#180: Implemented sample features for IDSR. Added suspected disease f…

…ield
ePareto-Information-System · Oct 14, 2024 · f60880c · f60880c
1 parent 8c2d769
commit f60880c
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Showing 5 changed files with 47 additions and 1 deletion.
diff --git a/sormas-app/app/src/main/java/de/symeda/sormas/app/backend/common/DatabaseHelper.java b/sormas-app/app/src/main/java/de/symeda/sormas/app/backend/common/DatabaseHelper.java
@@ -3462,9 +3462,12 @@ public void onUpgrade(SQLiteDatabase db, ConnectionSource connectionSource, int
 					getDao(Person.class).executeRaw("ALTER TABLE person ADD COLUMN applicable varchar(255);");
 				case 369:
 					currentVersion = 369;
+					getDao(Hospitalization.class).executeRaw("ALTER TABLE hospitalizations ADD COLUMN dateFormSentToDistrict Date;");
 					getDao(EpiData.class).executeRaw("ALTER TABLE epidata ADD COLUMN recentTravelOutbreak varchar(255);");
 					getDao(EpiData.class).executeRaw("ALTER TABLE epidata ADD COLUMN contactSimilarOutbreak varchar(255);");
 					getDao(EpiData.class).executeRaw("ALTER TABLE epidata ADD COLUMN contactSickAnimals varchar(255);");
+					getDao(Sample.class).executeRaw("ALTER TABLE samples ADD COLUMN suspectedDisease VARCHAR(255);");
+
 				// ATTENTION: break should only be done after last version
 				break;
 			default:

diff --git a/sormas-app/app/src/main/java/de/symeda/sormas/app/backend/sample/Sample.java b/sormas-app/app/src/main/java/de/symeda/sormas/app/backend/sample/Sample.java
@@ -36,6 +36,7 @@
 import javax.persistence.Enumerated;
 import javax.persistence.Transient;
 
+import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.sample.AdditionalTestType;
 import de.symeda.sormas.api.sample.IpSampleTestType;
 import de.symeda.sormas.api.sample.FilterChangingFrequency;
@@ -161,7 +162,8 @@ public class Sample extends PseudonymizableAdo {
 
 	@Enumerated(EnumType.STRING)
 	private PathogenTestResultType pathogenTestResult;
-
+	@Enumerated(EnumType.STRING)
+	private Disease suspectedDisease;
 	@DatabaseField
 	private Boolean pathogenTestingRequested;
 
@@ -478,6 +480,14 @@ public PathogenTestResultType getPathogenTestResult() {
 		return pathogenTestResult;
 	}
 
+	public Disease getSuspectedDisease() {
+		return suspectedDisease;
+	}
+
+	public void setSuspectedDisease(Disease suspectedDisease) {
+		this.suspectedDisease = suspectedDisease;
+	}
+
 	public void setPathogenTestResult(PathogenTestResultType pathogenTestResult) {
 		this.pathogenTestResult = pathogenTestResult;
 	}

diff --git a/sormas-app/app/src/main/java/de/symeda/sormas/app/backend/sample/SampleDtoHelper.java b/sormas-app/app/src/main/java/de/symeda/sormas/app/backend/sample/SampleDtoHelper.java
@@ -95,6 +95,7 @@ public void fillInnerFromDto(Sample target, SampleDto source) {
 		target.setShipped(source.isShipped());
 		target.setReceived(source.isReceived());
 		target.setPathogenTestResult(source.getPathogenTestResult());
+		target.setSuspectedDisease(source.getSuspectedDisease());
 		target.setPathogenTestingRequested(source.getPathogenTestingRequested());
 		target.setAdditionalTestingRequested(source.getAdditionalTestingRequested());
 		target.setRequestedPathogenTests(source.getRequestedPathogenTests());
@@ -195,6 +196,7 @@ public void fillInnerFromAdo(SampleDto target, Sample source) {
 		target.setShipped(source.isShipped());
 		target.setReceived(source.isReceived());
 		target.setPathogenTestResult(source.getPathogenTestResult());
+		target.setSuspectedDisease(source.getSuspectedDisease());
 		target.setPathogenTestingRequested(source.getPathogenTestingRequested());
 		target.setAdditionalTestingRequested(source.getAdditionalTestingRequested());
 		target.setRequestedPathogenTests(source.getRequestedPathogenTests());

diff --git a/sormas-app/app/src/main/java/de/symeda/sormas/app/sample/edit/SampleEditFragment.java b/sormas-app/app/src/main/java/de/symeda/sormas/app/sample/edit/SampleEditFragment.java
@@ -82,13 +82,15 @@ public class SampleEditFragment extends BaseEditFragment<FragmentSampleEditLayou
 
 	private List<Item> sampleMaterialList;
 	private List<Item> sampleSourceList;
+	private List<Item> suspectedDiseaseList;
 	private List<Facility> labList;
 	private List<Item> samplePurposeList;
 	private List<Item> samplingReasonList;
 	private List<String> requestedPathogenTests = new ArrayList<>();
 	private List<String> requestedSampleMaterials = new ArrayList<>();
 	private List<String> requestedAdditionalTests = new ArrayList<>();
 	private List<Item> finalTestResults;
+	private List<Item> suspectedList;
 	private List<String> ipSampleTestResults = new ArrayList<>();
 	private List<Item> posNegList;
 	private List<Item> posNegEqList;
@@ -188,6 +190,7 @@ record = getActivityRootData();
 		labList = DatabaseHelper.getFacilityDao().getActiveLaboratories(true);
 		samplePurposeList = DataUtils.getEnumItems(SamplePurpose.class, true);
 		samplingReasonList = DataUtils.getEnumItems(SamplingReason.class, true, getFieldVisibilityCheckers());
+		suspectedList = DataUtils.getEnumItems(Disease.class, true);
 		posNegList = DataUtils.getEnumItems(PosNegEq.class, true);
 		posNegEqList = DataUtils.getEnumItems(PosNegEq.class, true);
 		posNegList.remove(new Item<>(PosNegEq.EQU.toString(), PosNegEq.EQU));
@@ -299,6 +302,7 @@ public void onAfterLayoutBinding(final FragmentSampleEditLayoutBinding contentBi
 			}
 		}*/
 		contentBinding.samplePathogenTestResult.initializeSpinner(finalTestResults);
+
 		contentBinding.samplePurpose.initializeSpinner(samplePurposeList, field -> {
 			SamplePurpose samplePurpose = (SamplePurpose) field.getValue();
 			if (SamplePurpose.EXTERNAL == samplePurpose) {
@@ -317,6 +321,7 @@ public void onAfterLayoutBinding(final FragmentSampleEditLayoutBinding contentBi
 			}
 		});
 
+		contentBinding.sampleSuspectedDisease.initializeSpinner(suspectedList);
 		contentBinding.sampleSamplingReason.initializeSpinner(samplingReasonList);
 
 
@@ -433,6 +438,8 @@ public void onAfterLayoutBinding(final FragmentSampleEditLayoutBinding contentBi
 		switch (record.getAssociatedCase().getDisease()){
 			case YELLOW_FEVER:
 				handleYellowFever();
+			case IMMEDIATE_CASE_BASED_FORM_OTHER_CONDITIONS:
+				handleIDSR();
 		}
 
 
@@ -488,4 +495,22 @@ private void handleYellowFever() {
 		getContentBinding().samplePurpose.setVisibility(GONE);
 		getContentBinding().samplePathogenTestingRequested.setVisibility(GONE);
 	}
+
+	private void handleIDSR() {
+		List<Disease> idsrSuspectedList = Arrays.asList(
+				Disease.AHF,
+				Disease.AFP,
+				Disease.CORONAVIRUS,
+				Disease.CHIKUNGUNYA,
+				Disease.CHOLERA,
+				Disease.CONGENITAL_RUBELLA,
+				Disease.DENGUE,
+				Disease.EVD,
+				Disease.FOODBORNE_ILLNESS
+		);
+		getContentBinding().sampleSuspectedDisease.initializeSpinner(DataUtils.toItems(idsrSuspectedList));
+		getContentBinding().samplePurpose.setValue(SamplePurpose.EXTERNAL);
+		getContentBinding().samplePurpose.setVisibility(GONE);
+		getContentBinding().samplePathogenTestingRequested.setVisibility(GONE);
+	}
 }
diff --git a/sormas-app/app/src/main/res/layout/fragment_sample_edit_layout.xml b/sormas-app/app/src/main/res/layout/fragment_sample_edit_layout.xml
@@ -250,6 +250,12 @@
                     app:value="@={data.pathogenTestResult}"
                     style="@style/ControlSingleColumnStyle" />
 
+                <de.symeda.sormas.app.component.controls.ControlSpinnerField
+                    android:id="@+id/sample_suspectedDisease"
+                    app:required="true"
+                    app:value="@={data.suspectedDisease}"
+                    style="@style/ControlSingleColumnStyle" />
+
                 <LinearLayout
                     android:id="@+id/external_sample_fields_layout"
                     android:orientation="vertical"