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[BI-1477] - Improve Experiments Table #230

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Merged
HMS17 merged 2 commits into from
Dec 18, 2022
Merged

[BI-1477] - Improve Experiments Table #230

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f83e80f
[BI-1477] - Improve Experiments Table
HMS17 Nov 28, 2022
e3321ec
Merge branch 'develop' into feature/BI-1477
HMS17 Dec 18, 2022
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5 changes: 1 addition & 4 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIV2Controller.java
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Expand Up @@ -27,11 +27,9 @@
import io.micronaut.security.rules.SecurityRule;
import lombok.extern.slf4j.Slf4j;
import okhttp3.*;
import org.brapi.client.v2.JSON;
import org.brapi.client.v2.model.exceptions.ApiException;
import org.brapi.v2.model.core.BrAPIListSummary;
import org.brapi.v2.model.core.BrAPIServerInfo;
import org.brapi.v2.model.core.response.BrAPIListsListResponse;
import org.brapi.v2.model.core.response.BrAPIServerInfoResponse;
import org.breedinginsight.api.auth.AuthenticatedUser;
import org.breedinginsight.api.auth.ProgramSecured;
Expand All @@ -40,8 +38,7 @@
import org.breedinginsight.api.model.v1.validators.QueryValid;
import org.breedinginsight.brapi.v1.controller.BrapiVersion;
import org.breedinginsight.brapi.v1.model.request.query.BrapiQuery;
import org.breedinginsight.brapi.v2.model.response.mappers.GermplasmQueryMapper;
import org.breedinginsight.brapi.v2.model.response.mappers.ListQueryMapper;
import org.breedinginsight.utilities.response.mappers.ListQueryMapper;
import org.breedinginsight.brapi.v2.services.BrAPIGermplasmService;
import org.breedinginsight.model.ProgramBrAPIEndpoints;
import org.breedinginsight.services.ProgramService;
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13 changes: 8 additions & 5 deletions src/main/java/org/breedinginsight/brapi/v2/ExperimentController.java
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Expand Up @@ -11,16 +11,19 @@
import org.brapi.v2.model.core.BrAPITrial;
import org.breedinginsight.api.auth.ProgramSecured;
import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
import org.breedinginsight.api.model.v1.request.query.SearchRequest;
import org.breedinginsight.api.model.v1.response.DataResponse;
import org.breedinginsight.api.model.v1.response.Response;
import org.breedinginsight.api.model.v1.validators.QueryValid;
import org.breedinginsight.brapi.v1.controller.BrapiVersion;
import org.breedinginsight.brapi.v1.model.request.query.BrapiQuery;
import org.breedinginsight.brapi.v2.model.request.query.ExperimentQuery;
import org.breedinginsight.brapi.v2.services.BrAPITrialService;
import org.breedinginsight.services.exceptions.DoesNotExistException;
import org.breedinginsight.utilities.response.ResponseUtils;
import org.breedinginsight.utilities.response.mappers.ExperimentQueryMapper;

import javax.inject.Inject;
import javax.validation.Valid;
import java.util.List;
import java.util.UUID;

Expand All @@ -42,14 +45,14 @@ public ExperimentController(BrAPITrialService experimentService, ExperimentQuery
@Produces(MediaType.APPLICATION_JSON)
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
public HttpResponse<Response<DataResponse<List<BrAPITrial>>>> getExperiments(
@PathVariable("programId") UUID programId, @QueryValue BrapiQuery queryParams,
@QueryValue boolean metadata) {
@PathVariable("programId") UUID programId,
@QueryValue @QueryValid(using = ExperimentQueryMapper.class) @Valid ExperimentQuery queryParams) {
try {
log.debug("fetching trials for program: " + programId);

List<BrAPITrial> experiments = experimentService.getExperiments(programId);
return ResponseUtils.getBrapiQueryResponse(experiments, experimentQueryMapper, queryParams);

SearchRequest searchRequest = queryParams.constructSearchRequest();
return ResponseUtils.getBrapiQueryResponse(experiments, experimentQueryMapper, queryParams, searchRequest);
} catch (ApiException e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving experiments");
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4 changes: 1 addition & 3 deletions src/main/java/org/breedinginsight/brapi/v2/GermplasmController.java
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Expand Up @@ -30,14 +30,12 @@
import org.breedinginsight.brapi.v1.model.request.query.BrapiQuery;
import org.breedinginsight.brapi.v2.dao.BrAPIGermplasmDAO;
import org.breedinginsight.brapi.v2.model.request.query.GermplasmQuery;
import org.breedinginsight.brapi.v2.model.response.mappers.GermplasmQueryMapper;
import org.breedinginsight.utilities.response.mappers.GermplasmQueryMapper;
import org.breedinginsight.brapi.v2.services.BrAPIGermplasmService;
import org.breedinginsight.brapps.importer.model.base.Germplasm;
import org.breedinginsight.brapps.importer.model.exports.FileType;
import org.breedinginsight.daos.ProgramDAO;
import org.breedinginsight.model.DownloadFile;
import org.breedinginsight.services.exceptions.DoesNotExistException;
import org.breedinginsight.utilities.Utilities;
import org.breedinginsight.utilities.response.ResponseUtils;

import javax.inject.Inject;
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29 changes: 29 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/model/request/query/ExperimentQuery.java
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@@ -0,0 +1,29 @@
package org.breedinginsight.brapi.v2.model.request.query;

import io.micronaut.core.annotation.Introspected;
import lombok.Getter;
import org.breedinginsight.api.model.v1.request.query.FilterRequest;
import org.breedinginsight.api.model.v1.request.query.SearchRequest;
import org.breedinginsight.brapi.v1.model.request.query.BrapiQuery;
import org.jooq.tools.StringUtils;

import java.util.ArrayList;
import java.util.List;

@Getter
@Introspected
public class ExperimentQuery extends BrapiQuery {
private String name;
private String active;

public SearchRequest constructSearchRequest() {
List<FilterRequest> filters = new ArrayList<>();
if (!StringUtils.isBlank(getName())) {
filters.add(constructFilterRequest("name", getName()));
}
if (!StringUtils.isBlank(getActive())) {
filters.add(constructFilterRequest("active", getActive()));
}
return new SearchRequest(filters);
}
}
11 changes: 10 additions & 1 deletion src/main/java/org/breedinginsight/utilities/response/mappers/ExperimentQueryMapper.java
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Expand Up @@ -19,6 +19,7 @@

import lombok.Getter;
import org.brapi.v2.model.core.BrAPITrial;
import org.breedinginsight.api.v1.controller.metadata.SortOrder;

import javax.inject.Singleton;
import java.util.Map;
Expand All @@ -28,9 +29,17 @@
@Singleton
public class ExperimentQueryMapper extends AbstractQueryMapper {

private final String defaultSortField = "name";
private final SortOrder defaultSortOrder = SortOrder.ASC;

private Map<String, Function<BrAPITrial,?>> fields;

public ExperimentQueryMapper() { fields = Map.ofEntries(); }
public ExperimentQueryMapper() {
fields = Map.ofEntries(
Map.entry("name", BrAPITrial::getTrialName),
Map.entry("active", BrAPITrial::isActive)
);
}

@Override
public boolean exists(String fieldName) {
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2 changes: 1 addition & 1 deletion ...esponse/mappers/GermplasmQueryMapper.java → ...esponse/mappers/GermplasmQueryMapper.java
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@@ -1,4 +1,4 @@
package org.breedinginsight.brapi.v2.model.response.mappers;
package org.breedinginsight.utilities.response.mappers;

import com.google.gson.JsonObject;
import lombok.Getter;
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2 changes: 1 addition & 1 deletion ...del/response/mappers/ListQueryMapper.java → ...ies/response/mappers/ListQueryMapper.java
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@@ -1,4 +1,4 @@
package org.breedinginsight.brapi.v2.model.response.mappers;
package org.breedinginsight.utilities.response.mappers;

import lombok.Getter;
import org.brapi.v2.model.core.BrAPIListSummary;
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3 changes: 1 addition & 2 deletions src/test/java/org/breedinginsight/brapi/v2/GermplasmControllerIntegrationTest.java
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Expand Up @@ -18,15 +18,14 @@
import org.breedinginsight.api.model.v1.request.query.FilterRequest;
import org.breedinginsight.api.model.v1.request.query.SearchRequest;
import org.breedinginsight.api.v1.controller.TestTokenValidator;
import org.breedinginsight.brapi.v2.model.response.mappers.GermplasmQueryMapper;
import org.breedinginsight.utilities.response.mappers.GermplasmQueryMapper;
import org.breedinginsight.brapi.v2.services.BrAPIGermplasmService;
import org.breedinginsight.brapps.importer.daos.BrAPIListDAO;
import org.breedinginsight.dao.db.tables.pojos.BiUserEntity;
import org.breedinginsight.daos.UserDAO;
import org.breedinginsight.model.Program;
import org.breedinginsight.model.Species;
import org.breedinginsight.services.SpeciesService;
import org.breedinginsight.utilities.response.mappers.FilterField;
import org.jooq.DSLContext;
import org.junit.jupiter.api.*;

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