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MAT-6206: Adding ability to export TestCases as type 'Collection' #165

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MAT-6206: Adding ability to export TestCases as type 'Collection' #165

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25 changes: 9 additions & 16 deletions src/main/java/gov/cms/madie/madiefhirservice/resources/MeasureBundleController.java
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@@ -1,33 +1,26 @@
package gov.cms.madie.madiefhirservice.resources;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.MethodOutcome;
import gov.cms.madie.madiefhirservice.services.ExportService;
import gov.cms.madie.madiefhirservice.services.MeasureBundleService;
import gov.cms.madie.madiefhirservice.utils.BundleUtil;
import gov.cms.madie.madiefhirservice.utils.ExportFileNamesUtil;
import gov.cms.madie.models.measure.Measure;
import io.swagger.v3.oas.annotations.tags.Tag;
import jakarta.servlet.http.HttpServletRequest;

import lombok.extern.slf4j.Slf4j;
import org.hl7.fhir.r4.model.Bundle;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.validation.annotation.Validated;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.PutMapping;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestHeader;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBody;

@Slf4j
import ca.uhn.fhir.context.FhirContext;
import gov.cms.madie.madiefhirservice.services.ExportService;
import gov.cms.madie.madiefhirservice.services.MeasureBundleService;
import gov.cms.madie.madiefhirservice.utils.ExportFileNamesUtil;
import gov.cms.madie.models.measure.Measure;
import io.swagger.v3.oas.annotations.tags.Tag;
import jakarta.servlet.http.HttpServletRequest;

@Controller
@RequestMapping(path = "/fhir/measures")
@Tag(name = "Measure-Controller", description = "Measure resources HAPI FHIR API")
Expand All @@ -47,7 +40,7 @@ public ResponseEntity<String> getMeasureBundle(
@RequestBody @Validated(Measure.ValidationSequence.class) Measure measure,
@RequestHeader(value = HttpHeaders.ACCEPT, required = false) String accept,
@RequestHeader("Authorization") String accessToken,
@RequestParam(required = false, defaultValue = "calculation", name = "bundleType")
@RequestParam(required = false, defaultValue = "CALCULATION", name = "bundleType")
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Not a big deal, this doesn't affect functionality, we can add tech debt. we have enum that maintains this https://github.com/MeasureAuthoringTool/madie-fhir-service/blob/develop/src/main/java/gov/cms/madie/madiefhirservice/utils/BundleUtil.java

String bundleType) {

Bundle bundle =
Expand Down
6 changes: 2 additions & 4 deletions src/main/java/gov/cms/madie/madiefhirservice/resources/TestCaseBundleController.java
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Expand Up @@ -50,9 +50,6 @@ public ResponseEntity<byte[]> getTestCaseExportBundle(
if (testCaseId == null || testCaseId.isEmpty()) {
throw new ResourceNotFoundException("test cases", "measure", measure.getId());
}
//MAT-6204 Here we're modifying the bundle based on export choice,
// but we don't want to modify it permanently
testCaseBundleService.setExportBundleType(exportDTO, measure);

List<TestCase> testCases =
Optional.ofNullable(measure.getTestCases())
Expand All @@ -62,7 +59,8 @@ public ResponseEntity<byte[]> getTestCaseExportBundle(
.filter(tc -> testCaseId.stream().anyMatch(id -> id.equals(tc.getId())))
.collect(Collectors.toList());
Map<String, Bundle> exportableTestCaseBundle =
testCaseBundleService.getTestCaseExportBundle(measure, testCases);
testCaseBundleService.getTestCaseExportBundle(
measure, testCases, exportDTO.getBundleType());
if (testCases.size() != exportableTestCaseBundle.size()) {
// remove the test cases that couldn't be parsed
testCases =
Expand Down
9 changes: 6 additions & 3 deletions src/main/java/gov/cms/madie/madiefhirservice/services/MeasureBundleService.java
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Expand Up @@ -4,6 +4,7 @@
import gov.cms.madie.madiefhirservice.utils.BundleUtil;
import gov.cms.madie.madiefhirservice.utils.FhirResourceHelpers;
import gov.cms.madie.madiefhirservice.utils.ResourceUtils;

import gov.cms.madie.models.library.CqlLibrary;
import gov.cms.madie.models.measure.Measure;
import gov.cms.mat.cql.CqlFormatter;
Expand Down Expand Up @@ -50,7 +51,7 @@ public Bundle createMeasureBundle(

// Bundle entry for Measure resource
Bundle.BundleEntryComponent measureEntryComponent =
FhirResourceHelpers.getBundleEntryComponent(measure, "Transaction");
FhirResourceHelpers.getBundleEntryComponent(measure, Bundle.BundleType.TRANSACTION);
Bundle bundle =
new Bundle().setType(Bundle.BundleType.TRANSACTION).addEntry(measureEntryComponent);
// Bundle entries for all the library resources of a MADiE Measure
Expand Down Expand Up @@ -91,13 +92,15 @@ public List<Bundle.BundleEntryComponent> createBundleComponentsForLibrariesOfMad
Measure madieMeasure, final String bundleType, final String accessToken) {
Library library = getMeasureLibraryResourceForMadieMeasure(madieMeasure);
Bundle.BundleEntryComponent mainLibraryBundleComponent =
FhirResourceHelpers.getBundleEntryComponent(library, "Transaction");
FhirResourceHelpers.getBundleEntryComponent(library, Bundle.BundleType.TRANSACTION);
Map<String, Library> includedLibraryMap = new HashMap<>();
libraryService.getIncludedLibraries(
madieMeasure.getCql(), includedLibraryMap, bundleType, accessToken);
List<Bundle.BundleEntryComponent> libraryBundleComponents =
includedLibraryMap.values().stream()
.map((lib) -> FhirResourceHelpers.getBundleEntryComponent(lib, "Transaction"))
.map(
(lib) ->
FhirResourceHelpers.getBundleEntryComponent(lib, Bundle.BundleType.TRANSACTION))
.collect(Collectors.toList());
// add main library first in the list
libraryBundleComponents.add(0, mainLibraryBundleComponent);
Expand Down
70 changes: 9 additions & 61 deletions src/main/java/gov/cms/madie/madiefhirservice/services/TestCaseBundleService.java
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Expand Up @@ -24,8 +24,6 @@
import org.apache.commons.lang3.time.DateFormatUtils;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Bundle;

import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.MarkdownType;
import org.hl7.fhir.r4.model.MeasureReport;
Expand All @@ -49,7 +47,6 @@
import gov.cms.madie.madiefhirservice.utils.ExportFileNamesUtil;
import gov.cms.madie.madiefhirservice.utils.FhirResourceHelpers;
import gov.cms.madie.models.common.BundleType;
import gov.cms.madie.models.dto.ExportDTO;
import gov.cms.madie.models.measure.Measure;
import gov.cms.madie.models.measure.TestCase;
import gov.cms.madie.packaging.utils.PackagingUtility;
Expand All @@ -64,7 +61,8 @@ public class TestCaseBundleService {

private final FhirContext fhirContext;

public Map<String, Bundle> getTestCaseExportBundle(Measure measure, List<TestCase> testCases) {
public Map<String, Bundle> getTestCaseExportBundle(
Measure measure, List<TestCase> testCases, BundleType bundleType) {
if (measure == null || testCases == null || testCases.isEmpty()) {
throw new InternalServerException("Unable to find Measure and/or test case");
}
Expand All @@ -85,6 +83,11 @@ public Map<String, Bundle> getTestCaseExportBundle(Measure measure, List<TestCas
throw new DataFormatException("TestCase Json is empty");
}
bundle = parser.parseResource(Bundle.class, testCase.getJson());
if (bundleType != null) {
bundle.setType(
org.hl7.fhir.r4.model.Bundle.BundleType.valueOf(bundleType.toString().toUpperCase()));
bundle = FhirResourceHelpers.setTestCaseBundleEntryComponent(bundle);
}
} catch (DataFormatException | ClassCastException ex) {
log.error(
"Unable to parse test case bundle resource for test case [{}] from Measure [{}]",
Expand All @@ -95,9 +98,9 @@ public Map<String, Bundle> getTestCaseExportBundle(Measure measure, List<TestCas

String fileName = ExportFileNamesUtil.getTestCaseExportFileName(measure, testCase);
var measureReport = buildMeasureReport(testCase, measure, bundle);

var bundleEntryComponent =
FhirResourceHelpers.getBundleEntryComponent(
measureReport, String.valueOf(bundle.getType()));
FhirResourceHelpers.getBundleEntryComponent(measureReport, bundle.getType());
bundle.getEntry().add(bundleEntryComponent);
testCaseBundle.put(fileName, bundle);
}
Expand All @@ -110,41 +113,6 @@ public Map<String, Bundle> getTestCaseExportBundle(Measure measure, List<TestCas
return testCaseBundle;
}

public void updateEntry(TestCase testCase, BundleType bundleType) {

// Convert Test case JSON to a BUndle
IParser parser =
fhirContext
.newJsonParser()
.setParserErrorHandler(new StrictErrorHandler())
.setPrettyPrint(true);
Bundle bundle = parser.parseResource(Bundle.class, testCase.getJson());

// modify the bundle
org.hl7.fhir.r4.model.Bundle.BundleType fhirBundleType =
org.hl7.fhir.r4.model.Bundle.BundleType.valueOf(bundleType.toString().toUpperCase());
bundle.setType(fhirBundleType);
bundle.setEntry(
bundle.getEntry().stream()
.map(
entry -> {
if (bundleType == BundleType.TRANSACTION) {


FhirResourceHelpers.setResourceEntry(entry.getResource(), entry);
return entry;
} else if (bundleType == BundleType.COLLECTION) {
entry.setRequest(null);
}
return entry;
})
.collect(Collectors.toList()));
// bundle to json
String json = parser.encodeResourceToString(bundle);

testCase.setJson(json);
}

private MeasureReport buildMeasureReport(
TestCase testCase, Measure measure, Bundle testCaseBundle) {
MeasureReport measureReport = new MeasureReport();
Expand Down Expand Up @@ -319,26 +287,6 @@ private String generateReadMe(List<TestCase> testCases) {
return readMe;
}

public void setExportBundleType(ExportDTO exportDTO, Measure measure) {
if (exportDTO.getBundleType() != null) {
BundleType bundleType = BundleType.valueOf(exportDTO.getBundleType().name());
switch (bundleType) {
case COLLECTION:
log.debug("You're exporting a Collection");
// update bundle type for each entry MAT 6405
break;
case TRANSACTION:
log.debug("You're exporting a Transaction");
// update bundle type and add entry.request for each entry
if (measure.getTestCases() != null) {
measure.getTestCases().stream().forEach(testCase -> updateEntry(testCase, bundleType));
}
break;
default:
}
}
}

/**
* Combines the zip from Packaging Utility and a generated ReadMe file for the testcases
*
Expand Down
49 changes: 40 additions & 9 deletions src/main/java/gov/cms/madie/madiefhirservice/utils/FhirResourceHelpers.java
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Expand Up @@ -2,6 +2,7 @@

import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Period;
Expand All @@ -11,6 +12,7 @@

import java.util.ArrayList;
import java.util.Date;
import java.util.stream.Collectors;

@Component
public class FhirResourceHelpers {
Expand All @@ -21,26 +23,55 @@ public void setMadieUrl(String url) {
FhirResourceHelpers.madieUrl = url;
}

public static Bundle setTestCaseBundleEntryComponent(Bundle bundle) {

// modify the bundle
org.hl7.fhir.r4.model.Bundle.BundleType fhirBundleType =
org.hl7.fhir.r4.model.Bundle.BundleType.valueOf(bundle.getType().toString().toUpperCase());
bundle.setType(fhirBundleType);
bundle.setEntry(
bundle.getEntry().stream()
.map(
entry -> {
if (org.hl7.fhir.r4.model.Bundle.BundleType.valueOf(
bundle.getType().toString().toUpperCase())
== BundleType.TRANSACTION) {
FhirResourceHelpers.setResourceEntry(entry.getResource(), entry);
return entry;
} else if (org.hl7.fhir.r4.model.Bundle.BundleType.valueOf(
bundle.getType().toString().toUpperCase())
== BundleType.COLLECTION) {
entry.setRequest(null);
}
return entry;
})
.collect(Collectors.toList()));
// bundle to json

return bundle;
}

public static Bundle.BundleEntryComponent getBundleEntryComponent(
Resource resource, String bundleType) {
Resource resource, Bundle.BundleType bundleType) {
Bundle.BundleEntryComponent entryComponent =
new Bundle.BundleEntryComponent()
.setFullUrl(buildResourceFullUrl(resource.fhirType(), resource.getIdPart()))
.setResource(resource);
// for the transaction bundles, add request object to the entry
if ("Transaction".equalsIgnoreCase(bundleType)) {
if (bundleType == Bundle.BundleType.TRANSACTION) {
setResourceEntry(resource, entryComponent);
}
return entryComponent;
}

public static void setResourceEntry(Resource resource, Bundle.BundleEntryComponent entryComponent) {
Bundle.BundleEntryRequestComponent requestComponent =
new Bundle.BundleEntryRequestComponent()
.setMethod(Bundle.HTTPVerb.POST)
.setUrl(resource.getResourceType() + "/" + resource.getIdPart());
entryComponent.setRequest(requestComponent);
}
public static void setResourceEntry(
Resource resource, Bundle.BundleEntryComponent entryComponent) {
Bundle.BundleEntryRequestComponent requestComponent =
new Bundle.BundleEntryRequestComponent()
.setMethod(Bundle.HTTPVerb.POST)
.setUrl(resource.getResourceType() + "/" + resource.getIdPart());
entryComponent.setRequest(requestComponent);
}

public static Period getPeriodFromDates(Date startDate, Date endDate) {
return new Period()
Expand Down
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