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Fixes #455 - Create Group for test patients (#458)
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* Fixes #455 - Created a Group for all patients for a measure, supports both individual resources and bundles

* Added some logic to check FHIR version, only implemented R4 for now but logic in place to handle others

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Co-authored-by: Michael Holck <[email protected]>
Co-authored-by: JP <[email protected]>
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@mholck @JPercival
3 people authored Nov 28, 2023
1 parent fa035c9 commit b0cd33d
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Showing 2 changed files with 92 additions and 12 deletions.
91 changes: 80 additions & 11 deletions tooling/src/main/java/org/opencds/cqf/tooling/processor/TestCaseProcessor.java
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Original file line number Diff line number Diff line change
@@ -1,14 +1,20 @@
package org.opencds.cqf.tooling.processor;

import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Optional;

import javax.annotation.Nullable;

import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.model.api.IFhirVersion;
import org.apache.commons.io.FilenameUtils;
import org.hl7.fhir.Patient;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import org.opencds.cqf.tooling.utilities.BundleUtils;
import org.opencds.cqf.tooling.utilities.IOUtils;
import org.opencds.cqf.tooling.utilities.LogUtils;
Expand All @@ -30,29 +36,92 @@ public void refreshTestCases(String path, IOUtils.Encoding encoding, FhirContext
{
logger.info("Refreshing tests");
List<String> resourceTypeTestGroups = IOUtils.getDirectoryPaths(path, false);
IFhirVersion version = fhirContext.getVersion();

for (String group : resourceTypeTestGroups) {
List<String> testArtifactPaths = IOUtils.getDirectoryPaths(group, false);
for (String testArtifactPath : testArtifactPaths) {
List<String> testCasePaths = IOUtils.getDirectoryPaths(testArtifactPath, false);
for (String testCasePath : testCasePaths) {
try {
List<String> paths = IOUtils.getFilePaths(testCasePath, true);
List<IBaseResource> resources = IOUtils.readResources(paths, fhirContext);
ensureIds(testCasePath, resources);
Object bundle = BundleUtils.bundleArtifacts(getId(FilenameUtils.getName(testCasePath)), resources, fhirContext, false);
IOUtils.writeBundle(bundle, testArtifactPath, encoding, fhirContext);
} catch (Exception e) {
LogUtils.putException(testCasePath, e);

org.hl7.fhir.r4.model.Group testGroup = null;

if (version.getVersion() == FhirVersionEnum.R4) {
testGroup = new org.hl7.fhir.r4.model.Group();
testGroup.setActive(true);
testGroup.setType(Group.GroupType.PERSON);
testGroup.setActual(true);
}

// For each test case we need to create a group
if (!testCasePaths.isEmpty()) {
String measureName = IOUtils.getMeasureTestDirectory(testCasePaths.get(0));
if (testGroup != null) {
testGroup.setId(measureName);

testGroup.addExtension("http://hl7.org/fhir/StructureDefinition/artifact-testArtifact",
new CanonicalType("http://ecqi.healthit.gov/ecqms/Measure/" + measureName));
}
finally {
LogUtils.warn(testCasePath);

for (String testCasePath : testCasePaths) {
try {
List<String> paths = IOUtils.getFilePaths(testCasePath, true);
List<IBaseResource> resources = IOUtils.readResources(paths, fhirContext);
ensureIds(testCasePath, resources);

// Loop through resources and any that are patients need to be added to the test Group
// Handle individual resources when they exist
for (IBaseResource resource : resources) {
if ((resource.fhirType() == "Patient") && (version.getVersion() == FhirVersionEnum.R4)) {
org.hl7.fhir.r4.model.Patient patient = (org.hl7.fhir.r4.model.Patient) resource;
addPatientToGroupR4(testGroup, patient);
}

// Handle bundled resources when that is how they are provided
if ((resource.fhirType() == "Bundle") && (version.getVersion() == FhirVersionEnum.R4)) {
org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) resource;
ArrayList<org.hl7.fhir.r4.model.Resource> bundleResources =
BundleUtils.getR4ResourcesFromBundle(bundle);
for (IBaseResource bundleResource : bundleResources) {
if (bundleResource.fhirType() == "Patient") {
org.hl7.fhir.r4.model.Patient patient = (org.hl7.fhir.r4.model.Patient) bundleResource;
addPatientToGroupR4(testGroup, patient);
}
}
}
}

Object bundle = BundleUtils.bundleArtifacts(getId(FilenameUtils.getName(testCasePath)), resources, fhirContext, false);
IOUtils.writeBundle(bundle, testArtifactPath, encoding, fhirContext);
} catch (Exception e) {
LogUtils.putException(testCasePath, e);
} finally {
LogUtils.warn(testCasePath);
}
}

// Need to output the Group if it exists
if (testGroup != null) {
IOUtils.writeResource(testGroup, testArtifactPath, encoding, fhirContext, true,
"Group-" + measureName);
}
}
}
}
}

private void addPatientToGroupR4(Group group, org.hl7.fhir.r4.model.Patient patient) {
IdType idType = patient.getIdElement();
org.hl7.fhir.r4.model.Group.GroupMemberComponent member = group.addMember();
org.hl7.fhir.r4.model.Reference patientRef = new Reference();
patientRef.setReference("Patient/" + idType.getIdPart());

// Get name for display value
org.hl7.fhir.r4.model.HumanName name = patient.getName().get(0);
patientRef.setDisplay(name.getNameAsSingleString());

member.setEntity(patientRef);
}

public static List<IBaseResource> getTestCaseResources(String path, FhirContext fhirContext)
{
List<IBaseResource> resources = new ArrayList<IBaseResource>();
Expand Down
13 changes: 12 additions & 1 deletion tooling/src/main/java/org/opencds/cqf/tooling/utilities/IOUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,10 @@
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.Optional;
import java.util.regex.Matcher;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;

import ca.uhn.fhir.util.BundleBuilder;
import com.google.gson.JsonObject;
Expand Down Expand Up @@ -1035,11 +1037,20 @@ public static boolean isXMLOrJson(String fileDirPath, String libraryName){
return false;
}

// Assumes the tests are structured as .../input/tests/measure/{MeasureName}/{TestName} and will extract
// the measure name
public static String getMeasureTestDirectory(String pathString) {
Path path = Paths.get(pathString);
String[] testDirs = StreamSupport.stream(path.spliterator(), false).map(Path::toString).toArray(String[]::new);
String testDir = testDirs[testDirs.length - 2];
return testDir;
}

public static String concatFilePath(String basePath, String... pathsToAppend) {
String filePath = basePath;
for (String pathToAppend: pathsToAppend) {
filePath = FilenameUtils.concat(filePath, pathToAppend);
}
return filePath;
}
}
}

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