SORMAS-Foundation#3957 Add typing ID to specific pathogen test types (SORMAS-Foundation#4232)

DavidBaldsiefen · web-flow · commit 832af4c529c8 · 2021-02-04T15:17:34.000+01:00
* Add basic event generator for devmode SORMAS-Foundation#4185 * Revert "Add basic event generator for devmode SORMAS-Foundation#4185" This reverts commit 0b75f28. * Add new pathogen test type, add typing id SORMAS-Foundation#3957 * Add typing ID to app SORMAS-Foundation#3957 * Add i18n translation SORMAS-Foundation#3957 * Add conditions to typing id display in app SORMAS-Foundation#3957 * Revert "Add conditions to typing id display in app SORMAS-Foundation#3957" This reverts commit 079b3aa. * Fix app display condition for typing id SORMAS-Foundation#3957 * Add basic event generator for devmode SORMAS-Foundation#4185 * Revert "Add basic event generator for devmode SORMAS-Foundation#4185" This reverts commit 0b75f28. * Merge development into feature-3957-pathogen-test-typingid * Fix Formatting SORMAS-Foundation#3957
diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/i18n/Captions.java b/sormas-api/src/main/java/de/symeda/sormas/api/i18n/Captions.java
@@ -1220,6 +1220,7 @@ public interface Captions {
 	String PathogenTest_testResultVerified = "PathogenTest.testResultVerified";
 	String PathogenTest_testType = "PathogenTest.testType";
 	String PathogenTest_testTypeText = "PathogenTest.testTypeText";
+	String PathogenTest_typingId = "PathogenTest.typingId";
 	String pathogenTestNewResult = "pathogenTestNewResult";
 	String pathogenTestNewTest = "pathogenTestNewTest";
 	String PathogenTests = "PathogenTests";
diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/sample/PathogenTestDto.java b/sormas-api/src/main/java/de/symeda/sormas/api/sample/PathogenTestDto.java
@@ -39,6 +39,7 @@ public class PathogenTestDto extends PseudonymizableDto {
 	public static final String SAMPLE = "sample";
 	public static final String TESTED_DISEASE = "testedDisease";
 	public static final String TESTED_DISEASE_DETAILS = "testedDiseaseDetails";
+	public static final String TYPING_ID = "typingId";
 	public static final String TEST_TYPE = "testType";
 	public static final String TEST_TYPE_TEXT = "testTypeText";
 	public static final String TEST_DATE_TIME = "testDateTime";
@@ -57,6 +58,7 @@ public class PathogenTestDto extends PseudonymizableDto {
 	@Required
 	private Disease testedDisease;
 	private String testedDiseaseDetails;
+	private String typingId;
 	@Required
 	private PathogenTestType testType;
 	@SensitiveData
@@ -133,6 +135,14 @@ public void setTestedDiseaseDetails(String testedDiseaseDetails) {
 		this.testedDiseaseDetails = testedDiseaseDetails;
 	}
 
+	public String getTypingId() {
+		return typingId;
+	}
+
+	public void setTypingId(String typingId) {
+		this.typingId = typingId;
+	}
+
 	public PathogenTestType getTestType() {
 		return testType;
 	}
diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/sample/PathogenTestType.java b/sormas-api/src/main/java/de/symeda/sormas/api/sample/PathogenTestType.java
@@ -41,6 +41,7 @@ public enum PathogenTestType {
 	LATEX_AGGLUTINATION,
 	CQ_VALUE_DETECTION,
 	SEQUENCING,
+	DNA_MICROARRAY,
 	OTHER;
 
 	public String toString() {
diff --git a/sormas-api/src/main/resources/captions.properties b/sormas-api/src/main/resources/captions.properties
@@ -1339,6 +1339,7 @@ PathogenTest.testType=Type of test
 PathogenTest.testTypeText=Specify test details
 PathogenTest.testedDisease=Tested disease
 PathogenTest.testedDiseaseDetails=Tested disease name
+PathogenTest.typingId=Typing ID
 PathogenTest.serotype=Serotype
 PathogenTest.cqValue=CQ/CT Value
 
diff --git a/sormas-api/src/main/resources/captions_de-DE.properties b/sormas-api/src/main/resources/captions_de-DE.properties
@@ -1329,6 +1329,7 @@ PathogenTest.testType=Art des Tests
 PathogenTest.testTypeText=Testdetails angeben
 PathogenTest.testedDisease=Getestete Krankheit
 PathogenTest.testedDiseaseDetails=Name der getesteten Krankheit
+PathogenTest.typingId=Typisierungs ID
 PathogenTest.serotype=Serotyp
 PathogenTest.cqValue=CQ/CT Wert
 
diff --git a/sormas-api/src/main/resources/enum.properties b/sormas-api/src/main/resources/enum.properties
@@ -733,6 +733,7 @@ PathogenTestType.ANTIGEN_DETECTION = Antigen detection test
 PathogenTestType.CULTURE = Culture
 PathogenTestType.DENGUE_FEVER_ANTIBODIES = Dengue fever neutralizing antibodies
 PathogenTestType.DENGUE_FEVER_IGM = Dengue fever IgM serum antibody
+PathogenTestType.DNA_MICROARRAY = DNA Microarray
 PathogenTestType.HISTOPATHOLOGY = Histopathology
 PathogenTestType.IGG_SERUM_ANTIBODY = IgG serum antibody
 PathogenTestType.IGM_SERUM_ANTIBODY = IgM serum antibody
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
@@ -153,7 +153,7 @@ public class DatabaseHelper extends OrmLiteSqliteOpenHelper {
 	public static final String DATABASE_NAME = "sormas.db";
 	// any time you make changes to your database objects, you may have to increase the database version
 
-	public static final int DATABASE_VERSION = 267;
+	public static final int DATABASE_VERSION = 268;
 
 	private static DatabaseHelper instance = null;
 
@@ -1910,6 +1910,10 @@ public void onUpgrade(SQLiteDatabase db, ConnectionSource connectionSource, int
 				getDao(Case.class).executeRaw(
 					"ALTER TABLE cases ADD COLUMN diseaseVariant_id bigint REFERENCES diseaseVariant(id);");
 
+		      case 267:
+			  	currentVersion = 267;
+			  	getDao(PathogenTest.class).executeRaw("ALTER TABLE pathogentest ADD COLUMN typingId text;");
+
 				// ATTENTION: break should only be done after last version
 				break;
 
diff --git a/sormas-app/app/src/main/java/de/symeda/sormas/app/backend/sample/PathogenTest.java b/sormas-app/app/src/main/java/de/symeda/sormas/app/backend/sample/PathogenTest.java
@@ -64,6 +64,9 @@ public class PathogenTest extends PseudonymizableAdo {
 	@Column(length = COLUMN_LENGTH_DEFAULT)
 	private String testedDiseaseDetails;
 
+	@Column
+	private String typingId;
+
 	@Enumerated(EnumType.STRING)
 	@Column
 	private PathogenTestResultType testResult;
@@ -127,6 +130,14 @@ public void setTestedDiseaseDetails(String testedDiseaseDetails) {
 		this.testedDiseaseDetails = testedDiseaseDetails;
 	}
 
+	public String getTypingId() {
+		return typingId;
+	}
+
+	public void setTypingId(String typingId) {
+		this.typingId = typingId;
+	}
+
 	public PathogenTestResultType getTestResult() {
 		return testResult;
 	}
diff --git a/sormas-app/app/src/main/java/de/symeda/sormas/app/backend/sample/PathogenTestDtoHelper.java b/sormas-app/app/src/main/java/de/symeda/sormas/app/backend/sample/PathogenTestDtoHelper.java
@@ -66,6 +66,7 @@ protected void fillInnerFromDto(PathogenTest target, PathogenTestDto source) {
 		target.setTestTypeText(source.getTestTypeText());
 		target.setTestedDisease(source.getTestedDisease());
 		target.setTestedDiseaseDetails(source.getTestedDiseaseDetails());
+		target.setTypingId(source.getTypingId());
 		target.setTestResultVerified(source.getTestResultVerified());
 		target.setTestResultText(source.getTestResultText());
 		target.setFourFoldIncreaseAntibodyTiter(source.isFourFoldIncreaseAntibodyTiter());
@@ -92,6 +93,7 @@ protected void fillInnerFromAdo(PathogenTestDto target, PathogenTest source) {
 		target.setTestTypeText(source.getTestTypeText());
 		target.setTestedDisease(source.getTestedDisease());
 		target.setTestedDiseaseDetails(source.getTestedDiseaseDetails());
+		target.setTypingId(source.getTypingId());
 
 		if (source.getLab() != null) {
 			Facility lab = DatabaseHelper.getFacilityDao().queryForId(source.getLab().getId());
diff --git a/sormas-app/app/src/main/res/layout/fragment_pathogen_test_edit_layout.xml b/sormas-app/app/src/main/res/layout/fragment_pathogen_test_edit_layout.xml
@@ -83,6 +83,15 @@
                     app:required="true"
                     app:value="@={data.testedDiseaseDetails}"/>
 
+                <de.symeda.sormas.app.component.controls.ControlTextEditField
+                        android:id="@+id/pathogenTest_typingId"
+                        style="@style/ControlSingleColumnStyle"
+                        app:dependencyParentField="@{pathogenTestTestType}"
+                        app:dependencyParentValue="@{PathogenTestType.DNA_MICROARRAY}"
+                        app:dependencyParentValue2="@{PathogenTestType.PCR_RT_PCR}"
+                        app:dependencyParentValue3="@{PathogenTestType.SEQUENCING}"
+                        app:value="@={data.typingId}"/>
+
                 <de.symeda.sormas.app.component.controls.ControlDateTimeField
                     android:id="@+id/pathogenTest_testDateTime"
                     app:dateHint="@string/caption_date_of_sampling"
diff --git a/sormas-app/app/src/main/res/layout/fragment_pathogen_test_read_layout.xml b/sormas-app/app/src/main/res/layout/fragment_pathogen_test_read_layout.xml
@@ -73,6 +73,16 @@
 
                 </LinearLayout>
 
+                <de.symeda.sormas.app.component.controls.ControlTextReadField
+                        android:id="@+id/pathogenTest_typingId"
+                        app:value="@{data.typingId}"
+                        app:dependencyParentField="@{pathogenTestTestType}"
+                        app:dependencyParentValue="@{PathogenTestType.DNA_MICROARRAY}"
+                        app:dependencyParentValue2="@{PathogenTestType.PCR_RT_PCR}"
+                        app:dependencyParentValue3="@{PathogenTestType.SEQUENCING}"
+                        app:valueFormat="@string/two_strings_with_hyphen_format"
+                        style="@style/ControlSingleColumnStyle" />
+
                 <LinearLayout
                     android:layout_width="match_parent"
                     android:layout_height="wrap_content"
diff --git a/sormas-backend/src/main/java/de/symeda/sormas/backend/sample/PathogenTest.java b/sormas-backend/src/main/java/de/symeda/sormas/backend/sample/PathogenTest.java
@@ -50,6 +50,7 @@ public class PathogenTest extends CoreAdo {
 
 	public static final String SAMPLE = "sample";
 	public static final String TESTED_DISEASE = "testedDisease";
+	public static final String TYPING_ID = "typingId";
 	public static final String TEST_TYPE = "testType";
 	public static final String TEST_TYPE_TEXT = "testTypeText";
 	public static final String TEST_DATE_TIME = "testDateTime";
@@ -66,6 +67,7 @@ public class PathogenTest extends CoreAdo {
 	private Sample sample;
 	private Disease testedDisease;
 	private String testedDiseaseDetails;
+	private String typingId;
 	private PathogenTestType testType;
 	private String testTypeText;
 	private Date testDateTime;
@@ -107,6 +109,15 @@ public void setTestedDiseaseDetails(String testedDiseaseDetails) {
 		this.testedDiseaseDetails = testedDiseaseDetails;
 	}
 
+	@Column
+	public String getTypingId() {
+		return typingId;
+	}
+
+	public void setTypingId(String typingId) {
+		this.typingId = typingId;
+	}
+
 	@Enumerated(EnumType.STRING)
 	@Column(nullable = false)
 	public PathogenTestType getTestType() {
diff --git a/sormas-backend/src/main/java/de/symeda/sormas/backend/sample/PathogenTestFacadeEjb.java b/sormas-backend/src/main/java/de/symeda/sormas/backend/sample/PathogenTestFacadeEjb.java
@@ -276,6 +276,7 @@ public PathogenTest fromDto(@NotNull PathogenTestDto source, boolean checkChange
 		target.setSample(sampleService.getByReferenceDto(source.getSample()));
 		target.setTestedDisease(source.getTestedDisease());
 		target.setTestedDiseaseDetails(source.getTestedDiseaseDetails());
+		target.setTypingId(source.getTypingId());
 		target.setTestType(source.getTestType());
 		target.setTestTypeText(source.getTestTypeText());
 		target.setTestDateTime(source.getTestDateTime());
@@ -326,6 +327,7 @@ public static PathogenTestDto toDto(PathogenTest source) {
 		target.setSample(SampleFacadeEjb.toReferenceDto(source.getSample()));
 		target.setTestedDisease(source.getTestedDisease());
 		target.setTestedDiseaseDetails(source.getTestedDiseaseDetails());
+		target.setTypingId(source.getTypingId());
 		target.setTestType(source.getTestType());
 		target.setTestTypeText(source.getTestTypeText());
 		target.setTestDateTime(source.getTestDateTime());
diff --git a/sormas-backend/src/main/resources/sql/sormas_schema.sql b/sormas-backend/src/main/resources/sql/sormas_schema.sql
@@ -6355,5 +6355,11 @@ ALTER TABLE cases_history ADD COLUMN diseasevariant_id bigint;
 ALTER TABLE cases ADD CONSTRAINT fk_cases_diseasevariant_id FOREIGN KEY (diseasevariant_id) REFERENCES diseasevariant(id);
 
 INSERT INTO schema_version (version_number, comment) VALUES (316, 'Add DiseaseVariant entity #4042');
+              
+ -- 2020-02-03
+ALTER TABLE pathogentest ADD COLUMN typingId text;
+ALTER TABLE pathogentest_history ADD COLUMN typingId text;
+
+INSERT INTO schema_version (version_number, comment) VALUES (317, 'Add typing ID to pathogen tests #3957');
 
 -- *** Insert new sql commands BEFORE this line ***
diff --git a/sormas-ui/src/main/java/de/symeda/sormas/ui/samples/PathogenTestForm.java b/sormas-ui/src/main/java/de/symeda/sormas/ui/samples/PathogenTestForm.java
@@ -58,6 +58,7 @@ public class PathogenTestForm extends AbstractEditForm<PathogenTestDto> {
 	//@formatter:off
 	private static final String HTML_LAYOUT = 
 			fluidRowLocs(PathogenTestDto.TEST_TYPE, PathogenTestDto.TESTED_DISEASE) +
+			fluidRowLocs("", PathogenTestDto.TYPING_ID) +
 			fluidRowLocs(PathogenTestDto.TEST_TYPE_TEXT, PathogenTestDto.TESTED_DISEASE_DETAILS) +
 			fluidRowLocs(PathogenTestDto.TEST_DATE_TIME, PathogenTestDto.LAB) +
 			fluidRowLocs("", PathogenTestDto.LAB_DETAILS) +
@@ -113,6 +114,8 @@ protected void addFields() {
 		lab.addItems(FacadeProvider.getFacilityFacade().getAllActiveLaboratories(true));
 		TextField labDetails = addField(PathogenTestDto.LAB_DETAILS, TextField.class);
 		labDetails.setVisible(false);
+		TextField typingIdField = addField(PathogenTestDto.TYPING_ID, TextField.class);
+		typingIdField.setVisible(false);
 		addDiseaseField(PathogenTestDto.TESTED_DISEASE, true);
 		addField(PathogenTestDto.TESTED_DISEASE_DETAILS, TextField.class);
 
@@ -141,7 +144,12 @@ protected void addFields() {
 			PathogenTestDto.TESTED_DISEASE,
 			Arrays.asList(Disease.OTHER),
 			true);
-
+		FieldHelper.setVisibleWhen(
+			getFieldGroup(),
+			PathogenTestDto.TYPING_ID,
+			PathogenTestDto.TEST_TYPE,
+			Arrays.asList(PathogenTestType.PCR_RT_PCR, PathogenTestType.DNA_MICROARRAY, PathogenTestType.SEQUENCING),
+			true);
 		Map<Object, List<Object>> serotypeVisibilityDependencies = new HashMap<Object, List<Object>>() {
 
 			private static final long serialVersionUID = 1967952323596082247L;
