Merge branch 'refs/heads/gh-release-1.87.0-disease-lab-linkage' into …

…gh-release-1.87.0

sormas-app/app/src/main/java/de/symeda/sormas/app/backend/common/DatabaseHelper.java

@@ -211,6 +211,7 @@
 import de.symeda.sormas.app.backend.vaccination.VaccinationDao;
 import de.symeda.sormas.app.backend.visit.Visit;
 import de.symeda.sormas.app.backend.visit.VisitDao;
+import de.symeda.sormas.app.backend.disease.DiseaseFacility;
 
 /**
  * Database helper class used to manage the creation and upgrading of your database. This class also usually provides
@@ -228,7 +229,7 @@ public class DatabaseHelper extends OrmLiteSqliteOpenHelper {
 	// public static final int DATABASE_VERSION = 307;
 	//public static final int DATABASE_VERSION = 343;
 	// public static final int DATABASE_VERSION = 410;
-	public static final int DATABASE_VERSION = 428;
+	public static final int DATABASE_VERSION = 429;
 
 	private static DatabaseHelper instance = null;
 	private final Context context;
@@ -339,6 +340,7 @@ public static void clearTables(boolean clearInfrastructure) {
 				TableUtils.clearTable(connectionSource, FormField.class);
 				TableUtils.clearTable(connectionSource, FormBuilder.class);
 				TableUtils.clearTable(connectionSource, FormBuilderFormField.class);
+				TableUtils.clearTable(connectionSource, DiseaseFacility.class);
 
 				ConfigProvider.init(instance.context);
 			}
@@ -794,6 +796,8 @@ public void onCreate(SQLiteDatabase db, ConnectionSource connectionSource) {
 			TableUtils.createTable(connectionSource, AfpImmunization.class);
 			TableUtils.createTable(connectionSource, SixtyDay.class);
 			TableUtils.createTable(connectionSource, PatientSymptomsPrecedence.class);
+			TableUtils.createTable(connectionSource, DiseaseFacility.class);
+
 		} catch (SQLException e) {
 			Log.e(DatabaseHelper.class.getName(), "Can't build database", e);
 			throw new RuntimeException(e);
@@ -4452,7 +4456,9 @@ public void onUpgrade(SQLiteDatabase db, ConnectionSource connectionSource, int
 					currentVersion = 427;
 					getDao(Facility.class).executeRaw(
 							"UPDATE facility SET type = 'HOSPITAL' WHERE type = null AND uuid NOT IN ('SORMAS-CONSTID-NOTBASED-FACILITY','SORMAS-CONSTID-NOTSET-FACILITY');");
-
+				case 428:
+					currentVersion = 428;
+					getDao(DiseaseConfiguration.class).executeRaw("CREATE TABLE IF NOT EXISTS facility_diseaseconfiguration(diseaseConfiguration_id integer, facility_id integer);");
 					// ATTENTION: break should only be done after last version
 				break;
 			default:
@@ -5337,7 +5343,7 @@ public <ADO extends AbstractDomainObject> AbstractAdoDao<ADO> getAdoDaoInner(Cla
 				} else if (type.equals(UserRole.class)) {
 					dao = (AbstractAdoDao<ADO>) new UserRoleDao((Dao<UserRole, Long>) innerDao);
 				} else if (type.equals(DiseaseConfiguration.class)) {
-					dao = (AbstractAdoDao<ADO>) new DiseaseConfigurationDao((Dao<DiseaseConfiguration, Long>) innerDao);
+					dao = (AbstractAdoDao<ADO>) new DiseaseConfigurationDao((Dao<DiseaseConfiguration, Long>) innerDao, super.getDao(DiseaseFacility.class));
 				} else if (type.equals(CustomizableEnumValue.class)) {
 					dao = (AbstractAdoDao<ADO>) new CustomizableEnumValueDao((Dao<CustomizableEnumValue, Long>) innerDao);
 				} else if (type.equals(FeatureConfiguration.class)) {

sormas-app/app/src/main/java/de/symeda/sormas/app/backend/disease/DiseaseConfigurationDao.java

@@ -16,8 +16,10 @@
 package de.symeda.sormas.app.backend.disease;
 
 import java.sql.SQLException;
-
+import java.util.List;
+import java.util.stream.Collectors;
 import com.j256.ormlite.dao.Dao;
+import com.j256.ormlite.stmt.DeleteBuilder;
 import com.j256.ormlite.stmt.QueryBuilder;
 import com.j256.ormlite.stmt.Where;
 
@@ -26,11 +28,17 @@
 import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.app.backend.common.AbstractAdoDao;
 import de.symeda.sormas.app.util.DiseaseConfigurationCache;
+import de.symeda.sormas.app.backend.common.DatabaseHelper;
+import de.symeda.sormas.app.backend.facility.Facility;
 
 public class DiseaseConfigurationDao extends AbstractAdoDao<DiseaseConfiguration> {
 
-	public DiseaseConfigurationDao(Dao<DiseaseConfiguration, Long> innerDao) {
+	private Dao<DiseaseFacility, Long> diseaseFacilityDao;
+
+
+	public DiseaseConfigurationDao(Dao<DiseaseConfiguration, Long> innerDao, Dao<DiseaseFacility, Long> diseaseFacilityDao) {
 		super(innerDao);
+		this.diseaseFacilityDao = diseaseFacilityDao;
 	}
 
 	@Override
@@ -57,13 +65,60 @@ public DiseaseConfiguration getDiseaseConfiguration(Disease disease) {
 
 	@Override
 	public void create(DiseaseConfiguration data) throws SQLException {
+		if (data == null)
+			return;
 		super.create(data);
 		DiseaseConfigurationCache.reset();
+		if (data.getFacilities() != null) {
+			for (Facility facility : data.getFacilities()) {
+				int resultRowCount = diseaseFacilityDao.create(new DiseaseFacility(data, facility));
+				if (resultRowCount < 1)
+					throw new SQLException(
+							"Database entry was not created - go back and try again.\n" + "Type: " + DiseaseFacility.class.getSimpleName() + ", Facility-UUID: "
+									+ data.getUuid());
+			}
+		}
 	}
 
 	@Override
 	protected void update(DiseaseConfiguration data) throws SQLException {
+		if (data == null)
+			return;
 		super.update(data);
 		DiseaseConfigurationCache.reset();
+		// 1. Delete existing DiseaseFacility
+		DeleteBuilder<DiseaseFacility, Long> diseaseFacilityLongDeleteBuilder = diseaseFacilityDao.deleteBuilder();
+		diseaseFacilityLongDeleteBuilder.where().eq(DiseaseFacility.DISEASE_CONFIGURATION + "_id", data);
+		diseaseFacilityLongDeleteBuilder.delete();
+		// 2. Create new DiseaseFacility
+		if (data.getFacilities() != null) {
+			for (Facility facility : data.getFacilities()) {
+				int resultRowCount = diseaseFacilityDao.create(new DiseaseFacility(data, facility));
+				if (resultRowCount < 1)
+					throw new SQLException(
+							"Database entry was not created - go back and try again.\n" + "Type: " + DiseaseFacility.class.getSimpleName() + ", Facility-UUID: "
+									+ data.getUuid());
+			}
+		}
+	}
+
+	public List<Facility> getDiseaseFacilities(DiseaseConfiguration diseaseConfiguration) {
+		diseaseConfiguration.setFacilities(
+				loadDiseaseFacility(diseaseConfiguration.getId()).stream()
+						.map(diseaseFacility -> DatabaseHelper.getFacilityDao().queryForId(diseaseFacility.getFacility().getId()))
+						.collect(Collectors.toList()));
+		List<Facility> facilities = diseaseConfiguration.getFacilities();
+		return facilities;
+	}
+	private List<DiseaseFacility> loadDiseaseFacility(Long diseaseId) {
+		try {
+			QueryBuilder builder = diseaseFacilityDao.queryBuilder();
+			Where where = builder.where();
+			where.eq(DiseaseConfiguration.TABLE_NAME + "_id", diseaseId);
+			return (List<DiseaseFacility>) builder.query();
+		} catch (SQLException e) {
+			Log.e(getTableName(), "Could not perform loadUserRoles");
+			throw new RuntimeException(e);
+		}
 	}
 }

sormas-app/app/src/main/java/de/symeda/sormas/app/backend/facility/FacilityDao.java

@@ -26,11 +26,15 @@
 import com.j256.ormlite.stmt.Where;
 
 import android.util.Log;
+
+import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.infrastructure.facility.FacilityDto;
 import de.symeda.sormas.api.infrastructure.facility.FacilityType;
 import de.symeda.sormas.app.backend.common.AbstractDomainObject;
 import de.symeda.sormas.app.backend.common.AbstractInfrastructureAdoDao;
+import de.symeda.sormas.app.backend.common.DatabaseHelper;
 import de.symeda.sormas.app.backend.common.InfrastructureAdo;
+import de.symeda.sormas.app.backend.disease.DiseaseConfiguration;
 import de.symeda.sormas.app.backend.region.Community;
 import de.symeda.sormas.app.backend.region.District;
 import de.symeda.sormas.app.backend.region.Region;
@@ -198,6 +202,16 @@ public List<Facility> getActiveLaboratories(boolean includeOtherFacility) {
 		}
 	}
 
+	public List<Facility> getActiveLaboratoriesByDisease(Disease disease, boolean includeOtherFacility) {
+		DiseaseConfiguration diseaseConfiguration = DatabaseHelper.getDiseaseConfigurationDao().getDiseaseConfiguration(disease);
+		List<Facility> facilities = DatabaseHelper.getDiseaseConfigurationDao().getDiseaseFacilities(diseaseConfiguration);
+		if (facilities.size() < 1) {
+			facilities = getActiveLaboratories(includeOtherFacility);
+		}
+		return facilities;
+	}
+
+
 	@Override
 	public Facility saveAndSnapshot(Facility facility) {
 		throw new UnsupportedOperationException();

sormas-app/app/src/main/java/de/symeda/sormas/app/pathogentest/edit/PathogenTestEditFragment.java

@@ -112,6 +112,7 @@ record = getActivityRootData();
 		sample = record.getSample();
 		testTypeList = DataUtils.getEnumItems(PathogenTestType.class, true, getFieldVisibilityCheckers());
 		pcrTestSpecificationList = DataUtils.getEnumItems(PCRTestSpecification.class, true);
+		labList = DatabaseHelper.getFacilityDao().getActiveLaboratories(true);
 		Disease incomingDisease = record.getSample().getAssociatedCase().getDisease();
 		Disease incomingTestedDisease = record.getTestedDisease();
 		testResultVariationList = DataUtils.getEnumItems(PathogenTestResultVariant.class, true);
@@ -140,7 +141,6 @@ record = getActivityRootData();
 		testResultList = DataUtils.toItems(
 			Arrays.stream(PathogenTestResultType.values()).filter(type -> type != PathogenTestResultType.NOT_DONE).collect(Collectors.toList()),
 			true);
-		labList = DatabaseHelper.getFacilityDao().getActiveLaboratories(true);
 
 		finalClassificationList = DataUtils.toItems(Arrays.asList(FinalClassification.values()));
 	}
@@ -178,6 +178,10 @@ public void onLayoutBinding(FragmentPathogenTestEditLayoutBinding contentBinding
 		contentBinding.pathogenTestLaboratoryDatePcrPerformed.initializeDateField(getFragmentManager());
 		contentBinding.pathogenTestLaboratoryDateResultsSentDSD.initializeDateTimeField(getFragmentManager());
 		contentBinding.pathogenTestDateSampleSentRegLab.initializeDateField(getFragmentManager());
+		if (contentBinding.pathogenTestTestedDisease.getValue() != null) {
+			labList = DatabaseHelper.getFacilityDao().getActiveLaboratoriesByDisease((Disease) contentBinding.pathogenTestTestedDisease.getValue(), true);
+			contentBinding.pathogenTestLab.setSpinnerData(DataUtils.toItems(labList));
+		}
 
 	}
 
@@ -223,6 +227,13 @@ public void onChange(ControlPropertyField field) {
 				}
 
 				updateDiseaseVariantsField(contentBinding);
+				if (contentBinding.pathogenTestTestedDisease.getValue() != null) {
+					labList = DatabaseHelper.getFacilityDao().getActiveLaboratoriesByDisease((Disease) contentBinding.pathogenTestTestedDisease.getValue(), true);
+					contentBinding.pathogenTestLab.setSpinnerData(DataUtils.toItems(labList));
+				}
+				if (this.currentDisease == null || contentBinding.pathogenTestTestedDisease.getValue() != currentDisease) {
+					updateDiseaseVariantsField(contentBinding);
+				}
 			if(caseDisease != Disease.NEW_INFLUENZA){
 				testTypeList = DataUtils.toItems(
 						Arrays.asList(PathogenTestType.values()),

sormas-app/app/src/main/java/de/symeda/sormas/app/sample/edit/SampleEditFragment.java

@@ -200,8 +200,7 @@ record = getActivityRootData();
 		}
 
 		sampleMaterialList = DataUtils.getEnumItems(SampleMaterial.class, true, getFieldVisibilityCheckers());
-		sampleSourceList = DataUtils.getEnumItems(SampleSource.class, true);
-		labList = DatabaseHelper.getFacilityDao().getActiveLaboratories(true);
+		labList = DatabaseHelper.getFacilityDao().getActiveLaboratoriesByDisease(getDiseaseOfAssociatedEntity(record), true);
 		samplePurposeList = DataUtils.getEnumItems(SamplePurpose.class, true);
 		samplingReasonList = DataUtils.getEnumItems(SamplingReason.class, true, getFieldVisibilityCheckers());
 		csfReasonList = DataUtils.getEnumItems(CsfReason.class, true, getFieldVisibilityCheckers());