merge development

Author: Pa-Touche

sormas-api/src/main/java/de/symeda/sormas/api/epipulse/EpipulseLaboratoryMapper.java

@@ -17,6 +17,8 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import de.symeda.sormas.api.epidata.CaseImportedStatus;
 import de.symeda.sormas.api.epidata.ClusterType;
@@ -997,4 +999,20 @@ public static String mapMicSign(Float micValue, float lowerBound, float upperBou
 	public static String mapMicSign(Float micValue) {
 		return mapMicSign(micValue, MIC_DILUTION_LOWER_BOUND, MIC_DILUTION_UPPER_BOUND);
 	}
+
+	/** Leading (optionally sign-prefixed) decimal at the start of a free-text MIC value; accepts "0.5", "5" and ".5". */
+	private static final Pattern MIC_NUMBER = Pattern.compile("^\\s*[<>=≤≥]*\\s*(\\d+(?:\\.\\d+)?|\\.\\d+)");
+
+	/**
+	 * Extracts the numeric MIC from a free-text MIC value for EpiPulse export. Since #14036 the MIC is
+	 * stored as free text (e.g. {@code "≤0.125 mg/L"} or a genotypic result like {@code "mecA detected"}),
+	 * so this reads the leading number and ignores any sign/unit; returns {@code null} when no number is present.
+	 */
+	public static Float parseMicValue(String micText) {
+		if (micText == null) {
+			return null;
+		}
+		Matcher matcher = MIC_NUMBER.matcher(micText);
+		return matcher.find() ? Float.valueOf(matcher.group(1)) : null;
+	}
 }

sormas-api/src/main/java/de/symeda/sormas/api/externalmessage/labmessage/TestReportDto.java

@@ -176,39 +176,39 @@ public class TestReportDto extends EntityDto {
 	private RsvSubtype rsvSubtype;
 
 	// Drug susceptibility fields
-	private Float amikacinMic;
+	private String amikacinMic;
 	private DrugSusceptibilityType amikacinSusceptibility;
-	private Float bedaquilineMic;
+	private String bedaquilineMic;
 	private DrugSusceptibilityType bedaquilineSusceptibility;
-	private Float capreomycinMic;
+	private String capreomycinMic;
 	private DrugSusceptibilityType capreomycinSusceptibility;
-	private Float ciprofloxacinMic;
+	private String ciprofloxacinMic;
 	private DrugSusceptibilityType ciprofloxacinSusceptibility;
-	private Float delamanidMic;
+	private String delamanidMic;
 	private DrugSusceptibilityType delamanidSusceptibility;
-	private Float ethambutolMic;
+	private String ethambutolMic;
 	private DrugSusceptibilityType ethambutolSusceptibility;
-	private Float gatifloxacinMic;
+	private String gatifloxacinMic;
 	private DrugSusceptibilityType gatifloxacinSusceptibility;
-	private Float isoniazidMic;
+	private String isoniazidMic;
 	private DrugSusceptibilityType isoniazidSusceptibility;
-	private Float kanamycinMic;
+	private String kanamycinMic;
 	private DrugSusceptibilityType kanamycinSusceptibility;
-	private Float levofloxacinMic;
+	private String levofloxacinMic;
 	private DrugSusceptibilityType levofloxacinSusceptibility;
-	private Float moxifloxacinMic;
+	private String moxifloxacinMic;
 	private DrugSusceptibilityType moxifloxacinSusceptibility;
-	private Float ofloxacinMic;
+	private String ofloxacinMic;
 	private DrugSusceptibilityType ofloxacinSusceptibility;
-	private Float rifampicinMic;
+	private String rifampicinMic;
 	private DrugSusceptibilityType rifampicinSusceptibility;
-	private Float streptomycinMic;
+	private String streptomycinMic;
 	private DrugSusceptibilityType streptomycinSusceptibility;
-	private Float ceftriaxoneMic;
+	private String ceftriaxoneMic;
 	private DrugSusceptibilityType ceftriaxoneSusceptibility;
-	private Float penicillinMic;
+	private String penicillinMic;
 	private DrugSusceptibilityType penicillinSusceptibility;
-	private Float erythromycinMic;
+	private String erythromycinMic;
 	private DrugSusceptibilityType erythromycinSusceptibility;
 
 	private SeroGroupSpecification seroGroupSpecification;
@@ -598,11 +598,11 @@ public void setRsvSubtype(RsvSubtype rsvSubtype) {
 	}
 
 	// Drug susceptibility getters and setters
-	public Float getAmikacinMic() {
+	public String getAmikacinMic() {
 		return amikacinMic;
 	}
 
-	public void setAmikacinMic(Float amikacinMic) {
+	public void setAmikacinMic(String amikacinMic) {
 		this.amikacinMic = amikacinMic;
 	}
 
@@ -614,11 +614,11 @@ public void setAmikacinSusceptibility(DrugSusceptibilityType amikacinSusceptibil
 		this.amikacinSusceptibility = amikacinSusceptibility;
 	}
 
-	public Float getBedaquilineMic() {
+	public String getBedaquilineMic() {
 		return bedaquilineMic;
 	}
 
-	public void setBedaquilineMic(Float bedaquilineMic) {
+	public void setBedaquilineMic(String bedaquilineMic) {
 		this.bedaquilineMic = bedaquilineMic;
 	}
 
@@ -630,11 +630,11 @@ public void setBedaquilineSusceptibility(DrugSusceptibilityType bedaquilineSusce
 		this.bedaquilineSusceptibility = bedaquilineSusceptibility;
 	}
 
-	public Float getCapreomycinMic() {
+	public String getCapreomycinMic() {
 		return capreomycinMic;
 	}
 
-	public void setCapreomycinMic(Float capreomycinMic) {
+	public void setCapreomycinMic(String capreomycinMic) {
 		this.capreomycinMic = capreomycinMic;
 	}
 
@@ -646,11 +646,11 @@ public void setCapreomycinSusceptibility(DrugSusceptibilityType capreomycinSusce
 		this.capreomycinSusceptibility = capreomycinSusceptibility;
 	}
 
-	public Float getCiprofloxacinMic() {
+	public String getCiprofloxacinMic() {
 		return ciprofloxacinMic;
 	}
 
-	public void setCiprofloxacinMic(Float ciprofloxacinMic) {
+	public void setCiprofloxacinMic(String ciprofloxacinMic) {
 		this.ciprofloxacinMic = ciprofloxacinMic;
 	}
 
@@ -662,11 +662,11 @@ public void setCiprofloxacinSusceptibility(DrugSusceptibilityType ciprofloxacinS
 		this.ciprofloxacinSusceptibility = ciprofloxacinSusceptibility;
 	}
 
-	public Float getDelamanidMic() {
+	public String getDelamanidMic() {
 		return delamanidMic;
 	}
 
-	public void setDelamanidMic(Float delamanidMic) {
+	public void setDelamanidMic(String delamanidMic) {
 		this.delamanidMic = delamanidMic;
 	}
 
@@ -678,11 +678,11 @@ public void setDelamanidSusceptibility(DrugSusceptibilityType delamanidSusceptib
 		this.delamanidSusceptibility = delamanidSusceptibility;
 	}
 
-	public Float getEthambutolMic() {
+	public String getEthambutolMic() {
 		return ethambutolMic;
 	}
 
-	public void setEthambutolMic(Float ethambutolMic) {
+	public void setEthambutolMic(String ethambutolMic) {
 		this.ethambutolMic = ethambutolMic;
 	}
 
@@ -694,11 +694,11 @@ public void setEthambutolSusceptibility(DrugSusceptibilityType ethambutolSuscept
 		this.ethambutolSusceptibility = ethambutolSusceptibility;
 	}
 
-	public Float getGatifloxacinMic() {
+	public String getGatifloxacinMic() {
 		return gatifloxacinMic;
 	}
 
-	public void setGatifloxacinMic(Float gatifloxacinMic) {
+	public void setGatifloxacinMic(String gatifloxacinMic) {
 		this.gatifloxacinMic = gatifloxacinMic;
 	}
 
@@ -710,11 +710,11 @@ public void setGatifloxacinSusceptibility(DrugSusceptibilityType gatifloxacinSus
 		this.gatifloxacinSusceptibility = gatifloxacinSusceptibility;
 	}
 
-	public Float getIsoniazidMic() {
+	public String getIsoniazidMic() {
 		return isoniazidMic;
 	}
 
-	public void setIsoniazidMic(Float isoniazidMic) {
+	public void setIsoniazidMic(String isoniazidMic) {
 		this.isoniazidMic = isoniazidMic;
 	}
 
@@ -726,11 +726,11 @@ public void setIsoniazidSusceptibility(DrugSusceptibilityType isoniazidSusceptib
 		this.isoniazidSusceptibility = isoniazidSusceptibility;
 	}
 
-	public Float getKanamycinMic() {
+	public String getKanamycinMic() {
 		return kanamycinMic;
 	}
 
-	public void setKanamycinMic(Float kanamycinMic) {
+	public void setKanamycinMic(String kanamycinMic) {
 		this.kanamycinMic = kanamycinMic;
 	}
 
@@ -742,11 +742,11 @@ public void setKanamycinSusceptibility(DrugSusceptibilityType kanamycinSusceptib
 		this.kanamycinSusceptibility = kanamycinSusceptibility;
 	}
 
-	public Float getLevofloxacinMic() {
+	public String getLevofloxacinMic() {
 		return levofloxacinMic;
 	}
 
-	public void setLevofloxacinMic(Float levofloxacinMic) {
+	public void setLevofloxacinMic(String levofloxacinMic) {
 		this.levofloxacinMic = levofloxacinMic;
 	}
 
@@ -758,11 +758,11 @@ public void setLevofloxacinSusceptibility(DrugSusceptibilityType levofloxacinSus
 		this.levofloxacinSusceptibility = levofloxacinSusceptibility;
 	}
 
-	public Float getMoxifloxacinMic() {
+	public String getMoxifloxacinMic() {
 		return moxifloxacinMic;
 	}
 
-	public void setMoxifloxacinMic(Float moxifloxacinMic) {
+	public void setMoxifloxacinMic(String moxifloxacinMic) {
 		this.moxifloxacinMic = moxifloxacinMic;
 	}
 
@@ -774,11 +774,11 @@ public void setMoxifloxacinSusceptibility(DrugSusceptibilityType moxifloxacinSus
 		this.moxifloxacinSusceptibility = moxifloxacinSusceptibility;
 	}
 
-	public Float getOfloxacinMic() {
+	public String getOfloxacinMic() {
 		return ofloxacinMic;
 	}
 
-	public void setOfloxacinMic(Float ofloxacinMic) {
+	public void setOfloxacinMic(String ofloxacinMic) {
 		this.ofloxacinMic = ofloxacinMic;
 	}
 
@@ -790,11 +790,11 @@ public void setOfloxacinSusceptibility(DrugSusceptibilityType ofloxacinSusceptib
 		this.ofloxacinSusceptibility = ofloxacinSusceptibility;
 	}
 
-	public Float getRifampicinMic() {
+	public String getRifampicinMic() {
 		return rifampicinMic;
 	}
 
-	public void setRifampicinMic(Float rifampicinMic) {
+	public void setRifampicinMic(String rifampicinMic) {
 		this.rifampicinMic = rifampicinMic;
 	}
 
@@ -806,11 +806,11 @@ public void setRifampicinSusceptibility(DrugSusceptibilityType rifampicinSuscept
 		this.rifampicinSusceptibility = rifampicinSusceptibility;
 	}
 
-	public Float getStreptomycinMic() {
+	public String getStreptomycinMic() {
 		return streptomycinMic;
 	}
 
-	public void setStreptomycinMic(Float streptomycinMic) {
+	public void setStreptomycinMic(String streptomycinMic) {
 		this.streptomycinMic = streptomycinMic;
 	}
 
@@ -822,11 +822,11 @@ public void setStreptomycinSusceptibility(DrugSusceptibilityType streptomycinSus
 		this.streptomycinSusceptibility = streptomycinSusceptibility;
 	}
 
-	public Float getCeftriaxoneMic() {
+	public String getCeftriaxoneMic() {
 		return ceftriaxoneMic;
 	}
 
-	public void setCeftriaxoneMic(Float ceftriaxoneMic) {
+	public void setCeftriaxoneMic(String ceftriaxoneMic) {
 		this.ceftriaxoneMic = ceftriaxoneMic;
 	}
 
@@ -838,11 +838,11 @@ public void setCeftriaxoneSusceptibility(DrugSusceptibilityType ceftriaxoneSusce
 		this.ceftriaxoneSusceptibility = ceftriaxoneSusceptibility;
 	}
 
-	public Float getPenicillinMic() {
+	public String getPenicillinMic() {
 		return penicillinMic;
 	}
 
-	public void setPenicillinMic(Float penicillinMic) {
+	public void setPenicillinMic(String penicillinMic) {
 		this.penicillinMic = penicillinMic;
 	}
 
@@ -854,11 +854,11 @@ public void setPenicillinSusceptibility(DrugSusceptibilityType penicillinSuscept
 		this.penicillinSusceptibility = penicillinSusceptibility;
 	}
 
-	public Float getErythromycinMic() {
+	public String getErythromycinMic() {
 		return erythromycinMic;
 	}
 
-	public void setErythromycinMic(Float erythromycinMic) {
+	public void setErythromycinMic(String erythromycinMic) {
 		this.erythromycinMic = erythromycinMic;
 	}
 

sormas-api/src/main/java/de/symeda/sormas/api/i18n/Strings.java

@@ -464,6 +464,9 @@ public interface Strings {
 	String headingArchiveImmunization = "headingArchiveImmunization";
 	String headingArchiveSelfReport = "headingArchiveSelfReport";
 	String headingArchiveTravelEntry = "headingArchiveTravelEntry";
+	String headingAstInterpretation = "headingAstInterpretation";
+	String headingAstMethod = "headingAstMethod";
+	String headingAstValue = "headingAstValue";
 	String headingAutomaticDeletionStarted = "headingAutomaticDeletionStarted";
 	String headingAutomaticVaccinationStatusDetermination = "headingAutomaticVaccinationStatusDetermination";
 	String headingBulkEmailMaxAttachedFiles = "headingBulkEmailMaxAttachedFiles";
@@ -1945,7 +1948,6 @@ public interface Strings {
 	String promptSelfReportEpiWeekFrom = "promptSelfReportEpiWeekFrom";
 	String promptSelfReportEpiWeekTo = "promptSelfReportEpiWeekTo";
 	String promptSelfReportFreeTextSearch = "promptSelfReportFreeTextSearch";
-	String promptSurveillanceInterpretation = "promptSurveillanceInterpretation";
 	String promptSurvey = "promptSurvey";
 	String promptSurveyAssignedFrom = "promptSurveyAssignedFrom";
 	String promptSurveyAssignedTo = "promptSurveyAssignedTo";
@@ -1969,7 +1971,6 @@ public interface Strings {
 	String promptTreatmentTextFilter = "promptTreatmentTextFilter";
 	String promptTypeToAdd = "promptTypeToAdd";
 	String promptUserSearch = "promptUserSearch";
-	String promptZoneDiameter = "promptZoneDiameter";
 	String promtSampleDataType = "promtSampleDataType";
 	String prophylaxisStatus = "prophylaxisStatus";
 	String pseudonymizedCasesSelectedWarning = "pseudonymizedCasesSelectedWarning";

sormas-api/src/main/java/de/symeda/sormas/api/person/PersonDto.java

@@ -290,6 +290,7 @@ public class PersonDto extends PseudonymizableDto implements IsPerson {
 		Disease.POLIO,
 		Disease.UNSPECIFIED_VHF,
 		Disease.CORONAVIRUS,
+		Disease.PERTUSSIS,
 		Disease.UNDEFINED,
 		Disease.OTHER })
 	private DeathPlaceType deathPlaceType;
@@ -300,6 +301,7 @@ public class PersonDto extends PseudonymizableDto implements IsPerson {
 		Disease.POLIO,
 		Disease.UNSPECIFIED_VHF,
 		Disease.CORONAVIRUS,
+		Disease.PERTUSSIS,
 		Disease.UNDEFINED,
 		Disease.OTHER })
 	@SensitiveData

sormas-api/src/main/java/de/symeda/sormas/api/symptoms/SymptomsDto.java

@@ -805,7 +805,8 @@ public static SymptomsDto build() {
 	@SymptomGrouping(SymptomGroup.OTHER)
 	private SymptomState eyesBleeding;
 
-	@Diseases({})
+	@Diseases({
+		SALMONELLOSIS })
 	@HideForCountriesExcept(countries = {
 		CountryHelper.COUNTRY_CODE_LUXEMBOURG })
 	@SymptomGrouping(SymptomGroup.OTHER)
@@ -1936,6 +1937,7 @@ public static SymptomsDto build() {
 		GIARDIASIS,
 		CRYPTOSPORIDIOSIS,
 		MALARIA,
+		SALMONELLOSIS,
 		SHIGELLOSIS,
 		UNDEFINED,
 		OTHER })