Merge branch 'plantbreeding:brapi-server-v2' into brapi-server-v2

nickpalladino · web-flow · commit 93dcd0561e2d · 2021-06-23T12:07:57.000-04:00
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/model/entity/pheno/ObservationUnitPositionEntity.java b/src/main/java/org/brapi/test/BrAPITestServer/model/entity/pheno/ObservationUnitPositionEntity.java
@@ -28,7 +28,7 @@ public class ObservationUnitPositionEntity extends BrAPIBaseEntity {
 	private ObservationUnitHierarchyLevelEnum levelName;
 	@Column
 	private Integer levelOrder;
-	@OneToMany(mappedBy = "position")
+	@OneToMany(mappedBy = "position", cascade = CascadeType.ALL)
 	private List<ObservationUnitLevelRelationshipEntity> observationLevelRelationships;
 	@Column
 	private String positionCoordinateX;
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/GeoJSONUtility.java b/src/main/java/org/brapi/test/BrAPITestServer/service/GeoJSONUtility.java
@@ -27,12 +27,10 @@ public static GeoJSONEntity convertToEntity(GeoJSON geojson) {
 			entity.setType(POLYGON);
 			// Only handles single polygons, most plots are rectangles
 			Polygon polygon = ((PolygonGeometry) geojson.getGeometry()).getCoordinates();
-			if (polygon.size() == 1) {
-				LinearRing ring = polygon.get(0);
-				for (Position point : ring) {
-					CoordinateEntity pointEntity = convertToEntiy(entity, point);
-					entity.addCoordinate(pointEntity);
-				}
+			LinearRing ring = polygon.get(0);
+			for (Position point : ring) {
+				CoordinateEntity pointEntity = convertToEntiy(entity, point);
+				entity.addCoordinate(pointEntity);
 			}
 		}
 		return entity;
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/SearchQueryBuilder.java b/src/main/java/org/brapi/test/BrAPITestServer/service/SearchQueryBuilder.java
@@ -40,7 +40,7 @@ public Map<String, Object> getParams() {
 	public Class<T> getClazz() {
 		return clazz;
 	}
-
+	
 	public SearchQueryBuilder<T> appendList(List<String> list, String columnName) {
 		String paramName = paramFilter(columnName);
 		if (list != null && !list.isEmpty()) {
@@ -156,6 +156,21 @@ public SearchQueryBuilder<T> appendNumberRange(BigDecimal min, BigDecimal max, S
 		return this;
 	}
 
+	public SearchQueryBuilder<T> appendPersonNamesList(List<String> list, String columnFirst, String columnMiddle, String columnLast) {
+		if (list != null && !list.isEmpty()) {
+			this.params.put("namesList", list);
+			this.query += "AND (" + entityPrefix(columnFirst) + " in :namesList ";
+			this.query += "OR " + entityPrefix(columnMiddle) + " in :namesList ";
+			this.query += "OR " + entityPrefix(columnLast) + " in :namesList ";
+			this.query += "OR concat(" + entityPrefix(columnFirst) + ", ' ', " + entityPrefix(columnMiddle) + ") in :namesList ";
+			this.query += "OR concat(" + entityPrefix(columnFirst) + ", ' ', " + entityPrefix(columnLast) + ") in :namesList ";
+			this.query += "OR concat(" + entityPrefix(columnMiddle) + ", ' ', " + entityPrefix(columnLast) + ") in :namesList ";
+			this.query += "OR concat(" + entityPrefix(columnFirst) + ", ' ', " + entityPrefix(columnMiddle) + ", ' ', " + entityPrefix(columnLast) + ") in :namesList ";
+			this.query += ") ";
+		}
+		return this;
+	}
+
 	public SearchQueryBuilder<T> appendGeoJSONArea(GeoJSONSearchArea area) {
 		// if (single != null && !single.isEmpty()) {
 		// this.query += "AND " + entityPrefix(columnName) + " = :" + columnName + " ";
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/core/LocationService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/core/LocationService.java
@@ -49,19 +49,23 @@ public List<Location> findLocations(String locationDbId, String locationType, St
 
 	public List<Location> findLocations(LocationSearchRequest request, Metadata metadata) {
 		Pageable pageReq = PagingUtility.getPageRequest(metadata);
-		SearchQueryBuilder<LocationEntity> searchQuery = new SearchQueryBuilder<LocationEntity>(LocationEntity.class)
-				.withExRefs(request.getExternalReferenceIDs(), request.getExternalReferenceSources())
-				.appendList(request.getAbbreviations(), "abbreviaion")
-				.appendList(request.getCountryCodes(), "countrycode")
-				.appendList(request.getCountryNames(), "countryname")
-				.appendList(request.getInstituteAddresses(), "instituteaddress")
-				.appendList(request.getInstituteNames(), "institutename")
+		SearchQueryBuilder<LocationEntity> searchQuery = new SearchQueryBuilder<LocationEntity>(LocationEntity.class);
+
+		if (request.getAltitudeMin() != null || request.getAltitudeMax() != null || request.getCoordinates() != null) {
+			searchQuery = searchQuery.join("coordinates.coordinates", "coordinates");
+			searchQuery = searchQuery.appendNumberRange(request.getAltitudeMin(), request.getAltitudeMax(), "*coordinates.altitude")
+			.appendGeoJSONArea(request.getCoordinates());
+		}
+		searchQuery = searchQuery.withExRefs(request.getExternalReferenceIDs(), request.getExternalReferenceSources())
+				.appendList(request.getAbbreviations(), "abbreviation")
+				.appendList(request.getCountryCodes(), "countryCode")
+				.appendList(request.getCountryNames(), "countryName")
+				.appendList(request.getInstituteAddresses(), "instituteAddress")
+				.appendList(request.getInstituteNames(), "instituteName")
 				.appendList(request.getLocationDbIds(), "id")
 				.appendList(request.getLocationNames(), "locationName")
-				.appendList(request.getLocationTypes(), "locationType")
-				.appendNumberRange(request.getAltitudeMin(), request.getAltitudeMax(), "altitude")
-				.appendGeoJSONArea(request.getCoordinates());
-
+				.appendList(request.getLocationTypes(), "locationType");
+				
 		Page<LocationEntity> entityPage = locationRepository.findAllBySearch(searchQuery, pageReq);
 
 		List<Location> data = entityPage.map(this::convertFromEntity).getContent();
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/core/ProgramService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/core/ProgramService.java
@@ -64,7 +64,7 @@ public List<Program> findPrograms(ProgramSearchRequest request, Metadata metadat
 				.appendList(request.getAbbreviations(), "abbreviation")
 				.appendList(request.getCommonCropNames(), "crop.cropName")
 				.appendList(request.getLeadPersonDbIds(), "leadPerson.id")
-				.appendList(request.getLeadPersonNames(), "leadPerson.lastName")
+				.appendPersonNamesList(request.getLeadPersonNames(), "leadPerson.firstName", "leadPerson.middleName", "leadPerson.lastName")
 				.appendList(request.getObjectives(), "objective").appendList(request.getProgramDbIds(), "id")
 				.appendList(request.getProgramNames(), "name");
 
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/core/StudyService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/core/StudyService.java
@@ -125,7 +125,7 @@ public List<Study> findStudies(StudySearchRequest request, Metadata metaData) {
 			searchQuery = searchQuery.join("observationUnits", "obsunit");
 		}
 		if (request.getObservationVariableDbIds() != null || request.getObservationVariableNames() != null) {
-			searchQuery = searchQuery.join("*ou.observations", "observation");
+			searchQuery = searchQuery.join("*obsunit.observations", "observation");
 		}
 
 		searchQuery = searchQuery.withExRefs(request.getExternalReferenceIDs(), request.getExternalReferenceSources())
@@ -141,7 +141,7 @@ public List<Study> findStudies(StudySearchRequest request, Metadata metaData) {
 				.appendList(request.getSeasonDbIds(), "*season.id").appendList(request.getStudyCodes(), "studyCode")
 				.appendList(request.getStudyDbIds(), "id").appendList(request.getStudyNames(), "studyName")
 				.appendList(request.getStudyPUIs(), "studyPUI").appendList(request.getStudyTypes(), "studyType")
-				.appendList(request.getTrialDbIds(), "trial.id").appendList(request.getTrialNames(), "trial.name")
+				.appendList(request.getTrialDbIds(), "trial.id").appendList(request.getTrialNames(), "trial.trialName")
 				.withSort(getSortByField(request.getSortBy()), request.getSortOrder());
 
 		Page<StudyEntity> studiesPage = studyRepository.findAllBySearch(searchQuery, pageReq);
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/geno/CallSetService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/geno/CallSetService.java
@@ -62,7 +62,7 @@ public List<CallSetEntity> findCallSetEntities(CallSetsSearchRequest request, Me
 				.appendList(request.getGermplasmDbIds(), "sample.germplasm.id")
 				.appendList(request.getGermplasmNames(), "sample.germplasm.germplasmName")
 				.appendList(request.getSampleDbIds(), "sample.id")
-				.appendList(request.getSampleNames(), "sample.name");
+				.appendList(request.getSampleNames(), "sample.sampleName");
 
 		Page<CallSetEntity> page = callSetRepository.findAllBySearch(searchQuery, pageReq);
 		PagingUtility.calculateMetaData(metadata, page);
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/geno/SampleService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/geno/SampleService.java
@@ -67,11 +67,11 @@ public List<Sample> findSamples(@Valid SampleSearchRequest request, Metadata met
 		SearchQueryBuilder<SampleEntity> searchQuery = new SearchQueryBuilder<SampleEntity>(SampleEntity.class)
 				.withExRefs(request.getExternalReferenceIDs(), request.getExternalReferenceSources())
 				.appendList(request.getGermplasmDbIds(), "germplasm.id")
-				.appendList(request.getGermplasmNames(), "germplasm.name")
+				.appendList(request.getGermplasmNames(), "germplasm.germplasmName")
 				.appendList(request.getObservationUnitDbIds(), "observationUnit.id")
 				.appendList(request.getPlateDbIds(), "plate.id").appendList(request.getSampleDbIds(), "id")
 				.appendList(request.getStudyDbIds(), "observationUnit.study.id")
-				.appendList(request.getStudyNames(), "observationUnit.study.name");
+				.appendList(request.getStudyNames(), "observationUnit.study.studyName");
 
 		Page<SampleEntity> page = sampleRepository.findAllBySearch(searchQuery, pageReq);
 		List<Sample> samples = page.map(this::convertFromEntity).getContent();
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/germ/GermplasmAttributeValueService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/germ/GermplasmAttributeValueService.java
@@ -73,7 +73,7 @@ public List<GermplasmAttributeValue> findGermplasmAttributeValues(
 						.appendList(request.getTraitClasses(), "attribute.trait.traitClass")
 						.appendList(request.getTraitDbIds(), "attribute.trait.id")
 						.appendList(request.getGermplasmDbIds(), "germplasm.id")
-						.appendList(request.getGermplasmNames(), "germplasm.name");
+						.appendList(request.getGermplasmNames(), "germplasm.germplasmName");
 
 		Page<GermplasmAttributeValueEntity> page = attributeValueRepository.findAllBySearch(searchQuery, pageReq);
 		List<GermplasmAttributeValue> attributeValues = page.map(this::convertFromEntity).getContent();
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/germ/GermplasmService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/germ/GermplasmService.java
@@ -129,7 +129,7 @@ public List<Germplasm> findGermplasm(@Valid GermplasmSearchRequest request, Meta
 		if (request.getStudyDbIds() != null || request.getStudyNames() != null) {
 			searchQuery = searchQuery.join("observationUnits", "obsunit")
 					.appendList(request.getStudyDbIds(), "*obsunit.study.id")
-					.appendList(request.getStudyNames(), "*obsunit.study.name");
+					.appendList(request.getStudyNames(), "*obsunit.study.studyName");
 		}
 		if (request.getSynonyms() != null) {
 			searchQuery = searchQuery.join("synonyms", "synonym")
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationService.java
@@ -129,49 +129,49 @@ public List<Observation> findObservations(@Valid ObservationSearchRequest reques
 					.appendEnumList(
 							request.getObservationLevels().stream().filter(r -> r.getLevelName() != null)
 									.map(r -> r.getLevelName()).collect(Collectors.toList()),
-							"observationUnit.position.level.name")
+							"observationUnit.position.level.levelName")
 					.appendList(
 							request.getObservationLevels().stream().filter(r -> r.getLevelCode() != null)
 									.map(r -> r.getLevelCode()).collect(Collectors.toList()),
-							"observationUnit.position.level.code")
+							"observationUnit.position.level.levelCode")
 					.appendIntList(
 							request.getObservationLevels().stream().filter(r -> r.getLevelOrder() != null)
 									.map(r -> r.getLevelOrder()).collect(Collectors.toList()),
-							"observationUnit.position.level.order");
+							"observationUnit.position.level.levelOrder");
 		}
 		if (request.getObservationLevelRelationships() != null) {
 			searchQuery = searchQuery.join("observationUnit.position.levelRelationships", "levelRelationship")
 					.appendEnumList(
 							request.getObservationLevelRelationships().stream().filter(r -> r.getLevelName() != null)
 									.map(r -> r.getLevelName()).collect(Collectors.toList()),
-							"levelRelationship.name")
+							"levelRelationship.levelName")
 					.appendList(
 							request.getObservationLevelRelationships().stream().filter(r -> r.getLevelCode() != null)
 									.map(r -> r.getLevelCode()).collect(Collectors.toList()),
-							"levelRelationship.code")
+							"levelRelationship.levelCode")
 					.appendIntList(
 							request.getObservationLevelRelationships().stream().filter(r -> r.getLevelOrder() != null)
 									.map(r -> r.getLevelOrder()).collect(Collectors.toList()),
-							"levelRelationship.order");
+							"levelRelationship.levelOrder");
 		}
 		searchQuery = searchQuery.withExRefs(request.getExternalReferenceIDs(), request.getExternalReferenceSources())
 				.appendList(request.getGermplasmDbIds(), "observationUnit.germplasm.id")
-				.appendList(request.getGermplasmNames(), "observationUnit.germplasm.name")
+				.appendList(request.getGermplasmNames(), "observationUnit.germplasm.germplasmName")
 				.appendList(request.getLocationDbIds(), "observationUnit.study.location.id")
-				.appendList(request.getLocationNames(), "observationUnit.study.location.name")
+				.appendList(request.getLocationNames(), "observationUnit.study.location.locationName")
 				.appendList(request.getObservationDbIds(), "id")
 				.appendList(request.getObservationUnitDbIds(), "observationUnit.id")
 				.appendDateRange(request.getObservationTimeStampRangeStart(), request.getObservationTimeStampRangeEnd(),
 						"observationTimeStamp")
 				.appendList(request.getObservationVariableDbIds(), "observationVariable.id")
 				.appendList(request.getObservationVariableNames(), "observationVariable.name")
 				.appendList(request.getProgramDbIds(), "observationUnit.study.trial.program.id")
-				.appendList(request.getProgramNames(), "observationUnit.study.trial.program.name")
+				.appendList(request.getProgramNames(), "observationUnit.study.trial.program.programName")
 				.appendList(request.getSeasonDbIds(), "season.id")
 				.appendList(request.getStudyDbIds(), "observationUnit.study.id")
-				.appendList(request.getStudyNames(), "observationUnit.study.name")
+				.appendList(request.getStudyNames(), "observationUnit.study.studyName")
 				.appendList(request.getTrialDbIds(), "observationUnit.study.trial.id")
-				.appendList(request.getTrialNames(), "observationUnit.study.trial.name");
+				.appendList(request.getTrialNames(), "observationUnit.study.trial.trialName");
 
 		Page<ObservationEntity> page = observationRepository.findAllBySearch(searchQuery, pageReq);
 		List<Observation> observations = page.map(this::convertFromEntity).getContent();
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationUnitService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationUnitService.java

Original file line number	Diff line number	Diff line change
`@@ -129,7 +129,7 @@ public List<Germplasm> findGermplasm(@Valid GermplasmSearchRequest request, Meta`
`129`	`129`	`if (request.getStudyDbIds() != null \|\| request.getStudyNames() != null) {`
`130`	`130`	`searchQuery = searchQuery.join("observationUnits", "obsunit")`
`131`	`131`	`.appendList(request.getStudyDbIds(), "*obsunit.study.id")`
`132`		`- .appendList(request.getStudyNames(), "*obsunit.study.name");`
	`132`	`+ .appendList(request.getStudyNames(), "*obsunit.study.studyName");`
`133`	`133`	`}`
`134`	`134`	`if (request.getSynonyms() != null) {`
`135`	`135`	`searchQuery = searchQuery.join("synonyms", "synonym")`