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EVA-1190 Report studies browsable since given date #89

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EVA-1190 Report studies browsable since given date #89

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b77ca49
Filter EVA browsable studies by date
Apr 23, 2018
9ca7701
Removed println statement
May 1, 2018
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13 changes: 11 additions & 2 deletions eva-server/src/main/java/uk/ac/ebi/eva/server/ws/ArchiveWSServer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
import io.swagger.annotations.Api;

import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.format.annotation.DateTimeFormat;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
Expand All @@ -39,6 +40,7 @@
import uk.ac.ebi.eva.lib.utils.QueryResult;

import java.io.IOException;
import java.util.Date;
import java.util.List;

@RestController
Expand Down Expand Up @@ -89,10 +91,17 @@ public QueryResponse getStudies(@RequestParam(name = "species", required = false
}

@RequestMapping(value = "/studies/list", method = RequestMethod.GET)
public QueryResponse getBrowsableStudies(@RequestParam("species") String species)
public QueryResponse getBrowsableStudies(@RequestParam(name = "species") String species,
@RequestParam(name = "fromDate", required = false)
@DateTimeFormat(pattern="yyyy-MM-dd") Date date)
throws IOException {
MultiMongoDbFactory.setDatabaseNameForCurrentThread(DBAdaptorConnector.getDBName(species));
List<VariantStudySummary> uniqueStudies = variantStudySummaryService.findAll();
List<VariantStudySummary> uniqueStudies;
if (date == null) {
uniqueStudies = variantStudySummaryService.findAll();
} else {
uniqueStudies = variantStudySummaryService.findByFromDate(date);
}
QueryResult<VariantStudySummary> result = buildQueryResult(uniqueStudies);
return setQueryResponse(result);
}
Expand Down
63 changes: 52 additions & 11 deletions eva-server/src/test/java/uk/ac/ebi/eva/server/ws/ArchiveWSServerTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.mockito.BDDMockito.given;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyObject;

@RunWith(SpringRunner.class)
Expand Down Expand Up @@ -165,18 +166,21 @@ public void setup() throws URISyntaxException, IOException {
given(archiveDgvaDBAdaptor.countStudiesPerType(anyObject()))
.willReturn(encapsulateInQueryResult(svStudiesGroupedByStudyType.entrySet().toArray()));

List<VariantStudySummary> studies = buildVariantStudySummaries();
given(service.findAll()).willReturn(studies);
given(service.findAll()).willReturn(buildVariantStudySummaries(study1, study2, study3));
given(service.findByFromDate(any())).willReturn(buildVariantStudySummaries(study1));
}

private List<VariantStudySummary> buildVariantStudySummaries() {
List<VariantStudySummary> studies = new ArrayList<>();
VariantStudySummary study = new VariantStudySummary();
study.setFilesCount(1);
study.setStudyId("studyId");
study.setStudyName("studyName");
studies.add(study);
return studies;
private List<VariantStudySummary> buildVariantStudySummaries(VariantStudy... studies) {
List<VariantStudySummary> summaries = new ArrayList<>();

for (VariantStudy study : studies) {
VariantStudySummary summary = new VariantStudySummary();
summary.setFilesCount(1);
summary.setStudyId(study.getId());
summary.setStudyName(study.getName());
summaries.add(summary);
}
return summaries;
}

private <T> QueryResult<T> encapsulateInQueryResult(T... results) {
Expand Down Expand Up @@ -281,7 +285,8 @@ public void testGetBrowsableStudiesBySpecies() throws URISyntaxException {
assertEquals(1, queryResponse.getResponse().size());

List<VariantStudySummary> results = queryResponse.getResponse().get(0).getResult();
assertTrue(results.size() >= 1);
System.out.println(results);
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remove or use logger

assertEquals(3, results.size());

for (VariantStudySummary variantStudySummary : results) {
assertTrue(variantStudySummary.getFilesCount() > 0);
Expand All @@ -290,6 +295,42 @@ public void testGetBrowsableStudiesBySpecies() throws URISyntaxException {
}
}

@Test
public void testGetBrowsableStudiesBySpeciesAndFromDate() throws URISyntaxException {
String url = "/v1/meta/studies/list?species=hsapiens_grch37&fromDate=2018-01-01";
ResponseEntity<QueryResponse<QueryResult<VariantStudySummary>>> response = restTemplate.exchange(
url, HttpMethod.GET, null,
new ParameterizedTypeReference<QueryResponse<QueryResult<VariantStudySummary>>>() {});
assertEquals(HttpStatus.OK, response.getStatusCode());

QueryResponse<QueryResult<VariantStudySummary>> queryResponse = response.getBody();
assertEquals(1, queryResponse.getResponse().size());

List<VariantStudySummary> results = queryResponse.getResponse().get(0).getResult();
assertEquals(1, results.size());

for (VariantStudySummary variantStudySummary : results) {
assertTrue(variantStudySummary.getFilesCount() > 0);
assertEquals("Human Test study 1", variantStudySummary.getStudyName());
assertEquals("S1", variantStudySummary.getStudyId());
}
}

@Test
public void testGetBrowsableStudiesBySpeciesAndFutureFromDate() throws URISyntaxException {
String url = "/v1/meta/studies/list?species=hsapiens_grch37&fromDate=3000-01-01";
ResponseEntity<QueryResponse<QueryResult<VariantStudySummary>>> response = restTemplate.exchange(
url, HttpMethod.GET, null,
new ParameterizedTypeReference<QueryResponse<QueryResult<VariantStudySummary>>>() {});
assertEquals(HttpStatus.OK, response.getStatusCode());

QueryResponse<QueryResult<VariantStudySummary>> queryResponse = response.getBody();
assertEquals(1, queryResponse.getResponse().size());

List<VariantStudySummary> results = queryResponse.getResponse().get(0).getResult();
assertEquals(0, results.size());
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this test failed in travis https://travis-ci.org/EBIvariation/eva-ws/builds/373408145#L4349

}

@Test
public void testGetStudies() throws URISyntaxException {
String url = "/v1/meta/studies/all";
Expand Down