Merge pull request #13385 from SORMAS-Foundation/feature-13317-integration-of-tuberculosis-disease

Feature 13317 integration of tuberculosis disease

Author: obinna-h-n

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

@@ -58,6 +58,7 @@ public enum Disease
 	SNAKE_BITE(true, false, false, true, false, 0, true, false, false),
 	RUBELLA(true, false, false, true, false, 0, true, false, false),
 	TUBERCULOSIS(true, true, true, true, false, 0, true, false, false),
+	LATENT_TUBERCULOSIS(true, true, true, true, false, 0, true, false, false),
 	LEPROSY(true, false, false, true, false, 0, true, false, false),
 	LYMPHATIC_FILARIASIS(true, false, false, true, false, 0, true, false, false),
 	BURULI_ULCER(true, false, false, true, false, 0, true, false, false),

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

@@ -233,6 +233,8 @@ public class CaseDataDto extends SormasToSormasShareableDto implements IsCase {
 	public static final String DEPARTMENT = "department";
 
 	public static final String NOTIFIER = "notifier";
+	public static final String RADIOGRAPHY_COMPATIBILITY = "radiographyCompatibility";
+	public static final String OTHER_DIAGNOSTIC_CRITERIA = "otherDiagnosticCriteria";
 
 	// Fields are declared in the order they should appear in the import template
 
@@ -639,6 +641,8 @@ public class CaseDataDto extends SormasToSormasShareableDto implements IsCase {
 	private String department;
 
 	private NotifierReferenceDto notifier;
+	private RadiographyCompatibility radiographyCompatibility;
+	private String otherDiagnosticCriteria;
 
 	public static CaseDataDto build(PersonReferenceDto person, Disease disease) {
 		return build(person, disease, HealthConditionsDto.build());
@@ -1820,6 +1824,22 @@ public void setDepartment(String department) {
 		this.department = department;
 	}
 
+	public RadiographyCompatibility getRadiographyCompatibility() {
+		return radiographyCompatibility;
+	}
+
+	public void setRadiographyCompatibility(RadiographyCompatibility radiographyCompatibility) {
+		this.radiographyCompatibility = radiographyCompatibility;
+	}
+
+	public String getOtherDiagnosticCriteria() {
+		return otherDiagnosticCriteria;
+	}
+
+	public void setOtherDiagnosticCriteria(String otherDiagnosticCriteria) {
+		this.otherDiagnosticCriteria = otherDiagnosticCriteria;
+	}
+
 	/**
 	 * Checks if the case is an invasive bacterial disease (meningococcal or pneumococcal)
 	 * @return boolean

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

@@ -0,0 +1,35 @@
+/*
+ * SORMAS® - Surveillance Outbreak Response Management & Analysis System
+ * Copyright © 2016-2024 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.Disease;
+import de.symeda.sormas.api.i18n.I18nProperties;
+import de.symeda.sormas.api.utils.Diseases;
+
+public enum RadiographyCompatibility {
+
+	@Diseases(value = {
+		Disease.TUBERCULOSIS })
+	COMPATIBLE_WITH_TB,
+	@Diseases(value = {
+		Disease.TUBERCULOSIS })
+	NOT_COMPATIBLE_WITH_TB;
+
+	@Override
+	public String toString() {
+		return I18nProperties.getEnumCaption(this);
+	}
+}

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

@@ -730,6 +730,7 @@ public interface Captions {
 	String CaseData_notifyingClinicDetails = "CaseData.notifyingClinicDetails";
 	String CaseData_numberOfVisits = "CaseData.numberOfVisits";
 	String CaseData_otherDeletionReason = "CaseData.otherDeletionReason";
+	String CaseData_otherDiagnosticCriteria = "CaseData.otherDiagnosticCriteria";
 	String CaseData_outcome = "CaseData.outcome";
 	String CaseData_outcomeDate = "CaseData.outcomeDate";
 	String CaseData_overwriteFollowUpUntil = "CaseData.overwriteFollowUpUntil";
@@ -773,6 +774,7 @@ public interface Captions {
 	String CaseData_quarantineTo = "CaseData.quarantineTo";
 	String CaseData_quarantineTypeDetails = "CaseData.quarantineTypeDetails";
 	String CaseData_rabiesType = "CaseData.rabiesType";
+	String CaseData_radiographyCompatibility = "CaseData.radiographyCompatibility";
 	String CaseData_region = "CaseData.region";
 	String CaseData_regionLevelDate = "CaseData.regionLevelDate";
 	String CaseData_reInfection = "CaseData.reInfection";
@@ -1381,6 +1383,14 @@ public interface Captions {
 	String devModeSampleSendDispatch = "devModeSampleSendDispatch";
 	String devModeSampleStartDate = "devModeSampleStartDate";
 	String devModeUseSeed = "devModeUseSeed";
+	String diagnosisCriteriaDetailTestResult = "diagnosisCriteriaDetailTestResult";
+	String diagnosisCriteriaDetailTestResultDate = "diagnosisCriteriaDetailTestResultDate";
+	String diagnosisCriteriaDetailTestResultNeg = "diagnosisCriteriaDetailTestResultNeg";
+	String diagnosisCriteriaDetailTestResultOngoing = "diagnosisCriteriaDetailTestResultOngoing";
+	String diagnosisCriteriaDetailTestResultPos = "diagnosisCriteriaDetailTestResultPos";
+	String diagnosisCriteriaDetailTestTypeNo = "diagnosisCriteriaDetailTestTypeNo";
+	String diagnosisCriteriaDetailTestTypeNotApplicable = "diagnosisCriteriaDetailTestTypeNotApplicable";
+	String diagnosisCriteriaDetailTestTypeYes = "diagnosisCriteriaDetailTestTypeYes";
 	String disease = "disease";
 	String DiseaseBurden_caseCount = "DiseaseBurden.caseCount";
 	String DiseaseBurden_caseDeathCount = "DiseaseBurden.caseDeathCount";
@@ -2190,12 +2200,15 @@ public interface Captions {
 	String PathogenTest_ctValueRdrpS = "PathogenTest.ctValueRdrpS";
 	String PathogenTest_ctValueS = "PathogenTest.ctValueS";
 	String PathogenTest_deletionReason = "PathogenTest.deletionReason";
+	String PathogenTest_drugSusceptibility = "PathogenTest.drugSusceptibility";
 	String PathogenTest_externalId = "PathogenTest.externalId";
 	String PathogenTest_externalOrderId = "PathogenTest.externalOrderId";
 	String PathogenTest_fourFoldIncreaseAntibodyTiter = "PathogenTest.fourFoldIncreaseAntibodyTiter";
+	String PathogenTest_isoniazidResistant = "PathogenTest.isoniazidResistant";
 	String PathogenTest_lab = "PathogenTest.lab";
 	String PathogenTest_labDetails = "PathogenTest.labDetails";
 	String PathogenTest_otherDeletionReason = "PathogenTest.otherDeletionReason";
+	String PathogenTest_patternProfile = "PathogenTest.patternProfile";
 	String PathogenTest_pcrTestSpecification = "PathogenTest.pcrTestSpecification";
 	String PathogenTest_preliminary = "PathogenTest.preliminary";
 	String PathogenTest_prescriber = "PathogenTest.prescriber";
@@ -2208,9 +2221,12 @@ public interface Captions {
 	String PathogenTest_prescriberPhysicianCode = "PathogenTest.prescriberPhysicianCode";
 	String PathogenTest_prescriberPostalCode = "PathogenTest.prescriberPostalCode";
 	String PathogenTest_reportDate = "PathogenTest.reportDate";
+	String PathogenTest_rifampicinResistant = "PathogenTest.rifampicinResistant";
 	String PathogenTest_seroGroupSpecification = "PathogenTest.seroGroupSpecification";
 	String PathogenTest_seroGroupSpecificationText = "PathogenTest.seroGroupSpecificationText";
 	String PathogenTest_serotype = "PathogenTest.serotype";
+	String PathogenTest_specie = "PathogenTest.specie";
+	String PathogenTest_strainCallStatus = "PathogenTest.strainCallStatus";
 	String PathogenTest_seroTypingMethod = "PathogenTest.seroTypingMethod";
 	String PathogenTest_seroTypingMethodText = "PathogenTest.seroTypingMethodText";
 	String PathogenTest_testDateTime = "PathogenTest.testDateTime";
@@ -2223,6 +2239,7 @@ public interface Captions {
 	String PathogenTest_testResult = "PathogenTest.testResult";
 	String PathogenTest_testResultText = "PathogenTest.testResultText";
 	String PathogenTest_testResultVerified = "PathogenTest.testResultVerified";
+	String PathogenTest_testScale = "PathogenTest.testScale";
 	String PathogenTest_testType = "PathogenTest.testType";
 	String PathogenTest_testTypeText = "PathogenTest.testTypeText";
 	String PathogenTest_typingId = "PathogenTest.typingId";
@@ -3052,6 +3069,9 @@ public interface Captions {
 	String TestReport_testLabPostalCode = "TestReport.testLabPostalCode";
 	String TestReport_testResult = "TestReport.testResult";
 	String TestReport_testType = "TestReport.testType";
+	String Therapy_beijingLineage = "Therapy.beijingLineage";
+	String Therapy_directlyObservedTreatment = "Therapy.directlyObservedTreatment";
+	String Therapy_mdrXdrTuberculosis = "Therapy.mdrXdrTuberculosis";
 	String titleAefiInvestigationBasicDetails = "titleAefiInvestigationBasicDetails";
 	String titleAefiInvestigationColdChainAndTransport = "titleAefiInvestigationColdChainAndTransport";
 	String titleAefiInvestigationColdChainAndTransportLastVaccineStoragePoint = "titleAefiInvestigationColdChainAndTransportLastVaccineStoragePoint";

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

@@ -589,6 +589,7 @@ public interface Strings {
 	String headingDeleteContacts = "headingDeleteContacts";
 	String headingDeleteUserRoleNotPossible = "headingDeleteUserRoleNotPossible";
 	String headingDeleteVaccinations = "headingDeleteVaccinations";
+	String headingDiagnosisCriteria = "headingDiagnosisCriteria";
 	String headingDisableLineListing = "headingDisableLineListing";
 	String headingDiscardUnsavedChanges = "headingDiscardUnsavedChanges";
 	String headingDocumentCreated = "headingDocumentCreated";
@@ -597,6 +598,7 @@ public interface Strings {
 	String headingDownloadErrorReport = "headingDownloadErrorReport";
 	String headingDownloadImportGuide = "headingDownloadImportGuide";
 	String headingDownloadImportTemplate = "headingDownloadImportTemplate";
+	String headingDrugSusceptibility = "headingDrugSusceptibility";
 	String headingEditAction = "headingEditAction";
 	String headingEditAdditionalTest = "headingEditAdditionalTest";
 	String headingEditAggregateReport = "headingEditAggregateReport";
@@ -1818,6 +1820,7 @@ public interface Strings {
 	String promptImmunizationRecoveryDateFrom = "promptImmunizationRecoveryDateFrom";
 	String promptImmunizationStartDateFrom = "promptImmunizationStartDateFrom";
 	String promptImmunizationValidFrom = "promptImmunizationValidFrom";
+	String promptMicValue = "promptMicValue";
 	String promptNamePhoneEmail = "promptNamePhoneEmail";
 	String promptNewCaseDateType = "promptNewCaseDateType";
 	String promptPersonDuplicateSearchIdExternalId = "promptPersonDuplicateSearchIdExternalId";
@@ -1826,6 +1829,7 @@ public interface Strings {
 	String promptRegion = "promptRegion";
 	String promptRelatedPersonLikeField = "promptRelatedPersonLikeField";
 	String promptRemarks = "promptRemarks";
+	String promptResistanceResult = "promptResistanceResult";
 	String promptSampleDashboardFilterDateType = "promptSampleDashboardFilterDateType";
 	String promptSampleDateFrom = "promptSampleDateFrom";
 	String promptSampleDateTo = "promptSampleDateTo";

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

@@ -202,6 +202,7 @@ public interface Validations {
 	String patchUnsupportedCollectionFieldType = "patchUnsupportedCollectionFieldType";
 	String patchWrongUuid = "patchWrongUuid";
 	String pathogenTestValidDisease = "pathogenTestValidDisease";
+	String pathogenTestValidDrugSusceptibility = "pathogenTestValidDrugSusceptibility";
 	String pathogenTestValidPathogen = "pathogenTestValidPathogen";
 	String pathogenTestValidSampleOrEnvironment = "pathogenTestValidSampleOrEnvironment";
 	String patternNotMatching = "patternNotMatching";

sormas-api/src/main/java/de/symeda/sormas/api/sample/PathogenSpecie.java

@@ -0,0 +1,63 @@
+/*
+ * SORMAS® - Surveillance Outbreak Response Management & Analysis System
+ * Copyright © 2016-2024 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.sample;
+
+import java.lang.reflect.Field;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import de.symeda.sormas.api.i18n.I18nProperties;
+import de.symeda.sormas.api.utils.ApplicableToPathogenTests;
+
+public enum PathogenSpecie {
+
+	@ApplicableToPathogenTests(value = {
+		PathogenTestType.SPOLIGOTYPING })
+	MYCOBATERIUM_AFRICANUM,
+	@ApplicableToPathogenTests(value = {
+		PathogenTestType.SPOLIGOTYPING })
+	MYCOBATERIUM_BOVIS,
+	@ApplicableToPathogenTests(value = {
+		PathogenTestType.SPOLIGOTYPING })
+	MYCOBATERIUM_TUBERCULOSIS,
+	@ApplicableToPathogenTests(value = {
+		PathogenTestType.SPOLIGOTYPING })
+	OTHER_MTBC_MEMBER,
+	@ApplicableToPathogenTests(value = {
+		PathogenTestType.SPOLIGOTYPING })
+	UNKNOWN,
+	@ApplicableToPathogenTests(value = {
+		PathogenTestType.SPOLIGOTYPING })
+	NOT_APPLICABLE;
+
+	@Override
+	public String toString() {
+		return I18nProperties.getEnumCaption(this);
+	}
+
+	public static List<PathogenSpecie> forPathogenTest(PathogenTestType pathogenTest) {
+		return Arrays.stream(values()).filter(status -> {
+			try {
+				Field f = PathogenSpecie.class.getField(status.name());
+				ApplicableToPathogenTests ann = f.getAnnotation(ApplicableToPathogenTests.class);
+				return ann != null && Arrays.asList(ann.value()).contains(pathogenTest);
+			} catch (NoSuchFieldException e) {
+				return false;
+			}
+		}).collect(Collectors.toList());
+	}
+}

sormas-api/src/main/java/de/symeda/sormas/api/sample/PathogenStrainCallStatus.java

@@ -0,0 +1,95 @@
+/*
+ * SORMAS® - Surveillance Outbreak Response Management & Analysis System
+ * Copyright © 2016-2024 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.sample;
+
+import java.lang.reflect.Field;
+import java.util.Arrays;
+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.ApplicableToPathogenTests;
+import de.symeda.sormas.api.utils.Diseases;
+
+public enum PathogenStrainCallStatus {
+
+	@Diseases(value = {
+		Disease.TUBERCULOSIS })
+	@ApplicableToPathogenTests(value = {
+		PathogenTestType.BEIJINGGENOTYPING })
+	BEIJING,
+	@Diseases(value = {
+		Disease.TUBERCULOSIS })
+	@ApplicableToPathogenTests(value = {
+		PathogenTestType.BEIJINGGENOTYPING })
+	NOBEIJING,
+	@Diseases(value = {
+		Disease.TUBERCULOSIS })
+	@ApplicableToPathogenTests(value = {
+		PathogenTestType.BEIJINGGENOTYPING })
+	POSSBEIJING,
+	@Diseases(value = {
+		Disease.TUBERCULOSIS })
+	@ApplicableToPathogenTests(value = {
+		PathogenTestType.BEIJINGGENOTYPING })
+	UNKNOWN;
+
+	@Override
+	public String toString() {
+		return I18nProperties.getEnumCaption(this);
+	}
+
+	public static List<PathogenStrainCallStatus> forDisease(Disease disease) {
+		return Arrays.stream(values()).filter(status -> {
+			try {
+				Field f = PathogenStrainCallStatus.class.getField(status.name());
+				Diseases ann = f.getAnnotation(Diseases.class);
+				return ann != null && Arrays.asList(ann.value()).contains(disease);
+			} catch (NoSuchFieldException e) {
+				return false;
+			}
+		}).collect(Collectors.toList());
+	}
+
+	public static List<PathogenStrainCallStatus> forPathogenTest(PathogenTestType pathogenTest) {
+		return Arrays.stream(values()).filter(status -> {
+			try {
+				Field f = PathogenStrainCallStatus.class.getField(status.name());
+				ApplicableToPathogenTests ann = f.getAnnotation(ApplicableToPathogenTests.class);
+				return ann != null && Arrays.asList(ann.value()).contains(pathogenTest);
+			} catch (NoSuchFieldException e) {
+				return false;
+			}
+		}).collect(Collectors.toList());
+	}
+
+	public static List<PathogenStrainCallStatus> forDiseaseAndTest(Disease disease, PathogenTestType pathogenTest) {
+		return Arrays.stream(values()).filter(status -> {
+			try {
+				Field f = PathogenStrainCallStatus.class.getField(status.name());
+				Diseases diseaseAnn = f.getAnnotation(Diseases.class);
+				ApplicableToPathogenTests testAnn = f.getAnnotation(ApplicableToPathogenTests.class);
+				return diseaseAnn != null
+					&& testAnn != null
+					&& Arrays.asList(diseaseAnn.value()).contains(disease)
+					&& Arrays.asList(testAnn.value()).contains(pathogenTest);
+			} catch (NoSuchFieldException e) {
+				return false;
+			}
+		}).collect(Collectors.toList());
+	}
+}