Merge pull request #129 from KPMP/develop

Release v2.3 merge

.dockerignore

@@ -0,0 +1,6 @@
+.*
+*.iml
+gradle
+src
+build/*
+!build/docker

.github/workflows/build-gradle-project.yml

@@ -0,0 +1,49 @@
+name: Build pegasus-data docker image
+
+on: 
+  push:
+
+jobs:
+  build-gradle-project:
+    env:
+      IMAGE_TAG: 2.3
+    runs-on: ubuntu-latest
+    steps:
+      - name: Get branch names
+        id: branch-names
+        uses: tj-actions/branch-names@v8
+
+      - name: Get current branch name
+        if: steps.branch-names.outputs.is_default == 'false'
+        run: |
+          echo "Running on branch: ${{ steps.branch-names.outputs.current_branch }}"
+      - name: Checkout project sources
+        uses: actions/checkout@v3
+      - uses: actions/setup-java@v3
+        with:
+          java-version: '8'
+          distribution: 'temurin'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
+        with:
+          gradle-version: 7.4
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ secrets.ENV_DOCKER_USER }}
+          password: ${{ secrets.ENV_DOCKER_PASS }}
+
+      - name: Run build with Gradle Wrapper
+        run: |
+         ./gradlew build docker
+
+      - name: Push to Docker Hub if branch is develop
+        if: steps.branch-names.outputs.current_branch == 'develop'
+        run: | 
+         docker push "kingstonduo/pegasus-data:$IMAGE_TAG"
+        
+      - name: Push to Docker Hub if branch is not develop
+        if: ${{ !steps.branch-names.outputs.current_branch == 'develop' }}
+        run: |
+          docker push "kingstonduo/pegasus-data:${{ steps.branch-names.outputs.current_branch }}"

Dockerfile

@@ -1,7 +1,6 @@
-FROM alpine
+FROM alpine:3.19.1
 
-RUN apk update && \
-    apk upgrade
+RUN apk update
 RUN apk add openjdk8
 
 VOLUME /tmp
@@ -15,4 +14,4 @@ RUN apk add --no-cache tzdata
 ENV TZ=America/Detroit
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
 
-ENTRYPOINT ["java","-cp","app:app/lib/*","org.kpmp.Application"]
+ENTRYPOINT ["java","-cp","app:app/lib/*","org.kpmp.Application"]

README.md

@@ -15,6 +15,9 @@ Repository for the Atlas Explorer Tool service layer
 # Build
 
 `./gradlew build docker`
+The default tag is the github branch name if no verison is provided
+To pass a version when building the docker image execute
+`./gradlew build docker -Ptag=<tagNumber>`
 
 # Restart Spring
 

build.gradle

@@ -21,7 +21,7 @@ apply plugin: 'io.spring.dependency-management'
 
 jar {
     baseName='pegasus-data'
-    version= '1.6.3'
+    version= '2.3'
 }
 
 repositories {
@@ -59,8 +59,31 @@ task unpack(type: Copy) {
     into("build/dependency")
 }
 
+def getTagInfo() {
+    if (project.hasProperty('tag')) {
+        def tagValue = project.property('tag')
+        return tagValue
+    } else {
+        def gitBranch = "Unknown branch"
+      try {
+        def workingDir = new File("${project.projectDir}")
+        def result = 'git rev-parse --abbrev-ref HEAD'.execute(null, workingDir)
+        result.waitFor()
+        if (result.exitValue() == 0) {
+            gitBranch = result.text.trim()
+        }
+      } catch (e) {
+        }
+        if (gitBranch  == "develop" || gitBranch == "master"){
+          return "${jar.version}"
+        }else{
+          return gitBranch
+        }
+    }
+}
+
 docker {
-    name "${project.group}/${jar.baseName}:latest"
+    name "${project.group}/${jar.baseName}:" + getTagInfo()
     copySpec.from(tasks.unpack.outputs).into("dependency")
     buildArgs(['DEPENDENCY': "dependency"])
-}
+}

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

@@ -195,10 +195,6 @@ public ParticipantSummaryDataset participantSummaryDataset(String redcap_id) thr
 		}
 	}
 
-	public ParticipantSummaryDataset participantClinicalDataset(String redcap_id) throws Exception {
-		return this.participantSummaryDataset(redcap_id);
-	}
-
 	public ParticipantRepoDataTypeInformation getTotalParticipantFilesCount(String redcap_id) throws Exception {
 		try {
 			return this.participantService.getTotalFilesCount(redcap_id);
@@ -234,4 +230,8 @@ public List<AtlasMessage> getAtlasMessages() throws Exception {
             throw e;
         }
     }
+
+	public List<ParticipantRepoDataTypeInformation> getExperimentalStrategyCountsByParticipant(String redcapId) {
+		return participantService.getExperimentalStrategyCountsByParticipant(redcapId);
+	}
 }

src/main/java/org/kpmp/WebConfig.java

@@ -1,9 +1,11 @@
 package org.kpmp;
 
+import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
 import org.springframework.web.servlet.config.annotation.CorsRegistration;
 import org.springframework.web.servlet.config.annotation.CorsRegistry;
 import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
 
+@EnableAutoConfiguration
 public class WebConfig extends Application implements WebMvcConfigurer {
 
 	@Override

src/main/java/org/kpmp/atlasMessage/AtlasMessageRepository.java

@@ -3,13 +3,12 @@
 
 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.stereotype.Repository;
 
 @Repository
-interface AtlasMessageRepository extends CrudRepository<AtlasMessage, List>{
+interface AtlasMessageRepository extends CrudRepository<AtlasMessage, List<AtlasMessage>>{
     @Query(value = "SELECT * FROM atlas_messages am WHERE start_date <= CURRENT_DATE() AND end_date >= CURRENT_DATE() ORDER BY start_date ASC", nativeQuery = true)
     List<AtlasMessage> getAtlasMessages();
 }

src/main/java/org/kpmp/atlasMessage/AtlasMessageService.java

@@ -1,11 +1,10 @@
 package org.kpmp.atlasMessage;
 
+import java.util.List;
+
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
-import java.util.ArrayList;
-import java.util.List;
-
 
 @Service
 public class AtlasMessageService {

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

@@ -13,6 +13,8 @@
 import javax.persistence.OneToMany;
 import javax.persistence.Table;
 
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+
 @Entity
 @Table(name = "cell_type")
 public class CellType implements Serializable {
@@ -120,7 +122,7 @@ public void setCellTypeOrdering(int cellTypeOrdering) {
 
 	@Override
 	public int hashCode() {
-		return cellType.hashCode();
+		return new HashCodeBuilder().append(cellTypeId).build();
 	}
 
 	@Override
@@ -130,7 +132,7 @@ public boolean equals(Object obj) {
 		if (!(obj instanceof CellType))
 			return false;
 		CellType cellType = (CellType) obj;
-		return cellType.getCellType().equals(this.getCellType());
+		return cellType.getCellTypeId() == (this.getCellTypeId());
 	}
 
 }

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

@@ -4,7 +4,8 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import com.google.common.base.Objects;
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
 
 public class CellTypeStructureSubregion implements Serializable {
 
@@ -46,13 +47,13 @@ public boolean equals(Object obj) {
 			return false;
 		}
 		CellTypeStructureSubregion other = (CellTypeStructureSubregion) obj;
-		return Objects.equal(this.subregionName, other.subregionName);
+		return new EqualsBuilder().append(this.subregionName, other.subregionName).build();
 
 	}
 
 	@Override
 	public int hashCode() {
-		return Objects.hashCode(subregionName);
+		return new HashCodeBuilder().append(this.subregionName).build();
 	}
 
 }

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

@@ -1,10 +1,14 @@
 package org.kpmp.cellTypeSummary;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 import org.kpmp.DataTypeEnum;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.test.autoconfigure.data.neo4j.DataNeo4jTypeExcludeFilter;
 import org.springframework.stereotype.Service;
 
 @Service

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

@@ -1,53 +1,63 @@
 package org.kpmp.dataSummary;
 
 public class AtlasRepoSummaryRow {
-	private int openCount;
-	private int controlledCount;
 	private String omicsType;
-	private AtlasRepoSummaryLinkInformation linkInformation;
+	private AtlasRepositoryLinkInformation linkInformation;
+	private Long akiCount;
+	private Long ckdCount;
+	private Long hrtCount;
+	private Long dmrCount;
 
-	public AtlasRepoSummaryRow(String omicsType, AtlasRepoSummaryLinkInformation linkInformation) {
+	public AtlasRepoSummaryRow(String omicsType, AtlasRepositoryLinkInformation linkInformation) {
 		this.omicsType = omicsType;
 		this.linkInformation = linkInformation;
 	}
 
-	public int getOpenCount() {
-		return openCount;
+	public Long getAkiCount() {
+		return this.akiCount;
 	}
 
-	public void setOpenCount(int openCount) {
-		this.openCount = openCount;
+	public void setAkiCount(Long akiCount) {
+		this.akiCount = akiCount;
 	}
 
-	public int getControlledCount() {
-		return controlledCount;
+	public Long getCkdCount() {
+		return this.ckdCount;
 	}
 
-	public void setControlledCount(int controlledCount) {
-		this.controlledCount = controlledCount;
+	public void setCkdCount(Long ckdCount) {
+		this.ckdCount = ckdCount;
 	}
 
-	public String getOmicsType() {
-		return omicsType;
+	public Long getHrtCount() {
+		return this.hrtCount;
 	}
 
-	public void setOmicsType(String omicsType) {
-		this.omicsType = omicsType;
+	public void setHrtCount(Long hrtCount) {
+		this.hrtCount = hrtCount;
+	}
+
+	public Long getDmrCount() {
+		return this.dmrCount;
 	}
 
-	public void addToControlledCount(int count) {
-		this.controlledCount = this.controlledCount + count;
+	public void setDmrCount(Long dmrCount) {
+		this.dmrCount = dmrCount;
 	}
 
-	public void addToOpenCount(int count) {
-		this.openCount = this.openCount + count;
+	public String getOmicsType() {
+		return omicsType;
+	}
+
+	public void setOmicsType(String omicsType) {
+		this.omicsType = omicsType;
 	}
 
-	public AtlasRepoSummaryLinkInformation getLinkInformation() {
+	public AtlasRepositoryLinkInformation getLinkInformation() {
 		return linkInformation;
 	}
 
-	public void setLinkInformation(AtlasRepoSummaryLinkInformation linkInformation) {
+	public void setLinkInformation(AtlasRepositoryLinkInformation linkInformation) {
 		this.linkInformation = linkInformation;
 	}
 }

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

@@ -3,12 +3,15 @@
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 
-public class AtlasRepoSummaryLinkInformation {
+public class AtlasRepositoryLinkInformation {
 
+	public static final String EXPERIMENTAL_STRATEGY = "experimental_strategy";
+	public static final String DATA_CATEGORY = "data_category";
+
 	private String linkType;
 	private String linkValue;
 
-	public AtlasRepoSummaryLinkInformation(String linkType, String linkValue) {
+	public AtlasRepositoryLinkInformation(String linkType, String linkValue) {
 		this.setLinkType(linkType);
 		this.setLinkValue(linkValue);
 	}
@@ -36,8 +39,8 @@ public int hashCode() {
 
 	@Override
 	public boolean equals(Object obj) {
-		if (obj instanceof AtlasRepoSummaryLinkInformation) {
-			final AtlasRepoSummaryLinkInformation other = (AtlasRepoSummaryLinkInformation) obj;
+		if (obj instanceof AtlasRepositoryLinkInformation) {
+			final AtlasRepositoryLinkInformation other = (AtlasRepositoryLinkInformation) obj;
 			return new EqualsBuilder().append(linkType, other.getLinkType()).append(linkValue, other.getLinkValue()).isEquals();
 		}
 		else {

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

@@ -16,6 +16,14 @@ public interface DataSummaryRepository extends CrudRepository<DataSummaryValue,
 			+ "join file f on f.file_id= fp.file_id " + "join sv_file_info sv on sv.file_id = f.file_id "
 			+ "where sv.config_type = :data_type " + "and p.tissue_type = :tissue_type", nativeQuery = true)
 	Long getDataSummaryCount(@Param("tissue_type") String tissue_type, @Param("data_type") String data_type);
+
+	@Cacheable("repoDataSummaryCount")
+	@Query(value = "select count(distinct(dl_file_id)) from repo_file_v where experimental_strategy = :exp_strat and tissue_type = :tissue_type", nativeQuery = true)
+	Long getRepoDataSummaryCount(@Param("tissue_type") String tissue_type, @Param("exp_strat") String exp_strat);
+
+	@Cacheable("repoBiomarkerSummaryCount")
+	@Query(value = "select count(distinct(dl_file_id)) from repo_file_v where data_category = 'Biomarker' and tissue_type = :tissue_type", nativeQuery = true)
+	Long getRepoBiomarkerSummaryCount(@Param("tissue_type") String tissue_type);
 
 	@Cacheable("dataSummaryLinkCount")
 	@Query(value = "select count(distinct(redcap_id)) " + "from sv_link_v " + "where data_type = :data_type "