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#6286 Change covid caseclassifications #6319

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Aug 10, 2021
Merged

#6286 Change covid caseclassifications #6319

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7edd6a9
Change covid caseclassification #6286
DavidBaldsiefen Aug 9, 2021
796ef27
#6286 - Added criteria to mobile app, caption changes
MateStrysewske Aug 10, 2021
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78 changes: 78 additions & 0 deletions ...java/de/symeda/sormas/api/caze/classification/ClassificationAnyOfSymptomsCriteriaDto.java
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@@ -0,0 +1,78 @@
package de.symeda.sormas.api.caze.classification;

import java.lang.reflect.Field;
import java.util.List;

import de.symeda.sormas.api.Disease;
import de.symeda.sormas.api.caze.CaseDataDto;
import de.symeda.sormas.api.event.EventDto;
import de.symeda.sormas.api.i18n.I18nProperties;
import de.symeda.sormas.api.i18n.Strings;
import de.symeda.sormas.api.person.PersonDto;
import de.symeda.sormas.api.sample.PathogenTestDto;
import de.symeda.sormas.api.symptoms.SymptomState;
import de.symeda.sormas.api.symptoms.SymptomsDto;
import de.symeda.sormas.api.utils.fieldvisibility.FieldVisibilityCheckers;

public class ClassificationAnyOfSymptomsCriteriaDto extends ClassificationCriteriaDto {

private SymptomState symptomState;
private FieldVisibilityCheckers fieldVisibilityCheckers;

public ClassificationAnyOfSymptomsCriteriaDto(SymptomState symptomState, Disease disease, String countryLocale) {
this.symptomState = symptomState;
fieldVisibilityCheckers = FieldVisibilityCheckers.withDisease(disease).andWithCountry(countryLocale);
}

@Override
public boolean eval(CaseDataDto caze, PersonDto person, List<PathogenTestDto> pathogenTests, List<EventDto> events) {

for (Field field : SymptomsDto.class.getDeclaredFields()) {

SymptomsDto symptomsDto = caze.getSymptoms();
if (field.getType() == SymptomState.class && fieldVisibilityCheckers.isVisible(SymptomsDto.class, field.getName())) {
field.setAccessible(true);
try {
boolean matchedFieldState = field.get(symptomsDto) == symptomState;
field.setAccessible(false);
if (matchedFieldState) {
return true;
}
} catch (IllegalAccessException e) {
throw new RuntimeException(e);
}
}
}
return false;
}

@Override
public String buildDescription() {
StringBuilder stringBuilder = new StringBuilder();

stringBuilder.append("<b> ")
.append(I18nProperties.getString(Strings.classificationSymptomsAnyOf).toUpperCase())
.append("</b>")
.append(" ")
.append(I18nProperties.getString(Strings.setTo))
.append(" ");

if (symptomState == null) {
stringBuilder.append("<b>").append(I18nProperties.getString(Strings.none).toUpperCase()).append("</b>").append("</br>");
} else {
stringBuilder.append("<b>").append(symptomState.toString().toUpperCase()).append("</b>").append("</br>");
}

for (Field field : SymptomsDto.class.getDeclaredFields()) {
if (field.getType() == SymptomState.class && fieldVisibilityCheckers.isVisible(SymptomsDto.class, field.getName())) {
stringBuilder.append(I18nProperties.getPrefixCaption(SymptomsDto.I18N_PREFIX, field.getName())).append("; ");
}
}

if (stringBuilder.length() > 0 && stringBuilder.charAt(stringBuilder.length() - 2) == ';') {
stringBuilder.delete(stringBuilder.length() - 2, stringBuilder.length() - 1);
}

return stringBuilder.toString();
}
}
1 change: 1 addition & 0 deletions sormas-api/src/main/java/de/symeda/sormas/api/i18n/Strings.java
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Expand Up @@ -44,6 +44,7 @@ public interface Strings {
String classificationRulesFor = "classificationRulesFor";
String classificationSuspect = "classificationSuspect";
String classificationSymptomsAllOf = "classificationSymptomsAllOf";
String classificationSymptomsAnyOf = "classificationSymptomsAnyOf";
String classificationYearsOrLess = "classificationYearsOrLess";
String classificationYearsOrMore = "classificationYearsOrMore";
String comparedTo = "comparedTo";
Expand Down
1 change: 1 addition & 0 deletions sormas-api/src/main/resources/strings.properties
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Expand Up @@ -107,6 +107,7 @@ classificationNotACase = Not a case Classification
classificationProbable = Probable Classification
classificationRulesFor = Classification Rules For
classificationSymptomsAllOf = All symptoms
classificationSymptomsAnyOf = Any symptom
classificationSuspect = Suspect Classification
classificationYearsOrLess = years or less
classificationYearsOrMore = years or more
Expand Down
25 changes: 13 additions & 12 deletions sormas-app/app/src/main/java/de/symeda/sormas/app/rest/RetroProvider.java
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Expand Up @@ -15,12 +15,10 @@

package de.symeda.sormas.app.rest;

import android.content.Context;
import android.net.ConnectivityManager;
import android.net.NetworkInfo;
import android.util.Log;

import androidx.fragment.app.FragmentActivity;
import java.io.IOException;
import java.lang.ref.WeakReference;
import java.util.Date;
import java.util.concurrent.TimeUnit;

import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
Expand All @@ -29,13 +27,16 @@
import com.google.gson.JsonPrimitive;
import com.google.gson.JsonSerializer;

import java.io.IOException;
import java.lang.ref.WeakReference;
import java.util.Date;
import java.util.concurrent.TimeUnit;
import android.content.Context;
import android.net.ConnectivityManager;
import android.net.NetworkInfo;
import android.util.Log;

import androidx.fragment.app.FragmentActivity;

import de.symeda.sormas.api.caze.classification.ClassificationAllOfCriteriaDto;
import de.symeda.sormas.api.caze.classification.ClassificationAllSymptomsCriteriaDto;
import de.symeda.sormas.api.caze.classification.ClassificationAnyOfSymptomsCriteriaDto;
import de.symeda.sormas.api.caze.classification.ClassificationCaseCriteriaDto;
import de.symeda.sormas.api.caze.classification.ClassificationCriteriaDto;
import de.symeda.sormas.api.caze.classification.ClassificationEpiDataCriteriaDto;
Expand Down Expand Up @@ -198,8 +199,8 @@ public static Gson initGson() {
.registerSubtype(ClassificationXOfCriteriaDto.ClassificationOneOfCompactCriteriaDto.class, "ClassificationOneOfCompactCriteriaDto")
.registerSubtype(ClassificationAllOfCriteriaDto.ClassificationAllOfCompactCriteriaDto.class, "ClassificationAllOfCompactCriteriaDto")
.registerSubtype(ClassificationEventClusterCriteriaDto.class, "ClassificationEventClusterCriteriaDto")
.registerSubtype(ClassificationAllSymptomsCriteriaDto.class, "ClassificationAllSymptomsCriteriaDto");

.registerSubtype(ClassificationAllSymptomsCriteriaDto.class, "ClassificationAllSymptomsCriteriaDto")
.registerSubtype(ClassificationAnyOfSymptomsCriteriaDto.class, "ClassificationAnyOfSymptomsCriteriaDto");

return new GsonBuilder().registerTypeAdapter(Date.class, (JsonDeserializer<Date>) (json, typeOfT, context1) -> {
if (json.isJsonNull()) {
Expand Down
24 changes: 11 additions & 13 deletions ...c/main/java/de/symeda/sormas/backend/caze/classification/CaseClassificationFacadeEjb.java
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Expand Up @@ -39,6 +39,7 @@
import de.symeda.sormas.api.caze.classification.ClassificationAllOfCriteriaDto;
import de.symeda.sormas.api.caze.classification.ClassificationAllOfCriteriaDto.ClassificationAllOfCompactCriteriaDto;
import de.symeda.sormas.api.caze.classification.ClassificationAllSymptomsCriteriaDto;
import de.symeda.sormas.api.caze.classification.ClassificationAnyOfSymptomsCriteriaDto;
import de.symeda.sormas.api.caze.classification.ClassificationCaseCriteriaDto;
import de.symeda.sormas.api.caze.classification.ClassificationCriteriaDto;
import de.symeda.sormas.api.caze.classification.ClassificationEpiDataCriteriaDto;
Expand Down Expand Up @@ -465,6 +466,7 @@ private void buildCriteria() {
PathogenTestType.SEQUENCING,
PathogenTestType.RAPID_TEST));

// confirmed_no_symptoms = positive test AND at least one symptom set to no AND all covid-relevant symptoms are anything but yes
confirmedNoSymptoms = allOf(
positiveTestResult(
Disease.CORONAVIRUS,
Expand All @@ -473,19 +475,10 @@ private void buildCriteria() {
PathogenTestType.ISOLATION,
PathogenTestType.SEQUENCING,
PathogenTestType.RAPID_TEST),
xOf(
1,
allOfSymptoms(SymptomState.NO, Disease.CORONAVIRUS),
xOf(
1,
symptom(SymptomsDto.FEVER),
symptom(SymptomsDto.DIARRHEA),
symptom(SymptomsDto.FAST_HEART_RATE),
symptom(SymptomsDto.RAPID_BREATHING),
symptom(SymptomsDto.OXYGEN_SATURATION_LOWER_94),
symptom(SymptomsDto.VOMITING),
symptom(SymptomsDto.CHILLS_SWEATS))));
anyOfSymptoms(SymptomState.NO, Disease.CORONAVIRUS),
noneOf(anyOfSymptoms(SymptomState.YES, Disease.CORONAVIRUS)));

// confirmed_unknown_symptoms = positive test AND at least one symptom set to null or unknown AND covid-relevant symptoms are anything but yes or no
confirmedUnknownSymptoms = allOf(
positiveTestResult(
Disease.CORONAVIRUS,
Expand All @@ -494,7 +487,8 @@ private void buildCriteria() {
PathogenTestType.ISOLATION,
PathogenTestType.SEQUENCING,
PathogenTestType.RAPID_TEST),
xOf(1, allOfSymptoms(null, Disease.CORONAVIRUS), allOfSymptoms(SymptomState.UNKNOWN, Disease.CORONAVIRUS)));
xOf(1, anyOfSymptoms(SymptomState.UNKNOWN, Disease.CORONAVIRUS), anyOfSymptoms(null, Disease.CORONAVIRUS)),
noneOf(anyOfSymptoms(SymptomState.NO, Disease.CORONAVIRUS), anyOfSymptoms(SymptomState.YES, Disease.CORONAVIRUS)));

addCriteria(
Disease.CORONAVIRUS,
Expand Down Expand Up @@ -614,6 +608,10 @@ private ClassificationPersonAgeBetweenYearsCriteriaDto personAgeBetweenYears(Int
return new ClassificationPersonAgeBetweenYearsCriteriaDto(lowerYearsThreshold, upperYearsThreshold);
}

private ClassificationAnyOfSymptomsCriteriaDto anyOfSymptoms(SymptomState symptomState, Disease disease) {
return new ClassificationAnyOfSymptomsCriteriaDto(symptomState, disease, configFacade.getCountryLocale());
}

private ClassificationAllSymptomsCriteriaDto allOfSymptoms(SymptomState symptomState, Disease disease) {
return new ClassificationAllSymptomsCriteriaDto(symptomState, disease, configFacade.getCountryLocale());
}
Expand Down