Merge remote-tracking branch 'origin/development' into 3610_BAG-export-rest

# Conflicts:
#	sormas-api/src/main/java/de/symeda/sormas/api/user/UserRole.java

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:

DEVELOPMENT_ENVIRONMENT.md

@@ -51,7 +51,7 @@
 - Clone the SORMAS-Project repository and open the project in IntelliJ
 	- make sure the under "File -> Project Structure -> Modules" all the modules (except the android app - this should not be added) are recognized, if not add the modules with +
 - Make sure under "File -> Settings -> Plugins" Glassfish & Ant integrations are enabled (look into the "Installed" tab)
-- Install the Vaadin Designer plugin
+- Install the Vaadin plugin (not the Vaadin Designer plugin!)
 - Make a copy of "build.properties.example" contained in "sormas-base", rename it to "build.properties" and set "glassfish.domain.root" to the location of the sormas domain located in the "glassfish/domains" folder inside your payara installation
 - Run "Maven install" on the sormas-base project
 - Add a Payara server to IntelliJ:

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/caze/CaseDataDto.java

@@ -127,6 +127,8 @@ public class CaseDataDto extends PseudonymizableDto {
 	public static final String ADDITIONAL_DETAILS = "additionalDetails";
 	public static final String EXTERNAL_ID = "externalID";
 	public static final String SHARED_TO_COUNTRY = "sharedToCountry";
+	public static final String NOSOCOMIAL_OUTBREAK = "nosocomialOutbreak";
+	public static final String INFECTION_SETTING = "infectionSetting";
 	public static final String QUARANTINE = "quarantine";
 	public static final String QUARANTINE_TYPE_DETAILS = "quarantineTypeDetails";
 	public static final String QUARANTINE_FROM = "quarantineFrom";
@@ -367,6 +369,10 @@ public class CaseDataDto extends PseudonymizableDto {
 		COUNTRY_CODE_SWITZERLAND })
 	private String externalID;
 	private boolean sharedToCountry;
+	@HideForCountriesExcept
+	private boolean nosocomialOutbreak;
+	@HideForCountriesExcept
+	private InfectionSetting infectionSetting;
 	private QuarantineType quarantine;
 	@SensitiveData
 	private String quarantineTypeDetails;
@@ -1008,6 +1014,22 @@ public void setSharedToCountry(boolean sharedToCountry) {
 		this.sharedToCountry = sharedToCountry;
 	}
 
+	public boolean isNosocomialOutbreak() {
+		return nosocomialOutbreak;
+	}
+
+	public void setNosocomialOutbreak(boolean nosocomialOutbreak) {
+		this.nosocomialOutbreak = nosocomialOutbreak;
+	}
+
+	public InfectionSetting getInfectionSetting() {
+		return infectionSetting;
+	}
+
+	public void setInfectionSetting(InfectionSetting infectionSetting) {
+		this.infectionSetting = infectionSetting;
+	}
+
 	public QuarantineType getQuarantine() {
 		return quarantine;
 	}

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

@@ -208,6 +208,9 @@ public class CaseExportDto implements Serializable {
 	private EmbeddedSampleExportDto sample3 = new EmbeddedSampleExportDto();
 	private List<EmbeddedSampleExportDto> otherSamples = new ArrayList<>();
 
+	private Boolean nosocomialOutbreak;
+	private InfectionSetting infectionSetting;
+
 	private QuarantineType quarantine;
 	@SensitiveData
 	private String quarantineTypeDetails;
@@ -252,6 +255,7 @@ public CaseExportDto(long id, long personId, long personAddressId, long epiDataI
 						 String pointOfEntryUuid, String pointOfEntryDetails, CaseClassification caseClassification,
 						 InvestigationStatus investigationStatus, CaseOutcome outcome,
 						 FollowUpStatus followUpStatus, Date followUpUntil,
+						 Boolean nosocomialOutbreak, InfectionSetting infectionSetting,
 						 // Quarantine
 						 QuarantineType quarantine, String quarantineTypeDetails, Date quarantineFrom, Date quarantineTo,
 						 boolean quarantineOrderedVerbally, boolean quarantineOrderedOfficialDocument, Date quarantineOrderedVerballyDate,
@@ -296,6 +300,8 @@ public CaseExportDto(long id, long personId, long personAddressId, long epiDataI
 		this.caseClassification = caseClassification;
 		this.investigationStatus = investigationStatus;
 		this.outcome = outcome;
+		this.nosocomialOutbreak = nosocomialOutbreak;
+		this.infectionSetting = infectionSetting;
 		this.quarantine = quarantine;
 		this.quarantineTypeDetails = quarantineTypeDetails;
 		this.quarantineFrom = quarantineFrom;
@@ -628,6 +634,28 @@ public CaseOutcome getOutcome() {
 	}
 
 	@Order(33)
+	@ExportTarget(caseExportTypes = {
+		CaseExportType.CASE_SURVEILLANCE,
+		CaseExportType.CASE_MANAGEMENT })
+	@ExportProperty(value = CaseDataDto.NOSOCOMIAL_OUTBREAK, combined = true)
+	@ExportGroup(ExportGroupType.ADDITIONAL)
+	@HideForCountriesExcept
+	public Boolean getNosocomialOutbreak() {
+		return nosocomialOutbreak;
+	}
+
+	@Order(34)
+	@ExportTarget(caseExportTypes = {
+		CaseExportType.CASE_SURVEILLANCE,
+		CaseExportType.CASE_MANAGEMENT })
+	@ExportProperty(value = CaseDataDto.INFECTION_SETTING, combined = true)
+	@ExportGroup(ExportGroupType.ADDITIONAL)
+	@HideForCountriesExcept
+	public InfectionSetting getInfectionSetting() {
+		return infectionSetting;
+	}
+
+	@Order(35)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -637,7 +665,7 @@ public QuarantineType getQuarantine() {
 		return quarantine;
 	}
 
-	@Order(34)
+	@Order(36)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -647,7 +675,7 @@ public String getQuarantineTypeDetails() {
 		return quarantineTypeDetails;
 	}
 
-	@Order(35)
+	@Order(37)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -657,7 +685,7 @@ public Date getQuarantineFrom() {
 		return quarantineFrom;
 	}
 
-	@Order(36)
+	@Order(38)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -667,7 +695,7 @@ public Date getQuarantineTo() {
 		return quarantineTo;
 	}
 
-	@Order(37)
+	@Order(39)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -680,7 +708,7 @@ public boolean isQuarantineOrderedVerbally() {
 		return quarantineOrderedVerbally;
 	}
 
-	@Order(38)
+	@Order(40)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -693,7 +721,7 @@ public boolean isQuarantineOrderedOfficialDocument() {
 		return quarantineOrderedOfficialDocument;
 	}
 
-	@Order(39)
+	@Order(41)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -706,7 +734,7 @@ public Date getQuarantineOrderedVerballyDate() {
 		return quarantineOrderedVerballyDate;
 	}
 
-	@Order(40)
+	@Order(42)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -719,7 +747,7 @@ public Date getQuarantineOrderedOfficialDocumentDate() {
 		return quarantineOrderedOfficialDocumentDate;
 	}
 
-	@Order(41)
+	@Order(43)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -732,7 +760,7 @@ public boolean isQuarantineOfficialOrderSent() {
 		return quarantineOfficialOrderSent;
 	}
 
-	@Order(42)
+	@Order(44)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -745,7 +773,7 @@ public Date getQuarantineOfficialOrderSentDate() {
 		return quarantineOfficialOrderSentDate;
 	}
 
-	@Order(43)
+	@Order(45)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -755,7 +783,7 @@ public boolean isQuarantineExtended() {
 		return quarantineExtended;
 	}
 
-	@Order(44)
+	@Order(46)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -765,7 +793,7 @@ public boolean isQuarantineReduced() {
 		return quarantineReduced;
 	}
 
-	@Order(45)
+	@Order(47)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE })
 	@ExportProperty(MAX_SOURCE_CASE_CLASSIFICATION)
@@ -774,7 +802,7 @@ public CaseClassification getMaxSourceCaseClassification() {
 		return maxSourceCaseClassification;
 	}
 
-	@Order(46)
+	@Order(48)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE })
 	@ExportProperty(ASSOCIATED_WITH_OUTBREAK)
@@ -787,7 +815,7 @@ public void setMaxSourceCaseClassification(CaseClassification maxSourceCaseClass
 		this.maxSourceCaseClassification = maxSourceCaseClassification;
 	}
 
-	@Order(47)
+	@Order(49)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -797,7 +825,7 @@ public YesNoUnknown getAdmittedToHealthFacility() {
 		return admittedToHealthFacility;
 	}
 
-	@Order(48)
+	@Order(50)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -807,7 +835,7 @@ public Date getAdmissionDate() {
 		return admissionDate;
 	}
 
-	@Order(49)
+	@Order(51)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -821,7 +849,7 @@ public void setDischargeDate(Date dischargeDate) {
 		this.dischargeDate = dischargeDate;
 	}
 
-	@Order(50)
+	@Order(52)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -835,7 +863,7 @@ public void setLeftAgainstAdvice(YesNoUnknown leftAgainstAdvice) {
 		this.leftAgainstAdvice = leftAgainstAdvice;
 	}
 
-	@Order(51)
+	@Order(53)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -845,7 +873,7 @@ public PresentCondition getPresentCondition() {
 		return presentCondition;
 	}
 
-	@Order(52)
+	@Order(54)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE })
 	@ExportProperty(PersonDto.DEATH_DATE)
@@ -854,7 +882,7 @@ public Date getDeathDate() {
 		return deathDate;
 	}
 
-	@Order(53)
+	@Order(55)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE })
 	@ExportProperty(BURIAL_INFO)

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

@@ -115,6 +115,8 @@ Map<PresentCondition, Long> getCaseCountPerPersonCondition(
 
 	Date getOldestCaseReportDate();
 
+	Date getOldestCaseOutcomeDate();
+
 	boolean isArchived(String caseUuid);
 
 	boolean isDeleted(String caseUuid);

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

@@ -0,0 +1,60 @@
+/*
+ * SORMAS® - Surveillance Outbreak Response Management & Analysis System
+ * Copyright © 2016-2020 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.caze;
+
+import de.symeda.sormas.api.i18n.I18nProperties;
+
+public enum InfectionSetting {
+
+	UNKNOWN(null),
+	AMBULATORY(null),
+	MEDICAL_PRACTICE(AMBULATORY),
+	OPERATIVE_1200(AMBULATORY),
+	HOSPITAL_1300(AMBULATORY),
+	OTHER_OUTPATIENT_FACILITY(AMBULATORY),
+	STATIONARY(null),
+	HOSPITAL_2100(STATIONARY),
+	NORMAL_WARD(HOSPITAL_2100),
+	OPERATIVE_2111(NORMAL_WARD),
+	NOT_OPERATIVE(NORMAL_WARD),
+	HEMATOLOGICAL_ONCOLOGY(NORMAL_WARD),
+	CHILDREN_WARD(HOSPITAL_2100),
+	NEONATOLOGY(HOSPITAL_2100),
+	INTENSIVE_CARE_UNIT(HOSPITAL_2100),
+	OTHER_STATION(HOSPITAL_2100),
+	NURSING_HOME(STATIONARY),
+	REHAB_FACILITY(STATIONARY),
+	OTHER_STATIONARY_FACILITY(STATIONARY);
+
+	private final InfectionSetting parent;
+
+	InfectionSetting(InfectionSetting parent) {
+		this.parent = parent;
+	}
+
+	public InfectionSetting getParent() {
+		return this.parent;
+	}
+
+	public String toString() {
+		String caption = I18nProperties.getEnumCaption(this);
+		if (this.parent != null) {
+			caption = this.parent.toString() + " / " + caption;
+		}
+
+		return caption;
+	}
+}