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Fixes to BrAPI v1 services
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BESOMBES Gabriel committed Dec 6, 2023
1 parent fded1f4 commit cfc5a50
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Showing 17 changed files with 646 additions and 281 deletions.
32 changes: 25 additions & 7 deletions opensilex-brapi/src/main/java/org/opensilex/brapi/api/GermplasmAPI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,15 +7,20 @@
package org.opensilex.brapi.api;

import io.swagger.annotations.*;
import org.opensilex.brapi.responses.BrAPIv1GermplasmListResponse;
import org.opensilex.brapi.model.BrAPIv1GermplasmDTO;
import org.opensilex.brapi.responses.BrAPIv1AccessionWarning;
import org.opensilex.brapi.responses.BrAPIv1GermplasmListResponse;
import org.opensilex.core.germplasm.dal.GermplasmDAO;
import org.opensilex.core.germplasm.dal.GermplasmModel;
import org.opensilex.nosql.mongodb.MongoDBService;
import org.opensilex.security.account.dal.AccountModel;
import org.opensilex.security.authentication.ApiProtected;
import org.opensilex.security.authentication.NotFoundURIException;
import org.opensilex.security.authentication.injection.CurrentUser;
import org.opensilex.server.exceptions.BadRequestException;
import org.opensilex.server.response.ErrorResponse;
import org.opensilex.sparql.SPARQLModule;
import org.opensilex.sparql.ontology.store.OntologyStore;
import org.opensilex.sparql.service.SPARQLService;
import org.opensilex.utils.ListWithPagination;

Expand Down Expand Up @@ -47,7 +52,7 @@ public class GermplasmAPI extends BrapiCall {
@GET
@Path("v1/germplasm")
@BrapiVersion("1.3")
@ApiOperation("Submit a search request for germplasm")
@ApiOperation("Submit a search request for germplasm (type accession in OpenSILEX")
@ApiProtected
@Produces(MediaType.APPLICATION_JSON)
@ApiResponses(value = {
Expand All @@ -56,13 +61,23 @@ public class GermplasmAPI extends BrapiCall {
@ApiResponse(code = 500, message = "Internal Server Error", response = ErrorResponse.class)})

public Response getGermplasmBySearch(
@ApiParam(value = "Search by germplasmDbId") @QueryParam("germplasmDbId") URI uri,
@ApiParam(value = "Search by germplasmPUI") @QueryParam("germplasmPUI") URI germplasmPUI,
@ApiParam(value = "Search by germplasmName") @QueryParam("germplasmName") String germplasmName,
@ApiParam(value = "Search by commonCropName") @QueryParam("commonCropName") String commonCropName,
@ApiParam(value = "Search by germplasmDbId (URI of an OpenSilex accession)") @QueryParam("germplasmDbId") URI uri,
@ApiParam(value = "Search by germplasmPUI (URI of an OpenSilex accession)") @QueryParam("germplasmPUI") URI germplasmPUI,
@ApiParam(value = "Search by germplasmName (name of an OpenSilex accession)") @QueryParam("germplasmName") String germplasmName,
@ApiParam(value = "Search by commonCropName (name of the species of an OpenSilex accession)") @QueryParam("commonCropName") String commonCropName,
@ApiParam(value = "Page number", example = "0") @QueryParam("page") @DefaultValue("0") @Min(0) int page,
@ApiParam(value = "Page size", example = "20") @QueryParam("page_size") @DefaultValue("20") @Min(0) int pageSize
) throws Exception {

OntologyStore ontologyStore = SPARQLModule.getOntologyStoreInstance();
if (!ontologyStore.classExist(
BrAPIv1AccessionWarning.ACCESSION_URI,
BrAPIv1AccessionWarning.GERMPLASM_URI
)) {
throw new BadRequestException(
"The 'Accession' notion doesn't exist in your ontology so this service is unavailable"
);
}
GermplasmDAO germplasmDAO = new GermplasmDAO(sparql, nosql);

if (germplasmPUI != null && uri == null) {
Expand All @@ -77,7 +92,10 @@ public Response getGermplasmBySearch(
page,
pageSize
);

if (resultList.getList().isEmpty()){
throw new NotFoundURIException("No accession could be found with this URI ", uri);
}

// Convert paginated list to DTO
ListWithPagination<BrAPIv1GermplasmDTO> resultDTOList = resultList.convert(
BrAPIv1GermplasmDTO.class,
Expand Down
63 changes: 51 additions & 12 deletions opensilex-brapi/src/main/java/org/opensilex/brapi/api/StudiesAPI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
import io.swagger.annotations.*;
import org.apache.commons.lang3.StringUtils;
import org.eclipse.rdf4j.query.MalformedQueryException;
import org.opensilex.brapi.responses.*;
import org.opensilex.brapi.model.*;
import org.opensilex.brapi.responses.*;
import org.opensilex.core.data.dal.DataDAO;
import org.opensilex.core.data.dal.DataModel;
import org.opensilex.core.event.dal.move.MoveEventDAO;
Expand All @@ -25,6 +25,8 @@
import org.opensilex.core.scientificObject.dal.ScientificObjectDAO;
import org.opensilex.core.scientificObject.dal.ScientificObjectModel;
import org.opensilex.core.scientificObject.dal.ScientificObjectSearchFilter;
import org.opensilex.core.variable.dal.BaseVariableDAO;
import org.opensilex.core.variable.dal.MethodModel;
import org.opensilex.core.variable.dal.VariableModel;
import org.opensilex.fs.service.FileStorageService;
import org.opensilex.nosql.mongodb.MongoDBService;
Expand All @@ -49,6 +51,7 @@
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Objects;

/**
* @see <a href="https://app.swaggerhub.com/apis/PlantBreedingAPI/BrAPI/1.3">BrAPI documentation 1.3</a>
Expand All @@ -74,6 +77,7 @@ public class StudiesAPI extends BrapiCall {
protected Response standardGetStudies(URI studyDbId, String active, String sortBy, String sortOrder, int page, int pageSize) throws Exception {

ExperimentDAO xpDao = new ExperimentDAO(sparql, nosql);
GermplasmDAO germplasmDAO = new GermplasmDAO(sparql, nosql);

ArrayList<OrderBy> orderByList = new ArrayList<>();

Expand Down Expand Up @@ -101,8 +105,15 @@ protected Response standardGetStudies(URI studyDbId, String active, String sortB

Boolean isEnded = !StringUtils.isEmpty(active) ? !Boolean.parseBoolean(active) : null;

if (studyDbId != null && xpDao.get(studyDbId, currentUser) == null) {
throw new NotFoundURIException(studyDbId);
ListWithPagination<ExperimentModel> resultList;

if (studyDbId != null) {
ExperimentModel expeModel = xpDao.get(studyDbId, currentUser);
if (Objects.nonNull(expeModel)){
resultList = new ListWithPagination<>(Collections.singletonList(expeModel));
} else {
throw new NotFoundURIException(studyDbId);
}
} else {
ExperimentSearchFilter filter = new ExperimentSearchFilter()
.setEnded(isEnded)
Expand All @@ -111,10 +122,18 @@ protected Response standardGetStudies(URI studyDbId, String active, String sortB
.setPage(page)
.setPageSize(pageSize);

ListWithPagination<ExperimentModel> resultList = xpDao.search(filter);
ListWithPagination<BrAPIv1StudyDTO> resultDTOList = resultList.convert(BrAPIv1StudyDTO.class, BrAPIv1StudyDTO::fromModel);
return new BrAPIv1StudyListResponse(resultDTOList).getResponse();
resultList = xpDao.search(filter);
}
ListWithPagination<BrAPIv1StudyDTO> resultDTOList = resultList.convert(BrAPIv1StudyDTO.class, experimentModel -> {
try {
return BrAPIv1StudyDTO.fromModel(experimentModel, germplasmDAO, currentUser);
} catch (Exception e) {
throw new RuntimeException(e);
}
});
BrAPIv1StudyListResponse responseClass = new BrAPIv1StudyListResponse(resultDTOList);
BrAPIv1AccessionWarning.setAccessionWarningIfNeeded(responseClass);
return responseClass.getResponse();
}


Expand Down Expand Up @@ -187,9 +206,14 @@ public Response getStudyDetails(
OrganizationDAO organisationDAO = new OrganizationDAO(sparql, nosql);
FacilityDAO facilityDAO = new FacilityDAO(sparql, nosql, organisationDAO);
ExperimentModel model = xpDao.get(studyDbId, currentUser);
GermplasmDAO germplasmDAO = new GermplasmDAO(sparql, nosql);

if (model != null) {
return new BrAPIv1SingleStudyResponse(BrAPIv1StudyDetailsDTO.fromModel(model, facilityDAO, organisationDAO, currentUser)).getResponse();
BrAPIv1SingleStudyResponse responseClass = new BrAPIv1SingleStudyResponse(
BrAPIv1StudyDetailsDTO.fromModel(model, facilityDAO, organisationDAO, currentUser, germplasmDAO)
);
BrAPIv1AccessionWarning.setAccessionWarningIfNeeded(responseClass);
return responseClass.getResponse();
} else {
throw new NotFoundURIException(studyDbId);
}
Expand Down Expand Up @@ -229,7 +253,9 @@ public Response getObservations(
throw new RuntimeException(e);
}
});
return new BrAPIv1ObservationListResponse(observations).getResponse();
BrAPIv1ObservationListResponse responseClass = new BrAPIv1ObservationListResponse(observations);
BrAPIv1AccessionWarning.setAccessionWarningIfNeeded(responseClass);
return responseClass.getResponse();

}

Expand All @@ -252,8 +278,18 @@ public Response getObservationVariables(
DataDAO dataDAO = new DataDAO(nosql, sparql, fs);
List<VariableModel> variables = dataDAO.getUsedVariables(currentUser, Collections.singletonList(studyDbId), null, null, null);

BaseVariableDAO<MethodModel> baseVariableDAO = new BaseVariableDAO<>(MethodModel.class, sparql);
ListWithPagination<VariableModel> variablesPaginated = new ListWithPagination<>(variables, page, pageSize, variables.size());
ListWithPagination<BrAPIv1ObservationVariableDTO> resultDTOList = variablesPaginated.convert(BrAPIv1ObservationVariableDTO.class, BrAPIv1ObservationVariableDTO::fromModel);
ListWithPagination<BrAPIv1ObservationVariableDTO> resultDTOList = variablesPaginated.convert(
BrAPIv1ObservationVariableDTO.class,
variableModel -> {
try {
return BrAPIv1ObservationVariableDTO.fromModel(variableModel, baseVariableDAO);
} catch (Exception e) {
throw new RuntimeException(e);
}
}
);
return new BrAPIv1ObservationVariableListResponse(resultDTOList).getResponse();
}

Expand Down Expand Up @@ -287,6 +323,7 @@ public Response getObservationUnits(
OntologyDAO ontologyDAO = new OntologyDAO(sparql);
MoveEventDAO moveEventDAO = new MoveEventDAO(sparql, nosql);
GeospatialDAO geospatialDAO = new GeospatialDAO(nosql);
GermplasmDAO germplasmDAO = new GermplasmDAO(sparql, nosql);

ScientificObjectSearchFilter searchFilter = new ScientificObjectSearchFilter()
.setExperiment(studyDbId)
Expand All @@ -307,13 +344,15 @@ public Response getObservationUnits(
dataDAO,
xpDao.get(studyDbId, currentUser),
ontologyDAO,
sparql,
moveEventDAO,
geospatialDAO);
geospatialDAO,
germplasmDAO);
} catch (Exception e) {
throw new RuntimeException(e);
}
});
return new BrAPIv1ObservationUnitListResponse(observations).getResponse();
BrAPIv1ObservationUnitListResponse responseClass = new BrAPIv1ObservationUnitListResponse(observations);
BrAPIv1AccessionWarning.setAccessionWarningIfNeeded(responseClass);
return responseClass.getResponse();
}
}
19 changes: 17 additions & 2 deletions opensilex-brapi/src/main/java/org/opensilex/brapi/api/VariablesAPI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@
import org.opensilex.brapi.responses.BrAPIv1ObservationVariableListResponse;
import org.opensilex.brapi.responses.BrAPIv1SingleObservationVariableResponse;
import org.opensilex.brapi.model.BrAPIv1ObservationVariableDTO;
import org.opensilex.core.variable.dal.BaseVariableDAO;
import org.opensilex.core.variable.dal.MethodModel;
import org.opensilex.core.variable.dal.VariableDAO;
import org.opensilex.core.variable.dal.VariableModel;
import org.opensilex.fs.service.FileStorageService;
Expand Down Expand Up @@ -77,7 +79,17 @@ public Response getVariablesList(
variables = varDAO.search(null, null, page, pageSize,currentUser.getLanguage());
}

ListWithPagination<BrAPIv1ObservationVariableDTO> resultDTOList = variables.convert(BrAPIv1ObservationVariableDTO.class, BrAPIv1ObservationVariableDTO::fromModel);
BaseVariableDAO<MethodModel> baseVariableDAO = new BaseVariableDAO<>(MethodModel.class, sparql);
ListWithPagination<BrAPIv1ObservationVariableDTO> resultDTOList = variables.convert(
BrAPIv1ObservationVariableDTO.class,
variableModel -> {
try {
return BrAPIv1ObservationVariableDTO.fromModel(variableModel, baseVariableDAO);
} catch (Exception e) {
throw new RuntimeException(e);
}
}
);
return new BrAPIv1ObservationVariableListResponse(resultDTOList).getResponse();
}

Expand All @@ -98,7 +110,10 @@ public Response getVariableDetails(

VariableModel variable = variableDAO.get(observationVariableDbId);
if (variable != null) {
return new BrAPIv1SingleObservationVariableResponse(BrAPIv1ObservationVariableDTO.fromModel(variable)).getResponse();
BaseVariableDAO<MethodModel> baseVariableDAO = new BaseVariableDAO<>(MethodModel.class, sparql);
return new BrAPIv1SingleObservationVariableResponse(
BrAPIv1ObservationVariableDTO.fromModel(variable, baseVariableDAO)
).getResponse();
} else {
throw new NotFoundURIException(observationVariableDbId);
}
Expand Down
7 changes: 6 additions & 1 deletion opensilex-brapi/src/main/java/org/opensilex/brapi/model/BrAPIv1ContactDTO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,12 @@ public BrAPIv1ContactDTO extractFromModel(PersonModel model, String role) {
this.setEmail(model.getEmail().toString());
}
this.setContactDbId(model.getUri().toString());
this.setName(model.getLastName().toUpperCase() + model.getFirstName().substring(0,1).toUpperCase() + model.getFirstName().substring(1));
this.setName(
model.getLastName().toUpperCase()
+ " "
+ model.getFirstName().substring(0,1).toUpperCase()
+ model.getFirstName().substring(1)
);
if (model.getOrcid() != null && !model.getOrcid().toString().isEmpty()){
this.setOrcid(model.getOrcid().toString());
}
Expand Down
5 changes: 3 additions & 2 deletions opensilex-brapi/src/main/java/org/opensilex/brapi/model/BrAPIv1LocationDTO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
import org.opensilex.core.organisation.dal.facility.FacilityModel;
import org.opensilex.core.organisation.dal.site.SiteAddressModel;
import org.opensilex.security.account.dal.AccountModel;
import org.opensilex.server.rest.validation.model.OpenSilexLocale;

import java.util.*;
import java.util.stream.Collectors;
Expand Down Expand Up @@ -188,7 +189,7 @@ public BrAPIv1LocationDTO extractFromModel(FacilityModel model, FacilityDAO faci
this.setInstituteName(institute.getName());
String countryName = parentAddress.getCountryName();
this.setCountryName(countryName);
this.setCountryCode(new Locale(countryName).getISO3Country());
this.setCountryCode(new OpenSilexLocale(countryName).getISO3Country());
directParentOrganizations.remove(parentsWithOneAddress.get(0));
} else if (parentsWithOneAddress.size()>1) { // If more than one, go an Organisation level above
Set<OrganizationModel> newParents = new HashSet<>();
Expand All @@ -206,7 +207,7 @@ public BrAPIv1LocationDTO extractFromModel(FacilityModel model, FacilityDAO faci
if (model.getAddress() != null && !model.getAddress().toString().isEmpty()){
String countryName = model.getAddress().getCountryName();
this.setCountryName(countryName);
this.setCountryCode(new Locale(countryName).getISO3Country());
this.setCountryCode(new OpenSilexLocale(countryName).getISO3Country());
}

return this;
Expand Down
8 changes: 5 additions & 3 deletions opensilex-brapi/src/main/java/org/opensilex/brapi/model/BrAPIv1MethodDTO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
package org.opensilex.brapi.model;

import com.fasterxml.jackson.annotation.JsonProperty;
import org.opensilex.core.variable.dal.BaseVariableDAO;
import org.opensilex.core.variable.dal.MethodModel;

/**
Expand Down Expand Up @@ -79,7 +80,8 @@ public void setReference(String reference) {
this.reference = reference;
}

public BrAPIv1MethodDTO extractFromModel(MethodModel methodModel){
public BrAPIv1MethodDTO extractFromModel(MethodModel methodModel, BaseVariableDAO<MethodModel> baseVariableDAO) throws Exception {
methodModel = baseVariableDAO.get(methodModel.getUri());

if (methodModel.getUri() != null){
this.setMethodDbId(methodModel.getUri().toString());
Expand All @@ -96,8 +98,8 @@ public BrAPIv1MethodDTO extractFromModel(MethodModel methodModel){
return this;
}

public static BrAPIv1MethodDTO fromModel(MethodModel methodModel){
public static BrAPIv1MethodDTO fromModel(MethodModel methodModel, BaseVariableDAO<MethodModel> baseVariableDAO) throws Exception {
BrAPIv1MethodDTO method = new BrAPIv1MethodDTO();
return method.extractFromModel(methodModel);
return method.extractFromModel(methodModel, baseVariableDAO);
}
}
8 changes: 6 additions & 2 deletions opensilex-brapi/src/main/java/org/opensilex/brapi/model/BrAPIv1ObservationDTO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import org.apache.jena.graph.Node;
import org.apache.jena.graph.NodeFactory;
import org.apache.jena.vocabulary.RDFS;
import org.opensilex.brapi.responses.BrAPIv1AccessionWarning;
import org.opensilex.core.data.dal.DataModel;
import org.opensilex.core.experiment.dal.ExperimentModel;
import org.opensilex.core.germplasm.dal.GermplasmDAO;
Expand All @@ -26,6 +27,7 @@
import java.time.LocalDateTime;
import java.time.ZoneId;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;

/**
Expand Down Expand Up @@ -212,8 +214,10 @@ public BrAPIv1ObservationDTO extractFromModel(DataModel dataModel, ExperimentMod
List<SPARQLModelRelation> germplasms = objectModel.getRelations(Oeso.hasGermplasm).distinct().collect(Collectors.toList());
if (germplasms.size() >= 1){
GermplasmModel germplasmModel = germplasmDAO.get(new URI(germplasms.get(0).getValue()), currentUser, false);
this.setGermplasmDbId(germplasmModel.getUri().toString());
this.setGermplasmName(germplasmModel.getName());
if (Objects.equals(germplasmModel.getType(), BrAPIv1AccessionWarning.ACCESSION_URI)) {
this.setGermplasmDbId(germplasmModel.getUri().toString());
this.setGermplasmName(germplasmModel.getName());
}
}
}

Expand Down
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