BI-2379 - Create Delete Endpoint for Deltabreed Sample Controller

src/main/java/org/breedinginsight/api/v1/controller/geno/SampleSubmissionController.java

@@ -281,4 +281,42 @@ public HttpResponse<Response<SampleSubmission>> checkVendorStatus(@PathVariable
             return HttpResponse.serverError();
         }
     }
+
+    /**
+     * Delete sample submission.
+     * Deletes the bidb submission record and BrAPI samples & plates
+     * @param programId bi-api id of program
+     * @param submissionId bi-api id of submission
+     * @return HttpResponse
+     * @throws ApiException
+     */
+    @Delete("programs/{programId}/submissions/{submissionId}")
+    @Produces(MediaType.APPLICATION_JSON)
+    // sys admin and program admin roles to match file import permissions
+    @ProgramSecured(roles = {ProgramSecuredRole.SYSTEM_ADMIN, ProgramSecuredRole.PROGRAM_ADMIN})
+    public HttpResponse deleteSubmissionById(@PathVariable UUID programId, @PathVariable UUID submissionId) throws ApiException {
+
+        // program validation
+        Optional<Program> program = programService.getById(programId);
+        if(program.isEmpty()) {
+            log.info(String.format("programId not found: %s", programId.toString()));
+            return HttpResponse.notFound();
+        }
+
+        // sample status validation
+        Optional<SampleSubmission> submissionOpt = sampleSubmissionService.getSampleSubmission(program.get(), submissionId, false);
+
+        if(submissionOpt.isEmpty()) {
+            return HttpResponse.notFound();
+        }
+        SampleSubmission submission = submissionOpt.get();
+        if (!submission.isDeletable()) {
+            return HttpResponse.notAllowed();
+        }
+
+        sampleSubmissionService.deleteSampleSubmission(program.get(), submissionId);
+
+        return HttpResponse.ok();
+    }
+
 }

src/main/java/org/breedinginsight/brapps/importer/daos/BrAPISampleDAO.java

@@ -17,8 +17,15 @@
 
 package org.breedinginsight.brapps.importer.daos;
 
+import com.google.gson.Gson;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParser;
 import io.micronaut.context.annotation.Property;
+import io.micronaut.http.server.exceptions.InternalServerException;
 import lombok.extern.slf4j.Slf4j;
+import okhttp3.*;
+import org.brapi.client.v2.JSON;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.brapi.client.v2.modules.genotype.SamplesApi;
 import org.brapi.v2.model.geno.BrAPISample;
@@ -33,9 +40,9 @@
 
 import javax.inject.Inject;
 import javax.inject.Singleton;
+import java.io.IOException;
 import java.util.Collections;
 import java.util.List;
-import java.util.UUID;
 
 @Slf4j
 @Singleton
@@ -47,6 +54,7 @@ public class BrAPISampleDAO {
     private final ImportDAO importDAO;
     private final BrAPIDAOUtil brAPIDAOUtil;
     private final BrAPIEndpointProvider brAPIEndpointProvider;
+    private final Gson gson = new JSON().getGson();
 
     @Inject
     public BrAPISampleDAO(ProgramDAO programDAO,
@@ -102,4 +110,149 @@ public List<BrAPISample> readSamplesBySubmissionIds(Program program, List<String
         SamplesApi samplesApi = brAPIEndpointProvider.get(programDAO.getSampleClient(program.getId()), SamplesApi.class);
         return brAPIDAOUtil.search(samplesApi::searchSamplesPost, samplesApi::searchSamplesSearchResultsDbIdGet, searchRequest);
     }
+
+    /**
+     * Deletes all samples specified in the brapi server
+     * @param program
+     * @param sampleDbIds
+     * @throws ApiException
+     */
+    public void deleteSamples(Program program, List<String> sampleDbIds) throws ApiException {
+        // create batch of samples, not yet included in brapi client TODO: switch to brapi client when available
+        String programBrAPIBaseUrl = brAPIDAOUtil.getProgramBrAPIBaseUrl(program.getId());
+        String batchDbId = postSamplesBatch(programBrAPIBaseUrl, sampleDbIds);
+
+        // delete samples specified in batch
+        deleteBatch(programBrAPIBaseUrl, batchDbId);
+    }
+
+    /**
+     * Deletes all plates specified in the brapi server
+     * @param program
+     * @param plateDbIds
+     * @throws ApiException
+     */
+    public void deletePlates(Program program, List<String> plateDbIds) throws ApiException {
+        // create batch of plates, not yet included in brapi client TODO: switch to brapi client when available
+        String programBrAPIBaseUrl = brAPIDAOUtil.getProgramBrAPIBaseUrl(program.getId());
+        String batchDbId = postPlatesBatch(programBrAPIBaseUrl, plateDbIds);
+
+        // delete plates specified in batch
+        deleteBatch(programBrAPIBaseUrl, batchDbId);
+    }
+
+
+    private String postSamplesBatch(String programBrAPIBaseUrl, List<String> sampleDbIds) throws ApiException {
+        HttpUrl.Builder requestUrl = HttpUrl.parse(programBrAPIBaseUrl + "/batchDeletes").newBuilder();
+        SampleBatchDeleteRequest requestBody = new SampleBatchDeleteRequest(sampleDbIds);
+        String json = gson.toJson(requestBody);
+        RequestBody body = RequestBody.create(json, MediaType.get("application/json"));
+        HttpUrl url = requestUrl.build();
+        return postBatch(url, body, programBrAPIBaseUrl);
+    }
+
+    private String postPlatesBatch(String programBrAPIBaseUrl, List<String> plateDbIds) throws ApiException {
+        HttpUrl.Builder requestUrl = HttpUrl.parse(programBrAPIBaseUrl + "/batchDeletes").newBuilder();
+        PlateBatchDeleteRequest requestBody = new PlateBatchDeleteRequest(plateDbIds);
+        String json = gson.toJson(requestBody);
+        RequestBody body = RequestBody.create(json, MediaType.get("application/json"));
+        HttpUrl url = requestUrl.build();
+        return postBatch(url, body, programBrAPIBaseUrl);
+    }
+
+    private String postBatch(HttpUrl url, RequestBody body, String programBrAPIBaseUrl) throws ApiException {
+
+        Request brapiRequest = new Request.Builder()
+                .url(url)
+                .post(body)
+                .addHeader("Content-Type", "application/json")
+                .build();
+
+        String jsonResponse = brAPIDAOUtil.makeCallWithResponse(brapiRequest);
+        JsonElement rootElement = JsonParser.parseString(jsonResponse);
+        JsonObject rootObject = rootElement.getAsJsonObject();
+        JsonObject resultObject = rootObject.getAsJsonObject("result");
+
+        // check to see if immediate response or searchResultId
+        if(resultObject.has("batchDeleteDbId")) {
+            return resultObject.get("batchDeleteDbId").getAsString();
+        } else if (resultObject.has("searchResultsDbId")) {
+            // TODO: once api stuff is in client use BrAPIDAOUtil::search to handle retries, for now just request once
+            // brapi server only returns immediate response for batchDeletes so this case won't happen
+            return getBatchDeleteDbIdFromSearchResult(programBrAPIBaseUrl, resultObject.get("searchResultsDbId").getAsString());
+        } else {
+            throw new InternalServerException("Expected batchDeleteDbId or searchResultsDbId but got " + resultObject);
+        }
+    }
+
+    private String getBatchDeleteDbIdFromSearchResult(String programBrAPIBaseUrl, String searchResultDbId) throws ApiException {
+        HttpUrl.Builder requestUrl = HttpUrl.parse(programBrAPIBaseUrl + "/search/batchDeletes/" + searchResultDbId).newBuilder();
+
+        HttpUrl url = requestUrl.build();
+        Request brapiRequest = new Request.Builder()
+                .url(url)
+                .method("GET", null)
+                .addHeader("Content-Type", "application/json")
+                .build();
+
+        String jsonResponse = brAPIDAOUtil.makeCallWithResponse(brapiRequest);
+        JsonElement rootElement = JsonParser.parseString(jsonResponse);
+        JsonObject rootObject = rootElement.getAsJsonObject();
+        JsonObject resultObject = rootObject.getAsJsonObject("result");
+        return resultObject.get("batchDeleteDbId").getAsString();
+    }
+
+    private void deleteBatch(String programBrAPIBaseUrl, String batchDbId) throws ApiException {
+        HttpUrl.Builder requestUrl = HttpUrl.parse(programBrAPIBaseUrl + "/batchDeletes/" + batchDbId).newBuilder();
+        requestUrl.addQueryParameter("hardDelete", "true");
+
+        HttpUrl url = requestUrl.build();
+        Request brapiRequest = new Request.Builder()
+                .url(url)
+                .method("DELETE", null)
+                .addHeader("Content-Type", "application/json")
+                .build();
+
+        brAPIDAOUtil.makeCall(brapiRequest);
+    }
+
+    /**
+     * TODO: temporary minimal model here until brapi client is updated with delete models
+     */
+    public class SampleBatchDeleteRequest {
+        private String batchDeleteType;
+        private Search search;
+
+        public SampleBatchDeleteRequest(List<String> sampleDbIds) {
+            this.batchDeleteType = "samples";
+            this.search = new Search(sampleDbIds);
+        }
+
+        private class Search {
+            private List<String> sampleDbIds;
+
+            public Search(List<String> sampleDbIds) {
+                this.sampleDbIds = sampleDbIds;
+            }
+        }
+    }
+
+    public class PlateBatchDeleteRequest {
+        private String batchDeleteType;
+        private Search search;
+
+        public PlateBatchDeleteRequest(List<String> plateDbIds) {
+            this.batchDeleteType = "plates";
+            this.search = new Search(plateDbIds);
+        }
+
+        private class Search {
+            private List<String> plateDbIds;
+
+            public Search(List<String> plateDbIds) {
+                this.plateDbIds = plateDbIds;
+            }
+        }
+    }
+
 }

src/main/java/org/breedinginsight/model/SampleSubmission.java

@@ -17,6 +17,7 @@
 
 package org.breedinginsight.model;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.google.gson.Gson;
 import com.google.gson.reflect.TypeToken;
@@ -79,6 +80,15 @@ private void parseShipmentForms(JSONB shipmentforms) {
         }
     }
 
+    /**
+     * Should only be deleted when status is not submitted and has no vendor status
+     */
+    @JsonIgnore
+    public boolean isDeletable() {
+        return (this.getSubmitted() == null || (this.getSubmitted() != null && !this.getSubmitted()))
+                && this.getVendorStatus() == null;
+    }
+
     public enum Status {
         NOT_SUBMITTED("NOT SUBMITTED"),
         SUBMITTED("SUBMITTED"),

src/main/java/org/breedinginsight/services/SampleSubmissionService.java

@@ -427,4 +427,28 @@ public Optional<SampleSubmission> updateSubmissionStatus(Program program, UUID s
 
         return submissionOptional;
     }
+
+    /**
+     * Deletes BrAPI plates and submission objects as well as sample submission record in bidb
+     * We do not currently cache plates or samples so don't need to worry about that
+     * @param submissionId sample submission UUID to delete
+     * @exception ApiException if a BrAPI call fails
+     */
+    public void deleteSampleSubmission(Program program, UUID submissionId) throws ApiException {
+        // create a batch of sampleIds and plateIds to delete
+        // get samples with the sample submission xref
+        List<BrAPISample> samples = sampleDAO.readSamplesBySubmissionIds(program, List.of(submissionId.toString()));
+
+        // extract sampleDbIds and plateDbIds to include in batches
+        List<String> sampleDbIds = samples.stream().map(BrAPISample::getSampleDbId).distinct().collect(Collectors.toList());
+        List<String> platesDbIds = samples.stream().map(BrAPISample::getPlateDbId).distinct().collect(Collectors.toList());
+
+        // delete samples and plates BrAPI objects in brapi server
+        sampleDAO.deleteSamples(program, sampleDbIds);
+        sampleDAO.deletePlates(program, platesDbIds);
+
+        // delete sample submission record from bidb
+        submissionDAO.deleteById(submissionId);
+    }
+
 }

src/main/java/org/breedinginsight/utilities/BrAPIDAOUtil.java

@@ -18,6 +18,7 @@
 package org.breedinginsight.utilities;
 
 import io.micronaut.context.annotation.Property;
+
 import io.micronaut.http.HttpResponse;
 import io.micronaut.http.HttpStatus;
 import io.micronaut.http.exceptions.HttpStatusException;
@@ -380,6 +381,28 @@ public <T> List<T> post(List<T> brapiObjects,
         return post(brapiObjects, null, postMethod, null);
     }
 
+    /**
+     * TODO: replace with brapi client methods when available, will do timeout spec from config at that point
+     * @param brapiRequest
+     * @return
+     * @throws ApiException
+     */
+    public String makeCallWithResponse(Request brapiRequest) throws ApiException {
+        OkHttpClient client = new OkHttpClient.Builder()
+                .readTimeout(5, TimeUnit.MINUTES)
+                .build();
+
+        // autoclose Response
+        try (Response response = client.newCall(brapiRequest).execute()) {
+            if (!response.isSuccessful()) {
+                throw new ApiException("Request failed with status code: " + response.code());
+            }
+            return response.body().string();
+        } catch (IOException e) {
+            throw new ApiException(e);
+        }
+    }
+
     public HttpResponse<String> makeCall(Request brapiRequest) {
         // Create OkHttpClient with timeout
         OkHttpClient client = new OkHttpClient.Builder()

src/main/resources/version.properties

@@ -15,5 +15,5 @@
 #
 
 
-version=v1.1.0+899
-versionInfo=https://github.com/Breeding-Insight/bi-api/commit/1d19a829223e99b09324a69b51fa47c6b965de64
+version=v1.1.0+901
+versionInfo=https://github.com/Breeding-Insight/bi-api/commit/9c0fdb5b160215a40e5f2df57a7e922ec0036052