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MAT-6916: Implement basic endpoint for triggering database update
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mcmcphillips committed Mar 27, 2024
1 parent aad60ab commit d38cc2c
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Showing 13 changed files with 196 additions and 147 deletions.
10 changes: 5 additions & 5 deletions src/main/java/gov/cms/madie/terminology/config/WebFluxConfiguration.java
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Expand Up @@ -6,8 +6,8 @@

@Configuration
public class WebFluxConfiguration implements WebFluxConfigurer {
@Override
public void configureHttpMessageCodecs(ServerCodecConfigurer configurer) {
configurer.defaultCodecs().maxInMemorySize(500 * 1024);
}
}
@Override
public void configureHttpMessageCodecs(ServerCodecConfigurer configurer) {
configurer.defaultCodecs().maxInMemorySize(500 * 1024);
}
}
50 changes: 17 additions & 33 deletions src/main/java/gov/cms/madie/terminology/controller/VsacController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,19 +38,19 @@ public class VsacController {

@GetMapping(path = "/valueset", produces = MediaType.APPLICATION_JSON_VALUE)
public ResponseEntity<String> getValueSet(
Principal principal,
@RequestParam String oid,
@RequestParam(required = false, name = "profile") String profile,
@RequestParam(required = false, name = "includeDraft") String includeDraft,
@RequestParam(required = false, name = "release") String release,
@RequestParam(required = false, name = "version") String version) {
Principal principal,
@RequestParam String oid,
@RequestParam(required = false, name = "profile") String profile,
@RequestParam(required = false, name = "includeDraft") String includeDraft,
@RequestParam(required = false, name = "release") String release,
@RequestParam(required = false, name = "version") String version) {
log.debug("Entering: getValueSet()");

final String username = principal.getName();
Optional<UmlsUser> umlsUser = vsacService.findByHarpId(username);
if (umlsUser.isPresent()) {
RetrieveMultipleValueSetsResponse valuesetResponse =
vsacService.getValueSet(oid, umlsUser.get(), profile, includeDraft, release, version);
vsacService.getValueSet(oid, umlsUser.get(), profile, includeDraft, release, version);

ValueSet fhirValueSet = vsacService.convertToFHIRValueSet(valuesetResponse);
log.debug("valueset id = " + fhirValueSet.getId());
Expand All @@ -67,19 +67,19 @@ protected String serializeFhirValueset(ValueSet fhirValueSet) {

@PutMapping(path = "/value-sets/searches", produces = MediaType.APPLICATION_JSON_VALUE)
public ResponseEntity<String> searchValueSets(
Principal principal, @RequestBody ValueSetsSearchCriteria searchCriteria) {
Principal principal, @RequestBody ValueSetsSearchCriteria searchCriteria) {
log.debug("VsacController::getValueSets");

final String username = principal.getName();
Optional<UmlsUser> umlsUser = vsacService.findByHarpId(username);
if (umlsUser.isPresent()) {

List<RetrieveMultipleValueSetsResponse> vsacValueSets =
vsacService.getValueSets(searchCriteria, umlsUser.get());
vsacService.getValueSets(searchCriteria, umlsUser.get());

List<ValueSet> fhirValueSets = vsacService.convertToFHIRValueSets(vsacValueSets);
String serializedValueSets =
fhirValueSets.stream().map(this::serializeFhirValueset).collect(Collectors.joining(", "));
fhirValueSets.stream().map(this::serializeFhirValueset).collect(Collectors.joining(", "));

return ResponseEntity.ok().body("[" + serializedValueSets + "]");
}
Expand All @@ -88,14 +88,14 @@ public ResponseEntity<String> searchValueSets(

@PutMapping("/qdm/value-sets/searches")
public ResponseEntity<List<QdmValueSet>> getQdmValueSets(
Principal principal, @RequestBody ValueSetsSearchCriteria searchCriteria) {
Principal principal, @RequestBody ValueSetsSearchCriteria searchCriteria) {
log.debug("VsacController::getQdmValueSets");

final String username = principal.getName();
Optional<UmlsUser> umlsUser = vsacService.findByHarpId(username);
if (umlsUser.isPresent()) {
List<QdmValueSet> qdmValueSets =
vsacService.getValueSetsInQdmFormat(searchCriteria, umlsUser.get());
vsacService.getValueSetsInQdmFormat(searchCriteria, umlsUser.get());

return ResponseEntity.ok().body(qdmValueSets);
}
Expand All @@ -104,9 +104,9 @@ public ResponseEntity<List<QdmValueSet>> getQdmValueSets(

@PutMapping(path = "/validations/codes", produces = MediaType.APPLICATION_JSON_VALUE)
public ResponseEntity<List<CqlCode>> validateCodes(
Principal principal,
@RequestBody List<CqlCode> cqlCodes,
@RequestParam(required = false, defaultValue = "FHIR") String model) {
Principal principal,
@RequestBody List<CqlCode> cqlCodes,
@RequestParam(required = false, defaultValue = "FHIR") String model) {
final String username = principal.getName();
Optional<UmlsUser> umlsUser = vsacService.findByHarpId(username);
if (umlsUser.isPresent() && umlsUser.get().getApiKey() != null) {
Expand All @@ -131,23 +131,7 @@ public ResponseEntity<String> umlsLogin(Principal principal, @RequestBody String
@GetMapping("/umls-credentials/status")
public ResponseEntity<Boolean> checkUserLogin(Principal principal) {
return vsacService.validateUmlsInformation(principal.getName())
? ResponseEntity.ok().body(Boolean.TRUE)
: new ResponseEntity<>(HttpStatus.UNAUTHORIZED);
}

@GetMapping(path = "/update-code-systems", produces = MediaType.APPLICATION_JSON_VALUE)
public ResponseEntity<List<ManifestExpansion>> retrieveAndUpdateCodeSystems(Principal principal) {
final String username = principal.getName();
Optional<UmlsUser> umlsUser = vsacService.findByHarpId(username);

if (umlsUser.isPresent() && !StringUtils.isBlank(umlsUser.get().getApiKey())) {
return ResponseEntity.ok().body(fhirTerminologyService.retrieveAllCodeSystems(umlsUser.get()));
}
else{
log.error(
"Unable to Retrieve List of code systems, "
+ "UMLS Authentication Key Not found for user : [{}}]",
username);
throw new VsacUnauthorizedException("Please login to UMLS before proceeding"); }
? ResponseEntity.ok().body(Boolean.TRUE)
: new ResponseEntity<>(HttpStatus.UNAUTHORIZED);
}
}
19 changes: 19 additions & 0 deletions src/main/java/gov/cms/madie/terminology/controller/VsacFhirTerminologyController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,14 @@
import gov.cms.madie.terminology.dto.QdmValueSet;
import gov.cms.madie.terminology.dto.ValueSetsSearchCriteria;
import gov.cms.madie.terminology.exceptions.VsacUnauthorizedException;
import gov.cms.madie.terminology.models.CodeSystem;
import gov.cms.madie.terminology.models.UmlsUser;
import gov.cms.madie.terminology.service.FhirTerminologyService;
import gov.cms.madie.terminology.service.VsacService;
import lombok.RequiredArgsConstructor;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.lang3.StringUtils;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;

Expand Down Expand Up @@ -59,4 +61,21 @@ public ResponseEntity<List<QdmValueSet>> getValueSetsExpansions(
username);
throw new VsacUnauthorizedException("Please login to UMLS before proceeding");
}

@GetMapping(path = "/update-code-systems", produces = MediaType.APPLICATION_JSON_VALUE)
public ResponseEntity<List<CodeSystem>> retrieveAndUpdateCodeSystems(Principal principal) {
final String username = principal.getName();
Optional<UmlsUser> umlsUser = vsacService.findByHarpId(username);

if (umlsUser.isPresent() && !StringUtils.isBlank(umlsUser.get().getApiKey())) {
return ResponseEntity.ok()
.body(fhirTerminologyService.retrieveAllCodeSystems(umlsUser.get()));
} else {
log.error(
"Unable to Retrieve List of code systems, "
+ "UMLS Authentication Key Not found for user : [{}}]",
username);
throw new VsacUnauthorizedException("Please login to UMLS before proceeding");
}
}
}
12 changes: 5 additions & 7 deletions src/main/java/gov/cms/madie/terminology/models/CodeSystem.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,10 @@
@Builder(toBuilder = true)
@NoArgsConstructor
@Document

public class CodeSystem {
@Id private String id; //version ID
private String name;
private String version;
private Identifier identifier; // identifier[0] of identifier List
private Meta meta;
private Instant lastUpdated;
@Id private String versionId; // meta().versionId
private String name;
private String version;
private String value; // identifier[0].value oid of identifier List
private Instant lastUpdated; // when we got it
}
5 changes: 0 additions & 5 deletions src/main/java/gov/cms/madie/terminology/models/Identifier.java
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This file was deleted.

9 changes: 0 additions & 9 deletions src/main/java/gov/cms/madie/terminology/models/Meta.java
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This file was deleted.

10 changes: 10 additions & 0 deletions src/main/java/gov/cms/madie/terminology/repositories/CodeSystemRepository.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
package gov.cms.madie.terminology.repositories;

import gov.cms.madie.terminology.models.CodeSystem;
import org.springframework.data.mongodb.repository.MongoRepository;
import java.util.Optional;

public interface CodeSystemRepository extends MongoRepository<CodeSystem, String> {
Optional<CodeSystem> findByVersionId(String versionId);

}
89 changes: 68 additions & 21 deletions src/main/java/gov/cms/madie/terminology/service/FhirTerminologyService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,13 @@

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import gov.cms.madie.models.cql.terminology.VsacCode;
import gov.cms.madie.models.mapping.CodeSystemEntry;
import gov.cms.madie.models.measure.ManifestExpansion;
import gov.cms.madie.terminology.dto.QdmValueSet;
import gov.cms.madie.terminology.dto.ValueSetsSearchCriteria;
import gov.cms.madie.terminology.models.CodeSystem;
import gov.cms.madie.terminology.models.UmlsUser;
import gov.cms.madie.terminology.repositories.CodeSystemRepository;
import gov.cms.madie.terminology.util.TerminologyServiceUtil;
import gov.cms.madie.terminology.webclient.FhirTerminologyServiceWebClient;
import lombok.RequiredArgsConstructor;
Expand All @@ -16,7 +17,9 @@
import org.hl7.fhir.r4.model.ValueSet;
import org.springframework.cache.annotation.Cacheable;
import org.springframework.stereotype.Service;
import org.springframework.web.util.UriComponentsBuilder;

import java.time.Instant;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
Expand All @@ -28,7 +31,7 @@ public class FhirTerminologyService {
private final FhirContext fhirContext;
private final FhirTerminologyServiceWebClient fhirTerminologyServiceWebClient;
private final MappingService mappingService;

private final CodeSystemRepository codeSystemRepository;
@Cacheable("manifest-list")
public List<ManifestExpansion> getManifests(UmlsUser umlsUser) {
IParser parser = fhirContext.newJsonParser();
Expand Down Expand Up @@ -110,28 +113,72 @@ private List<QdmValueSet.Concept> getValueSetConcepts(
return List.of();
}

// call individual
public List<ManifestExpansion> retrieveCodeSystemsPage(UmlsUser umlsUser){
// one to call only, one to mutate and build
public Bundle retrieveCodeSystemsPage(UmlsUser umlsUser, Integer offset, Integer count) {
IParser parser = fhirContext.newJsonParser();
String responseString = fhirTerminologyServiceWebClient.getCodeSystemsPage(0, 100, umlsUser.getApiKey());
Bundle CodeSystemsBundle = parser.parseResource(Bundle.class, responseString);
var CodeSystemsOptions = new ArrayList<ManifestExpansion>();
CodeSystemsBundle
.getEntry()
.forEach(
entry ->
CodeSystemsOptions.add(
ManifestExpansion.builder()
.id(entry.getResource().getIdPart())
.fullUrl(entry.getFullUrl())
.build()));
return CodeSystemsOptions;
String responseString =
fhirTerminologyServiceWebClient.getCodeSystemsPage(offset, count, umlsUser.getApiKey());
return parser.parseResource(
Bundle.class, responseString);
}

public List<ManifestExpansion> retrieveAllCodeSystems(UmlsUser umlsUser) {

return retrieveCodeSystemsPage(umlsUser);
// save
private void updateOrInsertAllCodeSystems(List<CodeSystem> codeSystemList){
for (CodeSystem codeSystem : codeSystemList) {
Optional<CodeSystem> existingCodeSystemOptional = codeSystemRepository.findByVersionId(codeSystem.getVersionId());
if (existingCodeSystemOptional.isPresent()) {
// Update existing CodeSystem
CodeSystem existingCodeSystem = existingCodeSystemOptional.get();
existingCodeSystem.setName(codeSystem.getName());
existingCodeSystem.setValue(codeSystem.getValue());
existingCodeSystem.setLastUpdated(Instant.now());
codeSystemRepository.save(existingCodeSystem);
log.info("CodeSystem updated: {}", existingCodeSystem);
} else {
// Insert new CodeSystem
codeSystemRepository.save(codeSystem);
log.info("New CodeSystem inserted: {}", codeSystem);
}
}
}
private void recursiveRetrieveCodeSystems(UmlsUser umlsUser, Integer offset, Integer count, List<CodeSystem> allCodeSystems) {
log.info("requesting page offset: {} count: {}", offset, count);
Bundle codeSystemBundle = retrieveCodeSystemsPage(umlsUser, offset, count);
List<CodeSystem> codeSystemsPage = new ArrayList<>(); // build small list
codeSystemBundle.getEntry().forEach(entry -> {
var codeSystem = (org.hl7.fhir.r4.model.CodeSystem) entry.getResource();
String codeSystemValue = "";
if (!codeSystem.getIdentifier().isEmpty()) {
codeSystemValue = codeSystem.getIdentifier().get(0).getValue();
}
codeSystemsPage.add(
CodeSystem.builder()
.versionId(codeSystem.getMeta().getVersionId())
.version(codeSystem.getVersion())
.name(codeSystem.getName())
.value(codeSystemValue)
.lastUpdated(Instant.now())
.build());
});
allCodeSystems.addAll(codeSystemsPage); // update big list
var links = codeSystemBundle.getLink();
links.forEach((l) -> {
if (l.getRelation().equals("next")){
// if next, call self and continue until fail.
UriComponentsBuilder builder = UriComponentsBuilder.fromHttpUrl(l.getUrl());
String newOffset = builder.build().getQueryParams().getFirst("_offset");
String newCount = builder.build().getQueryParams().getFirst("_count");
assert newOffset != null;
assert newCount != null;
recursiveRetrieveCodeSystems(umlsUser, Integer.parseInt(newOffset), Integer.parseInt(newCount), allCodeSystems);
}
});
}
public List<CodeSystem> retrieveAllCodeSystems(UmlsUser umlsUser) {
List<CodeSystem> allCodeSystems = new ArrayList<>();

recursiveRetrieveCodeSystems(umlsUser, 0, 50, allCodeSystems);
// Once we have all codeSystems, update DB using mongo
updateOrInsertAllCodeSystems(allCodeSystems);
return allCodeSystems;
}
}
11 changes: 7 additions & 4 deletions src/main/java/gov/cms/madie/terminology/util/TerminologyServiceUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -64,12 +64,15 @@ public static URI buildRetrieveCodeUri(String baseUrl, String codePath) {
}

public static URI buildRetrieveCodeSystemsUri(String baseUrl, Integer offset, Integer count) {
// http://uat-cts.nlm.nih.gov/fhir/res/CodeSystem?_offset=100&_count=100
// http://uat-cts.nlm.nih.gov/fhir/res/CodeSystem?_offset=100&_count=100
return UriComponentsBuilder.fromUriString(baseUrl)
.queryParam("_offset", Integer.toString(offset))
.queryParam("_count", Integer.toString(count))
.buildAndExpand().encode().toUri();
.queryParam("_offset", Integer.toString(offset))
.queryParam("_count", Integer.toString(count))
.buildAndExpand()
.encode()
.toUri();
}

public static String buildCodePath(
String codeSystemName, String codeSystemVersion, String codeId) {
// "/CodeSystem/LOINC22/Version/2.67/Code/21112-8/Info";
Expand Down
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