more changes to enable the import

rest_ocd_services/src/main/java/i5/las2peer/services/ocd/ServiceClass.java

@@ -600,15 +600,15 @@ public Response createMultiplexGraph(@DefaultValue("unnamed") @QueryParam("name"
 				log.setStatus(ExecutionStatus.COMPLETED);
 				graph.setCreationMethod(log);
 				GraphProcessor processor = new GraphProcessor();
-				processor.determineGraphTypes(graph);
+				//processor.determineGraphTypes(graph);
 				//if (doMakeUndirected) {
 				//	Set<GraphType> graphTypes = graph.getTypes();
 				//	if (graphTypes.remove(GraphType.DIRECTED)) {
 				//		processor.makeCompatible(graph, graphTypes);
 				//	}
 				//}
 				try {
-					database.storeGraph(graph);
+					database.storeMultiplexGraph(graph);
 					generalLogger.getLogger().log(Level.INFO, "user " + username + ": import graph " + graph.getKey() + " in format " + graphInputFormatStr);
 				} catch (Exception e) {
 					return requestHandler.writeError(Error.INTERNAL, "Could not store graph");
@@ -733,12 +733,15 @@ public Response processStoredGraph(@DefaultValue("unnamed") @QueryParam("name")
 				return requestHandler.writeError(Error.INTERNAL, "Internal system error.");
 			}
 			graphFile.delete();
-			if (graphInputFormatStr.equals("MULTIPLEX_WEIGHTED_EDGE_LIST" || graphInputFormatStr.equals("MULTIPLEX_UNWEIGHTED_EDGE_LIST"))
-				return createMultiplexGraph(nameStr, creationTypeStr, graphInputFormatStr, doMakeUndirectedStr, startDateStr,
+			Response response;
+			if (graphInputFormatStr.equals("MULTIPLEX_WEIGHTED_EDGE_LIST") || graphInputFormatStr.equals("MULTIPLEX_UNWEIGHTED_EDGE_LIST")){
+				response = createMultiplexGraph(nameStr, creationTypeStr, graphInputFormatStr, doMakeUndirectedStr, startDateStr,
+						endDateStr,involvedUserURIsStr, showUserNamesStr, indexPathStr, filePathStr, contentStr.toString());
+			}else{
+				response = createGraph(nameStr, creationTypeStr, graphInputFormatStr, doMakeUndirectedStr, startDateStr,
 						endDateStr,involvedUserURIsStr, showUserNamesStr, indexPathStr, filePathStr, contentStr.toString());
 			}
-			return createGraph(nameStr, creationTypeStr, graphInputFormatStr, doMakeUndirectedStr, startDateStr,
-					endDateStr,involvedUserURIsStr, showUserNamesStr, indexPathStr, filePathStr, contentStr.toString());
+			return response;
 		}
 
 		/**

rest_ocd_services/src/main/java/i5/las2peer/services/ocd/adapters/graphInput/GraphInputAdapter.java

@@ -10,7 +10,7 @@
 
 
 /**
- * The common interface of all graph input adapters.
+ * The common interface of all customgraph input adapters.
  * @author Sebastian
  *
  */

rest_ocd_services/src/main/java/i5/las2peer/services/ocd/adapters/graphInput/MultiplexGraphInputAdapter.java

@@ -9,7 +9,7 @@
 
 
 /**
- * The common interface of all graph input adapters.
+ * The common interface of all multiplexgraph input adapters.
  * @author Maren
  *
  */

rest_ocd_services/src/main/java/i5/las2peer/services/ocd/graphs/CustomGraph.java

@@ -47,7 +47,7 @@
 //TODO: Check whether UUIDs work out as unique edge IDs, collision chances should however be extremely low
 //TODO: Check whether UUIDs work out as unique node IDs, collision chances should however be extremely low. Check whether this could actually replace the current node names. Would however break style with the naming of the other classes.
 //TODO: Integrate graphstream attributes into persistence or not?
-public class CustomGraph extends MultiGraph{
+public class CustomGraph extends MultiGraph {
 
 	/////////////////// DATABASE COLUMN NAMES
 

rest_ocd_services/src/main/java/i5/las2peer/services/ocd/graphs/MultiplexGraph.java

@@ -1,30 +1,10 @@
 package i5.las2peer.services.ocd.graphs;
 
 import com.arangodb.ArangoCollection;
-import com.arangodb.ArangoCursor;
 import com.arangodb.ArangoDatabase;
 import com.arangodb.entity.BaseDocument;
-import com.arangodb.entity.BaseEdgeDocument;
 import com.arangodb.model.*;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import i5.las2peer.services.ocd.algorithms.utils.Termmatrix;
-import i5.las2peer.services.ocd.cooperation.data.simulation.SimulationSeries;
-import i5.las2peer.services.ocd.graphs.properties.AbstractProperty;
-import i5.las2peer.services.ocd.graphs.properties.GraphProperty;
-import org.graphstream.graph.Edge;
-import org.graphstream.graph.Node;
-import org.graphstream.graph.implementations.AbstractGraph;
-import org.graphstream.graph.implementations.AbstractNode;
-import org.graphstream.graph.implementations.MultiGraph;
-import org.graphstream.graph.implementations.MultiNode;
-import org.graphstream.ui.layout.Layout;
-import org.graphstream.ui.layout.springbox.implementations.SpringBox;
-import org.la4j.matrix.Matrix;
-import org.la4j.matrix.sparse.CCSMatrix;
-
 import java.util.*;
-import java.util.stream.Stream;
-
 
 /**
  * Represents a graph (or network), i.e. the node / edge structure and
@@ -34,7 +14,7 @@
  *
  */
 
-public class MultiplexGraph{
+public class MultiplexGraph {
 	public static final String idColumnName = "ID";
 	public static final String userColumnName = "USER_NAME";
 	public static final String nameColumnName = "NAME";
@@ -62,7 +42,7 @@ public class MultiplexGraph{
 	private String name = "";
 
 	/**
-	 * The number of layer of the graph.
+	 * The number of layers of the graph.
 	 */
 	private long layerCount;
 
@@ -84,7 +64,7 @@ public class MultiplexGraph{
 
 	private Map<String, CustomGraph> mapCustomGraphs = new HashMap<String, CustomGraph>();
 
-	private Map<CustomGraph, String> mapCustomGraphIds = new HashMap<CustomGraph, String>();
+	//private Map<CustomGraph, String> mapCustomGraphIds = new HashMap<CustomGraph, String>();
 
 	//////////////////////////////////////////////////////////////////
 	///////// Constructor
@@ -207,14 +187,14 @@ public Map<String, CustomGraph> getCustomGraphs() {
 		return mapCustomGraphs;
 	}
 
-	public void setCustomGraphs(Map<String, CustomGraph> customGraphs) {
-		this.mapCustomGraphs = customGraphs;
-	}
+	//public void setCustomGraphs(Map<String, CustomGraph> customGraphs) {
+	//	this.mapCustomGraphs = customGraphs;
+	//}
 	//protected CustomGraph getCustomGraph(CustomGraph customgraph) {
 	//	return mapCustomGraphs.get(customgraph.getId());
 	//}
 
-	public void persist( ArangoDatabase db, String transId) throws InterruptedException {
+	public void persist(ArangoDatabase db, String transId) throws InterruptedException {
 		ArangoCollection collection = db.collection(collectionName);
 		BaseDocument bd = new BaseDocument();
 		//options for the transaction
@@ -223,26 +203,17 @@ public void persist( ArangoDatabase db, String transId) throws InterruptedExcept
 		bd.addAttribute(userColumnName, this.userName);
 		bd.addAttribute(nameColumnName, this.name);
 		bd.addAttribute(typesColumnName, this.types);
-		bd.addAttribute(layerCount, this.layerCount);
 		this.creationMethod.persist(db, createOptions);
 		bd.addAttribute(creationMethodKeyColumnName, this.creationMethod.getKey());
 		collection.insertDocument(bd, createOptions);
 		this.key = bd.getKey();
 
 		bd = new BaseDocument();
 
-		List<CustomNode> nodes = new ArrayList<CustomNode>(this.customNodes.values());
-		for (CustomNode customNode : nodes) {
-			customNode.persist(db,createOptions);
+		List<CustomGraph> layers = new ArrayList<CustomGraph>(this.mapCustomGraphs.values());
+		for (CustomGraph customGraph : layers) {
+			customGraph.persist(db, transId);
 		}
-
-
-		List<CustomEdge> edges = new ArrayList<CustomEdge>(this.customEdges.values());
-		for (CustomEdge customEdge : edges) {
-			customEdge.persist(db, createOptions);
-		}
-
-		bd.addAttribute(propertiesColumnName, this.properties);
 		collection.updateDocument(this.key, bd, updateOptions);
 	}
 }

rest_ocd_services/src/main/java/i5/las2peer/services/ocd/utils/Database.java

@@ -67,7 +67,7 @@ public class Database {
 	private ArangoDB arangoDB;
 	public ArangoDatabase db;
 
-	private List<String> collectionNames =new ArrayList<String>(13);
+	private List<String> collectionNames =new ArrayList<String>(14);
 
 
 	public Database(boolean testDB) {
@@ -182,7 +182,11 @@ public void createCollections() {
 		if(!collection.exists()) {
 			collection.create();
 		}
-
+		collectionNames.add(MultiplexGraph.collectionName);		//13
+		collection = db.collection(MultiplexGraph.collectionName);
+		if(!collection.exists()) {
+			collection.create();
+		}
 	}
 
 
@@ -1742,10 +1746,7 @@ public void deleteUserInactivityData(String username, ThreadHandler threadHandle
 				throw e;
 			}
 		}
-	}	
-
-
-
+	}
 
 	public String getTransactionId(Class c, boolean write) {
 		String [] collections;
@@ -1779,6 +1780,9 @@ else if(c == SimulationSeries.class){
 		else if(c == SimulationSeriesGroup.class){
 			collections = collectionNames.subList(11,13).toArray(new String[1]);
 		}
+		//else if(c == MultiplexGraph.class) {
+			//collections = collectionNames.subList(0, 4).toArray(new String[4]);
+		//}
 		else {
 			collections = collectionNames.subList(0, 13).toArray(new String[10]);
 		}

rest_ocd_services/src/main/java/i5/las2peer/services/ocd/utils/RequestHandler.java

@@ -558,6 +558,20 @@ public String writeId(CustomGraph graph) throws ParserConfigurationException {
 		return writeDoc(doc);
 	}
 
+	/**
+	 * Creates an XML document containing the id of a single graph.
+	 *
+	 * @param graph
+	 *            The multiplex graph.
+	 * @return The document.
+	 * @throws ParserConfigurationException if parsing failed
+	 */
+	public String writeId(MultiplexGraph graph) throws ParserConfigurationException {
+		Document doc = getDocument();
+		doc.appendChild(getIdElt(graph, doc));
+		return writeDoc(doc);
+	}
+
 	/**
 	 * Creates an XML document containing the id of a single cover.
 	 * 
@@ -973,6 +987,23 @@ protected Node getIdElt(CustomGraph graph, Document doc) {
 		return graphElt;
 	}
 
+	/**
+	 * Returns an XML element node representing the id (key) of a multiplex graph.
+	 *
+	 * @param graph
+	 *            The multiplex graph.
+	 * @param doc
+	 *            The document to create the element node for.
+	 * @return The element node.
+	 */
+	protected Node getIdElt(MultiplexGraph graph, Document doc) {
+		Element graphElt = doc.createElement("Graph");
+		Element graphIdElt = doc.createElement("Id");
+		graphIdElt.appendChild(doc.createTextNode(graph.getKey()));
+		graphElt.appendChild(graphIdElt);
+		return graphElt;
+	}
+
 	/**
 	 * Returns an XML element node representing the id of a graph.
 	 *