Merge pull request #97 from KPMP/develop

Release v2.1

README.md

@@ -42,3 +42,8 @@ If you have already followed these steps and are still having trouble connecting
 1. Start up your atlas/knowledge-environment server
 2. Open a tool like GraphQLPlayground and connect to "http://localhost:3030/graphql"
 3. Write and execute your query
+
+# Buyer BEWARE
+Notes to ourselves about the non-dynamic nature of some things in the app (this is not exhaustive)
+
+1. The endpoint `getDataTypeInformationByParticipant` is only partially dynamic. If we add new data types to the Spatial Viewer, it will pick those up without an issue, BUT if/when we add new data types to the Explorer, we will need to update the code that gets counts for data types in Explorer to include the new one.

src/main/java/org/kpmp/Query.java

@@ -13,14 +13,14 @@
 import org.kpmp.dataSummary.AtlasRepoSummaryResult;
 import org.kpmp.dataSummary.DataSummaryService;
 import org.kpmp.dataSummary.DataTypeSummary;
-import org.kpmp.gene.GeneService;
-import org.kpmp.gene.MyGeneInfoHit;
 import org.kpmp.geneExpression.RTExpressionByTissueType;
 import org.kpmp.geneExpression.RTExpressionData;
 import org.kpmp.geneExpression.RTExpressionDataService;
 import org.kpmp.geneExpressionSummary.GeneExpressionSummary;
 import org.kpmp.geneExpressionSummary.GeneExpressionSummaryService;
 import org.kpmp.participant.ParticipantDataTypeSummary;
+import org.kpmp.participant.ParticipantRepoDataTypeInformation;
+import org.kpmp.participant.ParticipantRepoDataTypeSummary;
 import org.kpmp.participant.ParticipantService;
 import org.kpmp.participant.ParticipantSummaryDataset;
 import org.kpmp.participant.ParticipantTissueTypeSummary;
@@ -36,7 +36,6 @@
 @Component
 public class Query implements GraphQLQueryResolver {
 
-	private GeneService geneService;
 	private AutocompleteService autocompleteService;
 	private CellTypeService cellTypeService;
 	private GeneExpressionSummaryService geneExpressionSummaryService;
@@ -48,12 +47,11 @@ public class Query implements GraphQLQueryResolver {
 	private Logger logger = LoggerFactory.getLogger(Query.class);
 
 	@Autowired
-	public Query(GeneService geneService, AutocompleteService autocompleteService, CellTypeService cellTypeService,
+	public Query(AutocompleteService autocompleteService, CellTypeService cellTypeService,
 			UmapDataService umapService, GeneExpressionSummaryService geneExpressionSummaryService,
 			DataSummaryService dataSummaryService, ClusterHierarchyService clusterHierarchyService,
 			RTExpressionDataService rtExpressionDataService, ParticipantService participantService) {
 
-		this.geneService = geneService;
 		this.autocompleteService = autocompleteService;
 		this.cellTypeService = cellTypeService;
 		this.umapService = umapService;
@@ -64,10 +62,6 @@ public Query(GeneService geneService, AutocompleteService autocompleteService, C
 		this.participantService = participantService;
 	}
 
-	public List<MyGeneInfoHit> genes(String symbol) throws IOException, Exception {
-		return geneService.querySymbolAndAlias(symbol);
-	}
-
 	public List<AutocompleteResult> autocomplete(String searchTerm) throws IOException, Exception {
 		return autocompleteService.query(searchTerm);
 	}
@@ -152,6 +146,10 @@ public ParticipantDataTypeSummary getDataTypeInformationByParticipant(String red
 		return participantService.getExperimentCounts(redcapId);
 	}
 
+	public ParticipantRepoDataTypeSummary getRepoDataTypeInformationByParticipant(String redcapId) {
+		return participantService.getDataTypeCounts(redcapId);
+	}
+
 	public ParticipantSummaryDataset participantSummaryDataset(String redcap_id) throws Exception {
 		try {
 			return participantService.getParticipantSummaryDataset(redcap_id);
@@ -168,6 +166,15 @@ public ParticipantSummaryDataset participantClinicalDataset(String redcap_id) th
 		return this.participantSummaryDataset(redcap_id);
 	}
 
+	public ParticipantRepoDataTypeInformation getTotalParticipantFilesCount(String redcap_id) throws Exception {
+		try {
+			return this.participantService.getTotalFilesCount(redcap_id);
+		} catch (Exception e) {
+			logger.error(e.getMessage());
+			throw e;
+		}
+	}
+
 	public List<ParticipantTissueTypeSummary> getTissueTypeSummaryData() throws Exception {
 		try {
 			return participantService.getTissueData();

src/main/java/org/kpmp/cache/CacheController.java

@@ -0,0 +1,34 @@
+package org.kpmp.cache;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.cache.CacheManager;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.ResponseBody;
+
+import java.util.Collection;
+
+@Controller
+public class CacheController {
+
+    @Autowired
+    private CacheManager cacheManager;
+
+    @RequestMapping(value = "/v1/clearCache", method = RequestMethod.GET)
+    public @ResponseBody CacheResponse clearCache(){
+        Collection<String> cacheNames = cacheManager.getCacheNames();
+        CacheResponse clearCacheResponse = new CacheResponse();
+        clearCacheResponse.setMessage("Caches successfully cleared!");
+        for(String name:cacheNames){
+            if (cacheManager.getCache(name) != null) {
+                cacheManager.getCache(name).clear();
+            } else {
+                clearCacheResponse.setMessage("There was a problem getting the " + name + " cache.");
+                break;
+            }
+        }
+        clearCacheResponse.setCacheNames(cacheNames);
+        return clearCacheResponse;
+    }
+}

src/main/java/org/kpmp/cache/CacheResponse.java

@@ -0,0 +1,25 @@
+package org.kpmp.cache;
+
+import java.util.Collection;
+
+public class CacheResponse {
+
+        private String message;
+        private Collection<String> cacheNames;
+
+        public String getMessage() {
+            return message;
+        }
+
+        public void setMessage(String message) {
+            this.message = message;
+        }
+
+        public Collection<String> getCacheNames() {
+            return cacheNames;
+        }
+
+        public void setCacheNames(Collection<String> cacheNames) {
+            this.cacheNames = cacheNames;
+        }
+}

src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryLinkInformation.java

@@ -38,12 +38,11 @@ public int hashCode() {
 	public boolean equals(Object obj) {
 		if (obj instanceof AtlasRepoSummaryLinkInformation) {
 			final AtlasRepoSummaryLinkInformation other = (AtlasRepoSummaryLinkInformation) obj;
-			return new EqualsBuilder().append(linkType, other.getLinkType()).append(linkValue, other.getLinkValue())
-					.isEquals();
-		} else {
+			return new EqualsBuilder().append(linkType, other.getLinkType()).append(linkValue, other.getLinkValue()).isEquals();
+		}
+		else {
 			return false;
 		}
-
 	}
 
 }

src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java

@@ -1,5 +1,7 @@
 package org.kpmp.dataSummary;
 
+import java.util.List;
+
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
@@ -35,4 +37,22 @@ public interface DataSummaryRepository extends CrudRepository<DataSummaryValue,
 	@Cacheable("dataParticipantSvLinkDataTypeCount")
 	@Query(value = "SELECT count(*) from sv_link_v WHERE data_type= :data_type AND redcap_id= :redcap_id", nativeQuery = true)
 	Integer getParticipantSvLinkDataTypeCount(@Param("redcap_id") String redcapId, @Param("data_type") String dataType);
+
+	@Cacheable("dataParticipantRepoFileDataTypeCount")
+	@Query(value = "SELECT count(*) from (SELECT distinct(dl_file_id) FROM repo_file_v WHERE data_type= :data_type AND redcap_id= :redcap_id) a", nativeQuery = true)
+	Integer getParticipantRepoFileDataTypeCount(@Param("redcap_id") String redcapId, @Param("data_type") String dataType);
+
+    @Cacheable("repoDataTypes")
+	@Query(value = "SELECT distinct(data_type) FROM repository_summary_v ORDER BY data_type ASC", nativeQuery = true)
+	List<String> getRepoDataTypes();
+
+	@Cacheable("participantIDFromRedcapID")
+	@Query(value = "SELECT participant_id FROM participant WHERE redcap_id= :redcap_id LIMIT 1", nativeQuery = true)
+	String getParticipantIDString(@Param("redcap_id") String redcapId);
+
+	@Cacheable("participantTotalFileCount")
+	@Query(value = "SELECT count(DISTINCT fp.file_id) FROM file_participant fp JOIN ar_file_info ar ON fp.file_id = ar.file_id "
+				+ "WHERE fp.participant_id= :participant_id AND ar.release_sunset_version IS NULL", nativeQuery = true)
+	Integer getParticipantTotalFileCount(@Param("participant_id") String participantId);
+
 }

src/main/java/org/kpmp/participant/ParticipantDataTypeSummary.java

@@ -8,6 +8,7 @@
 public class ParticipantDataTypeSummary {
 	private List<ParticipantDataTypeInformation> spatialViewerDataTypes;
 	private List<ParticipantDataTypeInformation> explorerDataTypes;
+
 	public List<ParticipantDataTypeInformation> getSpatialViewerDataTypes() {
 		return spatialViewerDataTypes;
 	}

src/main/java/org/kpmp/participant/ParticipantRepoDataTypeInformation.java

@@ -0,0 +1,40 @@
+package org.kpmp.participant;
+
+import org.kpmp.dataSummary.AtlasRepoSummaryLinkInformation;
+
+public class ParticipantRepoDataTypeInformation {
+
+	private String dataType;
+	private Integer count;
+	private AtlasRepoSummaryLinkInformation linkInformation;
+
+	public ParticipantRepoDataTypeInformation(String dataType, Integer count, AtlasRepoSummaryLinkInformation linkInformation) {
+		this.dataType = dataType;
+		this.count = count;
+		this.linkInformation = linkInformation;
+	}
+
+	public String getDataType() {
+		return dataType;
+	}
+
+	public void setDataType(String dataType) {
+		this.dataType = dataType;
+	}
+
+	public Integer getCount() {
+		return count;
+	}
+
+	public void setCount(Integer count) {
+		this.count = count;
+	}
+
+	public AtlasRepoSummaryLinkInformation getLinkInformation() {
+		return linkInformation;
+	}
+
+	public void setLinkInformation(AtlasRepoSummaryLinkInformation linkInformation) {
+		this.linkInformation = linkInformation;
+	}
+}

src/main/java/org/kpmp/participant/ParticipantRepoDataTypeSummary.java

@@ -0,0 +1,15 @@
+package org.kpmp.participant;
+
+import java.util.List;
+
+public class ParticipantRepoDataTypeSummary {
+	private List<ParticipantRepoDataTypeInformation> repositoryDataTypes;
+
+	public List<ParticipantRepoDataTypeInformation> getRepositoryDataTypes() {
+		return repositoryDataTypes;
+	}
+
+	public void setRepositoryDataTypes(List<ParticipantRepoDataTypeInformation> repositoryDataTypes) {
+		this.repositoryDataTypes = repositoryDataTypes;
+	}
+}

src/main/java/org/kpmp/participant/ParticipantService.java

@@ -5,6 +5,7 @@
 
 import org.kpmp.FullDataTypeEnum;
 import org.kpmp.TissueTypeEnum;
+import org.kpmp.dataSummary.AtlasRepoSummaryLinkInformation;
 import org.kpmp.dataSummary.DataSummaryRepository;
 import org.kpmp.geneExpressionSummary.RTParticipantRepository;
 import org.slf4j.Logger;
@@ -37,22 +38,28 @@ public ParticipantService(DataSummaryRepository dataSummaryRepo, SpatialViewerTy
 		this.rtParticipantRepo = rtParticipantRepo;
 		this.participantSummaryDatasetRepository = participantSummaryDatasetRepository;
 	}
-  
+
 	public ParticipantSummaryDataset getParticipantSummaryDataset(String redcapId) {
 		return participantSummaryDatasetRepository.findByRedcapId(redcapId);
 	}
 
-	public List<ParticipantTissueTypeSummary> getTissueData(){
+	public List<ParticipantTissueTypeSummary> getTissueData() {
 		List<ParticipantTissueTypeSummary> tissueData = new ArrayList<>();
 
 		tissueData.add(new ParticipantTissueTypeSummary(
-			participantSummaryDatasetRepository.getDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType()), 
-			participantSummaryDatasetRepository.getDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType()), 
-			participantSummaryDatasetRepository.getDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType()),
-		    participantSummaryDatasetRepository.getDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType())));
+				participantSummaryDatasetRepository.getDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType()),
+				participantSummaryDatasetRepository.getDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType()),
+				participantSummaryDatasetRepository.getDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType()),
+				participantSummaryDatasetRepository.getDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType())));
 		return tissueData;
 	}
 
+	public ParticipantRepoDataTypeSummary getDataTypeCounts(String redcapId) {
+		ParticipantRepoDataTypeSummary summaryData = new ParticipantRepoDataTypeSummary();
+		summaryData.setRepositoryDataTypes(getRepositoryCounts(redcapId));
+		return summaryData;
+	}
+
 	public ParticipantDataTypeSummary getExperimentCounts(String redcapId) {
 		ParticipantDataTypeSummary summaryData = new ParticipantDataTypeSummary();
 		summaryData.setSpatialViewerDataTypes(getSpatialViewerCounts(redcapId));
@@ -61,6 +68,15 @@ public ParticipantDataTypeSummary getExperimentCounts(String redcapId) {
 		return summaryData;
 	}
 
+	public ParticipantRepoDataTypeInformation getTotalFilesCount(String redcapId) {
+		String participant_id = dataSummaryRepo.getParticipantIDString(redcapId);
+		Integer totalCount = dataSummaryRepo.getParticipantTotalFileCount(participant_id);
+		AtlasRepoSummaryLinkInformation linkInfo = new AtlasRepoSummaryLinkInformation("redcap_id", redcapId);
+		ParticipantRepoDataTypeInformation res = new ParticipantRepoDataTypeInformation("", totalCount, linkInfo);
+
+		return res;
+	}
+
 	private List<ParticipantDataTypeInformation> getExplorerCounts(String redcapId) {
 		List<ParticipantDataTypeInformation> explorerExperiments = new ArrayList<>();
 		int scCount = 0;
@@ -114,4 +130,17 @@ private List<ParticipantDataTypeInformation> getSpatialViewerCounts(String redca
 		}
 		return spatialViewerExperiments;
 	}
+
+	private List<ParticipantRepoDataTypeInformation> getRepositoryCounts(String redcapId) {
+		List<ParticipantRepoDataTypeInformation> repoCounts = new ArrayList<>();
+
+		List<String> repoDataTypes = dataSummaryRepo.getRepoDataTypes();
+		for (String repoDataType : repoDataTypes) {
+			Integer count = dataSummaryRepo.getParticipantRepoFileDataTypeCount(redcapId, repoDataType);
+			AtlasRepoSummaryLinkInformation linkInformation = new AtlasRepoSummaryLinkInformation("data_type", repoDataType);
+			ParticipantRepoDataTypeInformation dataTypeInfo = new ParticipantRepoDataTypeInformation(repoDataType, count, linkInformation);
+			repoCounts.add(dataTypeInfo);
+		}
+		return repoCounts;
+	}
 }

src/main/resources/knowledge_environment.graphqls

@@ -1,5 +1,4 @@
 type Query {
-  genes(symbol: String): [MyGeneInfoHit]
   autocomplete(searchTerm: String): [AutoCompleteResult]
   cellTypeHierarchy: CellTypeHierarchy
   geneExpressionSummary(dataType: String, geneSymbol: String, cellType: String, tissueType: String) : [GeneExpressionSummary]
@@ -11,8 +10,10 @@ type Query {
   getRTGeneExpressionByStructure(structure: String): [RTGeneExpression]
   getSummaryData: [GeneDatasetInformation]
   getDataTypeInformationByParticipant(redcapId: String!): ParticipantDataTypeSummary
+  getRepoDataTypeInformationByParticipant(redcapId: String!): ParticipantRepoDataTypeSummary
   participantSummaryDataset(redcapId: String): ParticipantSummaryDataset 
   participantClinicalDataset(redcapId: String): ParticipantSummaryDataset
+  getTotalParticipantFilesCount(redcapId: String): ParticipantRepoDataTypeInformation
   getTissueTypeSummaryData: [ParticipantTissueTypeSummary]
   getAtlasSummaryRows: AtlasRepoSummaryResult
 }
@@ -52,6 +53,15 @@ type ParticipantDataTypeInformation {
   isAggregatedData: Boolean
 }
 
+type ParticipantRepoDataTypeSummary {
+  repositoryDataTypes: [ParticipantRepoDataTypeInformation]
+}
+
+type ParticipantRepoDataTypeInformation {
+  dataType: String
+  count: Long
+  linkInformation: AtlasRepoSummaryLinkInformation
+}
 
 type GeneDatasetInformation {
   omicsType: String
@@ -64,14 +74,6 @@ type GeneDatasetInformation {
   participantCount: Long
 }
 
-type MyGeneInfoHit {
-  id: ID
-  symbol: String
-  name: String
-  entrezgene: String
-  alias: [String]
-}
-
 type AutoCompleteResult {
   value: String
   name: String