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Refresh exception fix #228

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merged 4 commits into from
May 14, 2021
Merged

Refresh exception fix #228

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3cdf9b8
try-catch to handle missing dataTYpe in Parameters and dataReqs
May 7, 2021
2a5e036
changes to suppress narrative in MAT extracted bundle measures
May 12, 2021
8e22ba7
added null checks for extension values
May 13, 2021
06e3641
Merge branch 'master' into refreshExceptionFix
brynrhodes May 14, 2021
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10 changes: 7 additions & 3 deletions src/main/java/org/opencds/cqf/tooling/common/r4/CqfmSoftwareSystemHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -111,9 +111,13 @@ public <T extends DomainResource> void ensureSoftwareSystemExtensionAndDevice(T
final List<Extension> extensions = resource.getExtension();
Extension softwareSystemExtension = null;
for (Extension ext : extensions) {
if (ext.getValue().fhirType().equals("Reference") && ((Reference) ext.getValue()).getReference().equals(systemReferenceID)) {
softwareSystemExtension = ext;
((Reference)softwareSystemExtension.getValue()).setResource(null);
if(ext.getValue() != null
&& ext.getValue().fhirType() != null
&& ext.getValue().fhirType().equals("Reference")
&& ((Reference)ext.getValue()).getReference() != null
&& ((Reference) ext.getValue()).getReference().equals(systemReferenceID)){
softwareSystemExtension = ext;
((Reference) softwareSystemExtension.getValue()).setResource(null);
}
}

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64 changes: 44 additions & 20 deletions src/main/java/org/opencds/cqf/tooling/operation/ExtractMatBundleOperation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,26 +24,49 @@ public class ExtractMatBundleOperation extends Operation {
private String version = "r4";
private FhirContext context;
private String encoding;
private boolean suppressNarrative = true;

@Override
public void execute(String[] args) {
// Set file to extract
inputFile = args[1];
if (inputFile == null) {
throw new IllegalArgumentException("The path to a bundle file is required");
}

// Set version
if (args.length > 2) {
if (args[2] != null) {
String[] flagAndValue = args[2].split("=");
String flag = flagAndValue[0];
String value = flagAndValue[1];
if (flag != "-v") {
throw new IllegalArgumentException("Invalid argument: " + flag);
} else {
version = value;
}
public void execute(String[] args) {

for (int i = 0; i < args.length;i++) {
if(i == 0 && args[i].equalsIgnoreCase("-ExtractMatBundle")){
continue; //
}
if(i == 1){
inputFile = args[i];
if (inputFile == null) {
throw new IllegalArgumentException("The path to a bundle file is required");
}
continue;
}

String[] flagAndValue = args[i].split("=");
if (flagAndValue.length < 2) {
throw new IllegalArgumentException("Invalid argument: " + args[i]);
}
String flag = flagAndValue[0];
String value = flagAndValue[1];

switch (flag.replace("-", "").toLowerCase()) {
case "encoding":
case "e":
encoding = value.toLowerCase();
break;
case "supressNarrative":
case "sn":
if(value.equalsIgnoreCase("false")) {
suppressNarrative = false;
}
break;
case "outputpath":
case "op":
setOutputPath(value);
break; // -outputpath (-op)
case "version": case "v":
version = value;
break;
default: throw new IllegalArgumentException("Unknown flag: " + flag);
}
}

Expand Down Expand Up @@ -99,14 +122,15 @@ else if (bundleFile.getPath().endsWith(".json")) {
// Now call the Bundle utilities to extract the bundle
String outputDir = bundleFile.getAbsoluteFile().getParent();
if (version == "stu3") {
BundleUtils.extractStu3Resources((org.hl7.fhir.dstu3.model.Bundle)bundle, encoding, outputDir);
BundleUtils.extractStu3Resources((org.hl7.fhir.dstu3.model.Bundle)bundle, encoding, outputDir, suppressNarrative);
} else if (version == "r4") {
BundleUtils.extractR4Resources((org.hl7.fhir.r4.model.Bundle)bundle, encoding, outputDir);
BundleUtils.extractR4Resources((org.hl7.fhir.r4.model.Bundle)bundle, encoding, outputDir, suppressNarrative);
}

// Now move and properly rename the files
moveAndRenameFiles(outputDir);


LogUtils.info("Extraction completed successfully");
}

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21 changes: 17 additions & 4 deletions src/main/java/org/opencds/cqf/tooling/processor/DataRequirementsProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -368,8 +368,15 @@ private ParameterDefinition toParameterDefinition(VersionedIdentifier libraryIde

private ParameterDefinition toOutputParameterDefinition(VersionedIdentifier libraryIdentifier, ExpressionDef def) {
AtomicBoolean isList = new AtomicBoolean(false);
Enumerations.FHIRAllTypes typeCode = Enumerations.FHIRAllTypes.fromCode(
toFHIRResultTypeCode(def.getResultType(), def.getName(), isList));
Enumerations.FHIRAllTypes typeCode = null;
try{
typeCode = Enumerations.FHIRAllTypes.fromCode(
toFHIRResultTypeCode(def.getResultType(), def.getName(), isList));
}catch(org.hl7.fhir.exceptions.FHIRException fhirException){
validationMessages.add(new ValidationMessage(ValidationMessage.Source.Publisher, ValidationMessage.IssueType.NOTSUPPORTED, "CQL Library Packaging",
String.format("Result type %s of library %s is not supported; implementations may not be able to use the result of this expression",
def.getResultType().toLabel(), libraryIdentifier.getId()), ValidationMessage.IssueSeverity.WARNING));
}

return new ParameterDefinition()
.setName(def.getName())
Expand Down Expand Up @@ -544,6 +551,14 @@ private String stripReference(String path) {
private org.hl7.fhir.r5.model.DataRequirement toDataRequirement(ElmRequirementsContext context,
VersionedIdentifier libraryIdentifier, Retrieve retrieve, Map<String, Retrieve> retrieveMap) {
org.hl7.fhir.r5.model.DataRequirement dr = new org.hl7.fhir.r5.model.DataRequirement();
try {
dr.setType(org.hl7.fhir.r5.model.Enumerations.FHIRAllTypes.fromCode(retrieve.getDataType().getLocalPart()));
}
catch(org.hl7.fhir.exceptions.FHIRException fhirException) {
validationMessages.add(new ValidationMessage(ValidationMessage.Source.Publisher, ValidationMessage.IssueType.NOTSUPPORTED, "CQL Library Packaging",
String.format("Result type %s of library %s is not supported; implementations may not be able to use the result of this expression",
retrieve.getDataType().getLocalPart(), libraryIdentifier.getId()), ValidationMessage.IssueSeverity.WARNING));
}

// Set the id attribute of the data requirement if it will be referenced from an included retrieve
if (retrieve.getLocalId() != null && retrieve.getInclude() != null && retrieve.getInclude().size() > 0) {
Expand All @@ -554,8 +569,6 @@ private org.hl7.fhir.r5.model.DataRequirement toDataRequirement(ElmRequirementsC
}
}

dr.setType(org.hl7.fhir.r5.model.Enumerations.FHIRAllTypes.fromCode(retrieve.getDataType().getLocalPart()));

// Set profile if specified
if (retrieve.getTemplateId() != null) {
dr.setProfile(Collections.singletonList(new org.hl7.fhir.r5.model.CanonicalType(retrieve.getTemplateId())));
Expand Down
20 changes: 14 additions & 6 deletions 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 @@ -141,20 +141,28 @@ public static void stampR4BundleEntriesWithSoftwareSystems(org.hl7.fhir.r4.model
}
}

public static void extractStu3Resources(org.hl7.fhir.dstu3.model.Bundle bundle, String encoding, String outputPath) {
public static void extractStu3Resources(org.hl7.fhir.dstu3.model.Bundle bundle, String encoding, String outputPath, boolean suppressNarrative) {
FhirContext context = FhirContext.forDstu3();
for (org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
if (entry.getResource() != null) {
ResourceUtils.outputResource(entry.getResource(), encoding, context, outputPath);
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);
}
ResourceUtils.outputResource(entryResource, encoding, context, outputPath);
}
}
}

public static void extractR4Resources(org.hl7.fhir.r4.model.Bundle bundle, String encoding, String outputPath) {
public static void extractR4Resources(org.hl7.fhir.r4.model.Bundle bundle, String encoding, String outputPath, boolean suppressNarrative) {
FhirContext context = FhirContext.forR4();
for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
if (entry.getResource() != null) {
ResourceUtils.outputResource(entry.getResource(), encoding, context, outputPath);
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);
}
ResourceUtils.outputResource(entryResource, encoding, context, outputPath);
}
}
}
Expand Down