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entities, dto for tb sample/test changes
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Lines changed: 770 additions & 63 deletions

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

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/*
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* SORMAS® - Surveillance Outbreak Response Management & Analysis System
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* Copyright © 2016-2024 Helmholtz-Zentrum für Infektionsforschung GmbH (HZI)
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* This program is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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* You should have received a copy of the GNU General Public License
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* along with this program. If not, see <https://www.gnu.org/licenses/>.
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*/
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package de.symeda.sormas.api.sample;
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import java.lang.reflect.Field;
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import java.util.Arrays;
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import java.util.List;
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import java.util.stream.Collectors;
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import de.symeda.sormas.api.i18n.I18nProperties;
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import de.symeda.sormas.api.utils.ApplicableToPathogenTests;
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public enum PathogenSpecie {
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@ApplicableToPathogenTests(value = {
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PathogenTestType.SPOLIGOTYPING })
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MYCOBATERIUM_AFRICANUM,
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@ApplicableToPathogenTests(value = {
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PathogenTestType.SPOLIGOTYPING })
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MYCOBATERIUM_BOVIS,
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@ApplicableToPathogenTests(value = {
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PathogenTestType.SPOLIGOTYPING })
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MYCOBATERIUM_TUBERCULOSIS,
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@ApplicableToPathogenTests(value = {
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PathogenTestType.SPOLIGOTYPING })
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OTHER_MTBC_MEMBER,
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@ApplicableToPathogenTests(value = {
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PathogenTestType.SPOLIGOTYPING })
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UNKNOWN,
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@ApplicableToPathogenTests(value = {
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PathogenTestType.SPOLIGOTYPING })
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NOT_APPLICABLE;
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@Override
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public String toString() {
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return I18nProperties.getEnumCaption(this);
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}
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public static List<PathogenSpecie> forPathogenTest(PathogenTestType pathogenTest) {
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return Arrays.stream(values()).filter(status -> {
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try {
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Field f = PathogenSpecie.class.getField(status.name());
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ApplicableToPathogenTests ann = f.getAnnotation(ApplicableToPathogenTests.class);
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return ann != null && Arrays.asList(ann.value()).contains(pathogenTest);
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} catch (NoSuchFieldException e) {
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return false;
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}
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}).collect(Collectors.toList());
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}
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}

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

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/*
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* SORMAS® - Surveillance Outbreak Response Management & Analysis System
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* Copyright © 2016-2024 Helmholtz-Zentrum für Infektionsforschung GmbH (HZI)
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* 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
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* (at your option) any later version.
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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* You should have received a copy of the GNU General Public License
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* along with this program. If not, see <https://www.gnu.org/licenses/>.
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*/
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package de.symeda.sormas.api.sample;
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import java.lang.reflect.Field;
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import java.util.Arrays;
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import java.util.List;
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import java.util.stream.Collectors;
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import de.symeda.sormas.api.Disease;
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import de.symeda.sormas.api.i18n.I18nProperties;
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import de.symeda.sormas.api.utils.ApplicableToPathogenTests;
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import de.symeda.sormas.api.utils.Diseases;
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public enum PathogenStrainCallStatus {
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@Diseases(value = {
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Disease.TUBERCULOSIS })
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@ApplicableToPathogenTests(value = {
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PathogenTestType.BEJINGGENOTYPING })
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BEIJING,
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@Diseases(value = {
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Disease.TUBERCULOSIS })
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@ApplicableToPathogenTests(value = {
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PathogenTestType.BEJINGGENOTYPING })
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NOBEIJING,
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@Diseases(value = {
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Disease.TUBERCULOSIS })
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@ApplicableToPathogenTests(value = {
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PathogenTestType.BEJINGGENOTYPING })
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POSSBEIJING,
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@Diseases(value = {
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Disease.TUBERCULOSIS })
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@ApplicableToPathogenTests(value = {
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PathogenTestType.BEJINGGENOTYPING })
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UNKNOWN;
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@Override
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public String toString() {
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return I18nProperties.getEnumCaption(this);
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}
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public static List<PathogenStrainCallStatus> forDisease(Disease disease) {
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return Arrays.stream(values()).filter(status -> {
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try {
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Field f = PathogenStrainCallStatus.class.getField(status.name());
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Diseases ann = f.getAnnotation(Diseases.class);
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return ann != null && Arrays.asList(ann.value()).contains(disease);
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} catch (NoSuchFieldException e) {
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return false;
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}
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}).collect(Collectors.toList());
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}
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public static List<PathogenStrainCallStatus> forPathogenTest(PathogenTestType pathogenTest) {
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return Arrays.stream(values()).filter(status -> {
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try {
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Field f = PathogenStrainCallStatus.class.getField(status.name());
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ApplicableToPathogenTests ann = f.getAnnotation(ApplicableToPathogenTests.class);
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return ann != null && Arrays.asList(ann.value()).contains(pathogenTest);
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} catch (NoSuchFieldException e) {
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return false;
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}
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}).collect(Collectors.toList());
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}
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public static List<PathogenStrainCallStatus> forDiseaseAndTest(Disease disease, PathogenTestType pathogenTest) {
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return Arrays.stream(values()).filter(status -> {
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try {
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Field f = PathogenStrainCallStatus.class.getField(status.name());
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Diseases diseaseAnn = f.getAnnotation(Diseases.class);
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ApplicableToPathogenTests testAnn = f.getAnnotation(ApplicableToPathogenTests.class);
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return diseaseAnn != null
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&& testAnn != null
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&& Arrays.asList(diseaseAnn.value()).contains(disease)
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&& Arrays.asList(testAnn.value()).contains(pathogenTest);
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} catch (NoSuchFieldException e) {
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return false;
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}
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}).collect(Collectors.toList());
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}
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}

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

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@@ -37,6 +37,7 @@
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import de.symeda.sormas.api.infrastructure.facility.FacilityReferenceDto;
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import de.symeda.sormas.api.sormastosormas.S2SIgnoreProperty;
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import de.symeda.sormas.api.sormastosormas.SormasToSormasConfig;
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import de.symeda.sormas.api.therapy.DrugSusceptibilityDto;
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import de.symeda.sormas.api.user.UserDto;
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import de.symeda.sormas.api.user.UserReferenceDto;
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import de.symeda.sormas.api.utils.DataHelper;
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import de.symeda.sormas.api.utils.FieldConstraints;
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import de.symeda.sormas.api.utils.HideForCountriesExcept;
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import de.symeda.sormas.api.utils.SensitiveData;
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import de.symeda.sormas.api.utils.YesNoUnknown;
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import de.symeda.sormas.api.utils.pseudonymization.PseudonymizableDto;
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@DependingOnFeatureType(featureType = FeatureType.SAMPLES_LAB)
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public static final String PRESCRIBER_CITY = "prescriberCity";
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public static final String PRESCRIBER_COUNTRY = "prescriberCountry";
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public static final String ENVIRONMENT_SAMPLE = "environmentSample";
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public static final String RIFAMPICIN_RESISTANT = "rifampicinResistant";
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public static final String ISONIAZID_RESISTANT = "isoniazidResistant";
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public static final String SPECIE = "specie";
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public static final String PATTERN_PROFILE = "patternProfile";
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public static final String STRAIN_CALL_STATUS = "strainCallStatus";
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public static final String TEST_SCALE = "testScale";
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public static final String DRUG_SUSCEPTIBILITY = "drugSusceptibility";
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public static final String SEROTYPING_METHOD = "seroTypingMethod";
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public static final String SERO_TYPING_METHOD_TEXT = "seroTypingMethodText";
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public static final String SERO_GROUP_SPECIFICATION = "seroGroupSpecification";
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private String prescriberCity;
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@HideForCountriesExcept(countries = CountryHelper.COUNTRY_CODE_LUXEMBOURG)
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private CountryReferenceDto prescriberCountry;
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private YesNoUnknown rifampicinResistant;
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private YesNoUnknown isoniazidResistant;
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private PathogenSpecie specie;
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private String patternProfile;
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private PathogenStrainCallStatus strainCallStatus;
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private PathogenTestScale testScale;
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private DrugSusceptibilityDto drugSusceptibility;
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@SensitiveData
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@HideForCountriesExcept(countries = CountryHelper.COUNTRY_CODE_LUXEMBOURG)
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@Diseases(value = {Disease.INVASIVE_PNEUMOCOCCAL_INFECTION})
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pathogenTest.setLabDetails(sample.getLabDetails());
234250
}
235251
pathogenTest.setLabUser(currentUser.toReference());
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pathogenTest.setDrugSusceptibility(DrugSusceptibilityDto.build());
236253
return pathogenTest;
237254
}
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242259
pathogenTest.setUuid(DataHelper.createUuid());
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pathogenTest.setSample(sample);
244261
pathogenTest.setLabUser(currentUser);
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pathogenTest.setDrugSusceptibility(DrugSusceptibilityDto.build());
245263
return pathogenTest;
246264
}
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this.prescriberCountry = prescriberCountry;
636654
}
637655

656+
public YesNoUnknown getRifampicinResistant() {
657+
return rifampicinResistant;
658+
}
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public void setRifampicinResistant(YesNoUnknown rifampicinResistant) {
661+
this.rifampicinResistant = rifampicinResistant;
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}
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664+
public YesNoUnknown getIsoniazidResistant() {
665+
return isoniazidResistant;
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}
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public void setIsoniazidResistant(YesNoUnknown isoniazidResistant) {
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this.isoniazidResistant = isoniazidResistant;
670+
}
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672+
public PathogenSpecie getSpecie() {
673+
return specie;
674+
}
675+
676+
public void setSpecie(PathogenSpecie specie) {
677+
this.specie = specie;
678+
}
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680+
public String getPatternProfile() {
681+
return patternProfile;
682+
}
683+
684+
public void setPatternProfile(String patternProfile) {
685+
this.patternProfile = patternProfile;
686+
}
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688+
public PathogenStrainCallStatus getStrainCallStatus() {
689+
return strainCallStatus;
690+
}
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692+
public void setStrainCallStatus(PathogenStrainCallStatus strainCallStatus) {
693+
this.strainCallStatus = strainCallStatus;
694+
}
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public PathogenTestScale getTestScale() {
697+
return testScale;
698+
}
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700+
public void setTestScale(PathogenTestScale testScale) {
701+
this.testScale = testScale;
702+
}
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public DrugSusceptibilityDto getDrugSusceptibility() {
705+
return drugSusceptibility;
706+
}
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708+
public void setDrugSusceptibility(DrugSusceptibilityDto drugSusceptibility) {
709+
this.drugSusceptibility = drugSusceptibility;
710+
}
711+
638712
public SerotypingMethod getSeroTypingMethod() {
639713
return seroTypingMethod;
640714
}

sormas-api/src/main/java/de/symeda/sormas/api/sample/SpoligotypeSpecie.java renamed to sormas-api/src/main/java/de/symeda/sormas/api/sample/PathogenTestScale.java

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@@ -15,19 +15,40 @@
1515

1616
package de.symeda.sormas.api.sample;
1717

18+
import java.lang.reflect.Field;
19+
import java.util.Arrays;
20+
import java.util.List;
21+
import java.util.stream.Collectors;
22+
1823
import de.symeda.sormas.api.i18n.I18nProperties;
24+
import de.symeda.sormas.api.utils.ApplicableToPathogenTests;
1925

20-
public enum SpoligotypeSpecie {
26+
public enum PathogenTestScale {
2127

22-
MYCOBATERIUM_AFRICANUM,
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MYCOBATERIUM_BOVIS,
24-
MYCOBATERIUM_TUBERCULOSIS,
25-
OTHER_MTBC_MEMBER,
26-
UNKNOWN,
27-
NOT_APPLICABLE;
28+
@ApplicableToPathogenTests(value = {
29+
PathogenTestType.MICROSCOPY })
30+
ONE_PLUS,
31+
@ApplicableToPathogenTests(value = {
32+
PathogenTestType.MICROSCOPY })
33+
TWO_PLUS,
34+
@ApplicableToPathogenTests(value = {
35+
PathogenTestType.MICROSCOPY })
36+
THREE_PLUS;
2837

2938
@Override
3039
public String toString() {
3140
return I18nProperties.getEnumCaption(this);
3241
}
42+
43+
public static List<PathogenTestScale> forPathogenTest(PathogenTestType pathogenTest) {
44+
return Arrays.stream(values()).filter(status -> {
45+
try {
46+
Field f = PathogenTestScale.class.getField(status.name());
47+
ApplicableToPathogenTests ann = f.getAnnotation(ApplicableToPathogenTests.class);
48+
return ann != null && Arrays.asList(ann.value()).contains(pathogenTest);
49+
} catch (NoSuchFieldException e) {
50+
return false;
51+
}
52+
}).collect(Collectors.toList());
53+
}
3354
}

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