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Merged
KarnaiahPesula merged 7 commits into from
Jun 4, 2026
Merged

Introduced new disease "shigellosis" to sormas. #13963

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539e713
Introduced new disease "shigellosis" to sormas.
KarnaiahPesula Jun 2, 2026
e9284a2
Merge branch 'development' into feature-13927-modify-disease-enum-for…
KarnaiahPesula Jun 2, 2026
72de892
fixed the review comments
KarnaiahPesula Jun 2, 2026
a5a9cea
code refactoring
KarnaiahPesula Jun 2, 2026
80e1495
Merge branch 'development' into feature-13927-modify-disease-enum-for…
KarnaiahPesula Jun 4, 2026
075c549
Fixed the caption issue for one of the symptoms of shigellosis.
KarnaiahPesula Jun 4, 2026
f86452d
Restoring the OTHER and UNKNOWN species to specific diseases and path…
KarnaiahPesula Jun 4, 2026
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160 changes: 91 additions & 69 deletions sormas-api/src/main/java/de/symeda/sormas/api/Disease.java
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Original file line number Diff line number Diff line change
Expand Up @@ -29,74 +29,75 @@ public enum Disease
implements
StatisticsGroupingKey {

AFP(true, true, true, false, true, 60, true, false, false, true, 7, 30),
CHOLERA(true, true, true, false, true, 5, true, false, false, true, 0, 5),
CONGENITAL_RUBELLA(true, true, true, false, true, 21, true, false, false, false, 0, 0),
CSM(true, true, true, false, true, 10, true, false, false, false, 0, 0),
DENGUE(true, true, true, false, false, 14, true, false, false, true, 2, 14),
EVD(true, true, true, false, true, 21, true, false, false, true, 2, 21),
GUINEA_WORM(true, true, true, false, false, 0, true, false, false, false, 0, 0),
LASSA(true, true, true, false, true, 21, true, false, false, true, 3, 21),
MEASLES(true, true, true, false, true, 21, true, true, false, true, 7, 21),
MONKEYPOX(true, true, true, false, true, 21, true, false, false, true, 5, 21),
NEW_INFLUENZA(true, true, true, false, true, 17, true, false, false, false, 0, 0),
PLAGUE(true, true, true, false, true, 7, true, false, false, true, 1, 7),
POLIO(true, true, true, false, true, 60, true, false, false, true, 7, 30),
UNSPECIFIED_VHF(true, true, true, false, true, 21, true, false, false, true, 2, 21),
WEST_NILE_FEVER(true, false, true, false, false, 0, true, false, false, true, 2, 14),
YELLOW_FEVER(true, true, true, false, false, 6, true, false, false, true, 3, 6),
RABIES(true, true, true, false, true, 6, true, false, false, true, 5, 730),
ANTHRAX(true, true, true, false, false, 0, true, false, false, true, 1, 60),
CORONAVIRUS(true, true, true, false, true, 14, true, true, true, true, 1, 14),
PNEUMONIA(true, false, true, true, false, 0, true, false, false, false, 0, 0),
MALARIA(true, true, false, true, false, 0, true, false, false, true, 7, 60),
TYPHOID_FEVER(true, false, false, true, false, 0, true, false, false, false, 0, 0),
ACUTE_VIRAL_HEPATITIS(true, false, false, true, false, 0, true, false, false, false, 0, 0),
NON_NEONATAL_TETANUS(true, false, false, true, false, 0, true, false, false, false, 0, 0),
HIV(true, false, false, true, false, 0, true, false, false, true, 10, 180),
SCHISTOSOMIASIS(true, false, false, true, false, 0, true, false, false, false, 0, 0),
SOIL_TRANSMITTED_HELMINTHS(true, false, false, true, false, 0, true, false, false, false, 0, 0),
TRYPANOSOMIASIS(true, false, false, true, false, 0, true, false, false, false, 0, 0),
DIARRHEA_DEHYDRATION(true, false, false, true, false, 0, true, false, false, false, 0, 0),
DIARRHEA_BLOOD(true, false, false, true, false, 0, true, false, false, false, 0, 0),
SNAKE_BITE(true, false, false, true, false, 0, true, false, false, false, 0, 0),
RUBELLA(true, false, false, true, false, 0, true, false, false, true, 14, 23),
TUBERCULOSIS(false, true, true, true, true, 365, true, false, false, true, 30, 730),
LATENT_TUBERCULOSIS(false, true, true, true, true, 30, true, false, false, false, 0, 0),
LEPROSY(true, false, false, true, false, 0, true, false, false, true, 18, 730),
LYMPHATIC_FILARIASIS(true, false, false, true, false, 0, true, false, false, false, 0, 0),
BURULI_ULCER(true, false, false, true, false, 0, true, false, false, false, 0, 0),
PERTUSSIS(true, false, false, true, true, 0, true, false, false, true, 4, 21),
NEONATAL_TETANUS(true, false, false, true, false, 0, true, false, false, true, 3, 21),
ONCHOCERCIASIS(true, false, false, true, false, 0, true, false, false, false, 0, 0),
DIPHTERIA(true, false, false, true, false, 0, true, false, false, true, 1, 10),
TRACHOMA(true, false, false, true, false, 0, true, false, false, false, 0, 0),
YAWS_ENDEMIC_SYPHILIS(true, false, false, true, false, 0, true, false, false, false, 0, 0),
MATERNAL_DEATHS(true, false, false, true, false, 0, true, false, false, false, 0, 0),
PERINATAL_DEATHS(true, false, false, true, false, 0, true, false, false, true, 1, 4),
INFLUENZA(true, false, false, false, false, 0, true, false, false, true, 1, 4),
INFLUENZA_A(false, true, true, false, false, 0, true, false, false, true, 1, 4),
INFLUENZA_B(false, true, true, false, false, 0, true, false, false, true, 1, 4),
H_METAPNEUMOVIRUS(true, false, true, true, false, 0, true, false, false, false, 0, 0),
RESPIRATORY_SYNCYTIAL_VIRUS(true, false, true, false, false, 0, true, false, false, true, 2, 8),
PARAINFLUENZA_1_4(false, false, true, true, false, 0, true, false, false, false, 0, 0),
ADENOVIRUS(true, false, true, true, false, 0, true, false, false, false, 0, 0),
RHINOVIRUS(true, false, true, true, false, 0, true, false, false, false, 0, 0),
ENTEROVIRUS(true, false, true, true, false, 0, true, false, false, false, 0, 0),
M_PNEUMONIAE(true, false, true, true, false, 0, true, false, false, false, 0, 0),
C_PNEUMONIAE(true, false, true, true, false, 0, true, false, false, false, 0, 0),
ARI(true, false, false, true, false, 0, true, false, false, false, 0, 0),
CHIKUNGUNYA(true, false, false, true, false, 0, true, false, false, true, 2, 14),
POST_IMMUNIZATION_ADVERSE_EVENTS_MILD(true, false, false, true, false, 0, true, false, false, false, 0, 0),
POST_IMMUNIZATION_ADVERSE_EVENTS_SEVERE(true, false, false, true, false, 0, true, false, false, false, 0, 0),
FHA(true, false, false, true, false, 0, true, false, false, false, 0, 0),
INVASIVE_PNEUMOCOCCAL_INFECTION(true, true, true, false, false, 0, false, false, false, true, 1, 3),
INVASIVE_MENINGOCOCCAL_INFECTION(true, true, true, false, true, 7, false, false, false, true, 1, 10),
GIARDIASIS(true, true, true, false, true, 14, false, false, false, true, 7, 21),
CRYPTOSPORIDIOSIS(true, true, true, false, true, 14, false, false, false, true, 2, 12),
SALMONELLOSIS(true, true, true, false, true, 14, false, false, false, true, 1, 3),
OTHER(true, true, true, false, true, 21, false, false, false, false, 0, 0),
UNDEFINED(true, true, true, false, true, 0, false, false, false, false, 0, 0);
AFP(true, true, true, false, true, 60, true, false, false, true, 7, 30, false, 0, 0),
CHOLERA(true, true, true, false, true, 5, true, false, false, true, 0, 5, false, 0, 0),
CONGENITAL_RUBELLA(true, true, true, false, true, 21, true, false, false, false, 0, 0, false, 0, 0),
CSM(true, true, true, false, true, 10, true, false, false, false, 0, 0, false, 0, 0),
DENGUE(true, true, true, false, false, 14, true, false, false, true, 2, 14, false, 0, 0),
EVD(true, true, true, false, true, 21, true, false, false, true, 2, 21, false, 0, 0),
GUINEA_WORM(true, true, true, false, false, 0, true, false, false, false, 0, 0, false, 0, 0),
LASSA(true, true, true, false, true, 21, true, false, false, true, 3, 21, false, 0, 0),
MEASLES(true, true, true, false, true, 21, true, true, false, true, 7, 21, false, 0, 0),
MONKEYPOX(true, true, true, false, true, 21, true, false, false, true, 5, 21, false, 0, 0),
NEW_INFLUENZA(true, true, true, false, true, 17, true, false, false, false, 0, 0, false, 0, 0),
PLAGUE(true, true, true, false, true, 7, true, false, false, true, 1, 7, false, 0, 0),
POLIO(true, true, true, false, true, 60, true, false, false, true, 7, 30, false, 0, 0),
UNSPECIFIED_VHF(true, true, true, false, true, 21, true, false, false, true, 2, 21, false, 0, 0),
WEST_NILE_FEVER(true, false, true, false, false, 0, true, false, false, true, 2, 14, false, 0, 0),
YELLOW_FEVER(true, true, true, false, false, 6, true, false, false, true, 3, 6, false, 0, 0),
RABIES(true, true, true, false, true, 6, true, false, false, true, 5, 730, false, 0, 0),
ANTHRAX(true, true, true, false, false, 0, true, false, false, true, 1, 60, false, 0, 0),
CORONAVIRUS(true, true, true, false, true, 14, true, true, true, true, 1, 14, false, 0, 0),
PNEUMONIA(true, false, true, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
MALARIA(true, true, false, true, false, 0, true, false, false, true, 7, 60, false, 0, 0),
TYPHOID_FEVER(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
ACUTE_VIRAL_HEPATITIS(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
NON_NEONATAL_TETANUS(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
HIV(true, false, false, true, false, 0, true, false, false, true, 10, 180, false, 0, 0),
SCHISTOSOMIASIS(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
SOIL_TRANSMITTED_HELMINTHS(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
TRYPANOSOMIASIS(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
DIARRHEA_DEHYDRATION(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
DIARRHEA_BLOOD(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
SNAKE_BITE(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
RUBELLA(true, false, false, true, false, 0, true, false, false, true, 14, 23, false, 0, 0),
TUBERCULOSIS(false, true, true, true, true, 365, true, false, false, true, 30, 730, false, 0, 0),
LATENT_TUBERCULOSIS(false, true, true, true, true, 30, true, false, false, false, 0, 0, false, 0, 0),
LEPROSY(true, false, false, true, false, 0, true, false, false, true, 18, 730, false, 0, 0),
LYMPHATIC_FILARIASIS(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
BURULI_ULCER(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
PERTUSSIS(true, false, false, true, true, 0, true, false, false, true, 4, 21, false, 0, 0),
NEONATAL_TETANUS(true, false, false, true, false, 0, true, false, false, true, 3, 21, false, 0, 0),
ONCHOCERCIASIS(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
DIPHTERIA(true, false, false, true, false, 0, true, false, false, true, 1, 10, false, 0, 0),
TRACHOMA(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
YAWS_ENDEMIC_SYPHILIS(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
MATERNAL_DEATHS(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
PERINATAL_DEATHS(true, false, false, true, false, 0, true, false, false, true, 1, 4, false, 0, 0),
INFLUENZA(true, false, false, false, false, 0, true, false, false, true, 1, 4, false, 0, 0),
INFLUENZA_A(false, true, true, false, false, 0, true, false, false, true, 1, 4, false, 0, 0),
INFLUENZA_B(false, true, true, false, false, 0, true, false, false, true, 1, 4, false, 0, 0),
H_METAPNEUMOVIRUS(true, false, true, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
RESPIRATORY_SYNCYTIAL_VIRUS(true, false, true, false, false, 0, true, false, false, true, 2, 8, false, 0, 0),
PARAINFLUENZA_1_4(false, false, true, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
ADENOVIRUS(true, false, true, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
RHINOVIRUS(true, false, true, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
ENTEROVIRUS(true, false, true, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
M_PNEUMONIAE(true, false, true, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
C_PNEUMONIAE(true, false, true, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
ARI(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
CHIKUNGUNYA(true, false, false, true, false, 0, true, false, false, true, 2, 14, false, 0, 0),
POST_IMMUNIZATION_ADVERSE_EVENTS_MILD(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
POST_IMMUNIZATION_ADVERSE_EVENTS_SEVERE(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
FHA(true, false, false, true, false, 0, true, false, false, false, 0, 0, false, 0, 0),
INVASIVE_PNEUMOCOCCAL_INFECTION(true, true, true, false, false, 0, false, false, false, true, 1, 3, false, 0, 0),
INVASIVE_MENINGOCOCCAL_INFECTION(true, true, true, false, true, 7, false, false, false, true, 1, 10, false, 0, 0),
GIARDIASIS(true, true, true, false, true, 14, false, false, false, true, 7, 21, false, 0, 0),
CRYPTOSPORIDIOSIS(true, true, true, false, true, 14, false, false, false, true, 2, 12, false, 0, 0),
SHIGELLOSIS(true, true, true, false, true, 14, false, false, false, true, 0, 7, true, 1, 7),
SALMONELLOSIS(true, true, true, false, true, 14, false, false, false, true, 1, 3, false, 0, 0),
OTHER(true, true, true, false, true, 21, false, false, false, false, 0, 0, false, 0, 0),
UNDEFINED(true, true, true, false, true, 0, false, false, false, false, 0, 0, false, 0, 0);

/**
* Immutable that eager loads all available diseases.
Expand All @@ -116,6 +117,9 @@ public enum Disease
private final boolean defaultIncubationPeriodEnabled;
private final int defaultMinIncubationPeriod;
private final int defaultMaxIncubationPeriod;
private final boolean isContagious;
private final int defaultMinContagiousPeriod;
private final int defaultMaxContagiousPeriod;

Disease(
boolean defaultActive,
Expand All @@ -129,7 +133,10 @@ public enum Disease
boolean defaultExtendedClassificationMulti,
boolean defaultIncubationPeriodEnabled,
int defaultMinIncubationPeriod,
int defaultMaxIncubationPeriod) {
int defaultMaxIncubationPeriod,
boolean isContagious,
int defaultMinContagiousPeriod,
int defaultMaxContagiousPeriod) {

this.defaultActive = defaultActive;
this.defaultPrimary = defaultPrimary;
Expand All @@ -143,6 +150,9 @@ public enum Disease
this.defaultIncubationPeriodEnabled = defaultIncubationPeriodEnabled;
this.defaultMinIncubationPeriod = defaultMinIncubationPeriod;
this.defaultMaxIncubationPeriod = defaultMaxIncubationPeriod;
this.isContagious = isContagious;
this.defaultMinContagiousPeriod = defaultMinContagiousPeriod;
this.defaultMaxContagiousPeriod = defaultMaxContagiousPeriod;
}

@Override
Expand Down Expand Up @@ -221,6 +231,18 @@ public int getDefaultMaxIncubationPeriod() {
return defaultMaxIncubationPeriod;
}

public boolean isContagious() {
return isContagious;
}

public int getDefaultMinContagiousPeriod() {
return defaultMinContagiousPeriod;
}

public int getDefaultMaxContagiousPeriod() {
return defaultMaxContagiousPeriod;
}

@Override
public int keyCompareTo(StatisticsGroupingKey o) {

Expand Down
63 changes: 63 additions & 0 deletions sormas-api/src/main/java/de/symeda/sormas/api/clinicalcourse/HealthConditionsDto.java
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Expand Up @@ -60,6 +60,10 @@ public class HealthConditionsDto extends PseudonymizableDto {
public static final String VACCINATED_AGAINST_MOSQUITO_BORNE_VIRUSES = "vaccinatedAgainstMosquitoBorneViruses";
public static final String MALARIA = "malaria";
public static final String MALARIA_INFECTED_YEAR = "malariaInfectedYear";
public static final String UNDER_MEDICATION = "underMedication";
public static final String MEDICATION_DETAILS = "medicationDetails";
public static final String CHRONIC_DISEASE = "chronicDisease";
public static final String CHRONIC_DISEASE_DETAILS = "chronicDiseaseDetails";

@HideForCountries(countries = {
CountryHelper.COUNTRY_CODE_GERMANY,
Expand All @@ -68,6 +72,8 @@ public class HealthConditionsDto extends PseudonymizableDto {
@HideForCountries(countries = {
CountryHelper.COUNTRY_CODE_GERMANY,
CountryHelper.COUNTRY_CODE_SWITZERLAND })
@Diseases(value = {
Disease.SHIGELLOSIS }, hide = true)
private YesNoUnknown asplenia;
@HideForCountries(countries = {
CountryHelper.COUNTRY_CODE_GERMANY,
Expand All @@ -82,20 +88,32 @@ public class HealthConditionsDto extends PseudonymizableDto {
CountryHelper.COUNTRY_CODE_GERMANY,
CountryHelper.COUNTRY_CODE_SWITZERLAND })
private YesNoUnknown hivArt;
@Diseases(value = {
Disease.SHIGELLOSIS }, hide = true)
private YesNoUnknown chronicLiverDisease;
private YesNoUnknown malignancyChemotherapy;

//TODO: rename ? general heart issue
@HideForCountries(countries = {
CountryHelper.COUNTRY_CODE_GERMANY,
CountryHelper.COUNTRY_CODE_SWITZERLAND })
@Diseases(value = {
Disease.SHIGELLOSIS }, hide = true)
private YesNoUnknown chronicHeartFailure;
@Diseases(value = {
Disease.SHIGELLOSIS }, hide = true)
private YesNoUnknown chronicPulmonaryDisease;
@Diseases(value = {
Disease.SHIGELLOSIS }, hide = true)
private YesNoUnknown chronicKidneyDisease;
@Diseases(value = {
Disease.SHIGELLOSIS }, hide = true)
private YesNoUnknown chronicNeurologicCondition;
@HideForCountries(countries = {
CountryHelper.COUNTRY_CODE_GERMANY,
CountryHelper.COUNTRY_CODE_SWITZERLAND })
@Diseases(value = {
Disease.SHIGELLOSIS }, hide = true)
private YesNoUnknown downSyndrome;
@HideForCountries(countries = {
CountryHelper.COUNTRY_CODE_GERMANY,
Expand Down Expand Up @@ -181,6 +199,18 @@ public class HealthConditionsDto extends PseudonymizableDto {
@Diseases(value = {
Disease.MALARIA })
private Integer malariaInfectedYear;
@Diseases(value = {
Disease.SHIGELLOSIS })
private YesNoUnknown underMedication;
@Diseases(value = {
Disease.SHIGELLOSIS })
private String medicationDetails;
@Diseases(value = {
Disease.SHIGELLOSIS })
private YesNoUnknown chronicDisease;
@Diseases(value = {
Disease.SHIGELLOSIS })
private String chronicDiseaseDetails;

public static HealthConditionsDto build() {
HealthConditionsDto healthConditions = new HealthConditionsDto();
Expand Down Expand Up @@ -475,4 +505,37 @@ public Integer getMalariaInfectedYear() {
public void setMalariaInfectedYear(Integer malariaInfectedYear) {
this.malariaInfectedYear = malariaInfectedYear;
}

public YesNoUnknown getUnderMedication() {
return underMedication;
}

public void setUnderMedication(YesNoUnknown underMedication) {
this.underMedication = underMedication;
}

public String getMedicationDetails() {
return medicationDetails;
}

public void setMedicationDetails(String medicationDetails) {
this.medicationDetails = medicationDetails;
}

public YesNoUnknown getChronicDisease() {
return chronicDisease;
}

public void setChronicDisease(YesNoUnknown chronicDisease) {
this.chronicDisease = chronicDisease;
}

public String getChronicDiseaseDetails() {
return chronicDiseaseDetails;
}

public void setChronicDiseaseDetails(String chronicDiseaseDetails) {
this.chronicDiseaseDetails = chronicDiseaseDetails;
}

}
31 changes: 31 additions & 0 deletions sormas-api/src/main/java/de/symeda/sormas/api/disease/DiseaseConfigurationDto.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,9 @@ public class DiseaseConfigurationDto extends EntityDto {
public static final String MAX_INCUBATION_PERIOD = "maxIncubationPeriod";
public static final String MIN_INCUBATION_PERIOD = "minIncubationPeriod";
public static final String CASE_DEFINITION_TEXT = "caseDefinitionText";
public static final String IS_CONTAGIOUS = "isContagious";
public static final String MIN_CONTAGIOUS_PERIOD = "minContagiousPeriod";
public static final String MAX_CONTAGIOUS_PERIOD = "maxContagiousPeriod";
public static final String EXTENDED_CLASSIFICATION = "extendedClassification";
public static final String EXTENDED_CLASSIFICATION_MULTI = "extendedClassificationMulti";
public static final String AGE_GROUPS = "ageGroups";
Expand All @@ -45,6 +48,9 @@ public class DiseaseConfigurationDto extends EntityDto {
private Integer maxIncubationPeriod;
private Integer minIncubationPeriod;
private String caseDefinitionText;
private Boolean isContagious;
private Integer minContagiousPeriod;
private Integer maxContagiousPeriod;
private Boolean extendedClassification;
private Boolean extendedClassificationMulti;
private List<String> ageGroups;
Expand Down Expand Up @@ -195,4 +201,29 @@ public Set<ExposureCategory> getExposureCategories() {
public void setExposureCategories(Set<ExposureCategory> exposureCategories) {
this.exposureCategories = exposureCategories;
}

public Boolean getIsContagious() {
return isContagious;
}

public void setIsContagious(Boolean isContagious) {
this.isContagious = isContagious;
}

public Integer getMinContagiousPeriod() {
return minContagiousPeriod;
}

public void setMinContagiousPeriod(Integer minContagiousPeriod) {
this.minContagiousPeriod = minContagiousPeriod;
}

public Integer getMaxContagiousPeriod() {
return maxContagiousPeriod;
}

public void setMaxContagiousPeriod(Integer maxContagiousPeriod) {
this.maxContagiousPeriod = maxContagiousPeriod;
}

}
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