Java tutorial
/* * * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The ASF licenses this file * to you under the Apache License, Version 2.0 (the * "License"); you may not use this file except in compliance * with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, * software distributed under the License is distributed on an * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY * KIND, either express or implied. See the License for the * specific language governing permissions and limitations * under the License. * */ package org.apache.airavata.workflow.model.graph.impl; import java.awt.Point; import java.util.ArrayList; import java.util.Collection; import java.util.Iterator; import java.util.LinkedList; import java.util.List; import com.google.gson.JsonArray; import com.google.gson.JsonElement; import com.google.gson.JsonObject; import com.google.gson.JsonPrimitive; import org.apache.airavata.common.utils.XMLUtil; import org.apache.airavata.workflow.model.exceptions.WorkflowRuntimeException; import org.apache.airavata.workflow.model.graph.ControlPort; import org.apache.airavata.workflow.model.graph.DataEdge; import org.apache.airavata.workflow.model.graph.DataPort; import org.apache.airavata.workflow.model.graph.Edge; import org.apache.airavata.workflow.model.graph.Graph; import org.apache.airavata.workflow.model.graph.GraphException; import org.apache.airavata.workflow.model.graph.GraphFactory; import org.apache.airavata.workflow.model.graph.GraphSchema; import org.apache.airavata.workflow.model.graph.Node; import org.apache.airavata.workflow.model.graph.Port; import org.apache.airavata.workflow.model.graph.Port.Kind; import org.apache.airavata.workflow.model.graph.system.InputNode; import org.apache.airavata.workflow.model.graph.system.OutputNode; import org.apache.airavata.workflow.model.graph.system.StreamSourceNode; import org.apache.airavata.workflow.model.graph.system.SystemDataPort; import org.apache.airavata.workflow.model.graph.util.GraphUtil; import org.apache.airavata.workflow.model.graph.ws.WSPort; import org.apache.airavata.workflow.model.utils.ApplicationVersion; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.xmlpull.infoset.XmlElement; public abstract class GraphImpl implements Graph { private static final Logger logger = LoggerFactory.getLogger(GraphImpl.class); /** * Unique ID of this workflow */ private String id; /** * Name of the workflow. It has to have one. */ private String name = "Workflow"; /** * Default to empty string to avoid null check. */ private String description = ""; private List<NodeImpl> nodes = new LinkedList<NodeImpl>(); private List<PortImpl> ports = new LinkedList<PortImpl>(); private List<EdgeImpl> edges = new LinkedList<EdgeImpl>(); private GraphFactory factory; /** * @param factory */ public GraphImpl(GraphFactory factory) { this.factory = factory; } /** * @see org.apache.airavata.workflow.model.graph.Graph#getID() */ public String getID() { if (this.id == null) { this.id = this.name; // If its still null if (null == this.id) { throw new WorkflowRuntimeException("The workflow ID is null"); } } return this.id; } /** * This will only be done for the ODE * * @param id */ public void setID(String id) { this.id = id; } /** * @see org.apache.airavata.workflow.model.graph.Graph#setName(java.lang.String) */ public void setName(String name) { this.name = name; } /** * @see org.apache.airavata.workflow.model.graph.Graph#getName() */ public String getName() { return this.name; } /** * @see org.apache.airavata.workflow.model.graph.Graph#getDescription() */ public String getDescription() { return this.description; } /** * @see org.apache.airavata.workflow.model.graph.Graph#setDescription(java.lang.String) */ public void setDescription(String description) { this.description = description; } /** * @see org.apache.airavata.workflow.model.graph.Graph#getNodes() */ public List<NodeImpl> getNodes() { return this.nodes; } /** * @see org.apache.airavata.workflow.model.graph.Graph#getPorts() */ public List<PortImpl> getPorts() { return this.ports; } /** * @see org.apache.airavata.workflow.model.graph.Graph#getEdges() */ public List<EdgeImpl> getEdges() { return this.edges; } /** * @see org.apache.airavata.workflow.model.graph.Graph#removeNode(org.apache.airavata.workflow.model.graph.Node) */ public void removeNode(Node node) throws GraphException { if (node == null) { throw new IllegalArgumentException("null"); } if (!this.nodes.contains(node)) { throw new GraphException("The graph doesn't contain the node that is being removed."); } NodeImpl nodeImpl = (NodeImpl) node; // Have to be very careful to remove the node. // The extended for loop cannot be used to remove the elements. // Remove edges connected to input ports. for (Iterator<DataPort> portItr = nodeImpl.getInputPorts().iterator(); portItr.hasNext();) { DataPort port = portItr.next(); for (Iterator<DataEdge> edgeItr = port.getEdges().iterator(); edgeItr.hasNext();) { DataEdge edge = edgeItr.next(); // Remove the edge from from-port. DataPort fromPort = edge.getFromPort(); fromPort.removeEdge(edge); // remove the edge from this port. This is necessary so that // type update works properly. edgeItr.remove(); // Remove the edge from the graph. this.edges.remove(edge); fromPort.getNode().edgeWasRemoved(edge); } // Remove the port from the node. portItr.remove(); // Remove the port from the graph. this.ports.remove(port); } // Remove edges connected to output ports. for (Iterator<DataPort> portItr = nodeImpl.getOutputPorts().iterator(); portItr.hasNext();) { DataPort port = portItr.next(); for (Iterator<DataEdge> edgeItr = port.getEdges().iterator(); edgeItr.hasNext();) { DataEdge edge = edgeItr.next(); DataPort toPort = edge.getToPort(); toPort.removeEdge(edge); edgeItr.remove(); this.edges.remove(edge); toPort.getNode().edgeWasRemoved(edge); } portItr.remove(); this.ports.remove(port); } for (Iterator<ControlPort> portItr = nodeImpl.getControlOutPorts().iterator(); portItr.hasNext();) { PortImpl port = portItr.next(); for (Iterator<? extends EdgeImpl> edgeItr = port.getEdges().iterator(); edgeItr.hasNext();) { EdgeImpl edge = edgeItr.next(); PortImpl toPort = edge.getToPort(); toPort.removeEdge(edge); edgeItr.remove(); this.edges.remove(edge); toPort.getNode().edgeWasRemoved(edge); } portItr.remove(); this.ports.remove(port); } PortImpl controlInPort = nodeImpl.getControlInPort(); if (controlInPort != null) { for (Iterator<? extends EdgeImpl> edgeItr = controlInPort.getEdges().iterator(); edgeItr.hasNext();) { EdgeImpl edge = edgeItr.next(); PortImpl fromPort = edge.getFromPort(); fromPort.removeEdge(edge); edgeItr.remove(); this.edges.remove(edge); fromPort.getNode().edgeWasRemoved(edge); } this.ports.remove(controlInPort); } PortImpl eprPort = nodeImpl.getEPRPort(); if (eprPort != null) { for (Iterator<? extends EdgeImpl> edgeItr = eprPort.getEdges().iterator(); edgeItr.hasNext();) { EdgeImpl edge = edgeItr.next(); PortImpl toPort = edge.getToPort(); toPort.removeEdge(edge); edgeItr.remove(); this.edges.remove(edge); toPort.getNode().edgeWasRemoved(edge); } this.ports.remove(eprPort); } this.nodes.remove(node); } /** * @see org.apache.airavata.workflow.model.graph.Graph#getNode(java.lang.String) */ public NodeImpl getNode(String nodeID) { for (NodeImpl node : this.nodes) { if (nodeID.equals(node.getID())) { return node; } } return null; } /** * @param port * @throws GraphException */ public void removePort(Port port) throws GraphException { if (port == null) { throw new IllegalArgumentException("null"); } if (!this.ports.contains(port)) { throw new GraphException("The graph doesn't contain the port that is being removed."); } // copy it so that we can remove edge without worrying about the // iteration issue. ArrayList<Edge> edgesToBeRemoved = new ArrayList<Edge>(port.getEdges()); for (Edge edge : edgesToBeRemoved) { removeEdge(edge); } this.ports.remove(port); } /** * @see org.apache.airavata.workflow.model.graph.Graph#getPort(java.lang.String) */ public PortImpl getPort(String portID) { for (PortImpl port : this.ports) { if (portID.equals(port.getID())) { return port; } } return null; } /** * @see org.apache.airavata.workflow.model.graph.Graph#addEdge(org.apache.airavata.workflow.model.graph.Port, * org.apache.airavata.workflow.model.graph.Port) */ public Edge addEdge(Port fromPort, Port toPort) throws GraphException { if (containsEdge(fromPort, toPort)) { // The edge already exists. Doesn't create a new one. return null; } if (!this.ports.contains(fromPort) || !this.ports.contains(toPort)) { // The specified port doesn't belong to the graph. throw new GraphException("The graph doesn't contain the specified port."); } PortImpl fromPortImpl = (PortImpl) fromPort; PortImpl toPortImpl = (PortImpl) toPort; NodeImpl fromNode = fromPortImpl.getNode(); NodeImpl toNode = toPortImpl.getNode(); EdgeImpl edge = this.factory.createEdge(fromPort, toPort); edge.setFromPort(fromPortImpl); edge.setToPort(toPortImpl); fromPortImpl.addEdge(edge); toPortImpl.addEdge(edge); addEdge(edge); try { fromNode.edgeWasAdded(edge); toNode.edgeWasAdded(edge); return edge; } catch (GraphException e) { removeEdge(edge); throw e; } } /** * @throws GraphException * @see org.apache.airavata.workflow.model.graph.Graph#removeEdge(org.apache.airavata.workflow.model.graph.Edge) */ public void removeEdge(Edge edge) throws GraphException { if (!this.edges.contains(edge)) { throw new GraphException("The graph doesn't contain the specified edge."); } EdgeImpl edgeImpl = (EdgeImpl) edge; PortImpl fromPort = edgeImpl.getFromPort(); PortImpl toPort = edgeImpl.getToPort(); NodeImpl fromNode = fromPort.getNode(); NodeImpl toNode = toPort.getNode(); fromPort.removeEdge(edgeImpl); toPort.removeEdge(edgeImpl); this.edges.remove(edgeImpl); // This has to be after removing edges. fromNode.edgeWasRemoved(edge); toNode.edgeWasRemoved(edge); } /** * @throws GraphException * @see org.apache.airavata.workflow.model.graph.Graph#removeEdge(org.apache.airavata.workflow.model.graph.Port, * org.apache.airavata.workflow.model.graph.Port) */ public void removeEdge(Port fromPort, Port toPort) throws GraphException { Collection<? extends Edge> fromEdges = fromPort.getEdges(); for (Edge fromEdge : fromEdges) { if (fromEdge.getToPort() == toPort) { // It's OK to remove this way because it will exit the loop // right away. removeEdge(fromEdge); return; } } throw new WorkflowRuntimeException("No edge exist between two ports."); } /** * @see org.apache.airavata.workflow.model.graph.Graph#containsEdge(org.apache.airavata.workflow.model.graph.Port, * org.apache.airavata.workflow.model.graph.Port) */ public boolean containsEdge(Port fromPort, Port toPort) { for (Edge fromEdge : fromPort.getEdges()) { Collection<? extends Edge> toEdges = toPort.getEdges(); if (toEdges.contains(fromEdge)) { return true; } } return false; } /** * @throws GraphException * @see org.apache.airavata.workflow.model.graph.Graph#importGraph(org.apache.airavata.workflow.model.graph.Graph) */ public void importGraph(Graph graph) throws GraphException { // Does not support other implementations. if (!(graph instanceof GraphImpl)) { throw new GraphException("Cannot import this graph implementation"); } GraphImpl graphImpl = (GraphImpl) graph; for (NodeImpl node : graphImpl.getNodes()) { addNode(node); // Recreates the ID so that it doesn't conflict with the existing // one. node.createID(); // Changes the position. Point position = node.getPosition(); node.setPosition(new Point(position.x + 5, position.y + 5)); } for (PortImpl port : graphImpl.getPorts()) { addPort(port); } for (EdgeImpl edge : graphImpl.getEdges()) { addEdge(edge); } } /** * @see org.apache.airavata.workflow.model.graph.Graph#toXML() */ public XmlElement toXML() { XmlElement graphElement = XMLUtil.BUILDER.newFragment(GraphSchema.NS, GraphSchema.GRAPH_TAG); graphElement.setAttributeValue(GraphSchema.NS, GraphSchema.XBAYA_VERSION_ATTRIBUTE, ApplicationVersion.VERSION.getVersion()); XmlElement idElement = graphElement.addElement(GraphSchema.NS, GraphSchema.GRAPH_ID_TAG); idElement.addChild(getID()); if (this.name != null) { XmlElement nameElement = graphElement.addElement(GraphSchema.NS, GraphSchema.GRAPH_NAME_TAG); nameElement.addChild(getName()); } if (this.description != null) { XmlElement descriptionElement = graphElement.addElement(GraphSchema.NS, GraphSchema.GRAPH_DESCRIPTION_TAG); descriptionElement.addChild(getDescription()); } toXML(graphElement); for (NodeImpl node : this.nodes) { XmlElement nodeElement = node.toXML(); graphElement.addChild(nodeElement); } for (PortImpl port : this.ports) { XmlElement portElement = port.toXML(); graphElement.addChild(portElement); } for (EdgeImpl edge : this.edges) { XmlElement edgeElement = edge.toXML(); graphElement.addChild(edgeElement); } return graphElement; } @Override public JsonObject toJSON() { JsonObject graphObject = new JsonObject(); graphObject.addProperty(GraphSchema.XBAYA_VERSION_ATTRIBUTE, ApplicationVersion.VERSION.getVersion()); graphObject.addProperty(GraphSchema.GRAPH_ID_TAG, getID()); graphObject.addProperty(GraphSchema.GRAPH_NAME_TAG, getName()); graphObject.addProperty(GraphSchema.GRAPH_DESCRIPTION_TAG, getDescription()); JsonArray nodeArray = new JsonArray(); for (NodeImpl node : this.nodes) { nodeArray.add(node.toJSON()); } graphObject.add(GraphSchema.NODE_TAG, nodeArray); JsonArray portArray = new JsonArray(); for (PortImpl port : this.ports) { portArray.add(port.toJSON()); } graphObject.add(GraphSchema.PORT_TAG, portArray); JsonArray edgeArray = new JsonArray(); for (EdgeImpl edge : this.edges) { edgeArray.add(edge.toJSON()); } graphObject.add(GraphSchema.EDGE_TAG, edgeArray); return graphObject; } /** * @param graphElement */ protected void toXML(@SuppressWarnings("unused") XmlElement graphElement) { // For subclass to overwrite. } /** * @param graphElement * @throws GraphException */ protected void parse(XmlElement graphElement) throws GraphException { String version = graphElement.attributeValue(GraphSchema.NS, GraphSchema.XBAYA_VERSION_ATTRIBUTE); logger.debug("parsing a workflow created by version " + version); XmlElement idElement = graphElement.element(GraphSchema.GRAPH_ID_TAG); if (idElement != null) { this.id = idElement.requiredText(); } XmlElement nameElement = graphElement.element(GraphSchema.GRAPH_NAME_TAG); if (nameElement != null) { this.name = nameElement.requiredText(); } XmlElement descriptionElement = graphElement.element(GraphSchema.GRAPH_DESCRIPTION_TAG); if (descriptionElement != null) { this.description = descriptionElement.requiredText(); } for (XmlElement nodeElement : graphElement.elements(null, GraphSchema.NODE_TAG)) { NodeImpl nodeImpl = this.factory.createNode(nodeElement); // need to call this to set this graph to the node. addNode(nodeImpl); } for (XmlElement portElement : graphElement.elements(null, GraphSchema.PORT_TAG)) { PortImpl port = this.factory.createPort(portElement); // need to call this to set this graph to the port. this.addPort(port); } for (XmlElement edgeElement : graphElement.elements(null, GraphSchema.EDGE_TAG)) { EdgeImpl edge = this.factory.createEdge(edgeElement); // need to call this to set this graph to the edge. this.addEdge(edge); } indexToPointer(); } protected void parse(JsonObject graphObject) throws GraphException { JsonPrimitive jsonPrimitive = graphObject.getAsJsonPrimitive(GraphSchema.GRAPH_ID_TAG); if (jsonPrimitive != null) { this.id = jsonPrimitive.getAsString(); } jsonPrimitive = graphObject.getAsJsonPrimitive(GraphSchema.GRAPH_NAME_TAG); if (jsonPrimitive != null) { this.name = jsonPrimitive.getAsString(); } jsonPrimitive = graphObject.getAsJsonPrimitive(GraphSchema.GRAPH_DESCRIPTION_TAG); if (jsonPrimitive != null) { this.description = jsonPrimitive.getAsString(); } JsonArray jArray = graphObject.getAsJsonArray(GraphSchema.NODE_TAG); for (JsonElement jsonElement : jArray) { addNode(this.factory.createNode((JsonObject) jsonElement)); } jArray = graphObject.getAsJsonArray(GraphSchema.PORT_TAG); for (JsonElement jsonElement : jArray) { addPort(this.factory.createPort((JsonObject) jsonElement)); } jArray = graphObject.getAsJsonArray(GraphSchema.EDGE_TAG); for (JsonElement jsonElement : jArray) { addEdge(this.factory.createEdge((JsonObject) jsonElement)); } indexToPointer(); } /** * Adds a node. * * @param node * the node to add */ protected void addNode(NodeImpl node) { node.setGraph(this); // if this is a Stream now put it at the begining if (node instanceof StreamSourceNode) { this.nodes.add(0, node); } else { this.nodes.add(node); } } /** * @param port */ protected void addPort(PortImpl port) { port.setGraph(this); this.ports.add(port); } /** * Converts indexes to references. This method is called after reading the graph from an XML file. * * @throws GraphException */ protected void indexToPointer() throws GraphException { for (NodeImpl node : this.nodes) { node.indexToPointer(); } for (PortImpl port : this.ports) { port.indexToPointer(); } for (EdgeImpl edge : this.edges) { edge.indexToPointer(); } } /** * @param edge */ private void addEdge(EdgeImpl edge) { edge.setGraph(this); this.edges.add(edge); } // private void createID() { // Date date = new Date(); // SimpleDateFormat format = new SimpleDateFormat("yyyyMMdd_HHmmss_S"); // String time = format.format(date); // // this.id = StringUtil.convertToJavaIdentifier(this.name) + "_" + time; // } /** * @throws GraphException */ public void fixParameterNodes() { // XXX fix the ports of parameter nodes for 2.6.3 or before. for (InputNode node : GraphUtil.getNodes(this, InputNode.class)) { DataPort oldPort = node.getOutputPort(0); if (oldPort instanceof WSPort) { node.getOutputPorts().remove(oldPort); this.ports.remove(oldPort); SystemDataPort newPort = new SystemDataPort(); this.ports.add(newPort); newPort.setKind(Kind.DATA_OUT); newPort.setName(oldPort.getName()); newPort.setGraph(this); newPort.setNode(node); newPort.createID(); node.getOutputPorts().add(newPort); for (DataEdge edge : oldPort.getEdges()) { edge.setFromPort(newPort); newPort.getEdges().add(edge); } } } for (OutputNode node : GraphUtil.getNodes(this, OutputNode.class)) { DataPort oldPort = node.getInputPort(0); if (oldPort instanceof WSPort) { node.getInputPorts().remove(oldPort); this.ports.remove(oldPort); SystemDataPort newPort = new SystemDataPort(); this.ports.add(newPort); newPort.setKind(Kind.DATA_IN); newPort.setName(oldPort.getName()); newPort.setGraph(this); newPort.setNode(node); newPort.createID(); node.getInputPorts().add(newPort); for (DataEdge edge : oldPort.getEdges()) { edge.setToPort(newPort); newPort.getEdges().add(edge); } } } } /** * This returns the number of input Nodes, this will be useful when adding unique Id for nodes * @return */ public int getCurrentInputNodeCount() { int index = 0; for (Node node : nodes) { if (node instanceof InputNode) { index++; } } return index; } /** * This returns the number of input Nodes, this will be useful when adding unique Id for nodes * @return */ public int getCurrentOutputNodeCount() { int index = 0; for (Node node : nodes) { if (node instanceof OutputNode) { index++; } } return index; } }