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Merge remote-tracking branch 'origin/development' into 3409_prohibition-to-work-fields
# Conflicts: # sormas-api/src/main/resources/captions.properties # sormas-api/src/main/resources/captions_de-DE.properties # sormas-app/app/src/main/java/de/symeda/sormas/app/backend/caze/Case.java # sormas-app/app/src/main/java/de/symeda/sormas/app/backend/common/DatabaseHelper.java # sormas-app/app/src/main/java/de/symeda/sormas/app/caze/edit/CaseEditFragment.java # sormas-app/app/src/main/res/layout/fragment_case_read_layout.xml # sormas-backend/src/main/java/de/symeda/sormas/backend/caze/Case.java # sormas-backend/src/main/java/de/symeda/sormas/backend/caze/CaseFacadeEjb.java # sormas-backend/src/main/resources/sql/sormas_schema.sql
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‎CONTRIBUTING.md‎

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@@ -110,6 +110,18 @@ The GitHub project has been configured to **automatically** move issues that are
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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.
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112112

113+
### Managing dependencies
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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.
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1. **Payara modules**: Provided by Payara in *{payara-home}/glassfish/modules* and used in that version by other libs.
118+
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.
119+
3. **Compile dependencies**: Bundled in respective artifacts who need the dependency explicitly. Usually for dependencies singularly needed in one artifact.
120+
4. **Test libraries**: Libraries used in automated tests in one or more modules.
121+
122+
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*.
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### Eclipse Troubleshooting
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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

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@@ -88,3 +88,14 @@ The following features are currently configurable:
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* **Case Follow-Up** `CASE_FOLLOWUP`: Enables the contact follow-up module for cases as well to allow a more detailed daily documentation of symptoms.
8989
* **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.
9090
* **Documents** `DOCUMENTS`: Enables document storage.
91+
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## Proxy Settings
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Some SORMAS integrations support proxy settings:
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* **Patient diary interface**
95+
* **Geocoding**
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* **SORMAS 2 SORMAS**
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The proxy can be configured through the following system properties which can be passed as JVM arguments to the server:
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* `org.jboss.resteasy.jaxrs.client.proxy.host`
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* `org.jboss.resteasy.jaxrs.client.proxy.port`
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* `org.jboss.resteasy.jaxrs.client.proxy.scheme`

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

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@@ -127,6 +127,8 @@ public class CaseDataDto extends PseudonymizableDto {
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public static final String ADDITIONAL_DETAILS = "additionalDetails";
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public static final String EXTERNAL_ID = "externalID";
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public static final String SHARED_TO_COUNTRY = "sharedToCountry";
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public static final String NOSOCOMIAL_OUTBREAK = "nosocomialOutbreak";
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public static final String INFECTION_SETTING = "infectionSetting";
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public static final String QUARANTINE = "quarantine";
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public static final String QUARANTINE_TYPE_DETAILS = "quarantineTypeDetails";
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public static final String QUARANTINE_FROM = "quarantineFrom";
@@ -371,6 +373,10 @@ public class CaseDataDto extends PseudonymizableDto {
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COUNTRY_CODE_SWITZERLAND })
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private String externalID;
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private boolean sharedToCountry;
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@HideForCountriesExcept
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private boolean nosocomialOutbreak;
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@HideForCountriesExcept
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private InfectionSetting infectionSetting;
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private QuarantineType quarantine;
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@SensitiveData
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private String quarantineTypeDetails;
@@ -1019,6 +1025,22 @@ public void setSharedToCountry(boolean sharedToCountry) {
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this.sharedToCountry = sharedToCountry;
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}
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public boolean isNosocomialOutbreak() {
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return nosocomialOutbreak;
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}
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public void setNosocomialOutbreak(boolean nosocomialOutbreak) {
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this.nosocomialOutbreak = nosocomialOutbreak;
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}
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public InfectionSetting getInfectionSetting() {
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return infectionSetting;
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}
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public void setInfectionSetting(InfectionSetting infectionSetting) {
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this.infectionSetting = infectionSetting;
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}
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public QuarantineType getQuarantine() {
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return quarantine;
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}

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

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@@ -206,6 +206,9 @@ public class CaseExportDto implements Serializable {
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private EmbeddedSampleExportDto sample3 = new EmbeddedSampleExportDto();
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private List<EmbeddedSampleExportDto> otherSamples = new ArrayList<>();
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209+
private Boolean nosocomialOutbreak;
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private InfectionSetting infectionSetting;
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private QuarantineType quarantine;
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@SensitiveData
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private String quarantineTypeDetails;
@@ -250,6 +253,7 @@ public CaseExportDto(long id, long personId, long personAddressId, long epiDataI
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String pointOfEntryUuid, String pointOfEntryDetails, CaseClassification caseClassification,
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InvestigationStatus investigationStatus, CaseOutcome outcome,
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FollowUpStatus followUpStatus, Date followUpUntil,
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Boolean nosocomialOutbreak, InfectionSetting infectionSetting,
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// Quarantine
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QuarantineType quarantine, String quarantineTypeDetails, Date quarantineFrom, Date quarantineTo,
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boolean quarantineOrderedVerbally, boolean quarantineOrderedOfficialDocument, Date quarantineOrderedVerballyDate,
@@ -293,6 +297,8 @@ public CaseExportDto(long id, long personId, long personAddressId, long epiDataI
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this.caseClassification = caseClassification;
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this.investigationStatus = investigationStatus;
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this.outcome = outcome;
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this.nosocomialOutbreak = nosocomialOutbreak;
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this.infectionSetting = infectionSetting;
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this.quarantine = quarantine;
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this.quarantineTypeDetails = quarantineTypeDetails;
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this.quarantineFrom = quarantineFrom;
@@ -624,6 +630,28 @@ public CaseOutcome getOutcome() {
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}
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@Order(33)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
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@ExportProperty(value = CaseDataDto.NOSOCOMIAL_OUTBREAK, combined = true)
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@ExportGroup(ExportGroupType.ADDITIONAL)
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@HideForCountriesExcept
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public Boolean getNosocomialOutbreak() {
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return nosocomialOutbreak;
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}
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@Order(34)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
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@ExportProperty(value = CaseDataDto.INFECTION_SETTING, combined = true)
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@ExportGroup(ExportGroupType.ADDITIONAL)
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@HideForCountriesExcept
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public InfectionSetting getInfectionSetting() {
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return infectionSetting;
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}
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@Order(35)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
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return quarantine;
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}
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@Order(34)
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@Order(36)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
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return quarantineTypeDetails;
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}
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@Order(35)
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@Order(37)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
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return quarantineFrom;
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}
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656-
@Order(36)
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@Order(38)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
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return quarantineTo;
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}
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666-
@Order(37)
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@Order(39)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
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return quarantineOrderedVerbally;
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}
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@Order(38)
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@Order(40)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
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return quarantineOrderedOfficialDocument;
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}
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692-
@Order(39)
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@Order(41)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
@@ -702,7 +730,7 @@ public Date getQuarantineOrderedVerballyDate() {
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return quarantineOrderedVerballyDate;
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}
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@Order(40)
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@Order(42)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
@@ -715,7 +743,7 @@ public Date getQuarantineOrderedOfficialDocumentDate() {
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return quarantineOrderedOfficialDocumentDate;
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}
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718-
@Order(41)
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@Order(43)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
@@ -728,7 +756,7 @@ public boolean isQuarantineOfficialOrderSent() {
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return quarantineOfficialOrderSent;
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}
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731-
@Order(42)
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@Order(44)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
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return quarantineOfficialOrderSentDate;
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}
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744-
@Order(43)
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@Order(45)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
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return quarantineExtended;
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}
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754-
@Order(44)
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@Order(46)
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@ExportTarget(caseExportTypes = {
756784
CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
@@ -761,7 +789,7 @@ public boolean isQuarantineReduced() {
761789
return quarantineReduced;
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}
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764-
@Order(45)
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@Order(47)
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@ExportTarget(caseExportTypes = {
766794
CaseExportType.CASE_SURVEILLANCE })
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@ExportProperty(MAX_SOURCE_CASE_CLASSIFICATION)
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770798
return maxSourceCaseClassification;
771799
}
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773-
@Order(46)
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@Order(48)
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@ExportTarget(caseExportTypes = {
775803
CaseExportType.CASE_SURVEILLANCE })
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@ExportProperty(ASSOCIATED_WITH_OUTBREAK)
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783811
this.maxSourceCaseClassification = maxSourceCaseClassification;
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}
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@Order(47)
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@Order(49)
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@ExportTarget(caseExportTypes = {
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CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
@@ -793,7 +821,7 @@ public YesNoUnknown getAdmittedToHealthFacility() {
793821
return admittedToHealthFacility;
794822
}
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796-
@Order(48)
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@Order(50)
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@ExportTarget(caseExportTypes = {
798826
CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
@@ -803,7 +831,7 @@ public Date getAdmissionDate() {
803831
return admissionDate;
804832
}
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806-
@Order(49)
834+
@Order(51)
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@ExportTarget(caseExportTypes = {
808836
CaseExportType.CASE_SURVEILLANCE,
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CaseExportType.CASE_MANAGEMENT })
@@ -817,7 +845,7 @@ public void setDischargeDate(Date dischargeDate) {
817845
this.dischargeDate = dischargeDate;
818846
}
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820-
@Order(50)
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@Order(52)
821849
@ExportTarget(caseExportTypes = {
822850
CaseExportType.CASE_SURVEILLANCE,
823851
CaseExportType.CASE_MANAGEMENT })
@@ -831,7 +859,7 @@ public void setLeftAgainstAdvice(YesNoUnknown leftAgainstAdvice) {
831859
this.leftAgainstAdvice = leftAgainstAdvice;
832860
}
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834-
@Order(51)
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@Order(53)
835863
@ExportTarget(caseExportTypes = {
836864
CaseExportType.CASE_SURVEILLANCE,
837865
CaseExportType.CASE_MANAGEMENT })
@@ -841,7 +869,7 @@ public PresentCondition getPresentCondition() {
841869
return presentCondition;
842870
}
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844-
@Order(52)
872+
@Order(54)
845873
@ExportTarget(caseExportTypes = {
846874
CaseExportType.CASE_SURVEILLANCE })
847875
@ExportProperty(PersonDto.DEATH_DATE)
@@ -850,7 +878,7 @@ public Date getDeathDate() {
850878
return deathDate;
851879
}
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853-
@Order(53)
881+
@Order(55)
854882
@ExportTarget(caseExportTypes = {
855883
CaseExportType.CASE_SURVEILLANCE })
856884
@ExportProperty(BURIAL_INFO)

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

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@@ -115,6 +115,8 @@ Map<PresentCondition, Long> getCaseCountPerPersonCondition(
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Date getOldestCaseReportDate();
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118+
Date getOldestCaseOutcomeDate();
119+
118120
boolean isArchived(String caseUuid);
119121

120122
boolean isDeleted(String caseUuid);

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

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1+
/*
2+
* SORMAS® - Surveillance Outbreak Response Management & Analysis System
3+
* Copyright © 2016-2020 Helmholtz-Zentrum für Infektionsforschung GmbH (HZI)
4+
* This program is free software: you can redistribute it and/or modify
5+
* it under the terms of the GNU General Public License as published by
6+
* the Free Software Foundation, either version 3 of the License, or
7+
* (at your option) any later version.
8+
* This program is distributed in the hope that it will be useful,
9+
* but WITHOUT ANY WARRANTY; without even the implied warranty of
10+
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11+
* GNU General Public License for more details.
12+
* You should have received a copy of the GNU General Public License
13+
* along with this program. If not, see <https://www.gnu.org/licenses/>.
14+
*/
15+
16+
package de.symeda.sormas.api.caze;
17+
18+
import de.symeda.sormas.api.i18n.I18nProperties;
19+
20+
public enum InfectionSetting {
21+
22+
UNKNOWN(null),
23+
AMBULATORY(null),
24+
MEDICAL_PRACTICE(AMBULATORY),
25+
OPERATIVE_1200(AMBULATORY),
26+
HOSPITAL_1300(AMBULATORY),
27+
OTHER_OUTPATIENT_FACILITY(AMBULATORY),
28+
STATIONARY(null),
29+
HOSPITAL_2100(STATIONARY),
30+
NORMAL_WARD(HOSPITAL_2100),
31+
OPERATIVE_2111(NORMAL_WARD),
32+
NOT_OPERATIVE(NORMAL_WARD),
33+
HEMATOLOGICAL_ONCOLOGY(NORMAL_WARD),
34+
CHILDREN_WARD(HOSPITAL_2100),
35+
NEONATOLOGY(HOSPITAL_2100),
36+
INTENSIVE_CARE_UNIT(HOSPITAL_2100),
37+
OTHER_STATION(HOSPITAL_2100),
38+
NURSING_HOME(STATIONARY),
39+
REHAB_FACILITY(STATIONARY),
40+
OTHER_STATIONARY_FACILITY(STATIONARY);
41+
42+
private final InfectionSetting parent;
43+
44+
InfectionSetting(InfectionSetting parent) {
45+
this.parent = parent;
46+
}
47+
48+
public InfectionSetting getParent() {
49+
return this.parent;
50+
}
51+
52+
public String toString() {
53+
String caption = I18nProperties.getEnumCaption(this);
54+
if (this.parent != null) {
55+
caption = this.parent.toString() + " / " + caption;
56+
}
57+
58+
return caption;
59+
}
60+
}

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