Merge pull request #448 from mcneilco/release/2023.3.x

⬆️ Upmerge release/2023.3.x to release/2023.4.x

src/main/java/com/labsynch/labseer/api/ApiExperimentController.java

@@ -44,6 +44,7 @@
 import com.labsynch.labseer.dto.TsvLoaderResponseDTO;
 import com.labsynch.labseer.exceptions.ErrorMessage;
 import com.labsynch.labseer.exceptions.NotFoundException;
+import com.labsynch.labseer.exceptions.TooManyResultsException;
 import com.labsynch.labseer.exceptions.UniqueNameException;
 import com.labsynch.labseer.service.AnalysisGroupService;
 import com.labsynch.labseer.service.AnalysisGroupValueService;
@@ -1634,20 +1635,19 @@ public ResponseEntity<java.lang.String> jsonFindExperimentByNameGet(@RequestPara
 	@RequestMapping(value = "/protocol/{codeName}", method = RequestMethod.GET, headers = "Accept=application/json")
 	@ResponseBody
 	public ResponseEntity<java.lang.String> jsonFindExperimentsByProtocolCodeName(
-			@PathVariable("codeName") String codeName, @RequestParam(value = "with", required = false) String with) {
+			@PathVariable("codeName") String codeName, @RequestParam(value = "projects", required = false) List<String> projects, @RequestParam(value = "with", required = false) String with) {
 		HttpHeaders headers = new HttpHeaders();
 		headers.add("Content-Type", "application/json; charset=utf-8");
-		List<Protocol> protocols = Protocol.findProtocolsByCodeNameEqualsAndIgnoredNot(codeName, true).getResultList();
-		if (protocols.size() == 1) {
+		try {
+			Collection<Experiment> experiments = experimentService.findExperimentsByProtocolCodeName(codeName, projects);
 			return new ResponseEntity<String>(
-					Experiment.toJsonArrayStub(Experiment.findExperimentsByProtocol(protocols.get(0)).getResultList()),
+					Experiment.toJsonArrayStub(experiments),
 					headers, HttpStatus.OK);
-		} else if (protocols.size() > 1) {
-			logger.error("ERROR: multiple protocols found with the same code name");
-			return new ResponseEntity<String>("[ ]", headers, HttpStatus.CONFLICT);
-		} else {
-			logger.warn("WARN: no protocols found with the query code name");
+		} catch (NoResultException e) {
 			return new ResponseEntity<String>("[ ]", headers, HttpStatus.NOT_FOUND);
+
+		} catch (TooManyResultsException e) {
+			return new ResponseEntity<String>("[ ]", headers, HttpStatus.CONFLICT);
 		}
 	}
 

src/main/java/com/labsynch/labseer/domain/SaltForm.java

@@ -29,7 +29,9 @@
 import javax.persistence.criteria.JoinType;
 import javax.persistence.criteria.ParameterExpression;
 import javax.persistence.criteria.Predicate;
+import javax.persistence.criteria.Expression;
 import javax.persistence.criteria.Root;
+import javax.persistence.criteria.Order;
 import javax.validation.constraints.Size;
 
 import com.labsynch.labseer.dto.SearchFormDTO;
@@ -239,6 +241,7 @@ public static TypedQuery<SaltForm> findSaltFormsByMeta(SearchFormDTO searchParam
 
 		Predicate[] predicates = new Predicate[0];
 		List<Predicate> predicateList = new ArrayList<Predicate>();
+		List<Order> orderList = new ArrayList<Order>();
 
 		if (searchParams.getChemist() != null && !searchParams.getChemist().equals("anyone")) {
 			logger.debug("incoming chemist :" + searchParams.getChemist().toString());
@@ -282,12 +285,34 @@ public static TypedQuery<SaltForm> findSaltFormsByMeta(SearchFormDTO searchParam
 			List<String> corpNames = searchParams.getFormattedCorpNameList();
 			logger.debug("incoming corpNameList :" + corpNames.toString());
 			ArrayList<Predicate> corpNameLikePredicates = new ArrayList<Predicate>();
+			Expression<Double> maxSimilarity = null;
 			for (String corpName : corpNames) {
 				Predicate predicate = criteriaBuilder.like(saltFormParent.get("corpName"), '%' + corpName);
 				corpNameLikePredicates.add(predicate);
+				// Using pg_trgm.similarity to order results based on how similar the value is to
+				// the formatted corporate names.
+				Expression<Double> similarity = criteriaBuilder.function(
+					"similarity",
+					Double.class,
+					saltFormParent.get("corpName"),
+					criteriaBuilder.literal(corpName)
+				);
+				if (maxSimilarity == null) {
+					maxSimilarity = similarity;
+				}
+				else {
+					maxSimilarity = criteriaBuilder.selectCase()
+						.when(criteriaBuilder.greaterThan(similarity, maxSimilarity), similarity)
+						.otherwise(maxSimilarity)
+						.as(Double.class);
+				}
 			}
 			Predicate predicate = criteriaBuilder.or(corpNameLikePredicates.toArray(new Predicate[0]));
 			predicateList.add(predicate);
+			if (maxSimilarity != null) {
+				// Rows with a higher similarity will be ordered first.
+				orderList.add(criteriaBuilder.desc(maxSimilarity));
+			}
 		}
 		if (searchParams.getAlias() != null && !searchParams.getAlias().equals("")) {
 			Predicate predicate = null;
@@ -335,6 +360,7 @@ public static TypedQuery<SaltForm> findSaltFormsByMeta(SearchFormDTO searchParam
 
 		predicates = predicateList.toArray(predicates);
 		criteria.where(criteriaBuilder.and(predicates));
+		criteria.orderBy(orderList);
 		TypedQuery<SaltForm> q = em.createQuery(criteria);
 
 		if (searchParams.getMaxSynthDate() != null) {

src/main/java/com/labsynch/labseer/dto/SearchFormReturnDTO.java

@@ -15,7 +15,7 @@
 
 public class SearchFormReturnDTO {
 
-	private Collection<SearchCompoundReturnDTO> foundCompounds = new HashSet<SearchCompoundReturnDTO>();
+	private Collection<SearchCompoundReturnDTO> foundCompounds = new ArrayList<SearchCompoundReturnDTO>();
 
 	private boolean lotsWithheld;
 

src/main/java/com/labsynch/labseer/service/ExperimentService.java

@@ -51,6 +51,10 @@ public Collection<JSTreeNodeDTO> getExperimentNodesByProtocolTree(
 	public Collection<Experiment> findExperimentsByMetadataJson(
 			List<StringCollectionDTO> metaDataList);
 
+
+    public Collection<Experiment> findExperimentsByProtocolCodeName(String query, List<String> projects)
+    throws TooManyResultsException;
+
 	public Collection<Experiment> findExperimentsByGenericMetaDataSearch(String query, String userName, Boolean includeDeleted)
 			throws TooManyResultsException;
 

src/main/java/com/labsynch/labseer/service/ExperimentServiceImpl.java

@@ -1118,6 +1118,45 @@ public Collection<Experiment> findExperimentsByGenericMetaDataSearch(String quer
 
 	}
 
+	public Collection<Experiment> findExperimentsByProtocolCodeName(String codeName, List<String> projects)
+			throws TooManyResultsException, NoResultException {
+		List<Protocol> protocols = Protocol.findProtocolsByCodeNameEqualsAndIgnoredNot(codeName, true).getResultList();
+
+		if (protocols.size() > 1) {
+			logger.error("ERROR: multiple protocols found with the same code name");
+			throw new TooManyResultsException("ERROR: multiple protocols found with the same code name");
+		} else if (protocols.size() < 1) {
+			logger.warn("WARN: no protocols found with the query code name");
+			throw new NoResultException("WARN: no protocols found with the query code name");
+		}
+
+		Collection<Experiment> rawResults = Experiment.findExperimentsByProtocol(protocols.get(0)).getResultList();
+		if (propertiesUtilService.getRestrictExperiments()) {
+			projects.add("unassigned");
+			Collection<Experiment> results = new HashSet<Experiment>();
+			for (Experiment rawResult : rawResults) {
+				String experimentProject = null;
+				for (ExperimentState state : rawResult.getLsStates()) {
+					if (!state.isIgnored() && !state.isDeleted()) {
+						for (ExperimentValue value : state.getLsValues()) {
+							if (value.getLsKind().equals("project") && !value.getDeleted() && !value.getIgnored()) {
+								experimentProject = value.getCodeValue();
+								break;
+							}
+						}
+					}
+				}
+				if (projects.contains(experimentProject)) {
+					results.add(rawResult);
+				}
+			}
+			return results;
+		} else {
+			return rawResults;
+		}
+
+	}
+
 	@Override
 	public Collection<Experiment> findExperimentsByGenericMetaDataSearch(String queryString, List<String> projects, Boolean includeDeleted)
 			throws TooManyResultsException {

src/main/java/com/labsynch/labseer/service/SearchFormServiceImpl.java

@@ -613,7 +613,7 @@ public SearchFormReturnDTO findQuerySaltForms(SearchFormDTO searchParams) throws
 
 	private SearchFormReturnDTO filterSearchResultsByProject(SearchFormReturnDTO searchResults, List<String> projects) {
 		if (!searchResults.getFoundCompounds().isEmpty()) {
-			Collection<SearchCompoundReturnDTO> filteredFoundCompounds = new HashSet<SearchCompoundReturnDTO>();
+			Collection<SearchCompoundReturnDTO> filteredFoundCompounds = new ArrayList<SearchCompoundReturnDTO>();
 			for (SearchCompoundReturnDTO foundCompound : searchResults.getFoundCompounds()) {
 				List<SearchLotDTO> filteredFoundLots = new ArrayList<SearchLotDTO>();
 				for (SearchLotDTO foundLot : foundCompound.getLotIDs()) {