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BI-2374 Add delete catch-all to deltabreed brapi controller #427

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BI-2374 Add delete catch-all to deltabreed brapi controller #427

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17e68b9
add delete catch-all endpoint to brapi proxy
dmeidlin Nov 1, 2024
d233d59
optimize imports and clean up code
dmeidlin Nov 6, 2024
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2 changes: 1 addition & 1 deletion src/main/java/org/breedinginsight/brapi/v2/BrAPIGermplasmController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -178,7 +178,7 @@ private void batchProcessGermplasm(List<BrAPIGermplasm> germplasmList, String pr
Pattern programKeyPattern = Utilities.getRegexPatternMatchAllProgramKeysAnyAccession(programKey);
germplasmList.parallelStream().forEach(germplasm -> {
// Set dbId
germplasm.germplasmDbId(Utilities.getExternalReference(germplasm.getExternalReferences(), "breedinginsight.org")
germplasm.germplasmDbId(Utilities.getExternalReference(germplasm.getExternalReferences(), "breeding-insight.net")
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What was the reason for this change? Should we be using the value defined in application.yml brapi.server.reference-source

.orElseThrow(() -> new IllegalStateException("No BI external reference found"))
.getReferenceId());
// Process synonyms
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26 changes: 26 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIV2Controller.java
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Expand Up @@ -17,6 +17,7 @@

package org.breedinginsight.brapi.v2;

import io.micronaut.context.annotation.Value;
import io.micronaut.http.HttpRequest;
import io.micronaut.http.HttpResponse;
import io.micronaut.http.HttpStatus;
Expand Down Expand Up @@ -186,6 +187,15 @@ public HttpResponse<?> getCatchall(@PathVariable("path") String path, @PathVaria
return executeRequest(path, programId, request, "GET");
}

@Delete("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/{+path}")
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When the delete pass through is overridden by specific implementations in future cards, is the plan to use the DeltaBreed external reference id rather than the DbId of the brapi service?

@Produces(MediaType.APPLICATION_JSON)
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As we discussed in standup, this currently won't delete the associated dataset and that should be captured in the the experiment delete endpoint implementation.

@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
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Is this something only a program or system admin should be allowed to do? Wondering if we should make a new role group that is system admin and program admin without readonly.

public HttpResponse<?> deleteCatchall(@PathVariable("path") String path,
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When testing I could do DELETE http://localhost:8081/v1/programs/9d4719fe-bd89-4d54-bbf6-e71f33f87b04/brapi/v2/trials/ with no trialDbId and get success. Seems like it should give an error in that case.

@PathVariable("programId") UUID programId,
HttpRequest<Void> request) {
return executeDeleteRequest(path, programId, request);
}

@Post("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/{+path}")
@Consumes(MediaType.ALL)
@Produces(MediaType.APPLICATION_JSON)
Expand Down Expand Up @@ -241,6 +251,22 @@ private HttpResponse<String> executeRequest(String path, UUID programId, HttpReq
throw new HttpStatusException(HttpStatus.UNAUTHORIZED, "Unauthorized BrAPI Request");
}

private HttpResponse<String> executeDeleteRequest(String path, UUID programId, HttpRequest<?> request) {
AuthenticatedUser actingUser = securityService.getUser();
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actingUser isn't used


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Maybe should add a logCall so behavior is consistent with executeByteRequest and executeRequest

if (programId != null) {
HttpUrl requestUrl = getUrl(programId, path, request);

var brapiRequest = new Request.Builder().url(requestUrl)
.method("DELETE", null)
.build();

return makeCall(brapiRequest);
}

throw new HttpStatusException(HttpStatus.UNAUTHORIZED, "Unauthorized BrAPI Request");
}

private HttpResponse<String> makeCall(Request brapiRequest) {
// TODO: use config parameter for timeout
OkHttpClient client = new OkHttpClient.Builder()
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