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EVA-3589: Set WriteConcern and ReadPreference for MongoTemplate #454

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merged 5 commits into from
Jun 27, 2024
Merged

EVA-3589: Set WriteConcern and ReadPreference for MongoTemplate #454

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1be9e49
set WriteConcern and ReadPreference for MongoTemplate
apriltuesday Jun 19, 2024
80c850c
fix count-stats in tests
apriltuesday Jun 20, 2024
01aec6a
clean up
apriltuesday Jun 20, 2024
95dfa93
add file cleanup to test
apriltuesday Jun 20, 2024
731a06d
delete files before test start
nitin-ebi Jun 27, 2024
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4 changes: 4 additions & 0 deletions ...src/main/java/uk/ac/ebi/eva/accession/core/configuration/nonhuman/MongoConfiguration.java
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Expand Up @@ -18,6 +18,8 @@
import com.mongodb.MongoClient;
import com.mongodb.MongoClientOptions;

import com.mongodb.ReadPreference;
import com.mongodb.WriteConcern;
import org.springframework.beans.factory.ObjectProvider;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
Expand Down Expand Up @@ -91,6 +93,8 @@ public MongoTemplate mongoTemplate(@Qualifier("primaryFactory") MongoDbFactory m
MappingMongoConverter converter) {
converter.setTypeMapper(new DefaultMongoTypeMapper(null));
MongoTemplate mongoTemplate = new MongoTemplate(mongoDbFactory, converter);
mongoTemplate.setWriteConcern(WriteConcern.MAJORITY);
mongoTemplate.setReadPreference(ReadPreference.valueOf(readPreference));
mongoTemplate.setWriteResultChecking(WriteResultChecking.EXCEPTION);
return mongoTemplate;
}
Expand Down
36 changes: 33 additions & 3 deletions ...onfiguration/batch/jobs/CreateSeveralIntervalsOfSubsnpAccessionsJobConfigurationTest.java
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Expand Up @@ -25,11 +25,17 @@
import org.springframework.batch.core.StepExecution;
import org.springframework.batch.test.JobLauncherTestUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.data.mongodb.core.MongoTemplate;
import org.springframework.http.HttpMethod;
import org.springframework.http.HttpStatus;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.TestPropertySource;
import org.springframework.test.context.junit4.SpringRunner;
import org.springframework.test.web.client.ExpectedCount;
import org.springframework.test.web.client.MockRestServiceServer;
import org.springframework.web.client.RestTemplate;

import uk.ac.ebi.eva.accession.core.configuration.nonhuman.SubmittedVariantAccessioningConfiguration;
import uk.ac.ebi.eva.accession.core.repository.nonhuman.eva.SubmittedVariantAccessioningRepository;
Expand All @@ -38,11 +44,13 @@
import uk.ac.ebi.eva.accession.pipeline.parameters.InputParameters;
import uk.ac.ebi.eva.accession.pipeline.test.BatchTestConfiguration;
import uk.ac.ebi.eva.commons.core.utils.FileUtils;
import uk.ac.ebi.eva.metrics.count.CountServiceParameters;

import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.URI;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.Arrays;
Expand All @@ -52,6 +60,9 @@
import java.util.TreeSet;

import static org.junit.Assert.assertEquals;
import static org.springframework.test.web.client.match.MockRestRequestMatchers.method;
import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo;
import static org.springframework.test.web.client.response.MockRestResponseCreators.withStatus;
import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.ACCESSIONING_SHUTDOWN_STEP;
import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.BUILD_REPORT_STEP;
import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.CHECK_SUBSNP_ACCESSION_STEP;
Expand All @@ -76,19 +87,38 @@ public class CreateSeveralIntervalsOfSubsnpAccessionsJobConfigurationTest {
@Autowired
private MongoTemplate mongoTemplate;

@Autowired
private CountServiceParameters countServiceParameters;

private final String URL_PATH_SAVE_COUNT = "/v1/bulk/count";

@Autowired
@Qualifier("COUNT_STATS_REST_TEMPLATE")
private RestTemplate restTemplate;

private MockRestServiceServer mockServer;

@Before
public void setUp() {
public void setUp() throws Exception {
this.cleanSlate();
mongoTemplate.dropCollection(SubmittedVariantEntity.class);
mockServer = MockRestServiceServer.createServer(restTemplate);
mockServer.expect(ExpectedCount.manyTimes(), requestTo(new URI(countServiceParameters.getUrl() + URL_PATH_SAVE_COUNT)))
.andExpect(method(HttpMethod.POST))
.andRespond(withStatus(HttpStatus.OK));
}

@After
public void tearDown() throws Exception {
this.cleanSlate();
mongoTemplate.dropCollection(SubmittedVariantEntity.class);
}

public void cleanSlate() throws Exception {
Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf()));
Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf() + AccessionReportWriter.VARIANTS_FILE_SUFFIX));
Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf() + AccessionReportWriter.CONTIGS_FILE_SUFFIX));
Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf()));
Files.deleteIfExists(Paths.get(inputParameters.getFasta() + ".fai"));
mongoTemplate.dropCollection(SubmittedVariantEntity.class);
}

@Test
Expand Down
35 changes: 33 additions & 2 deletions ...cession/pipeline/configuration/batch/jobs/CreateSubsnpAccessionsJobConfigurationTest.java
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Expand Up @@ -25,11 +25,17 @@
import org.springframework.batch.core.StepExecution;
import org.springframework.batch.test.JobLauncherTestUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.data.mongodb.core.MongoTemplate;
import org.springframework.http.HttpMethod;
import org.springframework.http.HttpStatus;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.TestPropertySource;
import org.springframework.test.context.junit4.SpringRunner;
import org.springframework.test.web.client.ExpectedCount;
import org.springframework.test.web.client.MockRestServiceServer;
import org.springframework.web.client.RestTemplate;

import uk.ac.ebi.eva.accession.core.configuration.nonhuman.SubmittedVariantAccessioningConfiguration;
import uk.ac.ebi.eva.accession.core.repository.nonhuman.eva.SubmittedVariantAccessioningRepository;
Expand All @@ -38,19 +44,24 @@
import uk.ac.ebi.eva.accession.pipeline.parameters.InputParameters;
import uk.ac.ebi.eva.accession.pipeline.test.BatchTestConfiguration;
import uk.ac.ebi.eva.commons.core.utils.FileUtils;
import uk.ac.ebi.eva.metrics.count.CountServiceParameters;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.URI;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.Iterator;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.springframework.test.web.client.match.MockRestRequestMatchers.method;
import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo;
import static org.springframework.test.web.client.response.MockRestResponseCreators.withStatus;
import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.ACCESSIONING_SHUTDOWN_STEP;
import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.BUILD_REPORT_STEP;
import static uk.ac.ebi.eva.accession.pipeline.configuration.BeanNames.CHECK_SUBSNP_ACCESSION_STEP;
Expand All @@ -75,18 +86,38 @@ public class CreateSubsnpAccessionsJobConfigurationTest {
@Autowired
private MongoTemplate mongoTemplate;

@Autowired
private CountServiceParameters countServiceParameters;

private final String URL_PATH_SAVE_COUNT = "/v1/bulk/count";

@Autowired
@Qualifier("COUNT_STATS_REST_TEMPLATE")
private RestTemplate restTemplate;

private MockRestServiceServer mockServer;

@Before
public void setUp() {
public void setUp() throws Exception {
this.cleanSlate();
mongoTemplate.dropCollection(SubmittedVariantEntity.class);
mockServer = MockRestServiceServer.createServer(restTemplate);
mockServer.expect(ExpectedCount.manyTimes(), requestTo(new URI(countServiceParameters.getUrl() + URL_PATH_SAVE_COUNT)))
.andExpect(method(HttpMethod.POST))
.andRespond(withStatus(HttpStatus.OK));
}

@After
public void tearDown() throws Exception {
this.cleanSlate();
mongoTemplate.dropCollection(SubmittedVariantEntity.class);
}

public void cleanSlate() throws Exception {
Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf()));
Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf() + AccessionReportWriter.VARIANTS_FILE_SUFFIX));
Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf() + AccessionReportWriter.CONTIGS_FILE_SUFFIX));
Files.deleteIfExists(Paths.get(inputParameters.getFasta() + ".fai"));
mongoTemplate.dropCollection(SubmittedVariantEntity.class);
}

@Test
Expand Down
6 changes: 5 additions & 1 deletion ...ssion/pipeline/configuration/batch/steps/CreateSubsnpAccessionsStepConfigurationTest.java
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Expand Up @@ -77,7 +77,11 @@ public class CreateSubsnpAccessionsStepConfigurationTest {
private MongoTemplate mongoTemplate;

@Before
public void setUp() {
public void setUp() throws Exception {
Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf()));
Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf() + AccessionReportWriter.VARIANTS_FILE_SUFFIX));
Files.deleteIfExists(Paths.get(inputParameters.getOutputVcf() + AccessionReportWriter.CONTIGS_FILE_SUFFIX));
Files.deleteIfExists(Paths.get(inputParameters.getFasta() + ".fai"));
mongoTemplate.dropCollection(SubmittedVariantEntity.class);
Mockito.when(jobExecution.getJobId()).thenReturn(1L);
accessionWriter.setJobExecution(jobExecution);
Expand Down
4 changes: 4 additions & 0 deletions ...ession-pipeline/src/test/resources/properties/accession-pipeline-interval-test.properties
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Expand Up @@ -4,6 +4,10 @@ accessioning.monotonic.test-pipeline-ss.blockSize=2
accessioning.monotonic.test-pipeline-ss.blockStartValue=500
accessioning.monotonic.test-pipeline-ss.nextBlockInterval=10

eva.count-stats.url=http://localhost:8080
eva.count-stats.username=username
eva.count-stats.password=password

parameters.assemblyAccession=assembly
parameters.taxonomyAccession=1111
parameters.projectAccession=project
Expand Down
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