Merge pull request #83 from KPMP/develop

Q1 2023 Atlas Release

.gitignore

@@ -31,3 +31,4 @@ build
 .settings
 bin
 .gradle
+.DS_Store

.project

@@ -2,29 +2,27 @@
 <projectDescription>
 	<name>pegasus-data</name>
 	<comment></comment>
-	<projects>
-	</projects>
+	<projects/>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
+	</natures>
 	<buildSpec>
 		<buildCommand>
 			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
+			<arguments/>
 		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.buildship.core.gradleprojectbuilder</name>
-			<arguments>
-			</arguments>
+			<arguments/>
 		</buildCommand>
 	</buildSpec>
-	<natures>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
-	</natures>
+	<linkedResources/>
 	<filteredResources>
 		<filter>
 			<id>1</id>
-			<name></name>
 			<type>30</type>
+			<name/>
 			<matcher>
 				<id>org.eclipse.core.resources.regexFilterMatcher</id>
 				<arguments>node_modules|.git|__CREATED_BY_JAVA_LANGUAGE_SERVER__</arguments>

README.md

@@ -34,3 +34,11 @@ Repository for the Atlas Explorer Tool service layer
 2. Update .env ENV_MYSQL_PASSWORD to the password for QA KE
 3. Add your IP address to a new security group called sg-0597e054f11d2e31a (Developer to KE Mariadb) 
 4. Restart your knowledge-environment (don't worry that you have your own copy of mariadb, it'll be ignored)
+
+If you have already followed these steps and are still having trouble connecting, check to see if your ip address has changed, you may need to update the security group rules
+
+# Talking to GraphQL 
+
+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

build.gradle

@@ -21,7 +21,7 @@ apply plugin: 'io.spring.dependency-management'
 
 jar {
     baseName='pegasus-data'
-    version= '2.0'
+    version= '1.7'
 }
 
 repositories {
@@ -46,6 +46,7 @@ dependencies {
     testImplementation 'org.mockito:mockito-core'
     testImplementation 'org.springframework.boot:spring-boot-starter-test:2.2.0.RELEASE'
     implementation 'org.springframework.boot:spring-boot-starter-cache'
+    implementation 'com.hazelcast:hazelcast-all:4.2.5'
 }
 
 springBoot {

gradle/wrapper/gradle-wrapper.properties

@@ -3,4 +3,4 @@ distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.1-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-all.zip

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

@@ -10,8 +10,9 @@
 import org.kpmp.cellType.CellTypeService;
 import org.kpmp.cellTypeSummary.ClusterHierarchy;
 import org.kpmp.cellTypeSummary.ClusterHierarchyService;
+import org.kpmp.dataSummary.AtlasRepoSummaryResult;
 import org.kpmp.dataSummary.DataSummaryService;
-import org.kpmp.datasetSummary.DatasetSummary;
+import org.kpmp.dataSummary.DataTypeSummary;
 import org.kpmp.gene.GeneService;
 import org.kpmp.gene.MyGeneInfoHit;
 import org.kpmp.geneExpression.RTExpressionByTissueType;
@@ -22,6 +23,7 @@
 import org.kpmp.participant.ParticipantDataTypeSummary;
 import org.kpmp.participant.ParticipantService;
 import org.kpmp.participant.ParticipantSummaryDataset;
+import org.kpmp.participant.ParticipantTissueTypeSummary;
 import org.kpmp.umap.PlotData;
 import org.kpmp.umap.UmapDataService;
 import org.slf4j.Logger;
@@ -99,7 +101,7 @@ public PlotData getUmapPlotData(String dataType, String geneSymbol, String tissu
 		}
 	}
 
-	public List<DatasetSummary> getGeneDatasetInformation(String geneSymbol) throws Exception {
+	public List<DataTypeSummary> getGeneDatasetInformation(String geneSymbol) throws Exception {
 		try {
 			return geneExpressionSummaryService.getGeneDatasetInformation(geneSymbol);
 		} catch (Exception e) {
@@ -108,7 +110,7 @@ public List<DatasetSummary> getGeneDatasetInformation(String geneSymbol) throws
 		}
 	}
 
-	public List<DatasetSummary> getSummaryData() throws Exception {
+	public List<DataTypeSummary> getSummaryData() throws Exception {
 		try {
 			return dataSummaryService.getSummaryData();
 		} catch (Exception e) {
@@ -165,4 +167,22 @@ public ParticipantSummaryDataset participantSummaryDataset(String redcap_id) thr
 	public ParticipantSummaryDataset participantClinicalDataset(String redcap_id) throws Exception {
 		return this.participantSummaryDataset(redcap_id);
 	}
-}
+
+	public List<ParticipantTissueTypeSummary> getTissueTypeSummaryData() throws Exception {
+		try {
+			return participantService.getTissueData();
+		} catch (Exception e) {
+			logger.error(e.getMessage());
+			throw e;
+		}
+	}
+
+	public AtlasRepoSummaryResult getAtlasSummaryRows() throws Exception {
+		try {
+			return dataSummaryService.getAtlasRepoSummary();
+		} catch (Exception e) {
+			logger.error("Unable to get Atlas Summary data: ", e.getMessage());
+			throw e;
+		}
+	}
+}

src/main/java/org/kpmp/autocomplete/AutocompleteResult.java

@@ -1,9 +1,11 @@
 package org.kpmp.autocomplete;
 
+import java.io.Serializable;
 import java.util.List;
 
-public class AutocompleteResult {
+public class AutocompleteResult implements Serializable {
 
+	private static final long serialVersionUID = 762733408490639258L;
 	private String value;
 	private String name;
 	private String id;

src/main/java/org/kpmp/autocomplete/AutocompleteService.java

@@ -11,6 +11,7 @@
 import org.kpmp.gene.GeneService;
 import org.kpmp.gene.MyGeneInfoHit;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Service;
 
 @Service
@@ -28,6 +29,7 @@ public AutocompleteService(GeneService geneService, CellTypeRepository cellTypeR
 		this.cellTypeRepository = cellTypeRepository;
 	}
 
+	@Cacheable("autocompleteQuery")
 	public List<AutocompleteResult> query(String searchTerm) throws IOException, Exception {
 		List<MyGeneInfoHit> myGeneInfoHits = geneService.querySymbolAndAlias(searchTerm);
 		List<CellType> cellTypes = cellTypeRepository.findByCellTypeContainingOrSynonymContaining(searchTerm);
@@ -40,6 +42,7 @@ public List<AutocompleteResult> query(String searchTerm) throws IOException, Exc
 		return myGeneResults;
 	}
 
+	@Cacheable("myGeneInfoHitsToAutocompleteResults")
 	public List<AutocompleteResult> convertMyGeneInfoHitsToAutocompleteResults(List<MyGeneInfoHit> hits) {
 		List<AutocompleteResult> autocompleteResults = new ArrayList<>();
 		for (MyGeneInfoHit hit : hits) {
@@ -49,6 +52,7 @@ public List<AutocompleteResult> convertMyGeneInfoHitsToAutocompleteResults(List<
 		return autocompleteResults;
 	}
 
+	@Cacheable("cellTypesToAutocompleteResults")
 	public List<AutocompleteResult> convertCellTypesToAutocompleteResults(List<CellType> cellTypes,
 			List<CellType> regions, List<CellType> subregions) {
 		List<CellType> cellTypeListNoDupes = cellTypes.stream().distinct().collect(Collectors.toList());

src/main/java/org/kpmp/cellType/CellType.java

@@ -1,5 +1,6 @@
 package org.kpmp.cellType;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
@@ -14,7 +15,9 @@
 
 @Entity
 @Table(name = "cell_type")
-public class CellType {
+public class CellType implements Serializable {
+
+	private static final long serialVersionUID = -7240769211757430938L;
 
 	@Id
 	@Column(name = "cell_type_id")

src/main/java/org/kpmp/cellType/CellTypeHierarchy.java

@@ -1,5 +1,6 @@
 package org.kpmp.cellType;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -8,8 +9,9 @@
 import org.springframework.stereotype.Component;
 
 @Component
-public class CellTypeHierarchy  {
-
+public class CellTypeHierarchy implements Serializable {
+
+	private static final long serialVersionUID = 4174487460309851924L;
 	private Map<String, CellTypeStructureRegion> cellTypeRegionMap = new HashMap<>();
 
 	public List<CellTypeStructureRegion> getCellTypeRegions() {
@@ -19,7 +21,7 @@ public List<CellTypeStructureRegion> getCellTypeRegions() {
 	}
 
 	public void addCellTypeStructureRegion(CellTypeStructureRegion region) {
-		
+
 		if (cellTypeRegionMap.containsKey(region.getRegionName())) {
 			CellTypeStructureRegion existingRegion = cellTypeRegionMap.get(region.getRegionName());
 			List<CellTypeStructureSubregion> subregions = region.getCellTypeSubregions();
@@ -31,7 +33,4 @@ public void addCellTypeStructureRegion(CellTypeStructureRegion region) {
 		}
 	}
 
-
-
 }
-

src/main/java/org/kpmp/cellType/CellTypeRepository.java

@@ -2,6 +2,7 @@
 
 import java.util.List;
 
+import org.springframework.cache.annotation.Cacheable;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
 import org.springframework.data.repository.query.Param;
@@ -10,17 +11,21 @@
 @Repository
 public interface CellTypeRepository extends CrudRepository<CellType, Integer> {
 
+	@Cacheable("cellTypeContainingOrSynonymContaining")
 	@Query(value = "SELECT ct.*, cs.* " + "    FROM cell_type ct "
 			+ "    JOIN celltype_synonym cs ON (ct.cell_type_id = cs.cell_type_id AND cs.cell_type_synonym LIKE %:searchTerm%) "
 			+ "    UNION " + "    SELECT ct.*, cs.* " + "    FROM cell_type ct "
 			+ "    LEFT JOIN celltype_synonym cs ON ct.cell_type_id = cs.cell_type_id "
 			+ "    WHERE ct.cell_type LIKE %:searchTerm% ", nativeQuery = true)
 	List<CellType> findByCellTypeContainingOrSynonymContaining(@Param("searchTerm") String searchTerm);
 
+	@Cacheable("cellTypeIsNotNullOrderByCellTypeOrdering")
 	List<CellType> findAllByCellTypeIsNotNullOrderByCellTypeOrdering();
 
+	@Cacheable("structureRegionContaining")
 	List<CellType> findByStructureRegionContaining(String searchTerm);
 
+	@Cacheable("structureSubregionContaining")
 	List<CellType> findByStructureSubregionContaining(String searchTerm);
 
 }

src/main/java/org/kpmp/cellType/CellTypeStructureRegion.java

@@ -1,12 +1,14 @@
 package org.kpmp.cellType;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-public class CellTypeStructureRegion {
+public class CellTypeStructureRegion implements Serializable {
 
+	private static final long serialVersionUID = 3141535632314917816L;
 	private String regionName;
 	private Map<String, CellTypeStructureSubregion> subregionMap = new HashMap<>();
 	private List<String> subregionOrderdList = new ArrayList<>();

src/main/java/org/kpmp/cellType/CellTypeStructureSubregion.java

@@ -1,12 +1,14 @@
 package org.kpmp.cellType;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
 import com.google.common.base.Objects;
 
-public class CellTypeStructureSubregion {
+public class CellTypeStructureSubregion implements Serializable {
 
+	private static final long serialVersionUID = 1366955014710403152L;
 	private String subregionName;
 	private List<CellType> cellTypes = new ArrayList<>();
 

src/main/java/org/kpmp/cellType/CellTypeSynonym.java

@@ -1,9 +1,11 @@
 package org.kpmp.cellType;
 
-import javax.persistence.FetchType;
-import javax.persistence.Id;
+import java.io.Serializable;
+
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.Id;
 import javax.persistence.IdClass;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
@@ -12,33 +14,35 @@
 @Entity
 @Table(name = "celltype_synonym")
 @IdClass(CellTypeSynonymId.class)
-public class CellTypeSynonym {
+public class CellTypeSynonym implements Serializable {
+
+	private static final long serialVersionUID = -5650797130903696615L;
 
-    @Id
-    @Column(name="cell_type_id")
-    private int cellTypeId;
+	@Id
+	@Column(name = "cell_type_id")
+	private int cellTypeId;
 
-    @Id
-    @Column(name="cell_type_synonym")
-    private String cellTypeSynonym;
+	@Id
+	@Column(name = "cell_type_synonym")
+	private String cellTypeSynonym;
 
-    @ManyToOne(fetch = FetchType.EAGER)
-    @JoinColumn(name="cell_type_id", nullable = false, insertable = false, updatable = false)
-    private CellType cellType;
+	@ManyToOne(fetch = FetchType.EAGER)
+	@JoinColumn(name = "cell_type_id", nullable = false, insertable = false, updatable = false)
+	private CellType cellType;
 
-    public int getCellTypeId() {
-        return cellTypeId;
-    }
+	public int getCellTypeId() {
+		return cellTypeId;
+	}
 
-    public void setCellTypeId(int cellTypeId) {
-        this.cellTypeId = cellTypeId;
-    }
+	public void setCellTypeId(int cellTypeId) {
+		this.cellTypeId = cellTypeId;
+	}
 
-    public String getCellTypeSynonym() {
-        return cellTypeSynonym;
-    }
+	public String getCellTypeSynonym() {
+		return cellTypeSynonym;
+	}
 
-    public void setCellTypeSynonym(String cellTypeSynonym) {
-        this.cellTypeSynonym = cellTypeSynonym;
-    }
+	public void setCellTypeSynonym(String cellTypeSynonym) {
+		this.cellTypeSynonym = cellTypeSynonym;
+	}
 }

src/main/java/org/kpmp/cellTypeSummary/ClusterHiearchyRepository.java

@@ -2,18 +2,22 @@
 
 import java.util.List;
 
+import org.springframework.cache.annotation.Cacheable;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
 import org.springframework.data.repository.query.Param;
 
 interface ClusterHiearchyRepository extends CrudRepository<ClusterHierarchy, ClusterHierarchyId> {
 
 	@Override
+	@Cacheable("clusterHierarchy")
 	List<ClusterHierarchy> findAll();
 
+	@Cacheable("clusterHierarchyCt")
 	@Query(value = "CALL cluster_hierarchy_sp(:cell_type);", nativeQuery = true)
 	List<ClusterHierarchy> findByCellType(@Param("cell_type") String cellType);
 
-    @Query(value = "CALL cluster_hierarchy_by_cluster_sp(:cluster);", nativeQuery = true)
+	@Cacheable("clusterHierarchyCluster")
+	@Query(value = "CALL cluster_hierarchy_by_cluster_sp(:cluster);", nativeQuery = true)
     ClusterHierarchy findFirstByClusterOrRegion(String cluster);
 }