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- add functions to handle biosample endpoint - add additional biospecimen filter
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| Original file line number | Diff line number | Diff line change |
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@@ -3,5 +3,6 @@ | |
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| public enum QueryType { | ||
| BEACON_INDIVIDUALS, | ||
| BEACON_CATALOG; | ||
| BEACON_BIOSAMPLE, | ||
| BEACON_CATALOG | ||
| } | ||
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165 changes: 165 additions & 0 deletions
165
...n/java/org/ejprarediseases/vpdpbackend/search/v1/handler/BeaconBiosampleQueryHandler.java
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| package org.ejprarediseases.vpdpbackend.search.v1.handler; | ||
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| import org.ejprarediseases.vpdpbackend.resource.v1.model.Resource; | ||
| import org.ejprarediseases.vpdpbackend.search.v1.model.SearchRequest; | ||
| import org.ejprarediseases.vpdpbackend.search.v1.model.beacon.enums.BiospecimenType; | ||
| import org.ejprarediseases.vpdpbackend.search.v1.model.beacon.request_body.BeaconRequestBody; | ||
| import org.ejprarediseases.vpdpbackend.search.v1.model.beacon.request_body.filters.BeaconRequestBodyFilter; | ||
| import org.ejprarediseases.vpdpbackend.search.v1.model.beacon.request_body.filters.ontology_filter.BeaconRequestBodyOntologyFilter; | ||
| import org.ejprarediseases.vpdpbackend.search.v1.model.beacon.request_body.sections.BeaconRequestBodyMetaSection; | ||
| import org.ejprarediseases.vpdpbackend.search.v1.model.beacon.request_body.sections.BeaconRequestBodyQuerySection; | ||
| import org.ejprarediseases.vpdpbackend.utils.UserHandler; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
| import org.springframework.http.MediaType; | ||
| import org.springframework.web.reactive.function.client.WebClient; | ||
| import reactor.core.publisher.Mono; | ||
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| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
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| import static org.ejprarediseases.vpdpbackend.search.v1.handler.BeaconFilterHandler.*; | ||
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| public class BeaconBiosampleQueryHandler { | ||
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| static Logger logger = LoggerFactory.getLogger(BeaconBiosampleQueryHandler.class); | ||
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| /** | ||
| * Retrieves a response from the specified beacon resource using the provided request body and authorization key. | ||
| * | ||
| * @param resource The resource to query. | ||
| * @param requestBody The request body for the query. | ||
| * @return The response string from the resource. | ||
| */ | ||
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| public static String getResponse(Resource resource, BeaconRequestBody requestBody) { | ||
| String response; | ||
| try { | ||
| WebClient client = WebClient.create(); | ||
| response = client.post() | ||
| .uri( resource.getResourceAddress()) | ||
| .bodyValue(requestBody) | ||
| .accept(MediaType.APPLICATION_JSON) | ||
| .header("Authorization", UserHandler.getBearerToken()) | ||
| .retrieve() | ||
| .onStatus(httpStatus -> httpStatus.value() == 403, | ||
| error -> Mono.error(new RuntimeException("error Body"))) | ||
| .bodyToMono(String.class) | ||
| .block(); | ||
| } catch (Exception e) { | ||
| logger.error("authKey for resource: " + resource.getResourceName() + " is not defined." + e); | ||
| return null; | ||
| } | ||
| return response; | ||
| } | ||
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| /** | ||
| * Builds and returns the meta section of a Beacon query request body. | ||
| * | ||
| * @return The constructed BeaconRequestBodyMetaSection. | ||
| */ | ||
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| public static BeaconRequestBodyMetaSection buildMetaSection() { | ||
| BeaconRequestBodyMetaSection metaSection = new BeaconRequestBodyMetaSection(); | ||
| metaSection.setApiVersion("v0.2"); | ||
| return metaSection; | ||
| } | ||
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| /** | ||
| * Builds and returns the query section of a Beacon query request body. | ||
| * | ||
| * @param searchRequest The search request containing filter criteria. | ||
| * @return The constructed BeaconRequestBodyQuerySection. | ||
| */ | ||
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| private static BeaconRequestBodyQuerySection buildQuerySection(SearchRequest searchRequest) { | ||
| BeaconRequestBodyQuerySection querySection = new BeaconRequestBodyQuerySection(); | ||
| List<BeaconRequestBodyFilter> filters = new ArrayList<>(); | ||
| filters.add(buildDiseaseFilter(searchRequest.getDiseases())); | ||
| if (searchRequest.getSexes() != null && !searchRequest.getSexes().isEmpty()) { | ||
| filters.add(buildSexFilter(searchRequest.getSexes())); | ||
| } | ||
| if (searchRequest.getAgeThisYear() != null && searchRequest.getAgeThisYear().size() == 2) { | ||
| filters.add(buildMinAgeFilter(searchRequest.getAgeThisYear().get(0))); | ||
| filters.add(buildMaxAgeFilter(searchRequest.getAgeThisYear().get(1))); | ||
| } | ||
| if (searchRequest.getSymptomOnset() != null && searchRequest.getSymptomOnset().size() == 2) { | ||
| filters.add(buildMinSymptomOnsetFilter(searchRequest.getSymptomOnset().get(0))); | ||
| filters.add(buildMaxSymptomOnsetFilter(searchRequest.getSymptomOnset().get(1))); | ||
| } | ||
| if (searchRequest.getAgeAtDiagnosis() != null && searchRequest.getAgeAtDiagnosis().size() == 2) { | ||
| filters.add(buildMinAgeAtDiagnosisFilter(searchRequest.getAgeAtDiagnosis().get(0))); | ||
| filters.add(buildMaxAgeAtDiagnosisFilter(searchRequest.getAgeAtDiagnosis().get(1))); | ||
| } | ||
| if (searchRequest.getBiospecimenTypes() != null && !searchRequest.getBiospecimenTypes().isEmpty()) { | ||
| filters.add(buildBiospecimenTypeFilter(searchRequest.getBiospecimenTypes())); | ||
| } | ||
| querySection.setFilters(filters); | ||
| return querySection; | ||
| } | ||
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| /** | ||
| * Converts a SearchRequest into a BeaconRequestBody. | ||
| * | ||
| * @param searchRequest The search request containing filter criteria. | ||
| * @return The constructed BeaconRequestBody. | ||
| */ | ||
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| public static BeaconRequestBody convertToBeaconRequestBody(SearchRequest searchRequest) { | ||
| BeaconRequestBody requestBody = new BeaconRequestBody(); | ||
| requestBody.setMeta(buildMetaSection()); | ||
| requestBody.setQuery(buildQuerySection(searchRequest)); | ||
| return requestBody; | ||
| } | ||
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| /** | ||
| * Builds and returns a default query section for Beacon query request body. | ||
| * | ||
| * @return The constructed BeaconRequestBodyQuerySection. | ||
| */ | ||
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| private static BeaconRequestBodyQuerySection getDefaultQuerySection() { | ||
| BeaconRequestBodyQuerySection querySection = new BeaconRequestBodyQuerySection(); | ||
| List<BeaconRequestBodyFilter> filters = new ArrayList<>(); | ||
| BeaconRequestBodyOntologyFilter filter = new BeaconRequestBodyOntologyFilter(); | ||
| List<String> ids = new ArrayList<>(); | ||
| ids.add("ordo:Orphanet_730"); | ||
| ids.add("ordo:Orphanet_635"); | ||
| filter.setId(ids); | ||
| filters.add(filter); | ||
| //filters.add(buildSexFilter(Arrays.asList(Sex.values()))); | ||
| filters.add(buildMinAgeFilter(0)); | ||
| filters.add(buildMaxAgeFilter(100)); | ||
| filters.add(buildMinSymptomOnsetFilter(0)); | ||
| filters.add(buildMaxSymptomOnsetFilter(100)); | ||
| filters.add(buildMinAgeAtDiagnosisFilter(0)); | ||
| filters.add(buildMaxAgeAtDiagnosisFilter(100)); | ||
| filters.add(buildBiospecimenTypeFilter(Arrays.asList(BiospecimenType.BLOOD_SPECIMEN))); | ||
| querySection.setFilters(filters); | ||
| return querySection; | ||
| } | ||
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| /** | ||
| * Builds and returns a default request body for Beacon query. | ||
| * | ||
| * @return The constructed BeaconRequestBody. | ||
| */ | ||
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| public static BeaconRequestBody getDefaultRequestBody() { | ||
| BeaconRequestBody requestBody = new BeaconRequestBody(); | ||
| requestBody.setMeta(buildMetaSection()); | ||
| requestBody.setQuery(getDefaultQuerySection()); | ||
| return requestBody; | ||
| } | ||
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| } | ||
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23 changes: 23 additions & 0 deletions
23
...in/java/org/ejprarediseases/vpdpbackend/search/v1/model/beacon/enums/BiospecimenType.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| package org.ejprarediseases.vpdpbackend.search.v1.model.beacon.enums; | ||
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| public enum BiospecimenType { | ||
| BLOOD_SPECIMEN, | ||
| BONE_MARROW, | ||
| BUFFY_COAT, | ||
| PERIPHERAL_BLOOD_MONONUCLEAR_CELL, | ||
| BLOOD_PLASMA_SPECIMEN, | ||
| BLOOD_SERUM, | ||
| ASCITES_FLUID, | ||
| CEREBROSSPINAL_FLUID, | ||
| SALVIA, | ||
| FECES, | ||
| URINE, | ||
| SWAB, | ||
| BODILY_FLUID_SPECIMEN, | ||
| FFPE_SPECIMEN, | ||
| FROZEN_SPECIMEN, | ||
| SPECIMEN_WITH_KNOWN_STORAGE_STATE, | ||
| DNA_EXTRACT, | ||
| RNA_EXTRACT, | ||
| SPECIMEN_FROM_ORGANISM | ||
| } |
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