Put DTO Functions in Separate Class

virtualcell · Jan 15, 2025 · bfcd643 · bfcd643
1 parent 04e086d
commit bfcd643
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Showing 11 changed files with 115 additions and 104 deletions.
diff --git a/vcell-core/src/main/java/cbit/vcell/field/io/FieldDataFileOperationResults.java b/vcell-core/src/main/java/cbit/vcell/field/io/FieldDataFileOperationResults.java
@@ -53,20 +53,4 @@ public FieldDataFileOperationResults() {
 	super();
 }
 
-	public static FieldDataFileOperationResults fieldDataInfoDTOToFileOperationResults(FieldDataShape dto){
-		FieldDataFileOperationResults results = new FieldDataFileOperationResults();
-		results.extent = Extent.dtoToExtent(dto.getExtent());
-		results.origin = Origin.dtoToOrigin(dto.getOrigin());
-		results.iSize = ISize.dtoToISize(dto.getIsize());
-		results.times = dto.getTimes().stream().mapToDouble(Double::doubleValue).toArray();
-		results.dataIdentifierArr = dto.getDataIdentifier().stream().map(DataIdentifier::dtoToDataIdentifier).toArray(DataIdentifier[]::new);
-		return results;
-	}
-
-	public static FieldDataFileOperationResults fieldDataSaveResultsDTOToFileOperationResults(FieldDataSaveResults dto, User owner){
-		FieldDataFileOperationResults fieldDataFileOperationResults = new FieldDataFileOperationResults();
-		fieldDataFileOperationResults.externalDataIdentifier = new ExternalDataIdentifier(new KeyValue(dto.getFieldDataID()), owner, dto.getFieldDataName());
-		return fieldDataFileOperationResults;
-	}
-
 }
diff --git a/vcell-core/src/main/java/cbit/vcell/field/io/FieldDataFileOperationSpec.java b/vcell-core/src/main/java/cbit/vcell/field/io/FieldDataFileOperationSpec.java
@@ -10,22 +10,15 @@
 
 package cbit.vcell.field.io;
 
-import org.vcell.restclient.model.AnalyzedResultsFromFieldData;
+import cbit.vcell.math.VariableType;
+import cbit.vcell.solvers.CartesianMesh;
 import org.vcell.util.Extent;
 import org.vcell.util.ISize;
 import org.vcell.util.Origin;
 import org.vcell.util.document.ExternalDataIdentifier;
 import org.vcell.util.document.KeyValue;
 import org.vcell.util.document.User;
 
-import cbit.vcell.math.VariableType;
-import cbit.vcell.solvers.CartesianMesh;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.stream.Collectors;
-
 /**
  * Insert the type's description here.
  * Creation date: (1/10/2007 11:00:51 AM)
@@ -88,24 +81,6 @@ public FieldDataFileOperationSpec(short[][][] shortSpecData, double[][][] double
 	this.sourceOwner = sourceOwner;
 }
 
-public static AnalyzedResultsFromFieldData fieldDataSpecToAnalyzedResultsDTO(FieldDataFileOperationSpec fieldDataFileOperationSpec){
-	List<List<List<Integer>>> listVersion = Arrays.stream(fieldDataFileOperationSpec.shortSpecData) // Stream of short[][]
-			.map(twoDArray -> Arrays.stream(twoDArray) // Stream of short[]
-					.map(oneDArray -> {
-						List<Integer> list = new ArrayList<>();
-						for (short j : oneDArray) {
-							list.add((int) j);
-						}
-						return list;
-					}).collect(Collectors.toList())).collect(Collectors.toList());
-	AnalyzedResultsFromFieldData analyzedResultsFromFieldData = new AnalyzedResultsFromFieldData();
-	analyzedResultsFromFieldData.annotation(fieldDataFileOperationSpec.annotation); analyzedResultsFromFieldData.isize(ISize.iSizeToDTO(fieldDataFileOperationSpec.isize));
-	analyzedResultsFromFieldData.extent(Extent.extentToDTO(fieldDataFileOperationSpec.extent)); analyzedResultsFromFieldData.origin(Origin.originToDTO(fieldDataFileOperationSpec.origin));
-	analyzedResultsFromFieldData.times(Arrays.stream(fieldDataFileOperationSpec.times).boxed().toList()); analyzedResultsFromFieldData.setName(fieldDataFileOperationSpec.fieldDataName);
-	analyzedResultsFromFieldData.varNames(Arrays.stream(fieldDataFileOperationSpec.varNames).toList()); analyzedResultsFromFieldData.shortSpecData(listVersion);
-	return analyzedResultsFromFieldData;
-}
-
 
 @Deprecated
 public static FieldDataFileOperationSpec createCopySimFieldDataFileOperationSpec(

diff --git a/vcell-core/src/main/java/cbit/vcell/math/Variable.java b/vcell-core/src/main/java/cbit/vcell/math/Variable.java
@@ -39,11 +39,6 @@ void rename(String newName) {
 
     public static class Domain implements Matchable, Serializable {
 		private String name = null;
-
-		public static Domain dtoToDomain(org.vcell.restclient.model.Domain dto){
-			return new Domain(dto.getName());
-		}
-
 
 		public Domain(String argName){
 			String nameWithPeriodsMangled = argName.replace('.','_');

diff --git a/vcell-core/src/main/java/cbit/vcell/math/VariableType.java b/vcell-core/src/main/java/cbit/vcell/math/VariableType.java
@@ -36,19 +36,6 @@ public class VariableType implements java.io.Serializable, org.vcell.util.Matcha
 
 	public VariableType(){}
 
-	public static org.vcell.restclient.model.VariableType variableTypeToDTO(VariableType vt) {
-		org.vcell.restclient.model.VariableType dto = new org.vcell.restclient.model.VariableType();
-		dto.setType(vt.type);
-		dto.setName(vt.name);
-		dto.setUnits(vt.units);
-		dto.setLabel(vt.label);
-		return dto;
-	}
-
-	public static VariableType dtoToVariableType(org.vcell.restclient.model.VariableType dto) {
-		return new VariableType(dto.getType(), dto.getName(), dto.getUnits(), dto.getLabel());
-	}
-
 	/**
 	 * mark types that were not previously supported by {@link #getVariableTypeFromInteger(int)}, issue warning if triggered
 	 */

diff --git a/vcell-core/src/main/java/cbit/vcell/simdata/DataIdentifier.java b/vcell-core/src/main/java/cbit/vcell/simdata/DataIdentifier.java
@@ -41,12 +41,6 @@ public DataIdentifier(String argName, VariableType argVariableType, Domain argDo
 	displayName = argDisplayName;
 }
 
-public static DataIdentifier dtoToDataIdentifier(org.vcell.restclient.model.DataIdentifier dto){
-	return new DataIdentifier(dto.getName(), VariableType.dtoToVariableType(dto.getVariableType()),
-			dto.getDomain() == null ? null : Domain.dtoToDomain(dto.getDomain()),
-			dto.getbFunction() == null ? false : dto.getbFunction(), dto.getDisplayName());
-}
-
 
 /**
  * Insert the method's description here.

diff --git a/vcell-core/src/main/java/org/vcell/util/document/ExternalDataIdentifier.java b/vcell-core/src/main/java/org/vcell/util/document/ExternalDataIdentifier.java
@@ -26,22 +26,6 @@ public class ExternalDataIdentifier implements SimResampleInfoProvider,java.io.S
 	private org.vcell.util.document.User owner;
 	private String name;
 
-	public static org.vcell.restclient.model.ExternalDataIdentifier externalDataIdentifierToDTO(ExternalDataIdentifier externalDataIdentifier) {
-		org.vcell.restclient.model.ExternalDataIdentifier dto = new org.vcell.restclient.model.ExternalDataIdentifier();
-		dto.key(KeyValue.keyValueToDTO(externalDataIdentifier.getKey()));
-		dto.owner(User.userToDTO(externalDataIdentifier.getOwner()));
-		dto.name(externalDataIdentifier.getName());
-		return dto;
-	}
-
-	public static ExternalDataIdentifier dtoToExternalDataIdentifier(org.vcell.restclient.model.ExternalDataIdentifier dto){
-		ExternalDataIdentifier externalDataIdentifier = new ExternalDataIdentifier();
-		externalDataIdentifier.key = KeyValue.dtoToKeyValue(dto.getDataKey());
-		externalDataIdentifier.name = dto.getName();
-		externalDataIdentifier.owner = User.dtoToUser(dto.getOwner());
-		return externalDataIdentifier;
-	}
-
 /**
  * FieldDataIdentifier constructor comment.
  */

diff --git a/vcell-core/src/main/java/org/vcell/util/document/KeyValue.java b/vcell-core/src/main/java/org/vcell/util/document/KeyValue.java
@@ -20,15 +20,6 @@
 public class KeyValue implements java.io.Serializable, Matchable {
 	private java.math.BigDecimal value = null;
 
-	public static org.vcell.restclient.model.KeyValue keyValueToDTO(KeyValue kv) {
-		org.vcell.restclient.model.KeyValue k = new org.vcell.restclient.model.KeyValue();
-		k.setValue(kv.value);
-		return k;
-	}
-	public static KeyValue dtoToKeyValue(org.vcell.restclient.model.KeyValue dto){
-		return dto == null ? null : new KeyValue(dto.getValue());
-	}
-
 
 public KeyValue(String value) throws NumberFormatException {
 	this.value = new java.math.BigDecimal(value);

diff --git a/vcell-core/src/main/java/org/vcell/util/document/User.java b/vcell-core/src/main/java/org/vcell/util/document/User.java
@@ -26,17 +26,6 @@ public class User implements java.io.Serializable, Matchable, Immutable {
 	private final static String PREVIOUS_DATABASE_VALUE_POWERUSER = "special1";
 	private final static String PREVIOUS_DATABASE_VALUE_PUBLICATION = "publication";
 
-	public static org.vcell.restclient.model.User userToDTO(User user) {
-		org.vcell.restclient.model.User userDTO = new org.vcell.restclient.model.User();
-		userDTO.setUserName(user.userName);
-		userDTO.setKey(KeyValue.keyValueToDTO(user.key));
-		return userDTO;
-	}
-
-	public static User dtoToUser(org.vcell.restclient.model.User dto){
-		return new User(dto.getUserName(), KeyValue.dtoToKeyValue(dto.getKey()));
-	}
-
 	public enum SPECIAL_CLAIM {
 		admins/*special0*/,
 		powerUsers/*special1*/,

diff --git a/vcell-restclient/pom.xml b/vcell-restclient/pom.xml
@@ -204,6 +204,11 @@
             <artifactId>vcell-util</artifactId>
             <version>0.0.1-SNAPSHOT</version>
         </dependency>
+        <dependency>
+            <groupId>org.vcell</groupId>
+            <artifactId>vcell-core</artifactId>
+            <version>0.0.1-SNAPSHOT</version>
+        </dependency>
 
         <!-- JSON processing: jackson -->
         <dependency>

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
@@ -1,8 +1,25 @@
 package org.vcell.restclient.utils;
 
 
+import cbit.vcell.field.io.FieldDataFileOperationResults;
+import cbit.vcell.field.io.FieldDataFileOperationSpec;
+import cbit.vcell.math.Variable;
+import cbit.vcell.math.VariableType;
+import cbit.vcell.simdata.DataIdentifier;
+import org.vcell.restclient.model.AnalyzedResultsFromFieldData;
+import org.vcell.restclient.model.FieldDataSaveResults;
+import org.vcell.restclient.model.FieldDataShape;
 import org.vcell.util.Extent;
 import org.vcell.util.Origin;
+import org.vcell.util.document.ExternalDataIdentifier;
+import org.vcell.util.document.KeyValue;
+import org.vcell.util.document.User;
+
+import java.math.BigDecimal;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
 
 public class DtoModelTransforms {
 
@@ -43,5 +60,95 @@ public static Extent dtoToExtent(org.vcell.restclient.model.Extent dto) {
         return new Extent(dto.getX(), dto.getY(), dto.getZ());
     }
 
+    public static DataIdentifier dtoToDataIdentifier(org.vcell.restclient.model.DataIdentifier dto){
+        return new DataIdentifier(dto.getName(), dtoToVariableType(dto.getVariableType()),
+                dto.getDomain() == null ? null : dtoToDomain(dto.getDomain()),
+                dto.getbFunction() == null ? false : dto.getbFunction(), dto.getDisplayName());
+    }
+
+    public static org.vcell.restclient.model.VariableType variableTypeToDTO(VariableType vt) {
+        org.vcell.restclient.model.VariableType dto = new org.vcell.restclient.model.VariableType();
+        dto.setType(vt.getType());
+        dto.setName(vt.getTypeName());
+        dto.setUnits(vt.getDefaultUnits());
+        dto.setLabel(vt.getDefaultLabel());
+        return dto;
+    }
+
+    public static VariableType dtoToVariableType(org.vcell.restclient.model.VariableType dto) {
+        return VariableType.getVariableTypeFromInteger(dto.getType());
+    }
+
+    public static Variable.Domain dtoToDomain(org.vcell.restclient.model.Domain dto){
+        return new Variable.Domain(dto.getName());
+    }
+
+    public static org.vcell.restclient.model.ExternalDataIdentifier externalDataIdentifierToDTO(ExternalDataIdentifier externalDataIdentifier) {
+        org.vcell.restclient.model.ExternalDataIdentifier dto = new org.vcell.restclient.model.ExternalDataIdentifier();
+        dto.key(keyValueToDTO(externalDataIdentifier.getKey()));
+        dto.owner(userToDTO(externalDataIdentifier.getOwner()));
+        dto.name(externalDataIdentifier.getName());
+        return dto;
+    }
+
+    public static ExternalDataIdentifier dtoToExternalDataIdentifier(org.vcell.restclient.model.ExternalDataIdentifier dto){
+        return new ExternalDataIdentifier(
+                dtoToKeyValue(dto.getKey()), dtoToUser(dto.getOwner()), dto.getName()
+        );
+    }
+
+    public static org.vcell.restclient.model.KeyValue keyValueToDTO(KeyValue kv) {
+        org.vcell.restclient.model.KeyValue k = new org.vcell.restclient.model.KeyValue();
+        k.setValue(kv.toString().transform(BigDecimal::new));
+        return k;
+    }
+    public static KeyValue dtoToKeyValue(org.vcell.restclient.model.KeyValue dto){
+        return dto == null ? null : new KeyValue(dto.getValue());
+    }
+
+    public static org.vcell.restclient.model.User userToDTO(User user) {
+        org.vcell.restclient.model.User userDTO = new org.vcell.restclient.model.User();
+        userDTO.setUserName(user.getName());
+        userDTO.setKey(keyValueToDTO(user.getID()));
+        return userDTO;
+    }
+
+    public static User dtoToUser(org.vcell.restclient.model.User dto){
+        return new User(dto.getUserName(), dtoToKeyValue(dto.getKey()));
+    }
+
+    public static FieldDataFileOperationResults fieldDataInfoDTOToFileOperationResults(FieldDataShape dto){
+        FieldDataFileOperationResults results = new FieldDataFileOperationResults();
+        results.extent = dtoToExtent(dto.getExtent());
+        results.origin = dtoToOrigin(dto.getOrigin());
+        results.iSize = dtoToISize(dto.getIsize());
+        results.times = dto.getTimes().stream().mapToDouble(Double::doubleValue).toArray();
+        results.dataIdentifierArr = dto.getDataIdentifier().stream().map(DtoModelTransforms::dtoToDataIdentifier).toArray(DataIdentifier[]::new);
+        return results;
+    }
+
+    public static FieldDataFileOperationResults fieldDataSaveResultsDTOToFileOperationResults(FieldDataSaveResults dto, User owner){
+        FieldDataFileOperationResults fieldDataFileOperationResults = new FieldDataFileOperationResults();
+        fieldDataFileOperationResults.externalDataIdentifier = new ExternalDataIdentifier(new KeyValue(dto.getFieldDataID()), owner, dto.getFieldDataName());
+        return fieldDataFileOperationResults;
+    }
+
+    public static AnalyzedResultsFromFieldData fieldDataSpecToAnalyzedResultsDTO(FieldDataFileOperationSpec fieldDataFileOperationSpec){
+        List<List<List<Integer>>> listVersion = Arrays.stream(fieldDataFileOperationSpec.shortSpecData) // Stream of short[][]
+                .map(twoDArray -> Arrays.stream(twoDArray) // Stream of short[]
+                        .map(oneDArray -> {
+                            List<Integer> list = new ArrayList<>();
+                            for (short j : oneDArray) {
+                                list.add((int) j);
+                            }
+                            return list;
+                        }).collect(Collectors.toList())).collect(Collectors.toList());
+        AnalyzedResultsFromFieldData analyzedResultsFromFieldData = new AnalyzedResultsFromFieldData();
+        analyzedResultsFromFieldData.annotation(fieldDataFileOperationSpec.annotation); analyzedResultsFromFieldData.isize(iSizeToDTO(fieldDataFileOperationSpec.isize));
+        analyzedResultsFromFieldData.extent(extentToDTO(fieldDataFileOperationSpec.extent)); analyzedResultsFromFieldData.origin(originToDTO(fieldDataFileOperationSpec.origin));
+        analyzedResultsFromFieldData.times(Arrays.stream(fieldDataFileOperationSpec.times).boxed().toList()); analyzedResultsFromFieldData.setName(fieldDataFileOperationSpec.fieldDataName);
+        analyzedResultsFromFieldData.varNames(Arrays.stream(fieldDataFileOperationSpec.varNames).toList()); analyzedResultsFromFieldData.shortSpecData(listVersion);
+        return analyzedResultsFromFieldData;
+    }
 
 }
diff --git a/vcell-util/pom.xml b/vcell-util/pom.xml
@@ -138,7 +138,7 @@
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-annotations</artifactId>
-			<version>${jackson-version}</version>
+			<version>${jackson-annotations.version}</version>
 		</dependency>
 		<dependency>
 		  <groupId>com.sun.xml.bind</groupId>