used to configure the context path of your external message adapter module.
-```xml
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE xml>
-<Context antiJARLocking="true" path="${myProject.apiRoot}"/>
-```
-
 ### pom.xml
 This is the maven project configuration file.
 
@@ -114,7 +103,7 @@ Example with default dependencies for java-ee, sormas-api, logging and testing:
 
         <properties>
             <sormas.version>1.85.0</sormas.version>
-            <myProject.apiRoot>/my-message-adapter</myProject.apiRoot>
+            <warName>my-message-adapter</warName>
 
             <javaee.version>8.0</javaee.version>
             <slf4j.version>1.7.30</slf4j.version>
@@ -171,7 +160,7 @@ Example with default dependencies for java-ee, sormas-api, logging and testing:
 
     <properties>
         <sormas.version>1.85.0</sormas.version>
-        <myProject.apiRoot>/my-message-adapter</myProject.apiRoot>
+        <warName>my-message-adapter</warName>
 
         <junit.version>4.13.1</junit.version>
         <mockito.version>3.6.0</mockito.version>
@@ -297,22 +286,15 @@ Example with default dependencies for java-ee, sormas-api, logging and testing:
         </resources>
 
         <plugins>
-            <!-- Provide WebApp context path via value of `myProject.apiRoot` property -->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-war-plugin</artifactId>
                 <version>3.2.3</version>
                 <configuration>
+                    <warName>${warName}</warName>
+
                     <filteringDeploymentDescriptors>true</filteringDeploymentDescriptors>
                     <webResources>
-                        <resource>
-                            <directory>src/main/webapp/META-INF</directory>
-                            <includes>
-                                <include>context.xml</include>
-                            </includes>
-                            <targetPath>/META-INF</targetPath>
-                            <filtering>true</filtering>
-                        </resource>
                         <resource>
                             <directory>src/main/webapp</directory>
                             <targetPath>/</targetPath>

docs/SERVER_SETUP.md

@@ -61,8 +61,8 @@ You can check your Java version from the shell/command-line using: ``java -versi
 
 ### Postgres Database
 
-* Install PostgreSQL (currently 9.5, 9.6 or 10 to 15) on your system (manuals for all OS can be found here: <https://www.postgresql.org/download>)
-* Set **max_connections = 288** and **max_prepared_transactions = 256** (at least, sum of all connection pools) in ``postgresql.conf`` (e.g. ``/etc/postgresql/10.0/main/postgresql.conf``; ``C:/Program Files/PostgreSQL/10.0/data``) - make sure the property is uncommented and restart the service to apply the changes.
+* Install PostgreSQL (currently 14 to 15) on your system (manuals for all OS can be found here: <https://www.postgresql.org/download>)
+* Set **max_connections = 288** and **max_prepared_transactions = 256** (at least, sum of all connection pools) in ``postgresql.conf`` (e.g. ``/etc/postgresql/14.0/main/postgresql.conf``; ``C:/Program Files/PostgreSQL/14.0/data``) - make sure the property is uncommented and restart the service to apply the changes.
 * Install the "temporal tables" extension for Postgres (<https://github.com/arkhipov/temporal_tables>)
   * **Windows**: Download the latest version for your Postgres version:
     * <https://github.com/arkhipov/temporal_tables/releases/latest>, then copy the DLL from the project into the PostgreSQL's lib directory and the .sql and .control files into the directory share\extension.

docs/SERVER_UPDATE.md

@@ -57,6 +57,9 @@ DROP EXTENSION IF EXISTS temporal_tables;
 Payara is updated from 5.2021.10 to 5.2022.5.
 If you are **not** using [SORMAS-Docker](https://github.com/SORMAS-Foundation/SORMAS-Docker), please follow the [Payara migration guide](SERVER_UPDATE.md#how-to-migrate-to-new-payara-server).
 
+### 1.89.0
+When installing this version on new systems or upgrading postgres version on Ubuntu make sure you have at least Ubuntu LTS 20 with postgres 14 (or 18 with postgres 12 from APT).
+
 ## Automatic Server Update
 * Navigate to the  folder containing the unzipped deploy files:
   ``cd /root/deploy/sormas/$(date +%F)``
@@ -155,4 +158,4 @@ For minor updates of the payara version, you will most often be able to keep the
 2. Undeploy all sormas modules from the payara domain and stop the domain.
 3. Replace your payara server in ``/opt/payara5`` (default path) with the downloaded one. Remove the default domain in ``opt/payara5/glassfish/domains`` as it is not needed.
 4. Replace the application server in your IDE with the new server. See [IDE setup guide](DEVELOPMENT_ENVIRONMENT.md#step-5-install-and-configure-your-ide)
-5. If you are facing any problems, restart your IDE and clean all generated files from the sormas domain.
+5. If you are facing any problems, restart your IDE and clean all generated files from the sormas domain.

sormas-api/pom.xml

@@ -2,7 +2,7 @@
 	<parent>
 		<groupId>de.symeda.sormas</groupId>
 		<artifactId>sormas-base</artifactId>
-		<version>1.88.1</version>
+		<version>1.89.0</version>
 		<relativePath>../sormas-base</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

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

@@ -17,15 +17,17 @@
 
 import java.util.List;
 
+import de.symeda.sormas.api.common.progress.ProcessedEntity;
+
 public interface ArchivableFacade {
 
-	void archive(String uuid);
+	ProcessedEntity archive(String uuid);
 
-	void dearchive(String uuid);
+	ProcessedEntity dearchive(String uuid);
 
-	List<String> archive(List<String> entityUuid);
+	List<ProcessedEntity> archive(List<String> entityUuid);
 
-	List<String> dearchive(List<String> entityUuids);
+	List<ProcessedEntity> dearchive(List<String> entityUuids);
 
 	boolean isArchived(String uuid);
 }

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

@@ -19,8 +19,8 @@
 import java.util.Date;
 import java.util.List;
 
+import de.symeda.sormas.api.common.progress.ProcessedEntity;
 import de.symeda.sormas.api.deletionconfiguration.DeletionInfoDto;
-import de.symeda.sormas.api.externalsurveillancetool.ExternalSurveillanceToolException;
 import de.symeda.sormas.api.utils.criteria.BaseCriteria;
 
 public interface CoreFacade<DTO extends EntityDto, INDEX_DTO extends Serializable, REF_DTO extends ReferenceDto, CRITERIA extends BaseCriteria>
@@ -34,19 +34,14 @@ public interface CoreFacade<DTO extends EntityDto, INDEX_DTO extends Serializabl
 
 	DeletionInfoDto getManuallyDeletionInfo(String uuid);
 
-	void archive(String entityUuid, Date endOfProcessingDate);
+	ProcessedEntity archive(String entityUuid, Date endOfProcessingDate);
 
-	void archive(List<String> entityUuid);
+	List<ProcessedEntity> archive(List<String> entityUuid);
 
-	void dearchive(List<String> entityUuids, String dearchiveReason);
+	List<ProcessedEntity> dearchive(List<String> entityUuids, String dearchiveReason);
 
 	List<String> getArchivedUuidsSince(Date since);
 
-	default void setArchiveInExternalSurveillanceToolForEntity(String uuid, boolean archived) throws ExternalSurveillanceToolException {
-	}
-
-	default void setArchiveInExternalSurveillanceToolForEntities(List<String> uuid, boolean archived) throws ExternalSurveillanceToolException {
-	}
-
 	Date calculateEndOfProcessingDate(String entityUuids);
+
 }

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

@@ -3,16 +3,17 @@
 import java.util.List;
 
 import de.symeda.sormas.api.common.DeletionDetails;
+import de.symeda.sormas.api.common.progress.ProcessedEntity;
 
 public interface DeletableFacade {
 
 	void delete(String uuid, DeletionDetails deletionDetails);
 
-    List<String> delete(List<String> uuids, DeletionDetails deletionDetails);
+	List<ProcessedEntity> delete(List<String> uuids, DeletionDetails deletionDetails);
 
 	void restore(String uuid);
 
-	List<String> restore(List<String> uuids);
+	List<ProcessedEntity> restore(List<String> uuids);
 
 	boolean isDeleted(String uuid);
 }

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

@@ -46,6 +46,7 @@
 import de.symeda.sormas.api.docgeneneration.QuarantineOrderFacade;
 import de.symeda.sormas.api.document.DocumentFacade;
 import de.symeda.sormas.api.environment.EnvironmentFacade;
+import de.symeda.sormas.api.environment.EnvironmentImportFacade;
 import de.symeda.sormas.api.environment.environmentsample.EnvironmentSampleFacade;
 import de.symeda.sormas.api.epidata.EpiDataFacade;
 import de.symeda.sormas.api.event.EventFacade;
@@ -509,6 +510,10 @@ public static EnvironmentSampleFacade getEnvironmentSampleFacade() {
 		return get().lookupEjbRemote(EnvironmentSampleFacade.class);
 	}
 
+	public static EnvironmentImportFacade getEnvironmentImportFacade() {
+		return get().lookupEjbRemote(EnvironmentImportFacade.class);
+	}
+
 	@SuppressWarnings("unchecked")
 	public <P> P lookupEjbRemote(Class<P> clazz) {
 		try {

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

@@ -2,9 +2,11 @@
 
 import java.util.List;
 
+import de.symeda.sormas.api.common.progress.ProcessedEntity;
+
 public interface PermanentlyDeletableFacade {
 
 	void delete(String uuid);
 
-	void delete(List<String> uuids);
+	List<ProcessedEntity> delete(List<String> uuids);
 }

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

@@ -38,6 +38,7 @@
 import de.symeda.sormas.api.MergeFacade;
 import de.symeda.sormas.api.common.DeletionDetails;
 import de.symeda.sormas.api.common.Page;
+import de.symeda.sormas.api.common.progress.ProcessedEntity;
 import de.symeda.sormas.api.contact.ContactReferenceDto;
 import de.symeda.sormas.api.event.EventParticipantReferenceDto;
 import de.symeda.sormas.api.externaldata.ExternalDataDto;
@@ -176,7 +177,7 @@ Page<CaseFollowUpDto> getCaseFollowUpIndexPage(
 
 	List<String> getUuidsNotShareableWithExternalReportingTools(List<String> caseUuids);
 
-	Integer saveBulkCase(
+	List<ProcessedEntity> saveBulkCase(
 		List<String> caseUuidList,
 		@Valid CaseBulkEditData updatedCaseBulkEditData,
 		boolean diseaseChange,
@@ -186,7 +187,7 @@ Integer saveBulkCase(
 		boolean outcomeChange,
 		boolean surveillanceOfficerChange);
 
-	Integer saveBulkEditWithFacilities(
+	List<ProcessedEntity> saveBulkEditWithFacilities(
 		List<String> caseUuidList,
 		@Valid CaseBulkEditData updatedCaseBulkEditData,
 		boolean diseaseChange,
@@ -215,11 +216,13 @@ Integer saveBulkEditWithFacilities(
 
 	PreviousCaseDto getMostRecentPreviousCase(PersonReferenceDto person, Disease disease, Date startDate);
 
-	void archive(String entityUuid, Date endOfProcessingDate, boolean includeContacts);
+	ProcessedEntity archive(String entityUuid, Date endOfProcessingDate, boolean includeContacts);
 
-	void archive(List<String> entityUuids, boolean includeContacts);
+	List<ProcessedEntity> archive(List<String> entityUuids, boolean includeContacts);
 
-	void dearchive(List<String> entityUuids, String dearchiveReason, boolean includeContacts);
+	ProcessedEntity dearchive(String entityUuid, String dearchiveReason, boolean includeContacts);
+
+	List<ProcessedEntity> dearchive(List<String> entityUuids, String dearchiveReason, boolean includeContacts);
 
 	void setResultingCase(EventParticipantReferenceDto eventParticipantReferenceDto, CaseReferenceDto caseReferenceDto);
 

sormas-api/src/main/java/de/symeda/sormas/api/common/CoreEntityType.java → sormas-api/src/main/java/de/symeda/sormas/api/common/DeletableEntityType.java

@@ -15,7 +15,7 @@
 
 package de.symeda.sormas.api.common;
 
-public enum CoreEntityType {
+public enum DeletableEntityType {
 
 	//ENTITY LIST
 	CASE,
@@ -25,5 +25,8 @@ public enum CoreEntityType {
 	IMMUNIZATION,
 	TRAVEL_ENTRY,
 	CAMPAIGN,
-	ENVIRONMENT;
+	SAMPLE,
+	PATHOGEN_TEST,
+	ENVIRONMENT,
+	ENVIRONMENT_SAMPLE;
 }

sormas-api/src/main/java/de/symeda/sormas/api/common/progress/ProcessedEntity.java

@@ -0,0 +1,34 @@
+package de.symeda.sormas.api.common.progress;
+
+import java.io.Serializable;
+
+import de.symeda.sormas.api.audit.AuditedClass;
+
+@AuditedClass
+public class ProcessedEntity implements Serializable {
+
+	String entityUuid;
+
+	ProcessedEntityStatus processedEntityStatus;
+
+	public ProcessedEntity(String entityUuid, ProcessedEntityStatus processedEntityStatus) {
+		this.entityUuid = entityUuid;
+		this.processedEntityStatus = processedEntityStatus;
+	}
+
+	public String getEntityUuid() {
+		return entityUuid;
+	}
+
+	public void setEntityUuid(String entityUuid) {
+		this.entityUuid = entityUuid;
+	}
+
+	public ProcessedEntityStatus getProcessedEntityStatus() {
+		return processedEntityStatus;
+	}
+
+	public void setProcessedEntityStatus(ProcessedEntityStatus processedEntityStatus) {
+		this.processedEntityStatus = processedEntityStatus;
+	}
+}

sormas-api/src/main/java/de/symeda/sormas/api/common/progress/ProcessedEntityStatus.java

@@ -0,0 +1,27 @@
+package de.symeda.sormas.api.common.progress;
+
+public enum ProcessedEntityStatus {
+
+	SUCCESS,
+	/**
+	 * The entity does not corresponds to the criterias needed in order to be processed (e.g. Events with Participants can not be deleted)
+	 */
+	NOT_ELIGIBLE,
+	/**
+	 * ExternalSurveillanceToolRuntimeException was thrown during the processing of the entity
+	 */
+	EXTERNAL_SURVEILLANCE_FAILURE,
+	/**
+	 * SormasToSormasRuntimeException was thrown during the processing of the entity
+	 */
+	SORMAS_TO_SORMAS_FAILURE,
+	/**
+	 * AccessDeniedException was thrown during the processing of the entity
+	 */
+	ACCESS_DENIED_FAILURE,
+	/**
+	 * An internal exception was thrown during the processing of the entity
+	 */
+	INTERNAL_FAILURE;
+
+}

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

@@ -34,6 +34,7 @@
 import de.symeda.sormas.api.caze.CaseReferenceDto;
 import de.symeda.sormas.api.caze.CoreAndPersonDto;
 import de.symeda.sormas.api.common.Page;
+import de.symeda.sormas.api.common.progress.ProcessedEntity;
 import de.symeda.sormas.api.dashboard.DashboardContactDto;
 import de.symeda.sormas.api.externaldata.ExternalDataDto;
 import de.symeda.sormas.api.externaldata.ExternalDataUpdateException;
@@ -146,7 +147,7 @@ List<MergeContactIndexDto[]> getContactsForDuplicateMerging(
 
 	void updateExternalData(@Valid List<ExternalDataDto> externalData) throws ExternalDataUpdateException;
 
-	Integer saveBulkContacts(
+	List<ProcessedEntity> saveBulkContacts(
 		List<String> contactUuidlist,
 		@Valid ContactBulkEditData updatedContacBulkEditData,
 		boolean classificationChange,

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

@@ -28,8 +28,9 @@
 import de.symeda.sormas.api.person.SymptomJournalStatus;
 import de.symeda.sormas.api.utils.PersonalData;
 import de.symeda.sormas.api.utils.pseudonymization.PseudonymizableIndexDto;
+import de.symeda.sormas.api.uuid.HasUuid;
 
-public class ContactIndexDto extends PseudonymizableIndexDto implements Serializable, Cloneable {
+public class ContactIndexDto extends PseudonymizableIndexDto implements HasUuid, Serializable, Cloneable {
 
 	private static final long serialVersionUID = 7511900591141885152L;
 

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

@@ -4,7 +4,10 @@
 
 import de.symeda.sormas.api.CoreFacade;
 
+import java.util.List;
+
 @Remote
 public interface EnvironmentFacade extends CoreFacade<EnvironmentDto, EnvironmentIndexDto, EnvironmentReferenceDto, EnvironmentCriteria> {
 
+    List<String> getAllActiveUuids();
 }