Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

-ExtractMatBundle modified to handle whole directory of files, test coverage added #475

Merged
merged 18 commits into from
Oct 13, 2023
Merged

-ExtractMatBundle modified to handle whole directory of files, test coverage added #475

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
18 commits
Select commit Hold shift + click to select a range
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
b682935
Added transactional bundle files for tests to POST
Sep 27, 2023
8f8c3a7
Added commented out line for localhost POST testing.
Sep 27, 2023
e255533
Updated ExtractMatBundle tests to cover wider range of file types and…
Oct 10, 2023
d18b300
Eliminating unused resource
Oct 10, 2023
76cd6ea
Added resource ID verification so resources aren't processed repeated…
Oct 11, 2023
afa52ff
Fixed failing tests elsewhere in the app on null outputpath
Oct 11, 2023
273985b
Removing RefreshIG work accidentally included in this branch
Oct 11, 2023
984e7ac
Restoring Main documentation for -dir
Oct 12, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 8 additions & 7 deletions tooling-cli/src/main/java/org/opencds/cqf/tooling/cli/Main.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -123,13 +123,14 @@
- This tooling decomposes a Bundle entry into separate resource files
- Accepts Bundles with .json or .xml extensions
- MAT Bundle extraction
- mvn exec:java -Dexec.args="[-ExtractMatBundle] [Bundle file path] (-v)
- 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
- MAT Bundle extraction
- 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)"
Expand Down
631 changes: 397 additions & 234 deletions tooling/src/main/java/org/opencds/cqf/tooling/operation/ExtractMatBundleOperation.java
View file
Open in desktop

Large diffs are not rendered by default.

102 changes: 54 additions & 48 deletions tooling/src/main/java/org/opencds/cqf/tooling/utilities/BundleUtils.java
View file
Open in desktop
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
Loading
Loading