Merge pull request #133 from KPMP/develop

Release v2.3.1
KPMP · May 21, 2024 · aa63786 · aa63786
2 parents 77c5438 + 8197b0d
commit aa63786
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Showing 7 changed files with 45 additions and 19 deletions.
diff --git a/.github/workflows/build-gradle-project.yml b/.github/workflows/build-gradle-project.yml
@@ -6,7 +6,7 @@ on:
 jobs:
   build-gradle-project:
     env:
-      IMAGE_TAG: 2.3
+      IMAGE_TAG: 2.3.1
     runs-on: ubuntu-latest
     steps:
       - name: Get branch names
@@ -42,8 +42,8 @@ jobs:
         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: ${{ !steps.branch-names.outputs.current_branch == 'develop' }}
+        if: steps.branch-names.outputs.current_branch != 'develop'
         run: |
-          docker push "kingstonduo/pegasus-data:${{ steps.branch-names.outputs.current_branch }}"
+          docker push "kingstonduo/pegasus-data:${{ steps.branch-names.outputs.current_branch }}"
diff --git a/build.gradle b/build.gradle
@@ -21,7 +21,7 @@ apply plugin: 'io.spring.dependency-management'
 
 jar {
     baseName='pegasus-data'
-    version= '2.3'
+    version= '2.3.1'
 }
 
 repositories {
@@ -59,12 +59,12 @@ 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"
+def getCurrentGitBranch() {
+  if (project.hasProperty('tag')) {
+    def tagValue = project.property('tag')
+    return tagValue
+  } else {
+      def gitBranch = "Unknown branch"
       try {
         def workingDir = new File("${project.projectDir}")
         def result = 'git rev-parse --abbrev-ref HEAD'.execute(null, workingDir)
@@ -74,16 +74,16 @@ def getTagInfo() {
         }
       } catch (e) {
         }
-        if (gitBranch  == "develop" || gitBranch == "master"){
-          return "${jar.version}"
+        if (gitBranch == "develop" || gitBranch == "master"){
+          return jar.version
         }else{
           return gitBranch
         }
     }
 }
 
 docker {
-    name "${project.group}/${jar.baseName}:" + getTagInfo()
+    name "kingstonduo/${jar.baseName}:" + getCurrentGitBranch()
     copySpec.from(tasks.unpack.outputs).into("dependency")
     buildArgs(['DEPENDENCY': "dependency"])
-}
+}
diff --git a/src/main/java/org/kpmp/DataTypeEnum.java b/src/main/java/org/kpmp/DataTypeEnum.java
@@ -14,6 +14,7 @@ public enum DataTypeEnum {
 	SPATIAL_LIPIDOMICS("sl"),
 	SPATIAL_METABOLOMICS("sm"),
 	SPATIAL_NGLYCOMICS("sng"),
+    IMAGING_MASS_CYTOMETRY("imc"),
 	UNKNOWN("");
 
 	private String abbreviation;
@@ -49,7 +50,9 @@ public static DataTypeEnum fromAbbreviation(String abbreviation) {
 			return SPATIAL_METABOLOMICS;
 		} else if (SPATIAL_NGLYCOMICS.abbreviation.equals(abbreviation)) {
 			return SPATIAL_NGLYCOMICS;
-		}
+		}else if (IMAGING_MASS_CYTOMETRY.abbreviation.equals(abbreviation)){
+            return IMAGING_MASS_CYTOMETRY;
+        }
 		return UNKNOWN;
 	}
 }
diff --git a/src/main/java/org/kpmp/FullDataTypeEnum.java b/src/main/java/org/kpmp/FullDataTypeEnum.java
@@ -14,6 +14,7 @@ public enum FullDataTypeEnum {
 	SPATIAL_LIPIDOMICS_FULL("Spatial Lipidomics"),
 	SPATIAL_METABOLOMICS_FULL("Spatial Metabolomics"),
 	SPATIAL_NGLYCOMICS_FULL("Spatial N-glycomics"),
+    IMAGING_MASS_CYTOMETRY_FULL("Imaging Mass Cytometry"),
 	UNKNOWN_FULL("");
 
 	private String dataEnum;
@@ -49,7 +50,9 @@ public static FullDataTypeEnum fromLong(String dataEnum) {
 			return SPATIAL_METABOLOMICS_FULL;
 		} else if (SPATIAL_NGLYCOMICS_FULL.dataEnum.equals(dataEnum)) {
 			return SPATIAL_NGLYCOMICS_FULL;
-		}
+		}else if (IMAGING_MASS_CYTOMETRY_FULL.dataEnum.equals(dataEnum)){
+            return IMAGING_MASS_CYTOMETRY_FULL;
+        }
 		return UNKNOWN_FULL;
 	}
 }
diff --git a/src/main/java/org/kpmp/dataSummary/DataSummaryService.java b/src/main/java/org/kpmp/dataSummary/DataSummaryService.java
@@ -240,6 +240,21 @@ public List<DataTypeSummary> getSummaryData() {
 						FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName()),
 				dataSummaryRepository
 						.getParticipantSummaryLinkCount(FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName())));
+
+        summaryData.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(),
+                FullDataTypeEnum.IMAGING_MASS_CYTOMETRY_FULL.getFullName(),
+                DataTypeEnum.IMAGING_MASS_CYTOMETRY.getAbbreviation(),
+                dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(),
+                        FullDataTypeEnum.IMAGING_MASS_CYTOMETRY_FULL.getFullName()),
+                dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(),
+                        FullDataTypeEnum.IMAGING_MASS_CYTOMETRY_FULL.getFullName()),
+                dataSummaryRepository.getDataSummaryCount(
+                        TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(),
+                        FullDataTypeEnum.IMAGING_MASS_CYTOMETRY_FULL.getFullName()),
+                dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType(),
+                        FullDataTypeEnum.IMAGING_MASS_CYTOMETRY_FULL.getFullName()),
+                dataSummaryRepository
+                        .getParticipantSummaryCount(FullDataTypeEnum.IMAGING_MASS_CYTOMETRY_FULL.getFullName())));
 		return summaryData;
 	}
 }
diff --git a/src/test/java/org/kpmp/DataTypeEnumTest.java b/src/test/java/org/kpmp/DataTypeEnumTest.java
@@ -4,11 +4,12 @@
 
 import org.junit.Test;
 
+
 public class DataTypeEnumTest {
 
 	@Test
 	public void testGetAbbreviation() {
-		assertEquals(12, DataTypeEnum.values().length);
+		assertEquals(13, DataTypeEnum.values().length);
 		assertEquals("sn", DataTypeEnum.SINGLE_NUCLEUS.getAbbreviation());
 		assertEquals("sc", DataTypeEnum.SINGLE_CELL.getAbbreviation());
 		assertEquals("rt", DataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation());
@@ -17,6 +18,7 @@ public void testGetAbbreviation() {
 		assertEquals("sm", DataTypeEnum.SPATIAL_METABOLOMICS.getAbbreviation());
 		assertEquals("sng", DataTypeEnum.SPATIAL_NGLYCOMICS.getAbbreviation());
 		assertEquals("rp", DataTypeEnum.REGIONAL_PROTEOMICS.getAbbreviation());
+        assertEquals("imc", DataTypeEnum.IMAGING_MASS_CYTOMETRY.getAbbreviation());
 		assertEquals("", DataTypeEnum.UNKNOWN.getAbbreviation());
 	}
 
@@ -30,6 +32,7 @@ public void testFromAbbreviation() {
 		assertEquals(DataTypeEnum.SPATIAL_METABOLOMICS, DataTypeEnum.fromAbbreviation("sm"));
 		assertEquals(DataTypeEnum.SPATIAL_NGLYCOMICS, DataTypeEnum.fromAbbreviation("sng"));
 		assertEquals(DataTypeEnum.REGIONAL_PROTEOMICS, DataTypeEnum.fromAbbreviation("rp"));
+        assertEquals(DataTypeEnum.IMAGING_MASS_CYTOMETRY, DataTypeEnum.fromAbbreviation("imc"));
 		assertEquals(DataTypeEnum.UNKNOWN, DataTypeEnum.fromAbbreviation("xxx"));
 		assertEquals(DataTypeEnum.UNKNOWN, DataTypeEnum.fromAbbreviation(""));
 		assertEquals(DataTypeEnum.UNKNOWN, DataTypeEnum.fromAbbreviation(null));

diff --git a/src/test/java/org/kpmp/FullDataTypeEnumTest.java b/src/test/java/org/kpmp/FullDataTypeEnumTest.java
@@ -8,7 +8,7 @@ public class FullDataTypeEnumTest {
 
 	@Test
 	public void testGetLong() {
-		assertEquals(12, FullDataTypeEnum.values().length);
+		assertEquals(13, FullDataTypeEnum.values().length);
 		assertEquals("Single-nucleus RNA-seq (snRNA-seq)", FullDataTypeEnum.SINGLE_NUCLEUS_FULL.getFullName());
 		assertEquals("Single-cell RNA-seq (scRNA-seq)", FullDataTypeEnum.SINGLE_CELL_FULL.getFullName());
 		assertEquals("Regional transcriptomics", FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS_FULL.getFullName());
@@ -17,6 +17,7 @@ public void testGetLong() {
 		assertEquals("Spatial Metabolomics", FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName());
 		assertEquals("Spatial N-glycomics", FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName());
 		assertEquals("Regional proteomics", FullDataTypeEnum.REGIONAL_PROTEOMICS_FULL.getFullName());
+        assertEquals("Imaging Mass Cytometry", FullDataTypeEnum.IMAGING_MASS_CYTOMETRY_FULL.getFullName());
 		assertEquals("", FullDataTypeEnum.UNKNOWN_FULL.getFullName());
 	}
 
@@ -29,6 +30,7 @@ public void testFromLong() {
 		assertEquals(FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL, FullDataTypeEnum.fromLong("Spatial Lipidomics"));
 		assertEquals(FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL, FullDataTypeEnum.fromLong("Spatial Metabolomics"));
 		assertEquals(FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL, FullDataTypeEnum.fromLong("Spatial N-glycomics"));	
+        assertEquals(FullDataTypeEnum.IMAGING_MASS_CYTOMETRY_FULL, FullDataTypeEnum.fromLong("Imaging Mass Cytometry"));
 		assertEquals(FullDataTypeEnum.UNKNOWN_FULL, FullDataTypeEnum.fromLong("xxx"));
 		assertEquals(FullDataTypeEnum.UNKNOWN_FULL, FullDataTypeEnum.fromLong(""));
 		assertEquals(FullDataTypeEnum.UNKNOWN_FULL, FullDataTypeEnum.fromLong(null));