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client/client/src/main/java/uk/ac/ebi/biosamples/client/BioSamplesWebinGetClient.java
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| /* | ||
| * Copyright 2021 EMBL - European Bioinformatics Institute | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this | ||
| * file except in compliance with the License. You may obtain a copy of the License at | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * Unless required by applicable law or agreed to in writing, software distributed under the | ||
| * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR | ||
| * CONDITIONS OF ANY KIND, either express or implied. See the License for the | ||
| * specific language governing permissions and limitations under the License. | ||
| */ | ||
| package uk.ac.ebi.biosamples.client; | ||
|
|
||
| import java.io.IOException; | ||
| import java.net.URI; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.Optional; | ||
| import javax.annotation.PreDestroy; | ||
| import lombok.Getter; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
| import org.springframework.boot.web.client.RestTemplateBuilder; | ||
| import org.springframework.hateoas.MediaTypes; | ||
| import org.springframework.hateoas.client.Traverson; | ||
| import org.springframework.http.HttpHeaders; | ||
| import org.springframework.http.HttpRequest; | ||
| import org.springframework.http.client.ClientHttpRequestExecution; | ||
| import org.springframework.http.client.ClientHttpRequestInterceptor; | ||
| import org.springframework.http.client.ClientHttpResponse; | ||
| import org.springframework.web.client.RestClientException; | ||
| import org.springframework.web.client.RestTemplate; | ||
| import org.springframework.web.util.UriComponentsBuilder; | ||
| import uk.ac.ebi.biosamples.client.service.ClientService; | ||
| import uk.ac.ebi.biosamples.client.service.SampleRetrievalServiceV2; | ||
| import uk.ac.ebi.biosamples.client.service.WebinAuthClientService; | ||
| import uk.ac.ebi.biosamples.client.utils.ClientProperties; | ||
| import uk.ac.ebi.biosamples.model.Sample; | ||
| import uk.ac.ebi.biosamples.service.SampleValidator; | ||
|
|
||
| public class BioSamplesWebinGetClient implements AutoCloseable { | ||
| private final Logger log = LoggerFactory.getLogger(getClass()); | ||
| private final SampleRetrievalServiceV2 sampleRetrievalServiceV2; | ||
| /** -- GETTER -- Gets the public client. */ | ||
| @Getter private final Optional<BioSamplesClient> publicClient; | ||
|
|
||
| /** | ||
| * Constructs a BioSamplesClient with the given parameters. | ||
| * | ||
| * @param uri the URI for BioSamples | ||
| * @param uriV2 the URI for BioSamples V2 | ||
| * @param restTemplateBuilder the RestTemplateBuilder | ||
| * @param sampleValidator the SampleValidator | ||
| * @param clientService the ClientService | ||
| * @param clientProperties the BioSamplesProperties | ||
| */ | ||
| public BioSamplesWebinGetClient( | ||
| final URI uri, | ||
| URI uriV2, | ||
| final RestTemplateBuilder restTemplateBuilder, | ||
| final SampleValidator sampleValidator, | ||
| final ClientService clientService, | ||
| final ClientProperties clientProperties) { | ||
| if (uriV2 == null) { | ||
| uriV2 = UriComponentsBuilder.fromUri(URI.create(uri + "/v2")).build().toUri(); | ||
| } | ||
|
|
||
| final RestTemplate restOperations = restTemplateBuilder.build(); | ||
|
|
||
| if (clientService != null) { | ||
| if (clientService instanceof WebinAuthClientService) { | ||
| log.trace("Adding WebinClientHttpRequestInterceptor"); | ||
| restOperations | ||
| .getInterceptors() | ||
| .add(new BioSamplesWebinGetClient.BsdClientHttpRequestInterceptor(clientService)); | ||
| } else { | ||
| log.trace("No ClientService available"); | ||
| } | ||
| } | ||
|
|
||
| final Traverson traverson = new Traverson(uri, MediaTypes.HAL_JSON); | ||
| traverson.setRestOperations(restOperations); | ||
|
|
||
| sampleRetrievalServiceV2 = new SampleRetrievalServiceV2(restOperations, uriV2); | ||
|
|
||
| if (clientService == null) { | ||
| publicClient = Optional.empty(); | ||
| } else { | ||
| publicClient = | ||
| Optional.of( | ||
| new BioSamplesClient( | ||
| uri, uriV2, restTemplateBuilder, sampleValidator, null, clientProperties)); | ||
| } | ||
| } | ||
|
|
||
| private static class BsdClientHttpRequestInterceptor implements ClientHttpRequestInterceptor { | ||
| private final ClientService clientService; | ||
|
|
||
| BsdClientHttpRequestInterceptor(final ClientService clientService) { | ||
| this.clientService = clientService; | ||
| } | ||
|
|
||
| @Override | ||
| public ClientHttpResponse intercept( | ||
| final HttpRequest request, final byte[] body, final ClientHttpRequestExecution execution) | ||
| throws IOException { | ||
| if (clientService != null && !request.getHeaders().containsKey(HttpHeaders.AUTHORIZATION)) { | ||
| final String jwt = clientService.getJwt(); | ||
| if (jwt != null) { | ||
| request.getHeaders().set(HttpHeaders.AUTHORIZATION, "Bearer " + jwt); | ||
| } | ||
| } | ||
|
|
||
| // pass along to the next interceptor | ||
| return execution.execute(request, body); | ||
| } | ||
| } | ||
|
|
||
| // TODO: we can think of using an interceptor to remove the cache from the biosamples client | ||
| @Override | ||
| @PreDestroy | ||
| public void close() { | ||
| // close down public client if present | ||
| publicClient.ifPresent(BioSamplesClient::close); | ||
| // close down our own thread pools | ||
| // threadPoolExecutor.shutdownNow(); | ||
| try { | ||
| // threadPoolExecutor.awaitTermination(1, TimeUnit.MINUTES); | ||
| } catch (final Exception e) { | ||
| throw new RuntimeException(e); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Fetches sample resources by accessions using BioSamples V2. | ||
| * | ||
| * @param accessions the list of accessions | ||
| * @return a map of sample accessions to samples | ||
| * @throws RestClientException if there is an error while fetching samples | ||
| */ | ||
| public Map<String, Sample> fetchSampleResourcesByAccessionsV2(final List<String> accessions) | ||
| throws RestClientException { | ||
| try { | ||
| return sampleRetrievalServiceV2.fetchSamplesByAccessions(accessions); | ||
| } catch (final Exception e) { | ||
| throw new RuntimeException(e); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Fetches sample resources by accessions using BioSamples V2 with JWT authentication. | ||
| * | ||
| * @param accessions the list of accessions | ||
| * @param jwt the JWT token | ||
| * @return a map of sample accessions to samples | ||
| * @throws RestClientException if there is an error while fetching samples | ||
| */ | ||
| public Map<String, Sample> fetchSampleResourcesByAccessionsV2( | ||
| final List<String> accessions, final String jwt) throws RestClientException { | ||
| try { | ||
| return sampleRetrievalServiceV2.fetchSamplesByAccessions(accessions, jwt); | ||
| } catch (final Exception e) { | ||
| throw new RuntimeException(e); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Fetches a sample resource by accession using BioSamples V2. | ||
| * | ||
| * @param accession the accession of the sample | ||
| * @return the sample | ||
| * @throws RestClientException if there is an error while fetching the sample | ||
| */ | ||
| public Sample fetchSampleResourceV2(final String accession) throws RestClientException { | ||
| try { | ||
| return sampleRetrievalServiceV2.fetchSampleByAccession(accession); | ||
| } catch (final Exception e) { | ||
| throw new RuntimeException(e); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Fetches a sample resource by accession using BioSamples V2 with JWT authentication. | ||
| * | ||
| * @param accession the accession of the sample | ||
| * @param jwt the JWT token | ||
| * @return the sample | ||
| * @throws RestClientException if there is an error while fetching the sample | ||
| */ | ||
| public Sample fetchSampleResourceV2(final String accession, final String jwt) | ||
| throws RestClientException { | ||
| try { | ||
| return sampleRetrievalServiceV2.fetchSampleByAccession(accession, jwt); | ||
| } catch (final Exception e) { | ||
| throw new RuntimeException(e); | ||
| } | ||
| } | ||
| } |
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