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-ExtractMatBundle modified to handle whole directory of files, test coverage added #460

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-ExtractMatBundle modified to handle whole directory of files, test coverage added #460

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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
f77bc4f
Merge pull request #1 from echicoine-icf/ExtractMatBundle-dir-processing
echicoine-icf Sep 13, 2023
a7aaea4
80% code coverage on ExtractMatBundleOperation class
Sep 13, 2023
3ac0b4f
Merge pull request #2 from echicoine-icf/code-coverage
echicoine-icf Sep 13, 2023
930c249
Added more robust tests for the supplied output directory by the user
Sep 13, 2023
32bbca6
Removed unused test
Sep 18, 2023
cce36d4
Added clarification for new -dir argument for processing whole direct…
Oct 9, 2023
5fe78b4
Fixed mvn exec line to include optional -dir arg
Oct 9, 2023
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5 changes: 3 additions & 2 deletions tooling-cli/src/main/java/org/opencds/cqf/tooling/cli/Main.java
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Original file line number Diff line number Diff line change
Expand Up @@ -124,13 +124,14 @@
- Accepts Bundles with .json or .xml extensions

- MAT Bundle extraction
- mvn exec:java -Dexec.args="[-ExtractMatBundle] [Bundle file path] (-v)
- mvn exec:java -Dexec.args="[-ExtractMatBundle] [Bundle file path] (-v) (-dir)
- Example: mvn exec:java -Dexec.args="-ExtractMatBundle /Users/mholck/Development/ecqm-content-r4/bundles/mat/EXM124/EXM124.json -v=r4"
- This tooling extracts out the resources and CQL from a MAT export bundle and puts them in the appropriate directories
- Accepts Bundles with .json or .xml extensions
- version = FHIR version { stu3, r4 }
Default version: r4

- dir = Directory indicator. To process the input location as a directory of files, the input should point to a valid directory
and the -dir flag should be present in the arguments list.
- Generate StructureDefinitions from ModelInfo
- command: mvn exec:java -Dexec.args="[-GenerateSDs] [path to modelinfo xml] (-outputpath | -op) (-encoding | -e)"
- TODO
Expand Down
523 changes: 295 additions & 228 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
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