Merge remote-tracking branch 'origin/development' into 3416_SurvNet-nosocomial-outbreak

Author: lgal

CONTRIBUTING.md

@@ -110,6 +110,18 @@ The GitHub project has been configured to **automatically** move issues that are
 The Development Team is responsible to keep the tickets up to date on this board and to assign the appropriate milestone in which the work is going to be released.
 
 
+### Managing dependencies
+
+For managing Java libraries as dependencies, they are managed by Maven and listed in *sormas-base/pom.xml*.  The purpose of a centralized management is to have an overview of the used libraries and adjust for new versions.
+
+1. **Payara modules**: Provided by Payara in *{payara-home}/glassfish/modules* and used in that version by other libs.
+2. **Domain libs**: Provided in Payara domain under *{payara-domain}/lib* to be usable by deployed artifacts (ear, war). They have to be listed in *sormas-base/dependencies/serverlibs.pom*. Usually for helper libraries that several artifacts need.
+3. **Compile dependencies**: Bundled in respective artifacts who need the dependency explicitly. Usually for dependencies singularly needed in one artifact.
+4. **Test libraries**: Libraries used in automated tests in one or more modules.
+
+Due to the separate build management tool Gradle for *sormas-app*, there exists a redundant listing of compile dependencies in *sormas-app/app/build.gradle*.
+
+
 ### Eclipse Troubleshooting
 
 Unfortunatley, when using eclipse together with the Payara Tools, there are a number of deployment problems that you might run into. Examples of these include:

SERVER_CUSTOMIZATION.md

@@ -88,3 +88,14 @@ The following features are currently configurable:
 * **Case Follow-Up** `CASE_FOLLOWUP`: Enables the contact follow-up module for cases as well to allow a more detailed daily documentation of symptoms.
 * **Line Listing** `LINE_LISTING`: Whether or not using line listing for case entry is enabled in the specified jurisdiction for the specified disease. Configurable from the UI, no database interaction needed.
 * **Documents** `DOCUMENTS`: Enables document storage.
+
+## Proxy Settings
+Some SORMAS integrations support proxy settings:
+* **Patient diary interface**
+* **Geocoding**
+* **SORMAS 2 SORMAS**
+
+The proxy can be configured through the following system properties which can be passed as JVM arguments to the server:
+* `org.jboss.resteasy.jaxrs.client.proxy.host`
+* `org.jboss.resteasy.jaxrs.client.proxy.port`
+* `org.jboss.resteasy.jaxrs.client.proxy.scheme`

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

@@ -138,7 +138,7 @@ public class ContactExportDto implements Serializable {
 
 	private ContactJurisdictionDto jurisdiction;
 
-	private final Long eventCount;
+	private Long eventCount;
 	private String latestEventId;
 	private String latestEventTitle;
 	private String externalID;
@@ -158,7 +158,7 @@ public ContactExportDto(long id, long personId, String uuid, String sourceCaseUu
 							String facility, String facilityUuid, String facilityDetails,
 							String phone, String phoneOwner, String emailAddress, OccupationType occupationType, String occupationDetails, ArmedForcesRelationType armedForcesRelationType,
 							String region, String district, String community,
-							long epiDataId, YesNoUnknown contactWithSourceCaseKnown, YesNoUnknown returningTraveler, long eventCount, String externalID,							
+							long epiDataId, YesNoUnknown contactWithSourceCaseKnown, YesNoUnknown returningTraveler, String externalID,							
 							String reportingUserUuid, String regionUuid, String districtUuid, String communityUuid,
 							String caseReportingUserUuid, String caseRegionUuid, String caseDistrictUuid, String caseCommunityUuid, String caseHealthFacilityUuid, String casePointOfEntryUuid
 	) {
@@ -221,7 +221,6 @@ public ContactExportDto(long id, long personId, String uuid, String sourceCaseUu
 		this.epiDataId = epiDataId;
 		this.contactWithSourceCaseKnown = contactWithSourceCaseKnown;
 		this.returningTraveler = returningTraveler;
-		this.eventCount = eventCount;
 		this.externalID = externalID;
 
 		CaseJurisdictionDto caseJurisdiction = caseReportingUserUuid != null
@@ -622,6 +621,10 @@ public long getEventCount() {
 		return this.eventCount;
 	}
 
+	public void setEventCount(Long eventCount) {
+		this.eventCount = eventCount;
+	}
+
 	public void setId(long id) {
 		this.id = id;
 	}

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

@@ -4,7 +4,6 @@
 
 import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.caze.CaseClassification;
-import de.symeda.sormas.api.location.LocationDto;
 import de.symeda.sormas.api.person.ApproximateAgeType;
 import de.symeda.sormas.api.person.Sex;
 import de.symeda.sormas.api.person.SymptomJournalStatus;
@@ -67,7 +66,7 @@ public ContactIndexDetailedDto(String uuid, String personFirstName, String perso
 								   String caseHealthFacilityUuid, String casePointOfEntryUuid, Date changeDate, String externalID,
 								   Sex sex, Integer approximateAge, ApproximateAgeType approximateAgeType,
 								   String city, String street, String houseNumber, String additionalInformation, String postalCode, String phone,
-								   String reportingUserFirstName, String reportingUserLastName, int visitCount, long eventCount
+								   String reportingUserFirstName, String reportingUserLastName, int visitCount
 	) {
 	//@formatter:on
 
@@ -87,7 +86,6 @@ public ContactIndexDetailedDto(String uuid, String personFirstName, String perso
 		this.postalCode = postalCode;
 		this.phone = phone;
 		this.reportingUser = new UserReferenceDto(reportingUserUuid, reportingUserFirstName, reportingUserLastName, null);
-		this.eventCount = eventCount;
 	}
 
 	public Sex getSex() {
@@ -134,6 +132,10 @@ public Long getEventCount() {
 		return eventCount;
 	}
 
+	public void setEventCount(Long eventCount) {
+		this.eventCount = eventCount;
+	}
+
 	public String getLatestEventId() {
 		return latestEventId;
 	}

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

@@ -151,5 +151,9 @@ public String getFirstName() {
 		public String getLastName() {
 			return lastName;
 		}
+
+		public String toString() {
+			return firstName + " " + lastName;
+		}
 	}
 }

sormas-api/src/main/java/de/symeda/sormas/api/epidata/EpiDataFacade.java

@@ -17,13 +17,9 @@
  *******************************************************************************/
 package de.symeda.sormas.api.epidata;
 
-import java.util.List;
-import java.util.Map;
-
 import javax.ejb.Remote;
 
 @Remote
 public interface EpiDataFacade {
 
-	Map<String, String> getExposureSourceCaseNames(List<String> exposureUuids);
 }

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

@@ -482,6 +482,7 @@ public interface Strings {
 	String infoEpiDataSourceCaseContacts = "infoEpiDataSourceCaseContacts";
 	String infoExportNoFilters = "infoExportNoFilters";
 	String infoExposureInvestigation = "infoExposureInvestigation";
+	String infoExposureInvestigationContacts = "infoExposureInvestigationContacts";
 	String infoExposuresRiskAreaHint = "infoExposuresRiskAreaHint";
 	String infoHowToMergeCases = "infoHowToMergeCases";
 	String infoImportAllCountries = "infoImportAllCountries";

sormas-api/src/main/resources/strings.properties

@@ -586,6 +586,7 @@ populationDataByRegion = Population data by Region
 populationDataByCommunity = No population data available for communities
 populationDataByDistrict = Population data by District
 infoExposureInvestigation = <i>Please document ALL relevant direct exposures (e.g. attended gatherings, travels, animal contacts, etc.) during the incubation period:</i>
+infoExposureInvestigationContacts = <i>Please document information about the exposure that led to this contact:</i>
 infoEpiDataFieldsHint = <i>Please indicate if any of the following is relevant for the patient during the incubation period:</i>
 infoEpiDataSourceCaseContacts = <i>Please indicate ALL contacts with potential source cases during the incubation period:</i>
 infoNoSourceCase = No source case

sormas-api/src/main/resources/strings_de-CH.properties

@@ -577,6 +577,7 @@ infoCreateNewSampleDiscardsChangesEventParticipant = Die Erstellung einer neuen
 infoUsageOfEditableCampaignGrids = Sie können die Kampagnendaten und Dashboard-Definitionen bearbeiten, indem Sie innerhalb einer der Zellen im Raster klicken, und Sie können die Dashboard-Elemente durch Ziehen und Ablegen der Gitterzeilen neu ordnen
 infoSaveOfTask = Speichern dieser Aufgabe wird alle ungespeicherten Änderungen zu diesem Fall verwerfen.
 infoExposureInvestigation = <i>Bitte dokumentieren Sie ALLE relevanten direkten Expositionen (z.B. besuchte Versammlungen, Reisen, Tierkontakte usw.) während der Inkubationszeit\:</i>
+infoExposureInvestigationContacts = <i>Bitte dokumentieren Sie die Exposition, die zu diesem Kontakt geführt hat:</i>
 infoEpiDataFieldsHint = <i>Bitte geben Sie an, ob einer der folgenden Punkte für den/die Patient*in während des Inkubationszeitraums relevant ist.</i>
 infoEpiDataSourceCaseContacts = <i>Bitte geben Sie ALLE Kontakte mit möglichen Indexfällen während des Inkubationszeitraums an\:</i>
 infoNoSourceCase = Kein Indexfall

sormas-api/src/main/resources/strings_de-DE.properties

@@ -577,6 +577,7 @@ infoCreateNewSampleDiscardsChangesEventParticipant = Die Erstellung neuer Proben
 infoUsageOfEditableCampaignGrids = Sie können die Kampagnendaten und Dashboard-Definitionen bearbeiten, indem Sie innerhalb einer der Zellen im Raster klicken, und Sie können die Dashboard-Elemente durch Ziehen und Ablegen der Gitterzeilen neu ordnen
 infoSaveOfTask = Speichern dieser Aufgabe wird alle ungespeicherten Änderungen zu diesem Fall verwerfen.
 infoExposureInvestigation = <i>Bitte dokumentieren Sie ALLE relevanten direkten Expositionen (z.B. besuchte Versammlungen, Reisen, Tierkontakte usw.) während der Inkubationszeit\:</i>
+infoExposureInvestigationContacts = <i>Bitte dokumentieren Sie die Exposition, die zu diesem Kontakt geführt hat:</i>
 infoEpiDataFieldsHint = <i>Bitte geben Sie an, ob einer der folgenden Punkte für den/die Patient*in während des Inkubationszeitraums relevant ist.</i>
 infoEpiDataSourceCaseContacts = <i>Bitte geben Sie ALLE Kontakte mit möglichen Indexfällen während des Inkubationszeitraums an\:</i>
 infoNoSourceCase = Kein Indexfall