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Updated /serverinfo #548

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e308963
Updated /serverinfo
nickpalladino Aug 13, 2026
76a1246
Only allow system admin access to brapi pass through calls
nickpalladino Aug 26, 2026
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86 changes: 22 additions & 64 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIV2Controller.java
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Original file line numberDiff line numberDiff line change
Expand Up@@ -65,11 +65,12 @@ public BrAPIV2Controller(SecurityService securityService, ProgramService program
public BrAPIServerInfoResponse serverinfo() {
BrAPIServerInfo serverInfo = new BrAPIServerInfo();
setBrAPIServerInfo(serverInfo);
serverInfo.setServerDescription("BrAPI endpoints are not implemented at the root of this domain. Please make BrAPI calls in the context of a program (ex: https://app.breedinginsight.net/v1/programs/{programId}/brapi/v2)");
serverInfo.setServerDescription("DeltaBreed provides server information and program discovery at this root. Program-scoped BrAPI calls use https://app.breedinginsight.net/v1/programs/{programId}/brapi/v2");

serverInfo.setCalls(
new ServiceBuilder().versions("2.0", "2.1")
.setBase("serverinfo").GET().build()
.setBase("programs").GET().POST().addPath("{programDbId}").GET().PUT().build()
);

return new BrAPIServerInfoResponse().result(serverInfo);
Expand All@@ -79,82 +80,39 @@ public BrAPIServerInfoResponse serverinfo() {
@Produces(MediaType.APPLICATION_JSON)
@Secured(SecurityRule.IS_ANONYMOUS)
public BrAPIServerInfoResponse programServerinfo(@PathVariable("programId") UUID programId) {
String programBrAPIBase = String.format("v1/programs/%s%s/", programId, BrapiVersion.BRAPI_V2);

List<BrAPIService> programServices = new ServiceBuilder()
.versions("2.0", "2.1")
//CORE
.setBase("serverinfo").GET().build()
.setBase("commoncropnames").GET().build()
.setBase("lists").GET().POST().addPath("{listDbId}").GET().PUT().withSearch()
.setBase("locations").GET().addPath("{locationDbId}").GET().withSearch()
.setBase("people").GET().addPath("{personDbId}").GET().withSearch()
.setBase("programs").GET().addPath("{programDbId}").GET().withSearch()
.setBase("seasons").GET().addPath("{seasonDbId}").GET().build()
.setBase("studies").GET().addPath("{studyDbId}").GET().withSearch()
.setBase("studytypes").GET().build()
.setBase("trials").GET().addPath("{trialDbId}").GET().withSearch()
.setBase("lists").GET().addPath("{listDbId}").DELETE().build()
.setBase("programs").GET().POST().addPath("{programDbId}").GET().PUT().build()
.setBase("studies").GET().POST().addPath("{studyDbId}").GET().PUT().build()
.setBase("trials").GET().POST().addPath("{trialDbId}").GET().PUT().build()
//GERMPLASM
.setBase("attributes").GET().addPath("{attributeDbId}").GET().setPath("categories").GET().withSearch()
.setBase("attributevalues").GET().addPath("{attributeValueDbId}").GET().withSearch()
.setBase("breedingmethods").GET().addPath("{breedingMethodDbId}").GET().build()
.setBase("crosses").GET().build()
.setBase("plannedcrosses").GET().build()
.setBase("crossingprojects").GET().addPath("{crossingProjectDbId}").GET().build()
.setBase("seedlots").GET().addPath("transactions").GET().setPath("{seedLotDbId}").GET().addPath("transactions").GET().build()
.setBase("germplasm").GET().addPath("{germplasmDbId}").GET().addPath("mcpd").GET().withSearch()
.setBase("germplasm").GET().addPath("{germplasmDbId}").GET().build()
.setBase("search/germplasm").POST().addPath("{searchResultId}").GET().build()
//PHENOTYPING
.setBase("events").GET().build()
.setBase("images").GET().addPath("{imageDbId}").GET().addPath("imagecontent").withSearch()
.setBase("ontologies").GET().build()
.setBase("traits").GET().addPath("{traitDbId}").GET().build()
.setBase("methods").GET().addPath("{methodDbId}").GET().build()
.setBase("scales").GET().addPath("{scaleDbId}").GET().build()
.setBase("variables").GET().addPath("{observationVariableDbId}").GET().withSearch()
.setBase("observationunits").GET().addPath("{observationUnitDbId}").GET().setPath("table").GET().withSearch()
.setBase("observations").GET().addPath("{observationDbId}").GET().setPath("table").GET().withSearch()
.setBase("observations").addPath("tables").GET()
.setBase("images").GET().POST().addPath("{imageDbId}").GET().PUT().addPath("imagecontent").PUT().build()
.setBase("observationlevels").GET().build()
//GENOTYPING - TODO
// .setBase("calls").GET().withSearch()
// .setBase("callsets").GET().addPath("{callSetDbId}").GET().addPath("calls").GET().withSearch()
// .setBase("maps").GET().addPath("{mapDbId}").GET().addPath("linkagegroups").GET().build()
// .setBase("markerpositions").GET().withSearch()
// .setBase("references").GET().addPath("{referenceDbId}").GET().addPath("bases").GET().withSearch()
// .setBase("referencesets").GET().addPath("{referenceSetDbId}").GET().withSearch()
// .setBase("samples").GET().addPath("{sampleDbId}").GET().withSearch()
// .setBase("variants").GET().addPath("{variantDbId}").GET().addPath("calls").GET().withSearch()
// .setBase("variantsets").GET().addPath("extract").setPath("{variantSetDbId}").GET()
// .addPath("calls").GET().setPath("callsets").GET().setPath("variants").GET().withSearch()
// .setBase("vendor").addPath("specifications").GET().setPath("plates").addPath("{submissionId}").build()
// .setBase("vendor/orders").GET().addPath("{orderId}").addPath("plates").GET().setPath("results").GET().setPath("status").GET().build()

.setBase("observationunits").GET().POST().PUT().addPath("{observationUnitDbId}").GET().PUT().build()
.setBase("observationunits/table").GET().build()
.setBase("variables").GET().POST().addPath("{observationVariableDbId}").GET().PUT().build()
.setBase("observations").GET().POST().PUT().addPath("{observationDbId}").GET().PUT().build()
.setBase("observations/table").GET().build()
//V2.0 only
.versions("2.0")
.setBase("germplasm").addPath("{germplasmDbId}").addPath("pedigree").GET().setPath("progeny").GET().build()
.setBase("lists").addPath("{listDbId}").addPath("items").build()
// .setBase("samples").addPath("{sampleDbId}").build() //TODO
//V2.1 only
.versions("2.1")
// .setBase("allelematrix").GET().withSearch() //TODO
// .setBase("calls").build() //TODO
.setBase("delete").addPath("images").setPath("observations").build()
.setBase("lists").addPath("{listDbId}").addPath("data").POST().build()
.setBase("ontologies").addPath("{ontologyDbId}").GET().build()
.setBase("pedigree").GET().withSearch()
// .setBase("plates").GET().addPath("{plateDbId}").GET().withSearch() //TODO
// .setBase("samples").build() //TODO
.setBase("pedigree").GET().POST().PUT()
.build();

for(BrAPIService service : programServices) {
service.setService(service.getService());
}

BrAPIServerInfo programServerInfo = new BrAPIServerInfo();
setBrAPIServerInfo(programServerInfo);
programServerInfo.setCalls(programServices);
BrAPIServerInfo programServerInfo = new BrAPIServerInfo();
setBrAPIServerInfo(programServerInfo);
programServerInfo.setCalls(programServices);

return new BrAPIServerInfoResponse().result(programServerInfo);
return new BrAPIServerInfoResponse().result(programServerInfo);
}

private void setBrAPIServerInfo(BrAPIServerInfo serverInfo) {
Expand All@@ -181,15 +139,15 @@ public HttpResponse<?> getSeasons(@PathVariable("programId") UUID programId, Htt

@Get("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/{+path}")
@Produces(MediaType.APPLICATION_JSON)
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
@ProgramSecured(roles = {ProgramSecuredRole.SYSTEM_ADMIN})
public HttpResponse<?> getCatchall(@PathVariable("path") String path, @PathVariable("programId") UUID programId, HttpRequest<String> request) {
return executeRequest(path, programId, request, "GET");
}

@Post("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/{+path}")
@Consumes(MediaType.ALL)
@Produces(MediaType.APPLICATION_JSON)
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
@ProgramSecured(roles = {ProgramSecuredRole.SYSTEM_ADMIN})
public HttpResponse<String> postCatchall(@PathVariable("path") String path, @PathVariable("programId") UUID programId, HttpRequest<byte[]> request,
@Header("Content-Type") String contentType) {
return executeByteRequest(path, programId, request, contentType, "POST");
Expand All@@ -198,7 +156,7 @@ public HttpResponse<String> postCatchall(@PathVariable("path") String path, @Pat
@Put("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/{+path}")
@Consumes(MediaType.ALL)
@Produces(MediaType.APPLICATION_JSON)
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
@ProgramSecured(roles = {ProgramSecuredRole.SYSTEM_ADMIN})
public HttpResponse<String> putCatchall(@PathVariable("path") String path, @PathVariable("programId") UUID programId, HttpRequest<byte[]> request,
@Header("Content-Type") String contentType) {
return executeByteRequest(path, programId, request, contentType, "PUT");
Expand Down
5 changes: 5 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/ServiceBuilder.java
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Original file line numberDiff line numberDiff line change
Expand Up@@ -47,6 +47,11 @@ public ServiceBuilder POST() {
return this;
}

public ServiceBuilder DELETE() {
methods.add(MethodsEnum.DELETE);
return this;
}

public ServiceBuilder GET() {
methods.add(MethodsEnum.GET);
return this;
Expand Down
106 changes: 102 additions & 4 deletions src/test/java/org/breedinginsight/brapi/v2/BrAPIV2ControllerIntegrationTest.java
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Original file line numberDiff line numberDiff line change
Expand Up@@ -20,6 +20,8 @@
import com.google.gson.*;
import io.kowalski.fannypack.FannyPack;
import io.micronaut.context.annotation.Property;
import io.micronaut.http.HttpMethod;
import io.micronaut.http.HttpRequest;
import io.micronaut.http.HttpResponse;
import io.micronaut.http.HttpStatus;
import io.micronaut.http.MediaType;
Expand All@@ -32,6 +34,8 @@
import org.brapi.client.v2.typeAdapters.PaginationTypeAdapter;
import org.brapi.v2.model.BrAPIExternalReference;
import org.brapi.v2.model.BrAPIPagination;
import org.brapi.v2.model.core.BrAPIService;
import org.brapi.v2.model.core.BrAPIService.MethodsEnum;
import org.brapi.v2.model.core.BrAPIServerInfo;
import org.brapi.v2.model.pheno.*;
import org.breedinginsight.BrAPITest;
Expand All@@ -42,12 +46,13 @@
import org.breedinginsight.model.User;
import org.jooq.DSLContext;
import org.junit.jupiter.api.*;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.EnumSource;

import javax.inject.Inject;
import java.time.OffsetDateTime;
import java.util.Arrays;
import java.util.Collections;
import java.util.UUID;
import java.util.*;
import java.util.stream.Collectors;

import static io.micronaut.http.HttpRequest.GET;
import static io.micronaut.http.HttpRequest.POST;
Expand DownExpand Up@@ -142,9 +147,76 @@ public void testRootServerInfo() {
assertEquals("DeltaBreed", serverInfo.getServerName());
assertEquals("bidevteam@cornell.edu", serverInfo.getContactEmail());
assertEquals("https://breedinginsight.org", serverInfo.getOrganizationURL());
assertEquals("BrAPI endpoints are not implemented at the root of this domain. Please make BrAPI calls in the context of a program (ex: https://app.breedinginsight.net/v1/programs/{programId}/brapi/v2)", serverInfo.getServerDescription());
assertEquals("DeltaBreed provides server information and program discovery at this root. Program-scoped BrAPI calls use https://app.breedinginsight.net/v1/programs/{programId}/brapi/v2", serverInfo.getServerDescription());
assertEquals("Cornell University, Ithaca, NY, USA", serverInfo.getLocation());
assertEquals("https://brapi.org/specification", serverInfo.getDocumentationURL());

assertEquals(Map.ofEntries(
Map.entry("serverinfo", Set.of(MethodsEnum.GET)),
Map.entry("programs", Set.of(MethodsEnum.GET, MethodsEnum.POST)),
Map.entry("programs/{programDbId}", Set.of(MethodsEnum.GET, MethodsEnum.PUT))
), getMethodsByService(serverInfo));
assertAllCallsHaveVersions(serverInfo, Set.of("2.0", "2.1"));
}

@Test
public void testProgramServerInfoOnlyListsExplicitOverrides() {
String path = String.format("%s/programs/%s/brapi/v2/serverinfo", biApiVersion, validProgram.getId());
Flowable<HttpResponse<String>> call = biClient.exchange(GET(path), String.class);

HttpResponse<String> response = call.blockingFirst();
assertEquals(HttpStatus.OK, response.getStatus());
assertNotNull(response.body(), "Response body is empty");

JsonObject result = JsonParser.parseString(response.body())
.getAsJsonObject()
.getAsJsonObject("result");
BrAPIServerInfo serverInfo = GSON.fromJson(result, BrAPIServerInfo.class);

assertEquals(Map.ofEntries(
Map.entry("serverinfo", Set.of(MethodsEnum.GET)),
Map.entry("commoncropnames", Set.of(MethodsEnum.GET)),
Map.entry("lists", Set.of(MethodsEnum.GET)),
Map.entry("lists/{listDbId}", Set.of(MethodsEnum.DELETE)),
Map.entry("programs", Set.of(MethodsEnum.GET, MethodsEnum.POST)),
Map.entry("programs/{programDbId}", Set.of(MethodsEnum.GET, MethodsEnum.PUT)),
Map.entry("studies", Set.of(MethodsEnum.GET, MethodsEnum.POST)),
Map.entry("studies/{studyDbId}", Set.of(MethodsEnum.GET, MethodsEnum.PUT)),
Map.entry("trials", Set.of(MethodsEnum.GET, MethodsEnum.POST)),
Map.entry("trials/{trialDbId}", Set.of(MethodsEnum.GET, MethodsEnum.PUT)),
Map.entry("germplasm", Set.of(MethodsEnum.GET)),
Map.entry("germplasm/{germplasmDbId}", Set.of(MethodsEnum.GET)),
Map.entry("search/germplasm", Set.of(MethodsEnum.POST)),
Map.entry("search/germplasm/{searchResultId}", Set.of(MethodsEnum.GET)),
Map.entry("images", Set.of(MethodsEnum.GET, MethodsEnum.POST)),
Map.entry("images/{imageDbId}", Set.of(MethodsEnum.GET, MethodsEnum.PUT)),
Map.entry("images/{imageDbId}/imagecontent", Set.of(MethodsEnum.PUT)),
Map.entry("observationlevels", Set.of(MethodsEnum.GET)),
Map.entry("observationunits", Set.of(MethodsEnum.GET, MethodsEnum.POST, MethodsEnum.PUT)),
Map.entry("observationunits/{observationUnitDbId}", Set.of(MethodsEnum.GET, MethodsEnum.PUT)),
Map.entry("observationunits/table", Set.of(MethodsEnum.GET)),
Map.entry("variables", Set.of(MethodsEnum.GET, MethodsEnum.POST)),
Map.entry("variables/{observationVariableDbId}", Set.of(MethodsEnum.GET, MethodsEnum.PUT)),
Map.entry("observations", Set.of(MethodsEnum.GET, MethodsEnum.POST, MethodsEnum.PUT)),
Map.entry("observations/{observationDbId}", Set.of(MethodsEnum.GET, MethodsEnum.PUT)),
Map.entry("observations/table", Set.of(MethodsEnum.GET)),
Map.entry("germplasm/{germplasmDbId}/pedigree", Set.of(MethodsEnum.GET)),
Map.entry("germplasm/{germplasmDbId}/progeny", Set.of(MethodsEnum.GET)),
Map.entry("pedigree", Set.of(MethodsEnum.GET, MethodsEnum.POST, MethodsEnum.PUT))
), getMethodsByService(serverInfo));

serverInfo.getCalls().forEach(service -> {
Set<String> expectedVersions;
if (service.getService().equals("germplasm/{germplasmDbId}/pedigree") ||
service.getService().equals("germplasm/{germplasmDbId}/progeny")) {
expectedVersions = Set.of("2.0");
} else if (service.getService().equals("pedigree")) {
expectedVersions = Set.of("2.1");
} else {
expectedVersions = Set.of("2.0", "2.1");
}
assertEquals(expectedVersions, new HashSet<>(service.getVersions()), service.getService());
});
}

@Test
Expand DownExpand Up@@ -185,6 +257,21 @@ public void testPutVariablesNotFound() {
assertEquals(HttpStatus.NOT_FOUND, e.getStatus());
}

@ParameterizedTest
@EnumSource(value = HttpMethod.class, names = {"GET", "POST", "PUT"})
public void testCatchallRequiresSystemAdmin(HttpMethod method) {
String path = String.format("%s/programs/%s/brapi/v2/unsupported", biApiVersion, validProgram.getId());
HttpRequest<?> request = HttpRequest.create(method, path)
.contentType(MediaType.APPLICATION_JSON)
.bearerAuth("other-registered-user");

HttpClientResponseException exception = Assertions.assertThrows(HttpClientResponseException.class,
() -> biClient.exchange(request, String.class)
.blockingFirst());

assertEquals(HttpStatus.FORBIDDEN, exception.getStatus());
}



private BrAPIObservationVariable generateVariable() {
Expand All@@ -202,4 +289,15 @@ private BrAPIObservationVariable generateVariable() {
.scale(new BrAPIScale().scaleName("test scale" + random)
.dataType(BrAPITraitDataType.NUMERICAL));
}

private Map<String, Set<MethodsEnum>> getMethodsByService(BrAPIServerInfo serverInfo) {
return serverInfo.getCalls().stream()
.collect(Collectors.toMap(BrAPIService::getService,
service -> new HashSet<>(service.getMethods())));
}

private void assertAllCallsHaveVersions(BrAPIServerInfo serverInfo, Set<String> versions) {
serverInfo.getCalls().forEach(service ->
assertEquals(versions, new HashSet<>(service.getVersions()), service.getService()));
}
}
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