Merge pull request #46 from Breeding-Insight/bug/BI-2422

BI-2422 - Add paging support for GET /observations/table

Author: nickpalladino

src/main/java/io/swagger/api/pheno/ObservationsApi.java

@@ -154,6 +154,8 @@ ResponseEntity<ObservationTableResponse> observationsTableGet(
 			@ApiParam(value = "observationUnitLevelRelationshipOrder") @Valid @RequestParam(value = "observationUnitLevelRelationshipOrder", required = false) String observationUnitLevelRelationshipOrder,
 			@ApiParam(value = "observationUnitLevelRelationshipCode") @Valid @RequestParam(value = "observationUnitLevelRelationshipCode", required = false) String observationUnitLevelRelationshipCode,
 			@ApiParam(value = "observationUnitLevelRelationshipDbId") @Valid @RequestParam(value = "observationUnitLevelRelationshipDbId", required = false) String observationUnitLevelRelationshipDbId,
+			@ApiParam(value = "page") @Valid @RequestParam(value = "page", required = false) Integer page,
+			@ApiParam(value = "pageSize") @Valid @RequestParam(value = "pageSize", required = false) Integer pageSize,
 			@ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
 			throws BrAPIServerException;
 

src/main/java/org/brapi/test/BrAPITestServer/controller/pheno/ObservationsApiController.java

@@ -173,11 +173,14 @@ public ResponseEntity observationsTableGet(@RequestHeader(value = "Accept", requ
 			@RequestParam(value = "observationUnitLevelRelationshipOrder", required = false) String observationUnitLevelRelationshipOrder,
 			@RequestParam(value = "observationUnitLevelRelationshipCode", required = false) String observationUnitLevelRelationshipCode,
 			@RequestParam(value = "observationUnitLevelRelationshipDbId", required = false) String observationUnitLevelRelationshipDbId,
+		    @RequestParam(value = "page", required = false) Integer page,
+		    @RequestParam(value = "pageSize", required = false) Integer pageSize,
 			@RequestHeader(value = "Authorization", required = false) String authorization)
 			throws BrAPIServerException {
 
 		log.debug("Request: " + request.getRequestURI());
 		validateSecurityContext(request, "ROLE_ANONYMOUS", "ROLE_USER");
+		Metadata metadata = generateMetaDataTemplate(page, pageSize);
 
 		String sep = "";
 		if ("text/csv".equals(accept)) {
@@ -193,7 +196,8 @@ public ResponseEntity observationsTableGet(@RequestHeader(value = "Accept", requ
 			SearchRequestEntity request = searchService.findById(searchResultsDbId);
 			if (request != null) {
 				ObservationSearchRequest body = request.getParameters(ObservationSearchRequest.class);
-				data = observationService.findObservationsTable(body);
+				//TODO: revisit paging for this case; metadata=null
+				data = observationService.findObservationsTable(body, null);
 			} else {
 				return responseAccepted(searchResultsDbId);
 			}
@@ -204,11 +208,11 @@ public ResponseEntity observationsTableGet(@RequestHeader(value = "Accept", requ
 					observationUnitLevelName, observationUnitLevelOrder, observationUnitLevelCode,
 					observationUnitLevelRelationshipName, observationUnitLevelRelationshipOrder,
 					observationUnitLevelRelationshipCode, observationUnitLevelRelationshipDbId,
-					observationTimeStampRangeStart, observationTimeStampRangeEnd, searchResultsDbId);
+					observationTimeStampRangeStart, observationTimeStampRangeEnd, searchResultsDbId, metadata);
 		}
 
 		if (sep.isEmpty()) {
-			return responseOK(new ObservationTableResponse(), data);
+			return responseOK(new ObservationTableResponse(), data, metadata);
 		} else {
 			String textTable = observationService.getObservationTableText(data, sep);
 			return new ResponseEntity<String>(textTable, HttpStatus.OK);

src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationService.java

@@ -1,6 +1,7 @@
 package org.brapi.test.BrAPITestServer.service.pheno;
 
 import io.swagger.model.Metadata;
+import io.swagger.model.Pagination;
 import io.swagger.model.pheno.*;
 import jakarta.validation.Valid;
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerDbIdNotFoundException;
@@ -22,11 +23,8 @@
 import org.springframework.http.HttpStatus;
 import org.springframework.stereotype.Service;
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 import java.util.Map.Entry;
-import java.util.Optional;
 import java.util.stream.Collectors;
 
 @Service
@@ -137,27 +135,30 @@ public ObservationTable findObservationsTable(String observationUnitDbId, String
 			String observationUnitLevelOrder, String observationUnitLevelCode,
 			String observationUnitLevelRelationshipName, String observationUnitLevelRelationshipOrder,
 			String observationUnitLevelRelationshipCode, String observationUnitLevelRelationshipDbId,
-			String observationTimeStampRangeStart, String observationTimeStampRangeEnd, String searchResultsDbId)
+			String observationTimeStampRangeStart, String observationTimeStampRangeEnd, String searchResultsDbId, Metadata metadata)
 			throws BrAPIServerException {
 		ObservationSearchRequest obsRequest = buildObservationsSearchRequest(null, observationUnitDbId, germplasmDbId,
 				observationVariableDbId, studyDbId, locationDbId, trialDbId, programDbId, seasonDbId,
 				observationUnitLevelName, observationUnitLevelOrder, observationUnitLevelCode,
 				observationTimeStampRangeStart, observationTimeStampRangeEnd, observationUnitLevelRelationshipName,
 				observationUnitLevelRelationshipOrder, observationUnitLevelRelationshipCode,
 				observationUnitLevelRelationshipDbId, null, null, null, null);
-		return findObservationsTable(obsRequest);
+		return findObservationsTable(obsRequest, metadata);
 	}
 
-	public ObservationTable findObservationsTable(ObservationSearchRequest obsRequest) {
-		Page<ObservationEntity> observations = findObservationEntities(obsRequest, null);
+	public ObservationTable findObservationsTable(ObservationSearchRequest obsRequest, Metadata metadata) {
+		Page<ObservationEntity> page = findObservationEntities(obsRequest, metadata);
+		log.debug("converting "+page.getSize()+" entities");
 
-		List<ObservationVariableEntity> variables = observations.stream().map(obs -> obs.getObservationVariable())
-				.filter(vid -> vid != null).distinct().collect(Collectors.toList());
+		List<ObservationVariableEntity> variables = page.stream().map(ObservationEntity::getObservationVariable)
+				.filter(Objects::nonNull).distinct().collect(Collectors.toList());
 
 		ObservationTable table = new ObservationTable();
-		table.setData(buildDataMatrix(observations, variables));
+		table.setData(buildDataMatrix(page, variables));
 		table.setHeaderRow(buildHeaderRow());
 		table.setObservationVariables(variables.stream().map(this::convertVariables).collect(Collectors.toList()));
+		log.debug("done converting entities");
+		PagingUtility.calculateMetaData(metadata, page);
 		return table;
 	}