Merge branch 'development' into #12414_generate_enum_values_based_on_…

…locale_in_dev_view

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>

sormas-api/pom.xml

@@ -2,7 +2,7 @@
 	<parent>
 		<groupId>de.symeda.sormas</groupId>
 		<artifactId>sormas-base</artifactId>
-		<version>1.89.0-SNAPSHOT</version>
+		<version>1.90.0-SNAPSHOT</version>
 		<relativePath>../sormas-base</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

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/environment/EnvironmentCriteria.java

@@ -6,6 +6,7 @@
 import de.symeda.sormas.api.EntityRelevanceStatus;
 import de.symeda.sormas.api.caze.InvestigationStatus;
 import de.symeda.sormas.api.infrastructure.community.CommunityReferenceDto;
+import de.symeda.sormas.api.infrastructure.country.CountryReferenceDto;
 import de.symeda.sormas.api.infrastructure.district.DistrictReferenceDto;
 import de.symeda.sormas.api.infrastructure.region.RegionReferenceDto;
 import de.symeda.sormas.api.user.UserReferenceDto;
@@ -32,6 +33,8 @@ public class EnvironmentCriteria extends BaseCriteria implements Serializable {
 	private static final long serialVersionUID = -2947852193651003088L;
 
 	private String freeText;
+	private String externalId;
+	private CountryReferenceDto country;
 	private RegionReferenceDto region;
 	private DistrictReferenceDto district;
 	private CommunityReferenceDto community;
@@ -47,6 +50,14 @@ public class EnvironmentCriteria extends BaseCriteria implements Serializable {
 	private Double gpsLatTo;
 	private Double gpsLonFrom;
 	private Double gpsLonTo;
+	/**
+	 * Used for similarity detection at import
+	 */
+	private Double gpsLat;
+	/**
+	 * Used for similarity detection at import
+	 */
+	private Double gpsLon;
 
 	@IgnoreForUrl
 	public String getFreeText() {
@@ -62,6 +73,33 @@ public void setFreeText(String freeText) {
 		this.freeText = freeText;
 	}
 
+	@IgnoreForUrl
+	public String getExternalId() {
+		return externalId;
+	}
+
+	public EnvironmentCriteria externalId(String externalId) {
+		this.externalId = externalId;
+		return this;
+	}
+
+	public void setExternalId(String externalId) {
+		this.externalId = externalId;
+	}
+
+	public CountryReferenceDto getCountry() {
+		return country;
+	}
+
+	public EnvironmentCriteria country(CountryReferenceDto country) {
+		this.country = country;
+		return this;
+	}
+
+	public void setCountry(CountryReferenceDto country) {
+		this.country = country;
+	}
+
 	public RegionReferenceDto getRegion() {
 		return region;
 	}
@@ -244,6 +282,32 @@ public void setGpsLonTo(Double gpsLonTo) {
 		this.gpsLonTo = gpsLonTo;
 	}
 
+	public Double getGpsLat() {
+		return gpsLat;
+	}
+
+	public EnvironmentCriteria gpsLat(Double gpsLat) {
+		this.gpsLat = gpsLat;
+		return this;
+	}
+
+	public void setGpsLat(Double gpsLat) {
+		this.gpsLat = gpsLat;
+	}
+
+	public Double getGpsLon() {
+		return gpsLon;
+	}
+
+	public EnvironmentCriteria gpsLon(Double gpsLon) {
+		this.gpsLon = gpsLon;
+		return this;
+	}
+
+	public void setGpsLon(Double gpsLon) {
+		this.gpsLon = gpsLon;
+	}
+
 	public void reportDateBetween(Date reportDateFrom, Date reportDateTo, DateFilterOption dateFilterOption) {
 		this.reportDateFrom = reportDateFrom;
 		this.reportDateTo = reportDateTo;

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

@@ -47,12 +47,12 @@ public class EnvironmentDto extends PseudonymizableDto {
 	public static final String DELETION_REASON = "deletionReason";
 	public static final String OTHER_DELETION_REASON = "otherDeletionReason";
 
-	@NotNull
+	@NotNull(message = Validations.validReportDateTime)
 	private Date reportDate;
-	@NotNull
+	@NotNull(message = Validations.validReportingUser)
 	private UserReferenceDto reportingUser;
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_TEXT, message = Validations.textTooLong)
-	@NotBlank
+	@NotBlank(message = Validations.environmentName)
 	private String environmentName;
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_TEXT, message = Validations.textTooLong)
 	private String description;
@@ -61,7 +61,7 @@ public class EnvironmentDto extends PseudonymizableDto {
 	private UserReferenceDto responsibleUser;
 	@NotNull
 	private InvestigationStatus investigationStatus;
-	@NotNull
+	@NotNull(message = Validations.environmentMedia)
 	private EnvironmentMedia environmentMedia;
 	private WaterType waterType;
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_TEXT, message = Validations.textTooLong)
@@ -85,6 +85,7 @@ public class EnvironmentDto extends PseudonymizableDto {
 	public static EnvironmentDto build() {
 		final EnvironmentDto environment = new EnvironmentDto();
 		environment.setUuid(DataHelper.createUuid());
+		environment.setReportDate(new Date());
 		environment.setLocation(LocationDto.build());
 		environment.setInvestigationStatus(InvestigationStatus.PENDING);
 

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

@@ -1,10 +1,14 @@
 package de.symeda.sormas.api.environment;
 
+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<String> getAllActiveUuids();
+
 }

sormas-api/src/main/java/de/symeda/sormas/api/environment/environmentsample/EnvironmentSampleCriteria.java

@@ -19,6 +19,7 @@
 import java.util.Date;
 
 import de.symeda.sormas.api.EntityRelevanceStatus;
+import de.symeda.sormas.api.environment.EnvironmentReferenceDto;
 import de.symeda.sormas.api.infrastructure.district.DistrictReferenceDto;
 import de.symeda.sormas.api.infrastructure.facility.FacilityReferenceDto;
 import de.symeda.sormas.api.infrastructure.region.RegionReferenceDto;
@@ -54,6 +55,7 @@ public class EnvironmentSampleCriteria extends BaseCriteria implements Serializa
 	private DateFilterOption dateFilterOption = DateFilterOption.DATE;
 	private Date reportDateFrom;
 	private Date reportDateTo;
+	private EnvironmentReferenceDto environment;
 
 	public EnvironmentSampleCriteria() {
 		super();
@@ -184,4 +186,17 @@ public void reportDateBetween(Date reportDateFrom, Date reportDateTo, DateFilter
 		this.reportDateTo = reportDateTo;
 		this.dateFilterOption = dateFilterOption;
 	}
+
+	public EnvironmentReferenceDto getEnvironment() {
+		return environment;
+	}
+
+	public void setEnvironment(EnvironmentReferenceDto environment) {
+		this.environment = environment;
+	}
+
+	public EnvironmentSampleCriteria withEnvironment(EnvironmentReferenceDto environment) {
+		this.environment = environment;
+		return this;
+	}
 }

sormas-api/src/main/java/de/symeda/sormas/api/environment/environmentsample/EnvironmentSampleDto.java

@@ -25,6 +25,7 @@
 import javax.validation.constraints.NotNull;
 import javax.validation.constraints.Size;
 
+import de.symeda.sormas.api.common.DeletionReason;
 import de.symeda.sormas.api.environment.EnvironmentReferenceDto;
 import de.symeda.sormas.api.feature.FeatureType;
 import de.symeda.sormas.api.i18n.Validations;
@@ -48,6 +49,36 @@ public class EnvironmentSampleDto extends PseudonymizableDto {
 
 	public static final long APPROXIMATE_JSON_SIZE_IN_BYTES = 2000;
 
+	public static final String I18N_PREFIX = "EnvironmentSample";
+
+	public static final String ENVIRONMENT = "environment";
+	public static final String SAMPLE_DATE_TIME = "sampleDateTime";
+	public static final String SAMPLE_MATERIAL = "sampleMaterial";
+	public static final String OTHER_SAMPLE_MATERIAL = "otherSampleMaterial";
+	public static final String SAMPLE_VOLUME = "sampleVolume";
+	public static final String FIELD_SAMPLE_ID = "fieldSampleId";
+	public static final String TURBIDITY = "turbidity";
+	public static final String PH_VALUE = "phValue";
+	public static final String SAMPLE_TEMPERATURE = "sampleTemperature";
+	public static final String CHLORINE_RESIDUALS = "chlorineResiduals";
+	public static final String LABORATORY = "laboratory";
+	public static final String LABORATORY_DETAILS = "laboratoryDetails";
+	public static final String REQUESTED_PATHOGEN_TESTS = "requestedPathogenTests";
+	public static final String OTHER_REQUESTED_PATHOGEN_TESTS = "otherRequestedPathogenTests";
+	public static final String WEATHER_CONDITIONS = "weatherConditions";
+	public static final String HEAVY_RAIN = "heavyRain";
+	public static final String DISPATCHED = "dispatched";
+	public static final String DISPATCH_DATE = "dispatchDate";
+	public static final String DISPATCH_DETAILS = "dispatchDetails";
+	public static final String RECEIVED = "received";
+	public static final String RECEIVAL_DATE = "receivalDate";
+	public static final String LAB_SAMPLE_ID = "labSampleId";
+	public static final String SPECIMEN_CONDITION = "specimenCondition";
+	public static final String LOCATION = "location";
+	public static final String GENERAL_COMMENT = "generalComment";
+	public static final String DELETION_REASON = "deletionReason";
+	public static final String OTHER_DELETION_REASON = "otherDeletionReason";
+
 	@NotNull
 	private EnvironmentReferenceDto environment;
 	@NotNull
@@ -104,6 +135,10 @@ public class EnvironmentSampleDto extends PseudonymizableDto {
 	@SensitiveData
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_TEXT, message = Validations.textTooLong)
 	private String generalComment;
+	private boolean deleted;
+	private DeletionReason deletionReason;
+	@Size(max = FieldConstraints.CHARACTER_LIMIT_TEXT, message = Validations.textTooLong)
+	private String otherDeletionReason;
 
 	public static EnvironmentSampleDto build(EnvironmentReferenceDto environment, UserReferenceDto reportingUser) {
 		EnvironmentSampleDto sample = new EnvironmentSampleDto();
@@ -333,4 +368,32 @@ public String getGeneralComment() {
 	public void setGeneralComment(String generalComment) {
 		this.generalComment = generalComment;
 	}
+
+	public boolean isDeleted() {
+		return deleted;
+	}
+
+	public void setDeleted(boolean deleted) {
+		this.deleted = deleted;
+	}
+
+	public DeletionReason getDeletionReason() {
+		return deletionReason;
+	}
+
+	public void setDeletionReason(DeletionReason deletionReason) {
+		this.deletionReason = deletionReason;
+	}
+
+	public String getOtherDeletionReason() {
+		return otherDeletionReason;
+	}
+
+	public void setOtherDeletionReason(String otherDeletionReason) {
+		this.otherDeletionReason = otherDeletionReason;
+	}
+
+	public EnvironmentSampleReferenceDto toReference() {
+		return new EnvironmentSampleReferenceDto(getUuid());
+	}
 }

sormas-api/src/main/java/de/symeda/sormas/api/environment/environmentsample/EnvironmentSampleFacade.java

@@ -19,8 +19,20 @@
 
 import de.symeda.sormas.api.BaseFacade;
 import de.symeda.sormas.api.DeletableFacade;
+import de.symeda.sormas.api.EditPermissionType;
+import de.symeda.sormas.api.deletionconfiguration.DeletionInfoDto;
 
 @Remote
 public interface EnvironmentSampleFacade
 	extends BaseFacade<EnvironmentSampleDto, EnvironmentSampleIndexDto, EnvironmentSampleReferenceDto, EnvironmentSampleCriteria>, DeletableFacade {
+
+	boolean exists(String uuid);
+
+	boolean isEditAllowed(String uuid);
+
+	EditPermissionType getEditPermissionType(String sampleUuid);
+
+	DeletionInfoDto getAutomaticDeletionInfo(String sampleUuid);
+
+	DeletionInfoDto getManuallyDeletionInfo(String sampleUuid);
 }