Merge pull request #82 from KPMP/KPMP-4001_GetRepoCounts

Kpmp 4001 get repo counts

.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

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;
@@ -20,9 +21,9 @@
 import org.kpmp.geneExpressionSummary.GeneExpressionSummary;
 import org.kpmp.geneExpressionSummary.GeneExpressionSummaryService;
 import org.kpmp.participant.ParticipantDataTypeSummary;
-import org.kpmp.participant.ParticipantTissueTypeSummary;
 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;
@@ -100,7 +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) {
@@ -109,7 +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) {
@@ -170,9 +171,18 @@ public ParticipantSummaryDataset participantClinicalDataset(String redcap_id) th
 	public List<ParticipantTissueTypeSummary> getTissueTypeSummaryData() throws Exception {
 		try {
 			return participantService.getTissueData();
-		}catch (Exception e) {
+		} 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

@@ -5,6 +5,7 @@
 
 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/cellType/CellType.java

@@ -17,6 +17,8 @@
 @Table(name = "cell_type")
 public class CellType implements Serializable {
 
+	private static final long serialVersionUID = -7240769211757430938L;
+
 	@Id
 	@Column(name = "cell_type_id")
 	private int cellTypeId;

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

@@ -10,7 +10,8 @@
 
 @Component
 public class CellTypeHierarchy implements Serializable {
-
+
+	private static final long serialVersionUID = 4174487460309851924L;
 	private Map<String, CellTypeStructureRegion> cellTypeRegionMap = new HashMap<>();
 
 	public List<CellTypeStructureRegion> getCellTypeRegions() {
@@ -20,7 +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();
@@ -32,7 +33,4 @@ public void addCellTypeStructureRegion(CellTypeStructureRegion region) {
 		}
 	}
 
-
-
 }
-

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

@@ -8,6 +8,7 @@
 
 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

@@ -8,6 +8,7 @@
 
 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

@@ -1,45 +1,48 @@
 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;
 import javax.persistence.Table;
-import java.io.Serializable;
 
 @Entity
 @Table(name = "celltype_synonym")
 @IdClass(CellTypeSynonymId.class)
 public class CellTypeSynonym implements Serializable {
 
-    @Id
-    @Column(name="cell_type_id")
-    private int cellTypeId;
+	private static final long serialVersionUID = -5650797130903696615L;
+
+	@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/ClusterHierarchy.java

@@ -1,19 +1,21 @@
 package org.kpmp.cellTypeSummary;
 
-import org.springframework.lang.Nullable;
+import java.io.Serializable;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.Id;
 import javax.persistence.IdClass;
 import javax.persistence.Table;
-import java.io.Serializable;
+
+import org.springframework.lang.Nullable;
 
 @Entity
 @Table(name = "cluster_hierarchy_v")
 @IdClass(ClusterHierarchyId.class)
 public class ClusterHierarchy implements Serializable {
 
+	private static final long serialVersionUID = -7707637379989017634L;
 	@Id
 	@Column(name = "cell_type_id")
 	private int cellTypeId;
@@ -31,11 +33,11 @@ public class ClusterHierarchy implements Serializable {
 	@Column(name = "is_single_nuc")
 	private String isSingleNucCluster;
 	@Column(name = "is_rt")
-    private String isRegionalTranscriptomics;
+	private String isRegionalTranscriptomics;
 	@Column(name = "cell_type")
 	private String cellType;
 	@Column(name = "cell_type_order")
-    private Double cellTypeOrder;
+	private Double cellTypeOrder;
 
 	public int getCellTypeId() {
 		return cellTypeId;
@@ -45,7 +47,7 @@ public void setCellTypeId(int cellTypeId) {
 		this.cellTypeId = cellTypeId;
 	}
 
-    @Nullable
+	@Nullable
 	public int getClusterId() {
 		return clusterId;
 	}
@@ -62,7 +64,7 @@ public void setStructureRegion(String structureRegion) {
 		this.structureRegion = structureRegion;
 	}
 
-    @Nullable
+	@Nullable
 	public String getStructureSubregion() {
 		return structureSubregion;
 	}
@@ -71,7 +73,7 @@ public void setStructureSubregion(String structureSubregion) {
 		this.structureSubregion = structureSubregion;
 	}
 
-    @Nullable
+	@Nullable
 	public String getClusterName() {
 		return clusterName;
 	}
@@ -96,29 +98,29 @@ public void setIsSingleNucCluster(String isSingleNucCluster) {
 		this.isSingleNucCluster = isSingleNucCluster;
 	}
 
-    public String getIsRegionalTranscriptomics() {
-        return isRegionalTranscriptomics;
-    }
+	public String getIsRegionalTranscriptomics() {
+		return isRegionalTranscriptomics;
+	}
 
-    public void setIsRegionalTranscriptomics(String isRegionalTranscriptomics) {
-        this.isRegionalTranscriptomics = isRegionalTranscriptomics;
-    }
+	public void setIsRegionalTranscriptomics(String isRegionalTranscriptomics) {
+		this.isRegionalTranscriptomics = isRegionalTranscriptomics;
+	}
 
-    @Nullable
-    public Double getCellTypeOrder() {
-        return cellTypeOrder;
-    }
+	@Nullable
+	public Double getCellTypeOrder() {
+		return cellTypeOrder;
+	}
 
-    public void setCellTypeOrder(Double cellTypeOrder) {
-        this.cellTypeOrder = cellTypeOrder;
-    }
+	public void setCellTypeOrder(Double cellTypeOrder) {
+		this.cellTypeOrder = cellTypeOrder;
+	}
 
-    @Nullable
-    public String getCellType() {
-        return cellType;
-    }
+	@Nullable
+	public String getCellType() {
+		return cellType;
+	}
 
-    public void setCellType(String cellType) {
-        this.cellType = cellType;
-    }
+	public void setCellType(String cellType) {
+		this.cellType = cellType;
+	}
 }