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Merged
timparsons merged 3 commits into from
Sep 25, 2023
Merged

BI-1909 - Unable to open observation dataset. #291

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311ff82
[BI-1909] small fix for changes made in the brapi-java-server
timparsons Sep 15, 2023
8de2b1f
[BI-1909] adding log messages to dataset fetch code
timparsons Sep 19, 2023
294172c
[BI-1909] cleanup and renaming method
timparsons Sep 21, 2023
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7 changes: 7 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,9 @@ public BrAPITrial getTrialDataByUUID(UUID programId, UUID trialId, boolean stats
//Remove the [program key] from the trial name
trial.setTrialName( Utilities.removeUnknownProgramKey( trial.getTrialName()) );
if( stats ){
log.debug("fetching experiment: " + trialId + " stats");
int environmentsCount = 1; // For now this is hardcoded to 1, because we are only supporting one environment per experiment
log.debug("fetching observation units for experiment: " + trialId);
long germplasmCount = countGermplasm(programId, trial.getTrialDbId());
trial.putAdditionalInfoItem("environmentsCount", environmentsCount);
trial.putAdditionalInfoItem("germplasmCount", germplasmCount);
Expand Down Expand Up @@ -296,11 +298,16 @@ private StreamedFile zipFiles(List<DownloadFile> files) throws IOException {
}

public Dataset getDatasetData(Program program, UUID experimentId, UUID datsetId, Boolean stats) throws ApiException, DoesNotExistException {
log.debug("fetching dataset: " + datsetId + " for experiment: " + experimentId + ". including stats: " + stats);
log.debug("fetching observationUnits for dataset: " + datsetId);
List<BrAPIObservationUnit> datasetOUs = ouDAO.getObservationUnitsForDataset(datsetId.toString(), program);
log.debug("fetching dataset variables dataset: " + datsetId);
List<BrAPIObservationVariable> datasetObsVars = getDatasetObsVars(datsetId.toString(), program);
List<String> ouDbIds = datasetOUs.stream().map(BrAPIObservationUnit::getObservationUnitDbId).collect(Collectors.toList());
List<String> obsVarDbIds = datasetObsVars.stream().map(BrAPIObservationVariable::getObservationVariableDbId).collect(Collectors.toList());
log.debug("fetching observations for dataset: " + datsetId);
List<BrAPIObservation> data = observationDAO.getObservationsByObservationUnitsAndVariables(ouDbIds, obsVarDbIds, program);
log.debug("building dataset object for dataset: " + datsetId);
Dataset dataset = new Dataset(experimentId.toString(), data, datasetOUs, datasetObsVars);
if (stats) {
Integer ouCount = datasetOUs.size();
Expand Down
81 changes: 54 additions & 27 deletions src/test/java/org/breedinginsight/DatabaseTest.java
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Expand Up @@ -31,10 +31,12 @@
import org.testcontainers.images.PullPolicy;

import javax.annotation.Nonnull;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.SQLException;
import java.time.Duration;
import java.time.temporal.ChronoUnit;
import java.util.HashMap;
import java.util.Map;
import java.util.*;

@Slf4j
public class DatabaseTest implements TestPropertyProvider {
Expand All @@ -43,36 +45,42 @@ public class DatabaseTest implements TestPropertyProvider {
private static final String dbPassword = "postgres";

@Getter
private GenericContainer dbContainer;
private static GenericContainer dbContainer;

@Getter
private Network network;
private static Network network;

@Getter
private GenericContainer redisContainer;
private static GenericContainer redisContainer;

@Getter
private RedissonClient redisConnection;

@SneakyThrows
public DatabaseTest() {
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@mlm483 mlm483 Sep 21, 2023

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Why is this capitalized and not databaseTest()?

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@timparsons timparsons Sep 21, 2023

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That's a constructor, so it has to match the class name

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@mlm483 mlm483 Sep 21, 2023

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🤦 thanks.

network = Network.newNetwork();
dbContainer = new GenericContainer<>("postgres:11.4")
.withNetwork(network)
.withNetworkAliases("testdb")
.withImagePullPolicy(PullPolicy.defaultPolicy())
.withExposedPorts(5432)
.withEnv("POSTGRES_DB", dbName)
.withEnv("POSTGRES_PASSWORD", dbPassword)
.waitingFor(Wait.forLogMessage(".*LOG: database system is ready to accept connections.*", 1).withStartupTimeout(Duration.of(2, ChronoUnit.MINUTES)));
dbContainer.start();
redisContainer = new GenericContainer<>("redis")
.withNetwork(network)
.withNetworkAliases("redis")
.withImagePullPolicy(PullPolicy.defaultPolicy())
.withExposedPorts(6379)
.waitingFor(Wait.forListeningPort());
redisContainer.start();
if(network == null) {
network = Network.newNetwork();
}
if(dbContainer == null) {
dbContainer = new GenericContainer<>("postgres:11.4")
.withNetwork(network)
.withNetworkAliases("testdb")
.withImagePullPolicy(PullPolicy.defaultPolicy())
.withExposedPorts(5432)
.withEnv("POSTGRES_DB", dbName)
.withEnv("POSTGRES_PASSWORD", dbPassword)
.waitingFor(Wait.forLogMessage(".*LOG: database system is ready to accept connections.*", 1)
.withStartupTimeout(Duration.of(2, ChronoUnit.MINUTES)));
dbContainer.start();
}
if(redisContainer == null) {
redisContainer = new GenericContainer<>("redis")
.withNetwork(network)
.withNetworkAliases("redis")
.withImagePullPolicy(PullPolicy.defaultPolicy())
.withExposedPorts(6379)
.waitingFor(Wait.forListeningPort());
redisContainer.start();
}

Integer redisContainerPort = redisContainer.getMappedPort(6379);
String redisContainerIp = redisContainer.getContainerIpAddress();
Expand Down Expand Up @@ -110,9 +118,28 @@ public Map<String, String> getProperties() {

@SneakyThrows
@AfterAll
public void stopContainers() {
redisContainer.stop();
dbContainer.stop();
network.close();
public void resetContainers() {
if(redisContainer != null) {
redisConnection.getKeys()
.flushall();
}
if(dbContainer != null) {
resetDb(dbName);
resetDb("postgres");
}
}

private void resetDb(String name) {
log.debug("resetting db: " + name);
try (Connection con = DriverManager.
getConnection(String.format("jdbc:postgresql://%s:%s/"+name,
dbContainer.getContainerIpAddress(), dbContainer.getMappedPort(5432)),
"postgres", dbPassword)) {

con.prepareStatement("drop schema public CASCADE").execute();
con.prepareStatement("create schema public").execute();
} catch (SQLException e) {
log.error("Error during reset", e);
}
}
}
4 changes: 3 additions & 1 deletion src/test/java/org/breedinginsight/api/v1/controller/TraitControllerIntegrationTest.java
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Expand Up @@ -1104,7 +1104,9 @@ public void checkTraitFullResponse(JsonObject traitJson, Trait trait) {
assertEquals(trait.getScale().getDataType().toString(), scaleJson.get("dataType").getAsString(), "Scale data types don't match");

List<JsonObject> jsonCategories = new ArrayList<>();
scaleJson.get("categories").getAsJsonArray().iterator().forEachRemaining(element -> jsonCategories.add(element.getAsJsonObject()));
if(scaleJson.has("categories")) {
scaleJson.get("categories").getAsJsonArray().iterator().forEachRemaining(element -> jsonCategories.add(element.getAsJsonObject()));
}
Collections.sort(jsonCategories, Comparator.comparing((x) -> x.get("label").getAsString()));
List<BrAPIScaleValidValuesCategories> brApiScaleCategories = new ArrayList<>(trait.getScale().getCategories());
Collections.sort(brApiScaleCategories, Comparator.comparing(BrAPIScaleValidValuesCategories::getLabel));
Expand Down