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Extract mat bundle dir processing #1

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merged 5 commits into from
Sep 13, 2023
Merged

Extract mat bundle dir processing #1

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6d49c36
Moved the processing of a file to its own method, incorporated a for …
Sep 12, 2023
1bea97f
Finished with directory processing, adding test.
Sep 12, 2023
566dff6
Fixed issue with test, now verify Bundle using instanceof
Sep 12, 2023
d818395
Removed member variable references for readability.
Sep 12, 2023
2631026
Validating input earlier, adjusted BundlUtils to handle logic about v…
Sep 13, 2023
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504 changes: 275 additions & 229 deletions tooling/src/main/java/org/opencds/cqf/tooling/operation/ExtractMatBundleOperation.java
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102 changes: 54 additions & 48 deletions tooling/src/main/java/org/opencds/cqf/tooling/utilities/BundleUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ public static Object bundleArtifacts(String id, List<IBaseResource> resources, F
case DSTU3:
return bundleStu3Artifacts(id, resources);
case R4:
if(identifiers != null && identifiers.length > 0){
if (identifiers != null && identifiers.length > 0) {
return bundleR4Artifacts(id, resources, identifiers[0], addBundleTimestamp);
}
return bundleR4Artifacts(id, resources, null, addBundleTimestamp);
Expand All @@ -42,53 +42,49 @@ public static Object bundleArtifacts(String id, List<IBaseResource> resources, F
}
}

public static org.hl7.fhir.dstu3.model.Bundle bundleStu3Artifacts(String id, List<IBaseResource> resources)
{
public static org.hl7.fhir.dstu3.model.Bundle bundleStu3Artifacts(String id, List<IBaseResource> resources) {
org.hl7.fhir.dstu3.model.Bundle bundle = new org.hl7.fhir.dstu3.model.Bundle();
ResourceUtils.setIgId(id, bundle, false);
bundle.setType(org.hl7.fhir.dstu3.model.Bundle.BundleType.TRANSACTION);
for (IBaseResource resource : resources)
{
for (IBaseResource resource : resources) {
bundle.addEntry(
new org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent()
.setResource((org.hl7.fhir.dstu3.model.Resource) resource)
.setRequest(
new org.hl7.fhir.dstu3.model.Bundle.BundleEntryRequestComponent()
.setMethod(org.hl7.fhir.dstu3.model.Bundle.HTTPVerb.PUT)
.setUrl(((org.hl7.fhir.dstu3.model.Resource) resource).getId())
)
new org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent()
.setResource((org.hl7.fhir.dstu3.model.Resource) resource)
.setRequest(
new org.hl7.fhir.dstu3.model.Bundle.BundleEntryRequestComponent()
.setMethod(org.hl7.fhir.dstu3.model.Bundle.HTTPVerb.PUT)
.setUrl(((org.hl7.fhir.dstu3.model.Resource) resource).getId())
)
);
}
return bundle;
}

public static org.hl7.fhir.r4.model.Bundle bundleR4Artifacts(String id, List<IBaseResource> resources, List<Object> identifiers, Boolean addBundleTimestamp)
{
public static org.hl7.fhir.r4.model.Bundle bundleR4Artifacts(String id, List<IBaseResource> resources, List<Object> identifiers, Boolean addBundleTimestamp) {
org.hl7.fhir.r4.model.Bundle bundle = new org.hl7.fhir.r4.model.Bundle();
ResourceUtils.setIgId(id, bundle, false);
bundle.setType(org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION);
if (addBundleTimestamp) {
bundle.setTimestamp((new Date()));
}
if (identifiers!= null && !identifiers.isEmpty()) {
if (identifiers != null && !identifiers.isEmpty()) {
org.hl7.fhir.r4.model.Identifier identifier = (org.hl7.fhir.r4.model.Identifier) identifiers.get(0);
if(identifier.hasValue()) {
if (identifier.hasValue()) {
identifier.setValue(identifier.getValue() + "-bundle");
}
bundle.setIdentifier(identifier);
}

for (IBaseResource resource : resources)
{
for (IBaseResource resource : resources) {
String resourceRef = (resource.getIdElement().getResourceType() == null) ? resource.fhirType() + "/" + resource.getIdElement().getIdPart() : resource.getIdElement().getValueAsString();
bundle.addEntry(
new org.hl7.fhir.r4.model.Bundle.BundleEntryComponent()
.setResource((org.hl7.fhir.r4.model.Resource) resource)
.setRequest(
new org.hl7.fhir.r4.model.Bundle.BundleEntryRequestComponent()
.setMethod(org.hl7.fhir.r4.model.Bundle.HTTPVerb.PUT)
.setUrl(resourceRef)
)
new org.hl7.fhir.r4.model.Bundle.BundleEntryComponent()
.setResource((org.hl7.fhir.r4.model.Resource) resource)
.setRequest(
new org.hl7.fhir.r4.model.Bundle.BundleEntryRequestComponent()
.setMethod(org.hl7.fhir.r4.model.Bundle.HTTPVerb.PUT)
.setUrl(resourceRef)
)
);
}
return bundle;
Expand Down Expand Up @@ -140,53 +136,63 @@ public static List<Map.Entry<String, IBaseResource>> GetBundlesInDir(String dire
}

public static void stampDstu3BundleEntriesWithSoftwareSystems(org.hl7.fhir.dstu3.model.Bundle bundle, List<CqfmSoftwareSystem> softwareSystems, FhirContext fhirContext, String rootDir) {
for (org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent entry: bundle.getEntry()) {
for (org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
org.hl7.fhir.dstu3.model.Resource resource = entry.getResource();
if ((resource.fhirType().equals("Library")) || ((resource.fhirType().equals("Measure")))) {
org.opencds.cqf.tooling.common.stu3.CqfmSoftwareSystemHelper cqfmSoftwareSystemHelper = new org.opencds.cqf.tooling.common.stu3.CqfmSoftwareSystemHelper(rootDir);
cqfmSoftwareSystemHelper.ensureSoftwareSystemExtensionAndDevice((org.hl7.fhir.dstu3.model.DomainResource)resource, softwareSystems, fhirContext);
cqfmSoftwareSystemHelper.ensureSoftwareSystemExtensionAndDevice((org.hl7.fhir.dstu3.model.DomainResource) resource, softwareSystems, fhirContext);
}
}
}

public static void stampR4BundleEntriesWithSoftwareSystems(org.hl7.fhir.r4.model.Bundle bundle, List<CqfmSoftwareSystem> softwareSystems, FhirContext fhirContext, String rootDir) {
for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent entry: bundle.getEntry()) {
for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
org.hl7.fhir.r4.model.Resource resource = entry.getResource();
if ((resource.fhirType().equals("Library")) || ((resource.fhirType().equals("Measure")))) {
org.opencds.cqf.tooling.common.r4.CqfmSoftwareSystemHelper cqfmSoftwareSystemHelper = new org.opencds.cqf.tooling.common.r4.CqfmSoftwareSystemHelper(rootDir);
cqfmSoftwareSystemHelper.ensureSoftwareSystemExtensionAndDevice((org.hl7.fhir.r4.model.DomainResource)resource, softwareSystems, fhirContext);
cqfmSoftwareSystemHelper.ensureSoftwareSystemExtensionAndDevice((org.hl7.fhir.r4.model.DomainResource) resource, softwareSystems, fhirContext);
}
}
}

public static void extractStu3Resources(org.hl7.fhir.dstu3.model.Bundle bundle, String encoding, String outputPath, boolean suppressNarrative) {
FhirContext context = FhirContext.forDstu3Cached();
for (org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
FhirContext context = FhirContext.forDstu3Cached();
for (org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
org.hl7.fhir.dstu3.model.Resource entryResource = entry.getResource();
if (entryResource != null) {
if(entryResource.fhirType().equals("Measure") && suppressNarrative){
((org.hl7.fhir.dstu3.model.Measure)entryResource).setText(null);
if (entryResource.fhirType().equals("Measure") && suppressNarrative) {
((org.hl7.fhir.dstu3.model.Measure) entryResource).setText(null);
}
ResourceUtils.outputResource(entryResource, encoding, context, outputPath);
}
}
ResourceUtils.outputResource(entryResource, encoding, context, outputPath);
}
}
}

public static void extractR4Resources(org.hl7.fhir.r4.model.Bundle bundle, String encoding, String outputPath, boolean suppressNarrative) {
FhirContext context = FhirContext.forR4Cached();
for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
FhirContext context = FhirContext.forR4Cached();
for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
org.hl7.fhir.r4.model.Resource entryResource = entry.getResource();
if (entryResource != null) {
if(entryResource.fhirType().equals("Measure") && suppressNarrative){
((org.hl7.fhir.r4.model.Measure)entryResource).setText(null);
if (entryResource != null) {
if (entryResource.fhirType().equals("Measure") && suppressNarrative) {
((org.hl7.fhir.r4.model.Measure) entryResource).setText(null);
}
ResourceUtils.outputResource(entryResource, encoding, context, outputPath);
}
}
ResourceUtils.outputResource(entryResource, encoding, context, outputPath);
}
}
}

public static void extractResources(Object bundle, String encoding, String outputDir, boolean suppressNarrative, String version) {
if (version.equals("stu3") && bundle instanceof org.hl7.fhir.dstu3.model.Bundle) {
BundleUtils.extractStu3Resources((org.hl7.fhir.dstu3.model.Bundle) bundle, encoding, outputDir, suppressNarrative);
} else if (version.equals("r4") && bundle instanceof org.hl7.fhir.r4.model.Bundle) {
BundleUtils.extractR4Resources((org.hl7.fhir.r4.model.Bundle) bundle, encoding, outputDir, suppressNarrative);
}else{
throw new IllegalArgumentException("Invalid bundle/version: " + bundle + "/" + version);
}
}

public static ArrayList<Resource> getR4ResourcesFromBundle(Bundle bundle){
ArrayList <Resource> resourceArrayList = new ArrayList<>();
public static ArrayList<Resource> getR4ResourcesFromBundle(Bundle bundle) {
ArrayList<Resource> resourceArrayList = new ArrayList<>();
FhirContext context = FhirContext.forR4Cached();
for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
org.hl7.fhir.r4.model.Resource entryResource = entry.getResource();
Expand All @@ -197,8 +203,8 @@ public static ArrayList<Resource> getR4ResourcesFromBundle(Bundle bundle){
return resourceArrayList;
}

public static ArrayList<org.hl7.fhir.dstu3.model.Resource> getStu3ResourcesFromBundle(org.hl7.fhir.dstu3.model.Bundle bundle){
ArrayList <org.hl7.fhir.dstu3.model.Resource> resourceArrayList = new ArrayList<>();
public static ArrayList<org.hl7.fhir.dstu3.model.Resource> getStu3ResourcesFromBundle(org.hl7.fhir.dstu3.model.Bundle bundle) {
ArrayList<org.hl7.fhir.dstu3.model.Resource> resourceArrayList = new ArrayList<>();
for (org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
org.hl7.fhir.dstu3.model.Resource entryResource = entry.getResource();
if (entryResource != null) {
Expand Down
6 changes: 6 additions & 0 deletions tooling/src/test/java/org/opencds/cqf/tooling/utilities/ECQMCreatorIT.java
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Original file line number Diff line number Diff line change
Expand Up @@ -130,6 +130,12 @@ private void checkExpectedResourcesPresent(List<DataRequirement> drs, List<Strin
}
}

@Test
public void TestExtractMatBundleWithDirectory(){
ExtractMatBundleOperation o = new ExtractMatBundleOperation();
o.execute(new String[] { "-ExtractMATBundle", this.getClass().getResource("ecqm-content-r4-2021/bundles_small/").getFile(), "-dir" });
}

@Test
public void TestCMS816HIR() {
List<DataRequirement> drs = StartMatOutputTest("HH-01FHIR-v0-0-010-FHIR-4-0-1.json", "HospitalHarmSevereHypoglycemiaFHIR");
Expand Down
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