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Merged
timparsons merged 12 commits into from
Jan 27, 2023
Merged

BI-1651 - Allow programs to choose/create breeding methods #236

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b33f77e
[BI-1651] - Introducing program defined breeding methods
timparsons Oct 28, 2022
72c0151
[BI-1651] - cleanup
timparsons Nov 1, 2022
3db629b
[BI-1651] Preventing editing of breeding methods in use by a germplasm
timparsons Nov 22, 2022
fde2de6
[BI-1651] Adding ability to delete a program breeding method
timparsons Dec 5, 2022
2a50ea5
[BI-1651] Adding unit tests
timparsons Dec 21, 2022
7ac0f7a
[BI-1651] Finishing implementation of integration tests
timparsons Jan 9, 2023
9e81a6c
[BI-1651] Renaming flyway script
timparsons Jan 9, 2023
156bde6
[BI-1651] Removing unused test class
timparsons Jan 9, 2023
05eb500
[BI-1651] updating delete program script for unit tests
timparsons Jan 9, 2023
3b78f84
[BI-1651] fixing unit tests
timparsons Jan 10, 2023
61acf9e
[BI-1651] Addressing PR change requests
timparsons Jan 24, 2023
db68d7b
[BI-1651] Updating script name
timparsons Jan 24, 2023
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174 changes: 174 additions & 0 deletions src/main/java/org/breedinginsight/api/v1/controller/BreedingMethodController.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,174 @@
package org.breedinginsight.api.v1.controller;

import io.micronaut.http.HttpResponse;
import io.micronaut.http.MediaType;
import io.micronaut.http.annotation.*;
import io.micronaut.http.server.exceptions.InternalServerException;
import io.micronaut.security.annotation.Secured;
import io.micronaut.security.rules.SecurityRule;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.lang3.StringUtils;
import org.brapi.client.v2.model.exceptions.ApiException;
import org.breedinginsight.api.auth.*;
import org.breedinginsight.api.model.v1.response.DataResponse;
import org.breedinginsight.api.model.v1.response.Response;
import org.breedinginsight.api.model.v1.response.metadata.Metadata;
import org.breedinginsight.api.model.v1.response.metadata.Pagination;
import org.breedinginsight.api.model.v1.response.metadata.Status;
import org.breedinginsight.api.model.v1.response.metadata.StatusCode;
import org.breedinginsight.api.v1.controller.metadata.AddMetadata;
import org.breedinginsight.dao.db.tables.pojos.BreedingMethodEntity;
import org.breedinginsight.dao.db.tables.pojos.ProgramBreedingMethodEntity;
import org.breedinginsight.daos.BreedingMethodDAO;
import org.breedinginsight.services.BreedingMethodService;
import org.breedinginsight.services.exceptions.BadRequestException;

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

@Slf4j
@Controller("/${micronaut.bi.api.version}")
public class BreedingMethodController {

private final SecurityService securityService;
private final BreedingMethodService breedingMethodService;

@Inject
public BreedingMethodController(SecurityService securityService, BreedingMethodService breedingMethodService) {
this.securityService = securityService;
this.breedingMethodService = breedingMethodService;
}

@Get("/breeding-methods")
@Produces(MediaType.APPLICATION_JSON)
@AddMetadata
@Secured(SecurityRule.IS_AUTHENTICATED)
public HttpResponse<Response<DataResponse<ProgramBreedingMethodEntity>>> getSystemBreedingMethods() {
log.debug("fetching system breeding methods");

try {
AuthenticatedUser actingUser = securityService.getUser();

List<ProgramBreedingMethodEntity> breedingMethods = breedingMethodService.getSystemBreedingMethods();
return buildResponse(breedingMethods);
} catch (Exception e) {
log.error(e.getMessage(), e);
throw new InternalServerException("Error fetching system breeding methods", e);
}
}

@Post("programs/{programId}/breeding-methods")
@Produces(MediaType.APPLICATION_JSON)
@ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
public HttpResponse<Response<ProgramBreedingMethodEntity>> createProgramBreedingMethod(@PathVariable UUID programId, @Body ProgramBreedingMethodEntity breedingMethod) throws BadRequestException, ApiException {
log.debug("Saving new program breeding method");

try {
AuthenticatedUser user = securityService.getUser();
Response<ProgramBreedingMethodEntity> response = new Response<>();
response.result = breedingMethodService.createBreedingMethod(breedingMethod, programId, user.getId());

List<Status> metadataStatus = new ArrayList<>();
metadataStatus.add(new Status(StatusCode.INFO, "Successful Creation"));
Pagination pagination = new Pagination(1, 1, 1, 0);
Metadata metadata = new Metadata(pagination, metadataStatus);
response.metadata = metadata;

return HttpResponse.ok(response);
} catch (Exception e) {
log.error("Error creating program breeding method", e);
throw e;
}
}

@Get("programs/{programId}/breeding-methods{?inUse}")
@Produces(MediaType.APPLICATION_JSON)
@AddMetadata
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
public HttpResponse<Response<DataResponse<ProgramBreedingMethodEntity>>> getProgramBreedingMethods(@PathVariable UUID programId, @QueryValue(defaultValue = "false") Boolean inUse) {
log.debug(String.format("fetching breeding methods for program: %s", programId));

try {
AuthenticatedUser actingUser = securityService.getUser();
List<ProgramBreedingMethodEntity> breedingMethods;
if(inUse) {
breedingMethods = breedingMethodService.fetchBreedingMethodsInUse(programId);
} else {
breedingMethods = breedingMethodService.getBreedingMethods(programId);
}
return buildResponse(breedingMethods);
} catch (Exception e) {
log.error(e.getMessage(), e);
throw new InternalServerException("Error fetching breeding methods", e);
}
}

@Put("programs/{programId}/breeding-methods/{breedingMethodId}")
@Produces(MediaType.APPLICATION_JSON)
@ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
public HttpResponse<Response<ProgramBreedingMethodEntity>> updateProgramBreedingMethod(@PathVariable UUID programId, @PathVariable UUID breedingMethodId, @Body ProgramBreedingMethodEntity breedingMethod) throws BadRequestException, ApiException {
log.debug("Saving new program breeding method");

try {
AuthenticatedUser user = securityService.getUser();

breedingMethod.setId(breedingMethodId);

Response<ProgramBreedingMethodEntity> response = new Response<>();
response.result = breedingMethodService.updateBreedingMethod(breedingMethod, programId, user.getId());

List<Status> metadataStatus = new ArrayList<>();
metadataStatus.add(new Status(StatusCode.INFO, "Successful Update"));
Pagination pagination = new Pagination(1, 1, 1, 0);
Metadata metadata = new Metadata(pagination, metadataStatus);
response.metadata = metadata;

return HttpResponse.ok(response);
} catch (Exception e) {
log.error("Error updating program breeding method", e);
throw e;
}
}

@Put("programs/{programId}/breeding-methods/enable")
@ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
public HttpResponse enableSystemBreedingMethods(@PathVariable UUID programId, @Body List<UUID> systemBreedingMethodIds) throws ApiException, BadRequestException {
log.debug("enabling system breeding methods for program: "+programId);

try {
AuthenticatedUser user = securityService.getUser();

breedingMethodService.enableSystemMethods(systemBreedingMethodIds, programId, user.getId());
return HttpResponse.ok();
} catch (Exception e) {
log.error("Error enabling system breeding methods for program: "+programId, e);
throw e;
}
}

@Delete("programs/{programId}/breeding-methods/{breedingMethodId}")
@ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
public HttpResponse deleteProgramBreedingMethod(@PathVariable UUID programId, @PathVariable UUID breedingMethodId) throws BadRequestException, ApiException {
try {
AuthenticatedUser user = securityService.getUser();
breedingMethodService.deleteBreedingMethod(programId, breedingMethodId);
return HttpResponse.ok();
} catch (Exception e) {
log.error("Error deleting breeding method.\n\tprogramId: " + programId + "\n\tbreedingMethodId: " + breedingMethodId);
throw e;
}
}

private HttpResponse<Response<DataResponse<ProgramBreedingMethodEntity>>> buildResponse(List<ProgramBreedingMethodEntity> breedingMethods) {
List<Status> metadataStatus = new ArrayList<>();
metadataStatus.add(new Status(StatusCode.INFO, "Successful Query"));
Pagination pagination = new Pagination(breedingMethods.size(), breedingMethods.size(), 1, 0);
Metadata metadata = new Metadata(pagination, metadataStatus);
Response<DataResponse<ProgramBreedingMethodEntity>> response = new Response<>(metadata, new DataResponse<>(breedingMethods));
return HttpResponse.ok(response);
}
}
20 changes: 10 additions & 10 deletions src/main/java/org/breedinginsight/brapps/importer/model/base/Germplasm.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@
import org.brapi.v2.model.germ.BrAPIGermplasmSynonyms;
import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
import org.breedinginsight.brapps.importer.model.config.*;
import org.breedinginsight.dao.db.tables.pojos.BreedingMethodEntity;
import org.breedinginsight.dao.db.tables.pojos.ProgramBreedingMethodEntity;
import org.breedinginsight.model.Program;
import org.breedinginsight.model.User;
import org.breedinginsight.utilities.Utilities;
Expand Down Expand Up @@ -143,7 +143,7 @@ public static String constructGermplasmListName(String listName, Program program
return String.format("%s [%s-germplasm]", listName, program.getKey());
}

public BrAPIGermplasm constructBrAPIGermplasm(BreedingMethodEntity breedingMethod, User user) {
private BrAPIGermplasm constructBrAPIGermplasm(ProgramBreedingMethodEntity breedingMethod, User user) {
BrAPIGermplasm germplasm = new BrAPIGermplasm();
germplasm.setGermplasmName(getGermplasmName());
germplasm.setDefaultDisplayName(getGermplasmName());
Expand All @@ -163,8 +163,8 @@ public BrAPIGermplasm constructBrAPIGermplasm(BreedingMethodEntity breedingMetho
germplasm.setCountryOfOriginCode(getCountryOfOrigin());
if (additionalInfos != null) {
additionalInfos.stream()
.filter(additionalInfo -> additionalInfo.getAdditionalInfoValue() != null)
.forEach(additionalInfo -> germplasm.putAdditionalInfoItem(additionalInfo.getAdditionalInfoName(), additionalInfo.getAdditionalInfoValue()));
.filter(additionalInfo -> additionalInfo.getAdditionalInfoValue() != null)
.forEach(additionalInfo -> germplasm.putAdditionalInfoItem(additionalInfo.getAdditionalInfoName(), additionalInfo.getAdditionalInfoValue()));
}

// Seed Source
Expand All @@ -183,8 +183,8 @@ public BrAPIGermplasm constructBrAPIGermplasm(BreedingMethodEntity breedingMetho
germplasm.externalReferences(new ArrayList<>());
if (externalReferences != null) {
List<BrAPIExternalReference> brAPIExternalReferences = externalReferences.stream()
.map(externalReference -> externalReference.constructBrAPIExternalReference())
.collect(Collectors.toList());
.map(externalReference -> externalReference.constructBrAPIExternalReference())
.collect(Collectors.toList());
if (uidExternalReference != null) {
brAPIExternalReferences.add(uidExternalReference);
}
Expand All @@ -203,9 +203,9 @@ public BrAPIGermplasm constructBrAPIGermplasm(BreedingMethodEntity breedingMetho
List<BrAPIGermplasmSynonyms> brapiSynonyms = new ArrayList<>();
if (synonyms != null) {
List<String> synonyms = Arrays.asList(blobSynonyms.split(";")).stream()
.map(synonym -> synonym.strip())
.distinct()
.collect(Collectors.toList());
.map(synonym -> synonym.strip())
.distinct()
.collect(Collectors.toList());
// Create synonym
for (String synonym: synonyms) {
BrAPIGermplasmSynonyms brapiSynonym = new BrAPIGermplasmSynonyms();
Expand Down Expand Up @@ -246,7 +246,7 @@ private void setBrAPIGermplasmCommitFields(BrAPIGermplasm germplasm, String prog
}
}

public BrAPIGermplasm constructBrAPIGermplasm(Program program, BreedingMethodEntity breedingMethod, User user, boolean commit, String referenceSource, Supplier<BigInteger> nextVal) {
public BrAPIGermplasm constructBrAPIGermplasm(Program program, ProgramBreedingMethodEntity breedingMethod, User user, boolean commit, String referenceSource, Supplier<BigInteger> nextVal) {
BrAPIGermplasm germplasm = constructBrAPIGermplasm(breedingMethod, user);
if (commit) {
setBrAPIGermplasmCommitFields(germplasm, program.getKey(), referenceSource, nextVal);
Expand Down
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