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LNK-1871: Some more PR updates and some cleanup in ApplyConceptMaps a…
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…nd FHIRHelper.
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@ajagann1
ajagann1 committed Mar 13, 2024
1 parent fe591a8 commit 19277cd
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Showing 4 changed files with 64 additions and 84 deletions.
5 changes: 1 addition & 4 deletions core/src/main/java/com/lantanagroup/link/ApplyConceptMaps.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,6 @@

public class ApplyConceptMaps {
private static final Logger logger = LoggerFactory.getLogger(ApplyConceptMaps.class);
private final DefaultProfileValidationSupport validationSupport = new DefaultProfileValidationSupport(FhirContextProvider.getFhirContext());

private List<com.lantanagroup.link.db.model.ConceptMap> conceptMaps;

Expand All @@ -27,9 +26,7 @@ public static boolean isMapped(Coding coding, String system, String code) {
.anyMatch(mappedCoding -> mappedCoding.is(system, code));
}

public ApplyConceptMaps() {
validationSupport.fetchAllStructureDefinitions();
}
public ApplyConceptMaps() {}


private void translateCoding(ConceptMap map, Coding code) {
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132 changes: 56 additions & 76 deletions core/src/main/java/com/lantanagroup/link/FhirBundleProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,92 +39,72 @@ public class FhirBundleProcessor {
public FhirBundleProcessor(Bundle bundle) {
this.bundle = bundle;

this.linkOrganization = this.bundle.getEntry().stream()
.filter(e -> {
if(e.getResource().getResourceType().equals(ResourceType.Organization) &&
e.getResource().getMeta().hasProfile(Constants.SubmittingOrganizationProfile)){
int index = bundle.getEntry().indexOf(e);
bundleEntryIndexToFileMap.put(index, Constants.ORGANIZATION_FILE_NAME);
return true;
}
else return false;
})
.findFirst()
.orElse(null);

this.linkDevice = this.bundle.getEntry().stream()
.filter(e -> {

if(e.getResource().getResourceType().equals(ResourceType.Device) &&
e.getResource().getMeta().hasProfile(Constants.SubmittingDeviceProfile)){
int index = bundle.getEntry().indexOf(e);
bundleEntryIndexToFileMap.put(index, Constants.DEVICE_FILE_NAME);
return true;
}
else return false;
})
.findFirst()
.orElse(null);

this.linkQueryPlanLibrary = this.bundle.getEntry().stream()
.filter(e -> e.getResource().getResourceType().equals(ResourceType.Library))
.filter(e -> {
Library library = (Library) e.getResource();
if(library.getType().getCoding().stream()
.anyMatch(c -> c.getCode().equals(Constants.LibraryTypeModelDefinitionCode))){
int index = bundle.getEntry().indexOf(e);
bundleEntryIndexToFileMap.put(index, Constants.QUERY_PLAN_FILE_NAME);
return true;
}
else return false;
})
.findFirst()
.orElse(null);

this.linkCensusLists = this.bundle.getEntry().stream()
.filter(e -> {
if(e.getResource().getResourceType().equals(ResourceType.List) &&
e.getResource().getMeta().getProfile().stream()
.anyMatch(p -> p.getValue().equals(Constants.CensusProfileUrl))){
int index = bundle.getEntry().indexOf(e);
bundleEntryIndexToFileMap.put(index, String.format("census-%s.json",
e.getResource().getIdElement().getIdPart()));
return true;
}
else return false;
})
.sorted(new FhirBundlerEntrySorter.ResourceComparator())
.collect(Collectors.toList());

this.aggregateMeasureReports = this.bundle.getEntry().stream()
.filter(e -> {
if(e.getResource().getResourceType().equals(ResourceType.MeasureReport)
&& ((MeasureReport) e.getResource()).getType().equals(MeasureReport.MeasureReportType.SUBJECTLIST)){
int index = bundle.getEntry().indexOf(e);
bundleEntryIndexToFileMap.put(index, String.format("aggregate-%s.json",
e.getResource().getIdElement().getIdPart()));
return true;
}
else return false;
})
.sorted(new FhirBundlerEntrySorter.ResourceComparator())
.collect(Collectors.toList());

for (Bundle.BundleEntryComponent e : bundle.getEntry()) {
String patientReference = FhirHelper.getPatientReference(e.getResource());
int index = this.bundle.getEntry().indexOf(e);
if (patientReference != null) {
Bundle.BundleEntryComponent linkOrganization = null;
Bundle.BundleEntryComponent linkDevice = null;
Bundle.BundleEntryComponent linkQueryPlanLibrary = null;
List<Bundle.BundleEntryComponent> linkCensusLists = new ArrayList<>();
List<Bundle.BundleEntryComponent> aggregateMeasureReports = new ArrayList<>();

for (int index = 0; index < bundle.getEntry().size(); index++) {
Bundle.BundleEntryComponent e = bundle.getEntry().get(index);
Resource resource = e.getResource();
ResourceType resourceType = resource.getResourceType();
String patientReference = FhirHelper.getPatientReference(resource);
if(resourceType.equals(ResourceType.Organization) &&
resource.getMeta().hasProfile(Constants.SubmittingOrganizationProfile)){
if(linkOrganization == null){
linkOrganization = e;
bundleEntryIndexToFileMap.put(index, Constants.ORGANIZATION_FILE_NAME);
}
}
else if(resourceType.equals(ResourceType.Device) &&
resource.getMeta().hasProfile(Constants.SubmittingDeviceProfile)){
if(linkDevice == null){
linkDevice = e;
bundleEntryIndexToFileMap.put(index, Constants.DEVICE_FILE_NAME);
}
}
else if(resourceType.equals(ResourceType.Library) && ((Library) resource).getType().getCoding().stream()
.anyMatch(c -> c.getCode().equals(Constants.LibraryTypeModelDefinitionCode))){
if(linkQueryPlanLibrary == null){
linkQueryPlanLibrary = e;
bundleEntryIndexToFileMap.put(index, String.format("census-%s.json",
e.getResource().getIdElement().getIdPart()));
}
}
else if(resourceType.equals(ResourceType.List) &&
resource.getMeta().getProfile().stream()
.anyMatch(p -> p.getValue().equals(Constants.CensusProfileUrl))){
linkCensusLists.add(e);
bundleEntryIndexToFileMap.put(index, String.format("census-%s.json",
resource.getIdElement().getIdPart()));
} else if(resourceType.equals(ResourceType.MeasureReport)
&& ((MeasureReport) resource).getType().equals(MeasureReport.MeasureReportType.SUBJECTLIST)) {
aggregateMeasureReports.add(e);
bundleEntryIndexToFileMap.put(index, String.format("aggregate-%s.json",
resource.getIdElement().getIdPart()));
} else if (patientReference != null) {
String patientId = patientReference.replace("Patient/", "");
if (!this.patientResources.containsKey(patientId)) {
this.patientResources.put(patientId, new ArrayList<>());
}
this.patientResources.get(patientId).add(e);
bundleEntryIndexToFileMap.put(index, String.format("patient-%s.json", patientId));
} else if (isOtherResource(e)) {
} else {
this.otherResources.add(e);
bundleEntryIndexToFileMap.put(index, "other-resources.json");
}
}

//Cleanup
this.linkOrganization = linkOrganization;
this.linkDevice = linkDevice;
this.linkQueryPlanLibrary = linkQueryPlanLibrary;
this.linkCensusLists = linkCensusLists.stream()
.sorted(new FhirBundlerEntrySorter.ResourceComparator()).collect(Collectors.toList());
this.aggregateMeasureReports = aggregateMeasureReports.stream()
.sorted(new FhirBundlerEntrySorter.ResourceComparator()).collect(Collectors.toList());

}

private static boolean isSameResource(Bundle.BundleEntryComponent e1, Bundle.BundleEntryComponent e2) {
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1 change: 1 addition & 0 deletions core/src/main/java/com/lantanagroup/link/FhirHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -346,6 +346,7 @@ private static void addEventNotesToDevice(Device device, String eventCategory, L
}

public static FHIRPathEngine getFhirPathEngine() {
validationSupport.fetchAllStructureDefinitions();
HapiWorkerContext workerContext = new HapiWorkerContext(FhirContextProvider.getFhirContext(), validationSupport);
return new FHIRPathEngine(workerContext);
}
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10 changes: 6 additions & 4 deletions core/src/main/java/com/lantanagroup/link/sender/FileSystemSender.java
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Original file line number Diff line number Diff line change
Expand Up @@ -230,10 +230,12 @@ private void saveToFolder(Bundle bundle, OperationOutcome outcome, String path)
logger.debug("Annotating and saving validation results");
List<OperationOutcome.OperationOutcomeIssueComponent> issues = outcome.getIssue();
issues.forEach(i -> {
String expression = i.getExpression().get(0).toString();
if(expression.contains("Bundle.entry[")){
String entryIndex = expression.substring(expression.indexOf("Bundle.entry[") + 13, expression.indexOf("]"));
i.setDiagnostics(fhirBundleProcessor.getBundleEntryIndexToFileMap().get(Integer.parseInt(entryIndex)));
if(i.hasExpression()){
String expression = i.getExpression().get(0).toString();
if(expression.contains("Bundle.entry[")){
String entryIndex = expression.substring(expression.indexOf("Bundle.entry[") + 13, expression.indexOf("]"));
i.setDiagnostics(fhirBundleProcessor.getBundleEntryIndexToFileMap().get(Integer.parseInt(entryIndex)));
}
}
});
this.saveToFile(outcome, Paths.get(path, "validation-results.json").toString());
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