WIP: some changes to pom.xml files

virtualcell · Jan 14, 2025 · 04e086d · 04e086d
1 parent 49a20b3
commit 04e086d
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Showing 9 changed files with 73 additions and 74 deletions.
diff --git a/pom.xml b/pom.xml
@@ -124,6 +124,8 @@
 		<jackson-core.version>2.15.2</jackson-core.version>
 		<jackson-databind.version>2.15.2</jackson-databind.version>
 		<jackson-dataformat-yaml.version>2.15.2</jackson-dataformat-yaml.version>
+		<jackson-datatype.version>2.15.2</jackson-datatype.version>
+		<jakarta-annotation.version>1.3.5</jakarta-annotation.version>
 		<jama.version>1.0.3</jama.version>
 		<jaxb-api.version>2.3.0</jaxb-api.version>
 		<jaxb-core.version>2.3.0</jaxb-core.version>

diff --git a/vcell-core/pom.xml b/vcell-core/pom.xml
@@ -102,11 +102,6 @@
 			<artifactId>vcell-util</artifactId>
 			<version>${project.version}</version>
 		</dependency>
-		<dependency>
-			<groupId>org.vcell</groupId>
-			<artifactId>vcell-apiclient</artifactId>
-			<version>${project.version}</version>
-		</dependency>
 		<dependency>
 			<groupId>com.google.inject</groupId>
 			<artifactId>guice</artifactId>
@@ -656,12 +651,6 @@
 			<artifactId>commons-codec</artifactId>
 			<version>${commons-codec.version}</version>
 		</dependency>
-		<dependency>
-			<groupId>org.vcell</groupId>
-			<artifactId>vcell-restclient</artifactId>
-			<version>0.0.1-SNAPSHOT</version>
-		</dependency>
-
     </dependencies>
 
 	<profiles>

diff --git a/vcell-rest/src/test/java/org/vcell/restq/apiclient/FieldDataAPITest.java b/vcell-rest/src/test/java/org/vcell/restq/apiclient/FieldDataAPITest.java
@@ -17,6 +17,7 @@
 import org.vcell.restclient.model.FieldDataReference;
 import org.vcell.restclient.model.FieldDataSaveResults;
 import org.vcell.restclient.model.FieldDataShape;
+import org.vcell.restclient.utils.DtoModelTransforms;
 import org.vcell.restq.TestEndpointUtils;
 import org.vcell.restq.config.CDIVCellConfigProvider;
 import org.vcell.restq.db.AgroalConnectionFactory;
@@ -115,16 +116,16 @@ public void testAddAndDeleteFieldDataFromFile() throws ApiException {
         ///////////////////
         AnalyzedResultsFromFieldData saveFieldDataFromFile = new AnalyzedResultsFromFieldData();
         saveFieldDataFromFile.setShortSpecData(matrix); saveFieldDataFromFile.varNames(varNames);
-        saveFieldDataFromFile.times(times); saveFieldDataFromFile.origin(Origin.originToDTO(origin)); saveFieldDataFromFile.extent(Extent.extentToDTO(extent));
-        saveFieldDataFromFile.isize(ISize.iSizeToDTO(iSize)); saveFieldDataFromFile.annotation("test annotation"); saveFieldDataFromFile.name("TestFile");
+        saveFieldDataFromFile.times(times); saveFieldDataFromFile.origin(DtoModelTransforms.originToDTO(origin)); saveFieldDataFromFile.extent(DtoModelTransforms.extentToDTO(extent));
+        saveFieldDataFromFile.isize(DtoModelTransforms.iSizeToDTO(iSize)); saveFieldDataFromFile.annotation("test annotation"); saveFieldDataFromFile.name("TestFile");
         FieldDataSaveResults results = fieldDataResourceApi.createFieldDataFromAnalyzedFile(saveFieldDataFromFile);
 
         // File is Saved on File System
         FieldDataShape fieldDataInfo = fieldDataResourceApi.getFieldDataShapeFromID(results.getFieldDataID());
         Assertions.assertEquals(saveFieldDataFromFile.getName(), results.getFieldDataName());
-        Assertions.assertTrue(origin.compareEqual(Origin.dtoToOrigin(fieldDataInfo.getOrigin())));
-        Assertions.assertTrue(extent.compareEqual(Extent.dtoToExtent(fieldDataInfo.getExtent())));
-        Assertions.assertTrue(iSize.compareEqual(ISize.dtoToISize(fieldDataInfo.getIsize())));
+        Assertions.assertTrue(origin.compareEqual(DtoModelTransforms.dtoToOrigin(fieldDataInfo.getOrigin())));
+        Assertions.assertTrue(extent.compareEqual(DtoModelTransforms.dtoToExtent(fieldDataInfo.getExtent())));
+        Assertions.assertTrue(iSize.compareEqual(DtoModelTransforms.dtoToISize(fieldDataInfo.getIsize())));
         Assertions.assertEquals(times, fieldDataInfo.getTimes());
 
         // It's in the DB
@@ -171,9 +172,9 @@ public void testFileUploading() throws ApiException, IOException {
 
         FieldDataShape fieldDataInfo = fieldDataResourceApi.getFieldDataShapeFromID(saveResults.getFieldDataID());
         Assertions.assertNotNull(fieldDataInfo);
-        Assertions.assertTrue(Origin.dtoToOrigin(fieldDataInfo.getOrigin()).compareEqual(new Origin(0.0, 0.0, 0.0)));
-        Assertions.assertTrue(Extent.dtoToExtent(fieldDataInfo.getExtent()).compareEqual(new Extent(684.9333393978472, 684.9333393978472, 1)));
-        Assertions.assertTrue(ISize.dtoToISize(fieldDataInfo.getIsize()).compareEqual(new ISize(256, 256, 1)));
+        Assertions.assertTrue(DtoModelTransforms.dtoToOrigin(fieldDataInfo.getOrigin()).compareEqual(new Origin(0.0, 0.0, 0.0)));
+        Assertions.assertTrue(DtoModelTransforms.dtoToExtent(fieldDataInfo.getExtent()).compareEqual(new Extent(684.9333393978472, 684.9333393978472, 1)));
+        Assertions.assertTrue(DtoModelTransforms.dtoToISize(fieldDataInfo.getIsize()).compareEqual(new ISize(256, 256, 1)));
         Assertions.assertEquals(1, fieldDataInfo.getTimes().size());
 
         fieldDataResourceApi.deleteFieldData(saveResults.getFieldDataID());

diff --git a/vcell-restclient/pom.xml b/vcell-restclient/pom.xml
@@ -199,27 +199,32 @@
 <!--    </profiles>-->
 
     <dependencies>
+        <dependency>
+            <groupId>org.vcell</groupId>
+            <artifactId>vcell-util</artifactId>
+            <version>0.0.1-SNAPSHOT</version>
+        </dependency>
 
         <!-- JSON processing: jackson -->
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-core</artifactId>
-            <version>${jackson-version}</version>
+            <version>${jackson-core.version}</version>
         </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-annotations</artifactId>
-            <version>${jackson-version}</version>
+            <version>${jackson-annotations.version}</version>
         </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>${jackson-version}</version>
+            <version>${jackson-databind.version}</version>
         </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.datatype</groupId>
             <artifactId>jackson-datatype-jsr310</artifactId>
-            <version>${jackson-version}</version>
+            <version>${jackson-datatype.version}</version>
         </dependency>
         <dependency>
             <groupId>com.nimbusds</groupId>
@@ -242,7 +247,7 @@
         <dependency>
             <groupId>jakarta.annotation</groupId>
             <artifactId>jakarta.annotation-api</artifactId>
-            <version>${jakarta-annotation-version}</version>
+            <version>${jakarta-annotation.version}</version>
             <scope>provided</scope>
         </dependency>
 
@@ -274,16 +279,6 @@
             <scope>compile</scope>
         </dependency>
 
-
     </dependencies>
 
-    <properties>
-<!--        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>-->
-<!--        <maven.compiler.source>11</maven.compiler.source>-->
-<!--        <maven.compiler.target>11</maven.compiler.target>-->
-        <jackson-version>2.15.2</jackson-version>
-<!--        <jackson-databind-nullable-version>0.2.6</jackson-databind-nullable-version>-->
-        <jakarta-annotation-version>1.3.5</jakarta-annotation-version>
-<!--        <spotless.version>2.27.2</spotless.version>-->
-    </properties>
 </project>
diff --git a/vcell-restclient/src/main/java/org/vcell/restclient/utils/DtoModelTransforms.java b/vcell-restclient/src/main/java/org/vcell/restclient/utils/DtoModelTransforms.java
@@ -0,0 +1,47 @@
+package org.vcell.restclient.utils;
+
+
+import org.vcell.util.Extent;
+import org.vcell.util.Origin;
+
+public class DtoModelTransforms {
+
+    public static org.vcell.restclient.model.ISize iSizeToDTO(org.vcell.util.ISize iSize){
+        org.vcell.restclient.model.ISize iSizeDTO = new org.vcell.restclient.model.ISize();
+        iSizeDTO.setX(iSize.getX());
+        iSizeDTO.setY(iSize.getY());
+        iSizeDTO.setZ(iSize.getZ());
+        return iSizeDTO;
+    }
+
+    public static org.vcell.util.ISize dtoToISize(org.vcell.restclient.model.ISize dto){
+        return new org.vcell.util.ISize(dto.getX(), dto.getY(), dto.getZ());
+    }
+
+    public static org.vcell.restclient.model.Origin originToDTO(Origin origin){
+        org.vcell.restclient.model.Origin dtoOrigin = new org.vcell.restclient.model.Origin();
+        dtoOrigin.setX(origin.getX());
+        dtoOrigin.setY(origin.getY());
+        dtoOrigin.setZ(origin.getZ());
+        return dtoOrigin;
+    }
+
+    public static Origin dtoToOrigin(org.vcell.restclient.model.Origin dtoOrigin){
+        return new Origin(dtoOrigin.getX(), dtoOrigin.getY(), dtoOrigin.getZ());
+    }
+
+
+    public static org.vcell.restclient.model.Extent extentToDTO(Extent extent) {
+        org.vcell.restclient.model.Extent newExtent = new org.vcell.restclient.model.Extent();
+        newExtent.setX(extent.getX());
+        newExtent.setY(extent.getY());
+        newExtent.setZ(extent.getZ());
+        return newExtent;
+    }
+
+    public static Extent dtoToExtent(org.vcell.restclient.model.Extent dto) {
+        return new Extent(dto.getX(), dto.getY(), dto.getZ());
+    }
+
+
+}
diff --git a/vcell-util/pom.xml b/vcell-util/pom.xml
@@ -135,15 +135,15 @@
 		  <artifactId>jaxb-core</artifactId>
 		  <version>${jaxb-core.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-annotations</artifactId>
+			<version>${jackson-version}</version>
+		</dependency>
 		<dependency>
 		  <groupId>com.sun.xml.bind</groupId>
 		  <artifactId>jaxb-impl</artifactId>
 		  <version>${jaxb-impl.version}</version>
 		</dependency>
-		<dependency>
-			<groupId>org.vcell</groupId>
-			<artifactId>vcell-restclient</artifactId>
-			<version>0.0.1-SNAPSHOT</version>
-		</dependency>
 	</dependencies>
 </project>
diff --git a/vcell-util/src/main/java/org/vcell/util/Extent.java b/vcell-util/src/main/java/org/vcell/util/Extent.java
@@ -25,18 +25,6 @@ public class Extent implements java.io.Serializable, Matchable {
 	private double z;
 	public Extent() {}//For jaxb
 
-	public static org.vcell.restclient.model.Extent extentToDTO(Extent extent) {
-		org.vcell.restclient.model.Extent newExtent = new org.vcell.restclient.model.Extent();
-		newExtent.setX(extent.getX());
-		newExtent.setY(extent.getY());
-		newExtent.setZ(extent.getZ());
-		return newExtent;
-	}
-
-	public static Extent dtoToExtent(org.vcell.restclient.model.Extent dto) {
-        return new Extent(dto.getX(), dto.getY(), dto.getZ());
-	}
-
 /**
  * Origin constructor comment.
  */

diff --git a/vcell-util/src/main/java/org/vcell/util/ISize.java b/vcell-util/src/main/java/org/vcell/util/ISize.java
@@ -21,17 +21,6 @@ public class ISize implements java.io.Serializable, Matchable {
 	private int y;
 	private int z;
 
-	public static org.vcell.restclient.model.ISize iSizeToDTO(ISize iSize){
-		org.vcell.restclient.model.ISize iSizeDTO = new org.vcell.restclient.model.ISize();
-		iSizeDTO.setX(iSize.getX());
-		iSizeDTO.setY(iSize.getY());
-		iSizeDTO.setZ(iSize.getZ());
-		return iSizeDTO;
-	}
-
-	public static ISize dtoToISize(org.vcell.restclient.model.ISize dto){
-        return new ISize(dto.getX(), dto.getY(), dto.getZ());
-	}
 	public ISize(){}
 
 /**

diff --git a/vcell-util/src/main/java/org/vcell/util/Origin.java b/vcell-util/src/main/java/org/vcell/util/Origin.java
@@ -24,18 +24,6 @@ public class Origin implements java.io.Serializable, Matchable {
 	private double z;
 	public Origin() {}//For jaxb
 
-public static org.vcell.restclient.model.Origin originToDTO(Origin origin){
-	org.vcell.restclient.model.Origin dtoOrigin = new org.vcell.restclient.model.Origin();
-	dtoOrigin.setX(origin.getX());
-	dtoOrigin.setY(origin.getY());
-	dtoOrigin.setZ(origin.getZ());
-	return dtoOrigin;
-}
-
-public static Origin dtoToOrigin(org.vcell.restclient.model.Origin dtoOrigin){
-    return new Origin(dtoOrigin.getX(), dtoOrigin.getY(), dtoOrigin.getZ());
-}
-
 /**
  * Origin constructor comment.
  */