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59 changes: 0 additions & 59 deletions
59
src/main/java/org/ehrbase/fhirbridge/ehr/converter/ContextConverter.java
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76 changes: 76 additions & 0 deletions
76
src/main/java/org/ehrbase/fhirbridge/ehr/converter/specific/antibodypanel/AntiBodyPanel.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,76 @@ | ||
| package org.ehrbase.fhirbridge.ehr.converter.specific.antibodypanel; | ||
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| import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException; | ||
| import org.ehrbase.fhirbridge.ehr.opt.geccoserologischerbefundcomposition.definition.VirusnachweistestDefiningCode; | ||
| import org.hl7.fhir.r4.model.Observation; | ||
| import org.hl7.fhir.r4.model.Resource; | ||
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| import java.util.List; | ||
| import java.util.Optional; | ||
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| public class AntiBodyPanel { | ||
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| private Optional<Observation> antiBodyPanel = Optional.empty(); | ||
| private Optional<Immunoassay> aBPresence = Optional.empty(); | ||
| private Optional<Immunoassay> aBUnitsVolume = Optional.empty(); | ||
| private Optional<Immunoassay> igAAbPresence = Optional.empty(); | ||
| private Optional<Immunoassay> igAAbUnitVolume = Optional.empty(); | ||
| private Optional<Immunoassay> igMAbPresence = Optional.empty(); | ||
| private Optional<Immunoassay> igMAbUnitsVolume = Optional.empty(); | ||
| private Optional<Immunoassay> igGAbPresence = Optional.empty(); | ||
| private Optional<Immunoassay> igGAbUnitsVolume = Optional.empty(); | ||
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| public AntiBodyPanel(Observation observation) { | ||
| setObservations(observation); | ||
| } | ||
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| private void setObservations(Observation observation) { | ||
| antiBodyPanel = Optional.of(observation); | ||
| for (Resource resource : observation.getContained()) { | ||
| setProfiles(resource); | ||
| } | ||
| } | ||
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| private void setProfiles(Resource resource) { | ||
| try { | ||
| String profileUrl = resource.getMeta().getProfile().get(0).getValue(); | ||
| resoulveProfile(resource, profileUrl); | ||
| } catch (IndexOutOfBoundsException e) { | ||
| throw new UnprocessableEntityException("Make sure only the for Anti body panel supported Profiles are contained in the Bundle"); | ||
| } | ||
| } | ||
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| private void resoulveProfile(Resource resource, String profileUrl) { | ||
| if (AntiBodyProfileUrl.AB_PRESENCE.getUrl().equals(profileUrl)) { | ||
| this.aBPresence = Optional.of(new Immunoassay((Observation) resource, VirusnachweistestDefiningCode.SARS_COV2_COVID19_AB_PRESENCE_IN_SERUM_OR_PLASMA_BY_IMMUNOASSAY)); | ||
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| } else if (AntiBodyProfileUrl.AB_UNITS_VOLUME.getUrl().equals(profileUrl)) { | ||
| this.aBUnitsVolume = Optional.of(new Immunoassay((Observation) resource, VirusnachweistestDefiningCode.SARS_COV2_COVID19_AB_UNITS_VOLUME_IN_SERUM_OR_PLASMA_BY_IMMUNOASSAY)); | ||
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| } else if (AntiBodyProfileUrl.IGA_AB_PRESENCE.getUrl().equals(profileUrl)) { | ||
| this.igAAbPresence = Optional.of(new Immunoassay((Observation) resource, VirusnachweistestDefiningCode.SARS_COV2_COVID19_IGA_AB_PRESENCE_IN_SERUM_OR_PLASMA_BY_IMMUNOASSAY)); | ||
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| } else if (AntiBodyProfileUrl.IGA_AB_UNITS_VOLUME.getUrl().equals(profileUrl)) { | ||
| this.igAAbUnitVolume = Optional.of(new Immunoassay((Observation) resource, VirusnachweistestDefiningCode.SARS_COV2_COVID19_IGA_AB_UNITS_VOLUME_IN_SERUM_OR_PLASMA_BY_IMMUNOASSAY)); | ||
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| } else if (AntiBodyProfileUrl.IGM_AB_PRESENCE.getUrl().equals(profileUrl)) { | ||
| this.igMAbPresence = Optional.of(new Immunoassay((Observation) resource, VirusnachweistestDefiningCode.SARS_COV2_COVID19_IGM_AB_PRESENCE_IN_SERUM_OR_PLASMA_BY_IMMUNOASSAY)); | ||
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| } else if (AntiBodyProfileUrl.IGM_AB_UNITS_VOLUME.getUrl().equals(profileUrl)) { | ||
| this.igMAbUnitsVolume = Optional.of(new Immunoassay((Observation) resource, VirusnachweistestDefiningCode.SARS_COV2_COVID19_IGM_AB_UNITS_VOLUME_IN_SERUM_OR_PLASMA_BY_IMMUNOASSAY)); | ||
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| } else if (AntiBodyProfileUrl.IGG_AB_PRESENCE.getUrl().equals(profileUrl)) { | ||
| this.igGAbPresence = Optional.of(new Immunoassay((Observation) resource, VirusnachweistestDefiningCode.SARS_COV2_COVID19_IGG_AB_PRESENCE_IN_SERUM_OR_PLASMA_BY_IMMUNOASSAY)); | ||
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| } else if (AntiBodyProfileUrl.IGG_AB_UNITS_VOLUME.getUrl().equals(profileUrl)) { | ||
| this.igGAbUnitsVolume = Optional.of(new Immunoassay((Observation) resource, VirusnachweistestDefiningCode.SARS_COV2_COVID19_IGG_AB_UNITS_VOLUME_IN_SERUM_OR_PLASMA_BY_IMMUNOASSAY)); | ||
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| } else { | ||
| throw new UnprocessableEntityException("Anti body panel bundle needs to contain only the profiles for the Anti body panel. Please delete profile " + profileUrl + " from the Bundle."); | ||
| } | ||
| } | ||
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| public List<Optional<Immunoassay>> getAllNonPanel() { | ||
| return List.of(aBPresence, aBUnitsVolume, igAAbPresence, igAAbUnitVolume, igMAbPresence, igMAbUnitsVolume, igGAbPresence, igGAbUnitsVolume); | ||
| } | ||
| } |
25 changes: 25 additions & 0 deletions
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...n/java/org/ehrbase/fhirbridge/ehr/converter/specific/antibodypanel/AntiBodyPanelCode.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| package org.ehrbase.fhirbridge.ehr.converter.specific.antibodypanel; | ||
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| import org.ehrbase.fhirbridge.ehr.converter.specific.CodeSystem; | ||
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| public enum AntiBodyPanelCode { | ||
| LABORATORY_STUDIES(CodeSystem.LOINC.getUrl(), "26436-6"); | ||
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| private final String system; | ||
| private final String code; | ||
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| AntiBodyPanelCode( String system, String code) { | ||
| this.code = code; | ||
| this.system = system; | ||
| } | ||
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| public String getSystem() { | ||
| return system; | ||
| } | ||
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| public String getCode() { | ||
| return code; | ||
| } | ||
| } |
24 changes: 24 additions & 0 deletions
24
.../java/org/ehrbase/fhirbridge/ehr/converter/specific/antibodypanel/AntiBodyProfileUrl.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| package org.ehrbase.fhirbridge.ehr.converter.specific.antibodypanel; | ||
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| public enum AntiBodyProfileUrl { | ||
| AB_PRESENCE("https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-ab-ser-pl-ql-ia"), | ||
| AB_UNITS_VOLUME("https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-ab-ser-pl-ia-acnc"), | ||
| IGA_AB_PRESENCE("https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-iga-ser-pl-ql-ia"), | ||
| IGA_AB_UNITS_VOLUME("https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-iga-ser-pl-ia-acnc"), | ||
| IGM_AB_PRESENCE("https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-igm-ser-pl-ql-ia"), | ||
| IGM_AB_UNITS_VOLUME("https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-igm-ser-pl-ia-acnc"), | ||
| IGG_AB_PRESENCE("https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-igg-ser-pl-ql-ia"), | ||
| IGG_AB_UNITS_VOLUME("https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-igg-ser-pl-ia-acnc"); | ||
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| private final String url; | ||
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| AntiBodyProfileUrl(String url) { | ||
| this.url = url; | ||
| } | ||
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| public String getUrl() { | ||
| return url; | ||
| } | ||
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| } |
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