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Merge pull request #13386 from SORMAS-Foundation/feature-13317-integration-of-tuberculosis-disease
pathogen test form bug fixes from previous merge
2 parents 3b63518 + 8d9f578 commit fdb6573

1 file changed

Lines changed: 60 additions & 25 deletions

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‎sormas-ui/src/main/java/de/symeda/sormas/ui/samples/PathogenTestForm.java‎

Lines changed: 60 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -30,8 +30,6 @@
3030
import java.util.Map;
3131
import java.util.function.Consumer;
3232

33-
import de.symeda.sormas.api.sample.SeroGroupSpecification;
34-
import de.symeda.sormas.api.sample.SerotypingMethod;
3533
import org.apache.commons.collections4.CollectionUtils;
3634

3735
import com.vaadin.ui.Label;
@@ -61,6 +59,8 @@
6159
import de.symeda.sormas.api.sample.PathogenTestType;
6260
import de.symeda.sormas.api.sample.SampleDto;
6361
import de.symeda.sormas.api.sample.SamplePurpose;
62+
import de.symeda.sormas.api.sample.SeroGroupSpecification;
63+
import de.symeda.sormas.api.sample.SerotypingMethod;
6464
import de.symeda.sormas.api.utils.fieldaccess.UiFieldAccessCheckers;
6565
import de.symeda.sormas.api.utils.fieldvisibility.FieldVisibilityCheckers;
6666
import de.symeda.sormas.ui.therapy.DrugSusceptibilityForm;
@@ -96,15 +96,13 @@ public class PathogenTestForm extends AbstractEditForm<PathogenTestDto> {
9696
fluidRowLocs(PathogenTestDto.TYPING_ID, "") +
9797
fluidRowLocs(PathogenTestDto.TEST_DATE_TIME, PathogenTestDto.LAB) +
9898
fluidRowLocs("", PathogenTestDto.LAB_DETAILS) +
99-
fluidRowLocs(PathogenTestDto.TEST_RESULT, PathogenTestDto.TEST_RESULT_VERIFIED) +
100-
fluidRowLocs(PathogenTestDto.RIFAMPICIN_RESISTANT, PathogenTestDto.ISONIAZID_RESISTANT) +
99+
fluidRowLocs(6,PathogenTestDto.TEST_RESULT, 4, PathogenTestDto.TEST_RESULT_VERIFIED, 2,PathogenTestDto.PRELIMINARY) +
100+
fluidRowLocs(PathogenTestDto.RIFAMPICIN_RESISTANT, PathogenTestDto.ISONIAZID_RESISTANT, "", "") +
101101
fluidRowLocs(PathogenTestDto.TEST_SCALE, "") +
102102
fluidRowLocs(PathogenTestDto.STRAIN_CALL_STATUS, "") +
103103
fluidRowLocs(PathogenTestDto.SPECIE, "") +
104104
fluidRowLocs(PathogenTestDto.PATTERN_PROFILE, "") +
105105
fluidRowLocs(PathogenTestDto.DRUG_SUSCEPTIBILITY) +
106-
fluidRowLocs(PathogenTestDto.PRELIMINARY, "") +
107-
fluidRowLocs(5,PathogenTestDto.TEST_RESULT, 4, PathogenTestDto.TEST_RESULT_VERIFIED, 3,PathogenTestDto.PRELIMINARY) +
108106
fluidRowLocs(4,PathogenTestDto.SEROTYPE, 4,PathogenTestDto.SEROTYPING_METHOD, 4,PathogenTestDto.SERO_TYPING_METHOD_TEXT) +
109107
fluidRowLocs(6,PathogenTestDto.SERO_GROUP_SPECIFICATION , 6, PathogenTestDto.SERO_GROUP_SPECIFICATION_TEXT) +
110108
fluidRowLocs(PathogenTestDto.FOUR_FOLD_INCREASE_ANTIBODY_TITER, "") +
@@ -140,12 +138,23 @@ public class PathogenTestForm extends AbstractEditForm<PathogenTestDto> {
140138
private Disease disease;
141139
private TextField typingIdField;
142140
// List of tests that are used for serogrouping
143-
List<PathogenTestType> seroGrpTests = Arrays.asList(PathogenTestType.SEROGROUPING, PathogenTestType.MULTILOCUS_SEQUENCE_TYPING, PathogenTestType.SLIDE_AGGLUTINATION, PathogenTestType.WHOLE_GENOME_SEQUENCING, PathogenTestType.SEQUENCING);
144-
145-
public PathogenTestForm(AbstractSampleForm sampleForm, boolean create, int caseSampleCount, boolean isPseudonymized, boolean inJurisdiction, Disease disease) {
141+
List<PathogenTestType> seroGrpTests = Arrays.asList(
142+
PathogenTestType.SEROGROUPING,
143+
PathogenTestType.MULTILOCUS_SEQUENCE_TYPING,
144+
PathogenTestType.SLIDE_AGGLUTINATION,
145+
PathogenTestType.WHOLE_GENOME_SEQUENCING,
146+
PathogenTestType.SEQUENCING);
147+
148+
public PathogenTestForm(
149+
AbstractSampleForm sampleForm,
150+
boolean create,
151+
int caseSampleCount,
152+
boolean isPseudonymized,
153+
boolean inJurisdiction,
154+
Disease disease) {
146155
this(create, caseSampleCount, isPseudonymized, inJurisdiction, disease);
147156
this.sampleForm = sampleForm;
148-
this.disease = disease;
157+
this.disease = disease;
149158
addFields();
150159
if (create) {
151160
hideValidationUntilNextCommit();
@@ -286,11 +295,10 @@ protected void addFields() {
286295
addField(PathogenTestDto.EXTERNAL_ID);
287296
addField(PathogenTestDto.EXTERNAL_ORDER_ID);
288297
testTypeField = addField(PathogenTestDto.TEST_TYPE, ComboBox.class);
289-
TextField seroTypingMethodText = addField(PathogenTestDto.SERO_TYPING_METHOD_TEXT);
290-
seroTypingMethodText.setVisible(false);
291-
ComboBox testTypeField = addField(PathogenTestDto.TEST_TYPE, ComboBox.class);
292298
testTypeField.setItemCaptionMode(ItemCaptionMode.ID_TOSTRING);
293299
testTypeField.setImmediate(true);
300+
TextField seroTypingMethodText = addField(PathogenTestDto.SERO_TYPING_METHOD_TEXT);
301+
seroTypingMethodText.setVisible(false);
294302
pcrTestSpecification = addField(PathogenTestDto.PCR_TEST_SPECIFICATION, ComboBox.class);
295303
testTypeTextField = addField(PathogenTestDto.TEST_TYPE_TEXT, TextField.class);
296304
FieldHelper.addSoftRequiredStyle(testTypeTextField);
@@ -355,7 +363,7 @@ protected void addFields() {
355363
if (!FacadeProvider.getConfigFacade().isConfiguredCountry(CountryHelper.COUNTRY_CODE_LUXEMBOURG)) {
356364
testResultField.removeItem(PathogenTestResultType.NOT_APPLICABLE);
357365
}
358-
addField(PathogenTestDto.SEROTYPE, TextField.class);
366+
TextField seroTypeTF = addField(PathogenTestDto.SEROTYPE, TextField.class);
359367

360368
NullableOptionGroup rifampicinResistantField = addField(PathogenTestDto.RIFAMPICIN_RESISTANT, NullableOptionGroup.class);
361369
rifampicinResistantField.setVisible(false);
@@ -471,7 +479,6 @@ protected void addFields() {
471479
FieldHelper.setReadOnlyWhen(getFieldGroup(), PathogenTestDto.TEST_RESULT, tuberculosisTestResultReadOnlyDependencies, false, false);
472480
}
473481

474-
TextField seroTypeTF = addField(PathogenTestDto.SEROTYPE, TextField.class);
475482
seroTypeTF.setVisible(false);
476483
ComboBox seroTypeMetCB = addField(PathogenTestDto.SEROTYPING_METHOD, ComboBox.class);
477484
seroTypeMetCB.setVisible(false);
@@ -491,8 +498,15 @@ protected void addFields() {
491498
FieldConfiguration.withConversionError(PathogenTestDto.CT_VALUE_ORF_1, Validations.onlyNumbersAllowed),
492499
FieldConfiguration.withConversionError(PathogenTestDto.CT_VALUE_RDRP_S, Validations.onlyNumbersAllowed));
493500

494-
setVisibleClear(false, PathogenTestDto.CQ_VALUE, PathogenTestDto.CT_VALUE_E, PathogenTestDto.CT_VALUE_N, PathogenTestDto.CT_VALUE_RDRP
495-
, PathogenTestDto.CT_VALUE_S, PathogenTestDto.CT_VALUE_ORF_1, PathogenTestDto.CT_VALUE_RDRP_S);
501+
setVisibleClear(
502+
false,
503+
PathogenTestDto.CQ_VALUE,
504+
PathogenTestDto.CT_VALUE_E,
505+
PathogenTestDto.CT_VALUE_N,
506+
PathogenTestDto.CT_VALUE_RDRP,
507+
PathogenTestDto.CT_VALUE_S,
508+
PathogenTestDto.CT_VALUE_ORF_1,
509+
PathogenTestDto.CT_VALUE_RDRP_S);
496510
NullableOptionGroup testResultVerifiedField = addField(PathogenTestDto.TEST_RESULT_VERIFIED, NullableOptionGroup.class);
497511
testResultVerifiedField.setRequired(true);
498512
addField(PathogenTestDto.PRELIMINARY).addStyleName(CssStyles.VSPACE_4);
@@ -564,8 +578,18 @@ protected void addFields() {
564578
}
565579
};
566580
FieldHelper.setVisibleWhen(getFieldGroup(), PathogenTestDto.SEROTYPE, serotypeVisibilityDependencies, true);
567-
FieldHelper.setVisibleWhen(getFieldGroup(), PathogenTestDto.SERO_TYPING_METHOD_TEXT, PathogenTestDto.SEROTYPING_METHOD, SerotypingMethod.OTHER, true);
568-
FieldHelper.setVisibleWhen(getFieldGroup(), PathogenTestDto.SERO_GROUP_SPECIFICATION_TEXT, PathogenTestDto.SERO_GROUP_SPECIFICATION, SeroGroupSpecification.OTHER, true);
581+
FieldHelper.setVisibleWhen(
582+
getFieldGroup(),
583+
PathogenTestDto.SERO_TYPING_METHOD_TEXT,
584+
PathogenTestDto.SEROTYPING_METHOD,
585+
SerotypingMethod.OTHER,
586+
true);
587+
FieldHelper.setVisibleWhen(
588+
getFieldGroup(),
589+
PathogenTestDto.SERO_GROUP_SPECIFICATION_TEXT,
590+
PathogenTestDto.SERO_GROUP_SPECIFICATION,
591+
SeroGroupSpecification.OTHER,
592+
true);
569593

570594
Consumer<Disease> updateDiseaseVariantField = disease -> {
571595
List<DiseaseVariant> diseaseVariants =
@@ -580,7 +604,7 @@ protected void addFields() {
580604
diseaseField.addValueChangeListener((ValueChangeListener) valueChangeEvent -> {
581605
Disease latestDisease = (Disease) valueChangeEvent.getProperty().getValue();
582606
// If the disease changed, test type field should be updated with its respective test types
583-
if(latestDisease != disease) {
607+
if (latestDisease != disease) {
584608
testTypeField.clear();
585609
}
586610
disease = latestDisease;
@@ -609,7 +633,7 @@ protected void addFields() {
609633

610634
testTypeField.addValueChangeListener(e -> {
611635
PathogenTestType testType = (PathogenTestType) e.getProperty().getValue();
612-
if(testType !=null) {
636+
if (testType != null) {
613637
if (testType == PathogenTestType.IGM_SERUM_ANTIBODY || testType == PathogenTestType.IGG_SERUM_ANTIBODY) {
614638
fourFoldIncrease.setVisible(true);
615639
fourFoldIncrease.setEnabled(caseSampleCount >= 2);
@@ -627,10 +651,21 @@ protected void addFields() {
627651
seroTypeTF.setVisible(disease == Disease.INVASIVE_PNEUMOCOCCAL_INFECTION && seroGrpTests.contains(testType));
628652
seroGrpSepcCB.setVisible(disease == Disease.INVASIVE_MENINGOCOCCAL_INFECTION && seroGrpTests.contains(testType));
629653
testResultField.setEnabled(!seroGrpTests.contains(testType));
630-
setVisibleClear(PathogenTestType.PCR_RT_PCR == testType, PathogenTestDto.CQ_VALUE, PathogenTestDto.CT_VALUE_E, PathogenTestDto.CT_VALUE_N, PathogenTestDto.CT_VALUE_RDRP
631-
, PathogenTestDto.CT_VALUE_S, PathogenTestDto.CT_VALUE_ORF_1, PathogenTestDto.CT_VALUE_RDRP_S);
632-
}else{
633-
setVisibleClear(testTypeField.getValue() != null, PathogenTestDto.SEROTYPE, PathogenTestDto.SEROTYPING_METHOD, PathogenTestDto.SERO_GROUP_SPECIFICATION);
654+
setVisibleClear(
655+
PathogenTestType.PCR_RT_PCR == testType,
656+
PathogenTestDto.CQ_VALUE,
657+
PathogenTestDto.CT_VALUE_E,
658+
PathogenTestDto.CT_VALUE_N,
659+
PathogenTestDto.CT_VALUE_RDRP,
660+
PathogenTestDto.CT_VALUE_S,
661+
PathogenTestDto.CT_VALUE_ORF_1,
662+
PathogenTestDto.CT_VALUE_RDRP_S);
663+
} else {
664+
setVisibleClear(
665+
testTypeField.getValue() != null,
666+
PathogenTestDto.SEROTYPE,
667+
PathogenTestDto.SEROTYPING_METHOD,
668+
PathogenTestDto.SERO_GROUP_SPECIFICATION);
634669
testResultField.clear();
635670
testResultField.setEnabled(true);
636671
}

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