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net.maizegenetics.pipeline.TasselPipelineXMLUtil Maven / Gradle / Ivy
/*
* TasselPipelineXMLUtil
*/
package net.maizegenetics.pipeline;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import net.maizegenetics.plugindef.Plugin;
import net.maizegenetics.util.Utils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
/**
*
* @author Terry Casstevens
*/
public class TasselPipelineXMLUtil {
private static final Logger myLogger = LogManager.getLogger(TasselPipelineXMLUtil.class);
private TasselPipelineXMLUtil() {
// Utility Class
}
public static void writeArgsAsXML(String filename, String[] args) {
try {
DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder docBuilder = docFactory.newDocumentBuilder();
Document doc = docBuilder.newDocument();
Element rootElement = doc.createElement("TasselPipeline");
doc.appendChild(rootElement);
createXML(doc, rootElement, args);
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(new File(filename));
transformer.transform(source, result);
} catch (Exception e) {
e.printStackTrace();
}
}
private static void createXML(Document doc, Element element, String[] args) throws IOException {
int index = 0;
while (index < args.length) {
String current = args[index];
if (!isFork(current)) {
throw new IllegalArgumentException("TasselPipelineXMLUtil: createXML: this flag should be either -fork, -combine, or -runfork: " + current);
}
Element newElement = createTag(doc, element, current);
while (true) {
index++;
if (index >= args.length) {
break;
}
if (isFork(args[index])) {
break;
} else if (isSelfDescribingPlugin(args[index])) {
index = createSelfDescribingPluginXML(doc, newElement, args, index);
} else if (isModifier(args[index])) {
index = createString(doc, newElement, args, index);
} else {
index = createXML(doc, newElement, args, index);
}
}
}
}
private static int createXML(Document doc, Element element, String[] args, int index) throws IOException {
String current = args[index];
Element newElement = createTag(doc, element, current);
while (true) {
index++;
if (index >= args.length) {
break;
}
if (isModifier(args[index])) {
index = createString(doc, newElement, args, index);
} else {
break;
}
}
return index - 1;
}
private static int createSelfDescribingPluginXML(Document doc, Element element, String[] args, int index) throws IOException {
String current = args[index];
Element newElement = createTag(doc, element, current);
while (true) {
index++;
if (index >= args.length) {
break;
}
if (args[index].equalsIgnoreCase("-endPlugin")) {
index++;
break;
}
if (args[index].startsWith("-runfork")) {
break;
}
index = createString(doc, newElement, args, index);
}
return index - 1;
}
private static boolean isFork(String str) {
if ((str.startsWith("-fork")) || (str.startsWith("-runfork")) || (str.startsWith("-combine"))) {
return true;
} else {
return false;
}
}
private static boolean isModifier(String str) {
if (str.startsWith("-")) {
TasselPipeline.FLAGS temp = null;
try {
temp = TasselPipeline.FLAGS.valueOf(str.substring(1));
} catch (Exception e) {
temp = null;
}
if ((str.startsWith("-fork")) || (str.startsWith("-runfork")) || (str.startsWith("-combine"))) {
return false;
} else if (temp != null) {
return false;
} else {
return !isSelfDescribingPlugin(str);
}
} else {
return true;
}
}
private static boolean isSelfDescribingPlugin(String str) {
if (str.startsWith("-")) {
str = str.substring(1);
}
List matches = Utils.getFullyQualifiedClassNames(str);
for (String current : matches) {
if (Plugin.isPlugin(current)) {
return true;
}
}
return false;
}
private static Element createTag(Document doc, Element element, String tag) {
String str = tag.substring(tag.lastIndexOf('-') + 1);
Element tagElement = doc.createElement(str);
element.appendChild(tagElement);
return tagElement;
}
private static int createString(Document doc, Element element, String[] args, int index) throws IOException {
String current = args[index].substring(args[index].lastIndexOf('-') + 1);
if (args[index].startsWith("-")) {
Element newElement = createTag(doc, element, current);
while (true) {
index++;
if (index >= args.length) {
return index - 1;
}
if (args[index].startsWith("-")) {
return index - 1;
}
newElement.appendChild(doc.createTextNode(args[index]));
}
} else {
element.appendChild(doc.createTextNode(current));
return index;
}
}
public static String[][] readXMLAsArgs(String filename) {
try {
File fXmlFile = new File(filename);
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
Document doc = dBuilder.parse(fXmlFile);
return readXMLAsArgs(doc);
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
throw new IllegalStateException("TasselPipelineXMLUtil: readXMLAsArgs: Problem reading XML file: " + filename + "\n" + e.getMessage());
}
}
public static String[][] readXMLAsArgsFromResource(String filename) {
try {
InputStream input = TasselPipelineXMLUtil.class.getResourceAsStream(filename);
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
Document doc = dBuilder.parse(input);
return readXMLAsArgs(doc);
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
throw new IllegalStateException("TasselPipelineXMLUtil: readXMLAsArgsFromResource: Problem reading XML file: " + filename + "\n" + e.getMessage());
}
}
private static String[][] readXMLAsArgs(Document doc) {
try {
doc.getDocumentElement().normalize();
Element rootElement = doc.getDocumentElement();
if (!(rootElement.getNodeName().equalsIgnoreCase("TasselPipeline"))) {
throw new IllegalArgumentException("TasselPipelineXMLUtil: readXMLAsArgs: Root Node must be TasselPipeline: " + rootElement.getNodeName());
}
List temp = new ArrayList<>();
List workflow = new ArrayList<>();
NodeList children = rootElement.getChildNodes();
String overallDescription = null;
String citation = null;
for (int i = 0; i < children.getLength(); i++) {
Node current = children.item(i);
if ((current.getNodeType() == Node.ELEMENT_NODE) && (current.getNodeName().trim().equals("workflow"))) {
NodeList descNodes = current.getChildNodes();
for (int j = 0; j < descNodes.getLength(); j++) {
Node currentDesc = descNodes.item(j);
if (currentDesc.getNodeType() == Node.TEXT_NODE) {
String value = currentDesc.getNodeValue().trim();
overallDescription = formatDescription(value);
break;
}
}
} else if ((current.getNodeType() == Node.ELEMENT_NODE) && (current.getNodeName().trim().equals("citation"))) {
NodeList descNodes = current.getChildNodes();
for (int j = 0; j < descNodes.getLength(); j++) {
Node currentDesc = descNodes.item(j);
if (currentDesc.getNodeType() == Node.TEXT_NODE) {
String value = "Citation: " + currentDesc.getNodeValue().trim();
citation = formatDescription(value);
break;
}
}
} else {
getFlags(current, temp, workflow);
}
}
if (temp.size() != workflow.size()) {
throw new IllegalStateException("TasselPipelineXMLUtil: readXMLAsArgs: number of flags and descriptions should be the same.");
}
String[] args = new String[temp.size()];
temp.toArray(args);
String[] descriptions = new String[workflow.size()];
workflow.toArray(descriptions);
String[][] result = new String[3][];
result[0] = args;
result[1] = descriptions;
result[2] = new String[]{overallDescription, citation};
return result;
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
throw new IllegalStateException("TasselPipelineXMLUtil: readXMLAsArgs: Problem converting XML to Args: " + e.getMessage());
}
}
private static void getFlags(Node node, List flags, List workflow) {
if (node.getNodeType() != Node.ELEMENT_NODE) {
return;
}
String flagName = node.getNodeName().trim();
final int workflowIndex = flags.size();
flags.add("-" + flagName);
workflow.add(null);
NodeList children = node.getChildNodes();
for (int i = 0; i < children.getLength(); i++) {
Node current = children.item(i);
if (current.getNodeType() == Node.TEXT_NODE) {
String temp = current.getNodeValue().trim();
if (temp.length() != 0) {
flags.add(temp);
workflow.add(null);
}
} else if ((current.getNodeType() == Node.ELEMENT_NODE) && (current.getNodeName().trim().equals("workflow"))) {
NodeList descNodes = current.getChildNodes();
for (int j = 0; j < descNodes.getLength(); j++) {
Node currentDesc = descNodes.item(j);
if (currentDesc.getNodeType() == Node.TEXT_NODE) {
workflow.remove(workflowIndex);
String value = currentDesc.getNodeValue().trim();
workflow.add(workflowIndex, formatDescription(value));
break;
}
}
} else {
getFlags(current, flags, workflow);
}
}
if (isSelfDescribingPlugin(flagName)) {
flags.add("-endPlugin");
workflow.add(null);
}
}
private static final int DEFAULT_LINE_LENGTH = 50;
private static String formatDescription(String description) {
description = description.replaceAll("\\s+", " ");
int count = 0;
StringBuilder builder = new StringBuilder();
for (int i = 0, n = description.length(); i < n; i++) {
count++;
if (description.charAt(i) == '\n') {
builder.append("
