Merge pull request #131 from openworm/development

Release 0.3.6

LICENSE

@@ -1,15 +1,15 @@
 The MIT License (MIT)
 
-Copyright (c) 2011, 2013 OpenWorm.
-http://openworm.org
+Copyright © 2011, 2017 Geppetto authors
+http://geppetto.org
 
 All rights reserved. This program and the accompanying materials
 are made available under the terms of the MIT License
 which accompanies this distribution, and is available at
 http://opensource.org/licenses/MIT
 
 Contributors:
-     OpenWorm - http://openworm.org/people.html
+     Geppetto - http://contributors.geppetto.org
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

pom.xml

@@ -4,7 +4,7 @@
 	<groupId>org.geppetto</groupId>
 	<artifactId>core</artifactId>
 	<name>Geppetto Core Bundle</name>
-	<version>0.3.5</version>
+	<version>0.3.6</version>
 	<packaging>bundle</packaging>
 	<properties>
 		<github.global.server>github</github.global.server>
@@ -163,6 +163,11 @@
 			<artifactId>jackson-databind</artifactId>
 			<version>2.5.3</version>
 		</dependency>
+		<dependency>
+			<groupId>uk.com.robust-it</groupId>
+			<artifactId>cloning</artifactId>
+			<version>1.9.3</version>
+		</dependency>
 	</dependencies>
 	<repositories>
 		<repository>

src/main/java/org/geppetto/core/beans/PathConfiguration.java

@@ -226,6 +226,20 @@ public static File createFolderInProjectTmpFolder(Scope scope, long projectId, S
 		return folder;
 	}
 
+	/**
+	 * @param scope
+	 * @param projectId
+	 * @param folderName
+	 * @return
+	 */
+	public static File createFolderInExperimentTmpFolder(Scope scope, long projectId, long experimentId, String instancePath, String folderName)
+	{
+		File folder = new File(createExperimentTmpPath(scope, projectId, experimentId, instancePath, folderName) + File.separator);
+		// createProjectTmpFolder creates only up to the project level, the following mkdir will create also folderName
+		folder.mkdir();
+		return folder;
+	}
+
 	public static URL getModelSchemaURL()
 	{
 		return PathConfiguration.class.getResource("/schema/geppettoModel/geppettoModelSchema.xsd");

src/main/java/org/geppetto/core/common/HDF5Reader.java

@@ -68,7 +68,7 @@ public static H5File readHDF5File(URL url, long projectId) throws GeppettoExecut
 				// https://github.com/jrmartin/hdf5-java-bindings/blob/master/src/main/java/ncsa/hdf/hdf5lib/H5.java#L2566
 
 				// The scope is CONNECTION since if we are reading a recording the simulation has already happened
-				url = URLReader.createLocalCopy(Scope.CONNECTION, projectId, url);
+				url = URLReader.createLocalCopy(Scope.CONNECTION, projectId, url, true);
 			}
 			H5File testFile = (H5File) fileFormat.createInstance(url.getPath(), FileFormat.READ);
 

src/main/java/org/geppetto/core/conversion/AConversion.java

@@ -34,6 +34,7 @@
 package org.geppetto.core.conversion;
 
 import org.geppetto.core.beans.PathConfiguration;
+import org.geppetto.core.data.model.IExperiment;
 import org.geppetto.core.services.AService;
 import org.geppetto.model.ModelFormat;
 
@@ -45,6 +46,7 @@ public abstract class AConversion extends AService implements IConversion
 {
 
 	protected boolean convertModel = true;
+	private IExperiment experiment;
 
 	public void checkSupportedFormat(ModelFormat input) throws ConversionException
 	{
@@ -64,4 +66,14 @@ public void setConvertModel(boolean convert)
 		this.convertModel = convert;
 	}
 
+	public void setExperiment(IExperiment experiment)
+	{
+		this.experiment=experiment;
+	}
+
+	public IExperiment getExperiment()
+	{
+		return this.experiment;
+	}
+
 }

src/main/java/org/geppetto/core/data/DefaultGeppettoDataManager.java

@@ -59,6 +59,7 @@
 import org.geppetto.core.data.model.ISimulatorConfiguration;
 import org.geppetto.core.data.model.IUser;
 import org.geppetto.core.data.model.IUserGroup;
+import org.geppetto.core.data.model.IView;
 import org.geppetto.core.data.model.PersistedDataType;
 import org.geppetto.core.data.model.ResultsFormat;
 import org.geppetto.core.data.model.UserPrivileges;
@@ -71,9 +72,12 @@
 import org.geppetto.core.data.model.local.LocalSimulatorConfiguration;
 import org.geppetto.core.data.model.local.LocalUser;
 import org.geppetto.core.data.model.local.LocalUserGroup;
+import org.geppetto.core.data.model.local.LocalView;
+import org.geppetto.core.utilities.LocalViewSerializer;
 import org.springframework.http.HttpStatus;
 
 import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
 
 public class DefaultGeppettoDataManager implements IGeppettoDataManager
 {
@@ -139,15 +143,16 @@ public IUser getUserByLogin(String login)
 
 		return user;
 	}
-	
+
 	/*
 	 * (non-Javadoc)
 	 * 
 	 * @see org.geppetto.core.data.IGeppettoDataManager#getUserGroupById(long)
 	 */
 	@Override
-	public IUserGroup getUserGroupById(long id){
-		return getUserGroup();	
+	public IUserGroup getUserGroupById(long id)
+	{
+		return getUserGroup();
 	}
 
 	/*
@@ -226,8 +231,6 @@ public List<? extends IExperiment> getExperimentsForProject(long projectId)
 		return project.getExperiments();
 	}
 
-
-
 	/*
 	 * (non-Javadoc)
 	 * 
@@ -256,8 +259,7 @@ public IExperiment newExperiment(String name, String description, IGeppettoProje
 	/*
 	 * (non-Javadoc)
 	 * 
-	 * @see org.geppetto.core.data.IGeppettoDataManager#cloneExperiment(java.lang.String, java.lang.String,
-	 * 		org.geppetto.core.data.model.IGeppettoProject,org.geppetto.core.data.model.IExperiment)
+	 * @see org.geppetto.core.data.IGeppettoDataManager#cloneExperiment(java.lang.String, java.lang.String, org.geppetto.core.data.model.IGeppettoProject,org.geppetto.core.data.model.IExperiment)
 	 */
 	@Override
 	public IExperiment cloneExperiment(String name, String description, IGeppettoProject project, IExperiment e)
@@ -268,7 +270,7 @@ public IExperiment cloneExperiment(String name, String description, IGeppettoPro
 		((LocalGeppettoProject) project).getExperiments().add(experiment);
 		return experiment;
 	}
-	
+
 	/*
 	 * (non-Javadoc)
 	 * 
@@ -349,10 +351,15 @@ private void loadGeppettoProjects() throws IOException, URISyntaxException
 	@Override
 	public IGeppettoProject getProjectFromJson(Gson gson, String json)
 	{
-		LocalGeppettoProject project = gson.fromJson(json, LocalGeppettoProject.class);
+		GsonBuilder gsonBuilder = new GsonBuilder();
+		gsonBuilder.registerTypeAdapter(LocalGeppettoProject.class, new LocalViewSerializer());
+
+		LocalGeppettoProject project = gsonBuilder.create().fromJson(json, LocalGeppettoProject.class);
 		project.setId(getRandomId());
 		project.setVolatile(true);
-
+		if(project.getView()==null){
+			DataManagerHelper.getDataManager().newView(null, project);
+		}
 		// set project as parent for experiments
 		for(IExperiment e : project.getExperiments())
 		{
@@ -375,12 +382,18 @@ private long getRandomId()
 	 * @see org.geppetto.core.data.IGeppettoDataManager#getProjectFromJson(com.google.gson.Gson, java.io.Reader)
 	 */
 	@Override
-	public IGeppettoProject getProjectFromJson(Gson gson, Reader json)
+	public IGeppettoProject getProjectFromJson(Gson gson, Reader json, String baseURL)
 	{
-		LocalGeppettoProject project = gson.fromJson(json, LocalGeppettoProject.class);
+		GsonBuilder gsonBuilder = new GsonBuilder();
+		gsonBuilder.registerTypeAdapter(LocalGeppettoProject.class, new LocalViewSerializer());
+
+		LocalGeppettoProject project = gsonBuilder.create().fromJson(json, LocalGeppettoProject.class);
 		project.setId(getRandomId());
 		project.setVolatile(true);
-
+		project.setBaseURL(baseURL);
+		if(project.getView()==null){
+			DataManagerHelper.getDataManager().newView(null, project);
+		}
 		// set project as parent for experiments
 		for(IExperiment e : project.getExperiments())
 		{
@@ -399,8 +412,7 @@ public IGeppettoProject getProjectFromJson(Gson gson, Reader json)
 	@Override
 	public void clearWatchedVariables(IAspectConfiguration aspectConfig)
 	{
-		// TODO Auto-generated method stub
-
+		// Cannot do watch without db, cannot clear watched
 	}
 
 	@Override
@@ -436,16 +448,15 @@ public void saveEntity(IGeppettoProject entity)
 	@Override
 	public IAspectConfiguration newAspectConfiguration(IExperiment experiment, String instancePath, ISimulatorConfiguration simulatorConfiguration)
 	{
-		LocalAspectConfiguration ac = new LocalAspectConfiguration(0l, instancePath, new ArrayList<String>(), new ArrayList<LocalParameter>(),
-				(LocalSimulatorConfiguration) simulatorConfiguration);
+		LocalAspectConfiguration ac = new LocalAspectConfiguration(0l, instancePath, new ArrayList<String>(), new ArrayList<LocalParameter>(), (LocalSimulatorConfiguration) simulatorConfiguration);
 		((LocalExperiment) experiment).getAspectConfigurations().add(ac);
 		return ac;
 	}
 
 	@Override
-	public ISimulatorConfiguration newSimulatorConfiguration(String simulator, String conversionService, float timestep, float length,Map<String, String> parameters)
+	public ISimulatorConfiguration newSimulatorConfiguration(String simulator, String conversionService, float timestep, float length, Map<String, String> parameters)
 	{
-		return new LocalSimulatorConfiguration(0l, simulator, conversionService, timestep, length,parameters);
+		return new LocalSimulatorConfiguration(0l, simulator, conversionService, timestep, length, parameters);
 	}
 
 	@Override
@@ -489,9 +500,25 @@ private static IUserGroup getUserGroup()
 	}
 
 	@Override
-	public void makeGeppettoProjectPublic(long projectId, boolean isPublic)
-			throws GeppettoExecutionException {
+	public void makeGeppettoProjectPublic(long projectId, boolean isPublic) throws GeppettoExecutionException
+	{
 		// TODO Auto-generated method stub
-
+
+	}
+
+	@Override
+	public IView newView(String view, IExperiment experiment)
+	{
+		IView v = new LocalView(1, view);
+		experiment.setView(v);
+		return v;
+	}
+
+	@Override
+	public IView newView(String view, IGeppettoProject project)
+	{
+		IView v = new LocalView(1, view);
+		project.setView(v);
+		return v;
 	}
 }

src/main/java/org/geppetto/core/data/FindLocalProjectsVisitor.java

@@ -46,6 +46,10 @@
 
 import org.geppetto.core.data.model.IExperiment;
 import org.geppetto.core.data.model.IGeppettoProject;
+import org.geppetto.core.data.model.IView;
+import org.geppetto.core.data.model.local.LocalGeppettoProject;
+import org.geppetto.core.data.model.local.LocalView;
+import org.geppetto.core.utilities.LocalViewSerializer;
 
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
@@ -85,10 +89,14 @@ public Date deserialize(JsonElement json, Type typeOfT, JsonDeserializationConte
 				}
 
 			});
-			Gson gson = builder.create();
-
 			BufferedReader reader = Files.newBufferedReader(file, StandardCharsets.UTF_8);
-			T project = gson.fromJson(reader, type);
+
+			builder.registerTypeAdapter(LocalGeppettoProject.class, new LocalViewSerializer());
+			T project = builder.create().fromJson(reader, type);
+			if(project.getView() == null)
+			{
+				project.setView(new LocalView(0, null));
+			}
 			for(IExperiment e : project.getExperiments())
 			{
 				e.setParentProject(project);

src/main/java/org/geppetto/core/data/IGeppettoDataManager.java

@@ -49,6 +49,7 @@
 import org.geppetto.core.data.model.ISimulatorConfiguration;
 import org.geppetto.core.data.model.IUser;
 import org.geppetto.core.data.model.IUserGroup;
+import org.geppetto.core.data.model.IView;
 import org.geppetto.core.data.model.PersistedDataType;
 import org.geppetto.core.data.model.ResultsFormat;
 import org.geppetto.core.data.model.UserPrivileges;
@@ -82,7 +83,7 @@ public interface IGeppettoDataManager
 
 	IGeppettoProject getProjectFromJson(Gson gson, String json);
 
-	IGeppettoProject getProjectFromJson(Gson gson, Reader json);
+	IGeppettoProject getProjectFromJson(Gson gson, Reader json, String baseURL);
 
 	List<? extends IExperiment> getExperimentsForProject(long projectId);
 
@@ -95,6 +96,10 @@ public interface IGeppettoDataManager
 	IParameter newParameter(String parameterPath, String value);
 
 	IExperiment newExperiment(String name, String description, IGeppettoProject project);
+
+	IView newView(String view, IGeppettoProject project);
+
+	IView newView(String view, IExperiment experiment);
 
 	IUser newUser(String name, String password, boolean persistent, IUserGroup group);
 
@@ -123,5 +128,7 @@ public interface IGeppettoDataManager
 	void saveEntity(IGeppettoProject entity);
 
 	IExperiment cloneExperiment(String name, String description,
-			IGeppettoProject project, IExperiment originalExperiment);	
+			IGeppettoProject project, IExperiment originalExperiment);
+
+
 }

src/main/java/org/geppetto/core/data/model/IExperiment.java

@@ -88,4 +88,8 @@ public interface IExperiment extends IDataEntity
 	void updateEndDate();
 
 	boolean isPublic();
+
+	void setView(IView view);
+
+	IView getView();
 }

src/main/java/org/geppetto/core/data/model/IGeppettoProject.java

@@ -54,4 +54,12 @@ public interface IGeppettoProject extends IDataEntity
 	void setVolatile(boolean volatileProject);
 
 	boolean isPublic();
+
+	void setView(IView view);
+
+	IView getView();
+
+	String getBaseURL();
+
+	void setBaseURL(String baseURL);
 }

src/main/java/org/geppetto/core/data/model/IView.java

@@ -0,0 +1,13 @@
+package org.geppetto.core.data.model;
+
+public interface IView {
+
+
+	long getId();
+
+	String getView();
+
+	void setView(String string);
+
+
+}