Code refactoring

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

@@ -70,4 +70,13 @@ public static String toString(Disease disease, String diseaseDetails, DiseaseVar
 	public static String variantInBrackets(DiseaseVariant diseaseVariant) {
 		return diseaseVariant == null ? StringUtils.EMPTY : String.format("(%s)", diseaseVariant.getCaption());
 	}
+
+	/**
+	 * Checks if the case is an invasive bacterial disease (meningococcal or pneumococcal)
+	 * @return boolean
+	 */
+	public static boolean checkDiseaseIsInvasiveBacterialDiseases(Disease disease){
+		return disease != null && (disease == Disease.INVASIVE_MENINGOCOCCAL_INFECTION ||
+				disease == Disease.INVASIVE_PNEUMOCOCCAL_INFECTION);
+	}
 }

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

@@ -1840,14 +1840,7 @@ public void setOtherDiagnosticCriteria(String otherDiagnosticCriteria) {
 		this.otherDiagnosticCriteria = otherDiagnosticCriteria;
 	}
 
-	/**
-	 * Checks if the case is an invasive bacterial disease (meningococcal or pneumococcal)
-	 * @return boolean
-	 */
-	public boolean checkDiseaseIsInvasiveBacterialDiseases(){
-		return disease != null && (disease == Disease.INVASIVE_MENINGOCOCCAL_INFECTION ||
-				disease == Disease.INVASIVE_PNEUMOCOCCAL_INFECTION);
-	}
+
 
 	@JsonIgnore
 	public String i18nPrefix() {

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

@@ -34,6 +34,7 @@
 import de.symeda.sormas.api.infrastructure.region.RegionReferenceDto;
 import de.symeda.sormas.api.person.PersonReferenceDto;
 import de.symeda.sormas.api.person.SymptomJournalStatus;
+import de.symeda.sormas.api.therapy.Drug;
 import de.symeda.sormas.api.user.UserReferenceDto;
 import de.symeda.sormas.api.user.UserRoleReferenceDto;
 import de.symeda.sormas.api.utils.DateFilterOption;
@@ -153,7 +154,7 @@ public class ContactCriteria extends BaseCriteria implements Serializable {
 	private String caseReferenceNumber;
 	private Boolean withCase;
 	private Boolean prophylaxisPrescribed;
-	private PrescribedDrug prescribedDrug;
+	private Drug prescribedDrug;
 	private String prescribedDrugText;
 
 	public UserRoleReferenceDto getReportingUserRole() {
@@ -814,19 +815,19 @@ public void setProphylaxisPrescribed(Boolean prophylaxisPrescribed) {
 		this.prophylaxisPrescribed = prophylaxisPrescribed;
 	}
 
-	public PrescribedDrug getPrescribedDrug() {
-		return prescribedDrug;
-	}
-
-	public void setPrescribedDrug(PrescribedDrug prescribedDrug) {
-		this.prescribedDrug = prescribedDrug;
-	}
-
 	public String getPrescribedDrugText() {
 		return prescribedDrugText;
 	}
 
 	public void setPrescribedDrugText(String prescribedDrugText) {
 		this.prescribedDrugText = prescribedDrugText;
 	}
+
+	public Drug getPrescribedDrug() {
+		return prescribedDrug;
+	}
+
+	public void setPrescribedDrug(Drug prescribedDrug) {
+		this.prescribedDrug = prescribedDrug;
+	}
 }

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

@@ -47,6 +47,7 @@
 import de.symeda.sormas.api.sormastosormas.S2SIgnoreProperty;
 import de.symeda.sormas.api.sormastosormas.SormasToSormasConfig;
 import de.symeda.sormas.api.sormastosormas.SormasToSormasShareableDto;
+import de.symeda.sormas.api.therapy.Drug;
 import de.symeda.sormas.api.user.UserReferenceDto;
 import de.symeda.sormas.api.utils.DataHelper;
 import de.symeda.sormas.api.utils.DependingOnFeatureType;
@@ -379,7 +380,7 @@ public class ContactDto extends SormasToSormasShareableDto implements IsContact
 	@HideForCountriesExcept(countries = {COUNTRY_CODE_LUXEMBOURG})
 	@SensitiveData
 	@Diseases(Disease.INVASIVE_MENINGOCOCCAL_INFECTION)
-	private PrescribedDrug prescribedDrug;
+	private Drug prescribedDrug;
 	@HideForCountriesExcept(countries = {COUNTRY_CODE_LUXEMBOURG})
 	@SensitiveData
 	@Diseases(Disease.INVASIVE_MENINGOCOCCAL_INFECTION)
@@ -1092,11 +1093,11 @@ public void setProphylaxisPrescribed(Boolean prophylaxisPrescribed) {
 		this.prophylaxisPrescribed = prophylaxisPrescribed;
 	}
 
-	public PrescribedDrug getPrescribedDrug() {
+	public Drug getPrescribedDrug() {
 		return prescribedDrug;
 	}
 
-	public void setPrescribedDrug(PrescribedDrug prescribedDrug) {
+	public void setPrescribedDrug(Drug prescribedDrug) {
 		this.prescribedDrug = prescribedDrug;
 	}
 

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

@@ -9,6 +9,7 @@
 import de.symeda.sormas.api.person.ApproximateAgeType;
 import de.symeda.sormas.api.person.Sex;
 import de.symeda.sormas.api.person.SymptomJournalStatus;
+import de.symeda.sormas.api.therapy.Drug;
 import de.symeda.sormas.api.user.UserReferenceDto;
 import de.symeda.sormas.api.utils.PersonalData;
 import de.symeda.sormas.api.utils.SensitiveData;
@@ -74,7 +75,7 @@ public ContactIndexDetailedDto(String uuid, String personUuid, String personFirs
 								   Sex sex, Integer approximateAge, ApproximateAgeType approximateAgeType,
 								   String city, String street, String houseNumber, String additionalInformation, String postalCode, String phone,
 								   String reportingUserFirstName, String reportingUserLastName, ContactRelation relationToCase, int visitCount,
-								   Boolean prophylaxisPrescribed, PrescribedDrug prescribedDrug, String prescribedDrugText
+								   Boolean prophylaxisPrescribed, Drug prescribedDrug, String prescribedDrugText
 	) {
 	//@formatter:on
 

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

@@ -26,6 +26,7 @@
 import de.symeda.sormas.api.caze.VaccinationStatus;
 import de.symeda.sormas.api.common.DeletionReason;
 import de.symeda.sormas.api.person.SymptomJournalStatus;
+import de.symeda.sormas.api.therapy.Drug;
 import de.symeda.sormas.api.utils.PersonalData;
 import de.symeda.sormas.api.utils.pseudonymization.PseudonymizableIndexDto;
 import de.symeda.sormas.api.uuid.HasUuid;
@@ -102,7 +103,7 @@ public class ContactIndexDto extends PseudonymizableIndexDto implements IsContac
 	private DeletionReason deletionReason;
 	private String otherDeletionReason;
 	private Boolean prophylaxisPrescribed;
-	private PrescribedDrug prescribedDrug;
+	private Drug prescribedDrug;
 	private String prescribedDrugText;
 
 	private ContactJurisdictionFlagsDto contactJurisdictionFlagsDto;
@@ -117,7 +118,7 @@ public ContactIndexDto(String uuid, String personUuid, String personFirstName, S
 						   CaseClassification caseClassification, String caseRegionName, String caseDistrictName,
 						   Date changeDate, // XXX: unused, only here for TypedQuery mapping
 						   String externalID, String externalToken, String internalToken,String caseReferenceNumber, DeletionReason deletionReason, String otherDeletionReason, boolean isInJurisdiction, boolean isCaseInJurisdiction,
-						   int visitCount, Boolean prophylaxisPrescribed, PrescribedDrug prescribedDrug, String prescribedDrugText
+						   int visitCount, Boolean prophylaxisPrescribed, Drug prescribedDrug, String prescribedDrugText
 	) {
 	//@formatter:on
 
@@ -436,11 +437,11 @@ public void setProphylaxisPrescribed(Boolean prophylaxisPrescribed) {
 		this.prophylaxisPrescribed = prophylaxisPrescribed;
 	}
 
-	public PrescribedDrug getPrescribedDrug() {
+	public Drug getPrescribedDrug() {
 		return prescribedDrug;
 	}
 
-	public void setPrescribedDrug(PrescribedDrug prescribedDrug) {
+	public void setPrescribedDrug(Drug prescribedDrug) {
 		this.prescribedDrug = prescribedDrug;
 	}
 

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

@@ -2831,6 +2831,7 @@ public interface Captions {
 	String Symptoms_coughWithoutSputum = "Symptoms.coughWithoutSputum";
 	String Symptoms_coughWithSputum = "Symptoms.coughWithSputum";
 	String Symptoms_darkUrine = "Symptoms.darkUrine";
+	String Symptoms_dateOfOnsetKnown = "Symptoms.dateOfOnsetKnown";
 	String Symptoms_dehydration = "Symptoms.dehydration";
 	String Symptoms_delirium = "Symptoms.delirium";
 	String Symptoms_developmentalDelay = "Symptoms.developmentalDelay";

sormas-api/src/main/java/de/symeda/sormas/api/therapy/Drug.java

@@ -20,61 +20,77 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
+import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.i18n.I18nProperties;
+import de.symeda.sormas.api.utils.Diseases;
 import de.symeda.sormas.api.utils.DrugTypes;
 
 public enum Drug {
 
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+			@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	AMIKACIN,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	BEDAQUILINE,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	CAPREOMYCIN,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
 	CIPROFLOXACIN,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	DELAMANID,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	ETHAMBUTOL,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	GATIFLOXACIN,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	ISONIAZID,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	KANAMYCIN,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	LEVOFLOXACIN,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	MOXIFLOXACIN,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	OFLOXACIN,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
 	RIFAMPICIN,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	STREPTOMYCIN,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
 	CEFTRIAXONE,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	PENICILLIN,
 	@DrugTypes(value = {
 		TypeOfDrug.ANTIBIOTIC })
+	@Diseases(value = {Disease.INVASIVE_MENINGOCOCCAL_INFECTION}, hide = true)
 	ERYTHROMYCIN,
 	@DrugTypes(value = {
 			TypeOfDrug.ANTIBIOTIC })

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

@@ -1151,12 +1151,6 @@ PresentCondition.BURIED=Buried
 PresentCondition.DEAD=Dead
 PresentCondition.UNKNOWN=Unknown
 
-# PrescribedDrug
-PrescribedDrug.CIPROFLOXACIN = Ciprofloxacin
-PrescribedDrug.RIFAMPICIN  =  Rifampicin
-PrescribedDrug.CEFTRIAXONE   = Ceftriaxone
-PrescribedDrug.OTHER = Other
-
 # QuarantineType
 QuarantineType.HOME = Home
 QuarantineType.INSTITUTIONELL = Institutional

sormas-backend/src/main/java/de/symeda/sormas/backend/contact/Contact.java

@@ -54,9 +54,9 @@
 import de.symeda.sormas.api.contact.FollowUpStatus;
 import de.symeda.sormas.api.contact.IsContact;
 import de.symeda.sormas.api.contact.QuarantineType;
-import de.symeda.sormas.api.contact.PrescribedDrug;
 import de.symeda.sormas.api.contact.TracingApp;
 import de.symeda.sormas.api.externaldata.HasExternalData;
+import de.symeda.sormas.api.therapy.Drug;
 import de.symeda.sormas.api.utils.Diseases;
 import de.symeda.sormas.api.utils.Outbreaks;
 import de.symeda.sormas.api.utils.YesNoUnknown;
@@ -274,7 +274,7 @@ public class Contact extends CoreAdo implements IsContact, SormasToSormasShareab
 
 	private List<SelfReport> selfReport;
 
-	private PrescribedDrug prescribedDrug;
+	private Drug prescribedDrug;
 	private String prescribedDrugText;
 	private Boolean prophylaxisPrescribed;
 
@@ -1120,11 +1120,11 @@ public void setProphylaxisPrescribed(Boolean prophylaxisPrescribed) {
 		this.prophylaxisPrescribed = prophylaxisPrescribed;
 	}
 
-	public PrescribedDrug getPrescribedDrug() {
+	public Drug getPrescribedDrug() {
 		return prescribedDrug;
 	}
 
-	public void setPrescribedDrug(PrescribedDrug prescribedDrug) {
+	public void setPrescribedDrug(Drug prescribedDrug) {
 		this.prescribedDrug = prescribedDrug;
 	}
 

sormas-backend/src/main/java/de/symeda/sormas/backend/contact/ContactFacadeEjb.java

@@ -68,7 +68,6 @@
 import javax.validation.constraints.NotNull;
 
 import de.symeda.sormas.api.CountryHelper;
-import de.symeda.sormas.api.contact.PrescribedDrug;
 import org.apache.commons.collections4.CollectionUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

sormas-backend/src/main/java/de/symeda/sormas/backend/contact/ContactIndexDetailedDtoResultTransformer.java

@@ -18,7 +18,7 @@
 import java.util.Date;
 import java.util.List;
 
-import de.symeda.sormas.api.contact.PrescribedDrug;
+import de.symeda.sormas.api.therapy.Drug;
 import org.hibernate.transform.ResultTransformer;
 
 import de.symeda.sormas.api.Disease;
@@ -57,7 +57,7 @@ public ContactIndexDetailedDto transformTuple(Object[] tuple, String[] aliases)
                 (String) tuple[++index], (String) tuple[++index], (String) tuple[++index], (String) tuple[++index], (DeletionReason) tuple[++index], (String) tuple[++index], (Boolean) tuple[++index], (Boolean) tuple[++index],
                 (Sex) tuple[++index], (Integer) tuple[++index], (ApproximateAgeType) tuple[++index],
                 (String) tuple[++index], (String) tuple[++index], (String) tuple[++index], (String) tuple[++index], (String) tuple[++index], (String) tuple[++index],
-                (String) tuple[++index], (String) tuple[++index], (ContactRelation) tuple[++index], (Integer) tuple[++index], (Boolean) tuple[++index], (PrescribedDrug) tuple[++index], (String) tuple[++index]
+                (String) tuple[++index], (String) tuple[++index], (ContactRelation) tuple[++index], (Integer) tuple[++index], (Boolean) tuple[++index], (Drug) tuple[++index], (String) tuple[++index]
                 );
         //@formatter:on
 	}

sormas-backend/src/main/java/de/symeda/sormas/backend/contact/ContactIndexDtoResultTransformer.java

@@ -18,7 +18,7 @@
 import java.util.Date;
 import java.util.List;
 
-import de.symeda.sormas.api.contact.PrescribedDrug;
+import de.symeda.sormas.api.therapy.Drug;
 import org.hibernate.transform.ResultTransformer;
 
 import de.symeda.sormas.api.Disease;
@@ -51,7 +51,7 @@ public ContactIndexDto transformTuple(Object[] tuple, String[] aliases) {
                 (CaseClassification) tuple[++index], (String) tuple[++index], (String) tuple[++index],
                 (Date) tuple[++index],
                 (String) tuple[++index], (String) tuple[++index], (String) tuple[++index], (String) tuple[++index], (DeletionReason) tuple[++index], (String) tuple[++index], (Boolean) tuple[++index], (Boolean) tuple[++index],
-                (Integer) tuple[++index], (Boolean) tuple[++index], (PrescribedDrug) tuple[++index], (String) tuple[++index]
+                (Integer) tuple[++index], (Boolean) tuple[++index], (Drug) tuple[++index], (String) tuple[++index]
         );
         //@formatter:on
 	}

sormas-ui/src/main/java/de/symeda/sormas/ui/caze/AbstractCaseView.java

@@ -25,6 +25,7 @@
 
 import de.symeda.sormas.api.CoreFacade;
 import de.symeda.sormas.api.Disease;
+import de.symeda.sormas.api.DiseaseHelper;
 import de.symeda.sormas.api.FacadeProvider;
 import de.symeda.sormas.api.caze.CaseDataDto;
 import de.symeda.sormas.api.caze.CaseOrigin;
@@ -199,7 +200,7 @@ public void refreshMenu(SubMenu menu, String params) {
 		if (showExtraMenuEntries) {
 			if (UiUtil.permitted(
 				EnumSet.of(FeatureType.VIEW_TAB_CASES_FOLLOW_UP, FeatureType.VIEW_TAB_CASES_CLINICAL_COURSE, FeatureType.CLINICAL_MANAGEMENT),
-				UserRight.CLINICAL_COURSE_VIEW) && !caze.checkIsUnreferredPortHealthCase() && !caze.checkDiseaseIsInvasiveBacterialDiseases()) {
+				UserRight.CLINICAL_COURSE_VIEW) && !caze.checkIsUnreferredPortHealthCase() && !DiseaseHelper.checkDiseaseIsInvasiveBacterialDiseases(caze.getDisease())) {
 				menu.addView(
 					ClinicalCourseView.VIEW_NAME,
 					I18nProperties.getPrefixCaption(CaseDataDto.I18N_PREFIX, CaseDataDto.CLINICAL_COURSE),