[GITFLOW]merging 'release-1.80.0' into 'master'

.github/workflows/ci.yml

@@ -60,14 +60,55 @@ jobs:
           key: ${{ runner.os }}-java-${{ env.JAVA }}-m2-${{ hashFiles('**/pom.xml', '**/*.pom') }}
           restore-keys: ${{ runner.os }}-java-${{ env.JAVA }}-m2
 
-      - name: Run mvn verify
+      - name: Cache SonarCloud packages
+        # Check if PR results from the repository: if yes, it is safe to cache dependencies.
+        # This is to keep us safe from cache poisoning through 3rd party PRs.
+        if: ${{ fromJSON(env.PRIVILEGED_RUN) }}
+        uses: actions/cache@v2
+        with:
+          path: ~/.sonar/cache
+          key: ${{ runner.os }}-sonar
+          restore-keys: ${{ runner.os }}-sonar
+      - name: Run mvn verify and sonar analysis
         # FIXME(@JonasCir) see https://github.com/hzi-braunschweig/SORMAS-Project/issues/3730#issuecomment-745165678
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         working-directory: ./sormas-base
-        run: mvn verify -B -ntp
+        run: mvn -B -ntp verify org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=SORMAS-Project
+
+      - name: Comment with SonarCloud analysis
+        uses: actions/github-script@v6
+        if: github.event_name == 'pull_request'
+        with:
+          github-token: ${{ secrets.SORMAS_VITAGROUP_TOKEN }}
+          script: |
+            github.rest.issues.createComment({
+              issue_number: context.issue.number,
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              body: `SonarCloud analysis: https://sonarcloud.io/dashboard?id=SORMAS-Project&pullRequest=${{ github.event.pull_request.number }}`
+            })
 
       - name: Perform CodeQL Analysis
         uses: github/codeql-action/analyze@v1
 
+      - name: Run Trivy vulnerability scanner in repo mode
+        uses: aquasecurity/trivy-action@master
+        with:
+          scan-type: 'fs'
+          ignore-unfixed: true
+          format: 'sarif'
+          output: 'trivy-results.sarif'
+          security-checks: 'vuln,secret,config'
+
+      - name: Upload Trivy scan results to GitHub Security tab
+        uses: github/codeql-action/upload-sarif@v2
+        with:
+          sarif_file: 'trivy-results.sarif'
+          # needed as codeQL also performs an upload and they clash otherwise
+          category: 'code-scanning/trivy-repo'
+
       - name: Commit external visits API spec to development
         # Privileged action needing a secret token. Since this only runs on development in our own repo
         # the token will be available through a privileged checkout.

sormas-api/pom.xml

@@ -2,7 +2,7 @@
 	<parent>
 		<groupId>de.symeda.sormas</groupId>
 		<artifactId>sormas-base</artifactId>
-		<version>1.79.0</version>
+		<version>1.80.0</version>
 		<relativePath>../sormas-base</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

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

@@ -18,6 +18,7 @@
 package de.symeda.sormas.api.caze;
 
 import java.util.Date;
+import java.util.Set;
 
 import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.EntityRelevanceStatus;
@@ -149,6 +150,10 @@ public class CaseCriteria extends CriteriaWithDateType implements ExternalShareC
 	private Boolean onlyShowCasesWithFulfilledReferenceDefinition;
 	private String personLike;
 	private Boolean withOwnership;
+	/**
+	 * Used for filtering merge-able cases to filter both lead and similar cases.
+	 */
+	private Set<String> caseUuidsForMerge;
 
 	public CaseCriteria() {
 		super(NewCaseDateType.class);
@@ -772,4 +777,15 @@ public Boolean getWithOwnership() {
 	public void setWithOwnership(Boolean withOwnership) {
 		this.withOwnership = withOwnership;
 	}
+
+	@IgnoreForUrl
+	public Set<String> getCaseUuidsForMerge() {
+		return caseUuidsForMerge;
+	}
+
+	public CaseCriteria caseUuidsForMerge(Set<String> caseUuidsForMerge) {
+		this.caseUuidsForMerge = caseUuidsForMerge;
+
+		return this;
+	}
 }

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

@@ -147,6 +147,8 @@ public class CaseExportDto extends AbstractUuidDto {
 	@PersonalData
 	@SensitiveData
 	private String community;
+	@PersonalData
+	@SensitiveData
 	private FacilityType facilityType;
 	@PersonalData
 	@SensitiveData

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

@@ -25,6 +25,8 @@
 
 import javax.ejb.Remote;
 import javax.validation.Valid;
+import javax.validation.constraints.Max;
+import javax.validation.constraints.Min;
 import javax.validation.constraints.NotNull;
 
 import com.fasterxml.jackson.databind.JsonNode;
@@ -57,6 +59,9 @@
 @Remote
 public interface CaseFacade extends CoreFacade<CaseDataDto, CaseIndexDto, CaseReferenceDto, CaseCriteria> {
 
+	int DUPLICATE_MERGING_LIMIT_DEFAULT = 100;
+	int DUPLICATE_MERGING_LIMIT_MAX = 1000;
+
 	long count(CaseCriteria caseCriteria, boolean ignoreUserFilter);
 
 	List<CaseSelectionDto> getCaseSelectionList(CaseCriteria caseCriteria);
@@ -148,7 +153,7 @@ Long countCasesForMap(
 
 	List<CaseSelectionDto> getSimilarCases(CaseSimilarityCriteria criteria);
 
-	List<CaseIndexDto[]> getCasesForDuplicateMerging(CaseCriteria criteria, boolean showDuplicatesWithDifferentRegion);
+	List<CaseIndexDto[]> getCasesForDuplicateMerging(CaseCriteria criteria, @Min(1) @Max(DUPLICATE_MERGING_LIMIT_MAX) int limit, boolean showDuplicatesWithDifferentRegion);
 
 	void updateCompleteness(String caseUuid);
 

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

@@ -19,6 +19,7 @@
 
 import java.io.Serializable;
 import java.util.Date;
+import java.util.Set;
 
 import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.EntityRelevanceStatus;
@@ -140,6 +141,12 @@ public class ContactCriteria extends BaseCriteria implements Serializable {
 	private boolean excludeLimitedSyncRestrictions;
 	private Boolean withOwnership = true;
 
+	private Set<String> uuids;
+	/**
+	 * Used for filtering merge-able cases to filter both lead and similar cases.
+	 */
+	private Set<String> contactUuidsForMerge;
+
 	public UserRoleReferenceDto getReportingUserRole() {
 		return reportingUserRole;
 	}
@@ -723,4 +730,26 @@ public Boolean getWithOwnership() {
 	public void setWithOwnership(Boolean withOwnership) {
 		this.withOwnership = withOwnership;
 	}
+
+	@IgnoreForUrl
+	public Set<String> getUuids() {
+		return uuids;
+	}
+
+	public ContactCriteria uuids(Set<String> uuids) {
+		this.uuids = uuids;
+
+		return this;
+	}
+
+	@IgnoreForUrl
+	public Set<String> getContactUuidsForMerge() {
+		return contactUuidsForMerge;
+	}
+
+	public ContactCriteria contactUuidsForMerge(Set<String> contactUuidsForMerge) {
+		this.contactUuidsForMerge = contactUuidsForMerge;
+
+		return this;
+	}
 }

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

@@ -1,5 +1,6 @@
 package de.symeda.sormas.api.contact;
 
+import java.util.Collection;
 import java.util.Date;
 import java.util.List;
 
@@ -14,7 +15,7 @@ public class ContactSimilarityCriteria extends BaseCriteria implements Cloneable
 	private static final long serialVersionUID = 6902101244020083789L;
 
 	private PersonReferenceDto person;
-	private List<PersonReferenceDto> persons;
+	private Collection<PersonReferenceDto> persons;
 	private CaseReferenceDto caze;
 	private List<CaseReferenceDto> resultingCases;
 	private Disease disease;
@@ -52,11 +53,11 @@ public ContactSimilarityCriteria withPerson(PersonReferenceDto person) {
 		return this;
 	}
 
-	public List<PersonReferenceDto> getPersons() {
+	public Collection<PersonReferenceDto> getPersons() {
 		return persons;
 	}
 
-	public ContactSimilarityCriteria withPersons(List<PersonReferenceDto> persons) {
+	public ContactSimilarityCriteria withPersons(Collection<PersonReferenceDto> persons) {
 		this.persons = persons;
 		return this;
 	}

sormas-api/src/main/java/de/symeda/sormas/api/i18n/Captions.java

@@ -1764,6 +1764,7 @@ public interface Captions {
 	String personLinkToCases = "personLinkToCases";
 	String personLinkToContacts = "personLinkToContacts";
 	String personLinkToEvents = "personLinkToEvents";
+	String personLinkToSamples = "personLinkToSamples";
 	String personNoCaseLinkedToPerson = "personNoCaseLinkedToPerson";
 	String personNoContactLinkedToPerson = "personNoContactLinkedToPerson";
 	String personNoEventParticipantLinkedToPerson = "personNoEventParticipantLinkedToPerson";
@@ -1839,6 +1840,7 @@ public interface Captions {
 	String prescriptionNewPrescription = "prescriptionNewPrescription";
 	String prescriptionWithTreatment = "prescriptionWithTreatment";
 	String prescriptionWithTreatmentTitleDelete = "prescriptionWithTreatmentTitleDelete";
+	String QueryDetails_resultLimit = "QueryDetails.resultLimit";
 	String Region = "Region";
 	String Region_archived = "Region.archived";
 	String Region_country = "Region.country";
@@ -1989,6 +1991,7 @@ public interface Captions {
 	String sampleNoSamplesForCase = "sampleNoSamplesForCase";
 	String sampleNoSamplesForContact = "sampleNoSamplesForContact";
 	String sampleNoSamplesForEventParticipant = "sampleNoSamplesForEventParticipant";
+	String sampleNoSamplesForPerson = "sampleNoSamplesForPerson";
 	String sampleNotShipped = "sampleNotShipped";
 	String sampleNotShippedLong = "sampleNotShippedLong";
 	String samplePending = "samplePending";

sormas-api/src/main/java/de/symeda/sormas/api/i18n/Strings.java

@@ -978,6 +978,7 @@ public interface Strings {
 	String messageCaseFound = "messageCaseFound";
 	String messageCaseFoundNoValidPathogenTest = "messageCaseFoundNoValidPathogenTest";
 	String messageCaseIncidenceUnsupportedAgeGroup = "messageCaseIncidenceUnsupportedAgeGroup";
+	String messageCaseOutsideJurisdictionDeletionDenied = "messageCaseOutsideJurisdictionDeletionDenied";
 	String messageCaseReferredFromPoe = "messageCaseReferredFromPoe";
 	String messageCaseRelationToEventWithoutDisease = "messageCaseRelationToEventWithoutDisease";
 	String messageCasesArchived = "messageCasesArchived";
@@ -1017,6 +1018,7 @@ public interface Strings {
 	String messageContactDearchived = "messageContactDearchived";
 	String messageContactDuplicateDeleted = "messageContactDuplicateDeleted";
 	String messageContactExternalTokenWarning = "messageContactExternalTokenWarning";
+	String messageContactOutsideJurisdictionDeletionDenied = "messageContactOutsideJurisdictionDeletionDenied";
 	String messageContactSaved = "messageContactSaved";
 	String messageContactsDeleted = "messageContactsDeleted";
 	String messageContactsEdited = "messageContactsEdited";
@@ -1181,6 +1183,7 @@ public interface Strings {
 	String messagePathogenTestSaved = "messagePathogenTestSaved";
 	String messagePathogenTestSavedShort = "messagePathogenTestSavedShort";
 	String messagePathogenTestsDeleted = "messagePathogenTestsDeleted";
+	String messagePathogenTestsSavedShort = "messagePathogenTestsSavedShort";
 	String messagePersonAddedAsEventParticipant = "messagePersonAddedAsEventParticipant";
 	String messagePersonAlreadyCaseInEvent = "messagePersonAlreadyCaseInEvent";
 	String messagePersonAlreadyEventParticipant = "messagePersonAlreadyEventParticipant";

sormas-api/src/main/java/de/symeda/sormas/api/location/LocationDto.java

@@ -142,6 +142,7 @@ public class LocationDto extends PseudonymizableDto {
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_SMALL, message = Validations.textTooLong)
 	private String addressTypeDetails;
 	@PersonalData
+	@SensitiveData
 	private FacilityType facilityType;
 	@PersonalData
 	@SensitiveData

sormas-api/src/main/java/de/symeda/sormas/api/person/PersonCriteria.java

@@ -1,8 +1,11 @@
 package de.symeda.sormas.api.person;
 
+import java.util.Set;
+
 import de.symeda.sormas.api.infrastructure.community.CommunityReferenceDto;
 import de.symeda.sormas.api.infrastructure.district.DistrictReferenceDto;
 import de.symeda.sormas.api.infrastructure.region.RegionReferenceDto;
+import de.symeda.sormas.api.utils.IgnoreForUrl;
 import de.symeda.sormas.api.utils.criteria.BaseCriteria;
 
 public class PersonCriteria extends BaseCriteria implements Cloneable {
@@ -33,6 +36,7 @@ public class PersonCriteria extends BaseCriteria implements Cloneable {
 	private DistrictReferenceDto district;
 	private CommunityReferenceDto community;
 	private PersonAssociation personAssociation;
+	private Set<String> uuids;
 
 	public PersonCriteria() {
 
@@ -123,6 +127,17 @@ public PersonCriteria personAssociation(PersonAssociation personAssociation) {
 		return this;
 	}
 
+	@IgnoreForUrl
+	public Set<String> getUuids() {
+		return uuids;
+	}
+
+	public PersonCriteria uuids(Set<String> uuids) {
+		this.uuids = uuids;
+
+		return this;
+	}
+
 	private void validate(PersonAssociation personAssociation) {
 
 		if (personAssociation == null) {

sormas-api/src/main/java/de/symeda/sormas/api/sample/SampleAssociationType.java

@@ -7,7 +7,8 @@ public enum SampleAssociationType {
 	ALL,
 	CASE,
 	CONTACT,
-	EVENT_PARTICIPANT;
+	EVENT_PARTICIPANT,
+	PERSON;
 
 	@Override
 	public String toString() {

sormas-api/src/main/java/de/symeda/sormas/api/sample/SampleCriteria.java

@@ -260,6 +260,7 @@ public String getCaseCodeIdLike() {
 		return caseCodeIdLike;
 	}
 
+	@IgnoreForUrl
 	public List<String> getCaseUuids() {
 		return caseUuids;
 	}
@@ -270,6 +271,7 @@ public SampleCriteria caseUuids(List<String> caseUuids) {
 		return this;
 	}
 
+	@IgnoreForUrl
 	public List<String> getContactUuids() {
 		return contactUuids;
 	}
@@ -280,6 +282,7 @@ public SampleCriteria contactUuids(List<String> contactUuids) {
 		return this;
 	}
 
+	@IgnoreForUrl
 	public List<String> getEventParticipantUuids() {
 		return eventParticipantUuids;
 	}

sormas-api/src/main/java/de/symeda/sormas/api/sormastosormas/DuplicateResult.java

@@ -0,0 +1,50 @@
+/*
+ * SORMAS® - Surveillance Outbreak Response Management & Analysis System
+ * Copyright © 2016-2023 Helmholtz-Zentrum für Infektionsforschung GmbH (HZI)
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package de.symeda.sormas.api.sormastosormas;
+
+import java.io.Serializable;
+import java.util.Collections;
+import java.util.Set;
+
+import de.symeda.sormas.api.audit.AuditedClass;
+import de.symeda.sormas.api.sormastosormas.entities.DuplicateResultType;
+
+@AuditedClass
+public class DuplicateResult implements Serializable {
+
+	private static final long serialVersionUID = 1647535939211815787L;
+
+	private final DuplicateResultType type;
+
+	private final Set<String> uuids;
+
+	public DuplicateResult(DuplicateResultType type, Set<String> uuids) {
+		this.type = type;
+		this.uuids = uuids;
+	}
+
+	public static DuplicateResult none() {
+		return new DuplicateResult(DuplicateResultType.NONE, Collections.emptySet());
+	}
+
+	public DuplicateResultType getType() {
+		return type;
+	}
+
+	public Set<String> getUuids() {
+		return uuids;
+	}
+}