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ALS-4978: Move genomic client from genomic processor project
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6 changes: 2 additions & 4 deletions
6
processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessor.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,19 +1,17 @@ | ||
| package edu.harvard.hms.dbmi.avillach.hpds.processing; | ||
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| import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; | ||
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| import java.math.BigInteger; | ||
| import java.util.Collection; | ||
| import java.util.Set; | ||
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| public interface GenomicProcessor { | ||
| BigInteger getPatientMaskForVariantInfoFilters(DistributableQuery distributableQuery); | ||
| BigInteger getPatientMask(DistributableQuery distributableQuery); | ||
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| Set<Integer> patientMaskToPatientIdSet(BigInteger patientMask); | ||
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| BigInteger createMaskForPatientSet(Set<Integer> patientSubset); | ||
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| Collection<String> processVariantList(DistributableQuery distributableQuery); | ||
| Collection<String> getVariantList(DistributableQuery distributableQuery); | ||
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| String[] getPatientIds(); | ||
| } |
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63 changes: 63 additions & 0 deletions
63
...ava/edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClient.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| package edu.harvard.hms.dbmi.avillach.hpds.processing.genomic; | ||
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| import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; | ||
| import edu.harvard.hms.dbmi.avillach.hpds.processing.DistributableQuery; | ||
| import edu.harvard.hms.dbmi.avillach.hpds.processing.GenomicProcessor; | ||
| import org.springframework.http.HttpHeaders; | ||
| import org.springframework.http.MediaType; | ||
| import org.springframework.web.reactive.function.client.WebClient; | ||
| import reactor.core.publisher.Mono; | ||
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| import java.math.BigInteger; | ||
| import java.util.Collection; | ||
| import java.util.Set; | ||
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| public class GenomicProcessorRestClient implements GenomicProcessor { | ||
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| private final WebClient webClient; | ||
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| public GenomicProcessorRestClient(String serviceUrl) { | ||
| this.webClient = WebClient.builder() | ||
| .baseUrl(serviceUrl) | ||
| .defaultHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE) | ||
| .build(); | ||
| } | ||
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| @Override | ||
| public BigInteger getPatientMask(DistributableQuery distributableQuery) { | ||
| return webClient.post() | ||
| .uri("/patients") | ||
| .contentType(MediaType.APPLICATION_JSON) | ||
| .body(Mono.just(distributableQuery), DistributableQuery.class) | ||
| .retrieve() | ||
| .bodyToMono(BigInteger.class) | ||
| .block(); | ||
| } | ||
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| @Override | ||
| public Set<Integer> patientMaskToPatientIdSet(BigInteger patientMask) { | ||
| return null; | ||
| } | ||
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| @Override | ||
| public BigInteger createMaskForPatientSet(Set<Integer> patientSubset) { | ||
| return null; | ||
| } | ||
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| @SuppressWarnings("unchecked") | ||
| @Override | ||
| public Collection<String> getVariantList(DistributableQuery distributableQuery) { | ||
| return webClient.post() | ||
| .uri("/variants") | ||
| .contentType(MediaType.APPLICATION_JSON) | ||
| .body(Mono.just(distributableQuery), DistributableQuery.class) | ||
| .retrieve() | ||
| .bodyToMono(Collection.class) | ||
| .block(); | ||
| } | ||
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| @Override | ||
| public String[] getPatientIds() { | ||
| return new String[0]; | ||
| } | ||
| } |
39 changes: 39 additions & 0 deletions
39
...edu/harvard/hms/dbmi/avillach/hpds/processing/genomic/GenomicProcessorRestClientTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| package edu.harvard.hms.dbmi.avillach.hpds.processing.genomic; | ||
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| import com.fasterxml.jackson.core.JsonProcessingException; | ||
| import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; | ||
| import edu.harvard.hms.dbmi.avillach.hpds.processing.DistributableQuery; | ||
| import org.junit.Test; | ||
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| import java.math.BigInteger; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.Set; | ||
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| public class GenomicProcessorRestClientTest { | ||
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| private GenomicProcessorRestClient genomicProcessorRestClient = new GenomicProcessorRestClient("http://localhost:8090/"); | ||
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| @Test | ||
| public void test() throws JsonProcessingException { | ||
| DistributableQuery distributableQuery = new DistributableQuery(); | ||
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| List<Query.VariantInfoFilter> variantInfoFilters = new ArrayList<>(); | ||
| Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); | ||
| variantInfoFilter.categoryVariantInfoFilters = Map.of( | ||
| "Gene_with_variant", new String[]{"FRG1FP"} | ||
| ); | ||
| Query.VariantInfoFilter variantInfoFilter2 = new Query.VariantInfoFilter(); | ||
| variantInfoFilter2.categoryVariantInfoFilters = Map.of( | ||
| "Gene_with_variant", new String[]{"ACTG1P3"} | ||
| ); | ||
| variantInfoFilters.add(variantInfoFilter2); | ||
| distributableQuery.setVariantInfoFilters(variantInfoFilters); | ||
| distributableQuery.setPatientIds(Set.of(1, 2, 3, 4, 5, 6, 7, 8, 9, 10)); | ||
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| BigInteger patientMaskForVariantInfoFilters = genomicProcessorRestClient.getPatientMask(distributableQuery); | ||
| System.out.println(patientMaskForVariantInfoFilters); | ||
| } | ||
| } |