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0.8.2
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@holger-stenzhorn
holger-stenzhorn committed Jul 26, 2022
1 parent 505c350 commit 3032815
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Showing 9 changed files with 195 additions and 194 deletions.
8 changes: 4 additions & 4 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,15 @@

<groupId>de.difuture.uds</groupId>
<artifactId>odm2fhir</artifactId>
<version>0.8.1</version>
<version>0.8.2</version>

<name>ODM2FHIR</name>
<description>Mapper for GECCO based study/patient data in CDISC ODM to HL7 FHIR</description>

<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.7.1</version>
<version>2.7.2</version>
</parent>

<properties>
Expand All @@ -25,12 +25,12 @@
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>

<hapi-fhir.version>6.0.2</hapi-fhir.version>
<hapi-fhir.version>6.0.4</hapi-fhir.version>
<jackson.version>2.13.3</jackson.version>
<lombok.version>1.18.24</lombok.version>
<spring-boot.version>${project.parent.version}</spring-boot.version>
<spring-retry.version>1.3.3</spring-retry.version>
<woodstox.version>6.2.8</woodstox.version>
<woodstox.version>6.3.0</woodstox.version>

<maven-antrun-plugin.version>3.1.0</maven-antrun-plugin.version>
<maven-compiler-plugin.version>3.10.1</maven-compiler-plugin.version>
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13 changes: 7 additions & 6 deletions src/main/java/de/difuture/uds/odm2fhir/fhir/util/ResourceValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -122,11 +122,11 @@ private void init() throws IOException {
.forEach(prePopulatedValidationSupport::addResource);

var validationSupportChain = new ValidationSupportChain(
prePopulatedValidationSupport,
new DefaultProfileValidationSupport(forR4Cached()),
new InMemoryTerminologyServerValidationSupport(forR4Cached()),
new CommonCodeSystemsTerminologyService(forR4Cached()),
new SnapshotGeneratingValidationSupport(forR4Cached()),
prePopulatedValidationSupport);
new InMemoryTerminologyServerValidationSupport(forR4Cached()),
new SnapshotGeneratingValidationSupport(forR4Cached()));

if (terminologyserverUrl.isAbsolute()) {
forR4Cached().getRestfulClientFactory().setHttpClient(HTTP_CLIENT_BUILDER.build());
Expand Down Expand Up @@ -165,13 +165,14 @@ public boolean validate(DomainResource domainResource) {
case INFORMATION -> log.info(message.toString());
}
})
.sorted(comparing(SingleValidationMessage::getSeverity).reversed());
.sorted(comparing(SingleValidationMessage::getSeverity))
.toList();

if (!isEmpty(validationResult.getMessages())) {
if (!isEmpty(messages)) {
log.debug(JSON_PARSER.encodeResourceToString(domainResource));
}

return validationResult.isSuccessful() || messages.noneMatch(message -> message.getSeverity() == ERROR);
return messages.stream().map(SingleValidationMessage::getSeverity).noneMatch(ERROR::equals);
}

}
2 changes: 1 addition & 1 deletion src/main/resources/odm/redcap/datadictionary-pre.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -498,7 +498,7 @@ pa_co2_unit,vitalparameter,PaCO2,dropdown,Kohlendioxidpartialdruck (PaCO2) Einhe
pa_co2_code,vitalparameter,,text,2.16.840.1.113883.6.1_11557-6,,,,,,,,,,,,,"@HIDDEN @DEFAULT=""2.16.840.1.113883.6.1_11557-6"""
pa_co2,vitalparameter,,text,Kohlendioxidpartialdruck (PaCO2),,mm[Hg]PaCO2,integer,0,200,,,,,,,,
pa_o2_unit,vitalparameter,PaO2,dropdown,Sauerstoffpartialdruck (PaO2) Einheit,"1,mm[Hg]",,,,,,,,,,,,"@DEFAULT=""1""@READONLY"
pa_o2_code,vitalparameter,,text,2.16.840.1.113883.6.1_11557-8,,,,,,,,,,,,,"@HIDDEN @DEFAULT=""2.16.840.1.113883.6.1_11557-8"""
pa_o2_code,vitalparameter,,text,2.16.840.1.113883.6.1_11556-8,,,,,,,,,,,,,"@HIDDEN @DEFAULT=""2.16.840.1.113883.6.1_11556-8"""
pa_o2,vitalparameter,,text,Sauerstoffpartialdruck (PaO2),,mm[Hg]PaO2,integer,0,200,,,,,,,,
fi_o2_unit,vitalparameter,FiO2,dropdown,Inspiratorische Sauerstoffkonzentration (FiO2) Einheit,"1,%",,,,,,,,,,,,"@DEFAULT=""1""@READONLY"
fi_o2_code,vitalparameter,,text,2.16.840.1.113883.6.1_3150-0__2.16.840.1.113883.6.96_250774007,,,,,,,,,,,,,"@HIDDEN @DEFAULT=""2.16.840.1.113883.6.1_3150-0__2.16.840.1.113883.6.96_250774007"""
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2 changes: 1 addition & 1 deletion src/main/resources/odm/redcap/mapping.properties
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Original file line number Diff line number Diff line change
Expand Up @@ -244,7 +244,7 @@ organtransplantiert_nieren=1.2.276.0.76.5.502_Z94.0__2.16.840.1.113883.6.96_1814
organtransplantiert_sehne=1.2.276.0.76.5.502_Z94.9__2.16.840.1.113883.6.96_13024002__2.16.840.1.113883.6.96_410605003,1.2.276.0.76.5.502_Z94.9__2.16.840.1.113883.6.96_13024002__2.16.840.1.113883.6.96_410594000,1.2.276.0.76.5.502_Z94.9__2.16.840.1.113883.6.96_13024002__2.16.840.1.113883.6.96_261665006
p_hwert_code=2.16.840.1.113883.6.1_11558-4
pa_co2_code=2.16.840.1.113883.6.1_11557-6
pa_o2_code=2.16.840.1.113883.6.1_11557-8
pa_o2_code=2.16.840.1.113883.6.1_11556-8
pct_procalcitonin_code=2.16.840.1.113883.6.1_75241-0__2.16.840.1.113883.6.1_33959-8
pct_procalcitonin_loinc_1=75241-0,33959-8
periphere_sauerstoffsattigung_code=2.16.840.1.113883.6.1_2708-6__2.16.840.1.113883.6.1_59408-5__2.16.840.1.113883.6.1_20564-1__2.16.840.1.113883.6.96_431314004
Expand Down
16 changes: 8 additions & 8 deletions src/test/resources/DIS_Synthetic_Data_2021-04-15.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -444,7 +444,7 @@
<ItemData ItemOID="pa_o2_unit" Value="1"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.pa_o2_code" ItemGroupRepeatKey="1">
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11557-8"/>
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11556-8"/>
<ItemData ItemOID="pa_o2" Value="119"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.fi_o2_unit" ItemGroupRepeatKey="1">
Expand Down Expand Up @@ -2129,7 +2129,7 @@
<ItemData ItemOID="pa_o2_unit" Value="1"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.pa_o2_code" ItemGroupRepeatKey="1">
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11557-8"/>
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11556-8"/>
<ItemData ItemOID="pa_o2" Value="50"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.fi_o2_unit" ItemGroupRepeatKey="1">
Expand Down Expand Up @@ -3814,7 +3814,7 @@
<ItemData ItemOID="pa_o2_unit" Value="1"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.pa_o2_code" ItemGroupRepeatKey="1">
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11557-8"/>
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11556-8"/>
<ItemData ItemOID="pa_o2" Value="149"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.fi_o2_unit" ItemGroupRepeatKey="1">
Expand Down Expand Up @@ -5499,7 +5499,7 @@
<ItemData ItemOID="pa_o2_unit" Value="1"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.pa_o2_code" ItemGroupRepeatKey="1">
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11557-8"/>
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11556-8"/>
<ItemData ItemOID="pa_o2" Value="97"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.fi_o2_unit" ItemGroupRepeatKey="1">
Expand Down Expand Up @@ -7184,7 +7184,7 @@
<ItemData ItemOID="pa_o2_unit" Value="1"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.pa_o2_code" ItemGroupRepeatKey="1">
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11557-8"/>
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11556-8"/>
<ItemData ItemOID="pa_o2" Value="93"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.fi_o2_unit" ItemGroupRepeatKey="1">
Expand Down Expand Up @@ -8869,7 +8869,7 @@
<ItemData ItemOID="pa_o2_unit" Value="1"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.pa_o2_code" ItemGroupRepeatKey="1">
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11557-8"/>
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11556-8"/>
<ItemData ItemOID="pa_o2" Value="56"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.fi_o2_unit" ItemGroupRepeatKey="1">
Expand Down Expand Up @@ -10554,7 +10554,7 @@
<ItemData ItemOID="pa_o2_unit" Value="1"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.pa_o2_code" ItemGroupRepeatKey="1">
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11557-8"/>
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11556-8"/>
<ItemData ItemOID="pa_o2" Value="148"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.fi_o2_unit" ItemGroupRepeatKey="1">
Expand Down Expand Up @@ -12239,7 +12239,7 @@
<ItemData ItemOID="pa_o2_unit" Value="1"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.pa_o2_code" ItemGroupRepeatKey="1">
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11557-8"/>
<ItemData ItemOID="pa_o2_code" Value="2.16.840.1.113883.6.1_11556-8"/>
<ItemData ItemOID="pa_o2" Value="124"/>
</ItemGroupData>
<ItemGroupData ItemGroupOID="vitalparameter.fi_o2_unit" ItemGroupRepeatKey="1">
Expand Down
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