[GITFLOW]merging 'release-0.17.0' into 'master'

README.md

@@ -1,4 +1,5 @@
 ## Project Structure
+<a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc/4.0/88x31.png" /></a><br /><span xmlns:dct="http://purl.org/dc/terms/" property="dct:title">SORMAS- Surveillance Outbreak Response Management and Analysis System</span> by <a xmlns:cc="http://creativecommons.org/ns#" href="https://www.helmholtz-hzi.de/de/forschung/forschungsprojekte/ansicht/projekt/detail/sormas/" property="cc:attributionName" rel="cc:attributionURL">Helmholtz Centre for Infection Research (HZI)</a> is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/">Creative Commons Attribution-NonCommercial 4.0 International License</a>.<br />Based on a work at <a xmlns:dct="http://purl.org/dc/terms/" href="www.sormas.org" rel="dct:source">www.sormas.org</a>.
 The project consists of the following modules:
 
 - sormas-api: general business logic and definitions for data exchange between app and server
@@ -67,7 +68,7 @@ For information on what libs are used see pom.xml in sormas-base project: https:
     * Edit sql/sormas_schema.sql
         * ``Remove everything until after the INSERT with the read schema version``
         * ``Surround the remaining with BEGIN; and COMMIT;``
-    * Update the Database schema: ``psql -U sormas_user -W sormas_db < sql/sormas_schema.sql``
+    * Update the Database schema: ``psql -U sormas_user -h localhost -W sormas_db < sql/sormas_schema.sql``
 * If something goes wrong, restorte the database using ``pg_restore -U sormas_user -Fc -d sormas_db < sormas_db_....``
 
 #### Web Applications

sormas-api/pom.xml

@@ -2,7 +2,7 @@
 	<parent>
 		<groupId>de.symeda.sormas</groupId>
 		<artifactId>sormas-base</artifactId>
-		<version>0.16.0</version>
+		<version>0.17.0</version>
 		<relativePath>../sormas-base</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

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

@@ -21,6 +21,6 @@ public interface ConfigFacade {
 
 	String getSmsAuthSecret();
 
-	String getExportPath();
+	String getTempFilesPath();
 
 }

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

@@ -43,6 +43,7 @@ public static int getIncubationPeriodDays(Disease disease, PlagueType plagueType
 		case EVD:
 		case MEASLES:
 		case MONKEYPOX:
+		case LASSA:
 		case OTHER:
 			return 21;
 		case AVIAN_INFLUENCA:
@@ -53,7 +54,6 @@ public static int getIncubationPeriodDays(Disease disease, PlagueType plagueType
 			return 10;
 		case PLAGUE:
 			return 7;
-		case LASSA:
 		case YELLOW_FEVER:
 			return 6;
 		case CHOLERA:

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

@@ -8,9 +8,9 @@
 import de.symeda.sormas.api.epidata.EpiDataFacade;
 import de.symeda.sormas.api.event.EventFacade;
 import de.symeda.sormas.api.event.EventParticipantFacade;
-import de.symeda.sormas.api.export.ExportFacade;
 import de.symeda.sormas.api.facility.FacilityFacade;
 import de.symeda.sormas.api.hospitalization.HospitalizationFacade;
+import de.symeda.sormas.api.importexport.ImportExportFacade;
 import de.symeda.sormas.api.outbreak.OutbreakFacade;
 import de.symeda.sormas.api.person.PersonFacade;
 import de.symeda.sormas.api.region.CommunityFacade;
@@ -137,8 +137,8 @@ public static ConfigFacade getConfigFacade() {
 		return get().lookupEjbRemote(ConfigFacade.class);
 	}
 
-	public static ExportFacade getExportFacade() {
-		return get().lookupEjbRemote(ExportFacade.class);
+	public static ImportExportFacade getImportExportFacade() {
+		return get().lookupEjbRemote(ImportExportFacade.class);
 	}
 
 	@SuppressWarnings("unchecked")

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

@@ -4,8 +4,8 @@
 import java.util.Date;
 
 import de.symeda.sormas.api.Disease;
-import de.symeda.sormas.api.person.PresentCondition;
 import de.symeda.sormas.api.region.DistrictReferenceDto;
+import de.symeda.sormas.api.region.RegionReferenceDto;
 import de.symeda.sormas.api.user.UserRole;
 
 public class CaseCriteria implements Serializable {
@@ -15,6 +15,7 @@ public class CaseCriteria implements Serializable {
 	private UserRole reportingUserRole;
 	private Disease disease;
 	private CaseOutcome outcome;
+	private RegionReferenceDto region;
 	private DistrictReferenceDto district;
 	private Date newCaseDateFrom;
 	private Date newCaseDateTo;
@@ -34,6 +35,11 @@ public CaseCriteria diseaseEquals(Disease disease) {
 		return this;
 	}
 
+	public CaseCriteria regionEquals(RegionReferenceDto region) {
+		this.region = region;
+		return this;
+	}
+
 	public CaseCriteria districtEquals(DistrictReferenceDto district) {
 		this.district = district;
 		return this;
@@ -57,6 +63,10 @@ public Disease getDisease() {
 		return disease;
 	}
 
+	public RegionReferenceDto getRegion() {
+		return region;
+	}
+
 	public DistrictReferenceDto getDistrict() {
 		return district;
 	}

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

@@ -40,9 +40,9 @@ public interface CaseFacade {
 
 	List<CaseDataDto> getByUuids(List<String> uuids);
 
-	List<DashboardCaseDto> getNewCasesForDashboard(DistrictReferenceDto districtRef, Disease disease, Date from, Date to, String userUuid);
+	List<DashboardCaseDto> getNewCasesForDashboard(RegionReferenceDto regionRef, DistrictReferenceDto districtRef, Disease disease, Date from, Date to, String userUuid);
 
-	List<MapCaseDto> getCasesForMap(DistrictReferenceDto districtRef, Disease disease, Date from, Date to, String userUuid);
+	List<MapCaseDto> getCasesForMap(RegionReferenceDto regionRef, DistrictReferenceDto districtRef, Disease disease, Date from, Date to, String userUuid);
 
 	List<StatisticsCaseDto> getCasesForStatistics(RegionReferenceDto regionRef, DistrictReferenceDto districtRef, Disease disease, Date from, Date to, String userUuid);
 

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

@@ -8,6 +8,7 @@
 import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.caze.MapCaseDto;
 import de.symeda.sormas.api.region.DistrictReferenceDto;
+import de.symeda.sormas.api.region.RegionReferenceDto;
 import de.symeda.sormas.api.user.UserReferenceDto;
 import de.symeda.sormas.api.visit.VisitReferenceDto;
 
@@ -32,7 +33,7 @@ public interface ContactFacade {
 
 	List<ContactDto> getByUuids(List<String> uuids);
 
-	List<MapContactDto> getContactsForMap(DistrictReferenceDto districtRef, Disease disease, Date fromDate, Date toDate, String userUuid, List<MapCaseDto> mapCaseDtos);
+	List<MapContactDto> getContactsForMap(RegionReferenceDto regionRef, DistrictReferenceDto districtRef, Disease disease, Date fromDate, Date toDate, String userUuid, List<MapCaseDto> mapCaseDtos);
 
 	void deleteContact(ContactReferenceDto contactRef, String userUuid);
 

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

@@ -7,6 +7,7 @@
 
 import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.region.DistrictReferenceDto;
+import de.symeda.sormas.api.region.RegionReferenceDto;
 import de.symeda.sormas.api.user.UserReferenceDto;
 
 @Remote
@@ -16,7 +17,7 @@ public interface EventFacade {
 
 	List<EventDto> getAllEventsBetween(Date fromDate, Date toDate, DistrictReferenceDto districtRef, Disease disease, String userUuid);
 
-	List<DashboardEventDto> getNewEventsForDashboard(DistrictReferenceDto districtRef, Disease disease, Date from, Date to, String userUuid);
+	List<DashboardEventDto> getNewEventsForDashboard(RegionReferenceDto regionRef, DistrictReferenceDto districtRef, Disease disease, Date from, Date to, String userUuid);
 
 	EventDto getEventByUuid(String uuid);
 

sormas-api/src/main/java/de/symeda/sormas/api/facility/FacilityFacade.java

@@ -27,4 +27,5 @@ public interface FacilityFacade {
 	FacilityDto getByUuid(String uuid);
 
 	List<String> getAllUuids(String userUuid);
+
 }

sormas-api/src/main/java/de/symeda/sormas/api/export/DatabaseTable.java → sormas-api/src/main/java/de/symeda/sormas/api/importexport/DatabaseTable.java

@@ -1,4 +1,4 @@
-package de.symeda.sormas.api.export;
+package de.symeda.sormas.api.importexport;
 
 import de.symeda.sormas.api.I18nProperties;
 

sormas-api/src/main/java/de/symeda/sormas/api/export/DatabaseTableType.java → sormas-api/src/main/java/de/symeda/sormas/api/importexport/DatabaseTableType.java

@@ -1,4 +1,4 @@
-package de.symeda.sormas.api.export;
+package de.symeda.sormas.api.importexport;
 
 public enum DatabaseTableType {
 

sormas-api/src/main/java/de/symeda/sormas/api/importexport/ImportExportFacade.java

@@ -0,0 +1,33 @@
+package de.symeda.sormas.api.importexport;
+
+import java.io.IOException;
+import java.util.List;
+
+import javax.ejb.Remote;
+
+import de.symeda.sormas.api.utils.ExportErrorException;
+
+@Remote
+public interface ImportExportFacade {
+
+	/**
+	 * Exports the passed database tables as .csv files to the export folder specified in the
+	 * properties file, creates a zip archive containing these .csv files and returns the path
+	 * to the zip archive that can then be used to offer it as a download.
+	 */
+	String generateDatabaseExportArchive(List<DatabaseTable> databaseTables) throws ExportErrorException, IOException;
+
+	/**
+	 * Creates a .csv file with one row containing all relevant column names of the case entity
+	 * and its sub-entities and returns the path to the .csv file that can then be used to offer
+	 * it as a download.
+	 */
+	void generateCaseImportTemplateFile() throws IOException;
+
+	String getCaseImportTemplateFilePath();
+
+	String getSormasImportGuideFilePath();
+
+	String importCasesFromCsvFile(String csvFilePath, String userUuid) throws IOException, InvalidColumnException;
+
+}

sormas-api/src/main/java/de/symeda/sormas/api/importexport/InvalidColumnException.java

@@ -0,0 +1,18 @@
+package de.symeda.sormas.api.importexport;
+
+public class InvalidColumnException extends Exception {
+
+	private static final long serialVersionUID = -1597100047088745699L;
+
+	private String columnName;
+
+	public InvalidColumnException(String columnName) {
+		super();
+		this.columnName = columnName;
+	}
+
+	public String getColumnName() {
+		return columnName;
+	}
+
+}

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

@@ -31,4 +31,6 @@ public interface PersonFacade {
 	List<String> getAllUuids(String userUuid);
 
 	List<PersonDto> getByUuids(List<String> uuids);
+
+	PersonDto buildPerson();
 }

sormas-api/src/main/java/de/symeda/sormas/api/region/CommunityFacade.java

@@ -16,4 +16,6 @@ public interface CommunityFacade {
 
 	List<String> getAllUuids(String userUuid);
 
-	CommunityReferenceDto getCommunityReferenceByUuid(String uuid);}
+	CommunityReferenceDto getCommunityReferenceByUuid(String uuid);
+
+}

sormas-api/src/main/java/de/symeda/sormas/api/region/DistrictFacade.java

@@ -21,5 +21,5 @@ public interface DistrictFacade {
 	List<DistrictReferenceDto> getAllAsReference();
 
 	List<String> getAllUuids(String userUuid);
-
+	
 }

sormas-api/src/main/java/de/symeda/sormas/api/region/RegionFacade.java

@@ -17,4 +17,5 @@ public interface RegionFacade {
 	RegionReferenceDto getRegionReferenceByUuid(String uuid);
 
 	List<String> getAllUuids(String userUuid);
+
 }

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

@@ -8,6 +8,7 @@
 import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.caze.CaseReferenceDto;
 import de.symeda.sormas.api.region.DistrictReferenceDto;
+import de.symeda.sormas.api.region.RegionReferenceDto;
 
 @Remote
 public interface SampleFacade {
@@ -30,7 +31,7 @@ public interface SampleFacade {
 
 	List<SampleDto> getByUuids(List<String> uuids);
 
-	List<DashboardSampleDto> getNewSamplesForDashboard(DistrictReferenceDto districtRef, Disease disease, Date from, Date to, String userUuid);
+	List<DashboardSampleDto> getNewSamplesForDashboard(RegionReferenceDto regionRef, DistrictReferenceDto districtRef, Disease disease, Date from, Date to, String userUuid);
 
 	void deleteSample(SampleReferenceDto sampleRef, String userUuid);
 

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

@@ -7,6 +7,7 @@
 
 import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.region.DistrictReferenceDto;
+import de.symeda.sormas.api.region.RegionReferenceDto;
 
 @Remote
 public interface SampleTestFacade {
@@ -23,7 +24,7 @@ public interface SampleTestFacade {
 
 	List<SampleTestDto> getByUuids(List<String> uuids);
 
-	List<DashboardTestResultDto> getNewTestResultsForDashboard(DistrictReferenceDto districtRef, Disease disease, Date from, Date to, String userUuid);
+	List<DashboardTestResultDto> getNewTestResultsForDashboard(RegionReferenceDto regionRef, DistrictReferenceDto districtRef, Disease disease, Date from, Date to, String userUuid);
 
 	void deleteSampleTest(SampleTestReferenceDto sampleTestRef, String userUuid);
 }

sormas-api/src/main/java/de/symeda/sormas/api/user/UserRight.java

@@ -97,6 +97,9 @@ public enum UserRight {
 	CASE_DELETE(
 			ADMIN
 	),
+	CASE_IMPORT(
+			ADMIN
+	),
 	SAMPLE_CREATE(
 			ADMIN,
 			NATIONAL_USER,

sormas-api/src/main/java/de/symeda/sormas/api/utils/DateHelper.java

@@ -21,6 +21,8 @@ public final class DateHelper {
 
 	private static final SimpleDateFormat SHORT_DATE_FORMAT = new SimpleDateFormat("dd/MM/yy");
 	private static final SimpleDateFormat DATE_FORMAT = new SimpleDateFormat("dd/MM/yyyy");
+	private static final SimpleDateFormat DATE_FORMAT_DOTS = new SimpleDateFormat("dd.MM.yyyy");
+	private static final SimpleDateFormat DATE_FORMAT_HYPHEN = new SimpleDateFormat("dd-MM-yyyy");
 	private static final SimpleDateFormat DATE_TIME_FORMAT = new SimpleDateFormat("dd/MM/yyyy HH:mm");
 	private static final SimpleDateFormat SHORT_DATE_TIME_FORMAT = new SimpleDateFormat("dd/MM/yyyy HH:mm");
 	private static final SimpleDateFormat TIME_FORMAT = new SimpleDateFormat("HH:mm");
@@ -60,6 +62,31 @@ public static Date parseDate(String date) {
 			return null;
 		}
 	}
+
+	public static Date parseDateWithException(String date) throws ParseException {
+		if (date != null) {
+			try {
+				SimpleDateFormat dateFormat = clone(DATE_FORMAT);
+				dateFormat.setLenient(false);
+				return dateFormat.parse(date);
+			} catch (ParseException e) {
+				// Try next format
+			}
+			try {
+				SimpleDateFormat dateFormat = clone(DATE_FORMAT_DOTS);
+				dateFormat.setLenient(false);
+				return dateFormat.parse(date);
+			} catch (ParseException e) {
+				// Try next format
+			}
+			// If this fails, an exception is thrown
+			SimpleDateFormat dateFormat = clone(DATE_FORMAT_HYPHEN);
+			dateFormat.setLenient(false);
+			return dateFormat.parse(date);
+		} else {
+			return null;
+		}
+	}
 
 	public static String formatShortDate(Date date) {
 		if (date != null) {

sormas-app/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>sormas-base</artifactId>
 		<groupId>de.symeda.sormas</groupId>
-		<version>0.16.0</version>
+		<version>0.17.0</version>
 		<relativePath>../sormas-base</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

sormas-backend/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>sormas-base</artifactId>
 		<groupId>de.symeda.sormas</groupId>
-		<version>0.16.0</version>
+		<version>0.17.0</version>
 		<relativePath>../sormas-base</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
@@ -50,6 +50,11 @@
 			<artifactId>client</artifactId>
 		</dependency>
 
+		<dependency>
+			<groupId>com.opencsv</groupId>
+			<artifactId>opencsv</artifactId>
+		</dependency>
+
 		<!-- Testing -->
 
 		<dependency>